[go: up one dir, main page]

WO2024258820A2 - Procédés de fabrication de produits de fermentation à l'aide d'une levure modifiée exprimant une bêta-xylosidase - Google Patents

Procédés de fabrication de produits de fermentation à l'aide d'une levure modifiée exprimant une bêta-xylosidase Download PDF

Info

Publication number
WO2024258820A2
WO2024258820A2 PCT/US2024/033350 US2024033350W WO2024258820A2 WO 2024258820 A2 WO2024258820 A2 WO 2024258820A2 US 2024033350 W US2024033350 W US 2024033350W WO 2024258820 A2 WO2024258820 A2 WO 2024258820A2
Authority
WO
WIPO (PCT)
Prior art keywords
seq
beta
xylosidase
mature polypeptide
sequence
Prior art date
Application number
PCT/US2024/033350
Other languages
English (en)
Other versions
WO2024258820A3 (fr
Inventor
Aidin BALO
Chee-Leong Soong
Xiangyu CAI
Yueming SUN
Ye Liu
Original Assignee
Novozymes A/S
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Novozymes A/S filed Critical Novozymes A/S
Publication of WO2024258820A2 publication Critical patent/WO2024258820A2/fr
Publication of WO2024258820A3 publication Critical patent/WO2024258820A3/fr

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/02—Preparation of oxygen-containing organic compounds containing a hydroxy group
    • C12P7/04—Preparation of oxygen-containing organic compounds containing a hydroxy group acyclic
    • C12P7/06—Ethanol, i.e. non-beverage
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2477—Hemicellulases not provided in a preceding group
    • C12N9/248—Xylanases
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/01—Glycosidases, i.e. enzymes hydrolysing O- and S-glycosyl compounds (3.2.1)
    • C12Y302/01037—Xylan 1,4-beta-xylosidase (3.2.1.37)
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02E—REDUCTION OF GREENHOUSE GAS [GHG] EMISSIONS, RELATED TO ENERGY GENERATION, TRANSMISSION OR DISTRIBUTION
    • Y02E50/00—Technologies for the production of fuel of non-fossil origin
    • Y02E50/10—Biofuels, e.g. bio-diesel

Definitions

  • the present invention relates to processes for producing fermentation products from starch-containing and cellulosic-containing material.
  • the invention also relates to a recombinant host cell or fermenting organism that expresses a GH120 or GH3 beta- xylosidase which is suitable for use in a process of the invention.
  • BACKGROUND OF THE INVENTION Processes for producing fermentation products, such as ethanol, from a starch or lignocellulose containing material are well known in the art.
  • the preparation of the starch containing material such as corn for utilization in such fermentation processes typically begins with grinding the corn in a dry-grind or wet-milling process.
  • Wet-milling processes involve fractionating the corn into different components where only the starch fraction enters the fermentation process.
  • Dry-grind processes involve grinding the corn kernels into meal and mixing the meal with water and enzymes. Generally, two different kinds of dry-grind processes are used.
  • the most commonly used process includes grinding the starch-containing grain and then liquefying gelatinized starch at a high temperature using typically a bacterial alpha-amylase, followed by simultaneous saccharification and fermentation (SSF) carried out in the presence of a glucoamylase and a fermentation organism.
  • SSF simultaneous saccharification and fermentation
  • Another well-known process often referred to as a “raw starch hydrolysis” process (RSH process) includes grinding the starch-containing grain and then simultaneously saccharifying and fermenting granular starch below the initial gelatinization temperature typically in the presence of an acid fungal alpha-amylase and a glucoamylase.
  • the liquid fermentation products are recovered from the fermented mash (often referred to as “beer mash”), e.g., by distillation, which separates the desired fermentation product, e.g., ethanol, from other liquids and/or solids.
  • the remaining fraction is referred to as “whole stillage”.
  • Whole stillage typically contains about 10 to 20% solids.
  • the whole stillage is separated into a solid and a liquid fraction, e.g., by centrifugation.
  • the separated solid fraction is referred to as “wet cake” (or “wet grains”) and the separated liquid fraction is referred to as “thin stillage”.
  • Wet cake and thin stillage contain about 35 and 7% solids, respectively.
  • Wet cake, with optional additional dewatering is used as a component in animal feed or is dried to provide “Distillers Dried Grains” (DDG) used as a component in animal feed.
  • DDG Disillers Dried Grains
  • Thin stillage is typically evaporated to provide evaporator condensate and syrup or may alternatively be recycled to the slurry tank as “backset”. Evaporator condensate may either be forwarded to a methanator before being discharged and/or may be recycled to the slurry tank as “cook water”.
  • the syrup may be blended into DDG or added to the wet cake before or during the drying process, which can comprise one or more dryers in sequence, to produce DDGS (Distillers Dried Grain with Solubles).
  • Syrup typically contains about 25% to 35% solids.
  • Oil can also be extracted from the thin stillage and/or syrup as a by-product for use in biodiesel production, as a feed or food additive or product, or other biorenewable products.
  • Yeast of the genus Saccharomyces exhibit many of the characteristics required for production of ethanol.
  • strains of Saccharomyces cerevisiae are widely used for the production of ethanol in the fuel ethanol industry.
  • Industrial strains of Saccharomyces cerevisiae have the ability to produce high yields of ethanol under fermentation conditions found in, for example, the fermentation of corn mash.
  • An example of such a strain is the is the commercially available product ETHANOL RED®.
  • Saccharomyces cerevisae yeast also have been genetically engineered to express alpha-amylase and/or glucoamylase to improve yield and decrease the amount of exogenously added enzymes necessary during SSF (e.g., WO2018/098381, WO2017/087330, WO2017/037614, WO2011/128712, WO2011/153516, US2018/0155744).
  • Yeast have also been engineered to express trehalase in an attempt to increase fermentation yield by breaking down residual trehalose (e.g., WO2017/077504).
  • Cellulases and hemicellualses are well-known for use in the conversion of lignocellulosic feedstocks into ethanol.
  • the present invention provides a solution to the above problem by fermenting a saccharified starch-containing material with a fermenting organism that expresses a beta- xylosidase.
  • a first aspect relates to a process for producing a fermentation product from starch- containing material comprising the steps of: (a) liquefying the starch-containing material at a temperature above the initial gelatinization temperature using an alpha-amylase; (b) saccharifying the liquefied starch-containing material; and (c) fermenting the saccharified starch-containing material using a fermenting organism; wherein the fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • a second aspect relates to a process for producing a fermentation product from starch-containing material, the process comprising the steps of: (a) saccharifying the starch-containing material at a temperature below the initial gelatination temperature; and (b) fermenting the saccharified starch-containing material using a fermenting organism; wherein the fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • a third aspect relates to a recombinant host cell comprising a heterologous polynucleotide encoding a beta-xylosidase.
  • FIG. 2 shows active site modeling according to Example 3 for the five beta- xylosidase enzymes having the highest activity. conserveed residues are shown as thin sticks and the variable residues are shown as thick sticks.
  • FIG.3 shows a table highlighting amino acids at positions 413, 416, 435 and 462 for the five beta-xylosidase enzymes having the highest activity.
  • FIG. 2 shows active site modeling according to Example 3 for the five beta- xylosidase enzymes having the highest activity. Conserved residues
  • Active pentose fermentation pathway As used herein, a host cell or fermenting organism having an “active pentose fermentation pathway” produces active enzymes necessary to catalyze each reaction of a metabolic pathway in a sufficient amount to produce a fermentation product (e.g., ethanol) from pentose, and therefore is capable of producing the fermentation product in measurable yields when cultivated under fermentation conditions in the presence of pentose.
  • a host cell or fermenting organism having an active pentose fermentation pathway comprises one or more active pentose fermentation pathway genes.
  • a “pentose fermentation pathway gene” as used herein refers to a gene that encodes an enzyme involved in an active pentose fermentation pathway.
  • the active pentose fermentation pathway is an “active xylose fermentation pathway” (i.e. produces a fermentation product, such as ethanol, from xylose) or an “active arabinose fermentation pathway (ie produces a fermentation product, such as ethanol, from arabinose).
  • the active enzymes necessary to catalyze each reaction in an active pentose fermentation pathway may result from activities of endogenous gene expression, activities of heterologous gene expression, or from a combination of activities of endogenous and heterologous gene expression.
  • Alpha-amylase means an 1,4-alpha-D-glucan glucanohydrolase, EC. 3.2.1.1, which catalyze hydrolysis of starch and other linear and branched 1,4-glucosidic oligo- and polysaccharides.
  • Alpha-amylase activity can be determined using methods known in the art (e.g., using an alpha amylase assay described WO2020/023411).
  • Beta-glucosidase means a beta-D-glucoside glucohydrolase (E.C.3.2.1.21) that catalyzes the hydrolysis of terminal non-reducing beta-D- glucose residues with the release of beta-D-glucose. Beta-glucosidase activity can be determined using p-nitrophenyl-beta-D-glucopyranoside as substrate according to the procedure of Venturi et al., 2002, J. Basic Microbiol.42: 55-66.
  • Beta-glucosidase One unit of beta-glucosidase is defined as 1.0 ⁇ mole of p-nitrophenolate anion produced per minute at 25°C, pH 4.8 from 1 mM p-nitrophenyl-beta-D-glucopyranoside as substrate in 50 mM sodium citrate containing 0.01% TWEEN® 20.
  • Beta-xylosidase means a xylanolytic enzyme of E.C. 3.2.1.37 that catalyzes the hydrolysis of (1,4)-beta-D-xylans to release D-xylose.
  • Beta- xylosidase activity can be determined using 4-nitrophenyl- ⁇ -D-xylopyranoside as substrate to release 4-nitrophenolate according to the procedure shown in the examples below.
  • Catalytic domain means the region of an enzyme containing the catalytic machinery of the enzyme.
  • Cellobiohydrolase means a 1,4-beta-D-glucan cellobiohydrolase (E.C. 3.2.1.91 and E.C.
  • Coding sequence means a polynucleotide sequence, which specifies the amino acid sequence of a polypeptide.
  • the boundaries of the coding sequence are generally determined by an open reading frame, which usually begins with the ATG start codon or alternative start codons such as GTG and TTG and ends with a stop codon such as TAA, TAG, and TGA.
  • the coding sequence may be a sequence of genomic DNA, cDNA, a synthetic polynucleotide, and/or a recombinant polynucleotide.
  • Control sequence means a nucleic acid sequence necessary for polypeptide expression. Control sequences may be native or foreign to the polynucleotide encoding the polypeptide, and native or foreign to each other. Such control sequences include, but are not limited to, a leader sequence, polyadenylation sequence, propeptide sequence, promoter sequence, signal peptide sequence, and transcription terminator sequence.
  • the control sequences may be provided with linkers for the purpose of introducing specific restriction sites facilitating ligation of the control sequences with the coding region of the polynucleotide encoding a polypeptide.
  • Disruption means that a coding region and/or control sequence of a referenced gene is partially or entirely modified (such as by deletion, insertion, and/or substitution of one or more nucleotides) resulting in the absence (inactivation) or decrease in expression, and/or the absence or decrease of enzyme activity of the encoded polypeptide.
  • the effects of disruption can be measured using techniques known in the art such as detecting the absence or decrease of enzyme activity using from cell-free extract measurements referenced herein; or by the absence or decrease of corresponding mRNA (e.g., at least 25% decrease, at least 50% decrease, at least 60% decrease, at least 70% decrease, at least 80% decrease, or at least 90% decrease); the absence or decrease in the amount of corresponding polypeptide having enzyme activity (e.g., at least 25% decrease, at least 50% decrease, at least 60% decrease, at least 70% decrease, at least 80% decrease, or at least 90% decrease); or the absence or decrease of the specific activity of the corresponding polypeptide having enzyme activity (e.g., at least 25% decrease, at least 50% decrease, at least 60% decrease, at least 70% decrease, at least 80% decrease, or at least 90% decrease).
  • corresponding mRNA e.g., at least 25% decrease, at least 50% decrease, at least 60% decrease, at least 70% decrease, at least 80% decrease, or at least 90% decrease
  • Endogenous gene means a gene that is native to the referenced host cell or fermenting organism. “Endogenous gene expression” means expression of an endogenous gene.
  • Endoglucanase means a 4-(1,3;1,4)-beta-D-glucan 4- glucanohydrolase (E.C.3.2.1.4) that catalyzes endohydrolysis of 1,4-beta-D-glycosidic linkages in cellulose, cellulose derivatives (such as carboxymethyl cellulose and hydroxyethyl cellulose), lichenin, beta-1,4 bonds in mixed beta-1,3-1,4 glucans such as cereal beta-D-glucans or xyloglucans, and other plant material containing cellulosic components.
  • cellulose derivatives such as carboxymethyl cellulose and hydroxyethyl cellulose
  • lichenin beta-1,4 bonds in mixed beta-1,3-1,4 glucans
  • cereal beta-D-glucans or xyloglucans and other plant material containing cellulosic components.
  • Endoglucanase activity can be determined by measuring reduction in substrate viscosity or increase in reducing ends determined by a reducing sugar assay (Zhang et al., 2006, Biotechnology Advances 24: 452-481). Endoglucanase activity can also be determined using carboxymethyl cellulose (CMC) as substrate according to the procedure of Ghose, 1987, Pure and Appl. Chem.59: 257-268, at pH 5, 40°C.
  • CMC carboxymethyl cellulose
  • Expression includes any step involved in the production of the polypeptide including, but not limited to, transcription, post-transcriptional modification, translation, post-translational modification, and secretion.
  • Expression can be measured—for example, to detect increased expression—by techniques known in the art, such as measuring levels of mRNA and/or translated polypeptide.
  • Expression vector means a linear or circular DNA molecule that comprises a polynucleotide encoding a polypeptide and is operably linked to control sequences that provide for its expression.
  • Fermentable medium refers to a medium comprising one or more (e.g., two, several) sugars, such as glucose, fructose, sucrose, cellobiose, xylose, xylulose, arabinose, mannose, galactose, and/or soluble oligosaccharides, wherein the medium is capable, in part, of being converted (fermented) by a host cell into a desired product, such as ethanol.
  • the fermentation medium is derived from a natural source, such as sugar cane, starch, or cellulose, and may be the result of pretreating the source by enzymatic hydrolysis (saccharification).
  • fermentation medium is understood herein to refer to a medium before the fermenting organism is added, such as, a medium resulting from a saccharification process, as well as a medium used in a simultaneous saccharification and fermentation process (SSF).
  • Fermentation product means a product produced by a process including fermenting using a fermenting organism.
  • Fermentation products include alcohols (e.g., ethanol, methanol, butanol); organic acids (e.g., citric acid, acetic acid, itaconic acid, lactic acid, succinic acid, gluconic acid); ketones (e.g., acetone); amino acids (e.g., glutamic acid); gases (e.g., H 2 and CO 2 ); antibiotics (e.g., penicillin and tetracycline); enzymes; vitamins (e.g., riboflavin, B 12 , beta-carotene); and hormones.
  • alcohols e.g., ethanol, methanol, butanol
  • organic acids e.g., citric acid, acetic acid, itaconic acid, lactic acid, succinic acid, gluconic acid
  • ketones e.g., acetone
  • amino acids e.g., glutamic acid
  • gases e.g., H 2 and CO 2
  • the fermentation product is ethanol, e.g., fuel ethanol; drinking ethanol, i.e., potable neutral spirits; or industrial ethanol or products used in the consumable alcohol industry (e.g., beer and wine), dairy industry (e.g., fermented dairy products), leather industry and tobacco industry.
  • Preferred beer types comprise ales, stouts, porters, lagers, bitters, malt liquors, happoushu, high-alcohol beer, low-alcohol beer, low-calorie beer or light beer.
  • the fermentation product is ethanol.
  • Fermenting organism refers to any organism, including bacterial and fungal organisms, especially yeast, suitable for use in a fermentation process and capable of producing the desired fermentation product.
  • Glucoamylase The term “glucoamylase” (1,4-alpha-D-glucan glucohydrolase, EC 3.2.1.3) is defined as an enzyme that catalyzes the release of D-glucose from the non- reducing ends of starch or related oligo- and polysaccharide molecules.
  • glucoamylase activity may be determined according to the procedures known in the art, such as those described in WO2020/023411.
  • Hemicellulolytic enzyme or hemicellulase means one or more (e.g., several) enzymes that hydrolyze a hemicellulosic material. See, for example, Shallom and Shoham, 2003, Current Opinion In Microbiology 6(3): 219-228). Hemicellulases are key components in the degradation of plant biomass.
  • hemicellulases include, but are not limited to, an acetylmannan esterase, an acetylxylan esterase, an arabinanase, an arabinofuranosidase, a coumaric acid esterase, a feruloyl esterase, a galactosidase, a glucuronidase, a glucuronoyl esterase, a mannanase, a mannosidase, a xylanase, and a xylosidase.
  • hemicelluloses are a heterogeneous group of branched and linear polysaccharides that are bound via hydrogen bonds to the cellulose microfibrils in the plant cell wall, crosslinking them into a robust network. Hemicelluloses are also covalently attached to lignin, forming together with cellulose a highly complex structure. The variable structure and organization of hemicelluloses require the concerted action of many enzymes for its complete degradation.
  • the catalytic modules of hemicellulases are either glycoside hydrolases (GHs) that hydrolyze glycosidic bonds, or carbohydrate esterases (CEs), which hydrolyze ester linkages of acetate or ferulic acid side groups.
  • GHs glycoside hydrolases
  • CEs carbohydrate esterases
  • catalytic modules based on homology of their primary sequence, can be assigned into GH and CE families. Some families, with an overall similar fold, can be further grouped into clans, marked alphabetically (e.g., GH-A). A most informative and updated classification of these and other carbohydrate active enzymes is available in the Carbohydrate-Active Enzymes (CAZy) database. Hemicellulolytic enzyme activities can be measured according to Ghose and Bisaria, 1987, Pure & AppI.
  • Chem.59: 1739-1752 at a suitable temperature such as 40°C-80°C, e.g., 50°C, 55°C, 60°C, 65°C, or 70°C, and a suitable pH such as 4-9, e.g., 5.0, 5.5, 6.0, 6.5, or 7.0.
  • a suitable temperature such as 40°C-80°C, e.g., 50°C, 55°C, 60°C, 65°C, or 70°C
  • a suitable pH such as 4-9, e.g., 5.0, 5.5, 6.0, 6.5, or 7.0.
  • Heterologous polynucleotide is defined herein as a polynucleotide that is not native to the host cell; a native polynucleotide in which structural modifications have been made to the coding region; a native polynucleotide whose expression is quantitatively altered as a result of a manipulation of the DNA by recombinant DNA techniques, e.g., a different (foreign) promoter; or a native polynucleotide in a host cell having one or more extra copies of the polynucleotide to quantitatively alter expression.
  • a “heterologous gene” is a gene comprising a heterologous polynucleotide.
  • High stringency conditions means for probes of at least 100 nucleotides in length, prehybridization and hybridization at 42°C in 5X SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide, following standard Southern blotting procedures for 12 to 24 hours. The carrier material is finally washed three times each for 15 minutes using 0.2X SSC, 0.2% SDS at 65°C.
  • host cell means any cell type that is susceptible to transformation, transfection, transduction, and the like with a nucleic acid construct or expression vector comprising a polynucleotide described herein.
  • host cell encompasses any progeny of a parent cell that is not identical to the parent cell due to mutations that occur during replication.
  • recombinant cell is defined herein as a non-naturally occurring host cell comprising one or more (e.g., two, several) heterologous polynucleotides.
  • Low stringency conditions means for probes of at least 100 nucleotides in length, prehybridization and hybridization at 42°C in 5X SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 25% formamide, following standard Southern blotting procedures for 12 to 24 hours. The carrier material is finally washed three times each for 15 minutes using 0.2X SSC, 0.2% SDS at 50°C.
  • Initial gelatinization temperature "Initial gelatinization temperature” means the lowest temperature at which gelatinization of the starch commences.
  • Starch heated in water begins to gelatinize between 50 degrees centigrade and 75 degrees C; the exact temperature of gelatinization depends on the specific starch, and can readily be determined by the skilled artisan.
  • the initial gelatinization temperature may vary according to the plant species, to the particular variety of the plant species as well as with the growth conditions.
  • the initial gelatinization temperature of a given starch-containing grain is the temperature at which birefringence is lost in 5 percent of the starch granules using the method described by Gorinstein. S. and Lii. C, Starch/Starke, Vol. 44 (12) pp.461-466 (1992).
  • Mature polypeptide means a polypeptide in its final form following translation and any post-translational modifications, such as N-terminal processing, C-terminal truncation, glycosylation, phosphorylation, etc.
  • the mature polypeptide sequence lacks a signal sequence, which may be determined using techniques known in the art (See, e.g., Zhang and Henzel, 2004, Protein Science 13: 2819-2824).
  • the term “mature polypeptide coding sequence” means a polynucleotide that encodes a mature polypeptide.
  • Medium stringency conditions means for probes of at least 100 nucleotides in length, prehybridization and hybridization at 42°C in 5X SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 35% formamide, following standard Southern blotting procedures for 12 to 24 hours. The carrier material is finally washed three times each for 15 minutes using 0.2X SSC, 0.2% SDS at 55°C.
  • Medium-high stringency conditions means for probes of at least 100 nucleotides in length, prehybridization and hybridization at 42°C in 5X SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 35% formamide, following standard Southern blotting procedures for 12 to 24 hours. The carrier material is finally washed three times each for 15 minutes using 0.2X SSC, 0.2% SDS at 60°C.
  • Nucleic acid construct means a polynucleotide comprises one or more (e.g., two, several) control sequences.
  • the polynucleotide may be single-stranded or double-stranded, and may be isolated from a naturally occurring gene, modified to contain segments of nucleic acids in a manner that would not otherwise exist in nature, or synthetic.
  • Operably linked means a configuration in which a control sequence is placed at an appropriate position relative to the coding sequence of a polynucleotide such that the control sequence directs expression of the coding sequence.
  • Protease is defined herein as an enzyme that hydrolyses peptide bonds. It includes any enzyme belonging to the EC 3.4 enzyme group (including each of the thirteen subclasses thereof).
  • the EC number refers to Enzyme Nomenclature 1992 from NC-IUBMB, Academic Press, San Diego, California, including supplements 1-5 published in Eur. J. Biochem.223: 1-5 (1994); Eur. J. Biochem.232: 1-6 (1995); Eur. J. Biochem.237: 1-5 (1996); Eur. J. Biochem.250: 1-6 (1997); and Eur. J. Biochem.264: 610- 650 (1999); respectively.
  • subtilases refer to a sub-group of serine protease according to Siezen et al., 1991, Protein Engng.4: 719-737 and Siezen et al., 1997, Protein Science 6: 501-523.
  • Serine proteases or serine peptidases is a subgroup of proteases characterised by having a serine in the active site, which forms a covalent adduct with the substrate. Further the subtilases (and the serine proteases) are characterised by having two active site amino acid residues apart from the serine, namely a histidine and an aspartic acid residue.
  • the subtilases may be divided into 6 sub-divisions, i.e. the Subtilisin family, the Thermitase family, the Proteinase K family, the Lantibiotic peptidase family, the Kexin family and the Pyrolysin family.
  • proteease activity means a proteolytic activity (EC 3.4).
  • Protease activity may be determined using methods described in the art (e.g., US 2015/0125925) or using commercially available assay kits (e.g., Sigma-Aldrich).
  • Pullulanase means a starch debranching enzyme having pullulan 6-glucano-hydrolase activity (EC 3.2.1.41) that catalyzes the hydrolysis the ⁇ -1,6- glycosidic bonds in pullulan, releasing maltotriose with reducing carbohydrate ends.
  • pullulanase activity can be determined according to a PHADEBAS assay or the sweet potato starch assay described in WO2016/087237.
  • Sequence identity The relatedness between two amino acid sequences or between two nucleotide sequences is described by the parameter “sequence identity”.
  • sequence identity is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol.48: 443-453) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, Trends Genet.16: 276-277), e.g., version 5.0.0 or later.
  • the parameters used are gap open penalty of 10, gap extension penalty of 0.5, and the EBLOSUM62 (EMBOSS version of BLOSUM62) substitution matrix.
  • Needle labeled “longest identity” (obtained using the –nobrief option) is used as the percent identity and is calculated as follows: (Identical Residues x 100)/(Length of Alignment – Total Number of Gaps in Alignment)
  • sequence identity between two deoxyribonucleotide sequences is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, supra) as implemented in the Needle program of the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al., 2000, supra), e.g., version 5.0.0 or later.
  • Signal peptide The term “signal peptide” is defined herein as a peptide linked (fused) in frame to the amino terminus of a polypeptide having biological activity and directs the polypeptide into the cell’s secretory pathway.
  • Thermostable means the enzyme is not denatured or deactivated when it is used in a liquefaction step of a process of the invention. In other words, a thermostable enzyme is suitable for liquefaction if it has a denaturation temperature (Td) that is compatible with the liquefaction temperature and retains its activity at that temperature.
  • Td denaturation temperature
  • Trehalase means an enzyme which degrades trehalose into its unit monosaccharides (i.e., glucose). Trehalases are classified in EC 3.2.1.28 (alpha,alpha-trehalase) and EC.3.2.1.93 (alpha,alpha-phosphotrehalase).
  • the EC classes are based on recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). Description of EC classes can be found on the internet, e.g., on “http://www.expasy.org/enzyme/”.
  • Trehalases are enzymes that catalyze the following reactions: EC 3.2.1.28: Alpha,alpha-trehalose + 2 D-glucose; EC 3.2.1.93: Alpha,alpha-trehalose 6-phosphate + H 2 O ⁇ D-glucose + D-glucose 6- phosphate.
  • Trehalase activity may be determined according to procedures known in the art.
  • Very high stringency conditions The term “very high stringency conditions” means for probes of at least 100 nucleotides in length, prehybridization and hybridization at 42°C in 5X SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 50% formamide, following standard Southern blotting procedures for 12 to 24 hours.
  • Very low stringency conditions means for probes of at least 100 nucleotides in length, prehybridization and hybridization at 42°C in 5X SSPE, 0.3% SDS, 200 micrograms/ml sheared and denatured salmon sperm DNA, and 25% formamide, following standard Southern blotting procedures for 12 to 24 hours.
  • the carrier material is finally washed three times each for 15 minutes using 0.2X SSC, 0.2% SDS at 45°C.
  • Xylanase encompasses endo-1,4- ⁇ -xylanases (EC 3.2.1.8) that catalyze the endohydrolysis of (1 ⁇ 4)- ⁇ -D-xylosidic linkages in xylans and glucuronoarabinoxylan endo-1,4-beta-xylanases (E.C.3.2.1.136) that catalyze the endohydrolysis of 1,4-beta-D-xylosyl links in some glucuronoarabinoxylans.
  • Activity of EC 3.2.1.8 xylanases can be determined using birchwood xylan as substrate.
  • One unit of xylanase is defined as 1.0 ⁇ mole of reducing sugar (measured in glucose equivalents as described by Lever, 1972, A new reaction for colorimetric determination of carbohydrates, Anal. Biochem 47: 273-279) produced per minute during the initial period of hydrolysis at 50° C., pH 5 from 2 g of birchwood xylan per liter as substrate in 50 mM sodium acetate containing 0.01% TWEEN® 2.
  • Activity of EC 3.2.1.136 xylanases can be determined with 0.2% AZCL-glucuronoxylan as substrate in 0.01% TRITON® X-100 and 200 mM sodium phosphate pH 6 at 37°C.
  • One unit of xylanase activity is defined as 1.0 ⁇ mole of azurine produced per minute at 37°C, pH 6 from 0.2% AZCL-glucuronoxylan as substrate in 200 mM sodium phosphate pH 6.
  • DESCRIPTION OF THE INVENTION The present invention relates to processes of producing fermentation products, such as ethanol from starch-containing and/or cellulosic-containing material using a fermenting organism.
  • beta-xylosidase enzymes provide exceptionial beta-xylosidase activity.
  • beta-xylosidases that contain four conserved residues: W413, V416, R435 and N462 corresponding to SEQ ID NO: 335, provide significantly higher beta- xylosidase hydrolysis activity compared to those beta-xylosidase enzymes that lack the conserved residues.
  • the Applicant has shown with structural modelling of the active site using AlphaFold predictions aligned to a solved crystal structure of a GH120 beta-xylosidase that the residues are superimposable despite the overall sequences having modest sequence identity.
  • the present invention contemplates using the fermenting organism in saccharification, fermentation, or simultaneous saccharification and fermentation, to improve product yield in conventional and raw-starch hydrolysis (RSH) ethanol production processes, as well as cellulosic ethanol processes.
  • RSH raw-starch hydrolysis
  • I. Process for producing a fermentation product from a gelatinized starch- containing grain An aspect of the invention relates to a process for producing a fermentation product, (e.g., fuel ethanol), from a gelatinized starch-containing grain, wherein the fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • This process of the invention contemplates any of the beta-xylosidase enzymes described herein, especially those described below.
  • a process for producing a fermentation product from starch- containing material comprising the steps of: (a) liquefying the starch-containing material at a temperature above the initial gelatinization temperature using an alpha-amylase; (b) saccharifying the liquefied starch-containing material; (c) fermenting saccharified starch-containing material using a fermenting organism; wherein the fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • steps (b) and (c) are performed simultaneously in a simultaneous saccharification and fermentation (SSF).
  • a thermostable endoglucanase is added during liquefying step (a).
  • thermostable lipase is added during liquefying step (a).
  • a thermostable phytase is added during liquefying step (a).
  • a thermostable protease is added during liquefying step (a).
  • a thermostable pullulanase is added during liquefying step (a).
  • a thermostable xylanase is added during liquefying step (a).
  • a thermostable alpha-amylase, a thermostable protease and a thermostable xylanase are added during liquefying step (a).
  • an alpha-amylase is added during step (b) and/or step (c).
  • a beta-glucosidase is added during step (a) and/or step (b).
  • a glucoamylase is added during step (b) and/or step (c).
  • a cellobiohydrolase is added during step (b) and/or step (c).
  • an endoglucanase is added during step (b) and/or step (c).
  • a trehalase is added during step (b) and/or step (c).
  • the beta-xylosidase is a GH3 beta-xylosidase.
  • the beta-xylosidase is a GH120 beta-xylosidase.
  • the beta- xylosidase comprises residues W413, V416, R435 and N462 corresponding SEQ ID NO: 335. Additional embodiments for the expressed beta-xylosidase are described below.
  • the fermenting organism is yeast.
  • the yeast expresses an alpha-amylase in situ during step (b) and/or step (c).
  • the yeast expresses a glucoamylase in situ during step (b) and/or step (c).
  • Starch-containing grain Any suitable starch-containing starting grain may be used. The grain is selected based on the desired fermentation product.
  • starch-containing grains include without limitation, barley, beans, cassava, cereals, corn, milo, peas, potatoes, rice, rye, sago, sorghum, sweet potatoes, tapioca, wheat, and whole grains, or any mixture thereof.
  • the starch-containing grain may also be a waxy or non-waxy type of corn and barley.
  • Commonly used commercial starch-containing grains include corn, milo and/or wheat.
  • Grain Particle Size Reduction Prior to liquefying step (a), the particle size of the starch-containing grain may be reduced, for example by dry milling.
  • a slurry comprising the starch-containing grain (e.g., preferably milled) and water may be formed.
  • Alpha-amylase and optionally protease may be added to the slurry.
  • the slurry may be heated to between to above the initial gelatinization temperature of the starch-containing grain to begin gelatinization of the starch.
  • Jet Cook The slurry may optionally be jet-cooked to further gelatinize the starch in the slurry before adding alpha-amylase during liquefying step (a). Jet cooking can be performed at temperatures ranging from 100 °C to 120 °C for up to at least 15 minutes.
  • the temperature used during liquefying step (a) may range from 70 oC to 110 oC, such as from 75 °C to 105 °C, from 80 °C to 100°C, from 85 °C to 95 °C, or from 88 °C to 92 °C.
  • the temperature is at least 70 °C, at least 80 °C, at least 85 °C, at least 88°C, or at least 90 °C.
  • Liquefaction pH The pH used during liquefying step (a) may range from 4 to 6, from 4.5 to 5.5, or from 4.8 to 5.2.
  • the pH is at least 4.5, at least 4.6, at least 4.7, at least 4.8, at least 4.9, at least 5.0, or at least 5.1.
  • Liquefaction Time The time for performing liquefying step (a) may range from 30 minutes to 5 hours, from 1 hour to 3 hours, or 90 minutes to 150 minutes. Preferably, the time is at least 30 minutes, at least about 45 minutes, at least about 60 minutes, at least about 90 minutes, or at least about 2 hours.
  • Liquefaction Enzymes The present invention contemplates the use of thermostable enzymes during liquefying step (a).
  • thermostable enzymes during liquefying step (a), including, for example, thermostable alpha-amylases, thermostable glucoamylases, thermostable endoglucanases, thermostable lipases, thermostable phytase, thermostable proteases, thermostable pullulanases, and/or thermostable xylanases.
  • the present invention contemplates the use of any thermostable enzyme in liquefying step (a).
  • Guidance for determining the denaturation temperature of a candidate thermostable enzyme for use in liquefying step (a) is provided in the Materials & Methods section below.
  • thermostable alpha-amylases include, without limitation, the alpha-amylases described in WO 1996/023873, WO 1996/023874, WO 1997/041213, WO 1999/019467, WO 2000/060059, WO 2002/010355, WO 2002/092797, WO 2009/149130, WO 2009/061379, WO 2010/115021, WO 2010/036515, WO 2011/082425, WO 2019/113413, WO 2019/113415, WO 2019/197318 (each of which is incorporated herein by reference).
  • thermostable glucoamylases include, without limitation, the glucoamylases described in WO 2011/127802, WO 2013/036526, WO 2013/053801, WO 2018/164737, WO 2020/010101, and WO 2022/090564 (each of which is incorporated herein by reference).
  • suitable thermostable endoglucanases include, without limitation, the endoglucanases described in WO 2015/035914 (which is incorporated herein by reference)
  • suitable thermostable lipases include, without limitation, the lipases described in WO 2017/112542 and WO 2020/014407 (which are both incorporated herein by reference).
  • thermostable phytases include, without limitation, the phytases described in WO 1996/28567, WO 1997/33976, WO 1997/38096, WO 1997/48812, WO 1998/05785, WO 1998/06856, WO 1998/13480, WO 1998/20139, WO 1998/028408, WO 1999/48330, WO 1999/49022, WO 2003/066847, WO 2004/085638, WO 2006/037327, WO 2006/037328, WO 2006/038062, WO 2006/063588, WO 2007/112739, WO 2008/092901, WO 2008/116878, WO 2009/129489, and WO 2010/034835 (each of which is incorporated by reference).
  • thermostable proteases include, without limitation, the proteases described in WO 1992/02614, WO 98/56926, WO 2001/151620, WO 2003/048353, WO 2006/086792, WO 2010/008841, WO 2011/076123, WO 2011/087836, WO 2012/088303, WO 2013/082486, WO 2014/209789, WO 2014/209800, WO 2018/098124, WO2018/118815 A1, and WO2018/169780A1 (each of which is incorporated herein by reference).
  • Suitable commercially available protease containing products include AVANTEC AMP®, FORTIVA REVO®, FORTIVA HEMI®.
  • thermostable pullulanases include, without limitation, the pullulanases described in WO 2015/007639, WO 2015/110473, WO 2016/087327, WO 2017/014974, and WO 2020/187883 (each of which is incorporated herein by reference in its entirety).
  • Suitable commercially available pullulanase products include PROMOZYME 400L, PROMOZYMETM D2 (Novozymes A/S, Denmark), OPTIMAX L-300 (Genencor Int., USA), and AMANO 8 (Amano, Japan).
  • thermostable xylanases examples include, without limitation, the xylanases described in WO 2017/112540 and WO 2021/126966 (each of which is incorporated herein by reference).
  • Suitable commercially available thermostable xylanase containing products include FORTIVA HEMI®.
  • the enzyme(s) described above are to be used in effective amounts in the processes of the present invention.
  • Guidance for determining effective amounts of enzymes to be used in liquefying step (a) can be found in the published patent applications cited for each of the different thermostable liquefaction enzymes, along with guidance for performing activity assays for determining the activity of those enzymes.
  • Saccharification Temperature Saccharification may be performed at temperatures ranging from 20 °C to 75 °C, from 30 °C to 70 °C, or from 40 °C to 65 °C.
  • the saccharification temperature is at least about 50 °C, at least about 55 °C, or at least about 60 °C.
  • Saccharification pH Saccharification may occur at a ph ranging from 4 to 5.
  • the pH is about 4.5.
  • Saccharification Time Saccharification may last from about 24 hours to about 72 hours. Fermentation Time Fermentation may last from 6 to 120 hours, from 24 hours to 96 hours, or from 35 hours to 60 hours.
  • Simultaneous Saccharification and Fermentation SSF may be performed at a temperature from 25 °C to 40 °C, from 28 °C to 35 °C, or from 30 °C to °C, at a pH from 3.5 to 5 or from 3.8 to 4.3., for 24 to 96 hours, 36 to 72 hours, or from 48 to 60 hours.
  • SSF is performed at about 32 °C, at a pH from 3.8 to 4.5 for from 48 to 60 hours.
  • Saccharification and/or Fermentation Enzymes contemplates the use of enzymes during saccharifying step (b) and/or fermenting step (c).
  • alpha-amylases alpha-glucosidases, beta-amylases, beta-glucanases, beta-glucosidases, cellobiohydrolases, endoglucanases, glucoamylases, lipases, lytic polysaccharide monooxygenases (LPMOs), maltogenic alpha-amylases, pectinases, peroxidases, phytases, proteases, and trehalases.
  • alpha-amylases alpha-glucosidases
  • beta-amylases beta-glucanases
  • beta-glucosidases cellobiohydrolases
  • endoglucanases glucoamylases
  • lipases lipases
  • LPMOs lytic polysaccharide monooxygenases
  • maltogenic alpha-amylases pectinases, peroxidases, phytases, proteases, and
  • the enzymes used in saccharifying step (b) and/or fermenting step (c) may be added exogenously as mono-components or formulated as compositions comprising the enzymes.
  • the enzymes used in saccharifying step (b) and/or fermenting step (c) may also be added via in situ expression from the fermenting organism (e.g., yeast). Examples of suitable yeast expressing enzymes include, without limitation, the yeast described herein.
  • alpha-amylases include, without limitation, the alpha-amylases described in WO 2004/055178, WO 2006/069290, WO 2013/006756, WO 2013/034106, WO 2013/044867, WO 2021/163011, and WO 2021/163030 (each of which is incorporated herein by reference). Additional examples of alpha-amylases are shown below.
  • glucoamylases include, without limitation, the glucoamylases described in WO 1984/02921, WO 1992/00381, WO 1999/28448, WO 2000/04136, WO 2001/04273, WO 2006/069289, WO 2011/066560, WO 2011/066576, WO 2011/068803, WO 2011/127802, WO 2012/064351, WO 2013/036526, WO 2013/053801, WO 2014/039773, WO 2014/177541, WO 2014/177546, WO 2016/062875, WO 2017/066255, and WO 2018/191215 (each of which is incorporated herein by reference.
  • glucoamylases are shown below.
  • suitable compositions comprising alpha-amylases and glucoamylases include, without limitation, the compositons described in WO 2006/069290, WO 2009/052101, WO 2011/068803, and WO 2013/006756 (each of which is incorporated by reference herein).
  • compositions comprising glucoamylase include AMG 200L; AMG 300 L; SANTM SUPER, SANTM EXTRA L, SPIRIZYMETM PLUS, SPIRIZYMETM FUEL, SPIRIZYMETM B4U, SPIRIZYMETM ULTRA, SPIRIZYMETM EXCEL, SPIRIZYME ACHIEVE and AMGTM E (from Novozymes A/S); OPTIDEXTM 300, GC480, GC417 (from DuPont-Genencor); AMIGASETM and AMIGASETM PLUS (from DSM); G- ZYMETM G900, G-ZYMETM and G990 ZR (from DuPont-Genencor).
  • beta-glucanases examples include, without limitation, the beta-glucanases described in WO 2021/055395 (which is incorporated herein by reference).
  • suitable beta-glucosidases include, without limitation, the beta- glucosidases described in WO 2005/047499, WO 2013/148993, WO 2014/085439 and WO 2012/044915 (each of which is incorporated herein by reference).
  • suitable cellobiohydrolases include, without limitation, the cellobiohydrolases described in WO 2013/148993, WO 2014/085439, WO 2014/138672, and WO 2016/040265 (each of which is incorporated herein by reference).
  • Suitable endoglucanases include, without limitation, the endoglucanases described in WO 2013/148993 and WO 2014/085439 (both of which are incorporated herein by reference).
  • suitable maltogenic alpha-amylases are described in US Patent nos. 4,598,048, 4,604,355 and 6,162,628, which are hereby incorporated by reference.
  • suitable lipases include, without limitation, the lipases described in WO 2017/112533, WO 2017/112539, and WO 2020/076697 (each of which is incorporated herein by reference).
  • suitable LPMOs include, without limitation, the LPMOs described in WO 2013/148993, WO 2014/085439, and WO 2019/083831 (each of which is incorporated herein by reference).
  • suitable phytases include, without limitation, the phytases described in WO 2001/62947 (which is incorporated herein by reference).
  • suitable pectinases include, without limitation, the pectinases described in WO 2022/173694 (which is incorporated herein by reference).
  • suitable peroxidases include, without limitation, the peroxidases described in WO 2019/231944 (which is incorporated herein by reference).
  • proteases examples include, without limitation, the proteases described in WO 2017/050291, WO 2017/148389, WO 2018/015303, and WO 2018/015304 (each of which is incorporated herein by reference).
  • suitable trehalases include, without limitation, the trehalases described in WO 2016/205127, WO 2019/005755, WO 2019/030165, and WO 2020/023411 (each of which is incorporated herein by reference). II.
  • An aspect of the invention relates to a process for producing a fermentation product from an ungelatinized starch-containing grain (i.e., granularized starch--often referred to as a “raw starch hydrolysis” process), wherein the fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • This process of the invention contemplates any of the beta-xylosidase enzymes described herein, especially those described below.
  • a process for producing a fermentation product from an ungelatinized starch-containging grain comprises the following steps: (a) saccharifying a starch-containing grain at a temperature below the initial gelatinization temperature using a glucoamylase and an alpha-amylase to produce a fermentable sugar; and (b) fermenting the sugar using a fermenting organism to produce a fermentation product; wherein the fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • steps (a) and (b) are performed simultaneously in a simultaneous saccharification and fermentation (SSF).
  • SSF simultaneous saccharification and fermentation
  • alpha-amylases that are preferably used in step (a) and/or step (b) include, without limitation, the alpha-amylases described in WO 2004/055178, WO 2005/003311, WO 2006/069290, WO 2013/006756, WO 2013/034106, WO 2021/163015, and WO 2021/163036 (each of which is incorporated by reference herein).
  • Examples of glucoamylases that are preferably used in step (a) and/or step (b) include, without limitation, WO 1999/28448, WO 2005/045018, WO2005/069840, WO 2006/069289 (each of which is incorporated by reference herein).
  • compositions comprising alpha-amylases and glucoamylase that are preferably used in step (a) and/or step (b) include, without limitation, the compositions described in WO 2015/031477 (which is incorporated by reference herein).
  • A. Host Cells and Fermenting Organisms The host cells and fermenting organisms described herein may be derived from any host cell known to the skilled artisan, such as a cell capable of producing a fermentation product (e.g., ethanol).
  • a “derivative” of strain is derived from a referenced strain, such as through mutagenesis, recombinant DNA technology, mating, cell fusion, or cytoduction between yeast strains.
  • the genetic alterations including metabolic modifications exemplified herein, may be described with reference to a suitable host organism and their corresponding metabolic reactions or a suitable source organism for desired genetic material such as genes for a desired metabolic pathway.
  • desired genetic material such as genes for a desired metabolic pathway.
  • those skilled in the art can apply the teachings and guidance provided herein to other organisms.
  • the metabolic alterations exemplified herein can readily be applied to other species by incorporating the same or analogous encoding nucleic acid from species other than the referenced species.
  • the host cells and fermenting organisms described herein can be from any suitable host, such as a yeast strain, including, but not limited to, a Saccharomyces, Rhodotorula, Schizosaccharomyces, Kluyveromyces, Pichia, Hansenula, Rhodosporidium, Candida, Yarrowia, Lipomyces, Cryptococcus, or Dekkera sp. cell.
  • Saccharomyces host cells are contemplated, such as Saccharomyces cerevisiae, bayanus or carlsbergensis cells.
  • the yeast cell is a Saccharomyces cerevisiae cell.
  • Suitable cells can, for example, be derived from commercially available strains and polyploid or aneuploid industrial strains, including but not limited to those from SuperstartTM, THERMOSACC®, C5 FUEL TM , XyloFerm®, etc. (Lallemand); RED STAR and ETHANOL RED® (Fermentis/Lesaffre); FALI (AB Mauri); Baker's Best Yeast, Baker's Compressed Yeast, etc. (Fleishmann's Yeast); BIOFERM AFT, XP, CF, and XR (North American Bioproducts Corp.); Turbo Yeast (Gert Strand AB); and FERMIOL® (DSM Specialties).
  • yeast strains are available from biological depositories such as the American Type Culture Collection (ATCC) or the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), such as, e.g., BY4741 (e.g., ATCC 201388); Y108-1 (ATCC PTA.10567) and NRRL YB-1952 (ARS Culture Collection). Still other S.
  • ATCC American Type Culture Collection
  • DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
  • BY4741 e.g., ATCC 201388
  • Y108-1 ATCC PTA.10567
  • NRRL YB-1952 NRRL YB-1952
  • cerevisiae strains suitable as host cells DBY746, [Alpha][Eta]22, S150-2B, GPY55-15Ba, CEN.PK, USM21, TMB3500, TMB3400, VTT-A-63015, VTT-A- 85068, VTT-c-79093 and their derivatives as well as Saccharomyces sp.1400, 424A (LNH- ST), 259A (LNH-ST) and derivatives thereof.
  • the recombinant cell is a derivative of a strain Saccharomyces cerevisiae CIBTS1260 (deposited under Accession No.
  • the host cell or fermenting organism may be a Saccharomyces strain, e.g., a Saccharomyces cerevisiae strain produced using the method described in US 8,257,959.
  • the strain may also be a derivative of Saccharomyces cerevisiae strain NMI V14/004037 (See, WO2015/143324 and WO2015/143317 each incorporated herein by reference), strain nos. V15/004035, V15/004036, and V15/004037 (See, WO 2016/153924 incorporated herein by reference), strain nos.
  • the fermenting organisms according to the invention have been generated in order to, e.g., improve fermentation yield and to improve process economy by cutting enzyme costs since part or all of the necessary enzymes needed to improve method performance are be produced by the fermenting organism.
  • the host cells and fermenting organisms described herein may utilize expression vectors comprising the coding sequence of one or more (e.g., two, several) heterologous genes linked to one or more control sequences that direct expression in a suitable cell under conditions compatible with the control sequence(s).
  • Such expression vectors may be used in any of the cells and methods described herein.
  • the polynucleotides described herein may be manipulated in a variety of ways to provide for expression of a desired polypeptide. Manipulation of the polynucleotide prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying polynucleotides utilizing recombinant DNA methods are well known in the art.
  • a construct or vector comprising the one or more (e.g., two, several) heterologous genes may be introduced into a cell so that the construct or vector is maintained as a chromosomal integrant or as a self-replicating extra-chromosomal vector as described earlier.
  • the various nucleotide and control sequences may be joined together to produce a recombinant expression vector that may include one or more (e.g., two, several) convenient restriction sites to allow for insertion or substitution of the polynucleotide at such sites.
  • the polynucleotide(s) may be expressed by inserting the polynucleotide(s) or a nucleic acid construct comprising the sequence into an appropriate vector for expression.
  • the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression.
  • the recombinant expression vector may be any vector (e.g., a plasmid or virus) that can be conveniently subjected to recombinant DNA procedures and can bring about expression of the polynucleotide.
  • the choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced.
  • the vector may be a linear or closed circular plasmid.
  • the vector may be an autonomously replicating vector, i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome.
  • the vector may contain any means for assuring self-replication.
  • the vector may be one that, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated.
  • a single vector or plasmid or two or more vectors or plasmids that together contain the total DNA to be introduced into the genome of the cell, or a transposon may be used.
  • the expression vector may contain any suitable promoter sequence that is recognized by a cell for expression of a gene described herein.
  • the promoter sequence contains transcriptional control sequences that mediate the expression of the polypeptide.
  • the promoter may be any polynucleotide that shows transcriptional activity in the cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extracellular or intracellular polypeptides either homologous or heterologous to the cell.
  • Each heterologous polynucleotide described herein may be operably linked to a promoter that is foreign to the polynucleotide.
  • the nucleic acid construct encoding the polypeptide of interest is operably linked to a promoter foreign to the polynucleotide.
  • the promoters may be identical to or share a high degree of sequence identity (e.g., at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) with a selected native promoter.
  • suitable promoters for directing the transcription of the nucleic acid constructs in a yeast cells include, but are not limited to, the promoters obtained from the genes for enolase, (e.g., S. cerevisiae enolase or I.
  • orientalis enolase ENO1
  • galactokinase e.g., S. cerevisiae galactokinase or I. orientalis galactokinase (GAL1)
  • alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase e.g., S. cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase or I. orientalis alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH1, ADH2/GAP)
  • triose phosphate isomerase e.g., S.
  • TPI I. orientalis triose phosphate isomerase
  • metallothionein e.g., S. cerevisiae metallothionein or I. orientalis metallothionein (CUP1)
  • 3-phosphoglycerate kinase e.g., S. cerevisiae 3-phosphoglycerate kinase or I.
  • orientalis 3-phosphoglycerate kinase PGK
  • PDC1 xylose reductase
  • XDH xylitol dehydrogenase
  • CYB2 L-(+)-lactate-cytochrome c oxidoreductase
  • TEF1 translation elongation factor-1
  • TEF2 translation elongation factor-2
  • GPDH glyceraldehyde-3-phosphate dehydrogenase
  • UAA3 orotidine 5'-phosphate decarboxylase
  • Other suitable promoters may be obtained from S. cerevisiae TDH3, HXT7, PGK1, RPL18B and CCW12 genes.
  • the control sequence may also be a suitable transcription terminator sequence, which is recognized by a host cell to terminate transcription.
  • the terminator sequence is operably linked to the 3’-terminus of the polynucleotide encoding the polypeptide. Any terminator that is functional in the yeast cell of choice may be used.
  • the terminator may be identical to or share a high degree of sequence identity (e.g., at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99%) with the selected native terminator.
  • Suitable terminators for yeast host cells may be obtained from the genes for enolase (e.g., S. cerevisiae or I. orientalis enolase cytochrome C (e.g., S. cerevisiae or I. orientalis cytochrome (CYC1)), glyceraldehyde-3-phosphate dehydrogenase (e.g., S. cerevisiae or I.
  • enolase e.g., S. cerevisiae or I. orientalis enolase cytochrome C (e.g., S. cerevisiae or I. orientalis cytochrome (CYC1)
  • glyceraldehyde-3-phosphate dehydrogenase e.g., S. cerevisiae or I.
  • orientalis glyceraldehyde-3-phosphate dehydrogenase gpd
  • PDC1 XR
  • XDH transaldolase
  • TAL transaldolase
  • TKL transketolase
  • RKI ribose 5-phosphate ketol-isomerase
  • CYB2 CYB2
  • galactose family of genes especially the GAL10 terminator.
  • Other suitable terminators may be obtained from S. cerevisiae ENO2 or TEF1 genes. Additional useful terminators for yeast host cells are described by Romanos et al., 1992, supra.
  • the control sequence may also be an mRNA stabilizer region downstream of a promoter and upstream of the coding sequence of a gene which increases expression of the gene.
  • Suitable mRNA stabilizer regions are obtained from a Bacillus thuringiensis cryIIIA gene (WO 94/25612) and a Bacillus subtilis SP82 gene (Hue et al., 1995, Journal of Bacteriology 177: 3465-3471).
  • the control sequence may also be a suitable leader sequence, when transcribed is a non-translated region of an mRNA that is important for translation by the host cell.
  • the leader sequence is operably linked to the 5’-terminus of the polynucleotide encoding the polypeptide. Any leader sequence that is functional in the yeast cell of choice may be used.
  • Suitable leaders for yeast host cells are obtained from the genes for enolase (e.g., S. cerevisiae or I.
  • orientalis enolase ENO-1
  • 3-phosphoglycerate kinase e.g., S. cerevisiae or I. orientalis 3-phosphoglycerate kinase
  • alpha-factor e.g., S. cerevisiae or I. orientalis alpha-factor
  • alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase e.g., S. cerevisiae or I. orientalis alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP)
  • the control sequence may also be a polyadenylation sequence; a sequence operably linked to the 3’-terminus of the polynucleotide and, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence that is functional in the host cell of choice may be used. Useful polyadenylation sequences for yeast cells are described by Guo and Sherman, 1995, Mol. Cellular Biol.15: 5983-5990.
  • the control sequence may also be a signal peptide coding region that encodes a signal peptide linked to the N-terminus of a polypeptide and directs the polypeptide into the cell’s secretory pathway.
  • the 5’-end of the coding sequence of the polynucleotide may inherently contain a signal peptide coding sequence naturally linked in translation reading frame with the segment of the coding sequence that encodes the polypeptide.
  • the 5’-end of the coding sequence may contain a signal peptide coding sequence that is foreign to the coding sequence.
  • a foreign signal peptide coding sequence may be required where the coding sequence does not naturally contain a signal peptide coding sequence.
  • a foreign signal peptide coding sequence may simply replace the natural signal peptide coding sequence in order to enhance secretion of the polypeptide.
  • any signal peptide coding sequence that directs the expressed polypeptide into the secretory pathway of a host cell may be used.
  • Useful signal peptides for yeast host cells are obtained from the genes for Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase. Other useful signal peptide coding sequences are described by Romanos et al., 1992, supra. Signal peptides are also described in WO2021/025872 “Fusion Proteins For Improved Enzyme Expression” (the content of which is hereby incorporated by reference.
  • the control sequence may also be a propeptide coding sequence that encodes a propeptide positioned at the N-terminus of a polypeptide. The resultant polypeptide is known as a proenzyme or propolypeptide (or a zymogen in some cases).
  • a propolypeptide is generally inactive and can be converted to an active polypeptide by catalytic or autocatalytic cleavage of the propeptide from the propolypeptide.
  • the propeptide coding sequence may be obtained from the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Myceliophthora thermophila laccase (WO95/33836), Rhizomucor miehei aspartic proteinase, and Saccharomyces cerevisiae alpha-factor.
  • the propeptide sequence is positioned next to the N-terminus of a polypeptide and the signal peptide sequence is positioned next to the N-terminus of the propeptide sequence. It may also be desirable to add regulatory sequences that allow the regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those that cause the expression of the gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. Regulatory systems in prokaryotic systems include the lac, tac, and trp operator systems. In yeast, the ADH2 system or GAL1 system may be used.
  • the vectors may contain one or more (e.g., two, several) selectable markers that permit easy selection of transformed, transfected, transduced, or the like cells.
  • a selectable marker is a gene the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like.
  • Suitable markers for yeast host cells include, but are not limited to, ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3.
  • the vectors may contain one or more (e.g., two, several) elements that permit integration of the vector into the host cell's genome or autonomous replication of the vector in the cell independent of the genome.
  • the vector may rely on the polynucleotide’s sequence encoding the polypeptide or any other element of the vector for integration into the genome by homologous or non-homologous recombination.
  • the vector may contain additional polynucleotides for directing integration by homologous recombination into the genome of the host cell at a precise location(s) in the chromosome(s).
  • the integrational elements should contain a sufficient number of nucleic acids, such as 100 to 10,000 base pairs, 400 to 10,000 base pairs, and 800 to 10,000 base pairs, which have a high degree of sequence identity to the corresponding target sequence to enhance the probability of homologous recombination.
  • the integrational elements may be any sequence that is homologous with the target sequence in the genome of the host cell. Furthermore, the integrational elements may be non-encoding or encoding polynucleotides.
  • the vector may be integrated into the genome of the host cell by non-homologous recombination. Potential integration loci include those described in the art (e.g., See US2012/0135481).
  • the vector may further comprise an origin of replication enabling the vector to replicate autonomously in the yeast cell.
  • the origin of replication may be any plasmid replicator mediating autonomous replication that functions in a cell.
  • organ of replication or “plasmid replicator” means a polynucleotide that enables a plasmid or vector to replicate in vivo.
  • origins of replication for use in a yeast host cell are the 2 micron origin of replication, ARS1, ARS4, the combination of ARS1 and CEN3, and the combination of ARS4 and CEN6. More than one copy of a polynucleotide described herein may be inserted into a host cell to increase production of a polypeptide.
  • An increase in the copy number of the polynucleotide can be obtained by integrating at least one additional copy of the sequence into the yeast cell genome or by including an amplifiable selectable marker gene with the polynucleotide where cells containing amplified copies of the selectable marker gene, and thereby additional copies of the polynucleotide, can be selected for by cultivating the cells in the presence of the appropriate selectable agent.
  • the procedures used to ligate the elements described above to construct the recombinant expression vectors described herein are well known to one skilled in the art (see, e.g., Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor, New York).
  • the host cell or fermenting organism may be in the form of a composition comprising a host cell or fermenting organism (e.g., a yeast strain described herein) and a naturally occurring and/or a non-naturally occurring component.
  • the host cell or fermenting organism described herein may be in any viable form, including crumbled, dry, including active dry and instant, compressed, cream (liquid) form etc.
  • the host cell or fermenting organism e.g., a Saccharomyces cerevisiae yeast strain
  • the host cell or fermenting organism is dry yeast, such as active dry yeast or instant yeast.
  • the host cell or fermenting organism e.g., a Saccharomyces cerevisiae yeast strain
  • the host cell or fermenting organism is crumbled yeast.
  • the host cell or fermenting organism e.g., a Saccharomyces cerevisiae yeast strain
  • the host cell or fermenting organism e.g., a Saccharomyces cerevisiae yeast strain
  • the host cell or fermenting organism is cream yeast.
  • compositions comprising a host cell or fermenting organism described herein (e.g., a Saccharomyces cerevisiae yeast strain), and one or more of the component selected from the group consisting of: surfactants, emulsifiers, gums, swelling agent, and antioxidants and other processing aids.
  • the compositions described herein may comprise a host cell or fermenting organism described herein (e.g., a Saccharomyces cerevisiae yeast strain) and any suitable surfactants.
  • the surfactant(s) is/are an anionic surfactant, cationic surfactant, and/or nonionic surfactant.
  • compositions described herein may comprise a host cell or fermenting organism described herein (e.g., a Saccharomyces cerevisiae yeast strain) and any suitable emulsifier.
  • the emulsifier is a fatty-acid ester of sorbitan.
  • the emulsifier is selected from the group of sorbitan monostearate (SMS), citric acid esters of monodiglycerides, polyglycerolester, fatty acid esters of propylene glycol.
  • the composition comprises a host cell or fermenting organism described herein (e.g., a Saccharomyces cerevisiae yeast strain), and Olindronal SMS, Olindronal SK, or Olindronal SPL including composition concerned in EP 1,724,336 (hereby incorporated by reference). These products are commercially available from Bussetti, Austria, for active dry yeast.
  • the compositions described herein may comprise a host cell or fermenting organism described herein (e.g., a Saccharomyces cerevisiae yeast strain) and any suitable gum.
  • the gum is selected from the group of carob, guar, tragacanth, arabic, xanthan and acacia gum, in particular for cream, compressed and dry yeast.
  • compositions described herein may comprise a host cell or fermenting organism described herein (e.g., a Saccharomyces cerevisiae yeast strain) and any suitable swelling agent.
  • the swelling agent is methyl cellulose or carboxymethyl cellulose.
  • the compositions described herein may comprise a host cell or fermenting organism described herein (e.g., a Saccharomyces cerevisiae yeast strain) and any suitable anti-oxidant.
  • the antioxidant is butylated hydroxyanisol (BHA) and/or butylated hydroxytoluene (BHT), or ascorbic acid (vitamin C), particular for active dry yeast.
  • compositions described herein may comprise a co-culture of a fermenting organism described herein together with a second non-identical organism.
  • co-culture refers to growing two different strains or species of host cells together in the same vessel.
  • the two different strains or species may be any organism described herein, or any organism described in the art.
  • the co-cultures can be from different, or same, domains, kingdoms, phylums, classes, subclasses, orders, families, genera, or species. They can also be from different strains of different species or different strains of the same species.
  • the co-culture comprises two non-identical yeast strains (e.g., two non- identical Saccharomyces cerevisiae yeast strains; or a Saccharomyces cerevisiae yeast strain together with a yeast strain of a different species).
  • the co- culture is capable of co-fermentation (ie two or more different strains are capable of fermentation, e.g., alcohol fermentation).
  • the co-culture comprises two or more organisms that express different heterologous polynucleotides (e.g., express any enzymes described herein). Methods of growing co-cultures are known in the art (e.g., WO2015/164058).
  • the various host cell strains in the co-culture can be present in about equal numbers or one strain or species of host cell significantly outnumber another second strain or species of host cells.
  • the ratio of one host cell to another can be about 1:1, 1:2, 1:3, 1:4, 1:5, 1:10, 1:100, 1:500, or 1:1000.
  • the strains or species of host cells can be present in about equal or unequal amounts.
  • Beta-xylosidases in some embodiments, the fermenting organism (e.g., recombinant yeast cell) comprises a genetic modification that increases the expression of a beta-xylosidase (BX).
  • the beta-xylosidase may be any suitable beta-xylosidase that is suitable for improving the ability to hydrolyze the nonreducing ends of xylo-oligosaccharides into xylose, such as a naturally occurring beta-xylosidase (e.g., a native beta-xylosidase from another species or an endogenous beta-xylosidase expressed from a modified expression vector) or a variant thereof that retains or has improved beta-xylosidase activity.
  • a naturally occurring beta-xylosidase e.g., a native beta-xylosidase from another species or an endogenous beta-xylosidase expressed from a modified expression vector
  • a variant thereof that retains or has
  • Beta-xylosidase activity can be measured using any suitable assay known in the art (e.g., Ndat et al., MBC Biotechnol, (2021) 21:61), or preferably with the assay shown in the examples below.
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a beta- xylosidase has an increased level of beta-xylosidase activity compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the beta-xylosidase, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of beta-xylosidase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to host cell or fermenting organism without the heterologous polynucleotide encoding the beta-xylosidase, when cultivated under the same conditions.
  • the beta-xylosidase is a glycosyl hydrolase family 120 (GH120) beta-xylosidase.
  • the beta-xylosidase is a glycosyl hydrolase family 3 (GH3) beta-xylosidase.
  • GH3 beta-xylosidase glycosyl hydrolase family 3
  • Exemplary beta-xylosidases that may be expressed with the host cells or fermenting organisms and methods of use described herein include, but are not limited to, the mature polypeptide of the beta-xylosidases shown in Table 1 (or derivatives thereof). Table 1. Additional polynucleotides encoding suitable beta-xylosidases may be derived from microorganisms of any suitable genus, including those readily available within the UniProtKB database.
  • the beta-xylosidases may be a bacterial beta-xylosidase.
  • the beta- xylosidases may be derived from a Gram-positive bacterium such as a Bacillus, Clostridium, Enterococcus, Geobacillus, Lactobacillus, Lactococcus, Oceanobacillus, Staphylococcus, Streptococcus, or Streptomyces, or a Gram-negative bacterium such as a Campylobacter, E. coli, Flavobacterium, Fusobacterium, Helicobacter, Ilyobacter, Neisseria, Pseudomonas, Salmonella, or Ureaplasma.
  • a Gram-positive bacterium such as a Bacillus, Clostridium, Enterococcus, Geobacillus, Lactobacillus, Lactococcus, Oceanobacillus, Staphylococcus, Streptococcus, or Streptomyces
  • a Gram-negative bacterium such as a Campylobacter, E. coli, Flavobacter
  • the beta-xylosidase is derived from Bacillus alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans, Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, or Bacillus thuringiensis.
  • the beta-xylosidase is derived from Streptococcus equisimilis, Streptococcus pyogenes, Streptococcus uberis, or Streptococcus equi subsp. Zooepidemicus.
  • the beta-xylosidase is derived from Streptomyces achromogenes, Streptomyces avermitilis, Streptomyces coelicolor, Streptomyces griseus, or Streptomyces lividans.
  • the beta-xylosidase may be a fungal beta-xylosidase.
  • the beta- xylosidase may be derived from a yeast such as a Candida, Kluyveromyces, Pichia, Saccharomyces, Schizosaccharomyces, Yarrowia or Issatchenkia; or derived from a filamentous fungus such as an Acremonium, Agaricus, Alternaria, Aspergillus, Aureobasidium, Botryospaeria, Ceriporiopsis, Chaetomidium, Chrysosporium, Claviceps, Cochliobolus, Coprinopsis, Coptotermes, Corynascus, Cryphonectria, Cryptococcus, Diplodia, Exidia, Filibasidium, Fusarium, Gibberella, Holomastigotoides, Humicola, Irpex, Lentinula, Leptospaeria, Magnaporthe, Melanocarpus, Meripilus, Mucor, Myceliophthora, Neocal
  • the beta-xylosidase is derived from Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis, or Saccharomyces oviformis.
  • the beta-xylosidase is derived from Acremonium cellulolyticus, Aspergillus aculeatus, Aspergillus awamori, Aspergillus foetidus, Aspergillus fumigatus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae, Chrysosporium inops, Chrysosporium keratinophilum, Chrysosporium lucknowense, Chrysosporium merdarium, Chrysosporium pannicola, Chrysosporium queenslandicum, Chrysosporium tropicum, Chrysosporium zonatum, Fusarium bactridioides, Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum, Fusarium
  • the invention encompasses both the perfect and imperfect states, and other taxonomic equivalents, e.g., anamorphs, regardless of the species name by which they are known. Those skilled in the art will readily recognize the identity of appropriate equivalents. Strains of these species are readily accessible to the public in a number of culture collections, such as the American Type Culture Collection (ATCC), Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ), Centraalbureau Voor Schimmelcultures (CBS), and Agricultural Research Service Patent Culture Collection, Northern Regional Research Center (NRRL).
  • ATCC American Type Culture Collection
  • DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
  • CBS Centraalbureau Voor Schimmelcultures
  • NRRL Northern Regional Research Center
  • the beta-xylosidase coding sequences described or referenced herein, or a subsequence thereof, as well as the transporter described or referenced herein, or a fragment thereof, may be used to design nucleic acid probes to identify and clone DNA encoding a glycerol transporter from strains of different genera or species according to methods well known in the art.
  • probes can be used for hybridization with the genomic DNA or cDNA of a cell of interest, following standard Southern blotting procedures, in order to identify and isolate the corresponding gene therein.
  • Such probes can be considerably shorter than the entire sequence, but should be at least 15, e.g., at least 25, at least 35, or at least 70 nucleotides in length.
  • the nucleic acid probe is at least 100 nucleotides in length, e.g., at least 200 nucleotides, at least 300 nucleotides, at least 400 nucleotides, at least 500 nucleotides, at least 600 nucleotides, at least 700 nucleotides, at least 800 nucleotides, or at least 900 nucleotides in length.
  • Both DNA and RNA probes can be used.
  • the probes are typically labeled for detecting the corresponding gene (for example, with 32 P, 3 H, 35 S, biotin, or avidin).
  • a genomic DNA or cDNA library prepared from such other strains may be screened for DNA that hybridizes with the probes described above and encodes a sugar transporter.
  • Genomic or other DNA from such other strains may be separated by agarose or polyacrylamide gel electrophoresis, or other separation techniques.
  • DNA from the libraries or the separated DNA may be transferred to and immobilized on nitrocellulose or other suitable carrier material.
  • the carrier material is used in a Southern blot.
  • the nucleic acid probe is a polynucleotide, or subsequence thereof, that encodes the the mature polypeptide of the beta-xylosidase of any one of SEQ ID NOs: 324-353, 365-437, or a fragment thereof.
  • hybridization indicates that the polynucleotide hybridizes to a labeled nucleic acid probe, or the full-length complementary strand thereof, or a subsequence of the foregoing; under very low to very high stringency conditions. Molecules to which the nucleic acid probe hybridizes under these conditions can be detected using, for example, X-ray film. Stringency and washing conditions are defined as described supra.
  • the beta-xylosidase is encoded by a polynucleotide that hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence for any one of the beta-xylosidases described or referenced herein (e.g., SEQ ID NOs: 324-353 or 365- 437). (Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor, New York).
  • the beta-xylosidase may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, silage, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, silage, etc.) using the above-mentioned probes. Techniques for isolating microorganisms and DNA directly from natural habitats are well known in the art.
  • the polynucleotide encoding a beta- xylosidase may then be derived by similarly screening a genomic or cDNA library of another microorganism or mixed DNA sample.
  • the sequence may be isolated or cloned by utilizing techniques that are known to those of ordinary skill in the art (See, e.g., Sambrook et al., 1989, supra). Techniques used to isolate or clone polynucleotides encoding beta-xylosidases include isolation from genomic DNA, preparation from cDNA, or a combination thereof.
  • the cloning of the polynucleotides from such genomic DNA can be affected, e.g., by using the well- known polymerase chain reaction (PCR) or antibody screening of expression libraries to detect cloned DNA fragments with shares structural features (See, e.g., Innis et al., 1990, PCR: A Guide to Methods and Application, Academic Press, New York).
  • PCR polymerase chain reaction
  • Other nucleic acid amplification procedures such as ligase chain reaction (LCR), ligated activated transcription (LAT) and nucleotide sequence-based amplification (NASBA) may be used.
  • the beta-xylosidase comprises or consists of the mature polypeptide of the amino acid sequence of any one of SEQ ID NOs: 324-353 or 365-437 (e.g., SEQ ID NO: 335, 339 or 340).
  • the beta-xylosidase is a fragment of the beta-xylosidase of the mature polypeptide of the any one of SEQ ID NOs: 324-353 or 365-437 (e.g., SEQ ID NO: 335, 339 or 340) wherein, e.g., the fragment has beta-xylosidase activity.
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length beta-xylosidase (e.g. any one of SEQ ID NOs: 324-353 or 365-437, such as SEQ ID NO: 335, 339 or 340).
  • the beta-xylosidase may comprise the catalytic domain of any beta-xylosidase described or referenced herein (e.g., the catalytic domain of any one of SEQ ID NOs: 324-353 or 365-437, such as SEQ ID NO: 335, 339 or 340).
  • the beta-xylosidase may be a variant of any one of the beta-xylosidase described supra (e.g., any one of SEQ ID NOs: 324-353 or 365-437, such as SEQ ID NO: 335, 339 or 340) or the mature polypeptide thereof.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the beta-xylosidase described supra (e.g., any one of SEQ ID NOs: 324-353 or 365-437, such as SEQ ID NO: 335, 339 or 340) or the mature polypeptide thereof.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 324, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-598 of SEQ ID NO: 324.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 325, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-591 of SEQ ID NO: 325.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 326, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-590 of SEQ ID NO: 326.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 327, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-595 of SEQ ID NO: 327.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 328, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-676 of SEQ ID NO: 328.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 329, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 28-678 of SEQ ID NO: 329.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 330, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-674 of SEQ ID NO: 330.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 331, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-674 of SEQ ID NO: 331.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 332, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-674 of SEQ ID NO: 332.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 333, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-674 of SEQ ID NO: 333.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 334, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-662 of SEQ ID NO: 334.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 335, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-680 of SEQ ID NO: 335.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 336, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-662 of SEQ ID NO: 336.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 337, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-676 of SEQ ID NO: 337.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 338, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-669 of SEQ ID NO: 338.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 339, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-679 of SEQ ID NO: 339.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 340, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-678 of SEQ ID NO: 340.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 341, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-647 of SEQ ID NO: 341.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 342, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-670 of SEQ ID NO: 342.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 343, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-668 of SEQ ID NO: 343.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 344, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-678 of SEQ ID NO: 344.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 345, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-666 of SEQ ID NO: 345.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 346, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-679 of SEQ ID NO: 346.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 347, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-667 of SEQ ID NO: 347.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 348, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-598 of SEQ ID NO: 348.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 349, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 25-616 of SEQ ID NO: 349.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 350, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-663 of SEQ ID NO: 350.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 351, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-642 of SEQ ID NO: 351.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 352, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-652 of SEQ ID NO: 352.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 353, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 28-622 of SEQ ID NO: 353.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 365, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 11-622 of SEQ ID NO: 365.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 366, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-654 of SEQ ID NO: 366.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 367, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-672 of SEQ ID NO: 367.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 368, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-656 of SEQ ID NO: 368.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 369, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-647 of SEQ ID NO: 369.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 370, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-640 of SEQ ID NO: 370.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 371, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-641 of SEQ ID NO: 371.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 372, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-646 of SEQ ID NO: 372.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 373, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-638 of SEQ ID NO: 373.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 374, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-637 of SEQ ID NO: 374.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 375, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-627 of SEQ ID NO: 375.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 376, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-688 of SEQ ID NO: 376.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 377, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 26-777 of SEQ ID NO: 377.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 378, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-657 of SEQ ID NO: 378.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 379, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-678 of SEQ ID NO: 379.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 380, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-672 of SEQ ID NO: 380.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 381, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-648 of SEQ ID NO: 381.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 382, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-645 of SEQ ID NO: 382.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 383, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-642 of SEQ ID NO: 383.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 384, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-659 of SEQ ID NO: 384.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 385, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-679 of SEQ ID NO: 385.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 386, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-679 of SEQ ID NO: 386.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 387, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 1-644 of SEQ ID NO: 387.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 388, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 23-766 of SEQ ID NO: 388.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 389, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-791 of SEQ ID NO: 389.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 390, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-757 of SEQ ID NO: 390.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 391, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 14-763 of SEQ ID NO: 391.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 392, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 23-768 of SEQ ID NO: 392.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 393, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 18-804 of SEQ ID NO: 393.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 394, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-792 of SEQ ID NO: 394.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 395, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-763 of SEQ ID NO: 395.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 396, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-795 of SEQ ID NO: 396.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 397, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 28-801 of SEQ ID NO: 397.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 398, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-903 of SEQ ID NO: 398.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 399, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-768 of SEQ ID NO: 399.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 400, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 17-796 of SEQ ID NO: 400.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 401, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-818 of SEQ ID NO: 401.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 402, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-801 of SEQ ID NO: 402.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 403, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 26-907 of SEQ ID NO: 403.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 404, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-797 of SEQ ID NO: 404.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 405, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-792 of SEQ ID NO: 405.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 406, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-792 of SEQ ID NO: 406.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 407, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-773 of SEQ ID NO: 407.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 408, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 19-787 of SEQ ID NO: 408.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 409, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-793 of SEQ ID NO: 409.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 410, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 27-908 of SEQ ID NO: 410.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 411, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-792 of SEQ ID NO: 411.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 412, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-786 of SEQ ID NO: 412.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 413, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 18-791 of SEQ ID NO: 413.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 414, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 27-769 of SEQ ID NO: 414.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 415, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-1003 of SEQ ID NO: 415.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 416, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-779 of SEQ ID NO: 416.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 417, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 23-894 of SEQ ID NO: 417.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 418, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-785 of SEQ ID NO: 418.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 419, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 24-797 of SEQ ID NO: 419.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 420, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 18-764 of SEQ ID NO: 420.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 421, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 18-778 of SEQ ID NO: 421.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 422, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-757 of SEQ ID NO: 422.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 423, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 23-805 of SEQ ID NO: 423.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 424, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 28-909 of SEQ ID NO: 424.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 425, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 15-890 of SEQ ID NO: 425.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 426, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 24-792 of SEQ ID NO: 426.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 427, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 25-915 of SEQ ID NO: 427.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 428, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 20-781 of SEQ ID NO: 428.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 429, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-756 of SEQ ID NO: 429.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 430, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 23-769 of SEQ ID NO: 430.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 431, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 19-765 of SEQ ID NO: 431.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 432, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 21-794 of SEQ ID NO: 432.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 433, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 27-788 of SEQ ID NO: 433.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 434, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-906 of SEQ ID NO: 434.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 435, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-869 of SEQ ID NO: 435.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 436, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 22-876 of SEQ ID NO: 436.
  • the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to the beta- xylosidase of SEQ ID NO: 437, or the mature polypeptide thereof.
  • the mature polypeptide is amino acids 23-884 of SEQ ID NO: 437.
  • the beta-xylosidase sequence differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the beta-xylosidase described supra, or the mature polypeptide thereof (e.g., any one of SEQ ID NOs: 324-353 or 365-437, such as SEQ ID NO: 335, 339 or 340).
  • the beta-xylosidase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of any one of the beta- xylosidases described supra, or the mature polypeptide thereof (e.g., any one of SEQ ID NOs: 324-353 or 365-437, such as SEQ ID NO: 335, 339 or 340).
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • amino acid changes are generally of a minor nature, that is conservative amino acid substitutions or insertions that do not significantly affect the folding and/or activity of the protein; small deletions, typically of one to about 30 amino acids; small amino-terminal or carboxyl-terminal extensions, such as an amino-terminal methionine residue; a small linker peptide of up to about 20-25 residues; or a small extension that facilitates purification by changing net charge or another function, such as a poly-histidine tract, an antigenic epitope or a binding domain.
  • conservative substitutions are within the group of basic amino acids (arginine, lysine and histidine), acidic amino acids (glutamic acid and aspartic acid), polar amino acids (glutamine and asparagine), hydrophobic amino acids (leucine, isoleucine and valine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and small amino acids (glycine, alanine, serine, threonine and methionine).
  • Amino acid substitutions that do not generally alter specific activity are known in the art and are described, for example, by H. Neurath and R.L. Hill, 1979, In, The Proteins, Academic Press, New York.
  • amino acid changes are of such a nature that the physico-chemical properties of the polypeptides are altered.
  • amino acid changes may improve the thermal stability of the glycerol transporters, alter the substrate specificity, change the pH optimum, and the like.
  • Essential amino acids can be identified according to procedures known in the art, such as site-directed mutagenesis or alanine-scanning mutagenesis (Cunningham and Wells, 1989, Science 244: 1081-1085). In the latter technique, single alanine mutations are introduced at every residue in the molecule, and the resultant mutant molecules are tested for activity to identify amino acid residues that are critical to the activity of the molecule. See also, Hilton et al., 1996, J. Biol. Chem.271: 4699-4708.
  • the active site or other biological interaction can also be determined by physical analysis of structure, as determined by such techniques as nuclear magnetic resonance, crystallography, electron diffraction, or photoaffinity labeling, in conjunction with mutation of putative contact site amino acids (See, for example, de Vos et al., 1992, Science 255: 306-312; Smith et al., 1992, J. Mol. Biol.224: 899-904; Wlodaver et al., 1992, FEBS Lett.309: 59-64).
  • the identities of essential amino acids can also be inferred from analysis of identities with other beta-xylosidases that are related to the referenced beta-xylosidase.
  • beta-xylosidases herein can be determined using multiple sequence alignment (MSA) techniques well-known in the art. Based on the teachings herein, the skilled artisan could make similar alignments with any number of beta-xylosidases described herein or known in the art. Such alignments aid the skilled artisan to determine potentially relevant domains (e.g., binding domains or catalytic domains), as well as which amino acid residues are conserved and not conserved among the different beta-xylosidase sequences.
  • MSA multiple sequence alignment
  • Predicted structures for millions of polypeptides deposited in the UniProt database have been deposited in the AlphaFold Protein Structure Database, using the AlphaFold Monomer v2.0 model (Varadi et al., Nucleic Acids Research, 50: D439-D444 (2021)).
  • the three-dimensional structure of a polypeptide can be obtained by searching for the UniProt accession number of the polypeptide.
  • code is available for reproducing and predicting structures of new polypeptides at source code repositories.
  • the relatedness between the three- dimensional structure of two polypeptides is described by the parameter “structural similarity”.
  • a three-dimensional structure of any polypeptide may be obtained experimentally via, e.g., X-ray crystallography or using in silico methods such as AlphaFold (vide supra).
  • the structural similarity between three-dimensional structures may then be determined by the TM-score, which is calculated using the following general formula (Zhang & Skolnick, Proteins, 57:702–710 where L N is the length of the native structure, L T is the length of the aligned residues to the template structure, d i is the distance between the ith pair of aligned residues and d O is a scale to normalize the match difference. ‘Max’ denotes the maximum value after optimal spatial superposition.
  • the beta-xylosidase has a TM-score of at least 0.60, e.g., at least 0.65, at least 0.70, at least 0.75, at least 0.80, at least 0.85, at least 0.90, at least 0.91, at least 0.92, at least 0.93, at least 0.94, at least 0.95, at least 0.96, at least 0.97, at least 0.98, at least 0.99, or even 1.0, compared to the three-dimensional structure of the beta- xylosidase of SEQ ID NO: 335, wherein the three-dimensional structure is calculated using Alphafold.
  • the highest performing beta-xylosidases contain four conserved residues corresponding to positions 413, 416, 435 and 462 of SEQ ID NO: 335.
  • the polypeptide disclosed in SEQ ID NO: 335 is used to determine the corresponding amino acid positions in another beta-xylosidase.
  • the amino acid sequence of another beta-xylosidase is aligned with the polypeptide disclosed in SEQ ID NO: 335, and based on the alignment, the amino acid position number corresponding to any amino acid residue in the polypeptide disclosed in SEQ ID NO: 335 is determined using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol.
  • the beta-xylosidase comprises a tryptophan (W) at a position corresponding to position 413 of SEQ ID NO: 335.
  • the beta- xylosidase comprises a valine (V) at a position corresponding to position 416 of SEQ ID NO: 335.
  • the beta-xylosidase comprises an arginine (R) at a position corresponding to position 435 of SEQ ID NO: 335. In another embodiment, the beta- xylosidase comprises an asparagine (N) at a position corresponding to position 435 of SEQ ID NO: 462. In one embodiment, the beta-xylosidase comprises one or more (e.g., 1, 2, 3 or 4) of the residues referenced above. In one embodiment, the beta-xylosidase comprises W413, V416, R435 and N462 corresponding SEQ ID NO: 335.
  • Single or multiple amino acid substitutions, deletions, and/or insertions can be made and tested using known methods of mutagenesis, recombination, and/or shuffling, followed by a relevant screening procedure, such as those disclosed by Reidhaar-Olson and Sauer, 1988, Science 241: 53-57; Bowie and Sauer, 1989, Proc. Natl. Acad. Sci. USA 86: 2152- 2156; WO95/17413; or WO95/22625.
  • Other methods that can be used include error-prone PCR, phage display (e.g., Lowman et al., 1991, Biochemistry 30: 10832-10837; U.S.
  • the heterologous polynucleotide encoding the beta- xylosidase comprises a coding sequence having at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to the coding sequence of any one of the beta-xylosidases described supra, or mature polypeptide coding sequence thereof (e.g., any one of SEQ ID NOs: 324-353 or 365-437, such as SEQ ID NO: 335, 339 or 340).
  • the heterologous polynucleotide encoding the beta-xylosidase comprises or consists of the coding sequence of any one of the beta-xylosidases described supra, or a mature polypeptide coding sequence thereof (e.g., any one of SEQ ID NOs: 324- 353 or 365-437, such as SEQ ID NO: 335, 339 or 340).
  • the heterologous polynucleotide encoding the beta-xylosidase comprises a subsequence of the coding sequence of any one of the beta-xylosidases described supra (e.g., any one of SEQ ID NOs: 324-353 or 365-437, such as SEQ ID NO: 335, 339 or 340) wherein the subsequence encodes a polypeptide having beta-xylosidase activity.
  • the number of nucleotides residues in the coding subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon- optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae). Codon-optimization for expression in yeast cells is known in the art (e.g., US 8,326,547).
  • the beta-xylosidase may be a fused polypeptide or cleavable fusion polypeptide in which another polypeptide is fused at the N-terminus or the C-terminus of the beta- xylosidase.
  • a fused polypeptide may be produced by fusing a polynucleotide encoding another polypeptide to a polynucleotide encoding the beta-xylosidase.
  • Techniques for producing fusion polypeptides are known in the art, and include ligating the coding sequences encoding the polypeptides so that they are in frame and that expression of the fused polypeptide is under control of the same promoter(s) and terminator. Fusion proteins may also be constructed using intein technology in which fusions are created post- translationally (Cooper et al., 1993, EMBO J.12: 2575-2583; Dawson et al., 1994, Science 266: 776-779).
  • the beta-xylosidase is a fusion protein comprising a signal peptide linked to the N-terminus of a mature polypeptide, such as any signal sequences described in WO2021/025872 “Fusion Proteins For Improved Enzyme Expression” (the content of which is hereby incorporated by reference).
  • the fermenting organism e.g., recombinant yeast cell
  • the transporter may be any suitable transporter that is suitable for improving the transport of glycerol, such as a naturally occurring transporter (e.g., a native transporter from another species or an endogenous transporter expressed from a modified expression vector) or a variant thereof that retains glycerol transporter activity.
  • Glycerol transporter activity can be measured using any suitable assay known in the art.
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a glycerol transporter.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a glycerol transporter has an increased level of glycerol transporter activity compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the glycerol transporter, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of glycerol transporter activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to host cell or fermenting organism without the heterologous polynucleotide encoding the glycerol transporter, when cultivated under the same conditions.
  • Exemplary glycerol transporters that may be expressed with the host cells or fermenting organisms and methods of use described herein include, but are not limited to, glycerol transporters shown in Table 2 (or derivatives thereof). Table 2.
  • Additional polynucleotides encoding suitable glycerol transporters may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the glycerol transporters coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding glycerol transporterss from strains of different genera or species, as described supra.
  • the polynucleotides encoding glycerol transporters may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra.
  • the glycerol transporter comprises or consists of the amino acid sequence of any one of SEQ ID NOs: 312-323 (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide thereof.
  • the transporter is a fragment of the glycerol transporter of any one of SEQ ID NOs: 312-323 (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), wherein, e.g., the fragment has glycerol transporter activity.
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length glycerol transporter (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323).
  • the glycerol transporter may comprise the catalytic domain of any glycerol transporter described or referenced herein (e.g., the catalytic domain of any one of SEQ ID NOs: 312-323; such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323).
  • the glycerol transporter may be a variant of any one of the glycerol transporters described supra (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide thereof.
  • the glycerol transporter has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the glycerol transporters described supra (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide thereof.
  • suitable amino acid changes such as conservative substitutions that do not significantly affect the folding and/or activity of the glycerol transporter, are described herein.
  • the glycerol transporter sequence differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the glycerol transporters described supra (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide thereof.
  • the glycerol transporter has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the glycerol transporters described supra (e.g., any one of SEQ ID NOs: 312-323; such as any one of SEQ ID NOs: 312-323 (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide thereof.
  • any one of the glycerol transporters described supra e.g., any one of SEQ ID NOs: 312-323; such as any one of SEQ ID NOs: 312-323 (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide thereof.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the glycerol transporter has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the glycerol transporter activity of any glycerol transporter described or referenced herein under the same conditions (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide thereof.
  • the glycerol transporter coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any glycerol transporter described or referenced herein (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323).
  • any one of SEQ ID NOs: 312-323 such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323
  • the glycerol transporter coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any glycerol transporter described or referenced herein (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide coding sequence thereof.
  • the glycerol transporter comprises the coding sequence of any glycerol transporter described or referenced herein (e.g., any one of SEQ ID NOs: 312-323, such as SEQ ID NO: 312, 313, 315, 317, 318, 319, 320 or 323), or the mature polypeptide coding sequence thereof.
  • the glycerol transporter comprises a coding sequence that is a subsequence of the coding sequence from any glycerol transporter described or referenced herein, wherein the subsequence encodes a polypeptide having glycerol transporter activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced glycerol transporter coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the glycerol transporter can also include fused polypeptides or cleavable fusion polypeptides, as described supra. D.
  • the fermenting organism e.g., recombinant yeast cell
  • the fermenting organism comprises a genetic modification that increases or decreases expression of a glucose transporter.
  • the glucose transporter is a sodium-coupled glucose transporter.
  • the transporter may be any suitable transporter that is suitable for improving the transport and/or utilization of glucose, such as a naturally occurring transporter (e.g., a native transporter from another species or an endogenous transporter expressed from a modified expression vector) or a variant thereof that retains sugar transporter activity.
  • Glucose transporter activity can be measured using any suitable assay known in the art.
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a glucose transporter.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a glucose transporter has an increased level of glucose transporter activity compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the glucose transporter, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of glucose transporter activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to host cell or fermenting organism without the heterologous polynucleotide encoding the glucose transporter, when cultivated under the same conditions.
  • Exemplary glucose transporters that may be expressed with the host cells or fermenting organisms and methods of use described herein include, but are not limited to, glucose transporters shown in Table 3 (or derivatives thereof). Table 3.
  • Additional polynucleotides encoding suitable glucose transporters may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the glucose transporters coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding glucose transporterss from strains of different genera or species, as described supra.
  • the polynucleotides encoding glucose transporterss may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra.
  • the glucose transporter has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any one of the glucose transporter described or referenced herein (e.g., any one of SEQ ID NOs: 354-364; such as any one of SEQ ID NOs: 361-364), or the mature polypeptide thereof.
  • the glucose transporter has a mature polypeptide sequence that is a fragment of the any one of the glucose transporters described or referenced herein (e.g., any one of SEQ ID NOs: 354- 364; such as any one of SEQ ID NOs: 361-364).
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length glucose transporter.
  • the glucose transporter may comprise the catalytic domain of any glucose transporter described or referenced herein (e.g., any one of SEQ ID NOs: 354-364; such as any one of SEQ ID NOs: 361-364).
  • the glucose transporter may be a variant of any one of the glucose transporters described supra (e.g., any one of SEQ ID NOs: 354-364; such as any one of SEQ ID NOs: 361-364), or the mature polypeptide thereof.
  • the glucose transporter has a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the glucose transporters described supra (e.g., any one of SEQ ID NOs: 354-364; such as any one of SEQ ID NOs: 361-364), or the mature polypeptide thereof.
  • suitable amino acid changes such as conservative substitutions that do not significantly affect the folding and/or activity of the glucose transporter, are described herein.
  • the glucose transporter has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the glucose transporters described supra (e.g., any one of SEQ ID NOs: 354-364; such as SEQ ID NO: 361, 362, 363, or 364).
  • the glucose transporter has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the glucose transporters described supra (e.g., any one of SEQ ID NOs: 354-364; such as SEQ ID NO: 361, 362, 363, or 364).
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the glucose transporter has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the glucose transporter activity of any glucose transporter described or referenced herein under the same conditions (e.g., any one of SEQ ID NOs: 354-364; such as SEQ ID NO: 361, 362, 363, or 364).
  • the glucose transporter coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any glucose transporter described or referenced herein (e.g., any one of SEQ ID NOs: 354-364; such as SEQ ID NO: 361, 362, 363, or 364), or the mature polypeptide coding sequence thereof.
  • any glucose transporter described or referenced herein e.g., any one of SEQ ID NOs: 354-364; such as SEQ ID NO: 361, 362, 363, or 364
  • the glucose transporter coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any glucose transporter described or referenced herein (e.g., any one of SEQ ID NOs: 354-364; such as SEQ ID NO: 361, 362, 363, or 364), or the mature polypeptide coding sequence thereof.
  • any glucose transporter described or referenced herein e.g., any one of SEQ ID NOs: 354-364; such as SEQ ID NO: 361, 362, 363, or 364
  • the glucose transporter comprises the coding sequence of any glucose transporter described or referenced herein (e.g., any one of SEQ ID NOs: 354-364; such as SEQ ID NO: 361, 362, 363, or 364), or the mature polypeptide coding sequence thereof.
  • the glucose transporter comprises a coding sequence that is a subsequence of the coding sequence from any glucose transporter described or referenced herein, wherein the subsequence encodes a polypeptide having glucose transporter activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced glucose transporter coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the glucose transporter can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • Non-phosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenases The host cells and fermenting organisms may express a heterologous glucoamylase non-phosphorylating NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPN).
  • the GAPN can be any GAPN that is suitable for the host cells and their methods of use described herein, such as a naturally occurring GAPN (e.g., an endogenous GAPN or a native GAPN from another species) or a variant thereof that retains GAPN activity.
  • GAPN is present in the cytosol of the host cells.
  • GAPN activity may be determined from cell-free extracts as described in the art, e.g., as described in Tamoi et al., 1996, Biochem. J.316, 685-690.
  • GAPN activity may be measured spectrophotometrically by monitoring the absorbance change following NADPH oxidation at 340 nm in a reaction mixture containing 100 mM Tris/HCl buffer (pH 8.0), 10 mM MgCl 2 , 10 mM GSH, 5 mM ATP, 0.2 mM NADPH, 2 units of 3- phosphoglyceric phosphokinase, 2 mM 3-phosphoglyceric acid and the enzyme.
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a GAPN.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a GAPN has an increased level of GAPN activity compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the GAPN, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of GAPN activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to host cell or fermenting organism without the heterologous polynucleotide encoding the GAPN, when cultivated under the same conditions.
  • Exemplary GAPNs that may be expressed with the host cells or fermenting organisms and methods of use described herein include, but are not limited to, GAPNs shown in Table 4 (or derivatives thereof). Table 4.
  • Additional polynucleotides encoding suitable GAPNs may be derived from microorganisms of any suitable genus, including those readily available within the UniProtKB database.
  • the GAPN coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding GAPNs from strains of different genera or species, as described supra.
  • the polynucleotides encoding GAPNs may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra.
  • the GAPN has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any one of the GAPNs described or referenced herein (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464), or the mature polypeptide thereof.
  • any one of the GAPNs described or referenced herein e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267
  • the GAPN has a mature polypeptide sequence that is a fragment of the any one of the GAPNs described or referenced herein (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464).
  • any one of SEQ ID NOs: 262-280 and 438-464 such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length GAPN (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464).
  • GAPN e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 2
  • the GAPN may comprise the catalytic domain of any GAPN described or referenced herein (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464).
  • any GAPN described or referenced herein e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278,
  • the GAPN may be a variant of any one of the GAPNs described supra (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464), or the mature polypeptide thereof.
  • any one of SEQ ID NOs: 262-280 and 438-464 such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 4
  • the GAPN has a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the GAPNs described supra (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464), or the mature polypeptide thereof.
  • any one of SEQ ID NOs: 262-280 and 438-464 such as any one of SEQ ID NOs: 262,
  • the GAPN has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the GAPNs described supra (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459,
  • any one of SEQ ID NOs: 262-280 and 438-464 such as any one of SEQ ID NOs: 262, 263, 264
  • the GAPN has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the GAPNs described supra (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464), or the mature polypeptide thereof.
  • any one of SEQ ID NOs: 262-280 and 438-464 such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271,
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the GAPN has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the GAPN activity of any GAPN described or referenced herein (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453,
  • the GAPN coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any GAPN described or referenced herein (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464) or the mature polypeptide coding sequence thereof.
  • any one of SEQ ID NOs: 262-280 and 438-464 such as any one of SEQ ID
  • the GAPN coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any GAPN described or referenced herein (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 46
  • the GAPN comprises the coding sequence of any GAPN described or referenced herein (e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462 and 464), or the mature polypeptide coding sequence thereof.
  • any GAPN described or referenced herein e.g., any one of SEQ ID NOs: 262-280 and 438-464; such as any one of SEQ ID NOs: 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274,
  • the GAPN comprises a coding sequence that is a subsequence of the coding sequence from any GAPN described or referenced herein, wherein the subsequence encodes a polypeptide having GAPN activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced GAPN coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the GAPN can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • F. Glucoamylases The host cells and fermenting organisms may express a heterologous glucoamylase.
  • the glucoamylase can be any glucoamylase that is suitable for the host cells, fermenting organisms and/or their methods of use described herein, such as a naturally occurring glucoamylase or a variant thereof that retains glucoamylase activity.
  • any glucoamylase contemplated for expression by a host cell or fermenting organism described below is also contemplated for embodiments of the invention involving exogenous addition of a glucoamylase (e.g., added before, during or after liquefaction and/or saccharification).
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a glucoamylase, for example, as described in WO2017/087330, the content of which is hereby incorporated by reference. Any glucoamylase described or referenced herein is contemplated for expression in the host cell or fermenting organism.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a glucoamylase has an increased level of glucoamylase activity compared to the host cells without the heterologous polynucleotide encoding the glucoamylase, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of glucoamylase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the glucoamylase, when cultivated under the same conditions.
  • Exemplary glucoamylases that can be used with the host cells and/or the methods described herein include bacterial, yeast, or filamentous fungal glucoamylases, e.g., obtained from any of the microorganisms described or referenced herein, as described supra.
  • Preferred glucoamylases are of fungal or bacterial origin, selected from the group consisting of Aspergillus glucoamylases, in particular Aspergillus niger G1 or G2 glucoamylase (Boel et al. (1984), EMBO J.3 (5), p.1097-1102), or variants thereof, such as those disclosed in WO 92/00381, WO 00/04136 and WO 01/04273 (from Novozymes, Denmark); the A. awamori glucoamylase disclosed in WO 84/02921, Aspergillus oryzae glucoamylase (Agric. Biol. Chem.
  • variants or fragments thereof include variants with enhanced thermal stability: G137A and G139A (Chen et al. (1996), Prot. Eng.9, 499-505); D257E and D293E/Q (Chen et al. (1995), Prot. Eng.8, 575-582); N182 (Chen et al. (1994), Biochem. J. 301, 275-281); disulphide bonds, A246C (Fierobe et al. (1996), Biochemistry, 35, 8698-8704; and introduction of Pro residues in position A435 and S436 (Li et al.
  • glucoamylases include Athelia rolfsii (previously denoted Corticium rolfsii) glucoamylase (see US patent no.4,727,026 and (Nagasaka et al. (1998) “Purification and properties of the raw-starch-degrading glucoamylases from Corticium rolfsii, Appl Microbiol Biotechnol 50:323-330), Talaromyces glucoamylases, in particular derived from Talaromyces emersonii (WO 99/28448), Talaromyces leycettanus (US patent no.
  • the glucoamylase used during saccharification and/or fermentation is the Talaromyces emersonii glucoamylase disclosed in WO 99/28448 or the Talaromyces emersonii glucoamylase of SEQ ID NO: 247.
  • Bacterial glucoamylases contemplated include glucoamylases from the genus Clostridium, in particular C. thermoamylolyticum (EP 135,138), and C. thermohydrosulfuricum (WO 86/01831).
  • Contemplated fungal glucoamylases include Trametes cingulate, Pachykytospora papyracea; and Leucopaxillus giganteus all disclosed in WO2006/069289; or Peniophora rufomarginata disclosed in WO2007/124285; or a mixture thereof. Also hybrid glucoamylase are contemplated. Examples include the hybrid glucoamylases disclosed in WO2005/045018.
  • the glucoamylase is derived from a strain of the genus Pycnoporus, in particular a strain of Pycnoporus as described in WO2011/066576 (SEQ ID NO: 2, 4 or 6 therein), including the Pycnoporus sanguineus glucoamylase, or from a strain of the genus Gloeophyllum, such as a strain of Gloeophyllum sepiarium or Gloeophyllum trabeum, in particular a strain of Gloeophyllum as described in WO 2011/068803 (SEQ ID NO: 2, 4, 6, 8, 10, 12, 14 or 16 therein).
  • the glucoamylase is SEQ ID NO: 2 in WO2011/068803 (i.e. Gloeophyllum sepiarium glucoamylase). In one embodiment, the glucoamylase is the Gloeophyllum sepiarium glucoamylase of SEQ ID NO: 8. In one embodiment, the glucoamylase is the Pycnoporus sanguineus glucoamylase of SEQ ID NO: 229. In one embodiment, the glucoamylase is a Gloeophyllum trabeum glucoamylase (disclosed as SEQ ID NO: 3 in WO2014/177546).
  • the glucoamylase is derived from a strain of the genus Nigrofomes, in particular a strain of Nigrofomes sp. disclosed in WO2012/064351 (disclosed as SEQ ID NO: 2 therein). Also contemplated are glucoamylases with a mature polypeptide sequence which exhibit a high identity to any of the above mentioned glucoamylases, i.e., at least 60%, such as at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or even 100% identity to any one of the mature polypeptide sequences mentioned above.
  • Glucoamylases may be added to the saccharification and/or fermentation in an amount of 0.0001-20 AGU/g DS, such as 0.001-10 AGU/g DS, 0.01-5 AGU/g DS, or 0.1-2 AGU/g DS.
  • Glucoamylases may be added to the saccharification and/or fermentation in an amount of 1-1,000 ⁇ g EP/g DS, such as 10-500 ⁇ g/gDS, or 25-250 ⁇ g/g DS.
  • Glucoamylases may be added to liquefaction in an amount of 0.1-100 ⁇ g EP/g DS, such as 0.5-50 ⁇ g EP/g DS, 1-25 ⁇ g EP/g DS, or 2-12 ⁇ g EP/g DS.
  • the glucoamylase is added as a blend further comprising an alpha-amylase (e.g., any alpha-amylase described herein).
  • the alpha- amylase is a fungal alpha-amylase, especially an acid fungal alpha-amylase.
  • the alpha- amylase is typically a side activity.
  • the glucoamylase is a blend comprising Talaromyces emersonii glucoamylase disclosed in WO 99/28448 as SEQ ID NO: 34 and Trametes cingulata glucoamylase disclosed as SEQ ID NO: 2 in WO06/069289.
  • the glucoamylase is a blend comprising Talaromyces emersonii glucoamylase disclosed in WO 99/28448, Trametes cingulata glucoamylase disclosed as SEQ ID NO: 2 in WO06/69289, and an alpha-amylase.
  • the glucoamylase is a blend comprising Talaromyces emersonii glucoamylase disclosed in WO99/28448, Trametes cingulata glucoamylase disclosed in WO 06/69289, and Rhizomucor pusillus alpha-amylase with Aspergillus niger glucoamylase linker and SBD disclosed as V039 in Table 5 in WO2006/069290.
  • the glucoamylase is a blend comprising Gloeophyllum sepiarium glucoamylase shown as SEQ ID NO: 2 in WO2011/068803 and an alpha-amylase, in particular Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), disclosed SEQ ID NO: 3 in WO2013/006756, in particular with the following substitutions: G128D+D143N.
  • SBD starch-binding domain
  • the alpha-amylase may be derived from a strain of the genus Rhizomucor, preferably a strain the Rhizomucor pusillus, such as the one shown in SEQ ID NO: 3 in WO2013/006756, or the genus Meripilus, preferably a strain of Meripilus giganteus.
  • the alpha-amylase is derived from a Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), disclosed as V039 in Table 5 in WO2006/069290.
  • the Rhizomucor pusillus alpha-amylase or the Rhizomucor pusillus alpha-amylase with an Aspergillus niger glucoamylase linker and starch-binding domain has at least one of the following substitutions or combinations of substitutions: D165M; Y141W; Y141R; K136F; K192R; P224A; P224R; S123H+Y141W; G20S + Y141W; A76G + Y141W; G128D + Y141W; G128D + D143N; P219C + Y141W; N142D + D143N; Y141W + K192R; Y141W + D143N; Y141W + N383R; Y141W + P219C + A265C; Y141W + N142D + D143N; Y141W + K192R V410A; G128D + Y141W + D143N; Y141W + K192R
  • the glucoamylase blend comprises Gloeophyllum sepiarium glucoamylase (e.g., SEQ ID NO: 2 in WO2011/068803) and Rhizomucor pusillus alpha- amylase.
  • the glucoamylase blend comprises Gloeophyllum sepiarium glucoamylase shown as SEQ ID NO: 2 in WO2011/068803 and Rhizomucor pusillus with an Aspergillus niger glucoamylase linker and starch-binding domain (SBD), disclosed SEQ ID NO: 3 in WO2013/006756 with the following substitutions: G128D+D143N.
  • compositions comprising glucoamylase include AMG 200L; AMG 300 L; SANTM SUPER, SANTM EXTRA L, SPIRIZYME® PLUS, SPIRIZYME® FUEL, SPIRIZYME® B4U, SPIRIZYME® ULTRA, SPIRIZYME® EXCEL, SPIRIZYME ACHIEVE®, and AMG® E (from Novozymes A/S); OPTIDEXTM 300, GC480, GC417 (from DuPont- Danisco); AMIGASETM and AMIGASETM PLUS (from DSM); G-ZYMETM G900, G-ZYMETM and G990 ZR (from DuPont-Danisco).
  • the glucoamylase is derived from the Debaryomyces occidentalis glucoamylase of SEQ ID NO: 102. In one embodiment, the glucoamylase is derived from the Saccharomycopsis fibuligera glucoamylase of SEQ ID NO: 103. In one embodiment, the glucoamylase is derived from the Saccharomycopsis fibuligera glucoamylase of SEQ ID NO: 104. In one embodiment, the glucoamylase is derived from the Saccharomyces cerevisiae glucoamylase of SEQ ID NO: 105.
  • the glucoamylase is derived from the Aspergillus niger glucoamylase of SEQ ID NO: 106. In one embodiment, the glucoamylase is derived from the Aspergillus oryzae glucoamylase of SEQ ID NO: 107. In one embodiment, the glucoamylase is derived from the Rhizopus oryzae glucoamylase of SEQ ID NO: 108 or SEQ ID NO: 250. In one embodiment, the glucoamylase is derived from the Clostridium thermocellum glucoamylase of SEQ ID NO: 109.
  • the glucoamylase is derived from the Clostridium thermocellum glucoamylase of SEQ ID NO: 110. In one embodiment, the glucoamylase is derived from the Arxula adeninivorans glucoamylase of SEQ ID NO: 111. In one embodiment, the glucoamylase is derived from the Hormoconis resinae glucoamylase of SEQ ID NO: 112. In one embodiment, the glucoamylase is derived from the Aureobasidium pullulans glucoamylase of SEQ ID NO: 113.
  • the glucoamylase is derived from the Rhizopus microsporus glucoamylase of SEQ ID NO: 248. In one embodiment, the glucoamylase is derived from the Rhizopus delemar glucoamylase of SEQ ID NO: 249. In one embodiment, the glucoamylase is derived from the Punctularia strigosozonata glucoamylase of SEQ ID NO: 244. In one embodiment, the glucoamylase is derived from the Fibroporia radiculosa glucoamylase of SEQ ID NO: 245.
  • the glucoamylase is derived from the Wolfiporia cocos glucoamylase of SEQ ID NO: 246. In one embodiment, the glucoamylase is a Trichoderma reesei glucoamylase, such as theTrichoderma reesei glucoamylase of SEQ ID NO: 230. In one embodiment, the glucoamylase has a Relative Activity heat stability at 85oC of at least 20%, at least 30%, or at least 35% determined as described in Example 4 of WO2018/098381 (heat stability).
  • the glucoamylase has a relative activity pH optimum at pH 5.0 of at least 90%, e.g., at least 95%, at least 97%, or 100% determined as described in Example 4 of WO2018/098381 (pH optimum). In one embodiment, the glucoamylase has a pH stability at pH 5.0 of at least 80%, at least 85%, at least 90% determined as described in Example 4 of WO2018/098381 (pH stability).
  • the glucoamylase used in liquefaction such as a Penicillium oxalicum glucoamylase variant, has a thermostability determined as DSC Td at pH 4.0 as described in Example 15 of WO2018/098381 of at least 70oC, preferably at least 75oC, such as at least 80oC, such as at least 81oC, such as at least 82oC, such as at least 83oC, such as at least 84oC, such as at least 85oC, such as at least 86oC, such as at least 87%, such as at least 88oC, such as at least 89oC, such as at least 90oC.
  • the glucoamylase such as a Penicillium oxalicum glucoamylase variant, has a thermostability determined as DSC Td at pH 4.0 as described in Example 15 of WO2018/098381 in the range between 70oC and 95oC, such as between 80oC and 90oC.
  • the glucoamylase such as a Penicillium oxalicum glucoamylase variant, used in liquefaction has a thermostability determined as DSC Td at pH 4.8 as described in Example 15 of WO2018/098381 of at least 70oC, preferably at least 75oC, such as at least 80oC, such as at least 81oC, such as at least 82oC, such as at least 83oC, such as at least 84oC, such as at least 85oC, such as at least 86oC, such as at least 87%, such as at least 88oC, such as at least 89oC, such as at least 90oC, such as at least 91oC.
  • the glucoamylase such as a Penicillium oxalicum glucoamylase variant
  • the glucoamylase, such as a Penicillium oxalicum glucoamylase variant, used in liquefaction has a residual activity determined as described in Example 16 of WO2018/098381, of at least 100% such as at least 105%, such as at least 110%, such as at least 115%, such as at least 120%, such as at least 125%.
  • the glucoamylase such as a Penicillium oxalicum glucoamylase variant, has a thermostability determined as residual activity as described in Example 16 of WO2018/098381, in the range between 100% and 130%.
  • the glucoamylase e.g., of fungal origin such as a filamentous fungi, from a strain of the genus Penicillium, e.g., a strain of Penicillium oxalicum, in particular the Penicillium oxalicum glucoamylase disclosed as SEQ ID NO: 2 in WO2011/127802 (which is hereby incorporated by reference).
  • the glucoamylase has a mature polypeptide sequence of at least 80%, e.g., at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% or 100% identity to the mature polypeptide shown in SEQ ID NO: 2 in WO2011/127802.
  • the glucoamylase is a variant of the Penicillium oxalicum glucoamylase disclosed as SEQ ID NO: 2 in WO2011/127802, having a K79V substitution.
  • the K79V glucoamylase variant has reduced sensitivity to protease degradation relative to the parent as disclosed in WO2013/036526 (which is hereby incorporated by reference).
  • the glucoamylase is derived from Penicillium oxalicum.
  • the glucoamylase is a variant of the Penicillium oxalicum glucoamylase disclosed as SEQ ID NO: 2 in WO2011/127802.
  • the Penicillium oxalicum glucoamylase is the one disclosed as SEQ ID NO: 2 in WO2011/127802 having Val (V) in position 79.
  • Penicillium oxalicum glucoamylase variants are disclosed in WO 2013/053801 which is hereby incorporated by reference. In one embodiment, these variants have reduced sensitivity to protease degradation. In one embodiment, these variants have improved thermostability compared to the parent.
  • the glucoamylase has a K79V substitution (using SEQ ID NO: 2 of WO2011/127802 for numbering), corresponding to the PE001 variant, and further comprises one of the following alterations or combinations of alterations: T65A; Q327F; E501V; Y504T; Y504*; T65A + Q327F; T65A + E501V; T65A + Y504T; T65A + Y504*; Q327F + E501V; Q327F + Y504T; Q327F + Y504*; E501V + Y504T; E501V + Y504*; T65A + Q327F + E501V; T65A + Q327F + Y504T; T65A + E501V + Y504T; Q327F + E501V + Y504T; T65A + Q327F + Y504T; T65A + E501V + Y504T
  • the Penicillium oxalicum glucoamylase variant has a K79V substitution (using SEQ ID NO: 2 of WO2011/127802 for numbering), corresponding to the PE001 variant, and further comprises one of the following substitutions or combinations of substitutions: P11F + T65A + Q327F; P2N + P4S + P11F + T65A + Q327F; P11F + D26C + K33C + T65A + Q327F; P2N + P4S + P11F + T65A + Q327W + E501V + Y504T; P2N + P4S + P11F + T65A + Q327F + E501V + Y504T; and P11F + T65A + Q327W + E501V + Y504T.
  • substitutions or combinations of substitutions P11F + T65A + Q327F; P2N + P4S + P11F + T65A + Q327F; P11F +
  • Additional glucoamylases contemplated for use with the present invention can be found in WO2011/153516 (the content of which is incorporated herein). Additional polynucleotides encoding suitable glucoamylases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database. The glucoamylase coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding glucoamylases from strains of different genera or species, as described supra.
  • polynucleotides encoding glucoamylases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc,) as described supra. Techniques used to isolate or clone polynucleotides encoding glucoamylases are described supra.
  • the glucoamylase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any one of the glucoamylases described or referenced herein (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244- 250), or the mature polypeptide thereof.
  • the glucoamylase has a mature polypeptide sequence that is a fragment of the any one of the glucoamylases described or referenced herein (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244- 250), or the mature polypeptide thereof.
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length glucoamylase (e.g. any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250).
  • the glucoamylase may comprise the catalytic domain of any glucoamylase described or referenced herein (e.g., the catalytic domain of any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250).
  • the glucoamylase may be a variant of any one of the glucoamylases described supra (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250), or the mature polypeptide thereof.
  • the glucoamylase has a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the glucoamylases described supra (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250), or the mature polypeptide thereof.
  • the glucoamylase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the glucoamylases described supra (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250), or the mature polypeptide thereof.
  • the glucoamylase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the glucoamylases described supra (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250), or the mature polypeptide thereof.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the glucoamylase has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the glucoamylase activity of any glucoamylase described or referenced herein (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250) under the same conditions.
  • any glucoamylase described or referenced herein e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250
  • the glucoamylase coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any glucoamylase described or referenced herein (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250), or the mature polypeptide coding sequence thereof.
  • any glucoamylase described or referenced herein e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250
  • the glucoamylase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any glucoamylase described or referenced herein (e.g., any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250), or the mature polypeptide coding sequence thereof.
  • the glucoamylase comprises the coding sequence of any glucoamylase described or referenced herein (any one of SEQ ID NOs: 8, 102-113, 229, 230 and 244-250), or the mature polypeptide coding sequence thereof.
  • the glucoamylase comprises a coding sequence that is a subsequence of the coding sequence from any glucoamylase described or referenced herein, wherein the subsequence encodes a polypeptide having glucoamylase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced glucoamylase coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the glucoamylase can also include fused polypeptides or cleavable fusion polypeptides, as described supra. G.
  • Alpha-amylases The host cells and fermenting organisms may express a heterologous alpha- amylase.
  • the alpha-amylase may be any alpha-amylase that is suitable for the host cells and/or the methods described herein, such as a naturally occurring alpha-amylase (e.g., a native alpha-amylase from another species or an endogenous alpha-amylase expressed from a modified expression vector) or a variant thereof that retains alpha-amylase activity.
  • Any alpha-amylase contemplated for expression by a host cell or fermenting organism described below is also contemplated for embodiments of the invention involving exogenous addition of an alpha-amylase.
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding an alpha-amylase, for example, as described in WO2017/087330 or WO2020/023411, the content of which is hereby incorporated by reference. Any alpha-amylase described or referenced herein is contemplated for expression in the host cell or fermenting organism.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding an alpha-amylase has an increased level of alpha- amylase activity compared to the host cells without the heterologous polynucleotide encoding the alpha-amylase, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of alpha-amylase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the alpha-amylase, when cultivated under the same conditions (e.g., as described in Example 2).
  • Exemplary alpha-amylases that can be used with the host cells and/or the methods described herein include bacterial, yeast, or filamentous fungal alpha-amylases, e.g., derived from any of the microorganisms described or referenced herein.
  • the term “bacterial alpha-amylase” means any bacterial alpha-amylase classified under EC 3.2.1.1.
  • a bacterial alpha-amylase used herein may, e.g., be derived from a strain of the genus Bacillus, which is sometimes also referred to as the genus Geobacillus.
  • the Bacillus alpha-amylase is derived from a strain of Bacillus amyloliquefaciens, Bacillus licheniformis, Bacillus stearothermophilus, or Bacillus subtilis, but may also be derived from other Bacillus sp.
  • bacterial alpha-amylases include the Bacillus stearothermophilus alpha-amylase (BSG) of SEQ ID NO: 3 in WO99/19467, the Bacillus amyloliquefaciens alpha-amylase (BAN) of SEQ ID NO: 5 in WO99/19467, and the Bacillus licheniformis alpha-amylase (BLA) of SEQ ID NO: 4 in WO99/19467 (all sequences are hereby incorporated by reference).
  • BSG Bacillus stearothermophilus alpha-amylase
  • BAN Bacillus amyloliquefaciens alpha-amylase
  • BLA Bacillus licheniformis alpha-amylase
  • the alpha-amylase may be an enzyme having a mature polypeptide sequence with a degree of identity of at least 60%, e.g., at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% to any of the sequences shown in SEQ ID NOs: 3, 4 or 5, in WO99/19467.
  • the alpha-amylase is derived from Bacillus stearothermophilus.
  • the Bacillus stearothermophilus alpha-amylase may be a mature wild-type or a mature variant thereof.
  • the mature Bacillus stearothermophilus alpha-amylases may naturally be truncated during recombinant production.
  • the Bacillus stearothermophilus alpha-amylase may be a truncated at the C-terminal, so that it is from 480-495 amino acids long, such as about 491 amino acids long, e.g., so that it lacks a functional starch binding domain (compared to SEQ ID NO: 3 in WO99/19467).
  • the Bacillus alpha-amylase may also be a variant and/or hybrid.
  • Patent Nos.6,093,562, 6,187,576, 6,297,038, and 7,713,723 include Bacillus stearothermophilus alpha- amylase (often referred to as BSG alpha-amylase) variants having a deletion of one or two amino acids at positions R179, G180, I181 and/or G182, preferably a double deletion disclosed in WO96/23873 – see, e.g., page 20, lines 1-10 (hereby incorporated by reference), such as corresponding to deletion of positions I181 and G182 compared to the amino acid sequence of Bacillus stearothermophilus alpha-amylase set forth in SEQ ID NO: 3 disclosed in WO99/19467 or the deletion of amino acids R179 and G180 using SEQ ID NO: 3 in WO99/19467 for numbering (which reference is hereby incorporated by reference).
  • BSG alpha-amylase Bacillus stearothermophilus alpha- amylase
  • the Bacillus alpha-amylases such as Bacillus stearothermophilus alpha-amylases, have a double deletion corresponding to a deletion of positions 181 and 182 and further optionally comprise a N193F substitution (also denoted I181* + G182* + N193F) compared to the wild-type BSG alpha-amylase amino acid sequence set forth in SEQ ID NO: 3 disclosed in WO 99/19467.
  • the bacterial alpha-amylase may also have a substitution in a position corresponding to S239 in the Bacillus licheniformis alpha-amylase shown in SEQ ID NO: 4 in WO99/19467, or a S242 and/or E188P variant of the Bacillus stearothermophilus alpha-amylase of SEQ ID NO: 3 in WO99/19467.
  • the variant is a S242A, E or Q variant, e.g., a S242Q variant, of the Bacillus stearothermophilus alpha-amylase.
  • the variant is a position E188 variant, e.g., E188P variant of the Bacillus stearothermophilus alpha-amylase.
  • the bacterial alpha-amylase may, in one embodiment, be a truncated Bacillus alpha-amylase.
  • the truncation is so that, e.g., the Bacillus stearothermophilus alpha-amylase shown in SEQ ID NO: 3 in WO99/19467, is about 491 amino acids long, such as from 480 to 495 amino acids long, or so it lacks a functional starch bind domain.
  • the bacterial alpha-amylase may also be a hybrid bacterial alpha-amylase, e.g., an alpha-amylase comprising 445 C-terminal amino acid residues of the Bacillus licheniformis alpha-amylase (shown in SEQ ID NO: 4 of WO99/19467) and the 37 N-terminal amino acid residues of the alpha-amylase derived from Bacillus amyloliquefaciens (shown in SEQ ID NO: 5 of WO99/19467).
  • an alpha-amylase comprising 445 C-terminal amino acid residues of the Bacillus licheniformis alpha-amylase (shown in SEQ ID NO: 4 of WO99/19467) and the 37 N-terminal amino acid residues of the alpha-amylase derived from Bacillus amyloliquefaciens (shown in SEQ ID NO: 5 of WO99/19467).
  • this hybrid has one or more, especially all, of the following substitutions: G48A+T49I+G107A+H156Y+A181T+N190F+I201F+A209V+Q264S (using the Bacillus licheniformis numbering in SEQ ID NO: 4 of WO 99/19467).
  • the variants have one or more of the following mutations (or corresponding mutations in other Bacillus alpha-amylases): H154Y, A181T, N190F, A209V and Q264S and/or the deletion of two residues between positions 176 and 179, e.g., deletion of E178 and G179 (using SEQ ID NO: 5 of WO99/19467 for position numbering).
  • the bacterial alpha-amylase is the mature part of the chimeric alpha-amylase disclosed in Richardson et al. (2002), The Journal of Biological Chemistry, Vol.277, No 29, Issue 19 July, pp.267501-26507, referred to as BD5088 or a variant thereof.
  • This alpha-amylase is the same as the one shown in SEQ ID NO: 2 in WO2007/134207.
  • the mature enzyme sequence starts after the initial “Met” amino acid in position 1.
  • the alpha-amylase may be a thermostable alpha-amylase, such as a thermostable bacterial alpha-amylase, e.g., from Bacillus stearothermophilus.
  • the alpha-amylase used in a process described herein has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 of at least 10 determined as described in Example 1 of WO2018/098381.
  • the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl2, of at least 15. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , of as at least 20. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , of as at least 25.
  • the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , of as at least 30. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , of as at least 40. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , of at least 50.
  • the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , of at least 60. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , between 10- 70. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , between 15-70.
  • the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , between 20-70. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , between 25- 70. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , between 30-70.
  • the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , between 40-70. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , between 50- 70. In one embodiment, the thermostable alpha-amylase has a T1 ⁇ 2 (min) at pH 4.5, 85°C, 0.12 mM CaCl 2 , between 60-70.
  • the alpha-amylase is a bacterial alpha-amylase, e.g., derived from the genus Bacillus, such as a strain of Bacillus stearothermophilus, e.g., the Bacillus stearothermophilus as disclosed in WO99/019467 as SEQ ID NO: 3 with one or two amino acids deleted at positions R179, G180, I181 and/or G182, in particular with R179 and G180 deleted, or with I181 and G182 deleted, with mutations in below list of mutations.
  • a bacterial alpha-amylase e.g., derived from the genus Bacillus, such as a strain of Bacillus stearothermophilus, e.g., the Bacillus stearothermophilus as disclosed in WO99/019467 as SEQ ID NO: 3 with one or two amino acids deleted at positions R179, G180, I181 and/or G182, in particular with R179 and G180
  • the Bacillus stearothermophilus alpha-amylases have double deletion I181 + G182, and optional substitution N193F, further comprising one of the following substitutions or combinations of substitutions: V59A+Q89R+G112D+E129V+K177L+R179E+K220P+N224L+Q254S; V59A+Q89R+E129V+K177L+R179E+H208Y+K220P+N224L+Q254S; V59A+Q89R+E129V+K177L+R179E+K220P+N224L+Q254S+D269E+D281N; V59A+Q89R+E129V+K177L+R179E+K220P+N224L+Q254S+I270L; V59A+Q89R+E129V+K177L+R179E+K220P+N224L+Q254S+I270L; V59A+Q89
  • the alpha-amylase is normally produced in truncated form.
  • the truncation may be so that the Bacillus stearothermophilus alpha-amylase shown in SEQ ID NO: 3 in WO99/19467, or variants thereof, are truncated in the C-terminal and are typically from 480- 495 amino acids long, such as about 491 amino acids long, e.g., so that it lacks a functional starch binding domain.
  • the alpha-amylase variant may be an enzyme having a mature polypeptide sequence with a degree of identity of at least 60%, e.g., at least 70%, at least 80%, at least 90%, at least 95%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99%, but less than 100% to the sequence shown in SEQ ID NO: 3 in WO99/19467.
  • the bacterial alpha-amylase e.g., Bacillus alpha-amylase, such as especially Bacillus stearothermophilus alpha-amylase, or variant thereof, is dosed to liquefaction in a concentration between 0.01-10 KNU-A/g DS, e.g., between 0.02 and 5 KNU-A/g DS, such as 0.03 and 3 KNU-A, preferably 0.04 and 2 KNU-A/g DS, such as especially 0.01 and 2 KNU-A/g DS.
  • a concentration between 0.01-10 KNU-A/g DS, e.g., between 0.02 and 5 KNU-A/g DS, such as 0.03 and 3 KNU-A, preferably 0.04 and 2 KNU-A/g DS, such as especially 0.01 and 2 KNU-A/g DS.
  • the bacterial alpha-amylase e.g., Bacillus alpha-amylase, such as especially Bacillus stearothermophilus alpha-amylases, or variant thereof, is dosed to liquefaction in a concentration of between 0.0001-1 mg EP (Enzyme Protein)/g DS, e.g., 0.0005-0.5 mg EP/g DS, such as 0.001-0.1 mg EP/g DS.
  • EP Enzyme Protein
  • the bacterial alpha-amylase is derived from the Bacillus subtilis alpha-amylase of SEQ ID NO: 76, the Bacillus subtilis alpha-amylase of SEQ ID NO: 82, the Bacillus subtilis alpha-amylase of SEQ ID NO: 83, the Bacillus subtilis alpha-amylase of SEQ ID NO: 84, or the Bacillus licheniformis alpha-amylase of SEQ ID NO: 85, the Clostridium phytofermentans alpha-amylase of SEQ ID NO: 89, the Clostridium phytofermentans alpha- amylase of SEQ ID NO: 90, the Clostridium phytofermentans alpha-amylase of SEQ ID NO: 91, the Clostridium phytofermentans alpha-amylase of SEQ ID NO: 92, the Clostridium phytofermentans alpha-amylase of SEQ ID NO: 93, the Clostridium phytofermentans alpha
  • the alpha-amylase is derived from Bacillus amyloliquefaciens, such as the Bacillus amyloliquefaciens alpha-amylase of SEQ ID NO: 231 (e.g., as described in WO2018/002360, or variants thereof as described in WO2017/037614).
  • the alpha-amylase is derived from a yeast alpha-amylase, such as the Saccharomycopsis fibuligera alpha-amylase of SEQ ID NO: 77, the Debaryomyces occidentalis alpha-amylase of SEQ ID NO: 78, the Debaryomyces occidentalis alpha- amylase of SEQ ID NO: 79, the Lipomyces kononenkoae alpha-amylase of SEQ ID NO: 80, the Lipomyces kononenkoae alpha-amylase of SEQ ID NO: 81.
  • yeast alpha-amylase such as the Saccharomycopsis fibuligera alpha-amylase of SEQ ID NO: 77, the Debaryomyces occidentalis alpha-amylase of SEQ ID NO: 78, the Debaryomyces occidentalis alpha- amylase of SEQ ID NO: 79, the Lipomyces kononenkoae alpha-amylase of SEQ ID NO: 80, the
  • the alpha-amylase is derived from a filamentous fungal alpha-amylase, such as the Aspergillus niger alpha-amylase of SEQ ID NO: 86, or the Aspergillus niger alpha-amylase of SEQ ID NO: 87. Additional alpha-amylases that may be expressed with the host cells and fermenting organisms and used with the methods described herein are described in the examples, and include, but are not limited to alpha-amylases shown in Table 5 (or derivatives thereof). Table 5.
  • alpha-amylases contemplated for use with the present invention can be found in WO2011/153516, WO2017/087330 and WO2020/023411 (the content of which is incorporated herein). Additional polynucleotides encoding suitable alpha-amylases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database. The alpha-amylase coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding alpha-amylases from strains of different genera or species, as described supra.
  • the polynucleotides encoding alpha-amylases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra. Techniques used to isolate or clone polynucleotides encoding alpha-amylases are described supra.
  • the alpha-amylase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any one of the alpha-amylases described or referenced herein (e.g., any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the alpha-amylase has a mature polypeptide sequence that is a fragment of the any one of the alpha-amylases described or referenced herein (e.g., any one of SEQ ID NOs: 76-101, 121- 174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length alpha-amylase (e.g. any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the alpha-amylase may comprise the catalytic domain of any alpha-amylase described or referenced herein (e.g., the catalytic domain of any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256).
  • the alpha-amylase may be a variant of any one of the alpha-amylases described supra (e.g., any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the alpha-amylase has a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the alpha-amylases described supra (e.g., any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the alpha-amylase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the alpha-amylases described supra (e.g., any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the alpha-amylase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the alpha-amylases described supra (e.g., any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the alpha-amylase has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the alpha-amylase activity of any alpha- amylase described or referenced herein (e.g., any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof, under the same conditions.
  • the alpha-amylase coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any alpha-amylase described or referenced herein (e.g., any one of SEQ ID NOs: 76-101, 121-174 and 231), or the mature polypeptide coding sequence thereof.
  • any alpha-amylase described or referenced herein e.g., any one of SEQ ID NOs: 76-101, 121-174 and 231
  • the alpha-amylase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any alpha-amylase described or referenced herein (e.g., any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the alpha-amylase comprises the coding sequence of any alpha-amylase described or referenced herein (any one of SEQ ID NOs: 76-101, 121-174, 231 and 251-256), or the mature polypeptide coding sequence thereof.
  • the alpha-amylase comprises a coding sequence that is a subsequence of the coding sequence from any alpha-amylase described or referenced herein, wherein the subsequence encodes a polypeptide having alpha-amylase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced alpha-amylase coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the alpha-amylase can also include fused polypeptides or cleavable fusion polypeptides, as described supra. H.
  • the host cells and fermenting organisms may express a heterologous phospholipase.
  • the phospholipase may be any phospholipase that is suitable for the host cells, fermenting organism, and/or the methods described herein, such as a naturally occurring phospholipase (e.g., a native phospholipase from another species or an endogenous phospholipase expressed from a modified expression vector) or a variant thereof that retains phospholipase activity.
  • any phospholipase contemplated for expression by a host cell or fermenting organism described below is also contemplated for embodiments of the invention involving exogenous addition of a phospholipase (e.g., added before, during or after liquefaction and/or saccharification).
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a phospholipase, for example, as described in WO2018/075430, the content of which is hereby incorporated by reference.
  • the phospholipase is classified as a phospholipase A.
  • the phospholipase is classified as a phospholipase C.
  • any phospholipase described or referenced herein is contemplated for expression in the host cell or fermenting organism.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a phospholipase has an increased level of phospholipase activity compared to the host cells without the heterologous polynucleotide encoding the phospholipase, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of phospholipase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the phospholipase, when cultivated under the same conditions.
  • Exemplary phospholipases that can be used with the host cells and/or the methods described herein include bacterial, yeast, or filamentous fungal phospholipases, e.g., derived from any of the microorganisms described or referenced herein.
  • Additional phospholipases that may be expressed with the host cells and fermenting organisms, and used with the methods described herein, and include, but are not limited to phospholipases shown in Table 6 (or derivatives thereof). Table 6. Additional phospholipases contemplated for use with the present invention can be found in WO2018/075430 (the content of which is incorporated herein). Additional polynucleotides encoding suitable phospholipases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database. The phospholipase coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding phospholipases from strains of different genera or species, as described supra.
  • polynucleotides encoding phospholipases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra. Techniques used to isolate or clone polynucleotides encoding phospholipases are described supra.
  • the phospholipase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any one of the phospholipases described or referenced herein (e.g., any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242), or the mature polypeptide thereof.
  • the phospholipase has a mature polypeptide sequence that is a fragment of the any one of the phospholipases described or referenced herein (e.g., any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242), or the mature polypeptide thereof.
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length phospholipase (e.g. any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242), or the mature polypeptide coding sequence thereof.
  • the phospholipase may comprise the catalytic domain of any phospholipase described or referenced herein (e.g., the catalytic domain of any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242).
  • the phospholipase may be a variant of any one of the phospholipases described supra (e.g., any one of SEQ ID NOs: SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242), or the mature polypeptide thereof.
  • the phospholipase has a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the phospholipases described supra (e.g., any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242), or the mature polypeptide thereof.
  • suitable amino acid changes such as conservative substitutions that do not significantly affect the folding and/or activity of the phospholipase, are described herein.
  • the phospholipase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the phospholipases described supra (e.g., any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242), or the mature polypeptide thereof.
  • the phospholipase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the phospholipases described supra (e.g., any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242), or the mature polypeptide thereof.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the phospholipase has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the phospholipase activity of any phospholipase described or referenced herein (e.g., any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242), or the mature polypeptide thereof, under the same conditions.
  • any phospholipase described or referenced herein e.g., any one of SEQ ID NOs: 235, 236, 237, 238, 239, 240, 241, and 242
  • the phospholipase coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any phospholipase described or referenced herein (e.g., a coding sequence for a phospholipase of SEQ ID NO: 235, 236, 237, 238, 239, 240, 241 or 242), or the mature polypeptide coding sequence thereof.
  • any phospholipase described or referenced herein e.g., a coding sequence for a phospholipase of SEQ ID NO: 235, 236, 237, 238, 239, 240, 241 or 242
  • the phospholipase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any phospholipase described or referenced herein (e.g., a coding sequence for a phospholipase of SEQ ID NO: 235, 236, 237, 238, 239, 240, 241 or 242), or the mature polypeptide coding sequence thereof.
  • any phospholipase described or referenced herein e.g., a coding sequence for a phospholipase of SEQ ID NO: 235, 236, 237, 238, 239, 240, 241 or 242
  • the phospholipase comprises the coding sequence of any phospholipase described or referenced herein (e.g., a coding sequence for a phospholipase of SEQ ID NO: 235, 236, 237, 238, 239, 240, 241 or 242), or the mature polypeptide coding sequence thereof.
  • the phospholipase comprises a coding sequence that is a subsequence of the coding sequence from any phospholipase described or referenced herein, wherein the subsequence encodes a polypeptide having phospholipase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced phospholipase coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the phospholipase can also include fused polypeptides or cleavable fusion polypeptides, as described supra. I.
  • the host cells and fermenting organisms may express a heterologous trehalase.
  • the trehalase can be any trehalase that is suitable for the host cells, fermenting organisms and/or their methods of use described herein, such as a naturally occurring trehalase or a variant thereof that retains trehalase activity.
  • Any trehalase contemplated for expression by a host cell or fermenting organism described below is also contemplated for embodiments of the invention involving exogenous addition of a trehalase (e.g., added before, during or after liquefaction and/or saccharification).
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a trehalase has an increased level of trehalase activity compared to the host cells without the heterologous polynucleotide encoding the trehalase, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of trehalase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the trehalase, when cultivated under the same conditions.
  • Trehalases that may be expressed with the host cells and fermenting organisms, and used with the methods described herein include, but are not limited to, trehalases shown in Table 7 (or derivatives thereof). Table 7.
  • Additional polynucleotides encoding suitable trehalases may be derived from microorganisms of any suitable genus, including those readily available within the UniProtKB database.
  • the trehalase coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding trehalases from strains of different genera or species, as described supra.
  • the polynucleotides encoding trehalases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra.
  • the trehalase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any one of the trehalases described or referenced herein (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide thereof.
  • the trehalase has a mature polypeptide sequence that is a fragment of the any one of the trehalases described or referenced herein (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide thereof.
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length trehalase (e.g. any one of SEQ ID NOs: 175-226), or the mature polypeptide thereof.
  • the trehalase may comprise the catalytic domain of any trehalase described or referenced herein (e.g., the catalytic domain of any one of SEQ ID NOs: 175-226).
  • the trehalase may be a variant of any one of the trehalases described supra (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide thereof.
  • the trehalase has a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the trehalases described supra (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide thereof.
  • suitable amino acid changes such as conservative substitutions that do not significantly affect the folding and/or activity of the trehalase, are described herein.
  • the trehalase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the trehalases described supra (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide thereof.
  • the trehalase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the trehalases described supra (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide thereof.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the trehalase has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the trehalase activity of any trehalase described or referenced herein (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide thereof, under the same conditions.
  • any trehalase described or referenced herein e.g., any one of SEQ ID NOs: 175-226
  • the trehalase coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any trehalase described or referenced herein (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide coding sequence thereof.
  • low stringency conditions e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions
  • any trehalase described or referenced herein e.g., any one of SEQ ID NOs: 175-226
  • the trehalase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any trehalase described or referenced herein (e.g., any one of SEQ ID NOs: 175-226), or the mature polypeptide coding sequence thereof.
  • the trehalase comprises the coding sequence of any trehalase described or referenced herein (any one of SEQ ID NOs: 175-226), or the mature polypeptide coding sequence thereof.
  • the trehalase comprises a coding sequence that is a subsequence of the coding sequence from any trehalase described or referenced herein, wherein the subsequence encodes a polypeptide having trehalase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced trehalase coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the protease can be any protease that is suitable for the host cells and fermenting organisms and/or their methods of use described herein, such as a naturally occurring protease or a variant thereof that retains protease activity. Any protease contemplated for expression by a host cell or fermenting organism described below is also contemplated for embodiments of the invention involving exogenous addition of a protease (e.g., added before, during or after liquefaction and/or saccharification).
  • Proteases are classified on the basis of their catalytic mechanism into the following groups: Serine proteases (S), Cysteine proteases (C), Aspartic proteases (A), Metallo proteases (M), and Unknown, or as yet unclassified, proteases (U), see Handbook of Proteolytic Enzymes, A.J.Barrett, N.D.Rawlings, J.F.Woessner (eds), Academic Press (1998), in particular the general introduction part. Protease activity can be measured using any suitable assay, in which a substrate is employed, that includes peptide bonds relevant for the specificity of the protease in question.
  • Assay-pH and assay-temperature are likewise to be adapted to the protease in question.
  • assay-pH-values are pH 6, 7, 8, 9, 10, or 11.
  • assay-temperatures are 30, 35, 37, 40, 45, 50, 55, 60, 65, 70 or 80°C.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a protease has an increased level of protease activity compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the protease, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of protease activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the protease, when cultivated under the same conditions.
  • Exemplary proteases that may be expressed with the host cells and fermenting organisms, and used with the methods described herein include, but are not limited to, proteases shown in Table 8 (or derivatives thereof). Table 8.
  • protease is derived from Aspergillus, such as the Aspergillus niger protease of SEQ ID NO: 9, the Aspergillus tamarii protease of SEQ ID NO: 41, or the Aspergillus denticulatus protease of SEQ ID NO: 45.
  • the protease is derived from Dichomitus, such as the Dichomitus squalens protease of SEQ ID NO: 12.
  • the protease is derived from Penicillium, such as the Penicillium simplicissimum protease of SEQ ID NO: 14, the Penicillium antarcticum protease of SEQ ID NO: 66, or the Penicillium sumatrense protease of SEQ ID NO: 67.
  • the protease is derived from Meriphilus, such as the Meriphilus giganteus protease of SEQ ID NO: 16.
  • the protease is derived from Talaromyces, such as the Talaromyces liani protease of SEQ ID NO: 21.
  • the protease is derived from Thermoascus, such as the Thermoascus thermophilus protease of SEQ ID NO: 22.
  • the protease is derived from Ganoderma, such as the Ganoderma lucidum protease of SEQ ID NO: 33.
  • the protease is derived from Hamigera, such as the Hamigera terricola protease of SEQ ID NO: 61.
  • the protease is derived from Trichoderma, such as the Trichoderma brevicompactum protease of SEQ ID NO: 69.
  • the protease coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding proteases from strains of different genera or species, as described supra.
  • the polynucleotides encoding proteases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra. Techniques used to isolate or clone polynucleotides encoding proteases are described supra.
  • the protease has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any one of SEQ ID NOs: 9-73 (e.g., any one of SEQ ID NOs: 9, 14, 16, 21, 22, 33, 41, 45, 61, 62, 66, 67, and 69; such as any one of SEQ NOs: 9, 14, 16, and 69), or the mature polypeptide thereof.
  • the protease has a mature polypeptide sequence that is a fragment of the protease of any one of SEQ ID NOs: 9-73 (e.g., wherein the fragment has protease activity), or the mature polypeptide thereof.
  • the number of amino acid residues in the fragment is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of amino acid residues in referenced full length protease (e.g. any one of SEQ ID NOs: 9-73), or the mature polypeptide thereof.
  • the protease may comprise the catalytic domain of any protease described or referenced herein (e.g., the catalytic domain of any one of SEQ ID NOs: 9-73).
  • the protease may be a variant of any one of the proteases described supra (e.g., any one of SEQ ID NOs: 9-73, or the mature polypeptide thereof.
  • the protease has a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the proteases described supra (e.g., any one of SEQ ID NOs: 9-73), or the mature polypeptide thereof.
  • suitable amino acid changes such as conservative substitutions that do not significantly affect the folding and/or activity of the protease, are described herein.
  • the protease has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the proteases described supra (e.g., any one of SEQ ID NOs: 9-73), or the mature polypeptide thereof.
  • the protease has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the proteases described supra (e.g., any one of SEQ ID NOs: 9-73), or the mature polypeptide thereof.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the protease coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any protease described or referenced herein (e.g., any one of SEQ ID NOs: 9-73), or the mature polypeptide coding sequence thereof.
  • the protease coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any protease described or referenced herein (e.g., any one of SEQ ID NOs: 9-73), or the mature polypeptide coding sequence thereof.
  • the protease comprises the coding sequence of any protease described or referenced herein (any one of SEQ ID NOs: 9-73), or the mature polypeptide coding sequence thereof.
  • the protease comprises a coding sequence that is a subsequence of the coding sequence from any protease described or referenced herein, wherein the subsequence encodes a polypeptide having protease activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced protease coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the protease can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • the protease used according to a process described herein is a Serine proteases.
  • the protease is a serine protease belonging to the family 53, e.g., an endo-protease, such as S53 protease from Meriphilus giganteus, Dichomitus squalens Trametes versicolor, Polyporus arcularius, Lenzites betulinus, Ganoderma lucidum, Neolentinus lepideus, or Bacillus sp.19138, in a process for producing ethanol from a starch-containing material, the ethanol yield was improved, when the S53 protease was present/or added during saccharification and/or fermentation of either gelatinized or un-gelatinized starch.
  • an endo-protease such as S53 protease from Meriphilus giganteus, Dichomitus squalens Trametes versicolor, Polyporus arcularius, Lenzites betulinus, Ganoderma lucidum, Neolentinus lepideus, or Bacillus
  • the protease is selected from: (a) proteases belonging to the EC 3.4.21 enzyme group; and/or (b) proteases belonging to the EC 3.4.14 enzyme group; and/or (c) Serine proteases of the peptidase family S53 that comprises two different types of peptidases: tripeptidyl aminopeptidases (exo-type) and endo-peptidases; as described in 1993, Biochem. J.290:205-218 and in MEROPS protease database, release, 9.4 (31 January 2011) (www.merops.ac.uk). The database is described in Rawlings, N.D., Barrett, A.J.
  • protease database Nucl. Acids Res.38: D227-D233.
  • Peptidase family S53 contains acid-acting endopeptidases and tripeptidyl- peptidases. The residues of the catalytic triad are Glu, Asp, Ser, and there is an additional acidic residue, Asp, in the oxyanion hole.
  • the order of the residues is Glu, Asp, Asp, Ser.
  • the Ser residue is the nucleophile equivalent to Ser in the Asp, His, Ser triad of subtilisin, and the Glu of the triad is a substitute for the general base, His, in subtilisin.
  • the peptidases of the S53 family tend to be most active at acidic pH (unlike the homologous subtilisins), and this can be attributed to the functional importance of carboxylic residues, notably Asp in the oxyanion hole.
  • the amino acid sequences are not closely similar to those in family S8 (i.e.
  • the protease used according to a process described herein is a Cysteine proteases.
  • the protease used according to a process described herein is a Aspartic proteases. Aspartic acid proteases are described in, for example, Hand-book of Proteolytic En-zymes, Edited by A.J. Barrett, N.D. Rawlings and J.F.
  • aspartic acid protease include, e.g., those disclosed in R.M. Berka et al. Gene, 96, 313 (1990)); (R.M. Berka et al. Gene, 125, 195-198 (1993)); and Gomi et al. Biosci. Biotech. Biochem.57, 1095-1100 (1993), which are hereby incorporated by reference.
  • the protease also may be a metalloprotease, which is defined as a protease selected from the group consisting of: (a) proteases belonging to EC 3.4.24 (metalloendopeptidases); preferably EC 3.4.24.39 (acid metallo proteinases); (b) metalloproteases belonging to the M group of the above Handbook; (c) metalloproteases not yet assigned to clans (designation: Clan MX), or belonging to either one of clans MA, MB, MC, MD, ME, MF, MG, MH (as defined at pp.989-991 of the above Handbook); (d) other families of metalloproteases (as defined at pp.1448-1452 of the above Handbook); (e) metalloproteases with a HEXXH motif; (f) metalloproteases with an HEFTH motif; (g) metalloproteases belonging to either one of families M3, M26, M27, M32, M34, M35,
  • metalloproteases are hydrolases in which the nucleophilic attack on a peptide bond is mediated by a water molecule, which is activated by a divalent metal cation.
  • divalent cations are zinc, cobalt or manganese.
  • the metal ion may be held in place by amino acid ligands.
  • the number of ligands may be five, four, three, two, one or zero. In a particular embodiment the number is two or three, preferably three.
  • the metalloprotease is classified as EC 3.4.24, preferably EC 3.4.24.39.
  • the metalloprotease is an acid-stable metalloprotease, e.g., a fungal acid-stable metalloprotease, such as a metalloprotease derived from a strain of the genus Thermoascus, preferably a strain of Thermoascus aurantiacus, especially Thermoascus aurantiacus CGMCC No.0670 (classified as EC 3.4.24.39).
  • the metalloprotease is derived from a strain of the genus Aspergillus, preferably a strain of Aspergillus oryzae.
  • the metalloprotease has a degree of sequence identity to amino acids -178 to 177, -159 to 177, or preferably amino acids 1 to 177 (the mature polypeptide) of SEQ ID NO: 1 of WO2010/008841 (a Thermoascus aurantiacus metalloprotease) of at least 80%, at least 82%, at least 85%, at least 90%, at least 95%, or at least 97%; and which have metalloprotease activity.
  • the metalloprotease consists of an amino acid sequence with a degree of identity to SEQ ID NO: 1 as mentioned above.
  • Thermoascus aurantiacus metalloprotease is a preferred example of a metalloprotease suitable for use in a process of the invention.
  • Another metalloprotease is derived from Aspergillus oryzae and comprises the sequence of SEQ ID NO: 11 disclosed in WO2003/048353, or amino acids -23-353; -23-374; -23-397; 1-353; 1-374; 1-397; 177-353; 177-374; or 177-397 thereof, and SEQ ID NO: 10 disclosed in WO2003/048353.
  • Another metalloprotease suitable for use in a process of the invention is the Aspergillus oryzae metalloprotease comprising SEQ ID NO: 5 of WO2010/008841, or a metalloprotease is an isolated polypeptide which has a degree of identity to SEQ ID NO: 5 of at least about 80%, at least 82%, at least 85%, at least 90%, at least 95%, or at least 97%; and which have metalloprotease activity.
  • the metalloprotease consists of the amino acid sequence of SEQ ID NO: 5 of WO2010/008841.
  • a metalloprotease has an amino acid sequence that differs by forty, thirty-five, thirty, twenty-five, twenty, or by fifteen amino acids from amino acids -178 to 177, -159 to 177, or +1 to 177 of the amino acid sequences of the Thermoascus aurantiacus or Aspergillus oryzae metalloprotease.
  • a metalloprotease has an amino acid sequence that differs by ten, or by nine, or by eight, or by seven, or by six, or by five amino acids from amino acids -178 to 177, -159 to 177, or +1 to 177 of the amino acid sequences of these metalloproteases, e.g., by four, by three, by two, or by one amino acid.
  • the metalloprotease a) comprises or b) consists of i) the amino acid sequence of amino acids -178 to 177, -159 to 177, or +1 to 177 of SEQ ID NO:1 of WO2010/008841; ii) the amino acid sequence of amino acids -23-353, -23-374, -23-397, 1-353, 1-374, 1-397, 177-353, 177-374, or 177-397 of SEQ ID NO: 3 of WO2010/008841; iii) the amino acid sequence of SEQ ID NO: 5 of WO2010/008841; or allelic variants, or fragments, of the sequences of i), ii), and iii) that have protease activity.
  • a fragment of amino acids -178 to 177, -159 to 177, or +1 to 177 of SEQ ID NO: 1 of WO2010/008841 or of amino acids -23-353, -23-374, -23-397, 1-353, 1-374, 1-397, 177-353, 177-374, or 177-397 of SEQ ID NO: 3 of WO2010/008841 is a polypeptide having one or more amino acids deleted from the amino and/or carboxyl terminus of these amino acid sequences.
  • a fragment contains at least 75 amino acid residues, or at least 100 amino acid residues, or at least 125 amino acid residues, or at least 150 amino acid residues, or at least 160 amino acid residues, or at least 165 amino acid residues, or at least 170 amino acid residues, or at least 175 amino acid residues.
  • the protease may be a variant of, e.g., a wild-type protease, having thermostability properties defined herein.
  • the thermostable protease is a variant of a metallo protease.
  • thermostable protease used in a process described herein is of fungal origin, such as a fungal metallo protease, such as a fungal metallo protease derived from a strain of the genus Thermoascus, preferably a strain of Thermoascus aurantiacus, especially Thermoascus aurantiacus CGMCC No.0670 (classified as EC 3.4.24.39).
  • thermostable protease is a variant of the mature part of the metallo protease shown in SEQ ID NO: 2 disclosed in WO2003/048353 or the mature part of SEQ ID NO: 1 in WO 2010/008841 further with one of the following substitutions or combinations of substitutions: S5*+D79L+S87P+A112P+D142L; D79L+S87P+A112P+T124V+D142L; S5*+N26R+D79L+S87P+A112P+D142L; N26R+T46R+D79L+S87P+A112P+D142L; T46R+D79L+S87P+T116V+D142L; D79L+P81R+S87P+A112P+D142L; A27K+D79L+S87P+A112P+T124V+D142L; D79L+Y82F+S87P+A112P+T124V+D142
  • thermostable protease is a variant of the metallo protease disclosed as the mature part of SEQ ID NO: 2 disclosed in WO2003/048353 or the mature part of SEQ ID NO: 1 in WO2010/008841 with one of the following substitutions or combinations of substitutions: D79L+S87P+A112P+D142L; D79L+S87P+D142L; and A27K+ D79L+Y82F+S87G+D104P+A112P+A126V+D142L.
  • the protease variant has at least 75% identity preferably at least 80%, more preferably at least 85%, more preferably at least 90%, more preferably at least 91%, more preferably at least 92%, even more preferably at least 93%, most preferably at least 94%, and even most preferably at least 95%, such as even at least 96%, at least 97%, at least 98%, at least 99%, but less than 100% identity to the mature part of the polypeptide of SEQ ID NO: 2 disclosed in WO2003/048353 or the mature part of SEQ ID NO: 1 in WO2010/008841.
  • the thermostable protease may also be derived from any bacterium as long as the protease has the thermostability properties.
  • thermostable protease is derived from a strain of the bacterium Pyrococcus, such as a strain of Pyrococcus furiosus (pfu protease).
  • the protease is one shown as SEQ ID NO: 1 in US 6,358,726 (Takara Shuzo Company).
  • the thermostable protease is a protease having a mature polypeptide sequence of at least 80% identity, such as at least 85%, such as at least 90%, such as at least 95%, such as at least 96%, such as at least 97%, such as at least 98%, such as at least 99% identity to SEQ ID NO: 1 in US 6,358,726.
  • the Pyroccus furiosus protease can be purchased from Takara Bio, Japan.
  • the Pyrococcus furiosus protease may be a thermostable protease as described in SEQ ID NO: 13 of WO2018/098381.
  • This protease (PfuS) was found to have a thermostability of 110% (80°C/70°C) and 103% (90°C/70°C) at pH 4.5 determined.
  • a thermostable protease used in a process described herein has a thermostability value of more than 20% determined as Relative Activity at 80oC/70oC determined as described in Example 2 of WO2018/098381.
  • the protease has a thermostability of more than 30%, more than 40%, more than 50%, more than 60%, more than 70%, more than 80%, more than 90%, more than 100%, such as more than 105%, such as more than 110%, such as more than 115%, such as more than 120% determined as Relative Activity at 80oC/70oC. In one embodiment, protease has a thermostability of between 20 and 50%, such as between 20 and 40%, such as 20 and 30% determined as Relative Activity at 80oC/70oC.
  • the protease has a thermostability between 50 and 115%, such as between 50 and 70%, such as between 50 and 60%, such as between 100 and 120%, such as between 105 and 115% determined as Relative Activity at 80oC/70oC. In one embodiment, the protease has a thermostability value of more than 10% determined as Relative Activity at 85oC/70oC determined as described in Example 2 of WO2018/098381.
  • the protease has a thermostability of more than 10%, such as more than 12%, more than 14%, more than 16%, more than 18%, more than 20%, more than 30%, more than 40%, more that 50%, more than 60%, more than 70%, more than 80%, more than 90%, more than 100%, more than 110% determined as Relative Activity at 85oC/70oC. In one embodiment, the protease has a thermostability of between 10% and 50%, such as between 10% and 30%, such as between 10% and 25% determined as Relative Activity at 85oC/70oC.
  • the protease has more than 20%, more than 30%, more than 40%, more than 50%, more than 60%, more than 70%, more than 80%, more than 90% determined as Remaining Activity at 80oC; and/or the protease has more than 20%, more than 30%, more than 40%, more than 50%, more than 60%, more than 70%, more than 80%, more than 90% determined as Remaining Activity at 84oC. Determination of “Relative Activity” and “Remaining Activity” is done as described in Example 2 of WO2018/098381.
  • the protease may have a thermostability for above 90, such as above 100 at 85oC as determined using the Zein-BCA assay as disclosed in Example 3 of WO2018/098381.
  • the protease has a thermostability above 60%, such as above 90%, such as above 100%, such as above 110% at 85oC as determined using the Zein-BCA assay of WO2018/098381.
  • protease has a thermostability between 60-120, such as between 70-120%, such as between 80-120%, such as between 90-120%, such as between 100-120%, such as 110-120% at 85oC as determined using the Zein-BCA assay of WO2018/098381.
  • thermostable protease has at least 20%, such as at least 30%, such as at least 40%, such as at least 50%, such as at least 60%, such as at least 70%, such as at least 80%, such as at least 90%, such as at least 95%, such as at least 100% of the activity of the JTP196 protease variant or Protease Pfu determined by the AZCL-casein assay of WO2018/098381, and described herein.
  • thermostable protease has at least 20%, such as at least 30%, such as at least 40%, such as at least 50%, such as at least 60%, such as at least 70%, such as at least 80%, such as at least 90%, such as at least 95%, such as at least 100% of the protease activity of the Protease 196 variant or Protease Pfu determined by the AZCL-casein assay of WO2018/098381.
  • K. Pullulanases The host cells and fermenting organisms may express a heterologous pullulanase.
  • the pullulanase can be any protease that is suitable for the host cells and fermenting organisms and/or their methods of use described herein, such as a naturally occurring pullulanase or a variant thereof that retains pullulanase activity.
  • Any pullulanase contemplated for expression by a host cell or fermenting organism described below is also contemplated for embodiments of the invention involving exogenous addition of a pullulanase (e.g., added before, during or after liquefaction and/or saccharification).
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a pullulanase has an increased level of pullulanase activity compared to the host cells without the heterologous polynucleotide encoding the pullulanase, when cultivated under the same conditions.
  • the host cell or fermenting organism has an increased level of pullulanase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cell or fermenting organism without the heterologous polynucleotide encoding the pullulanase, when cultivated under the same conditions.
  • Exemplary pullulanases that can be used with the host cells and/or the methods described herein include bacterial, yeast, or filamentous fungal pullulanases, e.g., obtained from any of the microorganisms described or referenced herein, such as a pullulanse of any one of SEQ ID NOs: 114-120.
  • Contemplated pullulanases include the pullulanases from Bacillus amyloderamificans disclosed in US 4,560,651 (hereby incorporated by reference), the pullulanase disclosed as SEQ ID NO: 2 in WO01/151620 (hereby incorporated by reference), the Bacillus deramificans disclosed as SEQ ID NO: 4 in WO01/151620 (hereby incorporated by reference), and the pullulanase from Bacillus acidopullulyticus disclosed as SEQ ID NO: 6 in WO01/151620 (hereby incorporated by reference) and also described in FEMS Mic. Let. (1994) 115, 97-106.
  • pullulanases contemplated include the pullulanases from Pyrococcus woesei, specifically from Pyrococcus woesei DSM No.3773 disclosed in WO92/02614.
  • the pullulanase is a family GH57 pullulanase.
  • the pullulanase includes an X47 domain as disclosed in US 61/289,040 published as WO2011/087836 (which are hereby incorporated by reference).
  • the pullulanase may be derived from a strain of the genus Thermococcus, including Thermococcus litoralis and Thermococcus hydrothermalis, such as the Thermococcus hydrothermalis pullulanase truncated at site X4 right after the X47 domain (i.e., amino acids 1-782).
  • the pullulanase may also be a hybrid of the Thermococcus litoralis and Thermococcus hydrothermalis pullulanases or a T. hydrothermalis/T.
  • the pullulanase is one comprising an X46 domain disclosed in WO2011/076123 (Novozymes).
  • the pullulanase may be added in an effective amount which include the preferred amount of about 0.0001-10 mg enzyme protein per gram DS, preferably 0.0001-0.10 mg enzyme protein per gram DS, more preferably 0.0001-0.010 mg enzyme protein per gram DS.
  • Pullulanase activity may be determined as NPUN. An Assay for determination of NPUN is described in WO2018/098381.
  • Suitable commercially available pullulanase products include PROMOZYME D, PROMOZYMETM D2 (Novozymes A/S, Denmark), OPTIMAX L-300 (DuPont-Danisco, USA), and AMANO 8 (Amano, Japan).
  • the pullulanase is derived from the Bacillus subtilis pullulanase of SEQ ID NO: 114, or the mature polypeptide thereof.
  • the pullulanase is derived from the Bacillus licheniformis pullulanase of SEQ ID NO: 115, or the mature polypeptide thereof.
  • the pullulanase is derived from the Oryza sativa pullulanase of SEQ ID NO: 116, or the mature polypeptide thereof. In one embodiment, the pullulanase is derived from the Triticum aestivum pullulanase of SEQ ID NO: 117, or the mature polypeptide thereof. In one embodiment, the pullulanase is derived from the Clostridium phytofermentans pullulanase of SEQ ID NO: 118, or the mature polypeptide thereof. In one embodiment, the pullulanase is derived from the Streptomyces avermitilis pullulanase of SEQ ID NO: 119, or the mature polypeptide thereof.
  • the pullulanase is derived from the Klebsiella pneumoniae pullulanase of SEQ ID NO: 120, or the mature polypeptide thereof.
  • the pullulanase may be a variant of any one of the pullulanases described supra (e.g., any one of SEQ ID NOs: 114-120), or the mature polypeptide thereof.
  • the pullulanase has a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of the pullulanases described supra (e.g., any one of SEQ ID NOs: 114-120), or the mature polypeptide thereof.
  • suitable amino acid changes such as conservative substitutions that do not significantly affect the folding and/or activity of the pullulanase, are described herein.
  • the pullulanase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of the pullulanases described supra (e.g., any one of SEQ ID NOs: 114-120), or the mature polypeptide thereof.
  • the protease has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) of amino acid sequence of any one of the pullulanases described supra (e.g., any one of SEQ ID NOs: 114-120), or the mature polypeptide thereof.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the pullulanase coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any pullulanase described or referenced herein (e.g., any one of SEQ ID NOs: 114-120), or the mature polypeptide coding sequence thereof.
  • low stringency conditions e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions
  • any pullulanase described or referenced herein e.g., any one of SEQ ID NOs: 114-120
  • the protease coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any pullulanase described or referenced herein (e.g., any one of SEQ ID NOs: 114-120), or the mature polypeptide coding sequence thereof.
  • any pullulanase described or referenced herein e.g., any one of SEQ ID NOs: 114-120
  • the pullulanase comprises the coding sequence of any pullulanase described or referenced herein (any one of SEQ ID NOs: 114-120), or the mature polypeptide coding sequence thereof.
  • the pullulanase comprises a coding sequence that is a subsequence of the coding sequence from any pullulanase described or referenced herein, wherein the subsequence encodes a polypeptide having pullulanase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the referenced pullulanase coding sequence of any related aspect or embodiment described herein can be the native coding sequence or a degenerate sequence, such as a codon-optimized coding sequence designed for use in a particular host cell (e.g., optimized for expression in Saccharomyces cerevisiae).
  • the pullulanase can also include fused polypeptides or cleavable fusion polypeptides, as described supra. Additional pullulanases contemplated for use with the present invention can be found in WO2011/153516 (the content of which is incorporated herein).
  • Additional polynucleotides encoding suitable pullulanases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the pullulanase coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding pullulanases from strains of different genera or species, as described supra.
  • the polynucleotides encoding pullulanases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra.
  • the host cells or fermenting organisms described herein may comprise an active pentose fermentation pathway, such as an active xylose fermentation pathway and/or and active arabinose fermentation pathway as described in more detail below.
  • active pentose fermentation pathways and pathway genes and corresponding engineered transformants for fermentation of pentose are known in the art.
  • Any suitable pentose fermentation pathway gene, endogenous or heterologous may be used and expressed in sufficient amount to produce an enzyme involved in a selected pentose fermentation pathway.
  • Routine experimental design can be employed to test expression of various genes and activity of various enzymes, including genes and enzymes that function in a pentose fermentation pathway. Experiments may be conducted wherein each enzyme is expressed in the cell individually and in blocks of enzymes up to and including preferably all pathway enzymes, to establish which are needed (or desired) for improved pentose fermentation.
  • One illustrative experimental design tests expression of each individual enzyme as well as of each unique pair of enzymes, and further can test expression of all required enzymes, or each unique combination of enzymes. A number of approaches can be taken, as will be appreciated.
  • the host cells of the invention can be produced by introducing heterologous polynucleotides encoding one or more of the enzymes participating in an active pentose fermentation pathway, as described below.
  • the heterologous expression of every gene shown in the active pentose fermentation may not be required since a host cell may have endogenous enzymatic activity from one or more pathway genes.
  • a host cell may have endogenous enzymatic activity from one or more pathway genes.
  • heterologous polynucleotides for the deficient enzyme(s) are introduced into the host for subsequent expression.
  • an encoding polynucleotide is needed for the deficient enzyme(s) to achieve pentose fermentation.
  • a recombinant host cell of the invention can be produced by introducing heterologous polynucleotides to obtain the enzyme activities of a desired biosynthetic pathway or a desired biosynthetic pathway can be obtained by introducing one or more heterologous polynucleotides that, together with one or more endogenous enzymes, produces a desired product such as ethanol.
  • the host cells of the invention will include at least one heterologous polynucleotide and optionally up to all encoding heterologous polynucleotides for the pentose fermentation pathway.
  • pentose fermentation can be established in a host deficient in a pentose fermentation pathway enzyme through heterologous expression of the corresponding polynucleotide.
  • heterologous expression of all enzymes in the pathway can be included, although it is understood that all enzymes of a pathway can be expressed even if the host contains at least one of the pathway enzymes.
  • the enzymes of the selected active pentose fermentation pathway, and activities thereof, can be detected using methods known in the art or as described herein. These detection methods may include use of specific antibodies, formation of an enzyme product, or disappearance of an enzyme substrate.
  • the active pentose fermentation pathway may be an active xylose fermentation pathway.
  • Exemplary xylose fermentation pathways are known in the art (e.g., WO2003/062430, WO2003/078643, WO2004/067760, WO2006/096130, WO2009/017441, WO2010/059095, WO2011/059329, WO2011/123715, WO2012/113120, WO2012/135110, WO2013/081700, WO2018/112638 and US2017/088866).
  • Any xylose fermentation pathway or gene thereof described in the foregoing references is incorporated herein by reference for use in Applicant’s active xylose fermentation pathway.
  • the oxido-reductase pathway uses an aldolase reductase (AR, such as xylose reductase (XR)) to reduce D-xylose to xylitol followed by oxidation of xylitol to D-xylulose with xylitol dehydrogenase (XDH; also known as D-xylulose reductase).
  • AR aldolase reductase
  • XR xylose reductase
  • XDH xylitol dehydrogenase
  • the isomerase pathway uses xylose isomerase (XI) to convert D-xylose into D-xylulose.
  • D-xylulose is then converted to D- xylulose-5-phosphate with xylulokinase (XK).
  • the host cell or fermenting organism e.g., yeast cell
  • the host cell or fermenting organism further comprises a heterologous polynucleotide encoding a xylose isomerase (XI).
  • the xylose isomerase may be any xylose isomerase that is suitable for the host cells and the methods described herein, such as a naturally occurring xylose isomerase or a variant thereof that retains xylose isomerase activity.
  • the xylose isomerase is present in the cytosol of the host cells.
  • the host cell or fermenting organism comprising a heterologous polynucleotide encoding a xylose isomerase has an increased level of xylose isomerase activity compared to the host cells without the heterologous polynucleotide encoding the xylose isomerase, when cultivated under the same conditions.
  • the host cells or fermenting organisms have an increased level of xylose isomerase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cells without the heterologous polynucleotide encoding the xylose isomerase, when cultivated under the same conditions.
  • Exemplary xylose isomerases that can be used with the recombinant host cells and methods of use described herein include, but are not limited to, XIs from the fungus Piromyces sp.
  • xylose isomerases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the xylose isomerases is a bacterial, a yeast, or a filamentous fungal xylose isomerase, e.g., obtained from any of the microorganisms described or referenced herein, as described supra.
  • the xylose isomerase coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding xylose isomerases from strains of different genera or species, as described supra.
  • the polynucleotides encoding xylose isomerases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra. Techniques used to isolate or clone polynucleotides encoding xylose isomerases are described supra.
  • the xylose isomerase has a mature polypeptide sequence of having at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to any xylose isomerase described or referenced herein (e.g., the xylose isomerase of SEQ ID NO: 74), or the mature polypeptide thereof.
  • the xylose isomerase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from any xylose isomerase described or referenced herein (e.g., the xylose isomerase of SEQ ID NO: 74), or the mature polypeptide thereof.
  • the xylose isomerase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any xylose isomerase described or referenced herein (e.g., the xylose isomerase of SEQ ID NO: 74), allelic variant, or a fragment thereof having xylose isomerase activity.
  • the xylose isomerase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) amino acids. In some embodiments, the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the xylose isomerase has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the xylose isomerase activity of any xylose isomerase described or referenced herein (e.g., the xylose isomerase of SEQ ID NO: 74) under the same conditions.
  • the xylose isomerase coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any xylose isomerase described or referenced herein (e.g., the xylose isomerase of SEQ ID NO: 74), or the mature polypeptide coding sequence thereof.
  • any xylose isomerase described or referenced herein e.g., the xylose isomerase of SEQ ID NO: 74
  • the xylose isomerase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any xylose isomerase described or referenced herein (e.g., the xylose isomerase of SEQ ID NO: 74), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the xylose isomerase comprises the coding sequence of any xylose isomerase described or referenced herein (e.g., the xylose isomerase of SEQ ID NO: 74), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the xylose isomerase comprises a subsequence of the coding sequence from any xylose isomerase described or referenced herein, or the mature polypeptide coding sequence thereof, wherein the subsequence encodes a polypeptide having xylose isomerase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the xylose isomerases can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • the host cell or fermenting organism e.g., yeast cell
  • the host cell or fermenting organism further comprises a heterologous polynucleotide encoding a xylulokinase (XK).
  • XK xylulokinase
  • a xylulokinase provides enzymatic activity for converting D-xylulose to xylulose 5-phosphate.
  • the xylulokinase may be any xylulokinase that is suitable for the host cells and the methods described herein, such as a naturally occurring xylulokinase or a variant thereof that retains xylulokinase activity.
  • the xylulokinase is present in the cytosol of the host cells.
  • the host cells or fermenting organisms comprising a heterologous polynucleotide encoding a xylulokinase have an increased level of xylulokinase activity compared to the host cells without the heterologous polynucleotide encoding the xylulokinase, when cultivated under the same conditions.
  • the host cells have an increased level of xylose isomerase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cells without the heterologous polynucleotide encoding the xylulokinase, when cultivated under the same conditions.
  • Exemplary xylulokinases that can be used with the host cells and fermenting organisms, and methods of use described herein include, but are not limited to, the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75, or the mature polypeptide thereof. Additional polynucleotides encoding suitable xylulokinases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the xylulokinases is a bacterial, a yeast, or a filamentous fungal xylulokinase, e.g., obtained from any of the microorganisms described or referenced herein, as described supra.
  • the xylulokinase coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding xylulokinases from strains of different genera or species, as described supra.
  • polynucleotides encoding xylulokinases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra. Techniques used to isolate or clone polynucleotides encoding xylulokinases are described supra.
  • the xylulokinase has a mature polypeptide sequence of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to any xylulokinase described or referenced herein (e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75), or the mature polypeptide thereof.
  • the xylulokinase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from any xylulokinase described or referenced herein (e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75), or the mature polypeptide thereof.
  • the xylulokinase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any xylulokinase described or referenced herein (e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75), or the mature polypeptide thereof, allelic variant, or a fragment thereof having xylulokinase activity.
  • the xylulokinase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) amino acids.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the xylulokinase has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the xylulokinase activity of any xylulokinase described or referenced herein (e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75) under the same conditions.
  • any xylulokinase described or referenced herein e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75
  • the xylulokinase coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any xylulokinase described or referenced herein (e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75), or the mature polypeptide thereof.
  • any xylulokinase described or referenced herein e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75
  • the xylulokinase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any xylulokinase described or referenced herein (e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75), or the mature polypeptide thereof.
  • any xylulokinase described or referenced herein e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75
  • the heterologous polynucleotide encoding the xylulokinase comprises the coding sequence of any xylulokinase described or referenced herein (e.g., the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the xylulokinase comprises a subsequence of the coding sequence from any xylulokinase described or referenced herein, wherein the subsequence encodes a polypeptide having xylulokinase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the xylulokinases can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • the host cell or fermenting organism e.g., yeast cell
  • a ribulose 5 phosphate 3-epimerase provides enzymatic activity for converting L-ribulose 5-phosphate to L-xylulose 5-phosphate (EC 5.1.3.22).
  • the RPE1 may be any RPE1 that is suitable for the host cells and the methods described herein, such as a naturally occurring RPE1 or a variant thereof that retains RPE1 activity. In one embodiment, the RPE1 is present in the cytosol of the host cells.
  • the recombinant cell comprises a heterologous polynucleotide encoding a ribulose 5 phosphate 3-epimerase (RPE1), wherein the RPE1 is Saccharomyces cerevisiae RPE1, or an RPE1 having at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to a Saccharomyces cerevisiae RPE1.
  • the host cell or fermenting organism e.g., yeast cell
  • a ribulose 5 phosphate isomerase provides enzymatic activity for converting ribose-5-phophate to ribulose 5-phosphate.
  • the RKI1 may be any RKI1 that is suitable for the host cells and the methods described herein, such as a naturally occurring RKI1 or a variant thereof that retains RKI1 activity. In one embodiment, the RKI1 is present in the cytosol of the host cells.
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a ribulose 5 phosphate isomerase (RKI1), wherein the RKI1 is a Saccharomyces cerevisiae RKI1, or an RKI1 having a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to a Saccharomyces cerevisiae RKI1.
  • the host cell or fermenting organism e.g., yeast cell
  • the TKL1 may be any TKL1 that is suitable for the host cells and the methods described herein, such as a naturally occurring TKL1 or a variant thereof that retains TKL1 activity.
  • the TKL1 is present in the cytosol of the host cells.
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a transketolase (TKL1), wherein the TKL1 is a Saccharomyces cerevisiae TKL1, or a TKL1 having a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to a Saccharomyces cerevisiae TKL1.
  • the host cell or fermenting organism e.g., yeast cell
  • TAL1 transaldolase
  • the TAL1 may be any TAL1 that is suitable for the host cells and the methods described herein, such as a naturally occurring TAL1 or a variant thereof that retains TAL1 activity.
  • the TAL1 is present in the cytosol of the host cells.
  • the host cell or fermenting organism comprises a heterologous polynucleotide encoding a transketolase (TAL1), wherein the TAL1 is a Saccharomyces cerevisiae TAL1, or a TAL1 having a mature polypeptide sequence of at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to a Saccharomyces cerevisiae TAL1.
  • the active pentose fermentation pathway may be an active arabinose fermentation pathway.
  • Exemplary arabinose fermentation pathways are known in the art (e.g., WO2002/066616; WO2003/095627; WO2007/143245; WO2008/041840; WO2009/011591; WO2010/151548; WO2011/003893; WO2011/131674; WO2012/143513; US2012/225464; US 7,977,083).
  • Any arabinose fermentation pathway or gene thereof described in the foregoing references is incorporated herein by reference for use in Applicant’s active xylose fermentation pathway.
  • the bacterial arabinose fermentation pathway utilizes genes L- arabinose isomerase (AI, such as araA), L-ribulokinase (RK, such as araB), and L-ribulose- 5-P4-epimerase (R5PE, such as araD) to convert L-arabinose to D-xylulose 5-phosphate.
  • AI such as araA
  • RK L-ribulokinase
  • R5PE L-ribulose- 5-P4-epimerase
  • the fungal arabinose fermentation pathway proceeds using aldose reductase (AR), L- arabinitol 4-dehydrogenase (LAD), L-xylulose reductase (LXR), xylitol dehydrogenase (XDH, also known as D-xylulose reductase) and xylulokinase (XK).
  • AR aldose reductase
  • LAD L- arabinitol 4-dehydrogenase
  • LXR L-xylulose reductase
  • XDH xylitol dehydrogenase
  • XK xylulokinase
  • the host cell or fermenting organism e.g., yeast cell
  • yeast cell further comprises a heterologous polynucleotide encoding a L-xylulose reductase (LXR).
  • a L- xylulose reductase provides enzymatic activity for converting L-xylulose to xylitol.
  • the L-xylulose reductase may be any L-xylulose reductase that is suitable for the host cells and the methods described herein, such as a naturally occurring xylulokinase or a variant thereof that retains L-xylulose reductase activity.
  • the L-xylulose reductase is present in the cytosol of the host cells.
  • the host cells or fermenting organisms comprising a heterologous polynucleotide encoding a L-xylulose reductase have an increased level of L-xylulose reductase activity compared to the host cells without the heterologous polynucleotide encoding the L-xylulose reductase, when cultivated under the same conditions.
  • LXR L-xylulose reductase
  • the host cells have an increased level of L-xylulose reductase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cells without the heterologous polynucleotide encoding the L-xylulose reductase, when cultivated under the same conditions.
  • LXRs L-xylulose reductases
  • Exemplary L-xylulose reductases (LXRs) that can be used with the host cells and fermenting organisms, and methods of use described herein include, but are not limited to, the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75, the Scheffersomyces stipitis xylulokinase of SEQ ID NO: 310 and the Aspergillus niger xylulokinase of SEQ ID NO: 311.
  • L-xylulose reductases that may be expressed with the host cells or fermenting organisms and methods of use described herein include, but are not limited to the L-xylulose reductases (LXRs) shown in Table 9 (or derivatives thereof). Table 9. Additional polynucleotides encoding suitable L-xylulose reductases (LXRs) may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the L-xylulose reductase is a bacterial, a yeast, or a filamentous fungal L-xylulose reductase, e.g., obtained from any of the microorganisms described or referenced herein, as described supra.
  • the L-xylulose reductase (LXR) coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding L-xylulose reductases from strains of different genera or species, as described supra.
  • LXR L-xylulose reductases
  • the L-xylulose reductase has a mature polypeptide sequence of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to any xylulokinase described or referenced herein (e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304), or the mature polypeptide thereof.
  • any xylulokinase described or referenced herein e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302,
  • the L-xylulose reductase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from any L-xylulose reductase described or referenced herein (e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304), or the mature polypeptide thereof.
  • any L-xylulose reductase described or referenced herein e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304
  • the L-xylulose reductase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any L-xylulose reductase described or referenced herein (e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304), or the mature polypeptide thereof, allelic variant, or a fragment thereof having L-xylulose reductase activity.
  • any L-xylulose reductase described or referenced herein e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304
  • the mature polypeptide thereof allelic variant, or a fragment thereof having L-xylulose reductase activity.
  • the L-xylulose reductase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) amino acids, or the mature polypeptide thereof.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the L-xylulose reductase has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the L-xylulose reductase activity of any L-xylulose reductase described or referenced herein (e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304), or the mature polypeptide thereof, under the same conditions.
  • any L-xylulose reductase described or referenced herein e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304
  • the L-xylulose reductase (LXR) coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any L-xylulose reductase described or referenced herein (e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304), or the mature polypeptide coding sequence thereof.
  • L-xylulose reductase e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304
  • the L-xylulose reductase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any L-xylulose reductase described or referenced herein (e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304), or the mature polypeptide coding sequence thereof.
  • any L-xylulose reductase described or referenced herein e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO
  • the heterologous polynucleotide encoding the L-xylulose reductase comprises the coding sequence of any L-xylulose reductase described or referenced herein (e.g., the L-xylulose reductase of any one of SEQ ID NOs: 297-308; such as SEQ ID NO: 297, 300, 302, or 304), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the L-xylulose reductase comprises a subsequence of the coding sequence from any L-xylulose reductase described or referenced herein, wherein the subsequence encodes a polypeptide having L-xylulose reductase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • LXRs L-xylulose reductases
  • the host cell or fermenting organism e.g., yeast cell
  • the host cell or fermenting organism further comprises a heterologous polynucleotide encoding an aldose reductase (AR).
  • AR aldose reductase
  • An aldose reductase provides enzymatic activity for converting L-arabinose to L- arabitol, and may also have enzymatic activity for converting D-xylose to xylitol (known as a xylose reductase, XR).
  • the aldose reductase may be any aldose reductase that is suitable for the host cells and the methods described herein, such as a naturally occurring aldose reductase or a variant thereof that retains aldose reductase activity.
  • the aldose reductase is present in the cytosol of the host cells.
  • the host cells or fermenting organisms comprising a heterologous polynucleotide encoding an aldose reductase (AR) have an increased level of aldose reductase activity compared to the host cells without the heterologous polynucleotide encoding the aldose reductase, when cultivated under the same conditions.
  • the host cells have an increased level of aldose reductase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cells without the heterologous polynucleotide encoding the aldose reductase, when cultivated under the same conditions.
  • aldose reductases that can be used with the host cells and fermenting organisms, and methods of use described herein include, but are not limited to, the Aspergillus niger aldose reductase of SEQ ID NO: 281, the the Aspergillus oryzae aldose reductase of SEQ ID NO: 282, the Magnaporthe oryzae aldose reductase of SEQ ID NO: 283, the Meyerozyma guilliermondii aldose reductase of SEQ ID NO: 284 and the Scheffersomyces stipitis aldose reductase of SEQ ID NO: 285.
  • Aspergillus niger aldose reductase of SEQ ID NO: 281 the Aspergillus oryzae aldose reductase of SEQ ID NO: 282
  • the Magnaporthe oryzae aldose reductase of SEQ ID NO: 283 the Meyerozyma guilliermondii aldose
  • aldose reductase may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the aldose reductase is a bacterial, a yeast, or a filamentous fungal aldose reductase, e.g., obtained from any of the microorganisms described or referenced herein, as described supra.
  • the aldose reductase (AR) coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding aldose reductases from strains of different genera or species, as described supra.
  • the polynucleotides encoding the aldose reductases (ARs) may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra. Techniques used to isolate or clone polynucleotides encoding aldose reductases (ARs) are described supra.
  • the aldose reductase (AR) has a mature polypeptide sequence of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to any aldose reductase described or referenced herein (e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284 or 285), or the mature polypeptide thereof.
  • any aldose reductase described or referenced herein e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284 or 285
  • the aldose reductase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from any aldose reductase described or referenced herein (e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284 or 285), or the mature polypeptide thereof.
  • the aldose reductase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any aldose reductase described or referenced herein (e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284 or 285), or the mature polypeptide thereof, allelic variant, or a fragment thereof having aldose reductase activity.
  • the aldose reductase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) amino acids. In some embodiments, the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the aldose reductase (AR) has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the aldose reductase activity of any aldose reductase described or referenced herein (e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284 or 285), or the mature polypeptide thereof, under the same conditions.
  • any aldose reductase described or referenced herein e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284 or 285
  • the aldose reductase (AR) coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any aldose reductase described or referenced herein (e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284 or 285), or the mature polypeptide coding sequence thereof.
  • any aldose reductase described or referenced herein e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284 or 285
  • the aldose reductase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any aldose reductase described or referenced herein (e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284, or 285), or the mature polypeptide coding sequence thereof.
  • any aldose reductase described or referenced herein e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284, or 285
  • the heterologous polynucleotide encoding the aldose reductase comprises the coding sequence of any aldose reductase described or referenced herein (e.g., the aldose reductase of SEQ ID NO: 281, 282, 283, 284, or 285), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the aldose reductase comprises a subsequence of the coding sequence from any aldose reductase described or referenced herein, wherein the subsequence encodes a polypeptide having aldose reductase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the aldose reductases (ARs) can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • the host cell or fermenting organism e.g., yeast cell
  • the host cell or fermenting organism further comprises a heterologous polynucleotide encoding an L-arabinitol 4-dehydrogenase (LAD).
  • LAD L-arabinitol 4-dehydrogenase
  • a L-arabinitol 4-dehydrogenase provides enzymatic activity for converting L- arabitol to L-xylulose.
  • the L-arabinitol 4-dehydrogenase may be any L-arabinitol 4- dehydrogenase that is suitable for the host cells and the methods described herein, such as a naturally occurring L-arabinitol 4-dehydrogenase or a variant thereof that retains L- arabinitol 4-dehydrogenase activity.
  • the L-arabinitol 4-dehydrogenase is present in the cytosol of the host cells.
  • the host cells or fermenting organisms comprising a heterologous polynucleotide encoding a L-arabinitol 4-dehydrogenase have an increased level of L-arabinitol 4-dehydrogenase activity compared to the host cells without the heterologous polynucleotide encoding the L-arabinitol 4-dehydrogenase, when cultivated under the same conditions.
  • the host cells have an increased level of L-arabinitol 4-dehydrogenase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cells without the heterologous polynucleotide encoding the L-arabinitol 4-dehydrogenase, when cultivated under the same conditions.
  • L-arabinitol 4-dehydrogenases that can be used with the host cells and fermenting organisms, and methods of use described herein include, but are not limited to, the Meyerozyma caribbica LAD of SEQ ID NO: 286, the Trichoderma reesei LAD of SEQ ID NO: 287, the Meyerozyma guilliermondii LAD of SEQ ID NO: 288, the Candida arabinofermentans LAD of SEQ ID NO: 289, the Candida carpophila LAD of SEQ ID NO: 290, the Talaromyces emersonii LAD of SEQ ID NO: 291, the Aspergillus oryzae LAD of SEQ ID NO: 292, the Neurospora crassa LAD of SEQ ID NO: 293, the Trichoderma reesei LAD of SEQ ID NO: 294, the Aspergillus niger LAD of SEQ ID NO: 295 and the Penicillium
  • L-arabinitol 4- dehydrogenases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the L-arabinitol 4- dehydrogenase is a bacterial, a yeast, or a filamentous fungal L-arabinitol 4-dehydrogenase, e.g., obtained from any of the microorganisms described or referenced herein, as described supra.
  • L-arabinitol 4-dehydrogenase (LAD) coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding L-arabinitol 4- dehydrogenases from strains of different genera or species, as described supra.
  • the polynucleotides encoding L-arabinitol 4-dehydrogenases (LADs) may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra.
  • the L-arabinitol 4-dehydrogenase has a mature polypeptide sequence of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to any L-arabinitol 4-dehydrogenase described or referenced herein (e.g., the L-arabinitol 4- dehydrogenase of SEQ ID NO: 286, 287, 288, 289, 290, 291, 292, 293, 294, 295 or 296), or the mature polypeptide thereof.
  • L-arabinitol 4- dehydrogenase of SEQ ID NO: 286, 287, 288, 289, 290, 291, 292, 293, 294, 295 or 296
  • the L-arabinitol 4-dehydrogenase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from any L-arabinitol 4- dehydrogenase described or referenced herein (e.g., the L-arabinitol 4-dehydrogenase of SEQ ID NO: 286, 287, 288, 289, 290, 291, 292, 293, 294, 295 or 296), or the mature polypeptide thereof.
  • the L-arabinitol 4-dehydrogenase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any L- arabinitol 4-dehydrogenase described or referenced herein (e.g., the L-arabinitol 4- dehydrogenase of SEQ ID NO: 286, 287, 288, 289, 290, 291, 292, 293, 294, 295 or 296), or the mature polypeptide thereof, allelic variant, or a fragment thereof having L-arabinitol 4- dehydrogenase activity.
  • the L-arabinitol 4-dehydrogenase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) amino acids.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the L-arabinitol 4-dehydrogenase has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the L-arabinitol 4-dehydrogenase activity of any L-arabinitol 4-dehydrogenase described or referenced herein (e.g., the L-arabinitol 4-dehydrogenase of SEQ ID NO: 286, 287, 288, 289, 290, 291, 292, 293, 294, 295 or 296), or the mature polypeptide thereof, under the same conditions.
  • the L-arabinitol 4-dehydrogenase (LAD) coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any L- arabinitol 4-dehydrogenase described or referenced herein (e.g., the L-arabinitol 4- dehydrogenase of SEQ ID NO: 286, 287, 288, 289, 290, 291, 292, 293, 294, 295 or 296), or the mature polypeptide coding sequence thereof.
  • the L-arabinitol 4- dehydrogenase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any L-arabinitol 4-dehydrogenase described or referenced herein (e.g., the L-arabinitol 4-dehydrogenase of SEQ ID NO: 286, 287, 288, 289, 290, 291, 292, 293, 294, 295 or 296), or the mature polypeptide coding sequence thereof.
  • L-arabinitol 4-dehydrogenase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%,
  • the heterologous polynucleotide encoding the L-arabinitol 4- dehydrogenase comprises the coding sequence of any L-arabinitol 4-dehydrogenase described or referenced herein (e.g., the L-arabinitol 4-dehydrogenase of SEQ ID NO: 286, 287, 288, 289, 290, 291, 292, 293, 294, 295 or 296), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the L- arabinitol 4-dehydrogenase comprises a subsequence of the coding sequence from any L- arabinitol 4-dehydrogenase described or referenced herein, wherein the subsequence encodes a polypeptide having L-arabinitol 4-dehydrogenase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the L-arabinitol 4-dehydrogenases can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • the host cell or fermenting organism e.g., yeast cell
  • the host cell or fermenting organism further comprises a heterologous polynucleotide encoding a xylitol dehydrogenase (XDH).
  • XDH xylitol dehydrogenase
  • a xylitol dehydrogenase as used herein, provides enzymatic activity for converting xylitol to D- xylulose.
  • the xylitol dehydrogenase may be any xylitol dehydrogenase that is suitable for the host cells and the methods described herein, such as a naturally occurring xylitol dehydrogenase or a variant thereof that retains xylitol dehydrogenase activity.
  • the xylitol dehydrogenase is present in the cytosol of the host cells.
  • the host cells or fermenting organisms comprising a heterologous polynucleotide encoding a xylitol dehydrogenase have an increased level of xylitol dehydrogenase activity compared to the host cells without the heterologous polynucleotide encoding the xylitol dehydrogenase, when cultivated under the same conditions.
  • the host cells have an increased level of xylitol dehydrogenase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cells without the heterologous polynucleotide encoding the xylitol dehydrogenase, when cultivated under the same conditions.
  • xylitol dehydrogenases that can be used with the host cells and fermenting organisms, and methods of use described herein include, but are not limited to, the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309, the Trichoderma reesei xylitol dehydrogenase (Wang et al., 1998, Chin. J.
  • xylitol dehydrogenases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the xylitol dehydrogenase is a bacterial, a yeast, or a filamentous fungal xylitol dehydrogenase, e.g., obtained from any of the microorganisms described or referenced herein, as described supra.
  • the xylitol dehydrogenase (XDH) coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding xylitol dehydrogenases from strains of different genera or species, as described supra.
  • the polynucleotides encoding xylitol dehydrogenases (XDHs) may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra.
  • the xylitol dehydrogenase (XDH) has a mature polypeptide sequence of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to any xylitol dehydrogenase described or referenced herein (e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309), or the mature polypeptide thereof.
  • any xylitol dehydrogenase described or referenced herein e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309
  • the xylitol dehydrogenase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from any xylitol dehydrogenase described or referenced herein (e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309), or the mature polypeptide thereof.
  • any xylitol dehydrogenase described or referenced herein e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309
  • the xylitol dehydrogenase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any xylitol dehydrogenase described or referenced herein (e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309), or the mature polypeptide thereof, allelic variant, or a fragment thereof having xylitol dehydrogenase activity.
  • the xylitol dehydrogenase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) amino acids.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the xylitol dehydrogenase (XDH) has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the xylitol dehydrogenase activity of any xylitol dehydrogenase described or referenced herein (e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309), or the mature polypeptide thereof, under the same conditions.
  • the xylitol dehydrogenase (XDH) coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any xylitol dehydrogenase described or referenced herein (e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309), or the mature polypeptide coding sequence thereof.
  • any xylitol dehydrogenase described or referenced herein e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309
  • the xylitol dehydrogenase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any xylitol dehydrogenase described or referenced herein (e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309), or the mature polypeptide coding sequence thereof.
  • any xylitol dehydrogenase described or referenced herein e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309
  • the heterologous polynucleotide encoding the xylitol dehydrogenase comprises the coding sequence of any xylitol dehydrogenase described or referenced herein (e.g., the Scheffersomyces stipitis xylitol dehydrogenase of SEQ ID NO: 309), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the xylitol dehydrogenase comprises a subsequence of the coding sequence from any xylitol dehydrogenase described or referenced herein, wherein the subsequence encodes a polypeptide having xylitol dehydrogenase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the xylitol dehydrogenases can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • the host cell or fermenting organism e.g., yeast cell
  • the host cell or fermenting organism further comprises a heterologous polynucleotide encoding a xylulokinase (XK).
  • XK xylulokinase
  • the xylulokinase may be any xylulokinase that is suitable for the host cells and the methods described herein, such as a naturally occurring xylulokinase or a variant thereof that retains xylulokinase activity.
  • the xylulokinase is present in the cytosol of the host cells.
  • the host cells or fermenting organisms comprising a heterologous polynucleotide encoding a xylulokinase have an increased level of xylulokinase activity compared to the host cells without the heterologous polynucleotide encoding the xylulokinase, when cultivated under the same conditions.
  • the host cells have an increased level of xylulokinase activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cells without the heterologous polynucleotide encoding the xylulokinase, when cultivated under the same conditions.
  • Exemplary xylulokinases that can be used with the host cells and fermenting organisms, and methods of use described herein include, but are not limited to, the Saccharomyces cerevisiae xylulokinase of SEQ ID NO: 75, the Scheffersomyces stipitis xylulokinase of SEQ ID NO: 310 and the Aspergillus niger xylulokinase of SEQ ID NO: 311. Additional xylulokinases are known in the art.
  • xylulokinases may be obtained from microorganisms of any genus, including those readily available within the UniProtKB database.
  • the xylulokinases is a bacterial, a yeast, or a filamentous fungal xylulokinase, e.g., obtained from any of the microorganisms described or referenced herein, as described supra.
  • the xylulokinase (XK) coding sequences can also be used to design nucleic acid probes to identify and clone DNA encoding xylulokinases from strains of different genera or species, as described supra.
  • the polynucleotides encoding xylulokinases may also be identified and obtained from other sources including microorganisms isolated from nature (e.g., soil, composts, water, etc.) or DNA samples obtained directly from natural materials (e.g., soil, composts, water, etc.) as described supra. Techniques used to isolate or clone polynucleotides encoding xylulokinases (XKs) are described supra.
  • the xylulokinase (XK) has a mature polypeptide sequence of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to any xylulokinase described or referenced herein (e.g., the xylulokinase of SEQ ID NO: 75, 310 or 311), or the mature polypeptide thereof.
  • the xylulokinase has a mature polypeptide sequence that differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from any xylulokinase described or referenced herein (e.g., the xylulokinase of SEQ ID NO: 75, 310 or 311), or the mature polypeptide thereof.
  • the xylulokinase has a mature polypeptide sequence that comprises or consists of the amino acid sequence of any xylulokinase described or referenced herein (e.g., the xylulokinase of SEQ ID NO: 75, 310 or 311), or the mature polypeptide thereof, allelic variant, or a fragment thereof having xylulokinase activity.
  • the xylulokinase has an amino acid substitution, deletion, and/or insertion of one or more (e.g., two, several) amino acids.
  • the total number of amino acid substitutions, deletions and/or insertions is not more than 10, e.g., not more than 9, 8, 7, 6, 5, 4, 3, 2, or 1.
  • the xylulokinase (XK) has at least 20%, e.g., at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% of the xylulokinase activity of any xylulokinase described or referenced herein (e.g., the xylulokinase of SEQ ID NO: 75, 310 or 311), or the mature polypeptide thereof, under the same conditions.
  • the xylulokinase (XK) coding sequence hybridizes under at least low stringency conditions, e.g., medium stringency conditions, medium-high stringency conditions, high stringency conditions, or very high stringency conditions with the full-length complementary strand of the coding sequence from any xylulokinase described or referenced herein (e.g., the xylulokinase of SEQ ID NO: 75, 310 or 311), or the mature polypeptide coding sequence thereof.
  • any xylulokinase described or referenced herein e.g., the xylulokinase of SEQ ID NO: 75, 310 or 311
  • the xylulokinase coding sequence has at least 65%, e.g., at least 70%, at least 75%, at least 80%, at least 85%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity with the coding sequence from any xylulokinase described or referenced herein (e.g., the xylulokinase of SEQ ID NO: 75, 310 or 311), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the xylulokinase comprises the coding sequence of any xylulokinase described or referenced herein (e.g., the xylulokinase of SEQ ID NO: 75, 310 or 311), or the mature polypeptide coding sequence thereof.
  • the heterologous polynucleotide encoding the xylulokinase comprises a subsequence of the coding sequence from any xylulokinase described or referenced herein, wherein the subsequence encodes a polypeptide having xylulokinase activity.
  • the number of nucleotides residues in the subsequence is at least 75%, e.g., at least 80%, 85%, 90%, or 95% of the number of the referenced coding sequence.
  • the xylulokinases (XKs) can also include fused polypeptides or cleavable fusion polypeptides, as described supra.
  • the host cells or fermenting organisms described herein have an active arabinose fermentation pathway known as the “bacterial pathway” which utilizes genes L-arabinose isomerase (AI, such as araA), L-ribulokinase (RK, such as araB), and L-ribulose-5-P4-epimerase (R5PE, such as araD) to convert L-arabinose to D-xylulose 5-phosphate.
  • AI L-arabinose isomerase
  • RK L-ribulokinase
  • R5PE L-ribulose-5-P4-epimerase
  • exemplary arabinose fermentation pathways are known in the art (e.g., WO2002/066616; WO2003/095627; WO2007/143245; WO2008/041840; WO2009/011591; WO2010/151548; WO2011/003893; WO2011/131674; WO2012/143513; US2012/225464; US 7,977,083).
  • Any arabinose fermentation pathway or gene thereof described in the foregoing references is incorporated herein by reference for use in Applicant’s active arabinose fermentation pathway.
  • the recombinant cells described herein have improved anaerobic growth on a pentose (e.g., xylose and/or arabinose).
  • the recombinant cell is capable of higher anaerobic growth rate on a pentose (e.g., xylose and/or arabinose) compared to the same cell without the active pentose fermentation pathway.
  • the recombinant cells described herein have improved rate of pentose consumption (e.g., xylose and/or arabinose).
  • the recombinant cell is capable of higher rate of pentose consumption (e.g., xylose and/or arabinose) compared to the same cell without the active pentose fermentation pathway.
  • the rate of pentose consumption (e.g., xylose and/or arabinose) is at least 5%, e.g., at least 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 60%, 75% or 90% higher compared to the same cell without the active pentose fermentation pathway.
  • the recombinant cells described herein have higher pentose (e.g., xylose and/or arabinose) consumption.
  • the recombinant cell is capable of higher pentose (e.g., xylose and/or arabinose) consumption compared to the same cell without the active pentose fermentation pathway at about or after 120 hours fermentation (e.g., under conditions described in the examples herein). In one embodiment, the recombinant cell is capable of consuming more than 65%, e.g., at least 70%, 75%, 80%, 85%, 90%, 95% of pentose (e.g., xylose and/or arabinose) in the medium at about or after 120 hours fermentation (e.g., under conditions described in the examples herein). M.
  • pentose e.g., xylose and/or arabinose
  • the host cells and fermenting organisms described herein may also comprise one or more (e.g., two, several) gene disruptions, e.g., to divert sugar metabolism from undesired products to ethanol.
  • the recombinant host cells produce a greater amount of ethanol compared to the cell without the one or more disruptions when cultivated under identical conditions.
  • one or more of the disrupted endogenous genes is inactivated.
  • the host cell or fermenting organism is a diploid and has a disruption (e.g., inactivation) of both copies of the referenced gene.
  • the host cell or fermenting organism provided herein comprises a disruption of one or more endogenous genes encoding enzymes involved in producing alternate fermentative products such as glycerol or other byproducts such as acetate or diols.
  • the cells provided herein may comprise a disruption of one or more endogenous genes encoding a glycerol 3-phosphatase (GPP, E.C.3.1.3.21, catalyzes conversion of glycerol-3 phosphate to glycerol), a glycerol 3-phosphate dehydrogenase (GPD, catalyzes reaction of dihydroxyacetone phosphate to glycerol 3-phosphate), glycerol kinase (catalyzes conversion of glycerol 3-phosphate to glycerol), dihydroxyacetone kinase (catalyzes conversion of dihydroxyacetone phosphate to dihydroxyacetone), glycerol dehydrogenase (cataly).
  • GPP
  • the host cell or fermenting organism comprises a disruption to one or more endogenous genes encoding a glycerol 3-phosphatase (GPP).
  • GPP glycerol 3-phosphatase
  • Saccharomyces cerevisiae has two glycerol-3-phosphate phosphatase paralogs encoding GPP1 (UniProt No. P41277; SEQ ID NO: 257) and GPP2 (UniProt No. P40106; SEQ ID NO: 258) (Pahlman et al. (2001) J. Biol. Chem.276(5):3555-63; Norbeck et al. (1996) J. Biol. Chem. 271(23):13875-81).
  • the host cell or fermenting organism comprises a disruption to GPP1. In some embodiments, the host cell or fermenting organism comprises a disruption to GPP2. In some embodiments, the host cell or fermenting organism comprises a disruption to GPP1 and GPP2. In some embodiments, the host cell or fermenting organism comprises a disruption to one or more endogenous genes encoding a glycerol 3-phosphate dehydrogenase (GPD). Saccharomyces cerevisiae has two glycerol 3-phosphate dehydrogenases which encode GPD1 (UniProt No. Q00055; SEQ ID NO: 259) and GPD2 (UniProt No. P41911; SEQ ID NO: 260).
  • GPD glycerol 3-phosphate dehydrogenase
  • the host cell or fermenting organism comprises a disruption to GPD1. In some embodiments, the host cell or fermenting organism comprises a disruption to GPD2. In some embodiments, the host cell or fermenting organism comprises a disruption to GPD1 and GPD2.
  • the host cell or fermenting organism comprises a disruption to an endogenous gene encoding GPP (e.g., GPP1 and/or GPP2) and/or a GPD (GPD1 and/or GPD2), wherein the host cell or fermenting organism produces a decreased amount of glycerol (e.g., at least 25% less, at least 50% less, at least 60% less, at least 70% less, at least 80% less, or at least 90% less) compared to the cell without the disruption to the endogenous gene encoding the GPP and/or GPD when cultivated under identical conditions.
  • Modeling analysis can be used to design gene disruptions that additionally optimize utilization of the pathway.
  • One exemplary computational method for identifying and designing metabolic alterations favoring biosynthesis of a desired product is the OptKnock computational framework, Burgard et al., 2003, Biotechnol. Bioeng.84: 647-657.
  • the host cells and fermenting organisms comprising a gene disruption may be constructed using methods well known in the art, including those methods described herein.
  • a portion of the gene can be disrupted such as the coding region or a control sequence required for expression of the coding region.
  • Such a control sequence of the gene may be a promoter sequence or a functional part thereof, i.e., a part that is sufficient for affecting expression of the gene.
  • a promoter sequence may be inactivated resulting in no expression or a weaker promoter may be substituted for the native promoter sequence to reduce expression of the coding sequence.
  • Other control sequences for possible modification include, but are not limited to, a leader, propeptide sequence, signal sequence, transcription terminator, and transcriptional activator.
  • the host cells and fermenting organisms comprising a gene disruption may be constructed by gene deletion techniques to eliminate or reduce expression of the gene. Gene deletion techniques enable the partial or complete removal of the gene thereby eliminating their expression. In such methods, deletion of the gene is accomplished by homologous recombination using a plasmid that has been constructed to contiguously contain the 5' and 3' regions flanking the gene.
  • the host cells and fermenting organisms comprising a gene disruption may also be constructed by introducing, substituting, and/or removing one or more (e.g., two, several) nucleotides in the gene or a control sequence thereof required for the transcription or translation thereof.
  • nucleotides may be inserted or removed for the introduction of a stop codon, the removal of the start codon, or a frame-shift of the open reading frame.
  • Such a modification may be accomplished by site-directed mutagenesis or PCR generated mutagenesis in accordance with methods known in the art. See, for example, Botstein and Shortle, 1985, Science 229: 4719; Lo et al., 1985, Proc. Natl. Acad. Sci.
  • the host cells and fermenting organisms comprising a gene disruption may also be constructed by inserting into the gene a disruptive nucleic acid construct comprising a nucleic acid fragment homologous to the gene that will create a duplication of the region of homology and incorporate construct DNA between the duplicated regions.
  • a disrupting construct may be simply a selectable marker gene accompanied by 5’ and 3’ regions homologous to the gene. The selectable marker enables identification of transformants containing the disrupted gene.
  • the host cells and fermenting organisms comprising a gene disruption may also be constructed by the process of gene conversion (see, for example, Iglesias and Trautner, 1983, Molecular General Genetics 189: 73-76).
  • a nucleotide sequence corresponding to the gene is mutagenized in vitro to produce a defective nucleotide sequence, which is then transformed into the recombinant strain to produce a defective gene.
  • the defective nucleotide sequence replaces the endogenous gene.
  • the defective nucleotide sequence also comprises a marker for selection of transformants containing the defective gene.
  • the host cells and fermenting organisms comprising a gene disruption may be further constructed by random or specific mutagenesis using methods well known in the art, including, but not limited to, chemical mutagenesis (see, for example, Hopwood, The Isolation of Mutants in Methods in Microbiology (J.R.
  • Modification of the gene may be performed by subjecting the parent strain to mutagenesis and screening for mutant strains in which expression of the gene has been reduced or inactivated.
  • the mutagenesis which may be specific or random, may be performed, for example, by use of a suitable physical or chemical mutagenizing agent, use of a suitable oligonucleotide, or subjecting the DNA sequence to PCR generated mutagenesis.
  • the mutagenesis may be performed by use of any combination of these mutagenizing methods.
  • Examples of a physical or chemical mutagenizing agent suitable for the present purpose include ultraviolet (UV) irradiation, hydroxylamine, N-methyl-N'-nitro-N- nitrosoguanidine (MNNG), N-methyl-N’-nitrosogaunidine (NTG) O-methyl hydroxylamine, nitrous acid, ethyl methane sulphonate (EMS), sodium bisulphite, formic acid, and nucleotide analogues.
  • UV ultraviolet
  • MNNG N-methyl-N'-nitro-N- nitrosoguanidine
  • NVG N-methyl-N’-nitrosogaunidine
  • EMS ethyl methane sulphonate
  • sodium bisulphite formic acid
  • nucleotide analogues examples include ultraviolet (UV) irradiation, hydroxylamine, N-methyl-N'-nitro-N- nitrosoguanidine (MNNG), N-methyl-N’-nitrosogaunidine
  • a nucleotide sequence homologous or complementary to a gene described herein may be used from other microbial sources to disrupt the corresponding gene in a recombinant strain of choice.
  • the modification of a gene in the recombinant cell is unmarked with a selectable marker. Removal of the selectable marker gene may be accomplished by culturing the mutants on a counter-selection medium. Where the selectable marker gene contains repeats flanking its 5' and 3' ends, the repeats will facilitate the looping out of the selectable marker gene by homologous recombination when the mutant strain is submitted to counter-selection.
  • the selectable marker gene may also be removed by homologous recombination by introducing into the mutant strain a nucleic acid fragment comprising 5' and 3' regions of the defective gene, but lacking the selectable marker gene, followed by selecting on the counter-selection medium. By homologous recombination, the defective gene containing the selectable marker gene is replaced with the nucleic acid fragment lacking the selectable marker gene. Other methods known in the art may also be used. III. Backend or downstream processing A. Recovery of the fermentation product and production of whole stillage Subsequent to fermentation or SSF, the fermentation product may be separated from the fermentation medium.
  • the fermentation product e.g., ethanol
  • alcohol is separated from the fermented starch-containing grain and purified by conventional methods of distillation.
  • the method of the invention further comprises distillation to obtain the fermentation product, e.g., ethanol.
  • the fermentation and the distillation may be carried out simultaneously and/or separately/sequentially; optionally followed by one or more process steps for further refinement of the fermentation product. Following the completion of the distillation process, the material remaining is considered the whole stillage.
  • the desired fermentation product may be extracted from the fermentation medium by micro or membrane filtration techniques. Ethanol with a purity of up to about 96 vol. % can be obtained, which can be used as, for example, fuel ethanol, drinking ethanol, i.e., potable neutral spirits, or industrial ethanol.
  • the fermentation product after being recovered is substantially pure. With respect to the methods herein, "substantially pure" intends a recovered preparation that contains no more than 15% impurity, wherein impurity intends compounds other than the fermentation product (e.g., ethanol).
  • a substantially pure preparation wherein the preparation contains no more than 25% impurity, or no more than 20% impurity, or no more than 10% impurity, or no more than 5% impurity, or no more than 3% impurity, or no more than 1% impurity, or no more than 0.5% impurity.
  • Suitable assays to test for the production of ethanol and contaminants, and sugar consumption can be performed using methods known in the art.
  • ethanol product as well as other organic compounds, can be analyzed by methods such as HPLC (High Performance Liquid Chromatography), GC-MS (Gas Chromatography Mass Spectroscopy) and LC-MS (Liquid Chromatography-Mass Spectroscopy) or other suitable analytical methods using routine procedures well known in the art.
  • HPLC High Performance Liquid Chromatography
  • GC-MS Gas Chromatography Mass Spectroscopy
  • LC-MS Liquid Chromatography-Mass Spectroscopy
  • the whole stillage is separated or partitioned into a solid and liquid phase by one or more methods for separating the thin stillage from the wet cake. Separating whole stillage into thin stillage and wet cake to remove a significant portion of the liquid/water, may be done using any suitable separation technique, including centrifugation, pressing and filtration. In a preferred embodiment, the separation/dewatering is carried out by centrifugation.
  • Preferred centrifuges in industry are decanter type centrifuges, preferably high speed decanter type centrifuges.
  • a suitable centrifuge is the NX 400 steep cone series from Alfa Laval which is a high-performance decanter.
  • the separation is carried out using other conventional separation equipment such as a plate/frame filter presses, belt filter presses, screw presses, gravity thickeners and deckers, or similar equipment.
  • C. Processing of Thin Stillage is the term used for the supernatant of the centrifugation of the whole stillage.
  • the thin stillage contains 4-6 percent dry solids (DS) (mainly proteins, soluble fiber, fine fibers, and cell wall components) and has a temperature of about 60-90 degrees centigrade.
  • the thin stillage stream may be condensed by evaporation to provide two process streams including: (i) an evaporator condensate stream comprising condensed water removed from the thin stillage during evaporation, and (ii) a syrup stream, comprising a more concentrated stream of the non-volatile dissolved and non-dissolved solids, such as non-fermentable sugars and oil, remaining present from the thin stillage as the result of removing the evaporated water.
  • oil can be removed from the thin stillage or can be removed as an intermediate step to the evaporation process, which is typically carried out using a series of several evaporation stages.
  • Syrup and/or de-oiled syrup may be introduced into a dryer together with the wet grains (from the whole stillage separation step) to provide a product referred to as distillers dried grain with solubles, which also can be used as animal feed.
  • syrup and/or de-oiled syrup is sprayed into one or more dryers to combine the syrup and/or de- oiled syrup with the whole stillage to produce distillers dried grain with solubles.
  • Between 5-90 vol-%, such as between 10-80%, such as between 15-70%, such as between 20-60% of thin stillage (e.g., optionally hydrolyzed) may be recycled (as backset) to step (a).
  • the recycled thin stillage may constitute from about 1-70 vol.-%, preferably 15-60% vol.-%, especially from about 30 to 50 vol.-% of the slurry formed in step (a).
  • the process further comprises recycling at least a portion of the thin stillage stream to the slurry, optionally after oil has been extracted from the thin stillage stream.
  • DDG Drying of Wet Cake and Producing Distillers Dried Grains and Distillers Dried Grains with Solubles
  • the wet cake containing about 25-40 wt-%, preferably 30-38 wt-% dry solids, has been separated from the thin stillage (e.g., dewatered) it may be dried in a drum dryer, spray dryer, ring drier, fluid bed drier or the like in order to produce “Distillers Dried Grains” (DDG).
  • DDG is a valuable feed ingredient for animals, such as livestock, poultry and fish. It is preferred to provide DDG with a content of less than about 10-12 wt.-% moisture to avoid mold and microbial breakdown and increase the shelf life.
  • the wet cake is preferably dried under conditions that do not denature proteins in the wet cake.
  • the wet cake may be blended with syrup separated from the thin stillage and dried into DDG with Solubles (DDGS).
  • DDGS Solubles
  • Partially dried intermediate products such as are sometimes referred to as modified wet distillers grains, may be produced by partially drying wet cake, optionally with the addition of syrup before, during or after the drying process.
  • Yeast strain MEJI797 is MBG5012 of WO2019/161227 further expressing a Pycnopous sanguineus glucoamylase (SEQ ID NO: 4 of WO2011/066576) and a hybrid Rhizomucor pusillus alpha amylase expression cassette (as described in WO2013/006756).
  • SEQ ID NO: 4 of WO2011/066576 Pycnopous sanguineus glucoamylase
  • Rhizomucor pusillus alpha amylase expression cassette as described in WO2013/006756.
  • Example 1 Construction of yeast strains expressing a heterologous beta-xylosidase This example describes the construction of yeast cells containing a codon-optimized beta-xylosidase gene, listed in Table 1, under the control of the S.
  • TDH3 promoter (SEQ ID: 1), which is a strong constitutive yeast expression promoter from glyceraldehyde 3- phosphate dehydrogenase.
  • SEQ ID: 1 a strong constitutive yeast expression promoter from glyceraldehyde 3- phosphate dehydrogenase.
  • Four, five or six pieces of DNA containing the promoter, signal peptide, gene, and terminator were designed to allow for homologous recombination between the four, five or six fragments and into the X-3 locus of the yeast MEJI797.
  • the resulting strains contain one 5’ homology plus TDH promoter containing fragment (left fragment), EXG1 signal peptide plus gene containing fragments (middle fragments) and one PRM9 terminator plus 3’ homology containing fragment (right fragment) integrated into the S.
  • the left DNA fragment containing 500 bp homology to the X-3 integration site and the S. cerevisiae TDH3 promoter was PCR amplified from HP4 plasmid DNA.
  • the amplification reactions 50 ⁇ l were composed of 1X PhusionTM HF Buffer (Thermo Fisher Scientific), 0.4 mM dNTPs, 5 ng of plasmid DNA as template, 50 pmoles of forward primer, 50 pmoles of reverse primer, and one unit of PhusionTM High-Fidelity DNA Polymerase (Thermo Fisher Scientific).
  • the PCR was performed in a T100TM Thermal Cycler (Bio-Rad Laboratories, Inc.) programmed for 30 cycles each for 5 seconds at 98°C, 30 seconds at 55°C, and 30 seconds at 72°C (5 minute final extension).
  • a PCR product of 1180 bp was isolated by 1% agarose gel electrophoresis using TAE buffer and further purified using a QIAquick Gel Extraction kit (Qiagen). Construction of Beta-Xylosidase Containing Fragment (middle fragments) Synthetic linear DNA pieces containing 50 bp homology to the S. cerevisiae TDH3 promoter, the S.
  • Terminator Containing Fragment The right DNA fragment containing 500 bp homology to the X-3 integration site and the S. cerevisiae PRM9 terminator (SEQ ID NO: 243) was PCR amplified from TH37 plasmid.
  • the amplification reactions (50 ⁇ l) were composed of 1X PhusionTM HF Buffer (Thermo Fisher Scientific), 0.4 mM dNTPs, 5 ng of plasmid DNA as template, 50 pmoles of primer 1221473, 50 pmoles of primer 1230745, and one unit of PhusionTM High-Fidelity DNA Polymerase (Thermo Fisher Scientific).
  • the PCR was performed in a T100TM Thermal Cycler (Bio-Rad Laboratories, Inc.) programmed for 30 cycles each for 5 seconds at 98°C, 30 seconds at 55°C, and 30 seconds at 72°C (5 minute final extension).
  • a PCR product of 750 bp was isolated by 1% agarose gel electrophoresis using TAE buffer and further purified using a QIAquick Gel Extraction kit (Qiagen). Integration of the Left, Middle and Right Fragments to Generate a Library of Yeast Strains Expressing GH3 and GH120 Beta-Xylosidases
  • the yeast MEJI797 was transformed with the left, middle and right DNA fragments described above, using 100 ng of each fragment. To aid homologous recombination of these fragments at the genomic X-3 integration site, 300 ng of a plasmid containing MAD7 and guide RNA specific to X-3 (pMLBA647) was also used in the transformation. These components were transformed into the S.
  • Transformants were selected on YPD+clonNAT to select for transformants that contain the CRISPR/MAD7 plasmid pMLBA647. Transformants were picked using a Q-Pix Colony Picking System (Molecular Devices) to inoculate one well of 96- well plate containing YPD media. The plates were grown for 2 days then glycerol was added to 20% final concentration and the plates were stored at -80°C until needed. Integration of the beta-xylosidase constructs were verified by PCR using locus specific primers and subsequent sequencing.
  • BX Beta-xylosidase
  • yeast strains from Example 1 expressing a heterologous GH3 or GH120 enzyme were evaluated for the relative beta-xylosidase activities of their supernatants grown in 96-well microtiter plates. Each strain was grown in duplicate in 200 ⁇ L of YP medium + 2% glucose for 2 days at 30 °C. After which, the microtiter plates were centrifuged at 3000rpm for 5 min at ambient temperature. 130 ⁇ L of supernatant was transferred to Millipore Multiscreen HV plates (cat#MAHVN4550). The microtiter plates were centrifuged again at 3000rpm for 5 min into a sterile Costar 96WP.
  • the resulting solution is referred to henceforth as the supernatant.
  • 10 ⁇ L of 10 mM 4-nitrophenyl- ⁇ -D- xylopyranoside 10 ⁇ L of 1 M sodium acetate pH 5.0 and 60 ⁇ L of ddH2O were added to each well. Reactions were initiated by addition of 20 ⁇ L of S. cerevisiae supernatants. Upon initiation, the plates were incubated at 37 °C for 30 min. After this period, the reactions were quenched by addition of 100 ⁇ L of 4% Tris (pH 11).
  • panis to explore important active site residues
  • the structural models of the members of the GH120 enzyme library were predicted using AlphaFold.
  • the list of GH120 beta-xylosidase enzymes assayed in the previous example was converted into a phylogenetic tree using an in-house tool.
  • the closest phylogenetic relatives to the L. panis GH120(a) with conserved tertiary structure at the active site were compiled.
  • These conserved enzymes are GH120 beta-xylosidase enzymes from L. mucosae, L. ingluviei, B. wexlerae, and F. saccharivorans, and exhibit varying beta- xylosidase hydrolysis activity (Figure 1).
  • a process for producing a fermentation product from starch-containing material comprising the steps of: (a) liquefying the starch-containing material at a temperature above the initial gelatinization temperature using an alpha-amylase; (b) saccharifying the liquefied starch-containing material; and (c) fermenting saccharified starch-containing material using a fermenting organism; wherein the fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • Paragraph [2]. The process of paragraph 1, wherein steps (b) and (c) are performed simultaneously in a simultaneous saccharification and fermentation (SSF). Paragraph [3].
  • the process of any of paragraph 1 or 2 wherein a thermostable endoglucanase is added during liquefying step (a).
  • Paragraph [4]. The process of any of the preceding paragraphs, wherein a thermostable lipase is added during liquefying step (a).
  • Paragraph [5]. The process of any of the preceding paragraphs, wherein a thermostable phytase is added during liquefying step (a).
  • Paragraph [6]. The process of any of the preceding paragraphs, wherein a thermostable protease is added during liquefying step (a).
  • thermostable pullulanase is added during liquefying step (a).
  • Paragraph [8]. The process of any of the preceding paragraphs, wherein a thermostable xylanase is added during liquefying step (a).
  • Paragraph [9]. The process of any of the preceding paragraphs, wherein a thermostable alpha-amylase, a thermostable protease and a thermostable xylanase are added during liquefying step (a). Paragraph [10].
  • a glucoamylase is added during step (b) and/or step (c). Paragraph [11].
  • a process for producing a fermentation product from an ungelatinized starch-containging grain comprises the following steps: (a) saccharifying a starch-containing grain at a temperature below the initial gelatinization temperature to produce a fermentable sugar; and (b) fermenting the saccharified starch-containing material using a fermenting organism to produce a fermentation product; wherein the fermenting organism comprises a heterologous polynucleotide encoding a beta-xylosidase.
  • step (a) is conducted in the prescence of a glucoamylase and an alpha-amylase.
  • step (a) is conducted in the prescence of a glucoamylase and an alpha-amylase.
  • step (b) is conducted in the prescence of a glucoamylase and an alpha-amylase.
  • steps (a) and (b) are performed simultaneously in a simultaneous saccharification and fermentation (SSF).
  • SSF simultaneous saccharification and fermentation
  • Paragraph [19] The process of any one of the preceding paragraphs, wherein the beta- xylosidase is a glycosyl hydrolase family 120.
  • Paragraph [20]. The process of any one of the preceding paragraphs, wherein the beta- xylosidase is a glycosyl hydrolase family 3. Paragraph [21].
  • beta- xylosidase comprises one or more of residues W413, V416, R435 and N462 corresponding SEQ ID NO: 335.
  • Paragraph [22]. The process of any one of the preceding paragraphs, wherein the beta- xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to any one of SEQ ID NOs: 324-353 or 365-437, or the mature polypeptide thereof. Paragraph [23].
  • beta- xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 335, 339 or 340, or the mature polypeptide thereof.
  • beta- xylosidase sequence differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of SEQ ID NOs: 324-353 or 365-437, or the mature polypeptide sequence thereof (such as SEQ ID NO: 335, 339 or 340, or the mature polypeptide sequence thereof).
  • the mature polypeptide sequence thereof such as SEQ ID NO: 335, 339 or 340, or the mature polypeptide sequence thereof.
  • beta- xylosidase sequence comprises or consists of the amino acid sequence of any one of SEQ ID NOs: 324-353 or 365-437, or the mature polypeptide sequence thereof (such as SEQ ID NO: 335, 339 or 340, or the mature polypeptide sequence thereof).
  • the beta- xylosidase is a fragment of of any one of SEQ ID NOs: 324-353 or 365-437, or the mature polypeptide sequence thereof (such as a fragment of SEQ ID NO: 335, 339 or 340, or the mature polypeptide sequence thereof).
  • the beta- xylosidase has a TM-score of at least 0.60, e.g., at least 0.65, at least 0.70, at least 0.75, at least 0.80, at least 0.85, at least 0.90, at least 0.91, at least 0.92, at least 0.93, at least 0.94, at least 0.95, at least 0.96, at least 0.97, at least 0.98, at least 0.99, or even 1.0, compared to the three-dimensional structure of the beta-xylosidase of SEQ ID NO: 335, wherein the three-dimensional structure is calculated using Alphafold. Paragraph [28].
  • Paragraph [37]. The process of any of the preceding paragraphs, wherein the fermenting organism comprises a heterologous polynucleotide encoding a protease.
  • Paragraph [38]. The process of any of the preceding paragraphs, wherein the fermenting organism comprises a disruption to an endogenous gene encoding a glycerol 3-phosphate dehydrogenase (GPD).
  • GPD glycerol 3-phosphate dehydrogenase
  • Paragraph [39]. The process of any one of the preceding paragraphs, wherein the fermenting organism is yeast. Paragraph [40].
  • the starch- containing material comprises beets, maize, corn, wheat, rye, barley, oats, triticale, rice, sorghum, sweet potatoes, millet, pearl millet, and/or foxtail millet.
  • the starch- containing material comprises corn.
  • the fermentation product is ethanol, preferably fuel ethanol.
  • a recombinant host cell comprising a heterologous polynucleotide encoding a beta-xylosidase. Paragraph [46].
  • the recombinant host cell of paragraph 45, wherein the beta-xylosidase is a glycosyl hydrolase family 120. Paragraph [47]. The recombinant host cell of paragraph 45, wherein the beta-xylosidase is a glycosyl hydrolase family 3. Paragraph [48]. The recombinant host cell of any one of paragraphs 45-47, wherein the beta-xylosidase comprises one or more of residues W413, V416, R435 and N462 corresponding SEQ ID NO: 335. Paragraph [49].
  • Paragraph [51] the beta-xylosidase has at least 60%, e.g., at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% sequence identity to SEQ ID NO: 335, 339 or 340, or the mature polypeptide thereof.
  • beta-xylosidase sequence differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of SEQ ID NOs: 324-353 or 365-437, or the mature polypeptide sequence thereof (such as SEQ ID NO: 335, 339 or 340, or the mature polypeptide sequence thereof).
  • the beta-xylosidase sequence differs by no more than ten amino acids, e.g., by no more than five amino acids, by no more than four amino acids, by no more than three amino acids, by no more than two amino acids, or by one amino acid from the amino acid sequence of any one of SEQ ID NOs: 324-353 or 365-437, or the mature polypeptide sequence thereof (such as SEQ ID NO: 335, 339 or 340, or the mature polypeptide sequence thereof).
  • Paragraph [53]. The recombinant host cell of any one of paragraphs 45-52, wherein the beta-xylosidase is a fragment of of any one of SEQ ID NOs: 324-353 or 365-437, or the mature polypeptide sequence thereof (such as a fragment of SEQ ID NO: 335, 339 or 340, or the mature polypeptide sequence thereof).
  • Paragraph [54] The recombinant host cell of any one of paragraphs 45-53, wherein the beta-xylosidase has a TM-score of at least 0.60, e.g., at least 0.65, at least 0.70, at least 0.75, at least 0.80, at least 0.85, at least 0.90, at least 0.91, at least 0.92, at least 0.93, at least 0.94, at least 0.95, at least 0.96, at least 0.97, at least 0.98, at least 0.99, or even 1.0, compared to the three-dimensional structure of the beta-xylosidase of SEQ ID NO: 335, wherein the three-dimensional structure is calculated using Alphafold. Paragraph [55].
  • the recombinant host cell of any one of paragraphs 45-54 wherein the heterologous polynucleotide encoding the beta-xylosidase is operably linked to a promoter that is foreign to the polynucleotide.
  • Paragraph [56] The recombinant host cell of any one of paragraphs 45-55, wherein the fermenting organism comprises an active pentose fermentation pathway (e.g., an active xylose fermentation pathway and/or an active arabinose fermentation pathway).
  • GPD glycerol 3- phosphate dehydrogenase
  • GPP glycerol 3-phosphatase
  • Paragraph [63]. The recombinant host cell of any one of paragraphs 45-62, wherein the fermenting organism comprises a heterologous polynucleotide encoding a glycerol transporter.
  • Paragraph [64]. The recombinant host cell of any one of paragraphs 45-63, wherein the fermenting organism comprises a heterologous polynucleotide encoding a protease. Paragraph [65].
  • GPD glycerol 3- phosphate dehydrogenase
  • Paragraph [66] The recombinant host cell of any one of paragraphs 45-65, wherein the fermenting organism is yeast. Paragraph [67].
  • the recombinant host cell of any one of paragraphs 45-66 wherein the fermenting organism is a Saccharomyces, Rhodotorula, Schizosaccharomyces, Kluyveromyces, Pichia, Hansenula, Rhodosporidium, Candida, Yarrowia, Lipomyces, Cryptococcus, or Dekkera sp. cell. Paragraph [68].

Landscapes

  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

La présente invention concerne des procédés de fabrication de produits de fermentation, tels que l'éthanol, à partir d'une substance contenant de l'amidon, à l'aide d'organismes de fermentation qui expriment une bêta-xylosidase GH120 ou GH3.
PCT/US2024/033350 2023-06-13 2024-06-11 Procédés de fabrication de produits de fermentation à l'aide d'une levure modifiée exprimant une bêta-xylosidase WO2024258820A2 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202363507960P 2023-06-13 2023-06-13
US63/507,960 2023-06-13

Publications (2)

Publication Number Publication Date
WO2024258820A2 true WO2024258820A2 (fr) 2024-12-19
WO2024258820A3 WO2024258820A3 (fr) 2025-01-23

Family

ID=91829243

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2024/033350 WO2024258820A2 (fr) 2023-06-13 2024-06-11 Procédés de fabrication de produits de fermentation à l'aide d'une levure modifiée exprimant une bêta-xylosidase

Country Status (1)

Country Link
WO (1) WO2024258820A2 (fr)

Citations (182)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1984002921A2 (fr) 1983-01-28 1984-08-02 Cetus Corp cADN GLUCOAMYLASE
EP0135138A2 (fr) 1983-08-17 1985-03-27 Cpc International Inc. Glucoanylase thermostable et procédé pour sa production
US4560651A (en) 1981-04-20 1985-12-24 Novo Industri A/S Debranching enzyme product, preparation and use thereof
WO1986001831A1 (fr) 1984-09-18 1986-03-27 Michigan Biotechnology Institute Enzymes thermostables de conversion de l'amidon
US4587215A (en) 1984-06-25 1986-05-06 Uop Inc. Highly thermostable amyloglucosidase
USRE32153E (en) 1978-09-01 1986-05-20 Cpc International Inc. Highly thermostable glucoamylaseand process for its production
US4598048A (en) 1983-03-25 1986-07-01 Novo Industri A/S Preparation of a maltogenic amylase enzyme
US4727026A (en) 1985-11-26 1988-02-23 Godo Shusei Co., Ltd. Method for direct saccharification of raw starch using enzyme produced by a basidiomycete belonging to the genus Corticium
WO1992000381A1 (fr) 1990-06-29 1992-01-09 Novo Nordisk A/S Hydrolyse enzymatique de l'amidon en glucose a l'aide d'une enzyme produite par genie genetique
WO1992002614A1 (fr) 1990-08-01 1992-02-20 Novo Nordisk A/S Nouvelles pullulanases thermostables
WO1992006204A1 (fr) 1990-09-28 1992-04-16 Ixsys, Inc. Banques de recepteurs heteromeres a expression en surface
US5223409A (en) 1988-09-02 1993-06-29 Protein Engineering Corp. Directed evolution of novel binding proteins
WO1994025612A2 (fr) 1993-05-05 1994-11-10 Institut Pasteur Sequences de nucleotides pour le controle de l'expression de sequences d'adn dans un hote cellulaire
WO1995017413A1 (fr) 1993-12-21 1995-06-29 Evotec Biosystems Gmbh Procede permettant une conception et une synthese evolutives de polymeres fonctionnels sur la base d'elements et de codes de remodelage
WO1995022625A1 (fr) 1994-02-17 1995-08-24 Affymax Technologies N.V. Mutagenese d'adn par fragmentation aleatoire et reassemblage
WO1995033836A1 (fr) 1994-06-03 1995-12-14 Novo Nordisk Biotech, Inc. Phosphonyldipeptides efficaces dans le traitement de maladies cardiovasculaires
WO1996023874A1 (fr) 1995-02-03 1996-08-08 Novo Nordisk A/S Technique de mise au point de mutants d'amylase-alpha dotes de proprietes predefinies
WO1996023873A1 (fr) 1995-02-03 1996-08-08 Novo Nordisk A/S Alleles d'amylase-alpha
WO1996028567A1 (fr) 1995-03-09 1996-09-19 Genencor International, Inc. Procede de liquefaction de l'amidon
WO1997033976A1 (fr) 1996-03-14 1997-09-18 Korea Institute Of Science And Technology Ds11(kctc 0231bp), nouvelle souche de bacillus sp. et nouvelle phytase produite a partir de ladite souche
WO1997038096A1 (fr) 1996-04-05 1997-10-16 Kyowa Hakko Kogyo Co., Ltd. Nouvelle phytase et gene codant pour ladite phytase
WO1997041213A1 (fr) 1996-04-30 1997-11-06 Novo Nordisk A/S MUTANTS DUNE AMYLASE-$g(a)
WO1997048812A2 (fr) 1996-06-14 1997-12-24 Her Majesty The Queen In Right Of Canada, Represented By The Department Of Agriculture And Agri-Food Canada Sequences d'adn codant des phytases de micro-organismes de ruminants
WO1998005785A1 (fr) 1996-08-01 1998-02-12 Biocem Phytases de plantes et applications biotechnologiques
WO1998006856A1 (fr) 1996-08-13 1998-02-19 Finnfeeds International Ltd. Phytase, gene codant cette phytase, procede de production et utilisation de cette derniere
WO1998013480A1 (fr) 1996-09-25 1998-04-02 Kyowa Hakko Kogyo Co., Ltd. Nouvelle phytase et son procede de preparation
WO1998020139A2 (fr) 1996-11-05 1998-05-14 Finnfeeds International Ltd. Phytase obtenue a partir de germes de soja
WO1998028408A1 (fr) 1996-12-20 1998-07-02 Novo Nordisk A/S Phytase induite par peniophora
WO1998056926A1 (fr) 1997-06-10 1998-12-17 Takara Shuzo Co., Ltd. Systeme pour exprimer une proteine hyperthermostable
WO1999019467A1 (fr) 1997-10-13 1999-04-22 Novo Nordisk A/S MUTANTS D'α-AMYLASE
WO1999028448A1 (fr) 1997-11-26 1999-06-10 Novo Nordisk A/S Glucoamylase thermostable
WO1999048330A1 (fr) 1998-03-19 1999-09-23 Koninklijke Philips Electronics N.V. Prothese auditive a detecteur pour reception de signaux sans fil et dispositif associe
WO1999049022A1 (fr) 1998-03-23 1999-09-30 Novo Nordisk A/S Variant de phytase
WO2000004136A1 (fr) 1998-07-15 2000-01-27 Novozymes A/S Variants de glucoamylase
US6093562A (en) 1996-02-05 2000-07-25 Novo Nordisk A/S Amylase variants
WO2000060059A2 (fr) 1999-03-30 2000-10-12 NovozymesA/S Variantes d'alpha amylase
US6162628A (en) 1998-02-27 2000-12-19 Novo Nordisk A/S Maltogenic alpha-amylase variants
WO2001004273A2 (fr) 1999-07-09 2001-01-18 Novozymes A/S Variante de glucoamylase
WO2001062947A1 (fr) 2000-02-23 2001-08-30 Novozymes A/S Fermentation a l'aide de la phytase
WO2002010355A2 (fr) 2000-08-01 2002-02-07 Novozymes A/S Mutants d'alpha-amylase a proprietes modifiees
WO2002066616A2 (fr) 2001-02-16 2002-08-29 Valtion Teknillinen Tutkimuskeskus Genie de champignons destines a l'utilisation de l-arabinose
WO2002092797A2 (fr) 2001-05-15 2002-11-21 Novozymes A/S Variant d'alpha-amylases ayant des proprietes modifiees
WO2003048353A1 (fr) 2001-12-07 2003-06-12 Novozymes A/S Polypeptides a activite proteasique et acides nucleiques codant ces polypeptides
WO2003062430A1 (fr) 2002-01-23 2003-07-31 Royal Nedalco B.V. Fermentation de sucres pentose
WO2003066847A2 (fr) 2002-02-08 2003-08-14 Novozymes A/S Variants de phytase
WO2003078643A1 (fr) 2002-03-19 2003-09-25 Forskarpatent I Syd Ab Genie metabolique utile pour une utilisation amelioree du xylose dans saccharomyces cerevisiae
WO2003095627A1 (fr) 2002-05-08 2003-11-20 Forskarpatent I Syd Ab Levure modifiee consommant l-arabinose
WO2004055178A1 (fr) 2002-12-17 2004-07-01 Novozymes A/S Alpha-amylases thermostables
WO2004067760A2 (fr) 2003-01-21 2004-08-12 Wisconsin Alumni Research Foundation Souches de levure de fermentation du xylose de recombinaison
WO2004085638A1 (fr) 2003-03-25 2004-10-07 Republic Of National Fisheries Research And Development Institute Phytase obtenue a partir de citrobacter braakii
WO2004106533A1 (fr) 2003-05-30 2004-12-09 Novozymes A/S Procedes de fabrication de produits d'alcool
WO2005003311A2 (fr) 2003-06-25 2005-01-13 Novozymes A/S Enzymes de traitement d'amidon
WO2005045018A1 (fr) 2003-10-28 2005-05-19 Novozymes North America, Inc. Enzymes hybrides
WO2005047499A1 (fr) 2003-10-28 2005-05-26 Novozymes Inc. Polypeptides presentant une activite beta-glucosidase et polynucleotides codant pour ceux-ci
WO2005069840A2 (fr) 2004-01-16 2005-08-04 Novozymes North America, Inc Procedes destines a produire un produit de fermentation
WO2006038062A1 (fr) 2004-10-04 2006-04-13 Danisco A/S Phytase microbienne comme complement dans l'alimentation ou le fourrage
WO2006037327A2 (fr) 2004-10-04 2006-04-13 Novozymes A/S Polypeptides ayant une activite de phytase et polynucleotides codant ces polypeptides
WO2006037328A1 (fr) 2004-10-04 2006-04-13 Novozymes A/S Polypeptides presentant une activite phytase et polynucleotides codant pour ceux-ci
WO2006063588A1 (fr) 2004-12-13 2006-06-22 Novozymes A/S Polypeptides présentant une activité phosphatase acide et polynucléotides codant pour lesdits polypeptides
WO2006069289A2 (fr) 2004-12-22 2006-06-29 Novozymes North America, Inc Polypeptides presentant l'activite d'une glucoamylase, et polynucleotides encodant ces polypeptides
WO2006086792A2 (fr) 2005-02-07 2006-08-17 Novozymes North America, Inc. Procedes de production de produit de fermentation
WO2006096130A1 (fr) 2005-03-11 2006-09-14 Forskarpatent I Syd Ab Souches de saccharomyces cerevisiae capables de faire fermenter l'arabinose et le xylose
EP1724336A1 (fr) 2005-05-19 2006-11-22 Paul Dr. Fricko Procédé pour améliorer la qualité de séchage et de produit de microorganismes
WO2007112739A1 (fr) 2006-04-04 2007-10-11 Novozymes A/S Variants de phytase
WO2007124285A2 (fr) 2006-04-19 2007-11-01 Novozymes North America, Inc. Polypeptides ayant une activité de glucoamylase et polynucléotides codant pour ceux-ci
WO2007134207A2 (fr) 2006-05-12 2007-11-22 Novozymes North America, Inc. Procédé de production d'un produit de fermentation
WO2007143245A2 (fr) 2006-06-01 2007-12-13 Midwest Research Institute Levure fermentante de l-arabinose
WO2008041840A1 (fr) 2006-10-02 2008-04-10 Dsm Ip Assets B.V. Génie métabolique de cellules de levure induisant la fermentation de l'arabinose
WO2008092901A2 (fr) 2007-01-30 2008-08-07 Novozymes A/S Polypeptides ayant une activité phytase et polynucléotides codant pour ceux-ci
WO2008116878A1 (fr) 2007-03-26 2008-10-02 Novozymes A/S Phytase de hafnia
WO2009011591A2 (fr) 2007-07-19 2009-01-22 Royal Nedalco B.V. Nouvelles cellules eucaryotes fermentant l'arabinose
WO2009017441A1 (fr) 2007-07-31 2009-02-05 Bärbel Hahn Ab Polypeptide
WO2009052101A1 (fr) 2007-10-18 2009-04-23 Danisco Us, Inc. Mélanges d'enzymes pour fermentation
WO2009061379A2 (fr) 2007-11-05 2009-05-14 Danisco Us Inc., Genencor Division Variants d'alpha-amilase avec des propriétés modifiées
WO2009129489A2 (fr) 2008-04-18 2009-10-22 Danisco Us Inc., Genencor Division Variants dephytase de buttiauxella sp.
WO2009149130A2 (fr) 2008-06-06 2009-12-10 Danisco Us Inc. Variants d'alpha-amylase (amys) de geobacillus stearothermophilus présentant des propriétés améliorées
WO2010008841A2 (fr) 2008-06-23 2010-01-21 Novozymes A/S Procédés de production de produits de fermentation
WO2010036515A1 (fr) 2008-09-25 2010-04-01 Danisco Us Inc. Mélanges d'alpha-amylases, et leurs méthodes d'utilisation
WO2010034835A2 (fr) 2008-09-26 2010-04-01 Novozymes A/S Variant de phytase de hafnia
US7713723B1 (en) 2000-08-01 2010-05-11 Novozymes A/S Alpha-amylase mutants with altered properties
WO2010059095A1 (fr) 2008-11-24 2010-05-27 Bärbel Hahn Ab Souche de saccharomyces ayant la capacité de croître sur des glucides de pentose dans des conditions de culture anaérobies
WO2010115021A2 (fr) 2009-04-01 2010-10-07 Danisco Us Inc. Compositions et procédés comprenant des variantes alpha-amylases qui possèdent des propriétés modifiées
WO2010151548A1 (fr) 2009-06-22 2010-12-29 Engineered Products Of Virginia, Llc Ensemble de bobine de transformateur
WO2011003893A1 (fr) 2009-07-10 2011-01-13 Dsm Ip Assets B.V. Production par fermentation d'éthanol à partir de glucose, de galactose et d'arabinose employant une souche de levure recombinée
WO2011059329A2 (fr) 2009-11-12 2011-05-19 Universiteit Utrecht Holding B.V. Nouveaux transporteurs de pentose et leurs utilisations
WO2011066560A1 (fr) 2009-11-30 2011-06-03 Novozymes A/S Polypeptides a activite glucoamylase et polynucleotides codant pour lesdits polypeptides
WO2011066576A1 (fr) 2009-11-30 2011-06-03 Novozymes A/S Polypeptides a activite glucoamylase et polynucleotides codant pour lesdits polypeptides
WO2011068803A1 (fr) 2009-12-01 2011-06-09 Novozymes A/S Polypeptides possédant une activité de glucoamylase et polynucléotides codant pour ceux-ci
WO2011078262A1 (fr) 2009-12-22 2011-06-30 株式会社豊田中央研究所 Xylose isomérase et son utilisation
WO2011076123A1 (fr) 2009-12-22 2011-06-30 Novozymes A/S Compositions comprenant un polypeptide renforçateur et un enzyme dégradant l'amidon, et utilisations correspondantes
WO2011082425A2 (fr) 2010-01-04 2011-07-07 Novozymes A/S Variants d'alpha-amylase et polynucleotides les codant
US7977083B1 (en) 2006-12-28 2011-07-12 The United States Of America As Represented By The Secretary Of Agriculture Method for microbial production of xylitol from arabinose
WO2011123715A1 (fr) 2010-03-31 2011-10-06 The United States Of America As Represented By The Secretary Of Agriculture Levures au métabolisme modifié pour la fabrication d'éthanol et d'autres produits à partir de xylose et de cellobiose
WO2011127802A1 (fr) 2010-04-14 2011-10-20 Novozymes A/S Polypeptides présentant une activité glucoamylase et polynucléotides codant lesdits polypeptides
WO2011128712A1 (fr) 2010-04-12 2011-10-20 Stellenbosch University Production de biocarburant
WO2011131674A1 (fr) 2010-04-21 2011-10-27 Dsm Ip Assets B.V. Procédé de production de cellules qui sont capables de convertir l'arabinose
WO2011153516A2 (fr) 2010-06-03 2011-12-08 Mascoma Corporation Levure à expression d'enzymes saccharolytiques pour la transformation biologique consolidée au moyen d'amidon et de cellulose
WO2012009272A2 (fr) 2010-07-14 2012-01-19 Codexis, Inc. Fermentation de pentose par un micro-organisme recombinant
WO2012044915A2 (fr) 2010-10-01 2012-04-05 Novozymes, Inc. Variants de bêta-glucosidase et polynucléotides les codant
WO2012064351A1 (fr) 2010-11-08 2012-05-18 Novozymes A/S Polypeptides présentant une activité glucoamylase et polynucléotides codant lesdits polypeptides
US20120135481A1 (en) 2010-11-22 2012-05-31 Novozymes, Inc. Compositions and methods for 3-hydroxypropionic acid production
WO2012088303A2 (fr) 2010-12-22 2012-06-28 Novozymes North America, Inc. Procédés d'obtention de produits de fermentation
US20120184020A1 (en) 2009-07-09 2012-07-19 Verdezyne, Inc. Engineered microorganisms with enhanced fermentation activity
WO2012113120A1 (fr) 2011-02-22 2012-08-30 山东大学 Molécule d'acide nucléique codant pour la xylose isomérase et xylose isomérase ainsi codée
US8257959B2 (en) 2004-06-08 2012-09-04 Microbiogen Pty Ltd Non-recombinant Saccharomyces strains that grow on xylose
US20120225464A1 (en) 2011-03-04 2012-09-06 Eckhard Boles Specific Arabinose Transporter of the Plant Arabidopsis Thaliana for the Construction of Pentose-Fermenting Yeasts
WO2012135110A1 (fr) 2011-03-30 2012-10-04 Codexis, Inc. Fermentation des pentoses par un micro-organisme recombinant
WO2012143513A2 (fr) 2011-04-22 2012-10-26 Dsm Ip Assets B.V. Cellule de levure pouvant convertir des sucres comprenant l'arabinose et le xylose
US8326547B2 (en) 2009-10-07 2012-12-04 Nanjingjinsirui Science & Technology Biology Corp. Method of sequence optimization for improved recombinant protein expression using a particle swarm optimization algorithm
WO2013006756A2 (fr) 2011-07-06 2013-01-10 Novozymes A/S Variants d'alpha-amylase et polynucléotides codant ces variants
WO2013036526A1 (fr) 2011-09-06 2013-03-14 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci
WO2013034106A1 (fr) 2011-09-09 2013-03-14 Novozymes A/S Polypeptides ayant une activité alpha-amylase et polynucléotides codant pour ceux-ci
WO2013044867A1 (fr) 2011-09-30 2013-04-04 Novozymes A/S Polypeptides à activité alpha-amylase et polynucléotides codant pour ceux-ci
WO2013053801A1 (fr) 2011-10-11 2013-04-18 Novozymes A/S Variants de glucoamylase et polynucléotides les encodant
WO2013055676A1 (fr) 2011-10-11 2013-04-18 Novozymes North America, Inc. Procédés de production de produits de fermentation
WO2013081700A1 (fr) 2011-11-29 2013-06-06 Codexis, Inc. Surexpression des gènes qui améliorent la fermentation de levure au moyen de substrats cellulosiques
WO2013082486A1 (fr) 2011-12-02 2013-06-06 Novozymes A/S Procédés pour produire des produits de fermentation
WO2013148993A1 (fr) 2012-03-30 2013-10-03 Novozymes North America, Inc. Procédés de fabrication de produits de fermentation
WO2014039773A1 (fr) 2012-09-07 2014-03-13 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci et utilisations de ceux-ci
WO2014085439A1 (fr) 2012-11-30 2014-06-05 Novozymes A/S Procédés de production de produits de fermentation
WO2014138672A1 (fr) 2013-03-08 2014-09-12 Novozymes A/S Variantes de cellobiohydrolase et polynucléotides codant pour celles-ci
WO2014177546A2 (fr) 2013-04-30 2014-11-06 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ces derniers
WO2014177541A2 (fr) 2013-04-30 2014-11-06 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ces derniers
WO2014209789A1 (fr) 2013-06-24 2014-12-31 Novozymes A/S Procédé d'extraction d'huile à partir de résidus dilués de distillation
WO2015007639A1 (fr) 2013-07-17 2015-01-22 Novozymes A/S Chimères de pullulanase et polynucléotides les codant
WO2015031477A1 (fr) 2013-08-30 2015-03-05 Novozymes A/S Composition d'enzyme et utilisations de celle-ci
WO2015035914A1 (fr) 2013-09-11 2015-03-19 Novozymes A/S Procédés de production de produits de fermentation
US20150125925A1 (en) 2013-11-05 2015-05-07 The Procter & Gamble Company Compositions and methods comprising serine protease variants
WO2015110473A2 (fr) 2014-01-22 2015-07-30 Novozymes A/S Variants de pullulanase et polynucléotides les codant
WO2015143317A1 (fr) 2014-03-21 2015-09-24 Novozymes A/S Procédés de production d'éthanol à l'aide d'un organisme de fermentation
WO2015164058A1 (fr) 2014-04-21 2015-10-29 Danisco Us Inc. Saccharification et cofermentation simultanées de souches fongiques exprimant la glucoamylase avec un éthanologène pour produire de l'alcool à partir de maïs
WO2016040265A1 (fr) 2014-09-08 2016-03-17 Novozymes A/S Variants de cellobiohydrolase et polynucléotides codant pour ces derniers
WO2016045569A1 (fr) 2014-09-23 2016-03-31 Novozymes A/S Procédés de production d'éthanol et organismes de fermentation
WO2016062875A2 (fr) 2014-10-23 2016-04-28 Novozymes A/S Variants de glucoamylase et polynucléotides les encodant
WO2016087327A1 (fr) 2014-12-01 2016-06-09 Novozymes A/S Polypeptides ayant une activité pullulanase comprenant les domaines x25, x45 et cbm41
WO2016087237A1 (fr) 2014-12-02 2016-06-09 Mahle International Gmbh Procédé de fabrication d'un noyau de coulée perdu, noyau de coulée perdu et piston à conduit de refroidissement fabriqué à l'aide d'un tel noyau de coulée
WO2016138437A1 (fr) 2015-02-27 2016-09-01 Novozymes A/S Procédés de production d'éthanol à l'aide d'un organisme de fermentation
WO2016153924A1 (fr) 2015-03-20 2016-09-29 Novozymes A/S Procédés de production d'éthanol et levures produisant de l'éthanol
WO2016205127A1 (fr) 2015-06-18 2016-12-22 Novozymes A/S Polypeptides ayant une activité tréhalase et leur utilisation dans un procédé de production de produits de fermentation
WO2017014974A1 (fr) 2015-07-21 2017-01-26 Novozymes A/S Polypeptides présentant une activité de pullulanase appropriée pour une utilisation dans la liquéfaction
WO2017037614A1 (fr) 2015-09-04 2017-03-09 Lallemand Hungary Liquidity Management Llc Souches de levure destinées à l'expression et la sécrétion de protéines hétérologues à hautes températures
US20170088866A1 (en) 2015-09-30 2017-03-30 Alliance For Sustainable Energy, Llc Xylose utilizing oleaginous yeast
WO2017050291A1 (fr) 2015-09-25 2017-03-30 Novozymes A/S Utilisation de sérine protéases pour améliorer le rendement de l'éthanol
WO2017066255A1 (fr) 2015-10-14 2017-04-20 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci
WO2017077504A1 (fr) 2015-11-06 2017-05-11 Lallemand Hungary Liquidity Management Llc Limitation du tréhalose produit par des levures en fermentation
WO2017087330A1 (fr) 2015-11-17 2017-05-26 Novozymes A/S Souches de levure appropriées pour la saccharification et la fermentation exprimant une glucoamylase et/ou une alpha-amylase
WO2017112533A1 (fr) 2015-12-22 2017-06-29 Novozymes A/S Procédé d'extraction d'huile à partir de résidus de distillation fin
WO2017148389A1 (fr) 2016-03-01 2017-09-08 Novozymes A/S Utilisation combinée d'au moins une endoprotéase et d'au moins une exoprotéase dans un procédé de fermentation en milieu solide pour améliorer le rendement d'éthanol
WO2018002360A1 (fr) 2016-07-01 2018-01-04 Lallemand Hungary Liquidity Management Llc Alpha-amylases destinées à être combinées avec des glucoamylases pour améliorer la saccharification
WO2018015303A1 (fr) 2016-07-21 2018-01-25 Novozymes A/S Variants de sérine protéase et polynucléotides les codant
WO2018015304A1 (fr) 2016-07-21 2018-01-25 Novozymes A/S Variants de sérine protéase et polynucléotides codant pour ceux-ci
WO2018075430A1 (fr) 2016-10-17 2018-04-26 Novozymes A/S Procédés de réduction de la mousse pendant la fermentation d'éthanol
WO2018098381A1 (fr) 2016-11-23 2018-05-31 Novozymes A/S Levure améliorée pour la production d'éthanol
WO2018098124A1 (fr) 2016-11-23 2018-05-31 Novozymes A/S Polypeptides ayant une activité protéase et polynucléotides codant pour ceux-ci
US20180155744A1 (en) 2016-12-05 2018-06-07 Stellenbosch University Recombinant yeast and use thereof
WO2018112638A1 (fr) 2016-12-21 2018-06-28 Creatus Biosciences Inc. Procédés et organisme exprimant des gènes de metschnikowia pour une production accrue d'éthanol
WO2018118815A1 (fr) 2016-12-21 2018-06-28 Dupont Nutrition Biosciences Aps Procédés d'utilisation de sérine-protéases thermostables
WO2018164737A1 (fr) 2017-03-07 2018-09-13 Danisco Us Inc. Anglucoamylase thermostable et procédés d'utilisation associés
WO2018169780A1 (fr) 2017-03-15 2018-09-20 Dupont Nutrition Biosciences Aps Procédés d'utilisation d'une sérine protéase d'archaea
WO2018191215A1 (fr) 2017-04-11 2018-10-18 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci
WO2019005755A1 (fr) 2017-06-28 2019-01-03 Novozymes A/S Polypeptides présentant une activité tréhalase et polynucléotides codant pour ceux-ci
WO2019030165A1 (fr) 2017-08-08 2019-02-14 Novozymes A/S Polypeptides ayant une activité tréhalase et leur utilisation dans un procédé de production de produits de fermentation
WO2019083831A1 (fr) 2017-10-23 2019-05-02 Novozymes A/S Procédés pour la réduction d'acide lactique dans un système de fermentation de biocarburant
WO2019113415A1 (fr) 2017-12-08 2019-06-13 Novozymes A/S Variants d'alpha-amylase et polynucléotides codant pour ces derniers
WO2019113413A1 (fr) 2017-12-08 2019-06-13 Novozymes A/S Variants d'alpha-amylase et polynucléotides codant pour ces derniers
WO2019161227A1 (fr) 2018-02-15 2019-08-22 Novozymes A/S Levure améliorée pour la production d'éthanol
WO2019197318A1 (fr) 2018-04-09 2019-10-17 Novozymes A/S Polypeptides ayant une activité alpha-amylase et polynucléotides codant pour ceux-ci
WO2019231944A2 (fr) 2018-05-31 2019-12-05 Novozymes A/S Procédés d'amélioration de la croissance et de la productivité de levures
WO2020010101A2 (fr) 2018-07-04 2020-01-09 Danisco Us Inc Glucoamylases et leurs procédés d'utilisation
WO2020014407A1 (fr) 2018-07-11 2020-01-16 Novozymes A/S Procédés de production de produits de fermentation
WO2020023411A1 (fr) 2018-07-25 2020-01-30 Novozymes A/S Levure exprimant une enzyme pour la production d'éthanol
WO2020076697A1 (fr) 2018-10-08 2020-04-16 Novozymes A/S Levure exprimant une enzyme pour la production d'éthanol
WO2020187883A1 (fr) 2019-03-18 2020-09-24 Novozymes A/S Polypeptides présentant une activité de pullulanase appropriée pour une utilisation dans la liquéfaction
WO2021025872A1 (fr) 2019-08-06 2021-02-11 Novozymes A/S Protéines de fusion pour une expression enzymatique améliorée
WO2021055395A1 (fr) 2019-09-16 2021-03-25 Novozymes A/S Polypeptides dotés d'une activité bêta-glucanase et polynucléotides codant pour ces polypeptides
WO2021126966A1 (fr) 2019-12-16 2021-06-24 Novozymes A/S Procédés de production de produits de fermentation
WO2021163015A1 (fr) 2020-02-10 2021-08-19 Novozymes A/S Procédé de production d'éthanol à partir d'amidon brut à l'aide de variants d'alpha-amylase
WO2021163011A2 (fr) 2020-02-10 2021-08-19 Novozymes A/S Variants d'alpha-amylase et polynucléotides codant pour ceux-ci
WO2021163030A2 (fr) 2020-02-10 2021-08-19 Novozymes A/S Polypeptides ayant une activité alpha-amylase et polynucléotides codant pour ces derniers
WO2021163036A1 (fr) 2020-02-10 2021-08-19 Novozymes A/S Processus d'hydrolyse d'amidon brut de production d'un produit de fermentation
WO2022090564A1 (fr) 2020-11-02 2022-05-05 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci
WO2022173694A1 (fr) 2021-02-10 2022-08-18 Novozymes A/S Polypeptides ayant une activité de pectinase, polynucléotides codant pour ceux-ci et leurs utilisations

Family Cites Families (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
MX2012007224A (es) * 2009-12-23 2012-07-30 Danisco Us Inc Metodos para mejorar la eficacia de las reacciones de sacarificacion y fermentacion simultaneas.
BR112014031024A2 (pt) * 2012-06-11 2017-06-27 Codexis Inc xilanases e xilosidases fúngicas.
BR112022002203A2 (pt) * 2019-08-05 2022-09-06 Novozymes As Misturas de enzimas e processos para produção de um ingrediente alimentar com alto teor de proteína a partir de um subproduto de vinhaça completa

Patent Citations (194)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
USRE32153E (en) 1978-09-01 1986-05-20 Cpc International Inc. Highly thermostable glucoamylaseand process for its production
US4560651A (en) 1981-04-20 1985-12-24 Novo Industri A/S Debranching enzyme product, preparation and use thereof
WO1984002921A2 (fr) 1983-01-28 1984-08-02 Cetus Corp cADN GLUCOAMYLASE
US4598048A (en) 1983-03-25 1986-07-01 Novo Industri A/S Preparation of a maltogenic amylase enzyme
US4604355A (en) 1983-03-25 1986-08-05 Novo Industri A/S Maltogenic amylase enzyme, preparation and use thereof
EP0135138A2 (fr) 1983-08-17 1985-03-27 Cpc International Inc. Glucoanylase thermostable et procédé pour sa production
US4587215A (en) 1984-06-25 1986-05-06 Uop Inc. Highly thermostable amyloglucosidase
WO1986001831A1 (fr) 1984-09-18 1986-03-27 Michigan Biotechnology Institute Enzymes thermostables de conversion de l'amidon
US4727026A (en) 1985-11-26 1988-02-23 Godo Shusei Co., Ltd. Method for direct saccharification of raw starch using enzyme produced by a basidiomycete belonging to the genus Corticium
US5223409A (en) 1988-09-02 1993-06-29 Protein Engineering Corp. Directed evolution of novel binding proteins
WO1992000381A1 (fr) 1990-06-29 1992-01-09 Novo Nordisk A/S Hydrolyse enzymatique de l'amidon en glucose a l'aide d'une enzyme produite par genie genetique
WO1992002614A1 (fr) 1990-08-01 1992-02-20 Novo Nordisk A/S Nouvelles pullulanases thermostables
WO1992006204A1 (fr) 1990-09-28 1992-04-16 Ixsys, Inc. Banques de recepteurs heteromeres a expression en surface
WO1994025612A2 (fr) 1993-05-05 1994-11-10 Institut Pasteur Sequences de nucleotides pour le controle de l'expression de sequences d'adn dans un hote cellulaire
WO1995017413A1 (fr) 1993-12-21 1995-06-29 Evotec Biosystems Gmbh Procede permettant une conception et une synthese evolutives de polymeres fonctionnels sur la base d'elements et de codes de remodelage
WO1995022625A1 (fr) 1994-02-17 1995-08-24 Affymax Technologies N.V. Mutagenese d'adn par fragmentation aleatoire et reassemblage
WO1995033836A1 (fr) 1994-06-03 1995-12-14 Novo Nordisk Biotech, Inc. Phosphonyldipeptides efficaces dans le traitement de maladies cardiovasculaires
WO1996023873A1 (fr) 1995-02-03 1996-08-08 Novo Nordisk A/S Alleles d'amylase-alpha
WO1996023874A1 (fr) 1995-02-03 1996-08-08 Novo Nordisk A/S Technique de mise au point de mutants d'amylase-alpha dotes de proprietes predefinies
US6297038B1 (en) 1995-02-03 2001-10-02 Novozymes A/S Amylase variants
WO1996028567A1 (fr) 1995-03-09 1996-09-19 Genencor International, Inc. Procede de liquefaction de l'amidon
US6093562A (en) 1996-02-05 2000-07-25 Novo Nordisk A/S Amylase variants
WO1997033976A1 (fr) 1996-03-14 1997-09-18 Korea Institute Of Science And Technology Ds11(kctc 0231bp), nouvelle souche de bacillus sp. et nouvelle phytase produite a partir de ladite souche
WO1997038096A1 (fr) 1996-04-05 1997-10-16 Kyowa Hakko Kogyo Co., Ltd. Nouvelle phytase et gene codant pour ladite phytase
WO1997041213A1 (fr) 1996-04-30 1997-11-06 Novo Nordisk A/S MUTANTS DUNE AMYLASE-$g(a)
WO1997048812A2 (fr) 1996-06-14 1997-12-24 Her Majesty The Queen In Right Of Canada, Represented By The Department Of Agriculture And Agri-Food Canada Sequences d'adn codant des phytases de micro-organismes de ruminants
WO1998005785A1 (fr) 1996-08-01 1998-02-12 Biocem Phytases de plantes et applications biotechnologiques
WO1998006856A1 (fr) 1996-08-13 1998-02-19 Finnfeeds International Ltd. Phytase, gene codant cette phytase, procede de production et utilisation de cette derniere
WO1998013480A1 (fr) 1996-09-25 1998-04-02 Kyowa Hakko Kogyo Co., Ltd. Nouvelle phytase et son procede de preparation
WO1998020139A2 (fr) 1996-11-05 1998-05-14 Finnfeeds International Ltd. Phytase obtenue a partir de germes de soja
WO1998028408A1 (fr) 1996-12-20 1998-07-02 Novo Nordisk A/S Phytase induite par peniophora
WO1998056926A1 (fr) 1997-06-10 1998-12-17 Takara Shuzo Co., Ltd. Systeme pour exprimer une proteine hyperthermostable
US6358726B1 (en) 1997-06-10 2002-03-19 Takara Shuzo Co., Ltd. Thermostable protease
WO1999019467A1 (fr) 1997-10-13 1999-04-22 Novo Nordisk A/S MUTANTS D'α-AMYLASE
US6187576B1 (en) 1997-10-13 2001-02-13 Novo Nordisk A/S α-amylase mutants
WO1999028448A1 (fr) 1997-11-26 1999-06-10 Novo Nordisk A/S Glucoamylase thermostable
US6162628A (en) 1998-02-27 2000-12-19 Novo Nordisk A/S Maltogenic alpha-amylase variants
WO1999048330A1 (fr) 1998-03-19 1999-09-23 Koninklijke Philips Electronics N.V. Prothese auditive a detecteur pour reception de signaux sans fil et dispositif associe
WO1999049022A1 (fr) 1998-03-23 1999-09-30 Novo Nordisk A/S Variant de phytase
WO2000004136A1 (fr) 1998-07-15 2000-01-27 Novozymes A/S Variants de glucoamylase
WO2000060059A2 (fr) 1999-03-30 2000-10-12 NovozymesA/S Variantes d'alpha amylase
WO2001004273A2 (fr) 1999-07-09 2001-01-18 Novozymes A/S Variante de glucoamylase
WO2001062947A1 (fr) 2000-02-23 2001-08-30 Novozymes A/S Fermentation a l'aide de la phytase
WO2002010355A2 (fr) 2000-08-01 2002-02-07 Novozymes A/S Mutants d'alpha-amylase a proprietes modifiees
US7713723B1 (en) 2000-08-01 2010-05-11 Novozymes A/S Alpha-amylase mutants with altered properties
WO2002066616A2 (fr) 2001-02-16 2002-08-29 Valtion Teknillinen Tutkimuskeskus Genie de champignons destines a l'utilisation de l-arabinose
WO2002092797A2 (fr) 2001-05-15 2002-11-21 Novozymes A/S Variant d'alpha-amylases ayant des proprietes modifiees
WO2003048353A1 (fr) 2001-12-07 2003-06-12 Novozymes A/S Polypeptides a activite proteasique et acides nucleiques codant ces polypeptides
WO2003062430A1 (fr) 2002-01-23 2003-07-31 Royal Nedalco B.V. Fermentation de sucres pentose
WO2003066847A2 (fr) 2002-02-08 2003-08-14 Novozymes A/S Variants de phytase
WO2003078643A1 (fr) 2002-03-19 2003-09-25 Forskarpatent I Syd Ab Genie metabolique utile pour une utilisation amelioree du xylose dans saccharomyces cerevisiae
WO2003095627A1 (fr) 2002-05-08 2003-11-20 Forskarpatent I Syd Ab Levure modifiee consommant l-arabinose
WO2004055178A1 (fr) 2002-12-17 2004-07-01 Novozymes A/S Alpha-amylases thermostables
WO2004067760A2 (fr) 2003-01-21 2004-08-12 Wisconsin Alumni Research Foundation Souches de levure de fermentation du xylose de recombinaison
WO2004085638A1 (fr) 2003-03-25 2004-10-07 Republic Of National Fisheries Research And Development Institute Phytase obtenue a partir de citrobacter braakii
WO2004106533A1 (fr) 2003-05-30 2004-12-09 Novozymes A/S Procedes de fabrication de produits d'alcool
WO2005003311A2 (fr) 2003-06-25 2005-01-13 Novozymes A/S Enzymes de traitement d'amidon
WO2005045018A1 (fr) 2003-10-28 2005-05-19 Novozymes North America, Inc. Enzymes hybrides
WO2005047499A1 (fr) 2003-10-28 2005-05-26 Novozymes Inc. Polypeptides presentant une activite beta-glucosidase et polynucleotides codant pour ceux-ci
WO2005069840A2 (fr) 2004-01-16 2005-08-04 Novozymes North America, Inc Procedes destines a produire un produit de fermentation
US8257959B2 (en) 2004-06-08 2012-09-04 Microbiogen Pty Ltd Non-recombinant Saccharomyces strains that grow on xylose
WO2006038062A1 (fr) 2004-10-04 2006-04-13 Danisco A/S Phytase microbienne comme complement dans l'alimentation ou le fourrage
WO2006037327A2 (fr) 2004-10-04 2006-04-13 Novozymes A/S Polypeptides ayant une activite de phytase et polynucleotides codant ces polypeptides
WO2006037328A1 (fr) 2004-10-04 2006-04-13 Novozymes A/S Polypeptides presentant une activite phytase et polynucleotides codant pour ceux-ci
WO2006063588A1 (fr) 2004-12-13 2006-06-22 Novozymes A/S Polypeptides présentant une activité phosphatase acide et polynucléotides codant pour lesdits polypeptides
WO2006069290A2 (fr) 2004-12-22 2006-06-29 Novozymes A/S Enzymes pour le traitement d'amidon
WO2006069289A2 (fr) 2004-12-22 2006-06-29 Novozymes North America, Inc Polypeptides presentant l'activite d'une glucoamylase, et polynucleotides encodant ces polypeptides
WO2006086792A2 (fr) 2005-02-07 2006-08-17 Novozymes North America, Inc. Procedes de production de produit de fermentation
WO2006096130A1 (fr) 2005-03-11 2006-09-14 Forskarpatent I Syd Ab Souches de saccharomyces cerevisiae capables de faire fermenter l'arabinose et le xylose
EP1724336A1 (fr) 2005-05-19 2006-11-22 Paul Dr. Fricko Procédé pour améliorer la qualité de séchage et de produit de microorganismes
WO2007112739A1 (fr) 2006-04-04 2007-10-11 Novozymes A/S Variants de phytase
WO2007124285A2 (fr) 2006-04-19 2007-11-01 Novozymes North America, Inc. Polypeptides ayant une activité de glucoamylase et polynucléotides codant pour ceux-ci
WO2007134207A2 (fr) 2006-05-12 2007-11-22 Novozymes North America, Inc. Procédé de production d'un produit de fermentation
WO2007143245A2 (fr) 2006-06-01 2007-12-13 Midwest Research Institute Levure fermentante de l-arabinose
WO2008041840A1 (fr) 2006-10-02 2008-04-10 Dsm Ip Assets B.V. Génie métabolique de cellules de levure induisant la fermentation de l'arabinose
US7977083B1 (en) 2006-12-28 2011-07-12 The United States Of America As Represented By The Secretary Of Agriculture Method for microbial production of xylitol from arabinose
WO2008092901A2 (fr) 2007-01-30 2008-08-07 Novozymes A/S Polypeptides ayant une activité phytase et polynucléotides codant pour ceux-ci
WO2008116878A1 (fr) 2007-03-26 2008-10-02 Novozymes A/S Phytase de hafnia
WO2009011591A2 (fr) 2007-07-19 2009-01-22 Royal Nedalco B.V. Nouvelles cellules eucaryotes fermentant l'arabinose
WO2009017441A1 (fr) 2007-07-31 2009-02-05 Bärbel Hahn Ab Polypeptide
WO2009052101A1 (fr) 2007-10-18 2009-04-23 Danisco Us, Inc. Mélanges d'enzymes pour fermentation
WO2009061379A2 (fr) 2007-11-05 2009-05-14 Danisco Us Inc., Genencor Division Variants d'alpha-amilase avec des propriétés modifiées
WO2009129489A2 (fr) 2008-04-18 2009-10-22 Danisco Us Inc., Genencor Division Variants dephytase de buttiauxella sp.
WO2009149130A2 (fr) 2008-06-06 2009-12-10 Danisco Us Inc. Variants d'alpha-amylase (amys) de geobacillus stearothermophilus présentant des propriétés améliorées
WO2010008841A2 (fr) 2008-06-23 2010-01-21 Novozymes A/S Procédés de production de produits de fermentation
WO2010036515A1 (fr) 2008-09-25 2010-04-01 Danisco Us Inc. Mélanges d'alpha-amylases, et leurs méthodes d'utilisation
WO2010034835A2 (fr) 2008-09-26 2010-04-01 Novozymes A/S Variant de phytase de hafnia
WO2010059095A1 (fr) 2008-11-24 2010-05-27 Bärbel Hahn Ab Souche de saccharomyces ayant la capacité de croître sur des glucides de pentose dans des conditions de culture anaérobies
WO2010115021A2 (fr) 2009-04-01 2010-10-07 Danisco Us Inc. Compositions et procédés comprenant des variantes alpha-amylases qui possèdent des propriétés modifiées
WO2010151548A1 (fr) 2009-06-22 2010-12-29 Engineered Products Of Virginia, Llc Ensemble de bobine de transformateur
US20120184020A1 (en) 2009-07-09 2012-07-19 Verdezyne, Inc. Engineered microorganisms with enhanced fermentation activity
WO2011003893A1 (fr) 2009-07-10 2011-01-13 Dsm Ip Assets B.V. Production par fermentation d'éthanol à partir de glucose, de galactose et d'arabinose employant une souche de levure recombinée
US8326547B2 (en) 2009-10-07 2012-12-04 Nanjingjinsirui Science & Technology Biology Corp. Method of sequence optimization for improved recombinant protein expression using a particle swarm optimization algorithm
WO2011059329A2 (fr) 2009-11-12 2011-05-19 Universiteit Utrecht Holding B.V. Nouveaux transporteurs de pentose et leurs utilisations
WO2011066560A1 (fr) 2009-11-30 2011-06-03 Novozymes A/S Polypeptides a activite glucoamylase et polynucleotides codant pour lesdits polypeptides
WO2011066576A1 (fr) 2009-11-30 2011-06-03 Novozymes A/S Polypeptides a activite glucoamylase et polynucleotides codant pour lesdits polypeptides
WO2011068803A1 (fr) 2009-12-01 2011-06-09 Novozymes A/S Polypeptides possédant une activité de glucoamylase et polynucléotides codant pour ceux-ci
WO2011087836A2 (fr) 2009-12-22 2011-07-21 Novozymes A/S Variants de pullulanase et utilisations de ceux-ci
WO2011076123A1 (fr) 2009-12-22 2011-06-30 Novozymes A/S Compositions comprenant un polypeptide renforçateur et un enzyme dégradant l'amidon, et utilisations correspondantes
WO2011078262A1 (fr) 2009-12-22 2011-06-30 株式会社豊田中央研究所 Xylose isomérase et son utilisation
WO2011082425A2 (fr) 2010-01-04 2011-07-07 Novozymes A/S Variants d'alpha-amylase et polynucleotides les codant
WO2011123715A1 (fr) 2010-03-31 2011-10-06 The United States Of America As Represented By The Secretary Of Agriculture Levures au métabolisme modifié pour la fabrication d'éthanol et d'autres produits à partir de xylose et de cellobiose
WO2011128712A1 (fr) 2010-04-12 2011-10-20 Stellenbosch University Production de biocarburant
WO2011127802A1 (fr) 2010-04-14 2011-10-20 Novozymes A/S Polypeptides présentant une activité glucoamylase et polynucléotides codant lesdits polypeptides
WO2011131674A1 (fr) 2010-04-21 2011-10-27 Dsm Ip Assets B.V. Procédé de production de cellules qui sont capables de convertir l'arabinose
WO2011153516A2 (fr) 2010-06-03 2011-12-08 Mascoma Corporation Levure à expression d'enzymes saccharolytiques pour la transformation biologique consolidée au moyen d'amidon et de cellulose
WO2012009272A2 (fr) 2010-07-14 2012-01-19 Codexis, Inc. Fermentation de pentose par un micro-organisme recombinant
WO2012044915A2 (fr) 2010-10-01 2012-04-05 Novozymes, Inc. Variants de bêta-glucosidase et polynucléotides les codant
WO2012064351A1 (fr) 2010-11-08 2012-05-18 Novozymes A/S Polypeptides présentant une activité glucoamylase et polynucléotides codant lesdits polypeptides
US20120135481A1 (en) 2010-11-22 2012-05-31 Novozymes, Inc. Compositions and methods for 3-hydroxypropionic acid production
WO2012088303A2 (fr) 2010-12-22 2012-06-28 Novozymes North America, Inc. Procédés d'obtention de produits de fermentation
WO2012113120A1 (fr) 2011-02-22 2012-08-30 山东大学 Molécule d'acide nucléique codant pour la xylose isomérase et xylose isomérase ainsi codée
US8586336B2 (en) 2011-02-22 2013-11-19 Shandong University Nucleic acid molecule encoding xylose isomerase and xylose isomerase encoded by the nucleic acid molecule
US20120225464A1 (en) 2011-03-04 2012-09-06 Eckhard Boles Specific Arabinose Transporter of the Plant Arabidopsis Thaliana for the Construction of Pentose-Fermenting Yeasts
WO2012135110A1 (fr) 2011-03-30 2012-10-04 Codexis, Inc. Fermentation des pentoses par un micro-organisme recombinant
WO2012143513A2 (fr) 2011-04-22 2012-10-26 Dsm Ip Assets B.V. Cellule de levure pouvant convertir des sucres comprenant l'arabinose et le xylose
WO2013006756A2 (fr) 2011-07-06 2013-01-10 Novozymes A/S Variants d'alpha-amylase et polynucléotides codant ces variants
WO2013036526A1 (fr) 2011-09-06 2013-03-14 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci
WO2013034106A1 (fr) 2011-09-09 2013-03-14 Novozymes A/S Polypeptides ayant une activité alpha-amylase et polynucléotides codant pour ceux-ci
WO2013044867A1 (fr) 2011-09-30 2013-04-04 Novozymes A/S Polypeptides à activité alpha-amylase et polynucléotides codant pour ceux-ci
WO2013053801A1 (fr) 2011-10-11 2013-04-18 Novozymes A/S Variants de glucoamylase et polynucléotides les encodant
WO2013055676A1 (fr) 2011-10-11 2013-04-18 Novozymes North America, Inc. Procédés de production de produits de fermentation
WO2013081700A1 (fr) 2011-11-29 2013-06-06 Codexis, Inc. Surexpression des gènes qui améliorent la fermentation de levure au moyen de substrats cellulosiques
WO2013082486A1 (fr) 2011-12-02 2013-06-06 Novozymes A/S Procédés pour produire des produits de fermentation
WO2013148993A1 (fr) 2012-03-30 2013-10-03 Novozymes North America, Inc. Procédés de fabrication de produits de fermentation
WO2014039773A1 (fr) 2012-09-07 2014-03-13 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci et utilisations de ceux-ci
WO2014085439A1 (fr) 2012-11-30 2014-06-05 Novozymes A/S Procédés de production de produits de fermentation
WO2014138672A1 (fr) 2013-03-08 2014-09-12 Novozymes A/S Variantes de cellobiohydrolase et polynucléotides codant pour celles-ci
WO2014177546A2 (fr) 2013-04-30 2014-11-06 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ces derniers
WO2014177541A2 (fr) 2013-04-30 2014-11-06 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ces derniers
WO2014209789A1 (fr) 2013-06-24 2014-12-31 Novozymes A/S Procédé d'extraction d'huile à partir de résidus dilués de distillation
WO2014209800A1 (fr) 2013-06-24 2014-12-31 Novozymes A/S Procédés de récupération d'huile à partir de procédés de production de produits de fermentation et procédés de production de produits de fermentation
WO2015007639A1 (fr) 2013-07-17 2015-01-22 Novozymes A/S Chimères de pullulanase et polynucléotides les codant
WO2015031477A1 (fr) 2013-08-30 2015-03-05 Novozymes A/S Composition d'enzyme et utilisations de celle-ci
WO2015035914A1 (fr) 2013-09-11 2015-03-19 Novozymes A/S Procédés de production de produits de fermentation
US20150125925A1 (en) 2013-11-05 2015-05-07 The Procter & Gamble Company Compositions and methods comprising serine protease variants
WO2015110473A2 (fr) 2014-01-22 2015-07-30 Novozymes A/S Variants de pullulanase et polynucléotides les codant
WO2015143317A1 (fr) 2014-03-21 2015-09-24 Novozymes A/S Procédés de production d'éthanol à l'aide d'un organisme de fermentation
WO2015143324A1 (fr) 2014-03-21 2015-09-24 Novozymes A/S Procédés de production d'éthanol et de levure
WO2015164058A1 (fr) 2014-04-21 2015-10-29 Danisco Us Inc. Saccharification et cofermentation simultanées de souches fongiques exprimant la glucoamylase avec un éthanologène pour produire de l'alcool à partir de maïs
WO2016040265A1 (fr) 2014-09-08 2016-03-17 Novozymes A/S Variants de cellobiohydrolase et polynucléotides codant pour ces derniers
WO2016045569A1 (fr) 2014-09-23 2016-03-31 Novozymes A/S Procédés de production d'éthanol et organismes de fermentation
WO2016062875A2 (fr) 2014-10-23 2016-04-28 Novozymes A/S Variants de glucoamylase et polynucléotides les encodant
WO2016087327A1 (fr) 2014-12-01 2016-06-09 Novozymes A/S Polypeptides ayant une activité pullulanase comprenant les domaines x25, x45 et cbm41
WO2016087237A1 (fr) 2014-12-02 2016-06-09 Mahle International Gmbh Procédé de fabrication d'un noyau de coulée perdu, noyau de coulée perdu et piston à conduit de refroidissement fabriqué à l'aide d'un tel noyau de coulée
WO2016138437A1 (fr) 2015-02-27 2016-09-01 Novozymes A/S Procédés de production d'éthanol à l'aide d'un organisme de fermentation
WO2016153924A1 (fr) 2015-03-20 2016-09-29 Novozymes A/S Procédés de production d'éthanol et levures produisant de l'éthanol
WO2016205127A1 (fr) 2015-06-18 2016-12-22 Novozymes A/S Polypeptides ayant une activité tréhalase et leur utilisation dans un procédé de production de produits de fermentation
WO2017014974A1 (fr) 2015-07-21 2017-01-26 Novozymes A/S Polypeptides présentant une activité de pullulanase appropriée pour une utilisation dans la liquéfaction
WO2017037614A1 (fr) 2015-09-04 2017-03-09 Lallemand Hungary Liquidity Management Llc Souches de levure destinées à l'expression et la sécrétion de protéines hétérologues à hautes températures
WO2017050291A1 (fr) 2015-09-25 2017-03-30 Novozymes A/S Utilisation de sérine protéases pour améliorer le rendement de l'éthanol
US20170088866A1 (en) 2015-09-30 2017-03-30 Alliance For Sustainable Energy, Llc Xylose utilizing oleaginous yeast
WO2017066255A1 (fr) 2015-10-14 2017-04-20 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci
WO2017077504A1 (fr) 2015-11-06 2017-05-11 Lallemand Hungary Liquidity Management Llc Limitation du tréhalose produit par des levures en fermentation
WO2017087330A1 (fr) 2015-11-17 2017-05-26 Novozymes A/S Souches de levure appropriées pour la saccharification et la fermentation exprimant une glucoamylase et/ou une alpha-amylase
WO2017112539A1 (fr) 2015-12-22 2017-06-29 Novozymes A/S Procédé d'extraction d'huile de résidu de distillation soluble
WO2017112542A1 (fr) 2015-12-22 2017-06-29 Novozymes A/S Procédés pour améliorer le rendement en produits de fermentation mettant en oeuvre une phospholipase c
WO2017112533A1 (fr) 2015-12-22 2017-06-29 Novozymes A/S Procédé d'extraction d'huile à partir de résidus de distillation fin
WO2017112540A1 (fr) 2015-12-22 2017-06-29 Novozymes A/S Procédés de production de produits de fermentation
WO2017148389A1 (fr) 2016-03-01 2017-09-08 Novozymes A/S Utilisation combinée d'au moins une endoprotéase et d'au moins une exoprotéase dans un procédé de fermentation en milieu solide pour améliorer le rendement d'éthanol
WO2018002360A1 (fr) 2016-07-01 2018-01-04 Lallemand Hungary Liquidity Management Llc Alpha-amylases destinées à être combinées avec des glucoamylases pour améliorer la saccharification
WO2018015304A1 (fr) 2016-07-21 2018-01-25 Novozymes A/S Variants de sérine protéase et polynucléotides codant pour ceux-ci
WO2018015303A1 (fr) 2016-07-21 2018-01-25 Novozymes A/S Variants de sérine protéase et polynucléotides les codant
WO2018075430A1 (fr) 2016-10-17 2018-04-26 Novozymes A/S Procédés de réduction de la mousse pendant la fermentation d'éthanol
WO2018098381A1 (fr) 2016-11-23 2018-05-31 Novozymes A/S Levure améliorée pour la production d'éthanol
WO2018098124A1 (fr) 2016-11-23 2018-05-31 Novozymes A/S Polypeptides ayant une activité protéase et polynucléotides codant pour ceux-ci
US20180155744A1 (en) 2016-12-05 2018-06-07 Stellenbosch University Recombinant yeast and use thereof
WO2018112638A1 (fr) 2016-12-21 2018-06-28 Creatus Biosciences Inc. Procédés et organisme exprimant des gènes de metschnikowia pour une production accrue d'éthanol
WO2018118815A1 (fr) 2016-12-21 2018-06-28 Dupont Nutrition Biosciences Aps Procédés d'utilisation de sérine-protéases thermostables
WO2018164737A1 (fr) 2017-03-07 2018-09-13 Danisco Us Inc. Anglucoamylase thermostable et procédés d'utilisation associés
WO2018169780A1 (fr) 2017-03-15 2018-09-20 Dupont Nutrition Biosciences Aps Procédés d'utilisation d'une sérine protéase d'archaea
WO2018191215A1 (fr) 2017-04-11 2018-10-18 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci
WO2019005755A1 (fr) 2017-06-28 2019-01-03 Novozymes A/S Polypeptides présentant une activité tréhalase et polynucléotides codant pour ceux-ci
WO2019030165A1 (fr) 2017-08-08 2019-02-14 Novozymes A/S Polypeptides ayant une activité tréhalase et leur utilisation dans un procédé de production de produits de fermentation
WO2019083831A1 (fr) 2017-10-23 2019-05-02 Novozymes A/S Procédés pour la réduction d'acide lactique dans un système de fermentation de biocarburant
WO2019113415A1 (fr) 2017-12-08 2019-06-13 Novozymes A/S Variants d'alpha-amylase et polynucléotides codant pour ces derniers
WO2019113413A1 (fr) 2017-12-08 2019-06-13 Novozymes A/S Variants d'alpha-amylase et polynucléotides codant pour ces derniers
WO2019161227A1 (fr) 2018-02-15 2019-08-22 Novozymes A/S Levure améliorée pour la production d'éthanol
WO2019197318A1 (fr) 2018-04-09 2019-10-17 Novozymes A/S Polypeptides ayant une activité alpha-amylase et polynucléotides codant pour ceux-ci
WO2019231944A2 (fr) 2018-05-31 2019-12-05 Novozymes A/S Procédés d'amélioration de la croissance et de la productivité de levures
WO2020010101A2 (fr) 2018-07-04 2020-01-09 Danisco Us Inc Glucoamylases et leurs procédés d'utilisation
WO2020014407A1 (fr) 2018-07-11 2020-01-16 Novozymes A/S Procédés de production de produits de fermentation
WO2020023411A1 (fr) 2018-07-25 2020-01-30 Novozymes A/S Levure exprimant une enzyme pour la production d'éthanol
WO2020076697A1 (fr) 2018-10-08 2020-04-16 Novozymes A/S Levure exprimant une enzyme pour la production d'éthanol
WO2020187883A1 (fr) 2019-03-18 2020-09-24 Novozymes A/S Polypeptides présentant une activité de pullulanase appropriée pour une utilisation dans la liquéfaction
WO2021025872A1 (fr) 2019-08-06 2021-02-11 Novozymes A/S Protéines de fusion pour une expression enzymatique améliorée
WO2021055395A1 (fr) 2019-09-16 2021-03-25 Novozymes A/S Polypeptides dotés d'une activité bêta-glucanase et polynucléotides codant pour ces polypeptides
WO2021126966A1 (fr) 2019-12-16 2021-06-24 Novozymes A/S Procédés de production de produits de fermentation
WO2021163015A1 (fr) 2020-02-10 2021-08-19 Novozymes A/S Procédé de production d'éthanol à partir d'amidon brut à l'aide de variants d'alpha-amylase
WO2021163011A2 (fr) 2020-02-10 2021-08-19 Novozymes A/S Variants d'alpha-amylase et polynucléotides codant pour ceux-ci
WO2021163030A2 (fr) 2020-02-10 2021-08-19 Novozymes A/S Polypeptides ayant une activité alpha-amylase et polynucléotides codant pour ces derniers
WO2021163036A1 (fr) 2020-02-10 2021-08-19 Novozymes A/S Processus d'hydrolyse d'amidon brut de production d'un produit de fermentation
WO2022090564A1 (fr) 2020-11-02 2022-05-05 Novozymes A/S Variants de glucoamylase et polynucléotides codant pour ceux-ci
WO2022173694A1 (fr) 2021-02-10 2022-08-18 Novozymes A/S Polypeptides ayant une activité de pectinase, polynucléotides codant pour ceux-ci et leurs utilisations

Non-Patent Citations (76)

* Cited by examiner, † Cited by third party
Title
"UniProt", Database accession no. P41911
AGRIC. BIOL. CHEM, vol. 55, no. 4, 1991, pages 941 - 949
BIOCHEM. J., vol. 290, 1993, pages 205 - 218
BOEL ET AL., EMBO J., vol. 3, no. 5, 1984, pages 1097 - 1102
BOTSTEINSHORTLE, SCIENCE, vol. 229, 1985, pages 4719
BOWIESAUER, PROC. NATL. ACAD. SCI. USA, vol. 86, 1989, pages 2152 - 2156
BURGARD ET AL., BIOTECHNOL. BIOENG, vol. 84, 2003, pages 647 - 657
CHEN ET AL., BIOCHEM. J., vol. 301, 1994, pages 275 - 281
CHEN ET AL., PROT. ENG, vol. 8, 1995, pages 575 - 582
CHEN ET AL., PROT. ENG, vol. 9, 1996, pages 499 - 505
COOPER ET AL., EMBO J, vol. 12, 1993, pages 2575 - 2583
CUNNINGHAMWELLS, SCIENCE, vol. 244, 1989, pages 1081 - 1085
DAWSON ET AL., SCIENCE, vol. 266, 1994, pages 776 - 779
DERBYSHIRE ET AL., GENE, vol. 46, 1986, pages 145
EUR. J. BIOCHEM, vol. 232, 1995, pages 1 - 6
EUR. J. BIOCHEM, vol. 237, 1996, pages 1 - 5
EUR. J. BIOCHEM, vol. 250, 1997, pages 1 - 6
EUR. J. BIOCHEM, vol. 264, 1999, pages 610 - 650
FEMS MIC. LET., vol. 115, 1994, pages 97 - 106
FIEROBE ET AL., BIOCHEMISTRY, vol. 35, 1996, pages 8698 - 8704
GHOSE, PURE AND APPL. CHEM, vol. 59, 1987, pages 257 - 268
GHOSEBISARIA, PURE & APPL. CHEM, vol. 59, 1987, pages 1739 - 1752
GOMI ET AL., BIOSCI. BIOTECH. BIOCHEM., vol. 57, 1993, pages 1095 - 1100
GUOSHERMAN, MOL. CELLULAR BIOL, vol. 15, 1995, pages 5983 - 5990
H. NEURATHR.L. HILL: "In, The Proteins", 1979, ACADEMIC PRESS
HIGUCHI ET AL., NUCLEIC ACIDS RES, vol. 16, 1988, pages 7351
HOPWOOD: "The Isolation of Mutants in Methods in Microbiology", 1970, ACADEMIC PRESS, pages: 363 - 433
HORTON ET AL., GENE, vol. 77, 1989, pages 61
HUANG ET AL., BIOCHEM J, vol. 448, 2012, pages 401 - 407
HUE ET AL., JOURNAL OF BACTERIOLOGY, vol. 177, 1995, pages 3465 - 3471
IGLESIASTRAUTNER, MOLECULAR GENERAL GENETICS, vol. 189, 1983, pages 73 - 76
JUMPER ET AL., NATURE, vol. 596, 2021, pages 583 - 589
KARHUMAA ET AL., MICROB CELL FACT, vol. 73, 2007, pages 7814 - 7818
LEVER ET AL., ANAL. BIOCHEM., vol. 47, 1972, pages 273 - 279
LEVER: "A new reaction for colorimetric determination of carbohydrates", ANAL. BIOCHEM, vol. 47, 1972, pages 273 - 279, XP024820395, DOI: 10.1016/0003-2697(72)90301-6
LI ET AL., PROTEIN ENG, vol. 10, 1997, pages 1199 - 1204
LIN ET AL., BIOTECHNOL. BIOENG, vol. 90, 2005, pages 775 - 779
LOWMAN ET AL., BIOCHEMISTRY, vol. 30, 1991, pages 10832 - 10837
MADHAVAN ET AL., APPL MICROBIOL BIOTECHNOL, vol. 82, no. 6, 2009, pages 1067 - 1078
NAGASAKA ET AL.: "Purification and properties of the raw-starch-degrading glucoamylases from Corticium rolfsii", APPL MICROBIOL BIOTECHNOL, vol. 50, 1998, pages 323 - 330, XP002506425, DOI: 10.1007/s002530051299
NDAT ET AL., MBC BIOTECHNOL, vol. 21, 2021, pages 61
NEEDLEMANWUNSCH, J. MOL. BIOL., vol. 48, 1970, pages 443 - 453
NER ET AL., DNA, vol. 7, 1988, pages 127
NESS ET AL., NATURE BIOTECHNOLOGY, vol. 17, 1999, pages 893 - 896
NORBECK ET AL., J. BIOL. CHEM., vol. 271, no. 23, 1996, pages 13875 - 4708
PAHLMAN ET AL., J. BIOL. CHEM., vol. 276, no. 5, 2001, pages 3555 - 63
PROC. NATL. ACAD. SCI. U.S.A., vol. 81, 1985, pages 2285
R.M. BERKA ET AL., GENE, vol. 125, 1993, pages 195 - 198
R.M. BERKA ET AL., GENE, vol. 96, 1990, pages 313
RAWLINGS, N.DBARRETT, A.JBATEMAN, A: "MEROPS: the peptidase database", NUCL. ACIDS RES, vol. 38, 2010, pages D227 - D233
REIDHAAR-OLSONSAUER, SCIENCE, vol. 241, 1988, pages 1306 - 1310
RICE ET AL.: "EMBOSS: The European Molecular Biology Open Software Suite", TRENDS GENET, vol. 16, 2000, pages 276 - 277, XP004200114, DOI: 10.1016/S0168-9525(00)02024-2
RICHARD, FEBS LETTERS, vol. 457, 1999, pages 135 - 138
RICHARDSON ET AL., THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 277, no. 29, 19 June 2002 (2002-06-19), pages 267501 - 26507
ROMANOS ET AL., YEAST, vol. 8, 1992, pages 423 - 488
SARKARSOMMER, BIOTECHNIQUES, vol. 8, 1990, pages 404
SHALLOMSHOHAM, CURRENT OPINION IN MICROBIOLOGY, vol. 6, no. 3, 2003, pages 219 - 228
SHIMADA, METH. MOL. BIOL, vol. 57, 1996, pages 157
SIEZEN ET AL., PROTEIN ENGNG, vol. 4, 1991, pages 719 - 737
SIEZEN ET AL., PROTEIN SCIENCE, vol. 6, 1997, pages 501 - 523
SMITH ET AL., J. MOL. BIOL., vol. 224, 1992, pages 899 - 904
TAMOI ET AL., BIOCHEM. J., vol. 316, 1996, pages 685 - 690
TEERI ET AL., BIOCHEM. SOC. TRANS., vol. 26, 1998, pages 173 - 178
TEERI, TRENDS IN BIOTECHNOLOGY, vol. 15, 1997, pages 160 - 167
TOMME ET AL., EUR. J. BIOCHEM, vol. 170, 1988, pages 575 - 581
VAN TILBEURGH ET AL., FEBS LETTERS, vol. 149, 1982, pages 152 - 156
VAN TILBEURGHCLAEYSSENS, FEBS LETTERS, vol. 187, 1985, pages 283 - 288
VARADI ET AL., NUCLEIC ACIDS RESEARCH, vol. 50, 2021, pages D439 - D444
VENTURI ET AL., J. BASIC MICROBIOL, vol. 42, 2002, pages 55 - 66
VOS ET AL., SCIENCE, vol. 255, 1992, pages 306 - 312
WANG ET AL., CHIN. J. BIOTECHNOL, vol. 14, 1998, pages 179 - 185
WLODAVER ET AL., FEBS LETT, vol. 309, 1992, pages 59 - 64
YABLOCHKOVA ET AL., MICROBIOLOGY, vol. 72, no. 4, 2003, pages 414 - 417
ZHANG ET AL., BIOTECHNOLOGY ADVANCES, vol. 24, 2006, pages 452 - 481
ZHANGHENZEL, PROTEIN SCIENCE, vol. 13, 2004, pages 2819 - 2824
ZHANGSKOLNICK, PROTEINS, vol. 57, 2004, pages 702 - 710

Also Published As

Publication number Publication date
WO2024258820A3 (fr) 2025-01-23

Similar Documents

Publication Publication Date Title
US20240124902A1 (en) Enzyme-expressing yeast for ethanol production
US20240110204A1 (en) Yeast expressing a heterologous phospholipase for ethanol production
US20230193216A1 (en) Engineered microorganism for improved pentose fermentation
US20210198618A1 (en) Processes for enhancing yeast growth and productivity
US20200157581A1 (en) Improved Yeast For Ethanol Production
US20220348967A1 (en) Microorganisms With Improved Nitrogen Utilization For Ethanol Production
AU2020326511A1 (en) Fusion proteins for improved enzyme expression
US20230183639A1 (en) Improved microorganisms for arabinose fermentation
US20240279688A1 (en) Engineered microorganism for improved ethanol fermentation
US20230002794A1 (en) Microorganism for improved pentose fermentation
US20220251609A1 (en) Microorganisms with improved nitrogen transport for ethanol production
WO2024258820A2 (fr) Procédés de fabrication de produits de fermentation à l'aide d'une levure modifiée exprimant une bêta-xylosidase
WO2024137704A2 (fr) Procédés de production de produits de fermentation faisant appel à des enzymes de dégradation de fibres avec levure modifiée

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 24739342

Country of ref document: EP

Kind code of ref document: A2