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CN110157756B - Method for improving erythromycin yield by modifying saccharopolyspora erythraea SACE _0303 gene - Google Patents

Method for improving erythromycin yield by modifying saccharopolyspora erythraea SACE _0303 gene Download PDF

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CN110157756B
CN110157756B CN201910178832.5A CN201910178832A CN110157756B CN 110157756 B CN110157756 B CN 110157756B CN 201910178832 A CN201910178832 A CN 201910178832A CN 110157756 B CN110157756 B CN 110157756B
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张部昌
倪静姝
张万祥
吴杭
汪焰胜
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Abstract

The invention discloses a method for improving the yield of erythromycin by modifying a saccharopolyspora erythraea SACE _0303 gene, which comprises the steps of utilizing a screened erythromycin biosynthesis positive regulator SACE _0303, carrying out overexpression on a TetR family transcription gene SACE _0303 gene in the saccharopolyspora erythraea through a genetic engineering approach, obtaining a saccharopolyspora erythraea erythromycin high-yield engineering strain, and fermenting and producing erythromycin by using the strain to provide technical support for improving the yield of erythromycin in industrial production.

Description

Method for improving erythromycin yield by modifying saccharopolyspora erythraea SACE _0303 gene
Technical Field
The invention relates to the field of genetic engineering, in particular to a method for improving the yield of erythromycin by modifying saccharopolyspora erythraea SACE _0303 gene.
Background
Actinomycetes can produce abundant secondary metabolites, and the secondary metabolites and derivatives thereof have wide application, such as antibiotics, anticancer drugs, immunosuppressants and the like. Erythromycin is a macrolide antibiotic with broad-spectrum antibacterial action produced by saccharopolyspora erythraea. Since the discovery in 1952, erythromycin and its derivatives have been widely used clinically, and have been developed to the third generation. It follows that increasing the production of erythromycin is a problem that is urgently needed to be solved.
In the past, industrial production strains have been obtained mainly by physical or chemical mutagenesis methods. The traditional mutagenesis technology is time-consuming and has high randomness, and theoretical guidance cannot be provided for breeding. Through the gene engineering method, the modified antibiotic high-yield strain is obtained by inactivating certain regulatory genes or increasing the copy number of certain genes in the strain, and has good prospect. The invention aims to obtain the erythromycin high-producing strain by directionally changing genes through a genetic engineering way.
In the saccharopolyspora erythraea, no regulatory gene exists in an erythromycin biosynthesis gene cluster, and a high-yield strain obtained by modifying the gene of the saccharopolyspora erythraea through a genetic engineering approach can only modify other regulatory genes from the whole genome.
In 2005, Ramos et al, based on sequence similarity, structure and function, classified prokaryotic transcriptional regulators into 16 families, LysR, AraC/xylS, TetR, LuxR, LacI, ArsR, IcIR, MerR, AsnC, MarR, NtrC (EBP), OmpR, DeoR, Cold shock, GntR and Crp. Among them, the TetR family regulatory factors (TFRs) have high conservation in DNA binding domains and are widely involved in regulating biological activities such as multidrug resistance, antibiotic synthesis, osmotic stress response, and the like. In recent years, various TFRs involved in antibiotic production and morphological differentiation of Streptomyces have been reported, such as SAV _576, SAV _3619, SCO1712, AtrA, SLCG _2919, etc., suggesting the importance of TetR family regulatory genes in Streptomyces secondary metabolism and antibiotic biosynthesis. Among the Saccharopolyspora erythraea, there are 101 TFRs, and currently reported TFRs involved in spore morphological differentiation of Saccharopolyspora erythraea are SACE _0012 and SACE _7040, and TFRs involved in regulation of erythromycin biosynthesis are SACE _5599, SACE _3986, SACE _7301, SACE _3446, BldD (SACE _2077), PccD (SACE _3396), SACE _ Lrp (SACE _5388), SACE _5754 and the like. Indicating the importance of TFRs in erythromycin biosynthesis.
Disclosure of Invention
The invention aims to make up the defects of the prior art and provides a method for improving the yield of erythromycin by modifying a saccharopolyspora erythraea SACE _0303 gene.
The invention is realized by the following technical scheme:
a method for improving the yield of erythromycin by modifying a saccharopolyspora erythraea SACE _0303 gene comprises the steps of over-expressing the SACE _0303 gene in the saccharopolyspora erythraea through a genetic engineering approach to obtain a saccharopolyspora erythraea erythromycin high-yield engineering strain, and fermenting and producing erythromycin by using the strain.
The SACE _0303 gene product can positively regulate erythromycin biosynthesis.
The invention also provides application of the SACE _0303 gene in an industrial strain WB of saccharopolyspora erythraea, wherein the high-yield strain is obtained by over-expressing the TetR family transcriptional gene SACE _0303 gene in the industrial high-yield strain WB and can be used for producing erythromycin.
The invention has the advantages that:
in the research of the invention, an erythromycin biosynthesis positive regulator SACE _0303 is screened, and the saccharopolyspora erythraea SACE _0303 gene is overexpressed through a genetic engineering approach, so that a saccharopolyspora erythraea high-yield strain can be obtained, and a technical support is provided for improving the yield of erythromycin in industrial production.
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FIG. 1 shows the positional information of SACE _0303 gene and neighboring genes on chromosome.
FIG. 2 shows the construction of a Δ SACE _0303 mutant, wherein (A) is a schematic diagram of the construction of a Δ SACE _0303 mutant; (B) for PCR identification of Δ SACE _0303 mutants, M: 5000bp DNA Marker; 1: Δ SACE _0303 strain.
FIG. 3 shows the erythromycin production analysis of wild strain A226 and deletion mutant strain Δ SACE _ 0303.
FIG. 4 shows SACE _0303 gene complementation, construction of over-expressed strain and erythromycin yield analysis, wherein (A) is Δ SACE _0303/pIB139-0303 complementation, Δ SACE _0303/pIB139 empty load, A226/pIB139-0303 over-expression, PCR identification of A226/pIB139 empty load strain, and PCR product is apr resistance gene (776 bp); m: 5000bp DNA Marker; +: pIB139 plasmid; lane 1: Δ SACE _0303/pIB139 back-supplemented no-load control strains; 2: Δ SACE _0303/pIB139-0303 anaplerotic strains; 3: A226/pIB139 over-expressed empty control strain; 4: A226/pIB139-0303 overexpression strain; (B) erythromycin production analyses for strains A226,. DELTA.SACE _0303/pIB139-0303,. DELTA.SACE _0303/pIB139, A226/pIB 139-0303.
FIG. 5 shows the effect of SACE _0303 gene on biological and morphological differentiation, where (A) is a biomass assay of Δ SACE _0303 mutant and wild strain A226 mycelium; (B) is the spore growth of the mutant strain Δ SACE _0303 and wild strain A226.
FIG. 6 shows gene transcript level analysis, wherein (A) is the transcript levels of erythromycin biosynthetic enzyme gene eryAI (SACE _0721) and erythromycin resistance gene ermE (SACE _0733) in Δ SACE _ 0303; (B) is the self SACE _0303 transcript level in Δ SACE _ 0303.
FIG. 7 shows the purified expression of SACE _0303 protein and EMSA analysis of promoter region of related gene, in which (A) is the construction of SACE _0303 protein expression vector pET28 a-0303; (B) purifying SACE _0303 protein; (C) the EMSA analysis of SACE _0303 protein and eryAI promoter region, ermE promoter region, SACE _0303 promoter region.
FIG. 8 shows the modification of an industrial high-yielding strain WB of erythromycin using overexpression of SACE _0303 gene, wherein (A) is the PCR identification of WB/pIB139-0303 strain; SACE _0303 gene (420bp) was replaced by tsr resistance gene (1360 bp); m: 5000bp DNA Marker; 1: WB/pIB139-0303 strain; (B) the method is used for analyzing the yield of the erythromycin in the industrial high-yield strains WB and WB/pIB139-0303 of the erythromycin.
Detailed Description
The following examples are given for the detailed implementation and specific operation of the present invention, but the scope of the present invention is not limited to the following examples.
The strains and plasmids used in the examples are shown in Table 1. Coli were cultured on liquid LB medium at 37 ℃ or on solid LB plates supplemented with 1.25% agar. Erythromycin producing bacteria Rhodosporidium toruloides wild strain A226 and its engineered strain WB were cultured in Tryptone Soy Broth (TSBY) medium at 30 ℃ or on MGM plates containing 2.2% agar.
TABLE 1 strains and plasmids used in this example
Figure BDA0001990403110000031
Figure BDA0001990403110000041
Figure BDA0001990403110000042
Examples PEG3350, lysozyme, TES, casamino acids, thiostrepton, apramycin were purchased from Sigma. TSB, yeast extract, peptone were purchased from Oxoid. Glycine, agar powder, sodium chloride and other biological reagents were purchased from reagent companies. General procedures for E.coli and S.lincolnensis were performed according to standard protocols. The synthesis of primers and DNA sequencing were performed by Biotechnology engineering (Shanghai) Inc.
The sequences of the primers synthesized in the experiment are shown in Table 2:
TABLE 2 primer List
Figure BDA0001990403110000051
Figure BDA0001990403110000061
(1) Construction of SACE _0303 Gene deletion mutants:
the pUCTSR plasmid is obtained by inserting 1360bp thiostrepton resistance gene (tsr) between BamHI and SmaI cleavage sites of pUC 18. Using the genome of wild strain A226 as template, primers SACE _0303up-F/R and SACE _0303down-F/R were used to amplify homologous recombination upstream and downstream homologous fragments 0303-up and 0303-down of about 1500 bp.
Connecting the two segments 0303-up and 0303-down to two sides of tsr resistance gene sequence of pUCTSR in sequence to complete construction of plasmid pUCTS-SACE _0303 LR; the tsr-0303LR large fragment is transformed into saccharopolyspora erythraea A226 by utilizing chromosome homologous recombination technology, and a positive mutant strain is screened by thiostrepton, so that a genetic engineering strain with the SACE _0303 gene replaced by the tsr resistance gene is obtained. And c0303-F/R is used as an identification primer, plasmid pUCTS-SACE _0303LR is used as a positive template, A226 genome is used as a negative template for PCR identification, and the positive deletion mutant strain is named as delta SACE _ 0303.
(2) Construction of SACE _0303 Gene reverted and overexpressed strains:
the genome of the wild strain A226 is used as a template, and a complete SACE _0303 gene fragment is amplified by using a back-filling primer c 0303-F/R. The amplification product was electrophoresed and recovered using a kit. The recovered SACE _0303 fragment and plasmid pIB139 are subjected to NdeI and XbaI double enzyme digestion, and the double-enzyme digested SACE _0303 fragment is cloned onto the digested plasmid pIB 139. And (3) carrying out PCR verification on the selected monoclonal antibody, and screening the integrative plasmid pIB 139-0303.
The recombinant plasmid pIB139-0303 is transferred into wild strain A226 protoplast and mutant strain delta SACE _0303 protoplast, and the pIB139 no-load plasmid is transferred into A226 protoplast and mutant strain delta SACE _0303 protoplast in the same way. Approximately 24h after transformation, the medium was covered with an aqueous apramycin solution and cultured until transformants grew. And carrying out amplification culture on the picked transformant, and then carrying out bacteria liquid PCR identification and screening on strains delta SACE _0303/pIB139, delta SACE _0303/pIB139-0303, A226/pIB139 and A226/pIB139-0303 by using a pair of Apr primers Apr-p1/p2 designed on the pIB139 no-load plasmid.
(3) Construction of WB/pIB-0303 erythromycin high-producing strains in industrial high-producing strains WB:
the constructed pIB139-0303 plasmid is transferred into a saccharopolyspora erythraea industrial strain WB protoplast to construct a WB/pIB-0303 strain, and the steps are referred to for the construction and screening method.
(4) HPLC detection of the fermentation product of saccharopolyspora erythraea:
inoculating saccharopolyspora erythraea series strains into a TSB culture medium, carrying out shake culture at 30 ℃ for 48 hours, transferring to an R5 liquid culture medium, carrying out shake culture at 30 ℃ for 6 days, extracting fermentation liquor by using an organic solvent, evaporating to dryness by using a water bath kettle, adding 1mL of methanol for dissolving, treating by using a 0.22 mu m organic filter membrane, and then loading on a computer to detect the content of erythromycin A in a sample.
(5) And (3) detecting the biomass of saccharopolyspora erythraea mycelium:
inoculating the delta SACE _0303 mutant strain and A226 in 50mL of liquid TSR, carrying out shake cultivation at 30 ℃ for 48 hours, then transferring the mutant strain to R5 culture medium, carrying out shake cultivation at 30 ℃ and 240rpm for 6d, setting sampling at different time periods, washing with absolute ethyl alcohol, drying, weighing the dry weight of the thallus, repeatedly sampling twice each time, obtaining an average value, and drawing a thallus biomass curve according to experimental data after the measurement is finished.
(6) And (3) observing the spore morphology of saccharopolyspora erythraea:
marking on an R3 culture medium, respectively coating the spore glycerol bacterial liquids of the delta SACE _0303, the delta SACE _0303/pIB139-0303, the delta SACE _0303/pIB139 and the wild strain A226 on the R3M culture medium by the same inoculation amount, airing in a super clean bench, and then placing in a 30 ℃ constant temperature incubator for inverted growth. Spore growth was observed and recorded every 24 h.
(7) Transcriptional analysis of the relevant genes in Δ SACE _ 0303:
collecting the culture liquid of the delta SACE _0303 and the wild strain A226 which are cultured for 24h, obtaining the required RNA by adopting a full-type gold RNA extraction kit, inverting the RNA into cDNA, and detecting on a computer by using a real-time fluorescence quantitative PCR instrument.
(8) Protein expression of SACE _0303 and EMSA analysis of promoter regions of related genes:
according to the information noted on NCBI, a protein expression primer p28a-0303-F/R with NdeI and HindIII enzyme cutting sites is designed, and the SACE _0303 complete gene fragment is amplified and connected with pET28 a. And carrying out PCR verification on the selected monoclonal antibody.
The successfully constructed protein expression vector pET28a-0303 is transferred into a competent cell of escherichia coli BL21(DE3), a single colony is selected on a Kana resistant LB solid culture medium, after amplification culture, PCR identification of bacterial liquid is carried out by using pET28a-0303-F/R primers, and the screened bacterial strain is named as BL21/pET28 a-0303.
BL21/pET28a-0303 is inoculated in Kana resistance LB liquid culture medium and cultured overnight at 37 ℃; inoculating according to 2% of inoculum size the next day, and culturing at 37 deg.C to obtain thallus OD600Adding IPTG (final concentration 0.5mM) between 0.5 and 1, and inducing expression at 30 ℃ and 180rpm for 5 h; collecting thallus, ultrasonic crushing, centrifuging, taking supernatant, performing Ni-affinity chromatography, eluting with imidazole of different concentrations, and detecting by SDS-PAGE. The predicted protein size is 20.57kDa, plus a sequence on the vector of about 22 kDa.
Respectively carrying out PCR amplification on promoter regions of eryAI, ermE and SACE _0303 genes in an erythromycin cluster by using an eryAI-eryBIV-F/R primer and an ermE-eryCI-F/R, SACE _0303-SACE _0304-F/R primer, and carrying out electrophoresis and recovery on amplification products. The amplified fragment was named Probe PeryAI-eryBIV、PermE-eryCI、PSACE_0303-SACE_0304. And respectively incubating the probes with the purified SACE _0303 protein at the temperature of 30 ℃, wherein the incubation system is 20 mu L, and performing active PAGE detection after 10 min.
And (4) analyzing results:
the location of SACE _0303 and adjacent genes on the chromosome of Rhodosporidium saccharopolyspora is shown in FIG. 1. The construction process of SACE _0303 gene deletion mutant A226/delta SACE _0303 is shown in FIG. 2A. SACE _0303 gene deletion mutants were screened on R3M plates containing 30. mu.g/ml thiostrepton and confirmed by PCR (FIG. 2B).
After A226/delta SACE _0303 is fermented in R5 fermentation medium for 6d, the yield of erythromycin is detected by HPLC, and the yield of A226/delta SACE _0303 is reduced by 40% compared with the yield of wild strain A226 (FIG. 3), and the HPLC result shows that SACE _0303 is a positive regulator involved in erythromycin biosynthesis.
To further verify that the improvement of erythromycin production in mutant Δ SACE _0303 was due to SACE _0303 gene deletion, SACE _0303 gene expression vectors pIB139-0303 and pIB139 vector (control) were introduced into protoplasts of the Δ SACE _0303 mutant strain and wild strain A226, respectively, to obtain a revertant strain Δ SACE _0303/pIB139-0303 and an empty Δ SACE _0303/pIB139, and an over-expressed strain A226/pIB139-0303 and an empty A226/pIB 139. A226 and delta SACE _0303 series strains are subjected to shake flask fermentation, and HPLC detection results show that: the yield of the erythromycin A in the delta SACE _0303 is reduced by 37 percent compared with the yield of the A226; the yield of erythromycin A in the revertant strain Δ SACE _0303/pIB139-0303 was restored to the level of erythromycin A in A226; the yield of erythromycin A in A226/pIB139-0303 is improved by 30% compared with A226 (FIG. 4). These results indicate that SACE _0303 is positively regulating erythromycin biosynthesis.
The dry weight of cells of the mutant strain Δ SACE _0303 and the strain A226 were measured for 6 days of fermentation, and the results of plotting the corresponding change curves showed that the biomass of Δ SACE _0303 was not much different from that of A226 (FIG. 5A), suggesting that the deletion of SACE _0303 gene did not affect the growth of cells.
To determine whether SACE _0303 gene regulates the sporulation of the thallus, mutant strain Δ SACE _0303, anaplerotic strain Δ SACE _0303/pIB139-0303, empty load control strain Δ SACE _0303/pIB139 and wild type strain A226 were simultaneously smeared on an R3M plate, cultured at 30 ℃ for 72 hours, and the spore growth of the strain was observed. The results show no significant difference in spore morphology for the Δ SACE _0303 mutant compared to a226 (fig. 5B), indicating that the SACE _0303 gene deletion does not affect spore formation.
qRT-PCR data showed that the transcription levels of eryAI and ermE genes in the erythromycin gene cluster in the mutant strain Δ SACE _0303 were respectively down-regulated by 3.2-fold and 3.3-fold (FIG. 6A) compared to wild strain A226, indicating that SACE _0303 regulates the transcription level of genes in the cluster to control erythromycin biosynthesis; the SACE _0303 transcriptional level was down-regulated (FIG. 6B), indicating that SACE _0303 protein can promote the transcriptional expression of self-genes.
SACE _0303 protein expression vector construction is shown in FIG. 7A, protein purification is shown in FIG. 7B, and binding experiment with eryAI, ermE, SACE _0303 promoter region is shown in FIG. 7C; EMSA analysis shows that SACE _0303 protein does not bind to eryAI and ermE promoter regions and specifically binds to SACE _0303 promoter regions, which indicates that SACE _0303 indirectly regulates the transcriptional expression of genes in erythromycin biosynthesis clusters; directly promote the self gene transcription and then regulate the biosynthesis of erythromycin.
The constructed WB/pIB139-0303 strain was identified as shown in FIG. 8A. And carrying out shake flask parallel fermentation on the constructed WB/pIB139-0303 strain and the WB strain, and detecting the yield of the erythromycin A by HPLC. The results show that: the production of erythromycin A in WB/pIB139-0303 strain was improved by 27% compared to WB (FIG. 8B).
Sequence listing
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<120> a method for improving the yield of erythromycin by modifying saccharopolyspora erythraea SACE _0303 gene
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gacctgctcg ccaccggcga caccgaacgg gtgcgcgcgg gcttcgagtc actggtcgcc 540
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Claims (3)

1. A method for improving the yield of erythromycin through modifying a saccharopolyspora erythraea SACE _0303 gene is characterized in that a TetR family transcription gene SACE _0303 gene in the saccharopolyspora erythraea is overexpressed through a genetic engineering approach to obtain an engineering strain with improved saccharopolyspora erythraea erythromycin yield, and erythromycin is produced by fermenting the engineering strain, wherein the nucleotide sequence of the SACE _0303 gene is shown as a sequence 1.
2. The method of claim 1, wherein said SACE _0303 gene positively regulates erythromycin biosynthesis.
3. The method according to claim 1, characterized in that the use of SACE _0303 gene in the saccharopolyspora erythraea industrial strain WB overexpresses the TetR family transcriptional gene SACE _0303 gene in said industrial strain WB, obtaining an engineered strain for erythromycin production.
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CN111197019B (en) * 2020-01-10 2022-04-15 安徽大学 A kind of method of improving erythromycin yield through Saccharopolyspora SACE_1906 gene pathway
CN112458136A (en) * 2020-12-11 2021-03-09 安徽大学 Saccharopolyspora erythraea with modified SACE-1409 gene and application thereof
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CN116121163A (en) * 2022-12-29 2023-05-16 安徽农业大学 Alteration of thaxtomin A biosynthesis by the transcription factor gene bldD in Streptomyces scabies

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