Sphingomonas

Bacterial exopolysaccharides (EPS) are products of biotechnology that are of high interest due to their rheological properties. This is the case of sphingans, a group of structurally related EPS secreted by members of the genus Sphingomonas. Among these, gellan is a multifunctional gelling agent produced in high yields by the non-pathogenic strain Sphingomonas elodea ATCC 31461. In its native form, gellan is a linear anionic EPS based on a tetrasaccharide repeat unit composed of two molecules of d-glucose, one of l-rhamnose and one of d-glucuronic acid. The native gellan is partially esterified with acyl substituents (1 mol of glycerate and 0.5 mol of acetate) per repeat unit. Gellan has unique characteristics and has many applications, particularly in the food, pharmaceutical, and biomedical fields. This review summarizes current knowledge on the structure and properties of gellan and provides details about the biosynthesis of this exopolysaccharide. In addition, a highlight of the importance of gellan in industrial and medicinal applications is given.

Enrichment and elective culture for methylotrophs from sediment of the River Thames in central London yielded a diversity of pure cultures representing several genera of Gram-negative and Gram-positive bacteria, which were mainly of organisms not generally regarded as typically methylotrophic. Substrates leading to successful isolations included methanol, monomethylamine, dimethylamine, trimethylamine, methanesulfonate and dimethylsulfone. Several isolates were studied in detail and shown by their biochemical and morphological properties and 16S rRNA gene sequencing to be Sphingomonas melonis strain ET35, Mycobacterium fluoranthenivorans strain DSQ3, Rhodococcus erythropolis strain DSQ4, Brevibacterium casei strain MSQ5, Klebsiella oxytoca strains MMA/F and MMA/1, Pseudomonas mendocina strain TSQ4, and Flavobacterium sp. strains MSA/1 and MMA/2. The results show that facultative methylotrophy is present across a wide range of Bacteria, suggesting that turnover of diverse C1-compounds is of much greater microbiological and environmental significance than is generally thought. The origins of the genes encoding the enzymes of methylotrophy in diverse heterotrophs need further study, and could further our understanding of the phylogeny and antiquity of methylotrophic systems.

The genes encoding xylitol dehydrogenase (Texdh) and l-arabitol dehydrogenase (Telad) are involved in the fungal pentose pathway and were isolated from the thermophilic fungus Talaromyces emersonii, expressed in Escherichia coli, and the products purified to homogeneity. TeXDH showed activity toward xylitol and d-sorbitol. TeLAD was active with l-arabitol, xylitol, and d-sorbitol. Phylogenetic analysis showed TeLAD has evolved from d-sorbitol dehydrogenase as a result of environmental adaptation. Substrate specificity studies indicate that TeXDH is likely to have evolved from the more broadly acting TeLAD. Texdh and Telad expression was inducible by the same carbon sources responsible for induction of genes involved in biomass degradation, suggesting for the first time a coordinated regulatory control mechanism for expression of genes encoding extracellular hydrolases and intracellular metabolic genes in the pentose utilization pathways of T. emersonii. These data also suggest that TeXDH and TeLAD may be valuable in the production of xylitol, l-arabitol, and ethanol from renewable resources rich in pentose sugars.

Sphingomonas elodea ATCC 31461 synthesizes in high yield the exopolysaccharide gellan, which is a water-soluble gelling agent with many applications. In this study, we describe the cloning and sequence analysis of the ugdG gene, encoding a UDP-glucose dehydrogenase (47.2 kDa; UDPG-DH; EC 1.1.1.22), required for the synthesis of the gellan gum precursor UDP-glucuronic acid. UgdG protein shows homology to members of the UDP-glucose/GDP-mannose dehydrogenase superfamily. The Neighbor-Joining method was used to determine phylogenetic relationships among prokaryotic and eukaryotic UDPG-DHs. UgdG from S. elodea and UDPG-DHs from Novosphingobium, Zymomonas, Agrobacterium, and Caulobacter species form a divergent phylogenetic group with a close evolutionary relationship with eukaryotic UDPG-DHs. The ugdG gene was recombinantly expressed in Escherichia coli with and N-terminal 6-His tag and purified for biochemical characterization. The enzyme has an optimum temperature and pH of 37°C and 8.7, respectively. The estimated apparent K m values for UDP-glucose and NAD+ were 0.87 and 0.4 mM, respectively. DNA sequencing of chromosomal regions adjacent to ugdG gene and sequence similarity studies suggests that this gene maps together with others presumably involved in the biosynthesis of S. elodea cell wall polysaccharides.

An extension of the models developed by Guha and Jaffé (Biotechnol Bioeng [1996] 50:693–699) to describe the phenanthrene biodegradation kinetics for the cultures with variable fractional volumes is presented. Batch experiments were conducted with a culture capable of degrading the phenanthrene using a single culture vessel from which samples were withdrawn over time to monitor the disappearance of phenanthrene. For accurate measurement of phenanthrene concentrations, a sampling procedure designed for quantifying the sorption of phenanthrene onto glassware was also introduced. The Monod parameters were estimated by nonlinear regression analyses of simultaneous solutions to the substrate utilization/volatilization and Monod equations for growth of the cell mass. The results demonstrate that the models were able to be extended to phenanthrene-degrading cultures with variable fractional volumes. When the ratio between sampling volume and volume of the culture medium was relatively small, the parameters obtained were similar to those which would be obtained using constant fractional volumes of culture medium. It was also found that the model's fit to the phenanthrene disappearance data in this study were better than those obtained by Guha and Jaffé, implying that the sorption process of phenanthrene during the sampling period could significantly affect the measurement of phenanthrene concentrations. Failing to account for these losses led to less accurate measurements of substrate concentrations, which in turn resulted in a poor estimation of the parameters. The findings of this study reduce considerably the experimental work necessary in the estimation of Monod kinetic parameters for the purpose of modeling. © 2004 Wiley Periodicals, Inc.

Three dibenzofuran (DF)-degrading strains were newly isolated from roots of white clover (Trifolium repens L.) and poplar trees grown in DF-contaminated soil samples. These strains, designated KD2, KD7, and PD1, were characterized as Comamonas sp. on the basis of their 16S rDNA sequences and physiological characteristics. The metabolites produced when strain KD7 was incubated with DF were identified by gas chromatography–mass spectrometry (GC-MS) analysis. Interestingly, strain KD7 was found to have two pathways for DF degradation, beginning with angular dioxygenation at carbons 4 and 4a, and lateral dioxygenation at carbons 1 and 2, respectively. Furthermore, strains KD2 and KD7 not only achieved efficient root colonization in clover but also promoted clover growth. They are the first reported Comamonas sp. strains capable of utilizing DF as a sole carbon source. This provides additional information on the diversity of DF-degrading bacteria.

A bacterium possessing alginate-degrading activity was isolated from marine brown seaweed soup liquefied by salted and fermented anchovy. The isolated strain was designated as Sphingomonas sp. MJ-3 based on the analyses of 16S ribosomal DNA sequences, 16S-23S internal transcribed spacer region sequences, biochemical characteristics, and cellular fatty acid composition. A novel alginate lyase gene was cloned from genomic DNA library and then expressed in Escherichia coli. When the deduced amino acid sequence was compared with the sequences on the databases, interestingly, the cloned gene product was predicted to consist of AlgL (alginate lyase L)-like and heparinase-like protein domain. The MJ-3 alginate lyase gene shared below 27.0% sequence identity with exolytic alginate lyase of Sphingomonas sp. A1. The optimal pH and temperature for the recombinant MJ-3 alginate lyase were 6.5 and 50°C, respectively. The final degradation products of alginate oligosaccharides were analyzed by electrospray ionization mass spectrometry and proved to be alginate monosaccharides. Based on the results, the recombinant alginate lyase from Sphingomonas sp. MJ-3 is regarded as an oligoalginate lyase that can degrade oligoalginate and alginate into alginate monosaccharides.

The purpose of this study was to quantify and identify the airborne microbial contamination in Umbria Sawmills. In this paper we reported the preliminary results of our analysis. Microbial contaminants (fungi and bacteria) were assessed with passive (IMA Standard) and active (SAS microbial sampler) methods. There were significant differences of bacterial and/or fungal CFU/m3 values between the outdoor and indoor environments during the normal sawmills activity. Staphylococcus, Sphingomonas, Pasteurella, were the most predominant bacteria. The most predominant isolated fungi belong to Cladosporium, Penicillium, Alternaria and Aspergillus genus.

In the present paper, the effects of four factors, each at three levels, on biodegradation of phenanthrene, a 3-ring PAH, in contaminated mangrove sediment slurry were investigated using the orthogonal experimental design. The factors and levels were (i) sediment types (clay loam, clayey and sandy); (ii) different inoculums (Sphingomonas sp., a mixture of Sphingomonas sp. and Mycobacterium sp., and without inoculum); (iii) presence of other PAHs (fluorene, pyrene, and none); and (iv) different salinities (5, 15 and 25 ppt). Variance analysis based on the percentages of Phe biodegradation showed that the presence of other PAHs had little effect on phenanthrene biodegradation. The kinetics of phenanthrene biodegradation in all experiments was best fitted by the first order rate model. The highest first order rate constant, k value was 0.1172 h−1 with 97% Phe degradation; while the lowest k value was 0.0004 and phenanthrene was not degraded throughout the 7-d experiment. The p values of k for the four factors followed the same trend as that for the biodegradation percentage. Difference analysis revealed that optimal phenanthrene biodegradation would take place in clay loam sediment slurry at low salinity (5 to 15 ppt) with the inoculation of both Sphingomonas sp. and Mycobacterium sp.

With the aid of analysis software (Minitab 14.0), the formulation of pure culture in Mineral Salts Medium (MSM) can be optimized for several responses and the best formulation can be obtained. The influence of the different mixtures of three strains in the pure culture in MSM on the flavor components in decolorization of Methyl Red (with initial total cell density fixed at OD600 = 1 and in addition of 750 ppm of dye) was studied using equilateral triangle diagram and mixture experimental design to assess color and COD removal during species evolution. The regression model on microorganism composition and main metabolites was established. The results suggested that the highest predictable specific decolorization rate and Chemical Oxygen Demand (COD) were 77.97 and 93.77%. Based on these, the response values that satisfied all expectations were optimized, and the optimal composition of the mixed consortium for the dedolorization and COD removal were (Sphingomonas paucimobilis 45.20%, ...

A polyphasic approach was used to characterize an aerobic, Gram-stain-negative, rod-shaped bacterium (designed as strain CC-MHH0539T) isolated from the chopped tuber of taro (Colocasia esculanta) in Taiwan. Strain CC-MHH0539T was able to grow at 15-30 °C (optimum, 25 °C), at pH 6.0-9.0 (optimum, 7.0) and with 0-1 % (w/v) NaCl. Strain CC-MHH0539T showed highest 16S rRNA gene sequence similarity to Sphingomonas laterariae LNB2T (96.8 %), Sphingobium boeckii 469T (96.5 %), Sphingomonas faucium E62-3T (96.4 %) and Sphingosinicella vermicomposti YC7378T (96.2 %) and <96.1 % similarity to other sphingomonads. Strain CC-MHH0539T was found to cluster mainly with the clade that accommodated members of the genus Sphingomonas. The dominant cellular fatty acids were C16 : 0, C16 : 1ω5c, C14 : 0 2-OH, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two sphingoglyco...

The alkaline phosphatase (AP) is a bi-metalloenzyme of potential applications in biotechnology and bioremediation, in
which phosphate monoesters are nonspecifically hydrolysed under alkaline conditions to yield inorganic phosphate. The
hydrolysis occurs through an enzyme intermediate in which the catalytic residue is phosphorylated. The reaction, which also
requires a third metal ion, is proposed to proceed through a mechanism of in-line displacement involving a trigonal
bipyramidal transition state. Stabilizing the transition state by bidentate hydrogen bonding has been suggested to be the
reason for conservation of an arginine residue in the active site. We report here the first crystal structure of alkaline
phosphatase purified from the bacterium Sphingomonas. sp. Strain BSAR-1 (SPAP). The crystal structure reveals many
differences from other APs: 1) the catalytic residue is a threonine instead of serine, 2) there is no third metal ion binding
pocket, and 3) the arginine residue forming bidentate hydrogen bonding is deleted in SPAP. A lysine and an aspargine
residue, recruited together for the first time into the active site, bind the substrate phosphoryl group in a manner not
observed before in any other AP. These and other structural features suggest that SPAP represents a new class of APs.
Because of its direct contact with the substrate phosphoryl group, the lysine residue is proposed to play a significant role in
catalysis. The structure is consistent with a mechanism of in-line displacement via a trigonal bipyramidal transition state. The
structure provides important insights into evolutionary relationships between members of AP superfamily.

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated sediment is an attractive remediation technique and its success depends on biodegradation kinetics, and the optimal condition for the PAH-degrading isolates; however, information on this aspect is still scarce. The effects of multi-factors on biodegradation of phenanthrene, a 3-ring model PAH, in contaminated sediment slurry by Sphingomonas sp. a bacterial strain isolated from surface mangrove sediment, were investigated using the orthogonal experimental design (form L16(45)). The most significant factors were salinity and inoculum size, while the effects of phenanthrene concentrations, nutrient addition and temperatures were insignificant. The optimal biodegradation condition in contaminated mangrove sediment slurry was 30 °C, 15 ppt salinity, a carbon/nitrogen ratio of 100:1 (the background ratio in sediment) and an inoculum size of 106 most probable number g−1 sediment. The phenanthrene biodegradation could be best described by the first order rate model, C = C0e−kt, where k (the rate constant) is equaled to 0.1185, under the optimal condition. The kinetic model was verified and its validity in predicting biodegradation by Sphingomonas sp. at various phenanthrene concentrations was proved by experimental data.