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PubMed2003

Saccharin as a sole source of carbon and energy for Sphingomonas xenophaga SKN.

A bacterium, strain SKN, that was able to utilize saccharin as the sole source of carbon and energy for aerobic growth, was enriched and isolated from communal sewage. The isolate was identified as a strain of Sphingomonas xenophaga. Saccharin was quantitatively converted to cell material, sulfate, ammonium and, presumably, CO(2). The specific rate of saccharin-dependent oxygen uptake during growth reached a maximum before the culture entered the stationary phase and then fell to undetectable levels. Saccharin was degraded only in the presence of molecular oxygen. Catechol was detected as an intermediate during degradation of saccharin in whole cells and catechol 1,2-dioxygenase was expressed inducibly during growth with saccharin. There was an apparent requirement of 2 mol O(2)/mol saccharin to remove the substituents on the ring and to cleave the ring. We presume that S. xenophaga SKN synthesizes a multi-component saccharin dioxygenase that simultaneously cleaves off both vicinal substituents from the aromatic ring to yield catechol and the undefined precursor of CO(2) as well as sulfate and ammonium ions.

Aerobiosis↗
PubMed2004

Degradation of aromatic hydrocarbons by Sphingomonas paucimobilis strain EPA505.

To determine the substrate range capability of Sphingomonas paucimobilis strain EPA505, a number of aromatic compounds were tested as potential growth substrates. Strain EPA505 grew on phenanthrene, naphthalene, fluoranthene, toluene, benzoic acid, 2,3- and 3,4-dihydroxybenzoic acids, 1-chloro-2,4-dinitrobenzene, anthracene, 2-hydroxy-3-naphthoic acid and 1-hydroxy- 2-naphthoic acid, salicylic acid, and catechol. Strain EPA505 was unable to grow on coumarine 3-carboxylic acid, naphthalene dicarboxylic acid, acenaphthene, chrysene, pyrene, benzo[b]fluoranthene, and fluorene. Catabolic products were not detected or identified when the bacterium was incubated with coumarine 3-carboxylic acid, naphthalene dicarboxylic acid, acenaphthene, chrysene, or benzo[b]fluoranthene. Dihydroxypyrene, the ortho ring fission product of pyrene, and 10-hydroxy-1- phenanthroic acid were detected when the bacterium was incubated with pyrene. The open rings of benzo[b]fluoranthene, hydroxyacephenanthroic acid, hydroxyacephenanthrene, and phenanthrene anhydride, catabolites of benzo[b]fluoranthene degradation, were detected with Tn5 mutants of EPA505. With strain EPA505, both 9-fluorenone and an open ring fission product accumulated during incubation with fluorene. Other catabolites beyond the open ring of fluorene were detected, specifically dihydroxyfluorene, hydroxy-9-fluorenone, dihydroxy-9-fluorenone, hydroxyindane, and a putative glutathione-conjugated benzylanhydride. Benzylanhydride appeared to be a final end product of fluorene degradation by strain EPA505.

Molecular Weight↗
PubMed2003

Life under nutrient limitation in oligotrophic marine environments: an eco/physiological perspective of Sphingopyxis alaskensis (formerly Sphingomonas alaskensis).

The oceans of the world are nutrient-limited environments that support a dynamic diversity of microbial life. Heterotrophic prokaryotes proliferate in oligotrophic regions and affect nutrient transformation and remineralization thereby impacting directly on the all marine biota. An important challenge in studying the microbial ecology of oligotrophic environments has been the isolation of ecologically important species. This goal has been recognized not only for its relevance in defining the dynamics of community composition, but for enabling physiological studies of competitive species and inferring their impact on the microbial food web. This review describes the successful isolation attempts of the ultramicrobacterium, Sphingopyxis alaskensis (formerly described as Sphingomonas alaskensis) using extinction dilution culturing methods. It then provides a comprehensive perspective of the unique physiological and genetic properties that have been identified that distinguish it from typical copiotrophic species. These properties are described through studies of the growth phase and growth rate control of macromolecular synthesis, stress resistance and global gene expression (proteomics). We also discuss the importance of integrating ecological and physiological approaches for studying microorganisms in marine environments.

Alaska↗
PubMed2002

Use of a two-phase partitioning bioreactor for degrading polycyclic aromatic hydrocarbons by a Sphingomonas sp.

A two-phase partitioning bioreactor (TPPB) utilizing the bacterium Sphingomonas aromaticivorans B0695 was used to degrade four low molecular weight (LMW) polycyclic aromatic hydrocarbons (PAHs). The TPPB concept is based on the use of a biocompatible, immiscible organic solvent in which high concentrations of recalcitrant substrates are dissolved. These substances partition into the cell-containing aqueous phase at rates determined by the metabolic activity of the cells. Experiments showed that the selected solvent, dodecane, could be successfully used in both solvent extraction experiments (to remove PAHs from soil) and in a TPPB application. Further testing demonstrated that solvent extraction from spiked soil was enhanced when a solvent combination (dodecane and ethanol) was used, and it was shown that the co-solvent did not significantly affect TPPB performance. The TPPB achieved complete biodegradation of naphthalene, phenanthrene, acenaphthene and anthracene at a volumetric consumption rate of 90 mg l(-1) h(-1) in approximately 30 h. Additionally, a total of 20.0 g of LMW PAHs (naphthalene and phenanthrene) were biodegraded at an overall volumetric rate of 98 mg l(-1) h(-1) in less than 75 h. Degradation rates achieved using the TPPB and S. aromaticivorans B0695 are much greater than any others previously reported for an ex situ PAH biodegradation system operating with a single species.

Biodegradation, Environmental↗
PubMed2002

Biotransformation of p-xylene and 2,6-dimethylnaphthalene by xylene monooxygenase cloned from a Sphingomonas isolate.

Sphingomonas strain ASU1 was isolated from an industrial wastewater bioreactor and grew on 2,6-dimethylnaphthalene (2,6-DMN) as the sole carbon/energy source. The genes for a xylene monooxygenase were cloned from strain ASU1. Expression of the ASU1 xylene monooxygenase was compared to expression of the pWWO xylene monooxygenase in Escherichia coli. Both monooxygenases transformed p-xylene and 2,6-DMN by initially hydroxylating one methyl group. In addition, the ASU1 monooxygenase also hydroxylated the second methyl group on p-xylene and 2,6-DMN whereas the pWWO monooxygenase hydroxylated the second methyl group only on p-xylene. Endogenous E. coli enzymes contributed to further oxidation of the resulting aromatic alcohols to form aromatic carboxylates.

Chromosome Mapping↗
PubMed2003

Cloning and sequence analysis of the ces10 gene encoding a Sphingomonas paucimobilis esterase.

The ces10 gene of the gellan gum-producing strain Sphingomonas paucimobilis ATCC 31461 was cloned and sequenced. Multi-sequence alignment of the deduced protein indicated that Ces10 belongs to the serine hydrolase family with a potential catalytic triad comprising Ser(153) (within the G-X-S-X-G consensus sequence), His(75) and Asp(125). The mixed block results obtained following pattern search and the low identities detected in a BLAST analysis indicate that Ces10 is significantly different from other characterised bacterial esterases/lipases. Nevertheless, the Ces10 amino acid sequence showed 45% similarity with Rhodococcus sp. heroin esterase and 48% with Bacillus subtilis p-nitrobenzyl esterase. Ces10, with a predicted molecular mass of 30,641 Da, was overproduced in Escherichia coli and purified to homogeneity in a histidine-tagged form. Enzyme assays using p-nitrophenyl-esters (p-NP-esters) with different acyl chain-lengths as the substrate confirmed the anticipated esterase activity. Ces10 exhibited a marked preference for short-chain fatty acids, yielding the highest activity with p-NP-propionate (optimal pH 7.4, optimal temperature 37 degrees C).

Amino Acid Sequence↗
PubMed2003

Purification and characterization of arylsulfatase from Sphingomonas sp. AS6330.

Arylsulfatase was purified from Sphingomonas sp. AS6330 through ionic exchange, hydrophobic- and gel-chromatographies. The purity increased 12,800-fold with approximately 19.1% yield against cell homogenate. The enzyme was a monomeric protein with apparent molecular weight of 62 kDa as determined by sodium dodecylsulfate-polyacrylamide gel electrophoresis, and 41 kDa as determined by gel filtration. The enzyme had optimum reaction conditions for hydrolysis of sulfate ester bonds in agar and p-nitrophenyl sulfate (NPS) at pH 7.0 and 45 degrees C, with a specific activity of 3.93 and 97.2 U, respectively. The enzyme showed higher activity towards agar than other sulfated marine polysaccharides such as porphyran, fucoidan and carrageenan. The K(m) and V(max) of the enzyme for hydrolysis of NPS were 54.9 microM and 113 mM/min, respectively. With reaction of 200 g agar with 100 U arylsulfatase for 8 h at 45 degrees C, gel strength increased 2.44-fold, and 97.7% of the sulfate in the agar was hydrolyzed.

Agar↗
PubMed2005

The degradation of alpha-quaternary nonylphenol isomers by Sphingomonas sp. strain TTNP3 involves a type II ipso-substitution mechanism.

The degradation of radiolabeled 4(3',5'-dimethyl-3'-heptyl)-phenol [nonylphenol (NP)] was tested with resting cells of Sphingomonas sp. strain TTNP3. Concomitantly to the degradation of NP, a metabolite identified as hydroquinone transiently accumulated and short-chain organic acids were then produced at the expense of hydroquinone. Two other radiolabeled isomers of NP, 4(2',6'-dimethyl-2'-heptyl)-phenol and 4(3',6'-dimethyl-3'-heptyl)-phenol, were synthesized. In parallel experiments, the 4(2',6'-dimethyl-2'-heptyl)-phenol was degraded more slowly than the other isomers of NP by strain TTNP3, possibly because of effects of the side-chain structure on the kinetics of degradation. Alkylbenzenediol and alkoxyphenol derivatives identified as metabolites during previous studies were synthesized and tested as substrates. The derivatives were not degraded, which indicated that the mineralization of NP does not proceed via alkoxyphenol as the principal intermediate. The results obtained led to the elucidation of the degradation pathway of NP isomers with a quaternary alpha-carbon. The proposed mechanism is a type II ipso substitution, leading to hydroquinone and nonanol as the main metabolites and to the dead-end metabolites alkylbenzenediol or alkoxyphenol, depending on the substitution at the alpha-carbon of the carbocationic intermediate formed.

Biodegradation, Environmental↗
PubMed2005

Characterization of Sphingomonas aldehyde dehydrogenase catalyzing the conversion of various aromatic aldehydes to their carboxylic acids.

An aldehyde dehydrogenase gene, designated phnN, was isolated from a genome library of the 1,4-dimethylnaphthalene-utilizing soil bacterium, Sphingomonas sp. 14DN61. Escherichia coli expressing the phnN gene converted 1,4-dihydroxymethylnaphthalene to 1-hydroxymethyl-4-naphthoic acid. The putative amino acid sequence of the phnN gene product had 31-42% identity with those of NAD(+)-dependent short-chain aliphatic aldehyde dehydrogenases and a secondary alcohol dehydrogenase. The NAD(P)(+)-binding site and two consensus sequences involved in the active site for aldehyde dehydrogenase are conserved among these proteins. The PhnN enzyme purified from recombinant E. coli showed broad substrate specificity towards various aromatic aldehydes, i.e., 1- and 2-naphaldehydes, cinnamaldehyde, vanillin, syringaldehyde, benzaldehyde and benzaldehydes substituted with a hydroxyl, methyl, methoxy, chloro, fluoro, or nitro group were converted to their corresponding carboxylic acids. Interestingly, E. coli expressing phnN was able to biotransform a variety of not only aromatic aldehydes, but also aromatic alcohols to carboxylic acids.

Alcohols↗
PubMed2006

A gene linB2 responsible for the conversion of beta-HCH and 2,3,4,5,6-pentachlorocyclohexanol in Sphingomonas sp. BHC-A.

Commercial formulations of hexachlorocyclohexane (HCH) consist of a mixture of four isomers: alpha, beta, gamma, and delta. All four isomers are toxic and recalcitrant pollutants. beta-HCH is more problematic due to its longer persistence in the environment. Sphingomonas sp. BHC-A was able to degrade not only alpha-, gamma-, and delta-HCH but also beta-HCH. To clone a gene responsible for the degradation of beta-HCH, a Tn5 mutation was introduced into BHC-A, and one mutant BHC-A45 defective in beta-HCH degradation was selected. Sequencing analysis showed this mutant had a Tn5 insertion at the site of one haloalkane dehalogenase gene, designated linB2. linB2 was overexpressed in Escherichia coli and the 32-kDa product LinB2 showed the conversion activity of not only beta-HCH to beta-2,3,4,5,6-pentachlorocyclohexanol (beta-PCHL) but also beta-PCHL to beta-2,3,5,6-tetrachloro-1,4-cyclohexanediol.

Cloning, Molecular↗
PubMed2002

Recycle use of Sphingomonas sp. CDH-7 cells for continuous degradation of carbazole in the presence of MgCl2.

Carbazole (CA) is a heterocyclic nitrogen compound contained in the crude petroleum oil and recalcitrant to removal through the refinery processes. For development of the efficient CA-degradation bioprocess, conditions for the recycle use of Sphingomonas sp. CDH-7 resting cells were examined. When the resting cells (O.D.(660) 3.3) were shaken in 50 m M K2HPO4-KH2PO4 buffer (pH 7.0) containing CA 1000 mg/L, CA 880 mg/L was degraded within 3 h, but thereafter the activity decreased markedly. However, the activity was found to be restored to the initial level after the shaking treatment for 3 h in CA-free medium solution or in the buffer containing 20 m M MgCl2. Although the CA-degradation activity of CDH-7 resting cells was lost after 3 h of shaking in the buffer containing 100 m M EDTA, it was restored through the shaking treatment for 3 h in the buffer containing 20 m M MgCl2. When CA was periodically added eight times at a concentration of 100 mg/L (0.599 m M) to the reaction mixture containing the resting cells, CA 778 mg/L (4.66 m M) was continuously degraded within 35 h by the recycle use of resting cells, with the restoration treatment after each CA-degradation reaction by the resting cells.

Biodegradation, Environmental↗
PubMed2005

Degradation of chlorophenols using pentachlorophenol-degrading bacteria Sphingomonas chlorophenolica in a batch reactor.

Chlorophenols are common environmental contaminants that have been used as the major component in wide-spectrum biocides in industry and agriculture. Many chlorophenols tend to persist in the environment and may become public health hazards. This research studied the ability of the pentachlorophenol (PCP)-degrading bacterium Sphingomonas chlorophenolica to degrade and dechlorinate other chlorophenols. In addition, the characteristics of S. chlorophenolica were also investigated. When S. chlorophenolica cells were preincubated with PCP, the lag phase PCP degradation periods became shorter and the PCP concentrations that could be removed became higher. S. chlorophenolica was able to completely degrade 2,3,6-trichlorophenol (2,3,6-TCP), 2,4,6-trichlorophenol (2,4,6-TCP), 2,3,4,6-tetrachlorophenol (2,3,4,6-TeCP), and PCP within 38.1, 15.1, 11.8, and 11.8 h, and to release concentrations of 50.1, 60.9, 63.7, and 58.5 mg/L chloride at the same period of time. In the presence of supplementary carbon sources, the PCP removal efficiency increased with the presence of glucose or pyruvate. However, the removal efficiency of 75 mg/L 2,4-dichlorophenol did not increase with supplemental carbon sources.

Biodegradation, Environmental↗
PubMed2005

Cloning, sequence analysis, and expression of the gene encoding Sphingomonas paucimobilis FP2001 alpha-L -rhamnosidase.

The gene (rhaM) encoding the alpha-L-rhamnosidase of Sphingomonas paucimobilis FP2001 was cloned, sequenced, and expressed in Escherichia coli. The rhaM consisted of 3,354 nucleotides and had a promoter and Shine-Dalgarno sequences typical in bacteria. The rhaM encoding a protein (Rham) deducted from the sequence consisted of 1,117 amino acids and had a putative signal peptide of 25 amino acids. Rham has no similarity to other known rhamnosidases. Rham has a sugar-binding domain of glycoside hydrolase family 2, which has been well conserved in beta-glucuronidase, beta-mannosidase, and beta-galactosidase, in its C-terminal region. Rham is possibly a member of a new bacterial subfamily in glycoside hydrolase family 78 (alpha-L-rhamnosidase). RT-PCR analysis of rhaM mRNA indicated that the induction of alpha-L-rhamnosidase by the addition of L-rhamnose occurred on the transcriptional level.

Amino Acid Sequence↗
PubMed2000

Enhanced degradation of hexachlorocyclohexane isomers by Sphingomonas paucimobilis.

Hexachlorocyclohexane (HCH) has been banned for use in technologically advanced countries; however, it is still in use in tropical countries like India. Earlier we reported the degradation of HCH isomers by Sphingomonas paucimobilis within 12 days of incubation. Here we report the role of different factors that could enhance the degradation rate of HCH isomers. We found that an increase in the cell number from 10(2) to 10(8) cells/ml resulted in an increased degradation rate of HCH isomers viz. alpha, beta, gamma, and delta-HCH. While alpha-HCH and gamma-HCH disappeared completely from the medium within 3 days of incubation, a maximum of only 90% and 85% degradation was observed for beta and delta-HCH, respectively. We have also observed that adapted cultures degraded HCH isomers more efficiently than did the normal cultures.

Biodegradation, Environmental↗
PubMed2003

Characterization of the ugpG gene encoding a UDP-glucose pyrophosphorylase from the gellan gum producer Sphingomonas paucimobilis ATCC 31461.

The ugpGgene, which codes for a UDP-glucose pyrophosphorylase (UGP) (or glucose-1-phosphate uridylyltransferase; EC 2.7.7.9) in Sphingomonas paucimobilis ATCC 31461, was cloned and sequenced. This industrial strain produces the exopolysaccharide gellan, a new commercial gelling agent, and the ugpG gene may convert glucose-1-phosphate into UDP-glucose in the gellan biosynthetic pathway. The ugpG gene is capable of restoring the capacity of an Escherichia coli galU mutant to grow on galactose by functional complementation of its deficiency for UDP-glucose pyrophosphorylase activity. As expected, the predicted gene product shows strong homology to UDP-glucose pyrophosphorylases from several bacterial species. The N-terminal region of UgpG exhibits the motif GXGTRXLPXTK, which is highly conserved among bacterial XDP-sugar pyrophosphorylases, and a lysine residue (K(192)) is located within a VEKP motif predicted to be essential for substrate binding or catalysis. UgpG was purified to homogeneity as a heterologous fusion protein from crude cell extracts prepared from IPTG-induced cells of E. coli, using affinity chromatography. Under denaturing conditions, the fusion protein S-UgpG-His(6) migrated with an estimated molecular mass of 36 kDa [corresponding to the predicted molecular mass of native UgpG (31.2 kDa) plus 5 kDa for the S and histidine tags). Kinetic analysis of UgpG in the reverse reaction (pyrophosphorolysis) showed a typical Michaelis-Menten substrate saturation pattern. The apparent K(m) and V(max) values estimated for UDP-glucose were 7.5 microM and 1275 micromol/min/g.

Amino Acid Motifs↗
PubMed2000

Physiological and genetic comparison of two aromatic hydrocarbon-degrading Sphingomonas strains.

Sphingomonas yanoikuyae strain B1 is able to degrade a wider range of aromatic hydrocarbons than S. paucimobilis strain TNE12 can degrade. Various culture techniques were used to corroborate that B1 used m-xylene, biphenyl, toluene, naphthalene, and phenanthrene as sole carbon and energy sources. In contrast, TNE12 could not mineralize m-xylene, biphenyl, toluene, or naphthalene. However, fluoranthene served as carbon and energy source for TNE12 but not B1. Southern blots were performed using the cloned genomic region (approximately 23 kb) containing the degradative genes for the upstream pathways for biphenyl and m-xylene and a TOL plasmid-type meta operon from B1 as a probe against the KpnI restriction-digested total DNA of TNE12. This 23 kb probe hybridized to three KpnI-digested fragments of TNE12 DNA; thus significant homology existed between the aromatic hydrocarbon-degrading genes of B1 and TNE12. Further work with smaller probes revealed, however, that TNE12 DNA fragments did not hybridize with the probe containing the genes encoding for xylene monooxygenase and part of an aromatic dioxygenase. A recombinant plasmid, which contains only the genes for xylene monooxygenase, is able to complement TNE12 on m-xylene. These genes are, therefore, probably missing from TNE12. Hence, TNE12 cannot use monocyclic aromatics whereas B1 can. Pulsed field gel electrophoresis coupled with Southern blotting revealed that the aromatic degradative genes were on an approximately 240 kb plasmid of TNE12; the same genes in B1 are known to be chromosomal.

Biodegradation, Environmental↗
PubMed2003

Potential of a new biotreatment: Sphingomonas cloacae S-3T degrades nonylphenol in industrial wastewater.

Sphingomonas cloacae S-3(T), a nonylphenol (NP)-degrading bacterium, was evaluated for its utility in the remediation of NP-contaminated wastewater. In flask-scale experiments, S-3(T) cells immobilized on porous polypropylene carriers (beads) efficiently degraded NP to concentrations routinely measured in aquatic environments [a few parts per billion (ppb), or micrograms per liter). Therefore, we constructed and evaluated a laboratory-scale wastewater treatment system with a 3-l carrier-filled column. The system worked properly and consistently removed several hundred ppb of NP to ecologically safe concentrations of less than 10 ppb in industrial wastewater without the addition of nutrients. The effect of wastewater pH on the system performance was also evaluated; and wastewater samples with pH values of 6 or 8 were treated efficiently without pH adjustment. These results suggest that a biotreatment system using NP-degrading bacteria can efficiently remediate industrial wastewater and contribute to the preservation of aquatic environments.

Biomass↗
PubMed2006

Improvement in production and quality of gellan gum by Sphingomonas paucimobilis under high dissolved oxygen tension levels.

The effect of agitation rate and dissolved oxygen tension (DOT) on growth and gellan production by Sphingomonas paucimobilis was studied. Higher cell growth of 5.4 g l(-1) was obtained at 700 rpm but maximum gellan (15 g l(-1)) was produced at 500 rpm. DOT levels above 20% had no effect on cell growth but gellan yield was increased to 23 g l(-1 )with increase in DOT level to 100%. Higher DOT levels improved the viscosity and molecular weight of the polymer with change in acetate and glycerate content of the polymer.

Oxygen↗