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Evidence of histidine coordination to the catalytic ferrous ion in the ring-cleaving 2,2',3-trihydroxybiphenyl dioxygenase from the dibenzofuran-degrading bacterium Sphingomonas sp. strain RW1.

The 1H NMR spectra of an aromatic ring-cleaving extradiol dioxygenase, 2,2',3-trihydroxybiphenyl dioxygenase of the dibenzofuran-degrading bacterium Sphingomonas sp. strain RW1, are reported. In the catalytically active reduced form of the monomeric enzyme (MW = 32 kDa), three broad strongly downfield shifted signals were observed, two of which disappeared in D2O solution. Their shifts and linewidths are consistent with ring NH and meta-like protons of coordinated histidines. These signals show strong sensitivity to the presence of the substrate. The oxidized form of the enzyme shows no hyperfine shifted signals. It is suggested that the high spin Fe(II) ion present in the active form of the enzyme is coordinated by at least two histidines. This is the first report of hyperfine shifted NMR signals being detected for an extradiol dioxygenase.

Benzofurans↗

Novel polypeptides induced by the insecticide lindane (gamma-hexachlorocyclohexane) are required for its biodegradation by a Sphingomonas paucimobilis strain.

When exposed to the potent insecticide gamma-hexachlorocyclohexane or lindane, a Sphingomonas paucimobilis strain rapidly synthesized 7 novel polypeptides and concomitantly gained the ability to degrade lindane. Synthesis of these proteins was switched-off subsequent to the disappearance of lindane from the medium. Treatments which induced the synthesis of identical proteins also conferred on cells the ability to degrade lindane. In contrast, cells blocked in protein synthesis could not be induced to degrade lindane. The close correspondence observed between expression of lindane-induced proteins and gamma-hexachlorocyclohexane catabolism strongly implicates these novel proteins in lindane biodegradation.

Biodegradation, Environmental↗

Crystal structure of alginate lyase A1-III from Sphingomonas species A1 at 1.78 A resolution.

The three-dimensional structure of alginate lyase A1-III (ALYIII) from a Sphingomonas species A1 was determined by X-ray crystallography. The enzyme was crystallized by the hanging-drop vapour-diffusion method in the presence of 49% ammonium sulfate at 20 degrees C. The crystals are monoclinic and belong to the space group C2 with unit cell dimensions of a=49.18 A, b=93.08 A, c=82.10 A and beta=104.12 degrees. There was one molecule of alginate lyase in the asymmetric unit of the crystal. The diffraction data up to 1. 71 A were collected with Rsymof 5.0%. The crystal structure of ALYIII was solved by the multiple isomorphous replacement method and refined at 1.78 A resolution using X-PLOR with a final R -factor of 18.0% for 10.0 to 1.78 A resolution data. The refined model of ALYIII contained 351 amino acid residues, 299 water molecules and two sulfate ions. The three-dimensional structure of ALYIII was abundant in helices and had a deep tunnel-like cleft in a novel (alpha6/alpha5)-barrel structure, which was similar to the (alpha6/alpha6)-barrel found in glucoamylase and cellulase. This structure presented the possibility that alginate molecules might penetrate into the cleft to interact with the catalytic site of ALYIII.

Alginates↗

Cloning and sequence analysis of a novel insertion element from plasmids harbored by the carbofuran-degrading bacterium, Sphingomonas sp. CFO6.

Sphingomonas sp. CFO6 (a member of the alpha group of Proteobacteria) was isolated from a Washington soil by enrichment on the insecticide carbofuran as a sole source of carbon and energy. This strain has been shown to harbor five plasmids, at least some of which are required for catabolism of carbofuran. Rearrangements, deletions, and loss of individual plasmids resulting in the loss of the carbofuran-degrading phenotype were observed following treatment with heat or introduction of Tn5. Several putative insertion sequence elements of different sizes were cloned from these plasmids by trapping in pUCD800, a positive selection vector for isolation of transposable elements. Three of the most common putative IS elements (designated IS1412, IS1487, and IS1488) in the clone library were of different sizes and cross-hybridize with each other. An element hybridizing with IS1412, IS1487, and IS1488 was mobilized during growth of CFO6 at 42 degrees C and inserted into one of CFO6's plasmids (pCFO4), corresponding to a deletion in the plasmid and a loss of catabolic function. IS1412 was completely sequenced and its sequence analyzed. IS1412 is 1656 bp in length and possesses terminal partially matched inverted repeats of unequal length (17 and 18 bp). In addition, IS1412 contains an open reading frame which encodes a putative transposase with significant homology to the putative transposases of IS1380 from Acetobacter pasteurianus, HRS1 from Bradyrhizobium japonicum, and IS1247 from Xanthobacter autotrophicus. These related IS elements form part of a family of common IS elements distributed among members of the alpha group of the Proteobacteria.

Amino Acid Sequence↗

Purification of two isofunctional hydrolases (EC 3.7.1.8) in the degradative pathway for dibenzofuran in Sphingomonas sp. strain RW1.

Sphingomonas sp. strain RW1, when grown in salicylate-salts medium, synthesized the enzymes for the degradation of dibenzofuran. The reaction subsequent to meta cleavage of the first benzene ring was found to be catalyzed by two isofunctional hydrolases, H1 and H2, which were purified by chromatography on anion exchange, hydrophobic interaction and gel filtration media. Each enzyme was able to hydrolyze 2-hydroxy-6-oxo-6-(2-hydroxyphenyl)hexa-2,4-dienoate and 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate to produce salicylate and benzoate, respectively. SDS/PAGE of each purified enzyme showed a single band of M(r) 31,000 (H1) or 29,000 (H2). The N-terminal amino acid sequences of the two proteins showed 50% homology.

Bacteroidetes↗

Phototrophicity and genomic composition in plant-associated Sphingomonas faeni strains.

Solar radiation impacts most life forms on Earth as an energy source or a regulatory signal. Still, relatively little is known about phototrophic potential and strategies of environmental bacteria beyond cyanobacteria. This study explores the phototrophy related genomic diversity of Sphingomonas faeni strains from boreal, sub-arctic and arctic regions. We analyzed the genomes of 25 plant-associated S. faeni strains isolated from Vaccinium myrtillus, Oxyria digyna, V. vitis-idaea, and Bistorta vivipara, along with a reference S. faeni genome MA-Olki. The strains showed diversity both in overall genome level but also in phototrophic capabilities: Seven strains were identified as aerobic anoxygenic phototrophic bacteria with a complete photosynthesis gene cluster, 16 strains contained xanthorhodopsin genes, and three strains were non-phototrophic, possessing no aerobic anoxygenic phototrophic or xanthorhodopsin genes. Aerobic anoxygenic phototrophic strains were found exclusively in Vaccinium hosts. O. digyna contained only xanthorhodopsin containing strains and B. vivipara showed xanthorhodopsin genes and one non-phototrophic strain. V. vitis-idaea hosted strains for all three different phototrophy categories. Phylogenetic analyses showed aerobic anoxygenic phototrophic positive strains forming a tight phylogenetic group. Xanthorhodopsin strains and non-phototrophic strains clustered into three different subgroups. Phototrophic strains had more photoreceptors. Aerobic anoxygenic phototrophic strains encoded two 5-aminolevulinic acid synthase isoenzymes, one from a hemT-like gene within the photosynthesis gene cluster and one from a hemA-like gene elsewhere in the genome. Our genomic analysis reveals substantial diversity in phototrophic potential among strains of a single bacterial species isolated from different host plants, possibly reflecting the distinct environmental cues each strain encountered.

aerobic anoxygenic phototrophy↗

Structure and physical properties of the extracellular polysaccharide PS-P4 produced by Sphingomonas paucimobilis P4 (DSM 6418).

A new strain, Sphingomonas paucimobilis P4 (DSM 6418), was found during a screening programme for exopolysaccharide-producing bacteria. The highly viscous fermentation broth yields a polysaccharide (up to 10 kg/m3), named PS-P4, and shows thixotropic flow behaviour. In the presence of phosphate ions, PS-P4 forms aqueous gels after heating and cooling at alkaline pH. After isolation and purification of the exopolysaccharide, structural analysis by 1D and 2D 1H NMR spectroscopy and mass spectrometry was performed. The deacylated exopolysaccharide has the following repeating trisaccharide structure:-->4)-beta-D-Glcp-(1-->4)-alpha-L-Rhap-(1-->3)-beta-D- Glcp(1-->Additionally, the presence of ester-bound acetic acid, D-glyceric acid, and (R)-3-hydroxybutyric acid in the native polysaccharide was demonstrated.

Carbohydrate Sequence↗

Chemical structure of glycosphingolipids isolated from Sphingomonas paucimobilis.

Two novel glycosphingolipids were isolated from Sphingomonas paucimobilis and their structures were completely elucidated. The glycosyl portion of the glycosphingolipid consists of an alpha-D-Manp-[1----2)-alpha-D-Galp-(1----6)-alpha-D-GlcpN-(1 ----4)-alpha-D- GlcpA-R tetrasaccharide. The hydrophobic residue R was found to be heterogeneous with respect to the dihydrosphingosine residue. Erythro-1,3-dihydroxy-2-amino-octadecane and erythro-1,3-dihydroxy-2-amino-cis-13,14-methyleneoctadecane were identified in comparable amounts. Both dihydrosphingosine derivatives were quantitatively substituted by an (S)-2-hydroxymyristic acid in amide linkage.

Glycosphingolipids↗

Sequence and expression of an isocitrate dehydrogenase-encoding gene from a polycyclic aromatic hydrocarbon oxidizer, Sphingomonas yanoikuyae B1.

An 18.5-kb DNA fragment was cloned from Sphingomonas yanoikuyae (Sy) B1 (previously Beijerinckia B1). Analysis of a 4.3-kb sequence revealed an isocitrate dehydrogenase (Idh)-encoding gene (idhA), an unidentified open reading frame (ORF) and a partial glucosamine synthetase-encoding ORF (glmS). As in a number of bacteria, Tn7 insertion was found specifically at a site past the stop codon of glmS. The predicted 406-amino-acid sequence of IdhA shows, for the first time, an extensive sequence identity (66%) with an eukaryotic NADP+-specific Idh. The idhA gene was expressed in Escherichia coli. Identical restriction fragments carrying idhA were found in B1, Sy IFO15102 and Sy Q1 (formerly S. paucimobilis Q1), indicating a well-conserved idh gene.

Amino Acid Sequence↗

Structural studies of the exocellular polysaccharide from Sphingomonas paucimobilis strain I-886.

The exocellular polysaccharide from Sphingomonas paucimobilis strain I-886 has been studied using methylation analysis, Smith degradation, partial acid hydrolysis, NMR spectroscopy, and mass spectrometry as the principal methods. It is concluded that the repeating unit has the following structure: [formula: see text] The absolute configuration of the uronic acid was deduced from 1H NMR chemical shifts and is most likely D. Some preparations of the polysaccharide also contain phosphate and O-acyl groups which have not been identified or localised.

Carbohydrate Conformation↗

Identification of the catalytic triad in the haloalkane dehalogenase from Sphingomonas paucimobilis UT26.

The haloalkane dehalogenase from Sphingomonas paucimobilis UT26 (LinB) is the enzyme involved in the gamma-hexachlorocyclohexane degradation. This enzyme hydrolyses a broad range of halogenated aliphatic compounds via an alkyl-enzyme intermediate. LinB is believed to belong to the family of alpha/beta-hydrolases which employ a catalytic triad, i.e. nucleophile-histidine-acid, during the catalytic reaction. The position of the catalytic triad within the sequence of LinB was probed by a site-directed mutagenesis. The catalytic triad residues of the haloalkane dehalogenase LinB are proposed to be D108, H272 and E132. The topological location of the catalytic acid (E132) is after the beta-strand six which corresponds to the location of catalytic acid in the pancreatic lipase, but not in the haloalkane dehalogenase of Xanthobacter autotrophicus GJ10 which contains the catalytic acid after the beta-strand seven.

Binding Sites↗

Tracheal colonization with Sphingomonas paucimobilis in mechanically ventilated neonates due to contaminated ventilator temperature probes.

Sphingomonas paucimobilis was isolated from tracheal secretions of a total of 85 mechanically ventilated babies in a neonatal intensive-care unit (NICU) during a two-year-period. None of the neonates developed pneumonia or sepsis. After each increase in the fluctuating number of S. paucimobilis isolates, extra attention was paid to hand hygiene and to the maintenance of the ventilation equipment. This resulted in a reduction of the frequency of isolation each time. Cultures of all liquids in use and of the ventilation equipment were negative on several occasions. Fifteen months after the start of the outbreak, the NICU was moved to another building, and some older ventilation equipment was abandoned. After a period of six weeks without problems, S. paucimobilis was isolated in association with at least four ventilators. A new investigation showed that the ventilator temperature probes were the source of contamination. Once effective sterilization procedures for the temperature probes were introduced no new cases appeared, until a spare ventilator with an unautoclaved temperature probe was accidentally used and this caused contamination of one child. After correction, no further cases have occurred to date. The clonal relatedness of the outbreak isolates from patients and from ventilator temperature probes was documented by fingerprinting with the arbitrarily primed polymerase chain reaction.

DNA Fingerprinting↗

Emergence of Cu(++)-tolerant mutants defective in gellan synthesis in Cu(++)-stressed cultures of Sphingomonas paucimobilis.

Cells defective in gellan synthesis appeared during cultivation of the gellan gum-producing strain Sphingomonas paucimobilis R40 with inhibitory concentrations of copper, supplied as CuCl2. The percentage of less mucoid colonial variants dramatically increased with the increase in Cu++ supplementation, reaching 85% of total viable cells at the maximal concentration for growth. Results reported in this work indicate that emergence of colonial variants defective in gellan synthesis results from Cu(++)-induced mutation and the growth advantage of these mutants in Cu(++)-stressed cultures. In fact, DNA homologous recombination strongly increased with the increase in copper supplementation as indicated by the regeneration of kanamycin-resistant cells of R40 harbouring plasmid pBX404-7, which carries two non-overlapping truncated genes derived from a gene conferring kanamycin resistance. The four major groups of colonial mutants that emerged from Cu(++)-stressed cultures of R40 exhibited reduced growth rate and biomass yield in the absence of Cu++ stress and produced decreased levels of exopolysac-charide (EPS) which yielded solutions of lower or negligible viscosity. The level of increased Cu++ tolerance of these mutants, assessed by the inhibitory effect of Cu++ on growth, correlated with the degree of loss of the ability to secrete high-molecular-mass EPS. Consistent with the growth advantage of gellan-defective mutants in Cu(++)-stressed cultures, the non-producing strain RP10, spontaneously obtained during extended cultivation of R40, also exhibited a higher tolerance to Cu++. In addition, its non-mucoid phenotype was stably maintained during Cu(++)-stressed cultivation despite the stimulation of homologous recombination by Cu++.

Copper↗

Pyrimidine nucleoside catabolism in Sphingomonas paucimobilis: role of cytidine deaminase and uridine phosphorylase.

Pyrimidine nucleoside catabolism in the human pathogen Sphingomonas paucimobilis was studied. It was observed that S. paucimobilis was only capable of utilizing cytidine or deoxycytidine as a sole nitrogen source when glucose served as the carbon source. Thinlayer chromatographic analyses of cytidine and uridine catabolic products revealed that the enzymes cytidine deaminase and uridine phosphorylase were active in the extracts prepared from S. paucimobilis cells. The levels of cytidine deaminase and cytosine deaminase activities were lowered after growth on cytidine or deoxycytidine as a nitrogen source instead of ammonium sulfate. Uridine phosphorylase activity increased more than 4-fold after growth on deoxycytidine as a nitrogen source while growth on the nitrogen source cytidine caused a depression in phosphorylase activity.

Cytidine Deaminase↗

Comparison of biotin production by recombinant Sphingomonas sp. under various agitation conditions.

Biotin production by fermentation of recombinant Sphingomonas sp./pSP304 was investigated. A complex medium containing 60g/l of glycerol and 30g/l of yeast extract was suitable for biotin production. Biotin was produced in the late logarithmic or stationary phase after glycerol starvation. The optimum pH value for biotin production was 7.0. When the dissolved oxygen concentration (DO) was controlled at a constant level, the biotin concentration produced after 120h was significantly lower than that obtained in a test tube culture. Therefore, a batchwise jar-fermentor culture with a constant agitation speed and without DO control was conducted for investigating the effect of agitation conditions on biotin production. Six types of impeller were tested: turbine-blade type, turbo-lift type, rotating mesh type (EGSTAR((R))), screw with draft tube type, Maxblend((R))type, and anchor type. With some impellers, agitation speed was also changed. Both the maximum cell concentration and biotin production varied depending on agitation conditions. Relatively high cell concentrations were attained with four of the impeller types, turbine-blade type, rotating mesh type, Maxblend((R)) type, and anchor type. Among these impellers, the turbine-blade impeller with sintered sparger was suitable for biotin production. After 120h, the cell concentration reached an OD(660) of 43 and a biotin concentration of 66mg/l was obtained, which was comparable with the results from the test tube culture. Morphological variation was also observed depending on the agitation conditions: oval-shaped, rod-shaped, and elongated-shaped cells. Biotin production was relatively high in slightly long rod-shape cells but low in elongated cells. The difference in morphology appeared to depend on the shear stress. It was found that biotin production was strongly correlated with cell length and the oxygen transfer coefficient (k(L)a); cell lengths in the range 4-7µm and k(L)a values in the range 1.5-2.0/min were found to be suitable for biotin production in jar-fermentor culture.

Journal Article↗

Biodegradation of dibenzothiophene and 4,6-dimethyldibenzothiophene by Sphingomonas paucimobilis strain TZS-7.

Strain TZS-7, tentatively identified as Sphingomonas paucimobilis, was isolated from crude oil for its ability to degrade dibenzothiophene (DBT) and 4,6-dimethyldibenzothiophene (4,6-dmDBT). This strain did not utilize DBT or 4,6-dmDBT as the sole source of sulfur. However, the degradative activity was induced by various aromatic compounds, including DBT, fluorene, anthracene, naphthalene and toluene. Three products formed from 4,6-dmDBT degradation were detected and two of these were proposed to be 7-methyl-3-hydroxy-2-formylbenzothiophene and 7-methylbenzothiophene-2,3-dione by gas chromatography-mass spectrometry analysis. These findings proved that 4,6-dmDBT is degraded through a ring-destructive pathway by resting cells of strain TZS-7.

Journal Article↗

Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723.

An enzyme that catalyzes an Fe2+-dependent reaction of 2, 6-dichlorohydroquinone with O2 has been isolated from Sphingomonas chlorophenolica sp. strain ATCC 39723, a soil microorganism capable of complete mineralization of pentachlorophenol. The product of the reaction is too unstable to allow spectroscopic characterization, but is apparently negatively charged and retains the two chlorine atoms of the substrate. The enzyme was partially sequenced using electrospray LC-MS, and one peptide was used to search the NCBInr database. This peptide matched a part of PcpA, a protein of unknown function that is induced in S. chlorophenolica in response to pentachlorophenol. Several other peptides could also be mapped onto the sequence of PcpA, suggesting that the enzyme is encoded by pcpA. PcpA has low but significant sequence similarity to an unusual class of extradiol dioxygenases. On the basis of the sequence analysis, the Fe2+ and O2 dependence of the enzyme, and the characteristics of the product, the enzyme is proposed to be a 2,6-dichlorohydroquinone dioxygenase. The position of ring cleavage has not yet been identified.

Amino Acid Sequence↗

Practical syntheses of N-substituted 3-hydroxyazetidines and 4-hydroxypiperidines by hydroxylation with Sphingomonas sp. HXN-200.

[reaction: see text] Hydroxylation of N-substituted azetidines 11 and 12 and piperidines 15-19 with Sphingomonas sp. HXN-200 gave 91-98% of the corresponding 3-hydroxyazetidines 13 and 14 and 4-hydroxypiperidines 20-24, respectively, with high activity and excellent regioselectivity. High yields and high product concentrations (2 g/L) were achieved with frozen/thawed cells as biocatalyst. For the first time, rehydrated lyophilized cells were successfully used for the biohydroxylation.

Aldehydes↗