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Given the abundance of lignin in nature, multiple enzyme systems have been discovered to cleave the β-O-4 bonds, the most prevalent intermonomer linkage. In particular, stereospecific cleavage of lignin oligomers by glutathione S -transferases (GSTs) has been reported in several sphingomonads. Here, we apply quantum mechanics/molecular mechanics simulations to study the mechanism of two glutathione-dependent enzymes in the β-aryl ether catabolic pathway of Sphingomonas sp. SYK-6, namely, LigF, a β-etherase, and LigG, a lyase. For LigF, the free-energy landscape supports a S N 2 reaction mechanism, with the monoaromatic leaving group being promptly neutralized upon release. Specific interactions with conserved residues are responsible for stereoselectivity and for activation of the cofactor as a nucleophile. A glutathione conjugate is also released by LigF and serves the substrate of LigG, undergoing a S N 2-like reaction, in which Cys15 acts as the nucleophile, to yield the second monoaromatic product. The simulations suggest that the electron-donating substituent at the para-position found in lignin-derived aromatics and the interaction with Tyr217 are essential for reactivity in LigG. Overall, this work deepens the understanding of the stereospecific enzymatic mechanisms in the β-aryl ether cleavage pathway and reveals key structural features underpinning the ligninolytic activity detected in several sphingomonad GSTs.

β-1,2-Xylosidase activity has not been recorded as an EC subsubclass. In this study, phylogenetic analysis and multiple sequence alignments revealed that characterized β-xylosidases of glycoside hydrolase family (GH) 39 were classified into the same subgroup with conserved amino acid residue positions participating in substrate recognition. Protein-ligand docking revealed that seven of these positions were probably essential to bind xylose-glucose, which is linked by a β-1,2-glycosidic bond. Amino acid residues in five of the seven positions are invariant, while those in two of the seven positions are variable with low frequency. Both the wild-type β-xylosidase rJB13GH39 and its mutants with mutation at the two positions exhibited β-1,2-xylosidase activity, as they hydrolyzed o-nitrophenyl-β-d-xylopyranoside and transformed notoginsenosides R 1 and R 2 to ginsenosides Rg 1 and Rh 1 , respectively. The results suggest that all of these characterized GH 39 β-xylosidases probably show β-1,2-xylosidase activity, which should be assigned an EC number with these β-xylosidases as representatives.

Mining for novel enzymes from new microorganisms is a way to obtain β-xylosidases with promising applications. A Sphingomonas β-xylosidase was expressed in Escherichia coli. The purified recombinant enzyme (rJB13GH39) was most active at pH 4.5 and 50 °C, retaining 10%-50% of its maximum activity at 0-20 °C. Most salts and chemical reagents including 3.0%-20.0% (w/v) NaCl showed little or no effect on the enzymatic activity. rJB13GH39 exhibited 71.9% and 55.2% activity in 10.0% and 15.0% (v/v) ethanol, respectively. rJB13GH39 was stable below 60 °C in 3.0%-30.0% (w/v) NaCl, 3.0%-20.0% (v/v) ethanol, and 2.2-87.0 mg/mL trypsin. The enzyme transferred one xylosyl moiety to certain sugars and alcohols. The salt/ethanol tolerance and low-temperature activity of the enzyme may be attributed to its high structural flexibility caused by high proportions of small amino acids ACDGNSTV and random coils.

Alginate is a heteropolysaccharide that consists of β-D-mannuronate (M) and α-L-guluronate (G). The Gram-negative bacterium Sphingomonas sp. A1 directly incorporates alginate into the cytoplasm through the periplasmic solute-binding protein (AlgQ1 and AlgQ2)-dependent ABC transporter (AlgM1-AlgM2/AlgS-AlgS). Two binding proteins with at least four subsites strongly recognize the nonreducing terminal residue of alginate at subsite 1. Here, we show the broad substrate preference of strain A1 solute-binding proteins for M and G present in alginate and demonstrate the structural determinants in binding proteins for heteropolysaccharide recognition through X-ray crystallography of four AlgQ1 structures in complex with saturated and unsaturated alginate oligosaccharides. Alginates with different M/G ratios were assimilated by strain A1 cells and bound to AlgQ1 and AlgQ2. Crystal structures of oligosaccharide-bound forms revealed that in addition to interaction between AlgQ1 and unsaturated oligosaccharides, the binding protein binds through hydrogen bonds to the C4 hydroxyl group of the saturated nonreducing terminal residue at subsite 1. The M residue of saturated oligosaccharides is predominantly accommodated at subsite 1 because of the strict binding of Ser-273 to the carboxyl group of the residue. In unsaturated trisaccharide (ΔGGG or ΔMMM)-bound AlgQ1, the protein interacts appropriately with substrate hydroxyl groups at subsites 2 and 3 to accommodate M or G, while substrate carboxyl groups are strictly recognized by the specific residues Tyr-129 at subsite 2 and Lys-22 at subsite 3. Because of this substrate recognition mechanism, strain A1 solute-binding proteins can bind heteropolysaccharide alginate with different M/G ratios.

The synthesis of S-glycosphingolipids based on uronic acids is described. These compounds are analogous to the highly immunostimulatory antigens isolated from the cell walls of bacteria of the Sphingomonas family. Key to the synthetic route is a stereoselective anomerization to give α-glycosyl thiol precursors. A route to a sphinganine precursor from pseudoephedrine glycinamide is also described., (© 2011 American Chemical Society)

Bacterial glycolipids containing either alpha-glucuronic acid or alpha-galacturonic acid residues have an important role in the innate-type immune response to gram-negative bacteria. Synthesis of closely related compounds, including a novel alpha-SO(2) glycolipid mimetic, is described from carbohydrate precursors where anomerization is a key step. Very high stereoselectivites (>97:3 in favor of alpha) were observed from O-glycoside precursors.

A concise synthesis of a differentially protected D-galacturonic acid (D-GalA) thioglycoside and the construction of a potent immunomodulating glycosphingolipid are described. The key steps of the synthesis are an Evans aldol reaction between a C4 aldehyde and a PMB-protected glycolyloxazolidinone as well as a tandem-PMB-deprotection/cyclization to thioglycosides. The key glycosylation step is optimized by varying the anomeric leaving group, the activating agent, and the solvent system.

Bacterial flagellins are generally self-assembled into extracellular flagella for cell motility. However, the flagellin homologue p5 is found on the cell surface of Sphingomonas sp. A1 (strain A1) and binds tightly to the alginate polysaccharide. To assimilate alginate, strain A1 forms a mouthlike pit on the cell surface and concentrates the polymer in the pit. p5 is a candidate receptor that recognizes extracellular alginate and controls pit formation. To improve our understanding of the structure and function of p5, we determined the crystal structure of truncated p5 (p5DeltaN53C45) at 2.0 A resolution. This, to our knowledge, is the first structure of flagellin_IN motif-containing flagellin. p5DeltaN53C45 consists of two domains: an alpha-domain rich in alpha-helices that forms the N- and C-terminal regions and a beta-domain rich in beta-strands that constitutes the central region. The alpha-domain is structurally similar to the D1 domain of Salmonella typhimurium flagellin, while the beta-domain is structurally similar to the finger domain of the bacteriophage T4 baseplate protein that is important for intermolecular interactions between baseplate and a long or short tail fiber. Results from the deletion mutant analysis suggest that residues 20-40 and 353-363 are responsible for alginate binding. Truncated N- and C-terminal regions are thought to constitute alpha-helices extending from the alpha-domain. On the basis of the size and surface charge, the cleft in extended alpha-helices is proposed as an alginate binding site of p5. Structural similarity in the beta-domain suggests that the beta-domain is involved in the proper localization and/or orientation of p5 on the cell surface.

A nonmotile gram-negative bacterium, Sphingomonas sp. A1, directly incorporates macromolecules such as alginate through a "super-channel" consisting of a pit formed on the cell surface, alginate-binding proteins in the periplasm, and an ATP-binding cassette transporter in the inner membrane. Here, we demonstrate the proteomics-based identification of cell-surface proteins involved in the formation of the pit and/or import of alginate. Cell-surface proteins were prepared from the outer membrane released as vesicles during the conversion of intact cells to spheroplasts. Seven proteins (p1-p7) with acidic isoelectric points were inducibly expressed in the outer membrane of strain A1 cells grown on alginate and showed significant identity with bacterial cell-surface proteins (p1-p4, TonB-dependent outer-membrane transporter; p5 and p6, flagellin; and p7, lipoprotein). Each mutant with a disruption of the p1-p4 or p6 gene showed significant growth retardation in the alginate medium. Flagellin homologues (p5 and p6) were further analyzed because strain A1 forms no flagellum. p5 was found to be uniformly distributed on the cell surface by immunogold-labeling electron microscopy and to exhibit alginate binding with a nanomolar dissociation constant by a surface plasmon resonance sensor. The cell surface of the p6 gene disruptant differed from that of the wild-type strain A1 in that pit formation was incomplete and cell-surface structures shifted from pleats to networks. These results suggest that, distinct from bacterial flagellins constituting a helical filament of flagella, strain A1 cell-surface flagellin homologues function as receptors for alginate and/or regulators of cell-surface structures.

Physicochemical characteristics and biological activities of Sphingomonas gellan (S-gellan) were investigated. The S-gellan weight fractions of Glc and GlcUA were 0.45 and 0.25, respectively, and the molar ratio of Glc:Rha:GlcUA was approximately 4:2:3. The S-gellan was chemically derivatized with diethylaminoethyl chloride-HCl (DEAE-HCl), and the resulting modified S-gellan contained both positive and negative charges. The elemental and IR analyses were conducted to confirm the successful incorporation of DEAE groups into S-gellan. A large increase in nitrogen fraction was observed from the derivatized S-gellan by elemental analysis. The IR absorption bands induced by C-H, C-N, and C-O-C stretching were noticeable at 2950, 1310-1380, and 1000-1150 cm(-1), respectively, resulting from the DEAE substitution. The characteristic CH3 and CH2 peaks originated from the DEAE group were detected in the 1H NMR spectrum of the derivatized S-gellan as well. The solubility of native S-gellan was improved almost twice from 40% to 75% after DEAE derivatization, while water holding capacity (WHC) drastically decreased from 10026% to 245%. Oil binding capacity (OBC) of S-gellan also significantly dropped from 1528% to 331% after the derivatization. The bile acid binding capacity of S-gellan was indirectly determined by measuring the holding capability of cholic acid inside the dialysis membrane (MWCO 12,000-14,000 Da). Once S-gellan was DEAE derivatized, there was substantial increase in the cholic acid retardation index (CRI). Up to 9 h of dialysis, the derivatized S-gellan released 29.3% less of cholic acid compared to the control group that did not contain S-gellan. From these results of the improved water solubility and stronger bile acid binding capacity, it would be suggested that the DEAE-derivatized S-gellan has more advantages than gellan itself for functional food applications.

An investigation of the mobility, viability, and activity of polycyclic aromatic hydrocarbon (PAH) degrading bacteria in an electric field is presented. Bench-scale model aquifers were used to test electrophoresis and electroosmosis as potential mechanisms for bacterial dispersion in contaminated sites. Glass beads, alluvial sand from Lake Geneva, and historically polluted clayey soil were used as packing materials. The green-fluorescent protein labeled PAH-degrading bacteria Sphingomonas sp. L138 and Mycobacterium frederiksbergense LB501TG were used as test organisms because of the known differing physicochemical surface and adhesion properties of the corresponding wild-type strains. No adverse effects of the electric current on bacterial viability and PAH-degradation were observed in the system chosen. Up to 90% of the weakly negatively charged and moderately adhesive cells of strain L138 were transported by electroosmosis, whereas 0-20% were transported by electrophoresis. By contrast, poor electrokinetic transport of strongly charged and highly adhesive cells of M. frederiksbergense LB501TG occurred in the different model aquifers. Treatment of bacteria with the nonionic surfactant Brij35 resulted in up to 80% enhanced electrokinetic dispersion of both strains. Our findings demonstrate that electroosmosis may be a valuable mechanism to transport bacteria in the subsurface with transport efficiencies heavily depending on the retention of the bacteria by the solid phase.

The bacterial strain Sphingomonas sp. HXN-200 was used to catalyze the trans dihydroxylation ofN-substituted 1,2,5,6-tetrahydropyridines 1 and 3-pyrrolines 4 giving the corresponding 3,4-dihydroxypiperidines 3 and 3,4-dihydroxypyrrolidines 6, respectively, with high enantioselectivity and high activity. The trans dihydroxylation was sequentially catalyzed by a monooxygenase and an epoxide hydrolase in the strain with epoxide as intermediate. While both epoxidation and hydrolysis steps contributed to the overall enantioselectivity in trans dihydroxylation of 1, the enantioselectivity in trans dihydroxylation of the symmetric substrate 4 was generated only in the hydrolysis of meso-epoxide 5. The absolute configuration for the bioproducts (+)-3 and (+)-6 was established as (3R,4R) by chemical correlations. Preparative trans dihydroxylation of 1a and 4b with frozen/thawed cells of Sphingomonas sp. HXN-200 afforded the corresponding (+)-(3R,4R)-3,4-dihydroxypiperidine 3a and (+)-(3R,4R)-3,4-dihydroxy pyrrolidine 6b in 96% ee both and in 60% and 80% yield, respectively. These results represent first examples of enantioselective trans dihydroxylation with nonterpene substrates and with bacterial catalyst, thus significantly extending this methodology in practical synthesis of valuable and useful trans diols. Enantioselective hydrolysis of racemic epoxide 2a with Sphingomonas sp. HXN-200 gave 34% of (-)-2a in >99% ee, which is a versatile chiral building block. Further hydrolysis of (-)-2a with the same strain afforded (-)-(3S,4S)-3a in 96% ee and 92% yield. Thus, both enantiomers of 3a can be prepared by biotransformation with Sphingomonas sp. HXN-200.

Hydroxylation of N-benzylpyrrolidine 8 with resting cells of Sphingomonas sp. HXN-200 gave N-benzyl-3-hydroxypyrrolidine 15 in 53% ee (S) with an activity of 5.8 U/g CDW. By changing the "docking/protecting group" in pyrrolidines, hydroxylation activity and enantioselectivity were further improved and the enantiocomplementary formation of 3-hydroxypyrrolidines was achieved: hydroxylation of N-benzoyl-, N-benzyloxycarbonyl-, N-phenoxycarbonyl-, and N-tert-butoxycarbonyl-pyrrolidines 9-12 gave the corresponding 3-hydroxypyrrolidines 16-19 in ee of 52% (R), 75% (R), 39% (S), and 23% (R), respectively, with an activity of 2.2, 16, 14, and 24 U/g CDW, respectively. Simple crystallizations increased the ee of 16-18 to 95% (R), 98% (R), and 96% (S), respectively. Hydroxylation of pyrrolidines 8-12 with soluble cell-free extracts of Sphingomonas sp. HXN-200 and equimolar NADH gave 3-hydroxypyrrolidines 15-19 in nearly the same ee as the products generated by whole cell transformation, suggesting that this strain possesses a novel soluble alkane monooxygenase. Cells of Sphingomonas sp. HXN-200 were produced in large amounts and could be stored at -80 degrees C for 2 years without significant loss of activity. The frozen cells can be thawed and resuspended for biohydroxylation, providing a highly active and easy to handle biocatalyst for the regio- and stereoselective hydroxylation of nonactivated carbon atoms. These cells were used to prepare 1.0-3.2 g (66.4-93.5% yield) of 3-hydroxypyrrolidines 16-19 by hydroxylation of pyrrolidines 9-12 on 0.9-2 L scale. Preparative hydroxylation was also achieved with growing cells as biocatalysts; hydroxylation of pyrrolidine 11 on 1 L scale gave 1.970 g (79.7% yield) of 3-hydroxypyrrolidine 18.

Thermal, mechanical, turbidity, and microscope evidence is provided which strongly suggests molecular interpenetrating network (IPN) formation by mixtures of the bacterial and seaweed polysaccharides gellan and agarose. There is no evidence for synergistic coupling of the networks, and simple phase separation (demixing) can definitely be ruled out. Some changes in the gellan gelling behavior are suggested, however, by the increased gellan effective concentrations implicit in cure curve data. The dependence of this effect on the agarose nominal concentration seems consistent with a previous model that focused on gelling parameters, and changes in these rather than real concentration effects. In large deformation mechanical tests, the influence of agarose added to gellan is to re-enforce the network (higher compression and shear moduli, higher stresses-to-break) without significantly changing the strain to break, or the gellan brittle failure mechanism.

Two microbial strains with different substrate spectra were immobilized separately within a single biosensor chip featuring four individually addressable platinum electrodes. These were sputtered onto the inner surface of four isolated pyramidal cavities ("containments") micromachined on a silicon wafer. The biosensor chip was integrated into a flow-through system to measure the oxygen consumption of the immobilized microorganisms in the presence of assimilable analytes. As a model system, a yeast for the determination of biochemical oxygen demand (BOD) and a strain capable of degrading polycyclic aromatic hydrocarbons (PAH) were chosen. It was shown that the simple and mass-producible containment sensor exhibits good performance data: lower detection limit 0.1 mg/L naphthalene and 1 mg/L sensor-BOD; calibration range up to 30 mg/L; precision 3-6%; response time 2-3 min; service life up to 40 days; shelf life at 4 degrees C 6 months. The versatility of the multimicrobial sensor was demonstrated by measuring ordinary municipal wastewater samples as well as various aqueous samples contaminated with PAH. The concept of a multimicrobial sensor not only enlarges the substrate spectrum for sum parameters such as BOD but leads to additional information which allows for a more differentiated and immediate knowledge of sample composition. Using chemometrical data analysis, the multimicrobial sensor lays a foundation for developing an "electronic tongue".