Cloning, Sequencing, and Expression in
            <i>Escherichia coli</i>
            of the New Gene Encoding β-1,3-Xylanase from a Marine Bacterium,
            <i>Vibrio</i>
            sp. Strain XY-214

Araki, Toshimitsu; Hashikawa, Shinnosuke; Morishita, Tatsuo

doi:10.1128/aem.66.4.1741-1743.2000

Cited by 41 publications

(32 citation statements)

References 17 publications

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“…The polysaccharides were labeled with fluoresceinamine (isomer II; Sigma) and characterized as described previously (54,55). These polysaccharides are constituents of marine algae (2), and the activities of enzymes hydrolyzing these substrates have been demonstrated in marine bacteria (16,(56)(57)(58). Genes encoding enzymes that hydrolyze these polysaccharides have also been identified in the genomes of fully sequenced marine bacteria (13)(14)(15)(16).…”

Section: Methodsmentioning

confidence: 99%

Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard

Cardman

Arnosti

Durbin

et al. 2014

Appl Environ Microbiol

181

106

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In Arctic marine bacterial communities, members of the phylum Verrucomicrobia are consistently detected, although not typically abundant, in 16S rRNA gene clone libraries and pyrotag surveys of the marine water column and in sediments. In an Arctic fjord (Smeerenburgfjord) of Svalbard, members of the Verrucomicrobia, together with Flavobacteria and smaller proportions of Alpha-and Gammaproteobacteria, constituted the most frequently detected bacterioplankton community members in 16S rRNA gene-based clone library analyses of the water column. Parallel measurements in the water column of the activities of six endo-acting polysaccharide hydrolases showed that chondroitin sulfate, laminarin, and xylan hydrolysis accounted for most of the activity. Several Verrucomicrobia water column phylotypes were affiliated with previously sequenced, glycoside hydrolaserich genomes of individual Verrucomicrobia cells that bound fluorescently labeled laminarin and xylan and therefore constituted candidates for laminarin and xylan hydrolysis. In sediments, the bacterial community was dominated by different lineages of Verrucomicrobia, Bacteroidetes, and Proteobacteria but also included members of multiple phylum-level lineages not observed in the water column. This community hydrolyzed laminarin, xylan, chondroitin sulfate, and three additional polysaccharide substrates at high rates. Comparisons with data from the same fjord in the previous summer showed that the bacterial community in Smeerenburgfjord changed in composition, most conspicuously in the changing detection frequency of Verrucomicrobia in the water column. Nonetheless, in both years the community hydrolyzed the same polysaccharide substrates.A major fraction of heterotrophic activity in the ocean is carried out by marine microbial communities (1). These communities use substrates such as high-molecular-weight carbohydrates (polysaccharides), which constitute a large percentage of phytoplankton biomass, particulate organic matter, and dissolved organic matter (DOM) in the ocean (2-5) and therefore fuel a considerable proportion of heterotrophic activity. To initiate the degradation of complex organic matter, bacteria must initially hydrolyze high-molecular-weight substrates by using extracellular enzymes in order to yield substrates sufficiently small to be taken into the microbial cell for further processing (6).The substrate spectrum and the rates of polysaccharide-hydrolyzing extracellular enzymes produced by microbial communities vary by location and depth in the ocean (7-9, 83) and can change through processes such as aggregate formation (10). Bacterial groups differ in their enzymatic spectra, as shown through field studies (11, 12), as well as genomic and microbiological investigation (13-16). Microbial communities involved in polysaccharide degradation in the water column include heterotrophic Gammaproteobacteria, fast-growing opportunists that can adapt quickly to changing substrate availability (17) and that include isolates that grow on rich standard media (...

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Section: Methodsmentioning

confidence: 99%

Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard

Cardman

Arnosti

Durbin

et al. 2014

Appl Environ Microbiol

181

106

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“…These polysaccharides were selected because all come from marine sources, and/or their component monomers are common in marine systems. Laminarin, xylan, and fucoidan occur in marine algae (Painter 1983); laminarinase, pullulanase, and xylanase enzyme activities have been detected in marine bacteria (Wainwright 1981, Arnosti & Repeta 1994, Araki et al 2000; chondroitin sulfate is produced commercially (Fluka) from shark cartilage, and arabinose and galactose are among the monosaccharides most commonly detected in particles, sediments, seawater, and plankton (e.g. Cowie & Hedges 1984, Biersmith & Benner 1998).…”

Section: Introductionmentioning

confidence: 99%

Patterns of extracellular enzyme activities among pelagic marine microbial communities: implications for cycling of dissolved organic carbon

Arnosti¹,

Durkin²,

Jeffrey³

2005

Aquat. Microb. Ecol.

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The potential for pelagic microbial communities to hydrolyze high molecular weight substrates and therefore to initiate remineralization of high-molecular-weight dissolved organic carbon (DOC) was assessed at 8 different stations spanning a range of locations. Six structurally diverse polysaccharides were used to investigate activities and structural specificities of a related class of microbial extracellular enzymes, the polysaccharide hydrolases. Three high-latitude (57 to 79°N) stations showed similar rates and patterns of enzyme activity, with only 3 of 6 polysaccharides hydrolyzed. Hydrolysis at the other stations (39°S to 29°N) showed a variety of patterns, in which 2 to 5 of the polysaccharides were hydrolyzed. One of the polysaccharides, fucoidan, was not hydrolyzed at any station, while only laminarin was hydrolyzed at every station. A limited ability of microbial communities in some locations to hydrolyze high-molecular-weight substrates could help explain the persistence of a fraction of DOC in the ocean. Potential hydrolysis rates showed no correlation with factors such as environmental temperature or total cell numbers. Denaturing gradient gel electrophoresis analysis of community 16S rDNA indicated that the microbial communities at these locations were diverse, consistent with the diversity in patterns of enzyme activities.

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“…␤-Glycosidases from GH5 and GH26 are particularly fascinating since these families contain enzymes specific for both manno-and gluco-configured substrates, yet they appear to have structural invariance around the 2-position of the glycone in the Ϫ1 subsite. So, although in peripheral subsites substrate specificity simply reflects recognition of the axial versus equatorial nature of 4 C 1 (chair)-conformed glycoside moieties, in the catalytic Ϫ1 subsite similar recognition apparatus around O2 favors binding of transition states in which O2 lies pseudoequatorial, 4 H 3 for glucosides and B 2,5 for mannosides. GH5 and GH26 present different evolutionary routes to solve the conformational aspects of catalysis.…”

Section: Structure Of a Ctlic26a-inhibitor Complex; Molecular Basis Fmentioning

confidence: 99%

“…Glycoside hydrolases (GH) 4 are currently grouped into almost 100 sequence-based families (1). A further complexity of these GH families is that many different families, defined by sequence, display similar three-dimensional structures and catalytic apparatus leading to a "clan" classification, analogous to that used for proteases.…”

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confidence: 99%

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How Family 26 Glycoside Hydrolases Orchestrate Catalysis on Different Polysaccharides

Taylor

Goyal²,

Guerreiro³

et al. 2005

Journal of Biological Chemistry

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One of the most intriguing features of the 90 glycoside hydrolase families (GHs) is the range of specificities displayed by different members of the same family, whereas the catalytic apparatus and mechanism are often invariant. Family GH26 predominantly comprises ␤-1,4 mannanases; however, a bifunctional Clostridium thermocellum GH26 member (hereafter CtLic26A) displays a markedly different specificity. We show that CtLic26A is a lichenase, specific for mixed (Glc␤1,4Glc␤1,4Glc␤1,3) n oligo-and polysaccharides, and displays no activity on manno-configured substrates or ␤-1,4-linked homopolymers of glucose or xylose. The three-dimensional structure of the native form of CtLic26A has been solved at 1.50-Å resolution, revealing a characteristic (␤/␣) 8 barrel with Glu-109 and Glu-222 acting as the catalytic acid/base and nucleophile in a double-displacement mechanism. The complex with the competitive inhibitor, Glc-␤-1,3-isofagomine (K i 1 M), at 1.60 Å sheds light on substrate recognition in the ؊2 and ؊1 subsites and illuminates why the enzyme is specific for lichenan-based substrates. Hydrolysis of ␤-mannosides by GH26 members is thought to proceed through transition states in the B 2,5 (boat) conformation in which structural distinction of glucosides versus mannosides reflects not the configuration at C2 but the recognition of the pseudoaxial O3 of the B 2,5 conformation. We suggest a different conformational itinerary for the GH26 enzymes active on gluco-configured substrates.

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Cloning, Sequencing, and Expression in Escherichia coli of the New Gene Encoding β-1,3-Xylanase from a Marine Bacterium, Vibrio sp. Strain XY-214

Cited by 41 publications

References 17 publications

Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard

Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard

Patterns of extracellular enzyme activities among pelagic marine microbial communities: implications for cycling of dissolved organic carbon

How Family 26 Glycoside Hydrolases Orchestrate Catalysis on Different Polysaccharides

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