In vitro and in vivo characterization of three Cellvibrio japonicus glycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-02-17

AUTHORS

Mohamed A. Attia, Cassandra E. Nelson, Wendy A. Offen, Namrata Jain, Gideon J. Davies, Jeffrey G. Gardner, Harry Brumer

ABSTRACT

Background: Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo-xyloglucanases were unresolved. Results: Combined bioinformatic and transcriptomic analyses implicated three glycoside hydrolase family 5 subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone endo-xyloglucanases in C. japonicus. Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose. Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known exo-glycosidases. Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes. Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in C. japonicus. Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the endo-xyloglucanases characterized here. Conclusions: Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of C. japonicus. The detailed structural-functional characterization of three distinct GH5_4 endo-xyloglucanases will inform future bioinformatic predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications. More... »

PAGES

45

References to SciGraph publications

  • 2009-05-18. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass in BIOTECHNOLOGY FOR BIOFUELS
  • 2016-06-04. Polysaccharide degradation systems of the saprophytic bacterium Cellvibrio japonicus in WORLD JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
  • 2009-04-12. Enzymatic assembly of DNA molecules up to several hundred kilobases in NATURE METHODS
  • 2013-03-06. Characterization of two novel family 12 xyloglucanases from the thermophilic Rhizomucor miehei in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 2009-12-29. A novel xyloglucan-specific endo-β-1,4-glucanase: biochemical properties and inhibition studies in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 2008-06-27. Methods for the bioinformatic identification of bacterial lipoproteins encoded in the genomes of Gram-positive bacteria in WORLD JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY
  • 2011-09-29. SignalP 4.0: discriminating signal peptides from transmembrane regions in NATURE METHODS
  • 2016-03-07. Mechanisms involved in xyloglucan catabolism by the cellulosome-producing bacterium Ruminiclostridium cellulolyticum in SCIENTIFIC REPORTS
  • 2014-06-05. Characterisation of a novel endo-xyloglucanase (XcXGHA) from Xanthomonas that accommodates a xylosyl-substituted glucose at subsite −1 in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 1999-08-26. Flexible Sequence Similarity Searching with the FASTA3 Program Package in BIOINFORMATICS METHODS AND PROTOCOLS
  • 2009. A Family of LIC Vectors for High-Throughput Cloning and Purification of Proteins in HIGH THROUGHPUT PROTEIN EXPRESSION AND PURIFICATION
  • 2011-06-14. Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation in BMC MICROBIOLOGY
  • 2015-11-04. Privateer: software for the conformational validation of carbohydrate structures in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2012-07-02. Novel enzymes for the degradation of cellulose in BIOTECHNOLOGY FOR BIOFUELS
  • 2012-07-18. Developing inhibitors of glycan processing enzymes as tools for enabling glycobiology in NATURE CHEMICAL BIOLOGY
  • 2014-01-19. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes in NATURE
  • 2012-09-20. Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5) in BMC EVOLUTIONARY BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13068-018-1039-6

    DOI

    http://dx.doi.org/10.1186/s13068-018-1039-6

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1101082124

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29467823


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/09", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Engineering", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/10", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Technology", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0904", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Chemical Engineering", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/1003", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Industrial Biotechnology", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada", 
              "id": "http://www.grid.ac/institutes/grid.17091.3e", 
              "name": [
                "Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada", 
                "Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Attia", 
            "givenName": "Mohamed A.", 
            "id": "sg:person.01003031213.03", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01003031213.03"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA", 
              "id": "http://www.grid.ac/institutes/grid.266673.0", 
              "name": [
                "Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nelson", 
            "givenName": "Cassandra E.", 
            "id": "sg:person.01140625507.03", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01140625507.03"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Chemistry, University of York, Heslington, York, YO10 5DD UK", 
              "id": "http://www.grid.ac/institutes/grid.5685.e", 
              "name": [
                "Department of Chemistry, University of York, Heslington, York, YO10 5DD UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Offen", 
            "givenName": "Wendy A.", 
            "id": "sg:person.01065153725.14", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01065153725.14"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada", 
              "id": "http://www.grid.ac/institutes/grid.17091.3e", 
              "name": [
                "Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada", 
                "Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Jain", 
            "givenName": "Namrata", 
            "id": "sg:person.015245217253.82", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015245217253.82"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Chemistry, University of York, Heslington, York, YO10 5DD UK", 
              "id": "http://www.grid.ac/institutes/grid.5685.e", 
              "name": [
                "Department of Chemistry, University of York, Heslington, York, YO10 5DD UK"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Davies", 
            "givenName": "Gideon J.", 
            "id": "sg:person.01211607401.09", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01211607401.09"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA", 
              "id": "http://www.grid.ac/institutes/grid.266673.0", 
              "name": [
                "Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Gardner", 
            "givenName": "Jeffrey G.", 
            "id": "sg:person.01206740707.14", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01206740707.14"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4 Canada", 
              "id": "http://www.grid.ac/institutes/grid.17091.3e", 
              "name": [
                "Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada", 
                "Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada", 
                "Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada", 
                "Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4 Canada"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Brumer", 
            "givenName": "Harry", 
            "id": "sg:person.0652444461.83", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0652444461.83"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/s00253-013-4770-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040260499", 
              "https://doi.org/10.1007/s00253-013-4770-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/srep22770", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1005387179", 
              "https://doi.org/10.1038/srep22770"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-1-59745-196-3_7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011851259", 
              "https://doi.org/10.1007/978-1-59745-196-3_7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1385/1-59259-192-2:185", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037394637", 
              "https://doi.org/10.1385/1-59259-192-2:185"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00253-009-2364-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039242727", 
              "https://doi.org/10.1007/s00253-009-2364-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11274-016-2068-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039797446", 
              "https://doi.org/10.1007/s11274-016-2068-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11274-008-9795-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012876881", 
              "https://doi.org/10.1007/s11274-008-9795-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nsmb.3115", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010755414", 
              "https://doi.org/10.1038/nsmb.3115"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature12907", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026386111", 
              "https://doi.org/10.1038/nature12907"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2148-12-186", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051443156", 
              "https://doi.org/10.1186/1471-2148-12-186"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1701", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049894869", 
              "https://doi.org/10.1038/nmeth.1701"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nchembio.1029", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022078679", 
              "https://doi.org/10.1038/nchembio.1029"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1754-6834-5-45", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002219986", 
              "https://doi.org/10.1186/1754-6834-5-45"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00253-014-5825-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012782992", 
              "https://doi.org/10.1007/s00253-014-5825-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1754-6834-2-10", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007556277", 
              "https://doi.org/10.1186/1754-6834-2-10"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2180-11-134", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008052759", 
              "https://doi.org/10.1186/1471-2180-11-134"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1318", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040405189", 
              "https://doi.org/10.1038/nmeth.1318"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2018-02-17", 
        "datePublishedReg": "2018-02-17", 
        "description": "Background: Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte Cellvibrio japonicus has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of C. japonicus have been functionally characterized, the requisite backbone-cleaving endo-xyloglucanases were unresolved.\nResults: Combined bioinformatic and transcriptomic analyses implicated three glycoside hydrolase family 5 subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone endo-xyloglucanases in C. japonicus. Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose. Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known exo-glycosidases. Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes. Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in C. japonicus. Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the endo-xyloglucanases characterized here.\nConclusions: Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of C. japonicus. The detailed structural-functional characterization of three distinct GH5_4 endo-xyloglucanases will inform future bioinformatic predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s13068-018-1039-6", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2623099", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2780059", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.4319878", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1039046", 
            "issn": [
              "1754-6834"
            ], 
            "name": "Biotechnology for Biofuels", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "11"
          }
        ], 
        "keywords": [
          "reverse genetic analysis", 
          "cell wall glycans", 
          "plant cell walls", 
          "tractable model system", 
          "glycoside hydrolase family 5", 
          "structural-functional characterization", 
          "hydrolase family 5", 
          "potential keystone", 
          "growth defect", 
          "transcriptomic analysis", 
          "new CAZymes", 
          "molecular basis", 
          "bioinformatics prediction", 
          "biotechnological applications", 
          "cell wall", 
          "recombinant proteins", 
          "family 5", 
          "plant polysaccharides", 
          "debranching enzyme", 
          "complete deconstruction", 
          "xyloglucanases", 
          "enzymatic characterization", 
          "systems-based analysis", 
          "XyG", 
          "modular organization", 
          "biomass saccharification", 
          "enzyme", 
          "functional compensation", 
          "model system", 
          "structural complexity", 
          "new insights", 
          "innate capacity", 
          "utilization system", 
          "polysaccharides", 
          "crystallographic analysis", 
          "members", 
          "CAZymes", 
          "Cellvibrio", 
          "xyloglucan", 
          "species", 
          "specificity", 
          "growth", 
          "protein", 
          "glycans", 
          "high specificity", 
          "vivo characterization", 
          "component monosaccharides", 
          "systems-based approach", 
          "characterization", 
          "pathway", 
          "glycosidases", 
          "saccharification", 
          "keystone", 
          "subsequent saccharification", 
          "vitro", 
          "oligosaccharides", 
          "vivo", 
          "function", 
          "wide range", 
          "monosaccharides", 
          "soil", 
          "insights", 
          "analysis", 
          "defects", 
          "cellulose", 
          "product analysis", 
          "basis", 
          "wall", 
          "form", 
          "panel", 
          "system", 
          "organization", 
          "combination", 
          "capacity", 
          "part", 
          "study", 
          "deconstruction", 
          "module", 
          "range", 
          "complexity", 
          "prediction", 
          "approach", 
          "applications", 
          "compensation", 
          "cohort", 
          "fundamental polysaccharide", 
          "sidechain-debranching enzymes", 
          "downstream debranching enzymes", 
          "xyloglucan utilization system", 
          "distinct modular organization", 
          "XyG polysaccharide", 
          "wall glycans", 
          "XyG oligosaccharides", 
          "GH5D", 
          "active-site affinity-labelled forms", 
          "affinity-labelled forms", 
          "exquisite XyG specificity", 
          "XyG specificity", 
          "exhaustive reverse-genetic analysis", 
          "GH74 member", 
          "attack-mounting (GH5D) functions", 
          "molecular systems-based approach", 
          "saccharification pathway", 
          "detailed structural-functional characterization", 
          "future bioinformatic predictions", 
          "Cellvibrio japonicus glycoside hydrolase family 5 members", 
          "japonicus glycoside hydrolase family 5 members", 
          "glycoside hydrolase family 5 members", 
          "hydrolase family 5 members", 
          "family 5 members", 
          "potent xyloglucan backbone-cleaving functions", 
          "xyloglucan backbone-cleaving functions", 
          "backbone-cleaving functions"
        ], 
        "name": "In vitro and in vivo characterization of three Cellvibrio japonicus glycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions", 
        "pagination": "45", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1101082124"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s13068-018-1039-6"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "29467823"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s13068-018-1039-6", 
          "https://app.dimensions.ai/details/publication/pub.1101082124"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2021-11-01T18:32", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_775.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s13068-018-1039-6"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13068-018-1039-6'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13068-018-1039-6'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13068-018-1039-6'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13068-018-1039-6'


     

    This table displays all metadata directly associated to this object as RDF triples.

    308 TRIPLES      22 PREDICATES      158 URIs      131 LITERALS      7 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s13068-018-1039-6 schema:about anzsrc-for:09
    2 anzsrc-for:0904
    3 anzsrc-for:10
    4 anzsrc-for:1003
    5 schema:author N706a88a4889c4b4bafa6d3a8ad1909a9
    6 schema:citation sg:pub.10.1007/978-1-59745-196-3_7
    7 sg:pub.10.1007/s00253-009-2364-2
    8 sg:pub.10.1007/s00253-013-4770-8
    9 sg:pub.10.1007/s00253-014-5825-1
    10 sg:pub.10.1007/s11274-008-9795-2
    11 sg:pub.10.1007/s11274-016-2068-6
    12 sg:pub.10.1038/nature12907
    13 sg:pub.10.1038/nchembio.1029
    14 sg:pub.10.1038/nmeth.1318
    15 sg:pub.10.1038/nmeth.1701
    16 sg:pub.10.1038/nsmb.3115
    17 sg:pub.10.1038/srep22770
    18 sg:pub.10.1186/1471-2148-12-186
    19 sg:pub.10.1186/1471-2180-11-134
    20 sg:pub.10.1186/1754-6834-2-10
    21 sg:pub.10.1186/1754-6834-5-45
    22 sg:pub.10.1385/1-59259-192-2:185
    23 schema:datePublished 2018-02-17
    24 schema:datePublishedReg 2018-02-17
    25 schema:description Background: Xyloglucan (XyG) is a ubiquitous and fundamental polysaccharide of plant cell walls. Due to its structural complexity, XyG requires a combination of backbone-cleaving and sidechain-debranching enzymes for complete deconstruction into its component monosaccharides. The soil saprophyte <i>Cellvibrio japonicus</i> has emerged as a genetically tractable model system to study biomass saccharification, in part due to its innate capacity to utilize a wide range of plant polysaccharides for growth. Whereas the downstream debranching enzymes of the xyloglucan utilization system of <i>C. japonicus</i> have been functionally characterized, the requisite backbone-cleaving <i>endo</i>-xyloglucanases were unresolved. Results: Combined bioinformatic and transcriptomic analyses implicated three glycoside hydrolase family 5 subfamily 4 (GH5_4) members, with distinct modular organization, as potential keystone <i>endo</i>-xyloglucanases in <i>C. japonicus</i>. Detailed biochemical and enzymatic characterization of the GH5_4 modules of all three recombinant proteins confirmed particularly high specificities for the XyG polysaccharide versus a panel of other cell wall glycans, including mixed-linkage beta-glucan and cellulose. Moreover, product analysis demonstrated that all three enzymes generated XyG oligosaccharides required for subsequent saccharification by known <i>exo</i>-glycosidases. Crystallographic analysis of GH5D, which was the only GH5_4 member specifically and highly upregulated during growth on XyG, in free, product-complex, and active-site affinity-labelled forms revealed the molecular basis for the exquisite XyG specificity among these GH5_4 enzymes. Strikingly, exhaustive reverse-genetic analysis of all three GH5_4 members and a previously biochemically characterized GH74 member failed to reveal a growth defect, thereby indicating functional compensation in vivo, both among members of this cohort and by other, yet unidentified, xyloglucanases in <i>C. japonicus</i>. Our systems-based analysis indicates distinct substrate-sensing (GH74, GH5E, GH5F) and attack-mounting (GH5D) functions for the <i>endo</i>-xyloglucanases characterized here. Conclusions: Through a multi-faceted, molecular systems-based approach, this study provides a new insight into the saccharification pathway of xyloglucan utilization system of <i>C. japonicus</i>. The detailed structural-functional characterization of three distinct GH5_4 <i>endo</i>-xyloglucanases will inform future bioinformatic predictions across species, and provides new CAZymes with defined specificity that may be harnessed in industrial and other biotechnological applications.
    26 schema:genre article
    27 schema:inLanguage en
    28 schema:isAccessibleForFree true
    29 schema:isPartOf N0b4be72e22a241c28698ebf1395dce47
    30 Naa71b0bba2e0496d804fd9339b738f86
    31 sg:journal.1039046
    32 schema:keywords CAZymes
    33 Cellvibrio
    34 Cellvibrio japonicus glycoside hydrolase family 5 members
    35 GH5D
    36 GH74 member
    37 XyG
    38 XyG oligosaccharides
    39 XyG polysaccharide
    40 XyG specificity
    41 active-site affinity-labelled forms
    42 affinity-labelled forms
    43 analysis
    44 applications
    45 approach
    46 attack-mounting (GH5D) functions
    47 backbone-cleaving functions
    48 basis
    49 bioinformatics prediction
    50 biomass saccharification
    51 biotechnological applications
    52 capacity
    53 cell wall
    54 cell wall glycans
    55 cellulose
    56 characterization
    57 cohort
    58 combination
    59 compensation
    60 complete deconstruction
    61 complexity
    62 component monosaccharides
    63 crystallographic analysis
    64 debranching enzyme
    65 deconstruction
    66 defects
    67 detailed structural-functional characterization
    68 distinct modular organization
    69 downstream debranching enzymes
    70 enzymatic characterization
    71 enzyme
    72 exhaustive reverse-genetic analysis
    73 exquisite XyG specificity
    74 family 5
    75 family 5 members
    76 form
    77 function
    78 functional compensation
    79 fundamental polysaccharide
    80 future bioinformatic predictions
    81 glycans
    82 glycosidases
    83 glycoside hydrolase family 5
    84 glycoside hydrolase family 5 members
    85 growth
    86 growth defect
    87 high specificity
    88 hydrolase family 5
    89 hydrolase family 5 members
    90 innate capacity
    91 insights
    92 japonicus glycoside hydrolase family 5 members
    93 keystone
    94 members
    95 model system
    96 modular organization
    97 module
    98 molecular basis
    99 molecular systems-based approach
    100 monosaccharides
    101 new CAZymes
    102 new insights
    103 oligosaccharides
    104 organization
    105 panel
    106 part
    107 pathway
    108 plant cell walls
    109 plant polysaccharides
    110 polysaccharides
    111 potent xyloglucan backbone-cleaving functions
    112 potential keystone
    113 prediction
    114 product analysis
    115 protein
    116 range
    117 recombinant proteins
    118 reverse genetic analysis
    119 saccharification
    120 saccharification pathway
    121 sidechain-debranching enzymes
    122 soil
    123 species
    124 specificity
    125 structural complexity
    126 structural-functional characterization
    127 study
    128 subsequent saccharification
    129 system
    130 systems-based analysis
    131 systems-based approach
    132 tractable model system
    133 transcriptomic analysis
    134 utilization system
    135 vitro
    136 vivo
    137 vivo characterization
    138 wall
    139 wall glycans
    140 wide range
    141 xyloglucan
    142 xyloglucan backbone-cleaving functions
    143 xyloglucan utilization system
    144 xyloglucanases
    145 schema:name In vitro and in vivo characterization of three Cellvibrio japonicus glycoside hydrolase family 5 members reveals potent xyloglucan backbone-cleaving functions
    146 schema:pagination 45
    147 schema:productId N0381c86453184d22b5e8689db10cfc26
    148 N1f07c07febc74f7b9e79075293445ae4
    149 Nd26e0c27c72f4dc0b934cc10578ef3c4
    150 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101082124
    151 https://doi.org/10.1186/s13068-018-1039-6
    152 schema:sdDatePublished 2021-11-01T18:32
    153 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    154 schema:sdPublisher Nc4435423794942c8930e4b3fd8992bfd
    155 schema:url https://doi.org/10.1186/s13068-018-1039-6
    156 sgo:license sg:explorer/license/
    157 sgo:sdDataset articles
    158 rdf:type schema:ScholarlyArticle
    159 N0381c86453184d22b5e8689db10cfc26 schema:name pubmed_id
    160 schema:value 29467823
    161 rdf:type schema:PropertyValue
    162 N0b4be72e22a241c28698ebf1395dce47 schema:issueNumber 1
    163 rdf:type schema:PublicationIssue
    164 N0f9966bc3c7e475490e1f02774fb9a57 rdf:first sg:person.015245217253.82
    165 rdf:rest Nfb9890f24e944e4cb934b3c836542427
    166 N1f07c07febc74f7b9e79075293445ae4 schema:name doi
    167 schema:value 10.1186/s13068-018-1039-6
    168 rdf:type schema:PropertyValue
    169 N39ef376b01b9478d81183d7253d495ec rdf:first sg:person.01140625507.03
    170 rdf:rest N3e3f55e0f2c745bbb9620dc85af9fa47
    171 N3e3f55e0f2c745bbb9620dc85af9fa47 rdf:first sg:person.01065153725.14
    172 rdf:rest N0f9966bc3c7e475490e1f02774fb9a57
    173 N5267499c4af64336921c78c8e8703c19 rdf:first sg:person.0652444461.83
    174 rdf:rest rdf:nil
    175 N706a88a4889c4b4bafa6d3a8ad1909a9 rdf:first sg:person.01003031213.03
    176 rdf:rest N39ef376b01b9478d81183d7253d495ec
    177 Naa71b0bba2e0496d804fd9339b738f86 schema:volumeNumber 11
    178 rdf:type schema:PublicationVolume
    179 Nc4435423794942c8930e4b3fd8992bfd schema:name Springer Nature - SN SciGraph project
    180 rdf:type schema:Organization
    181 Nd26e0c27c72f4dc0b934cc10578ef3c4 schema:name dimensions_id
    182 schema:value pub.1101082124
    183 rdf:type schema:PropertyValue
    184 Ne7b17a352e894165a6637de992a4fbc9 rdf:first sg:person.01206740707.14
    185 rdf:rest N5267499c4af64336921c78c8e8703c19
    186 Nfb9890f24e944e4cb934b3c836542427 rdf:first sg:person.01211607401.09
    187 rdf:rest Ne7b17a352e894165a6637de992a4fbc9
    188 anzsrc-for:09 schema:inDefinedTermSet anzsrc-for:
    189 schema:name Engineering
    190 rdf:type schema:DefinedTerm
    191 anzsrc-for:0904 schema:inDefinedTermSet anzsrc-for:
    192 schema:name Chemical Engineering
    193 rdf:type schema:DefinedTerm
    194 anzsrc-for:10 schema:inDefinedTermSet anzsrc-for:
    195 schema:name Technology
    196 rdf:type schema:DefinedTerm
    197 anzsrc-for:1003 schema:inDefinedTermSet anzsrc-for:
    198 schema:name Industrial Biotechnology
    199 rdf:type schema:DefinedTerm
    200 sg:grant.2623099 http://pending.schema.org/fundedItem sg:pub.10.1186/s13068-018-1039-6
    201 rdf:type schema:MonetaryGrant
    202 sg:grant.2780059 http://pending.schema.org/fundedItem sg:pub.10.1186/s13068-018-1039-6
    203 rdf:type schema:MonetaryGrant
    204 sg:grant.4319878 http://pending.schema.org/fundedItem sg:pub.10.1186/s13068-018-1039-6
    205 rdf:type schema:MonetaryGrant
    206 sg:journal.1039046 schema:issn 1754-6834
    207 schema:name Biotechnology for Biofuels
    208 schema:publisher Springer Nature
    209 rdf:type schema:Periodical
    210 sg:person.01003031213.03 schema:affiliation grid-institutes:grid.17091.3e
    211 schema:familyName Attia
    212 schema:givenName Mohamed A.
    213 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01003031213.03
    214 rdf:type schema:Person
    215 sg:person.01065153725.14 schema:affiliation grid-institutes:grid.5685.e
    216 schema:familyName Offen
    217 schema:givenName Wendy A.
    218 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01065153725.14
    219 rdf:type schema:Person
    220 sg:person.01140625507.03 schema:affiliation grid-institutes:grid.266673.0
    221 schema:familyName Nelson
    222 schema:givenName Cassandra E.
    223 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01140625507.03
    224 rdf:type schema:Person
    225 sg:person.01206740707.14 schema:affiliation grid-institutes:grid.266673.0
    226 schema:familyName Gardner
    227 schema:givenName Jeffrey G.
    228 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01206740707.14
    229 rdf:type schema:Person
    230 sg:person.01211607401.09 schema:affiliation grid-institutes:grid.5685.e
    231 schema:familyName Davies
    232 schema:givenName Gideon J.
    233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01211607401.09
    234 rdf:type schema:Person
    235 sg:person.015245217253.82 schema:affiliation grid-institutes:grid.17091.3e
    236 schema:familyName Jain
    237 schema:givenName Namrata
    238 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015245217253.82
    239 rdf:type schema:Person
    240 sg:person.0652444461.83 schema:affiliation grid-institutes:grid.17091.3e
    241 schema:familyName Brumer
    242 schema:givenName Harry
    243 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0652444461.83
    244 rdf:type schema:Person
    245 sg:pub.10.1007/978-1-59745-196-3_7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011851259
    246 https://doi.org/10.1007/978-1-59745-196-3_7
    247 rdf:type schema:CreativeWork
    248 sg:pub.10.1007/s00253-009-2364-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039242727
    249 https://doi.org/10.1007/s00253-009-2364-2
    250 rdf:type schema:CreativeWork
    251 sg:pub.10.1007/s00253-013-4770-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040260499
    252 https://doi.org/10.1007/s00253-013-4770-8
    253 rdf:type schema:CreativeWork
    254 sg:pub.10.1007/s00253-014-5825-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012782992
    255 https://doi.org/10.1007/s00253-014-5825-1
    256 rdf:type schema:CreativeWork
    257 sg:pub.10.1007/s11274-008-9795-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012876881
    258 https://doi.org/10.1007/s11274-008-9795-2
    259 rdf:type schema:CreativeWork
    260 sg:pub.10.1007/s11274-016-2068-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039797446
    261 https://doi.org/10.1007/s11274-016-2068-6
    262 rdf:type schema:CreativeWork
    263 sg:pub.10.1038/nature12907 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026386111
    264 https://doi.org/10.1038/nature12907
    265 rdf:type schema:CreativeWork
    266 sg:pub.10.1038/nchembio.1029 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022078679
    267 https://doi.org/10.1038/nchembio.1029
    268 rdf:type schema:CreativeWork
    269 sg:pub.10.1038/nmeth.1318 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040405189
    270 https://doi.org/10.1038/nmeth.1318
    271 rdf:type schema:CreativeWork
    272 sg:pub.10.1038/nmeth.1701 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049894869
    273 https://doi.org/10.1038/nmeth.1701
    274 rdf:type schema:CreativeWork
    275 sg:pub.10.1038/nsmb.3115 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010755414
    276 https://doi.org/10.1038/nsmb.3115
    277 rdf:type schema:CreativeWork
    278 sg:pub.10.1038/srep22770 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005387179
    279 https://doi.org/10.1038/srep22770
    280 rdf:type schema:CreativeWork
    281 sg:pub.10.1186/1471-2148-12-186 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051443156
    282 https://doi.org/10.1186/1471-2148-12-186
    283 rdf:type schema:CreativeWork
    284 sg:pub.10.1186/1471-2180-11-134 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008052759
    285 https://doi.org/10.1186/1471-2180-11-134
    286 rdf:type schema:CreativeWork
    287 sg:pub.10.1186/1754-6834-2-10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007556277
    288 https://doi.org/10.1186/1754-6834-2-10
    289 rdf:type schema:CreativeWork
    290 sg:pub.10.1186/1754-6834-5-45 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002219986
    291 https://doi.org/10.1186/1754-6834-5-45
    292 rdf:type schema:CreativeWork
    293 sg:pub.10.1385/1-59259-192-2:185 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037394637
    294 https://doi.org/10.1385/1-59259-192-2:185
    295 rdf:type schema:CreativeWork
    296 grid-institutes:grid.17091.3e schema:alternateName Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4 Canada
    297 Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
    298 schema:name Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3 Canada
    299 Department of Botany, University of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4 Canada
    300 Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1 Canada
    301 Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4 Canada
    302 rdf:type schema:Organization
    303 grid-institutes:grid.266673.0 schema:alternateName Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA
    304 schema:name Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 USA
    305 rdf:type schema:Organization
    306 grid-institutes:grid.5685.e schema:alternateName Department of Chemistry, University of York, Heslington, York, YO10 5DD UK
    307 schema:name Department of Chemistry, University of York, Heslington, York, YO10 5DD UK
    308 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...