A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-12

AUTHORS

David J Studholme, Selena Gimenez Ibanez, Daniel MacLean, Jeffery L Dangl, Jeff H Chang, John P Rathjen

ABSTRACT

BACKGROUND: Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. P. syringae pathovar tabaci naturally causes disease on wild tobacco, the model member of the Solanaceae, a family that includes many crop species as well as on soybean. RESULTS: We used the 'next-generation' Illumina sequencing platform and the Velvet short-read assembly program to generate a 145X deep 6,077,921 nucleotide draft genome sequence for P. syringae pathovar tabaci strain 11528. From our draft assembly, we predicted 5,300 potential genes encoding proteins of at least 100 amino acids long, of which 303 (5.72%) had no significant sequence similarity to those encoded by the three previously fully sequenced P. syringae genomes. Of the core set of Hrp Outer Proteins that are conserved in three previously fully sequenced P. syringae strains, most were also conserved in strain 11528, including AvrE1, HopAH2, HopAJ2, HopAK1, HopAN1, HopI, HopJ1, HopX1, HrpK1 and HrpW1. However, the hrpZ1 gene is partially deleted and hopAF1 is completely absent in 11528. The draft genome of strain 11528 also encodes close homologues of HopO1, HopT1, HopAH1, HopR1, HopV1, HopAG1, HopAS1, HopAE1, HopAR1, HopF1, and HopW1 and a degenerate HopM1'. Using a functional screen, we confirmed that hopO1, hopT1, hopAH1, hopM1', hopAE1, hopAR1, and hopAI1' are part of the virulence-associated HrpL regulon, though the hopAI1' and hopM1' sequences were degenerate with premature stop codons. We also discovered two additional HrpL-regulated effector candidates and an HrpL-regulated distant homologue of avrPto1. CONCLUSION: The draft genome sequence facilitates the continued development of P. syringae pathovar tabaci on wild tobacco as an attractive model system for studying bacterial disease on plants. The catalogue of effectors sheds further light on the evolution of pathogenicity and host-specificity as well as providing a set of molecular tools for the study of plant defence mechanisms. We also discovered several large genomic regions in Pta 11528 that do not share detectable nucleotide sequence similarity with previously sequenced Pseudomonas genomes. These regions may include horizontally acquired islands that possibly contribute to pathogenicity or epiphytic fitness of Pta 11528. More... »

PAGES

395

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-10-395

DOI

http://dx.doi.org/10.1186/1471-2164-10-395

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1019815339

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19703286


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/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacterial Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Binding Sites", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Comparative Genomic Hybridization", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Conserved Sequence", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA-Binding Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Gene Expression Regulation, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome, Bacterial", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomic Islands", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Pseudomonas syringae", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Regulon", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sigma Factor", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Virulence", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Sainsbury Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.18888.31", 
          "name": [
            "The Sainsbury Laboratory, NR4 7UH, Norwich, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Studholme", 
        "givenName": "David J", 
        "id": "sg:person.01047645057.86", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01047645057.86"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Sainsbury Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.18888.31", 
          "name": [
            "The Sainsbury Laboratory, NR4 7UH, Norwich, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ibanez", 
        "givenName": "Selena Gimenez", 
        "id": "sg:person.01213377550.01", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01213377550.01"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Sainsbury Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.18888.31", 
          "name": [
            "The Sainsbury Laboratory, NR4 7UH, Norwich, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "MacLean", 
        "givenName": "Daniel", 
        "id": "sg:person.013574744257.00", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013574744257.00"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of North Carolina at Chapel Hill", 
          "id": "https://www.grid.ac/institutes/grid.10698.36", 
          "name": [
            "Department of Biology, CB# 3280, Coker Hall, The University of North Carolina at Chapel Hill, 27599-3280, Chapel Hill, North Carolina, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Dangl", 
        "givenName": "Jeffery L", 
        "id": "sg:person.015727674137.17", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015727674137.17"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Oregon State University", 
          "id": "https://www.grid.ac/institutes/grid.4391.f", 
          "name": [
            "Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, 97331, Corvallis, OR, USA", 
            "Center for Genome Research and Biocomputing, Oregon State University, 2082 Cordley Hall, 97331, Corvallis, OR, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chang", 
        "givenName": "Jeff H", 
        "id": "sg:person.010637573117.44", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010637573117.44"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Sainsbury Laboratory", 
          "id": "https://www.grid.ac/institutes/grid.18888.31", 
          "name": [
            "The Sainsbury Laboratory, NR4 7UH, Norwich, UK"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Rathjen", 
        "givenName": "John P", 
        "id": "sg:person.01031216266.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031216266.12"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1073/pnas.1731982100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000574692"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bti054", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002594133"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mib.2008.12.003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002962917"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.185.19.5772-5778.2003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003824909"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf01922457", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004216587", 
          "https://doi.org/10.1007/bf01922457"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/bf01922457", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004216587", 
          "https://doi.org/10.1007/bf01922457"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cell.2006.02.012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005835412"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/iai.69.12.7471-7480.2001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007356590"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aac.01643-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007429625"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.fmrre.2005.01.001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007522179"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0048-4059(84)90017-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007734413"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0504930102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008441401"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0504930102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008441401"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.phyto.41.052002.095652", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010416651"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.083311.108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011112451"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature07660", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011164954", 
          "https://doi.org/10.1038/nature07660"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.bbrc.2007.11.021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1011396487"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.403602", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012195556"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pcbi.1000186", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012210496"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.187.18.6488-6498.2005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012814363"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.micro.60.080805.142251", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013159069"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.96.19.10875", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013411703"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0022-2836(05)80360-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013618994"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.186.15.5101-5115.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014979544"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.genom.9.081307.164359", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015853776"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ja.2005.109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016226364", 
          "https://doi.org/10.1038/ja.2005.109"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/ja.2005.109", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016226364", 
          "https://doi.org/10.1038/ja.2005.109"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1574-6968.2008.01441.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016462719"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ijmm.2004.11.001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016577605"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl629", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017299791"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro2122", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017693818", 
          "https://doi.org/10.1038/nrmicro2122"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10327-005-0240-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018729069", 
          "https://doi.org/10.1007/s10327-005-0240-1"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10327-005-0240-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018729069", 
          "https://doi.org/10.1007/s10327-005-0240-1"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.00793-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018775269"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2006.02798.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020054544"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/aem.70.4.1999-2012.2004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022014193"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mib.2003.12.006", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022105930"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2004-5-2-r12", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022585853", 
          "https://doi.org/10.1186/gb-2004-5-2-r12"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-9-376", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023829631", 
          "https://doi.org/10.1186/1471-2105-9-376"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2105-9-376", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023829631", 
          "https://doi.org/10.1186/1471-2105-9-376"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.7088808", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025227180"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mmbr.69.1.155-194.2005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026986186"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.phyto.45.062806.094317", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028657088"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-9-603", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028935538", 
          "https://doi.org/10.1186/1471-2164-9-603"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1369-5274(02)00004-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030300320"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1574-6968.2006.00526.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030390124"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.95.7.3943", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031136183"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.97.9.4856", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032763876"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.6435207", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033023123"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.7337908", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035219026"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.00998-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036711998"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0966-842x(02)02451-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037348621"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.073262.107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037655071"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.072033.107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038496028"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/415497a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039822330", 
          "https://doi.org/10.1038/415497a"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/415497a", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1039822330", 
          "https://doi.org/10.1038/415497a"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0000484", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040432928"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1104/pp.71.4.912", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042838225"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.2000.02133.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042914038"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cub.2005.10.074", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044311052"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/emboj/19.13.3204", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1044703718"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1286-4579(03)00032-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045349230"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s1286-4579(03)00032-7", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045349230"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2006-7-4-r34", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046349148", 
          "https://doi.org/10.1186/gb-2006-7-4-r34"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.01282-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046584111"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.ygeno.2008.02.005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047387894"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.078212.108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047542880"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/pl00012997", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1047765556", 
          "https://doi.org/10.1007/pl00012997"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1105/tpc.13.5.1079", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048906839"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.185.3.1018-1026.2003", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048996782"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm960", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050102057"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm960", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050102057"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0409660102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050607248"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btm451", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051622036"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.074492.107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051720574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-313x.2007.03126.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052868330"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/bth205", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053359138"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1146/annurev.micro.54.1.735", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053645502"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.femsre.2004.12.004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1054735310"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1042/0264-6021:3440273", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1056714345"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi-18-0060", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060078192"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi-18-0275", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060078214"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi-19-1151", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060078433"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi-20-2-0146", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060078564"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi-21-6-0685", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060078754"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi-22-1-0052", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060078813"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi-4-553", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060079211"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi-8-0717", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060079571"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/mpmi.2000.13.12.1366", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060080184"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1094/phyto-69-208", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060105687"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1099/00207713-49-2-469", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060349923"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1099/00221287-146-10-2447", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060370182"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.170.8.3738-3741.1988", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062717155"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.2307/3871365", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1070469152"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1077155436", 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2009-12", 
    "datePublishedReg": "2009-12-01", 
    "description": "BACKGROUND: Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. P. syringae pathovar tabaci naturally causes disease on wild tobacco, the model member of the Solanaceae, a family that includes many crop species as well as on soybean.\nRESULTS: We used the 'next-generation' Illumina sequencing platform and the Velvet short-read assembly program to generate a 145X deep 6,077,921 nucleotide draft genome sequence for P. syringae pathovar tabaci strain 11528. From our draft assembly, we predicted 5,300 potential genes encoding proteins of at least 100 amino acids long, of which 303 (5.72%) had no significant sequence similarity to those encoded by the three previously fully sequenced P. syringae genomes. Of the core set of Hrp Outer Proteins that are conserved in three previously fully sequenced P. syringae strains, most were also conserved in strain 11528, including AvrE1, HopAH2, HopAJ2, HopAK1, HopAN1, HopI, HopJ1, HopX1, HrpK1 and HrpW1. However, the hrpZ1 gene is partially deleted and hopAF1 is completely absent in 11528. The draft genome of strain 11528 also encodes close homologues of HopO1, HopT1, HopAH1, HopR1, HopV1, HopAG1, HopAS1, HopAE1, HopAR1, HopF1, and HopW1 and a degenerate HopM1'. Using a functional screen, we confirmed that hopO1, hopT1, hopAH1, hopM1', hopAE1, hopAR1, and hopAI1' are part of the virulence-associated HrpL regulon, though the hopAI1' and hopM1' sequences were degenerate with premature stop codons. We also discovered two additional HrpL-regulated effector candidates and an HrpL-regulated distant homologue of avrPto1.\nCONCLUSION: The draft genome sequence facilitates the continued development of P. syringae pathovar tabaci on wild tobacco as an attractive model system for studying bacterial disease on plants. The catalogue of effectors sheds further light on the evolution of pathogenicity and host-specificity as well as providing a set of molecular tools for the study of plant defence mechanisms. We also discovered several large genomic regions in Pta 11528 that do not share detectable nucleotide sequence similarity with previously sequenced Pseudomonas genomes. These regions may include horizontally acquired islands that possibly contribute to pathogenicity or epiphytic fitness of Pta 11528.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2164-10-395", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.2517550", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "10"
      }
    ], 
    "name": "A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528", 
    "pagination": "395", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "5e6951f1d7ceb77457daf79e83860fb3870c591f0d7e1f67f3545d832443c078"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19703286"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965258"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2164-10-395"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1019815339"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2164-10-395", 
      "https://app.dimensions.ai/details/publication/pub.1019815339"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T23:22", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8693_00000504.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2164-10-395"
  }
]
 

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.10.1186/1471-2164-10-395'

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

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-10-395'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-10-395'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-10-395'


 

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

443 TRIPLES      21 PREDICATES      131 URIs      36 LITERALS      24 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2164-10-395 schema:about N130bd7498c0540f7917c527940600c3d
2 N182c79dc34b0414da10b04c83a7d3ead
3 N6ba5a3e87541491899b1392791df3b64
4 N83042db7b27a49b19c905f3cb6bebacf
5 N8ec2fe812b0c4fd38b6f6711a4c952d4
6 N98c7675a9a9e427c8412739b376350c3
7 N9ee4048c76544bd78459ab898ba49027
8 Nb0a95b15771340fbb1457f280a6f2ddf
9 Nb0d7c91fcbe74284a5d23307aee9c3bf
10 Nbd6e5434dd134634b8e1f987bb77cf34
11 Nbfff98773553471a9e608e94100c2e1c
12 Ndfb429423c104ab9ae0eef127443f243
13 Nf0cf83e9909044c28dbeefbc0fb2bfe5
14 Nf442c2110c7c478a926296912ed3fde8
15 Nf59fe8d2222a4578a429dfcc1978f2c1
16 anzsrc-for:06
17 anzsrc-for:0604
18 schema:author N2794a8edfd884159a4e763d4859a58c1
19 schema:citation sg:pub.10.1007/bf01922457
20 sg:pub.10.1007/pl00012997
21 sg:pub.10.1007/s10327-005-0240-1
22 sg:pub.10.1038/415497a
23 sg:pub.10.1038/ja.2005.109
24 sg:pub.10.1038/nature07660
25 sg:pub.10.1038/nrmicro2122
26 sg:pub.10.1186/1471-2105-9-376
27 sg:pub.10.1186/1471-2164-9-603
28 sg:pub.10.1186/gb-2004-5-2-r12
29 sg:pub.10.1186/gb-2006-7-4-r34
30 https://app.dimensions.ai/details/publication/pub.1077155436
31 https://doi.org/10.1016/0048-4059(84)90017-1
32 https://doi.org/10.1016/j.bbrc.2007.11.021
33 https://doi.org/10.1016/j.cell.2006.02.012
34 https://doi.org/10.1016/j.cub.2005.10.074
35 https://doi.org/10.1016/j.femsre.2004.12.004
36 https://doi.org/10.1016/j.fmrre.2005.01.001
37 https://doi.org/10.1016/j.ijmm.2004.11.001
38 https://doi.org/10.1016/j.mib.2003.12.006
39 https://doi.org/10.1016/j.mib.2008.12.003
40 https://doi.org/10.1016/j.ygeno.2008.02.005
41 https://doi.org/10.1016/s0022-2836(05)80360-2
42 https://doi.org/10.1016/s0966-842x(02)02451-4
43 https://doi.org/10.1016/s1286-4579(03)00032-7
44 https://doi.org/10.1016/s1369-5274(02)00004-8
45 https://doi.org/10.1042/0264-6021:3440273
46 https://doi.org/10.1046/j.1365-2958.2000.02133.x
47 https://doi.org/10.1073/pnas.0409660102
48 https://doi.org/10.1073/pnas.0504930102
49 https://doi.org/10.1073/pnas.1731982100
50 https://doi.org/10.1073/pnas.95.7.3943
51 https://doi.org/10.1073/pnas.96.19.10875
52 https://doi.org/10.1073/pnas.97.9.4856
53 https://doi.org/10.1093/bioinformatics/bth205
54 https://doi.org/10.1093/bioinformatics/bti054
55 https://doi.org/10.1093/bioinformatics/btl629
56 https://doi.org/10.1093/bioinformatics/btm451
57 https://doi.org/10.1093/emboj/19.13.3204
58 https://doi.org/10.1093/nar/gkm960
59 https://doi.org/10.1094/mpmi-18-0060
60 https://doi.org/10.1094/mpmi-18-0275
61 https://doi.org/10.1094/mpmi-19-1151
62 https://doi.org/10.1094/mpmi-20-2-0146
63 https://doi.org/10.1094/mpmi-21-6-0685
64 https://doi.org/10.1094/mpmi-22-1-0052
65 https://doi.org/10.1094/mpmi-4-553
66 https://doi.org/10.1094/mpmi-8-0717
67 https://doi.org/10.1094/mpmi.2000.13.12.1366
68 https://doi.org/10.1094/phyto-69-208
69 https://doi.org/10.1099/00207713-49-2-469
70 https://doi.org/10.1099/00221287-146-10-2447
71 https://doi.org/10.1101/gr.072033.107
72 https://doi.org/10.1101/gr.073262.107
73 https://doi.org/10.1101/gr.074492.107
74 https://doi.org/10.1101/gr.078212.108
75 https://doi.org/10.1101/gr.083311.108
76 https://doi.org/10.1101/gr.403602
77 https://doi.org/10.1101/gr.6435207
78 https://doi.org/10.1101/gr.7088808
79 https://doi.org/10.1101/gr.7337908
80 https://doi.org/10.1104/pp.71.4.912
81 https://doi.org/10.1105/tpc.13.5.1079
82 https://doi.org/10.1111/j.1365-313x.2006.02798.x
83 https://doi.org/10.1111/j.1365-313x.2007.03126.x
84 https://doi.org/10.1111/j.1574-6968.2006.00526.x
85 https://doi.org/10.1111/j.1574-6968.2008.01441.x
86 https://doi.org/10.1128/aac.01643-07
87 https://doi.org/10.1128/aem.70.4.1999-2012.2004
88 https://doi.org/10.1128/iai.69.12.7471-7480.2001
89 https://doi.org/10.1128/jb.00793-07
90 https://doi.org/10.1128/jb.00998-07
91 https://doi.org/10.1128/jb.01282-07
92 https://doi.org/10.1128/jb.170.8.3738-3741.1988
93 https://doi.org/10.1128/jb.185.19.5772-5778.2003
94 https://doi.org/10.1128/jb.185.3.1018-1026.2003
95 https://doi.org/10.1128/jb.186.15.5101-5115.2004
96 https://doi.org/10.1128/jb.187.18.6488-6498.2005
97 https://doi.org/10.1128/mmbr.69.1.155-194.2005
98 https://doi.org/10.1146/annurev.genom.9.081307.164359
99 https://doi.org/10.1146/annurev.micro.54.1.735
100 https://doi.org/10.1146/annurev.micro.60.080805.142251
101 https://doi.org/10.1146/annurev.phyto.41.052002.095652
102 https://doi.org/10.1146/annurev.phyto.45.062806.094317
103 https://doi.org/10.1371/journal.pcbi.1000186
104 https://doi.org/10.1371/journal.pone.0000484
105 https://doi.org/10.2307/3871365
106 schema:datePublished 2009-12
107 schema:datePublishedReg 2009-12-01
108 schema:description BACKGROUND: Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. P. syringae pathovar tabaci naturally causes disease on wild tobacco, the model member of the Solanaceae, a family that includes many crop species as well as on soybean. RESULTS: We used the 'next-generation' Illumina sequencing platform and the Velvet short-read assembly program to generate a 145X deep 6,077,921 nucleotide draft genome sequence for P. syringae pathovar tabaci strain 11528. From our draft assembly, we predicted 5,300 potential genes encoding proteins of at least 100 amino acids long, of which 303 (5.72%) had no significant sequence similarity to those encoded by the three previously fully sequenced P. syringae genomes. Of the core set of Hrp Outer Proteins that are conserved in three previously fully sequenced P. syringae strains, most were also conserved in strain 11528, including AvrE1, HopAH2, HopAJ2, HopAK1, HopAN1, HopI, HopJ1, HopX1, HrpK1 and HrpW1. However, the hrpZ1 gene is partially deleted and hopAF1 is completely absent in 11528. The draft genome of strain 11528 also encodes close homologues of HopO1, HopT1, HopAH1, HopR1, HopV1, HopAG1, HopAS1, HopAE1, HopAR1, HopF1, and HopW1 and a degenerate HopM1'. Using a functional screen, we confirmed that hopO1, hopT1, hopAH1, hopM1', hopAE1, hopAR1, and hopAI1' are part of the virulence-associated HrpL regulon, though the hopAI1' and hopM1' sequences were degenerate with premature stop codons. We also discovered two additional HrpL-regulated effector candidates and an HrpL-regulated distant homologue of avrPto1. CONCLUSION: The draft genome sequence facilitates the continued development of P. syringae pathovar tabaci on wild tobacco as an attractive model system for studying bacterial disease on plants. The catalogue of effectors sheds further light on the evolution of pathogenicity and host-specificity as well as providing a set of molecular tools for the study of plant defence mechanisms. We also discovered several large genomic regions in Pta 11528 that do not share detectable nucleotide sequence similarity with previously sequenced Pseudomonas genomes. These regions may include horizontally acquired islands that possibly contribute to pathogenicity or epiphytic fitness of Pta 11528.
109 schema:genre research_article
110 schema:inLanguage en
111 schema:isAccessibleForFree true
112 schema:isPartOf N443bcbc2ef984e4bac77ca4888c22cbe
113 Ne1fc1ee8b4414fbeacb4dc580df1f079
114 sg:journal.1023790
115 schema:name A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528
116 schema:pagination 395
117 schema:productId N18eaff36ec6f40c5a3e906c907d45479
118 N8bce073b20264329aa6b7ed763df06ce
119 Na7422ae82ea245ceb50454bd8ccecaf3
120 Nbf75b3459d48475f9e5b23e4d3bfed9b
121 Nf737d84346774f4f9e947b85963558db
122 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019815339
123 https://doi.org/10.1186/1471-2164-10-395
124 schema:sdDatePublished 2019-04-10T23:22
125 schema:sdLicense https://scigraph.springernature.com/explorer/license/
126 schema:sdPublisher N94786a3e64ba478ba2f4db0b36d5ab6a
127 schema:url http://link.springer.com/10.1186%2F1471-2164-10-395
128 sgo:license sg:explorer/license/
129 sgo:sdDataset articles
130 rdf:type schema:ScholarlyArticle
131 N075fc04711d94c59be915580c43af921 rdf:first sg:person.010637573117.44
132 rdf:rest N9afb9755c26442d4b4fe8f63a764e7b6
133 N0e541c095c0b4867b4fddb8d07e6b17e rdf:first sg:person.013574744257.00
134 rdf:rest Nb65056434eb84589a55366525ecb274a
135 N130bd7498c0540f7917c527940600c3d schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
136 schema:name Pseudomonas syringae
137 rdf:type schema:DefinedTerm
138 N182c79dc34b0414da10b04c83a7d3ead schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
139 schema:name DNA, Bacterial
140 rdf:type schema:DefinedTerm
141 N18eaff36ec6f40c5a3e906c907d45479 schema:name dimensions_id
142 schema:value pub.1019815339
143 rdf:type schema:PropertyValue
144 N2794a8edfd884159a4e763d4859a58c1 rdf:first sg:person.01047645057.86
145 rdf:rest Nad8fb5ee606149d2a6cf65ad71ca10c3
146 N443bcbc2ef984e4bac77ca4888c22cbe schema:issueNumber 1
147 rdf:type schema:PublicationIssue
148 N6ba5a3e87541491899b1392791df3b64 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
149 schema:name Sequence Analysis, DNA
150 rdf:type schema:DefinedTerm
151 N83042db7b27a49b19c905f3cb6bebacf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
152 schema:name DNA-Binding Proteins
153 rdf:type schema:DefinedTerm
154 N8bce073b20264329aa6b7ed763df06ce schema:name doi
155 schema:value 10.1186/1471-2164-10-395
156 rdf:type schema:PropertyValue
157 N8ec2fe812b0c4fd38b6f6711a4c952d4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name Virulence
159 rdf:type schema:DefinedTerm
160 N94786a3e64ba478ba2f4db0b36d5ab6a schema:name Springer Nature - SN SciGraph project
161 rdf:type schema:Organization
162 N98c7675a9a9e427c8412739b376350c3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
163 schema:name Comparative Genomic Hybridization
164 rdf:type schema:DefinedTerm
165 N9afb9755c26442d4b4fe8f63a764e7b6 rdf:first sg:person.01031216266.12
166 rdf:rest rdf:nil
167 N9ee4048c76544bd78459ab898ba49027 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
168 schema:name Binding Sites
169 rdf:type schema:DefinedTerm
170 Na7422ae82ea245ceb50454bd8ccecaf3 schema:name readcube_id
171 schema:value 5e6951f1d7ceb77457daf79e83860fb3870c591f0d7e1f67f3545d832443c078
172 rdf:type schema:PropertyValue
173 Nad8fb5ee606149d2a6cf65ad71ca10c3 rdf:first sg:person.01213377550.01
174 rdf:rest N0e541c095c0b4867b4fddb8d07e6b17e
175 Nb0a95b15771340fbb1457f280a6f2ddf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
176 schema:name Genomics
177 rdf:type schema:DefinedTerm
178 Nb0d7c91fcbe74284a5d23307aee9c3bf schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
179 schema:name Gene Expression Regulation, Bacterial
180 rdf:type schema:DefinedTerm
181 Nb65056434eb84589a55366525ecb274a rdf:first sg:person.015727674137.17
182 rdf:rest N075fc04711d94c59be915580c43af921
183 Nbd6e5434dd134634b8e1f987bb77cf34 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
184 schema:name Conserved Sequence
185 rdf:type schema:DefinedTerm
186 Nbf75b3459d48475f9e5b23e4d3bfed9b schema:name pubmed_id
187 schema:value 19703286
188 rdf:type schema:PropertyValue
189 Nbfff98773553471a9e608e94100c2e1c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
190 schema:name Genome, Bacterial
191 rdf:type schema:DefinedTerm
192 Ndfb429423c104ab9ae0eef127443f243 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
193 schema:name Regulon
194 rdf:type schema:DefinedTerm
195 Ne1fc1ee8b4414fbeacb4dc580df1f079 schema:volumeNumber 10
196 rdf:type schema:PublicationVolume
197 Nf0cf83e9909044c28dbeefbc0fb2bfe5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
198 schema:name Sigma Factor
199 rdf:type schema:DefinedTerm
200 Nf442c2110c7c478a926296912ed3fde8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
201 schema:name Genomic Islands
202 rdf:type schema:DefinedTerm
203 Nf59fe8d2222a4578a429dfcc1978f2c1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
204 schema:name Bacterial Proteins
205 rdf:type schema:DefinedTerm
206 Nf737d84346774f4f9e947b85963558db schema:name nlm_unique_id
207 schema:value 100965258
208 rdf:type schema:PropertyValue
209 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
210 schema:name Biological Sciences
211 rdf:type schema:DefinedTerm
212 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
213 schema:name Genetics
214 rdf:type schema:DefinedTerm
215 sg:grant.2517550 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-10-395
216 rdf:type schema:MonetaryGrant
217 sg:journal.1023790 schema:issn 1471-2164
218 schema:name BMC Genomics
219 rdf:type schema:Periodical
220 sg:person.01031216266.12 schema:affiliation https://www.grid.ac/institutes/grid.18888.31
221 schema:familyName Rathjen
222 schema:givenName John P
223 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031216266.12
224 rdf:type schema:Person
225 sg:person.01047645057.86 schema:affiliation https://www.grid.ac/institutes/grid.18888.31
226 schema:familyName Studholme
227 schema:givenName David J
228 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01047645057.86
229 rdf:type schema:Person
230 sg:person.010637573117.44 schema:affiliation https://www.grid.ac/institutes/grid.4391.f
231 schema:familyName Chang
232 schema:givenName Jeff H
233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010637573117.44
234 rdf:type schema:Person
235 sg:person.01213377550.01 schema:affiliation https://www.grid.ac/institutes/grid.18888.31
236 schema:familyName Ibanez
237 schema:givenName Selena Gimenez
238 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01213377550.01
239 rdf:type schema:Person
240 sg:person.013574744257.00 schema:affiliation https://www.grid.ac/institutes/grid.18888.31
241 schema:familyName MacLean
242 schema:givenName Daniel
243 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013574744257.00
244 rdf:type schema:Person
245 sg:person.015727674137.17 schema:affiliation https://www.grid.ac/institutes/grid.10698.36
246 schema:familyName Dangl
247 schema:givenName Jeffery L
248 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015727674137.17
249 rdf:type schema:Person
250 sg:pub.10.1007/bf01922457 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004216587
251 https://doi.org/10.1007/bf01922457
252 rdf:type schema:CreativeWork
253 sg:pub.10.1007/pl00012997 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047765556
254 https://doi.org/10.1007/pl00012997
255 rdf:type schema:CreativeWork
256 sg:pub.10.1007/s10327-005-0240-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018729069
257 https://doi.org/10.1007/s10327-005-0240-1
258 rdf:type schema:CreativeWork
259 sg:pub.10.1038/415497a schema:sameAs https://app.dimensions.ai/details/publication/pub.1039822330
260 https://doi.org/10.1038/415497a
261 rdf:type schema:CreativeWork
262 sg:pub.10.1038/ja.2005.109 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016226364
263 https://doi.org/10.1038/ja.2005.109
264 rdf:type schema:CreativeWork
265 sg:pub.10.1038/nature07660 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011164954
266 https://doi.org/10.1038/nature07660
267 rdf:type schema:CreativeWork
268 sg:pub.10.1038/nrmicro2122 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017693818
269 https://doi.org/10.1038/nrmicro2122
270 rdf:type schema:CreativeWork
271 sg:pub.10.1186/1471-2105-9-376 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023829631
272 https://doi.org/10.1186/1471-2105-9-376
273 rdf:type schema:CreativeWork
274 sg:pub.10.1186/1471-2164-9-603 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028935538
275 https://doi.org/10.1186/1471-2164-9-603
276 rdf:type schema:CreativeWork
277 sg:pub.10.1186/gb-2004-5-2-r12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022585853
278 https://doi.org/10.1186/gb-2004-5-2-r12
279 rdf:type schema:CreativeWork
280 sg:pub.10.1186/gb-2006-7-4-r34 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046349148
281 https://doi.org/10.1186/gb-2006-7-4-r34
282 rdf:type schema:CreativeWork
283 https://app.dimensions.ai/details/publication/pub.1077155436 schema:CreativeWork
284 https://doi.org/10.1016/0048-4059(84)90017-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007734413
285 rdf:type schema:CreativeWork
286 https://doi.org/10.1016/j.bbrc.2007.11.021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011396487
287 rdf:type schema:CreativeWork
288 https://doi.org/10.1016/j.cell.2006.02.012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005835412
289 rdf:type schema:CreativeWork
290 https://doi.org/10.1016/j.cub.2005.10.074 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044311052
291 rdf:type schema:CreativeWork
292 https://doi.org/10.1016/j.femsre.2004.12.004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1054735310
293 rdf:type schema:CreativeWork
294 https://doi.org/10.1016/j.fmrre.2005.01.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007522179
295 rdf:type schema:CreativeWork
296 https://doi.org/10.1016/j.ijmm.2004.11.001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016577605
297 rdf:type schema:CreativeWork
298 https://doi.org/10.1016/j.mib.2003.12.006 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022105930
299 rdf:type schema:CreativeWork
300 https://doi.org/10.1016/j.mib.2008.12.003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002962917
301 rdf:type schema:CreativeWork
302 https://doi.org/10.1016/j.ygeno.2008.02.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047387894
303 rdf:type schema:CreativeWork
304 https://doi.org/10.1016/s0022-2836(05)80360-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013618994
305 rdf:type schema:CreativeWork
306 https://doi.org/10.1016/s0966-842x(02)02451-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037348621
307 rdf:type schema:CreativeWork
308 https://doi.org/10.1016/s1286-4579(03)00032-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045349230
309 rdf:type schema:CreativeWork
310 https://doi.org/10.1016/s1369-5274(02)00004-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030300320
311 rdf:type schema:CreativeWork
312 https://doi.org/10.1042/0264-6021:3440273 schema:sameAs https://app.dimensions.ai/details/publication/pub.1056714345
313 rdf:type schema:CreativeWork
314 https://doi.org/10.1046/j.1365-2958.2000.02133.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1042914038
315 rdf:type schema:CreativeWork
316 https://doi.org/10.1073/pnas.0409660102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050607248
317 rdf:type schema:CreativeWork
318 https://doi.org/10.1073/pnas.0504930102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008441401
319 rdf:type schema:CreativeWork
320 https://doi.org/10.1073/pnas.1731982100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000574692
321 rdf:type schema:CreativeWork
322 https://doi.org/10.1073/pnas.95.7.3943 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031136183
323 rdf:type schema:CreativeWork
324 https://doi.org/10.1073/pnas.96.19.10875 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013411703
325 rdf:type schema:CreativeWork
326 https://doi.org/10.1073/pnas.97.9.4856 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032763876
327 rdf:type schema:CreativeWork
328 https://doi.org/10.1093/bioinformatics/bth205 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053359138
329 rdf:type schema:CreativeWork
330 https://doi.org/10.1093/bioinformatics/bti054 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002594133
331 rdf:type schema:CreativeWork
332 https://doi.org/10.1093/bioinformatics/btl629 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017299791
333 rdf:type schema:CreativeWork
334 https://doi.org/10.1093/bioinformatics/btm451 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051622036
335 rdf:type schema:CreativeWork
336 https://doi.org/10.1093/emboj/19.13.3204 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044703718
337 rdf:type schema:CreativeWork
338 https://doi.org/10.1093/nar/gkm960 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050102057
339 rdf:type schema:CreativeWork
340 https://doi.org/10.1094/mpmi-18-0060 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060078192
341 rdf:type schema:CreativeWork
342 https://doi.org/10.1094/mpmi-18-0275 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060078214
343 rdf:type schema:CreativeWork
344 https://doi.org/10.1094/mpmi-19-1151 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060078433
345 rdf:type schema:CreativeWork
346 https://doi.org/10.1094/mpmi-20-2-0146 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060078564
347 rdf:type schema:CreativeWork
348 https://doi.org/10.1094/mpmi-21-6-0685 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060078754
349 rdf:type schema:CreativeWork
350 https://doi.org/10.1094/mpmi-22-1-0052 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060078813
351 rdf:type schema:CreativeWork
352 https://doi.org/10.1094/mpmi-4-553 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060079211
353 rdf:type schema:CreativeWork
354 https://doi.org/10.1094/mpmi-8-0717 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060079571
355 rdf:type schema:CreativeWork
356 https://doi.org/10.1094/mpmi.2000.13.12.1366 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060080184
357 rdf:type schema:CreativeWork
358 https://doi.org/10.1094/phyto-69-208 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060105687
359 rdf:type schema:CreativeWork
360 https://doi.org/10.1099/00207713-49-2-469 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060349923
361 rdf:type schema:CreativeWork
362 https://doi.org/10.1099/00221287-146-10-2447 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060370182
363 rdf:type schema:CreativeWork
364 https://doi.org/10.1101/gr.072033.107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038496028
365 rdf:type schema:CreativeWork
366 https://doi.org/10.1101/gr.073262.107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037655071
367 rdf:type schema:CreativeWork
368 https://doi.org/10.1101/gr.074492.107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051720574
369 rdf:type schema:CreativeWork
370 https://doi.org/10.1101/gr.078212.108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1047542880
371 rdf:type schema:CreativeWork
372 https://doi.org/10.1101/gr.083311.108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011112451
373 rdf:type schema:CreativeWork
374 https://doi.org/10.1101/gr.403602 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012195556
375 rdf:type schema:CreativeWork
376 https://doi.org/10.1101/gr.6435207 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033023123
377 rdf:type schema:CreativeWork
378 https://doi.org/10.1101/gr.7088808 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025227180
379 rdf:type schema:CreativeWork
380 https://doi.org/10.1101/gr.7337908 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035219026
381 rdf:type schema:CreativeWork
382 https://doi.org/10.1104/pp.71.4.912 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042838225
383 rdf:type schema:CreativeWork
384 https://doi.org/10.1105/tpc.13.5.1079 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048906839
385 rdf:type schema:CreativeWork
386 https://doi.org/10.1111/j.1365-313x.2006.02798.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1020054544
387 rdf:type schema:CreativeWork
388 https://doi.org/10.1111/j.1365-313x.2007.03126.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1052868330
389 rdf:type schema:CreativeWork
390 https://doi.org/10.1111/j.1574-6968.2006.00526.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1030390124
391 rdf:type schema:CreativeWork
392 https://doi.org/10.1111/j.1574-6968.2008.01441.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1016462719
393 rdf:type schema:CreativeWork
394 https://doi.org/10.1128/aac.01643-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007429625
395 rdf:type schema:CreativeWork
396 https://doi.org/10.1128/aem.70.4.1999-2012.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022014193
397 rdf:type schema:CreativeWork
398 https://doi.org/10.1128/iai.69.12.7471-7480.2001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007356590
399 rdf:type schema:CreativeWork
400 https://doi.org/10.1128/jb.00793-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018775269
401 rdf:type schema:CreativeWork
402 https://doi.org/10.1128/jb.00998-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036711998
403 rdf:type schema:CreativeWork
404 https://doi.org/10.1128/jb.01282-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046584111
405 rdf:type schema:CreativeWork
406 https://doi.org/10.1128/jb.170.8.3738-3741.1988 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062717155
407 rdf:type schema:CreativeWork
408 https://doi.org/10.1128/jb.185.19.5772-5778.2003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003824909
409 rdf:type schema:CreativeWork
410 https://doi.org/10.1128/jb.185.3.1018-1026.2003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048996782
411 rdf:type schema:CreativeWork
412 https://doi.org/10.1128/jb.186.15.5101-5115.2004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014979544
413 rdf:type schema:CreativeWork
414 https://doi.org/10.1128/jb.187.18.6488-6498.2005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012814363
415 rdf:type schema:CreativeWork
416 https://doi.org/10.1128/mmbr.69.1.155-194.2005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026986186
417 rdf:type schema:CreativeWork
418 https://doi.org/10.1146/annurev.genom.9.081307.164359 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015853776
419 rdf:type schema:CreativeWork
420 https://doi.org/10.1146/annurev.micro.54.1.735 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053645502
421 rdf:type schema:CreativeWork
422 https://doi.org/10.1146/annurev.micro.60.080805.142251 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013159069
423 rdf:type schema:CreativeWork
424 https://doi.org/10.1146/annurev.phyto.41.052002.095652 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010416651
425 rdf:type schema:CreativeWork
426 https://doi.org/10.1146/annurev.phyto.45.062806.094317 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028657088
427 rdf:type schema:CreativeWork
428 https://doi.org/10.1371/journal.pcbi.1000186 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012210496
429 rdf:type schema:CreativeWork
430 https://doi.org/10.1371/journal.pone.0000484 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040432928
431 rdf:type schema:CreativeWork
432 https://doi.org/10.2307/3871365 schema:sameAs https://app.dimensions.ai/details/publication/pub.1070469152
433 rdf:type schema:CreativeWork
434 https://www.grid.ac/institutes/grid.10698.36 schema:alternateName University of North Carolina at Chapel Hill
435 schema:name Department of Biology, CB# 3280, Coker Hall, The University of North Carolina at Chapel Hill, 27599-3280, Chapel Hill, North Carolina, USA
436 rdf:type schema:Organization
437 https://www.grid.ac/institutes/grid.18888.31 schema:alternateName Sainsbury Laboratory
438 schema:name The Sainsbury Laboratory, NR4 7UH, Norwich, UK
439 rdf:type schema:Organization
440 https://www.grid.ac/institutes/grid.4391.f schema:alternateName Oregon State University
441 schema:name Center for Genome Research and Biocomputing, Oregon State University, 2082 Cordley Hall, 97331, Corvallis, OR, USA
442 Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, 97331, Corvallis, OR, USA
443 rdf:type schema:Organization
 




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


...