High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-12

AUTHORS

G. Salvadori, R. Junges, H. A. Åmdal, T. Chen, D. A. Morrison, F. C. Petersen

ABSTRACT

BACKGROUND: In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the absence of a widespread functional competence system have been reported for Streptococcus mitis, recent studies revealed that, at least for some strains, high efficiencies can be achieved following optimization protocols. To gain a deeper insight into competence in this species, we used RNA-seq, to map the global CSP response of two transformable strains: the type strain NCTC12261T and SK321. RESULTS: All known genes induced by ComE in Streptococcus pneumoniae, including sigX, were upregulated in the two strains. Likewise, all sets of streptococcal SigX core genes involved in extracellular DNA uptake, recombination, and fratricide were upregulated. No significant differences in the set of induced genes were observed when the type strain was grown in rich or semi-defined media. Five upregulated operons unique to S. mitis with a SigX-box in the promoter region were identified, including two specific to SK321, and one specific to NCTC12261T. Two of the strain-specific operons coded for different bacteriocins. Deletion of the unique S. mitis sigX regulated genes had no effect on transformation. CONCLUSIONS: Overall, comparison of the global transcriptome in response to CSP shows the conservation of the ComE and SigX-core regulons in competent S. mitis isolates, as well as species and strain-specific genes. Although some S. mitis exhibit truncations in key competence genes, this study shows that in transformable strains, competence seems to depend on the same core genes previously identified in S. pneumoniae. More... »

PAGES

453

Journal

TITLE

BMC Genomics

ISSUE

1

VOLUME

19

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s12864-018-4802-y

DOI

http://dx.doi.org/10.1186/s12864-018-4802-y

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1104559881

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/29898666


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"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "name": [
            "Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Salvadori", 
        "givenName": "G.", 
        "id": "sg:person.0655606014.41", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0655606014.41"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Junges", 
        "givenName": "R.", 
        "id": "sg:person.010466032505.86", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010466032505.86"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway"
          ], 
          "type": "Organization"
        }, 
        "familyName": "\u00c5mdal", 
        "givenName": "H. A.", 
        "id": "sg:person.01062515207.92", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01062515207.92"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Harvard University", 
          "id": "https://www.grid.ac/institutes/grid.38142.3c", 
          "name": [
            "Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chen", 
        "givenName": "T.", 
        "id": "sg:person.016673767277.23", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016673767277.23"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Illinois at Chicago", 
          "id": "https://www.grid.ac/institutes/grid.185648.6", 
          "name": [
            "Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Morrison", 
        "givenName": "D. A.", 
        "id": "sg:person.01072070075.19", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01072070075.19"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "name": [
            "Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Petersen", 
        "givenName": "F. C.", 
        "id": "sg:person.01035133120.07", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035133120.07"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1016/j.ijmm.2007.02.009", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001718464"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/iai.68.3.1374-1382.2000", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002244578"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/msystems.00038-15", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1004498950"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s12602-009-9021-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005215375", 
          "https://doi.org/10.1007/s12602-009-9021-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s12602-009-9021-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005215375", 
          "https://doi.org/10.1007/s12602-009-9021-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pgen.1005353", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1006177679"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.1998.00737.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007799876"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.1998.00737.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007799876"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.1993.tb01723.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008587535"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-60761-820-1_12", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008856508", 
          "https://doi.org/10.1007/978-1-60761-820-1_12"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-60761-820-1_12", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008856508", 
          "https://doi.org/10.1007/978-1-60761-820-1_12"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2005.05021.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009815984"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2005.05021.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009815984"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.1998.00904.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009902779"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.1998.00904.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009902779"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2672.2004.02420.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1012175245"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.1999.01528.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1013504478"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2005.04695.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016120659"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2005.04695.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016120659"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mbio.01490-14", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017607424"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0378-1119(92)90016-i", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018997382"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0378-1119(92)90016-i", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1018997382"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.ppat.1003596", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1019982093"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.01750-08", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021119305"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.06273-11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022314153"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2003.03892.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022826696"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.05968-11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022923642"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0500879102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023850937"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0500879102", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023850937"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2007.05757.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026802155"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.01023-07", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027094674"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.92.24.11140", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027843462"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.micinf.2014.11.002", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030244521"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.1996.501417.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031045089"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/gb-2010-11-10-r106", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031289083", 
          "https://doi.org/10.1186/gb-2010-11-10-r106"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btu153", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031501454"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.ppat.1003178", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038101516"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/0378-1119(94)00841-f", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040356030"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0167-7012(01)00369-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1040525782"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.3389/fmicb.2016.01009", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042431646"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.2041-1014.2011.00606.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042650982"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/mbio.00071-11", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043179028"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1365-2958.2008.06288.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043371868"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/iai.69.4.2477-2486.2001", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1043944239"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.2003.03714.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045581276"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.182.21.6192-6202.2000", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1046814739"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0002683", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048625490"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s12866-016-0771-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049832132", 
          "https://doi.org/10.1186/s12866-016-0771-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/s12866-016-0771-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049832132", 
          "https://doi.org/10.1186/s12866-016-0771-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.187.13.4338-4345.2005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051010097"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1046/j.1365-2958.2003.03907.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052705851"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0009426", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053359396"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1574-6968.1999.tb13460.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053483457"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1574-6968.1999.tb13460.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053483457"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1099/00222615-42-1-67", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060378648"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1099/ijsem.0.001433", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1060389451"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1061217", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062445088"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/jb.01174-06", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062711745"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1080101504", 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://app.dimensions.ai/details/publication/pub.1083255143", 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/s41598-017-04768-5", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1090717719", 
          "https://doi.org/10.1038/s41598-017-04768-5"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/msphere.00324-17", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1091691754"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2018-12", 
    "datePublishedReg": "2018-12-01", 
    "description": "BACKGROUND: In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the absence of a widespread functional competence system have been reported for Streptococcus mitis, recent studies revealed that, at least for some strains, high efficiencies can be achieved following optimization protocols. To gain a deeper insight into competence in this species, we used\u00a0RNA-seq, to map the\u00a0global CSP response of two transformable strains:\u00a0the type strain NCTC12261T and SK321.\nRESULTS: All known genes induced by ComE in Streptococcus pneumoniae, including sigX, were upregulated in the two strains. Likewise, all sets of streptococcal SigX core genes involved in extracellular DNA uptake, recombination, and fratricide were upregulated. No significant differences in the set of induced genes were observed when the type strain was grown in rich or semi-defined media. Five upregulated operons unique to S. mitis with a SigX-box in the promoter region were identified, including two specific to SK321, and one specific to NCTC12261T. Two of the strain-specific operons coded for different bacteriocins. Deletion of the unique S. mitis sigX regulated\u00a0genes had no effect on transformation.\nCONCLUSIONS: Overall, comparison of the global transcriptome in response to CSP shows the conservation of the ComE and SigX-core regulons in competent S. mitis isolates, as well as species and strain-specific genes. Although some\u00a0S. mitis exhibit truncations in key competence genes, this study shows that in transformable strains, competence seems to depend on the same core genes previously identified in S. pneumoniae.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/s12864-018-4802-y", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "19"
      }
    ], 
    "name": "High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes", 
    "pagination": "453", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "a0cc4069efb1b37db30e68d123e33be5ac30cc9af5f21fd4c373c859bab5d98e"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "29898666"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965258"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s12864-018-4802-y"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1104559881"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s12864-018-4802-y", 
      "https://app.dimensions.ai/details/publication/pub.1104559881"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T14:19", 
    "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_8660_00000570.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://link.springer.com/10.1186%2Fs12864-018-4802-y"
  }
]
 

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/s12864-018-4802-y'

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/s12864-018-4802-y'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12864-018-4802-y'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12864-018-4802-y'


 

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

273 TRIPLES      21 PREDICATES      81 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s12864-018-4802-y schema:about anzsrc-for:06
2 anzsrc-for:0604
3 schema:author N98b102ddcad74556ad1fe84da3461164
4 schema:citation sg:pub.10.1007/978-1-60761-820-1_12
5 sg:pub.10.1007/s12602-009-9021-z
6 sg:pub.10.1038/s41598-017-04768-5
7 sg:pub.10.1186/gb-2010-11-10-r106
8 sg:pub.10.1186/s12866-016-0771-y
9 https://app.dimensions.ai/details/publication/pub.1080101504
10 https://app.dimensions.ai/details/publication/pub.1083255143
11 https://doi.org/10.1016/0378-1119(92)90016-i
12 https://doi.org/10.1016/0378-1119(94)00841-f
13 https://doi.org/10.1016/j.ijmm.2007.02.009
14 https://doi.org/10.1016/j.micinf.2014.11.002
15 https://doi.org/10.1016/s0167-7012(01)00369-4
16 https://doi.org/10.1046/j.1365-2958.1996.501417.x
17 https://doi.org/10.1046/j.1365-2958.1998.00737.x
18 https://doi.org/10.1046/j.1365-2958.1998.00904.x
19 https://doi.org/10.1046/j.1365-2958.1999.01528.x
20 https://doi.org/10.1046/j.1365-2958.2003.03714.x
21 https://doi.org/10.1046/j.1365-2958.2003.03907.x
22 https://doi.org/10.1073/pnas.0500879102
23 https://doi.org/10.1073/pnas.92.24.11140
24 https://doi.org/10.1093/bioinformatics/btu153
25 https://doi.org/10.1099/00222615-42-1-67
26 https://doi.org/10.1099/ijsem.0.001433
27 https://doi.org/10.1111/j.1365-2672.2004.02420.x
28 https://doi.org/10.1111/j.1365-2958.1993.tb01723.x
29 https://doi.org/10.1111/j.1365-2958.2003.03892.x
30 https://doi.org/10.1111/j.1365-2958.2005.04695.x
31 https://doi.org/10.1111/j.1365-2958.2005.05021.x
32 https://doi.org/10.1111/j.1365-2958.2007.05757.x
33 https://doi.org/10.1111/j.1365-2958.2008.06288.x
34 https://doi.org/10.1111/j.1574-6968.1999.tb13460.x
35 https://doi.org/10.1111/j.2041-1014.2011.00606.x
36 https://doi.org/10.1126/science.1061217
37 https://doi.org/10.1128/iai.68.3.1374-1382.2000
38 https://doi.org/10.1128/iai.69.4.2477-2486.2001
39 https://doi.org/10.1128/jb.01023-07
40 https://doi.org/10.1128/jb.01174-06
41 https://doi.org/10.1128/jb.01750-08
42 https://doi.org/10.1128/jb.05968-11
43 https://doi.org/10.1128/jb.06273-11
44 https://doi.org/10.1128/jb.182.21.6192-6202.2000
45 https://doi.org/10.1128/jb.187.13.4338-4345.2005
46 https://doi.org/10.1128/mbio.00071-11
47 https://doi.org/10.1128/mbio.01490-14
48 https://doi.org/10.1128/msphere.00324-17
49 https://doi.org/10.1128/msystems.00038-15
50 https://doi.org/10.1371/journal.pgen.1005353
51 https://doi.org/10.1371/journal.pone.0002683
52 https://doi.org/10.1371/journal.pone.0009426
53 https://doi.org/10.1371/journal.ppat.1003178
54 https://doi.org/10.1371/journal.ppat.1003596
55 https://doi.org/10.3389/fmicb.2016.01009
56 schema:datePublished 2018-12
57 schema:datePublishedReg 2018-12-01
58 schema:description BACKGROUND: In streptococci of the mitis group, competence for natural transformation is a transient physiological state triggered by competence stimulating peptides (CSPs). Although low transformation yields and the absence of a widespread functional competence system have been reported for Streptococcus mitis, recent studies revealed that, at least for some strains, high efficiencies can be achieved following optimization protocols. To gain a deeper insight into competence in this species, we used RNA-seq, to map the global CSP response of two transformable strains: the type strain NCTC12261T and SK321. RESULTS: All known genes induced by ComE in Streptococcus pneumoniae, including sigX, were upregulated in the two strains. Likewise, all sets of streptococcal SigX core genes involved in extracellular DNA uptake, recombination, and fratricide were upregulated. No significant differences in the set of induced genes were observed when the type strain was grown in rich or semi-defined media. Five upregulated operons unique to S. mitis with a SigX-box in the promoter region were identified, including two specific to SK321, and one specific to NCTC12261T. Two of the strain-specific operons coded for different bacteriocins. Deletion of the unique S. mitis sigX regulated genes had no effect on transformation. CONCLUSIONS: Overall, comparison of the global transcriptome in response to CSP shows the conservation of the ComE and SigX-core regulons in competent S. mitis isolates, as well as species and strain-specific genes. Although some S. mitis exhibit truncations in key competence genes, this study shows that in transformable strains, competence seems to depend on the same core genes previously identified in S. pneumoniae.
59 schema:genre research_article
60 schema:inLanguage en
61 schema:isAccessibleForFree true
62 schema:isPartOf N45c0242cea804cf2a8687d200ba0cb21
63 N9a7247ec353e4510a32593bb6e5e4628
64 sg:journal.1023790
65 schema:name High-resolution profiles of the Streptococcus mitis CSP signaling pathway reveal core and strain-specific regulated genes
66 schema:pagination 453
67 schema:productId N48327e099d7e454ca5390c1a7091edba
68 N4a915f1772954c1ca69def85b52c9c6c
69 N5d78b7eda0a04bf9871d87500755fb72
70 N908d4b24963e462296e091360114ab6a
71 Ne148f918c38449cbb2f12d8f778a4557
72 schema:sameAs https://app.dimensions.ai/details/publication/pub.1104559881
73 https://doi.org/10.1186/s12864-018-4802-y
74 schema:sdDatePublished 2019-04-10T14:19
75 schema:sdLicense https://scigraph.springernature.com/explorer/license/
76 schema:sdPublisher Nbadd4ac7f3c443a28059c67554bda09b
77 schema:url https://link.springer.com/10.1186%2Fs12864-018-4802-y
78 sgo:license sg:explorer/license/
79 sgo:sdDataset articles
80 rdf:type schema:ScholarlyArticle
81 N14f06e97da1b4cbb9f64c9ec64934586 rdf:first sg:person.016673767277.23
82 rdf:rest N62c8436945ca48e0a15613da74ae2e3e
83 N1d1ee92cacd247a387f15fc8526559e3 schema:name Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
84 rdf:type schema:Organization
85 N2d17f36995ef4e2d8c1fda1c1d098c74 rdf:first sg:person.01062515207.92
86 rdf:rest N14f06e97da1b4cbb9f64c9ec64934586
87 N45c0242cea804cf2a8687d200ba0cb21 schema:issueNumber 1
88 rdf:type schema:PublicationIssue
89 N48327e099d7e454ca5390c1a7091edba schema:name dimensions_id
90 schema:value pub.1104559881
91 rdf:type schema:PropertyValue
92 N4a915f1772954c1ca69def85b52c9c6c schema:name doi
93 schema:value 10.1186/s12864-018-4802-y
94 rdf:type schema:PropertyValue
95 N4b94a6fcfa4248708a2d4cfec7ba6146 rdf:first sg:person.01035133120.07
96 rdf:rest rdf:nil
97 N5d78b7eda0a04bf9871d87500755fb72 schema:name nlm_unique_id
98 schema:value 100965258
99 rdf:type schema:PropertyValue
100 N62c8436945ca48e0a15613da74ae2e3e rdf:first sg:person.01072070075.19
101 rdf:rest N4b94a6fcfa4248708a2d4cfec7ba6146
102 N71d9493ed55343fa849e4ef22fc5be44 schema:name Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
103 rdf:type schema:Organization
104 N908d4b24963e462296e091360114ab6a schema:name pubmed_id
105 schema:value 29898666
106 rdf:type schema:PropertyValue
107 N98b102ddcad74556ad1fe84da3461164 rdf:first sg:person.0655606014.41
108 rdf:rest N9e4c04a39942475bb08d444b2ba87968
109 N9a7247ec353e4510a32593bb6e5e4628 schema:volumeNumber 19
110 rdf:type schema:PublicationVolume
111 N9e4c04a39942475bb08d444b2ba87968 rdf:first sg:person.010466032505.86
112 rdf:rest N2d17f36995ef4e2d8c1fda1c1d098c74
113 Nbadd4ac7f3c443a28059c67554bda09b schema:name Springer Nature - SN SciGraph project
114 rdf:type schema:Organization
115 Nce1e5905294e4af5bcc2a020dc0ea566 schema:name Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
116 rdf:type schema:Organization
117 Ne148f918c38449cbb2f12d8f778a4557 schema:name readcube_id
118 schema:value a0cc4069efb1b37db30e68d123e33be5ac30cc9af5f21fd4c373c859bab5d98e
119 rdf:type schema:PropertyValue
120 Nec247a6388d24cf091a633999eb8909f schema:name Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Postboks 1052, Blindern, 0316, Oslo, Norway
121 rdf:type schema:Organization
122 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
123 schema:name Biological Sciences
124 rdf:type schema:DefinedTerm
125 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
126 schema:name Genetics
127 rdf:type schema:DefinedTerm
128 sg:journal.1023790 schema:issn 1471-2164
129 schema:name BMC Genomics
130 rdf:type schema:Periodical
131 sg:person.01035133120.07 schema:affiliation N1d1ee92cacd247a387f15fc8526559e3
132 schema:familyName Petersen
133 schema:givenName F. C.
134 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035133120.07
135 rdf:type schema:Person
136 sg:person.010466032505.86 schema:affiliation Nce1e5905294e4af5bcc2a020dc0ea566
137 schema:familyName Junges
138 schema:givenName R.
139 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010466032505.86
140 rdf:type schema:Person
141 sg:person.01062515207.92 schema:affiliation N71d9493ed55343fa849e4ef22fc5be44
142 schema:familyName Åmdal
143 schema:givenName H. A.
144 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01062515207.92
145 rdf:type schema:Person
146 sg:person.01072070075.19 schema:affiliation https://www.grid.ac/institutes/grid.185648.6
147 schema:familyName Morrison
148 schema:givenName D. A.
149 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01072070075.19
150 rdf:type schema:Person
151 sg:person.016673767277.23 schema:affiliation https://www.grid.ac/institutes/grid.38142.3c
152 schema:familyName Chen
153 schema:givenName T.
154 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016673767277.23
155 rdf:type schema:Person
156 sg:person.0655606014.41 schema:affiliation Nec247a6388d24cf091a633999eb8909f
157 schema:familyName Salvadori
158 schema:givenName G.
159 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0655606014.41
160 rdf:type schema:Person
161 sg:pub.10.1007/978-1-60761-820-1_12 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008856508
162 https://doi.org/10.1007/978-1-60761-820-1_12
163 rdf:type schema:CreativeWork
164 sg:pub.10.1007/s12602-009-9021-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1005215375
165 https://doi.org/10.1007/s12602-009-9021-z
166 rdf:type schema:CreativeWork
167 sg:pub.10.1038/s41598-017-04768-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1090717719
168 https://doi.org/10.1038/s41598-017-04768-5
169 rdf:type schema:CreativeWork
170 sg:pub.10.1186/gb-2010-11-10-r106 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031289083
171 https://doi.org/10.1186/gb-2010-11-10-r106
172 rdf:type schema:CreativeWork
173 sg:pub.10.1186/s12866-016-0771-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1049832132
174 https://doi.org/10.1186/s12866-016-0771-y
175 rdf:type schema:CreativeWork
176 https://app.dimensions.ai/details/publication/pub.1080101504 schema:CreativeWork
177 https://app.dimensions.ai/details/publication/pub.1083255143 schema:CreativeWork
178 https://doi.org/10.1016/0378-1119(92)90016-i schema:sameAs https://app.dimensions.ai/details/publication/pub.1018997382
179 rdf:type schema:CreativeWork
180 https://doi.org/10.1016/0378-1119(94)00841-f schema:sameAs https://app.dimensions.ai/details/publication/pub.1040356030
181 rdf:type schema:CreativeWork
182 https://doi.org/10.1016/j.ijmm.2007.02.009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001718464
183 rdf:type schema:CreativeWork
184 https://doi.org/10.1016/j.micinf.2014.11.002 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030244521
185 rdf:type schema:CreativeWork
186 https://doi.org/10.1016/s0167-7012(01)00369-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040525782
187 rdf:type schema:CreativeWork
188 https://doi.org/10.1046/j.1365-2958.1996.501417.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1031045089
189 rdf:type schema:CreativeWork
190 https://doi.org/10.1046/j.1365-2958.1998.00737.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1007799876
191 rdf:type schema:CreativeWork
192 https://doi.org/10.1046/j.1365-2958.1998.00904.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1009902779
193 rdf:type schema:CreativeWork
194 https://doi.org/10.1046/j.1365-2958.1999.01528.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1013504478
195 rdf:type schema:CreativeWork
196 https://doi.org/10.1046/j.1365-2958.2003.03714.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1045581276
197 rdf:type schema:CreativeWork
198 https://doi.org/10.1046/j.1365-2958.2003.03907.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1052705851
199 rdf:type schema:CreativeWork
200 https://doi.org/10.1073/pnas.0500879102 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023850937
201 rdf:type schema:CreativeWork
202 https://doi.org/10.1073/pnas.92.24.11140 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027843462
203 rdf:type schema:CreativeWork
204 https://doi.org/10.1093/bioinformatics/btu153 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031501454
205 rdf:type schema:CreativeWork
206 https://doi.org/10.1099/00222615-42-1-67 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060378648
207 rdf:type schema:CreativeWork
208 https://doi.org/10.1099/ijsem.0.001433 schema:sameAs https://app.dimensions.ai/details/publication/pub.1060389451
209 rdf:type schema:CreativeWork
210 https://doi.org/10.1111/j.1365-2672.2004.02420.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1012175245
211 rdf:type schema:CreativeWork
212 https://doi.org/10.1111/j.1365-2958.1993.tb01723.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1008587535
213 rdf:type schema:CreativeWork
214 https://doi.org/10.1111/j.1365-2958.2003.03892.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1022826696
215 rdf:type schema:CreativeWork
216 https://doi.org/10.1111/j.1365-2958.2005.04695.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1016120659
217 rdf:type schema:CreativeWork
218 https://doi.org/10.1111/j.1365-2958.2005.05021.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1009815984
219 rdf:type schema:CreativeWork
220 https://doi.org/10.1111/j.1365-2958.2007.05757.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1026802155
221 rdf:type schema:CreativeWork
222 https://doi.org/10.1111/j.1365-2958.2008.06288.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1043371868
223 rdf:type schema:CreativeWork
224 https://doi.org/10.1111/j.1574-6968.1999.tb13460.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1053483457
225 rdf:type schema:CreativeWork
226 https://doi.org/10.1111/j.2041-1014.2011.00606.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1042650982
227 rdf:type schema:CreativeWork
228 https://doi.org/10.1126/science.1061217 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062445088
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1128/iai.68.3.1374-1382.2000 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002244578
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1128/iai.69.4.2477-2486.2001 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043944239
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1128/jb.01023-07 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027094674
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1128/jb.01174-06 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062711745
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1128/jb.01750-08 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021119305
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1128/jb.05968-11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022923642
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1128/jb.06273-11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022314153
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1128/jb.182.21.6192-6202.2000 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046814739
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1128/jb.187.13.4338-4345.2005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051010097
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1128/mbio.00071-11 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043179028
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1128/mbio.01490-14 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017607424
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1128/msphere.00324-17 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091691754
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1128/msystems.00038-15 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004498950
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1371/journal.pgen.1005353 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006177679
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1371/journal.pone.0002683 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048625490
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1371/journal.pone.0009426 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053359396
261 rdf:type schema:CreativeWork
262 https://doi.org/10.1371/journal.ppat.1003178 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038101516
263 rdf:type schema:CreativeWork
264 https://doi.org/10.1371/journal.ppat.1003596 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019982093
265 rdf:type schema:CreativeWork
266 https://doi.org/10.3389/fmicb.2016.01009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042431646
267 rdf:type schema:CreativeWork
268 https://www.grid.ac/institutes/grid.185648.6 schema:alternateName University of Illinois at Chicago
269 schema:name Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois at Chicago, Chicago, IL, USA
270 rdf:type schema:Organization
271 https://www.grid.ac/institutes/grid.38142.3c schema:alternateName Harvard University
272 schema:name Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
273 rdf:type schema:Organization
 




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


...