Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-11-14

AUTHORS

Kira S Makarova, Vivek Anantharaman, L Aravind, Eugene V Koonin

ABSTRACT

BACKGROUND: The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune systems that discriminate self DNA from nonself DNA and specifically destroy the foreign, in particular viral, genomes, whereas the host genome is protected, or ii) programmed cell suicide or dormancy induced by infection. PRESENTATION OF THE HYPOTHESIS: Almost all genomic loci encoding immunity systems such as CRISPR-Cas, restriction-modification and DNA phosphorothioation also encompass suicide genes, in particular those encoding known and predicted toxin nucleases, which do not appear to be directly involved in immunity. In contrast, the immunity systems do not appear to encode antitoxins found in typical toxin-antitoxin systems. This raises the possibility that components of the immunity system themselves act as reversible inhibitors of the associated toxin proteins or domains as has been demonstrated for the Escherichia coli anticodon nuclease PrrC that interacts with the PrrI restriction-modification system. We hypothesize that coupling of diverse immunity and suicide/dormancy systems in prokaryotes evolved under selective pressure to provide robustness to the antivirus response. We further propose that the involvement of suicide/dormancy systems in the coupled antivirus response could take two distinct forms:1) induction of a dormancy-like state in the infected cell to 'buy time' for activation of adaptive immunity; 2) suicide or dormancy as the final recourse to prevent viral spread triggered by the failure of immunity. TESTING THE HYPOTHESIS: This hypothesis entails many experimentally testable predictions. Specifically, we predict that Cas2 protein present in all cas operons is a mRNA-cleaving nuclease (interferase) that might be activated at an early stage of virus infection to enable incorporation of virus-specific spacers into the CRISPR locus or to trigger cell suicide when the immune function of CRISPR-Cas systems fails. Similarly, toxin-like activity is predicted for components of numerous other defense loci. IMPLICATIONS OF THE HYPOTHESIS: The hypothesis implies that antivirus response in prokaryotes involves key decision-making steps at which the cell chooses the path to follow by sensing the course of virus infection. REVIEWERS: This article was reviewed by Arcady Mushegian, Etienne Joly and Nick Grishin. For complete reviews, go to the Reviewers' reports section. More... »

PAGES

40-40

References to SciGraph publications

  • 2003-11-26. New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system in GENOME BIOLOGY
  • 2010-12-03. Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation in VIROLOGY JOURNAL
  • 2009-08-25. Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements in BIOLOGY DIRECT
  • 2005-09-14. Viruses in the sea in NATURE
  • 2012-06-25. Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics in BIOLOGY DIRECT
  • 2011-05-09. Evolution and classification of the CRISPR–Cas systems in NATURE REVIEWS MICROBIOLOGY
  • 2011-09-19. Regulation of growth and death in Escherichia coli by toxin–antitoxin systems in NATURE REVIEWS MICROBIOLOGY
  • 2003-03. Restriction endonuclease in MOLECULAR BIOTECHNOLOGY
  • 2012-01. Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system in NATURE COMMUNICATIONS
  • 2009-06-03. Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes in BIOLOGY DIRECT
  • 2012-02-15. RNA-guided genetic silencing systems in bacteria and archaea in NATURE
  • 2011-07-14. Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems in BIOLOGY DIRECT
  • 2012-01-30. Success of a suicidal defense strategy against infection in a structured habitat in SCIENTIFIC REPORTS
  • 2006-03-16. A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action in BIOLOGY DIRECT
  • 2007-10. Marine viruses — major players in the global ecosystem in NATURE REVIEWS MICROBIOLOGY
  • 2010-03-29. Bacteriophage resistance mechanisms in NATURE REVIEWS MICROBIOLOGY
  • 2011-09-21. Structures of the RNA-guided surveillance complex from a bacterial immune system in NATURE
  • 2010-03-18. Mathematical Modelling of the Sporulation-Initiation Network in Bacillus Subtilis Revealing the Dual Role of the Putative Quorum-Sensing Signal Molecule PhrA in BULLETIN OF MATHEMATICAL BIOLOGY
  • 2008-03-17. MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases in BIOLOGY DIRECT
  • 2012-06-09. Bacteria–Virus Coevolution in EVOLUTIONARY SYSTEMS BIOLOGY
  • 2005-05-10. Viral metagenomics in NATURE REVIEWS MICROBIOLOGY
  • 2005-05. Prokaryotic toxin–antitoxin stress response loci in NATURE REVIEWS MICROBIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1745-6150-7-40

    DOI

    http://dx.doi.org/10.1186/1745-6150-7-40

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1046031735

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23151069


    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/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Microbiology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Archaea", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Archaeal Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Bacteria", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Bacterial Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Catalytic Domain", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA Restriction-Modification Enzymes", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Enzyme Activation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Evolution, Molecular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Host-Pathogen Interactions", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Operon", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Toxins, Biological", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Virus Physiological Phenomena", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA", 
              "id": "http://www.grid.ac/institutes/grid.419234.9", 
              "name": [
                "National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Makarova", 
            "givenName": "Kira S", 
            "id": "sg:person.0676725351.01", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676725351.01"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA", 
              "id": "http://www.grid.ac/institutes/grid.419234.9", 
              "name": [
                "National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Anantharaman", 
            "givenName": "Vivek", 
            "id": "sg:person.0673016603.16", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0673016603.16"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA", 
              "id": "http://www.grid.ac/institutes/grid.419234.9", 
              "name": [
                "National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Aravind", 
            "givenName": "L", 
            "id": "sg:person.01106662166.38", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01106662166.38"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA", 
              "id": "http://www.grid.ac/institutes/grid.419234.9", 
              "name": [
                "National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Koonin", 
            "givenName": "Eugene V", 
            "id": "sg:person.01017015051.78", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01017015051.78"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1385/mb:23:3:225", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018624526", 
              "https://doi.org/10.1385/mb:23:3:225"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1743-422x-7-360", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011404836", 
              "https://doi.org/10.1186/1743-422x-7-360"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro1163", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017393430", 
              "https://doi.org/10.1038/nrmicro1163"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-1-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011010591", 
              "https://doi.org/10.1186/1745-6150-1-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro2651", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028527851", 
              "https://doi.org/10.1038/nrmicro2651"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2003-4-12-r81", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016542336", 
              "https://doi.org/10.1186/gb-2003-4-12-r81"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-4-29", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015797830", 
              "https://doi.org/10.1186/1745-6150-4-29"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-6-38", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036092892", 
              "https://doi.org/10.1186/1745-6150-6-38"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature04160", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043981198", 
              "https://doi.org/10.1038/nature04160"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro2315", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035378322", 
              "https://doi.org/10.1038/nrmicro2315"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro1750", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1049635150", 
              "https://doi.org/10.1038/nrmicro1750"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10886", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1053669571", 
              "https://doi.org/10.1038/nature10886"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature10402", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003817588", 
              "https://doi.org/10.1038/nature10402"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-7-18", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040385591", 
              "https://doi.org/10.1186/1745-6150-7-18"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro1147", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034055556", 
              "https://doi.org/10.1038/nrmicro1147"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11538-010-9530-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017081866", 
              "https://doi.org/10.1007/s11538-010-9530-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-1-4614-3567-9_16", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022742188", 
              "https://doi.org/10.1007/978-1-4614-3567-9_16"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/srep00238", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007703661", 
              "https://doi.org/10.1038/srep00238"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-3-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006845773", 
              "https://doi.org/10.1186/1745-6150-3-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro2577", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020345829", 
              "https://doi.org/10.1038/nrmicro2577"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-4-19", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025245856", 
              "https://doi.org/10.1186/1745-6150-4-19"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms1937", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026211758", 
              "https://doi.org/10.1038/ncomms1937"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2012-11-14", 
        "datePublishedReg": "2012-11-14", 
        "description": "BACKGROUND: The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune systems that discriminate self DNA from nonself DNA and specifically destroy the foreign, in particular viral, genomes, whereas the host genome is protected, or ii) programmed cell suicide or dormancy induced by infection.\nPRESENTATION OF THE HYPOTHESIS: Almost all genomic loci encoding immunity systems such as CRISPR-Cas, restriction-modification and DNA phosphorothioation also encompass suicide genes, in particular those encoding known and predicted toxin nucleases, which do not appear to be directly involved in immunity. In contrast, the immunity systems do not appear to encode antitoxins found in typical toxin-antitoxin systems. This raises the possibility that components of the immunity system themselves act as reversible inhibitors of the associated toxin proteins or domains as has been demonstrated for the Escherichia coli anticodon nuclease PrrC that interacts with the PrrI restriction-modification system. We hypothesize that coupling of diverse immunity and suicide/dormancy systems in prokaryotes evolved under selective pressure to provide robustness to the antivirus response. We further propose that the involvement of suicide/dormancy systems in the coupled antivirus response could take two distinct forms:1) induction of a dormancy-like state in the infected cell to 'buy time' for activation of adaptive immunity; 2) suicide or dormancy as the final recourse to prevent viral spread triggered by the failure of immunity.\nTESTING THE HYPOTHESIS: This hypothesis entails many experimentally testable predictions. Specifically, we predict that Cas2 protein present in all cas operons is a mRNA-cleaving nuclease (interferase) that might be activated at an early stage of virus infection to enable incorporation of virus-specific spacers into the CRISPR locus or to trigger cell suicide when the immune function of CRISPR-Cas systems fails. Similarly, toxin-like activity is predicted for components of numerous other defense loci.\nIMPLICATIONS OF THE HYPOTHESIS: The hypothesis implies that antivirus response in prokaryotes involves key decision-making steps at which the cell chooses the path to follow by sensing the course of virus infection.\nREVIEWERS: This article was reviewed by Arcady Mushegian, Etienne Joly and Nick Grishin. For complete reviews, go to the Reviewers' reports section.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/1745-6150-7-40", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2726065", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1036001", 
            "issn": [
              "1745-6150"
            ], 
            "name": "Biology Direct", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "7"
          }
        ], 
        "keywords": [
          "cell suicide", 
          "immunity system", 
          "virus-host arms race", 
          "Reviewers' Reports section", 
          "antivirus response", 
          "anticodon nuclease PrrC", 
          "toxin-antitoxin systems", 
          "CRISPR-Cas systems", 
          "restriction-modification system", 
          "key decision-making step", 
          "dormancy-like state", 
          "evolutionary innovation", 
          "Etienne Joly", 
          "genomic loci", 
          "DNA phosphorothioation", 
          "Arcady Mushegian", 
          "nonself DNA", 
          "Nick Grishin", 
          "defense loci", 
          "Cas2 proteins", 
          "cas operon", 
          "CRISPR loci", 
          "toxin proteins", 
          "host genome", 
          "selective pressure", 
          "CRISPR-Cas", 
          "prokaryotes", 
          "self DNA", 
          "report sections", 
          "antivirus immunity", 
          "arms race", 
          "dormancy", 
          "loci", 
          "failure of immunity", 
          "genome", 
          "infected cells", 
          "defense system", 
          "nuclease", 
          "protein", 
          "DNA", 
          "testable predictions", 
          "adaptive immunity", 
          "archaea", 
          "operon", 
          "reversible inhibitor", 
          "cells", 
          "phosphorothioation", 
          "immune system", 
          "suicide gene", 
          "immune function", 
          "PrrC", 
          "genes", 
          "viral spread", 
          "immunity", 
          "virus infection", 
          "hypothesis", 
          "bacteria", 
          "toxin-like activity", 
          "Grishin", 
          "early stages", 
          "response", 
          "activation", 
          "induction", 
          "inhibitors", 
          "domain", 
          "viral", 
          "Joly", 
          "spacer", 
          "general principles", 
          "antitoxin", 
          "infection", 
          "components", 
          "decision-making steps", 
          "activity", 
          "final recourse", 
          "function", 
          "contrast", 
          "stage", 
          "involvement", 
          "incorporation", 
          "spread", 
          "step", 
          "system", 
          "review", 
          "implications", 
          "possibility", 
          "complete review", 
          "prediction", 
          "major theatres", 
          "coupling", 
          "race", 
          "state", 
          "time", 
          "suicide", 
          "sections", 
          "principles", 
          "course", 
          "pressure", 
          "presentation", 
          "testing", 
          "failure", 
          "robustness", 
          "innovation", 
          "path", 
          "article", 
          "recourse", 
          "theatre", 
          "elaborate antivirus defense systems", 
          "antivirus defense systems", 
          "particular viral", 
          "toxin nucleases", 
          "typical toxin-antitoxin systems", 
          "Escherichia coli anticodon nuclease PrrC", 
          "coli anticodon nuclease PrrC", 
          "nuclease PrrC", 
          "PrrI restriction-modification system", 
          "diverse immunity", 
          "suicide/dormancy systems", 
          "dormancy systems", 
          "mRNA-cleaving nuclease", 
          "virus-specific spacers", 
          "Mushegian"
        ], 
        "name": "Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes", 
        "pagination": "40-40", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1046031735"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/1745-6150-7-40"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "23151069"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/1745-6150-7-40", 
          "https://app.dimensions.ai/details/publication/pub.1046031735"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2021-12-01T19:25", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20211201/entities/gbq_results/article/article_561.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/1745-6150-7-40"
      }
    ]
     

    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.10.1186/1745-6150-7-40'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-7-40'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-7-40'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-7-40'


     

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

    342 TRIPLES      22 PREDICATES      181 URIs      151 LITERALS      19 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/1745-6150-7-40 schema:about N0784533421c5403cb82f94b8134f1009
    2 N1cd2055b933f4023bb7466670b2bdd59
    3 N3e6a3618b7944c1ea1a60a3f28c7aaea
    4 N42862849f4f540ffb522f701708aaa12
    5 N6d085b220f7841349c478dfdbdb0db57
    6 N7677d1e7e6f943dca6ebd96d1fa172c7
    7 N7739bb0ccf03432aa39b96b74c67d74c
    8 N9b080145fdb24639b7f400778cd34717
    9 Na9a5117fca404ae8ace826fd6f28891a
    10 Neae16588c94e43798d57c790612072d1
    11 Nfa01f3029d974133941bba8b15ca6c26
    12 Nff86afdcca6c4a969c35f886b2833fe8
    13 anzsrc-for:06
    14 anzsrc-for:0605
    15 schema:author N56098c4a5482492ea47d5468985d3b36
    16 schema:citation sg:pub.10.1007/978-1-4614-3567-9_16
    17 sg:pub.10.1007/s11538-010-9530-7
    18 sg:pub.10.1038/nature04160
    19 sg:pub.10.1038/nature10402
    20 sg:pub.10.1038/nature10886
    21 sg:pub.10.1038/ncomms1937
    22 sg:pub.10.1038/nrmicro1147
    23 sg:pub.10.1038/nrmicro1163
    24 sg:pub.10.1038/nrmicro1750
    25 sg:pub.10.1038/nrmicro2315
    26 sg:pub.10.1038/nrmicro2577
    27 sg:pub.10.1038/nrmicro2651
    28 sg:pub.10.1038/srep00238
    29 sg:pub.10.1186/1743-422x-7-360
    30 sg:pub.10.1186/1745-6150-1-7
    31 sg:pub.10.1186/1745-6150-3-8
    32 sg:pub.10.1186/1745-6150-4-19
    33 sg:pub.10.1186/1745-6150-4-29
    34 sg:pub.10.1186/1745-6150-6-38
    35 sg:pub.10.1186/1745-6150-7-18
    36 sg:pub.10.1186/gb-2003-4-12-r81
    37 sg:pub.10.1385/mb:23:3:225
    38 schema:datePublished 2012-11-14
    39 schema:datePublishedReg 2012-11-14
    40 schema:description BACKGROUND: The virus-host arms race is a major theater for evolutionary innovation. Archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune systems that discriminate self DNA from nonself DNA and specifically destroy the foreign, in particular viral, genomes, whereas the host genome is protected, or ii) programmed cell suicide or dormancy induced by infection. PRESENTATION OF THE HYPOTHESIS: Almost all genomic loci encoding immunity systems such as CRISPR-Cas, restriction-modification and DNA phosphorothioation also encompass suicide genes, in particular those encoding known and predicted toxin nucleases, which do not appear to be directly involved in immunity. In contrast, the immunity systems do not appear to encode antitoxins found in typical toxin-antitoxin systems. This raises the possibility that components of the immunity system themselves act as reversible inhibitors of the associated toxin proteins or domains as has been demonstrated for the Escherichia coli anticodon nuclease PrrC that interacts with the PrrI restriction-modification system. We hypothesize that coupling of diverse immunity and suicide/dormancy systems in prokaryotes evolved under selective pressure to provide robustness to the antivirus response. We further propose that the involvement of suicide/dormancy systems in the coupled antivirus response could take two distinct forms:1) induction of a dormancy-like state in the infected cell to 'buy time' for activation of adaptive immunity; 2) suicide or dormancy as the final recourse to prevent viral spread triggered by the failure of immunity. TESTING THE HYPOTHESIS: This hypothesis entails many experimentally testable predictions. Specifically, we predict that Cas2 protein present in all cas operons is a mRNA-cleaving nuclease (interferase) that might be activated at an early stage of virus infection to enable incorporation of virus-specific spacers into the CRISPR locus or to trigger cell suicide when the immune function of CRISPR-Cas systems fails. Similarly, toxin-like activity is predicted for components of numerous other defense loci. IMPLICATIONS OF THE HYPOTHESIS: The hypothesis implies that antivirus response in prokaryotes involves key decision-making steps at which the cell chooses the path to follow by sensing the course of virus infection. REVIEWERS: This article was reviewed by Arcady Mushegian, Etienne Joly and Nick Grishin. For complete reviews, go to the Reviewers' reports section.
    41 schema:genre article
    42 schema:inLanguage en
    43 schema:isAccessibleForFree true
    44 schema:isPartOf N3dfda16de3664bd2a73840e00366a8de
    45 N8a32d6666e314f90a3f6fc8e1581ac61
    46 sg:journal.1036001
    47 schema:keywords Arcady Mushegian
    48 CRISPR loci
    49 CRISPR-Cas
    50 CRISPR-Cas systems
    51 Cas2 proteins
    52 DNA
    53 DNA phosphorothioation
    54 Escherichia coli anticodon nuclease PrrC
    55 Etienne Joly
    56 Grishin
    57 Joly
    58 Mushegian
    59 Nick Grishin
    60 PrrC
    61 PrrI restriction-modification system
    62 Reviewers' Reports section
    63 activation
    64 activity
    65 adaptive immunity
    66 anticodon nuclease PrrC
    67 antitoxin
    68 antivirus defense systems
    69 antivirus immunity
    70 antivirus response
    71 archaea
    72 arms race
    73 article
    74 bacteria
    75 cas operon
    76 cell suicide
    77 cells
    78 coli anticodon nuclease PrrC
    79 complete review
    80 components
    81 contrast
    82 coupling
    83 course
    84 decision-making steps
    85 defense loci
    86 defense system
    87 diverse immunity
    88 domain
    89 dormancy
    90 dormancy systems
    91 dormancy-like state
    92 early stages
    93 elaborate antivirus defense systems
    94 evolutionary innovation
    95 failure
    96 failure of immunity
    97 final recourse
    98 function
    99 general principles
    100 genes
    101 genome
    102 genomic loci
    103 host genome
    104 hypothesis
    105 immune function
    106 immune system
    107 immunity
    108 immunity system
    109 implications
    110 incorporation
    111 induction
    112 infected cells
    113 infection
    114 inhibitors
    115 innovation
    116 involvement
    117 key decision-making step
    118 loci
    119 mRNA-cleaving nuclease
    120 major theatres
    121 nonself DNA
    122 nuclease
    123 nuclease PrrC
    124 operon
    125 particular viral
    126 path
    127 phosphorothioation
    128 possibility
    129 prediction
    130 presentation
    131 pressure
    132 principles
    133 prokaryotes
    134 protein
    135 race
    136 recourse
    137 report sections
    138 response
    139 restriction-modification system
    140 reversible inhibitor
    141 review
    142 robustness
    143 sections
    144 selective pressure
    145 self DNA
    146 spacer
    147 spread
    148 stage
    149 state
    150 step
    151 suicide
    152 suicide gene
    153 suicide/dormancy systems
    154 system
    155 testable predictions
    156 testing
    157 theatre
    158 time
    159 toxin nucleases
    160 toxin proteins
    161 toxin-antitoxin systems
    162 toxin-like activity
    163 typical toxin-antitoxin systems
    164 viral
    165 viral spread
    166 virus infection
    167 virus-host arms race
    168 virus-specific spacers
    169 schema:name Live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes
    170 schema:pagination 40-40
    171 schema:productId N5ee4111bc71646bf9ba429c98e5345dd
    172 Nbfa3be0b4c8043c89ecb079dda9c6242
    173 Nc35e2412bb25477ca01fd12177157b07
    174 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046031735
    175 https://doi.org/10.1186/1745-6150-7-40
    176 schema:sdDatePublished 2021-12-01T19:25
    177 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    178 schema:sdPublisher N868c203a9e4249ef977e916dbc4a5ab1
    179 schema:url https://doi.org/10.1186/1745-6150-7-40
    180 sgo:license sg:explorer/license/
    181 sgo:sdDataset articles
    182 rdf:type schema:ScholarlyArticle
    183 N0784533421c5403cb82f94b8134f1009 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    184 schema:name Operon
    185 rdf:type schema:DefinedTerm
    186 N1cd2055b933f4023bb7466670b2bdd59 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    187 schema:name Archaea
    188 rdf:type schema:DefinedTerm
    189 N3dfda16de3664bd2a73840e00366a8de schema:volumeNumber 7
    190 rdf:type schema:PublicationVolume
    191 N3e6a3618b7944c1ea1a60a3f28c7aaea schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    192 schema:name Archaeal Proteins
    193 rdf:type schema:DefinedTerm
    194 N42862849f4f540ffb522f701708aaa12 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    195 schema:name Catalytic Domain
    196 rdf:type schema:DefinedTerm
    197 N56098c4a5482492ea47d5468985d3b36 rdf:first sg:person.0676725351.01
    198 rdf:rest N703bf6e8a8a9443793e9232e1c5edba5
    199 N5ee4111bc71646bf9ba429c98e5345dd schema:name doi
    200 schema:value 10.1186/1745-6150-7-40
    201 rdf:type schema:PropertyValue
    202 N6d085b220f7841349c478dfdbdb0db57 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    203 schema:name Toxins, Biological
    204 rdf:type schema:DefinedTerm
    205 N703bf6e8a8a9443793e9232e1c5edba5 rdf:first sg:person.0673016603.16
    206 rdf:rest Nfbd43cbab2524cf48679d1db49d89e1e
    207 N7677d1e7e6f943dca6ebd96d1fa172c7 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    208 schema:name Enzyme Activation
    209 rdf:type schema:DefinedTerm
    210 N7739bb0ccf03432aa39b96b74c67d74c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    211 schema:name Bacteria
    212 rdf:type schema:DefinedTerm
    213 N868c203a9e4249ef977e916dbc4a5ab1 schema:name Springer Nature - SN SciGraph project
    214 rdf:type schema:Organization
    215 N8a32d6666e314f90a3f6fc8e1581ac61 schema:issueNumber 1
    216 rdf:type schema:PublicationIssue
    217 N9b080145fdb24639b7f400778cd34717 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    218 schema:name Evolution, Molecular
    219 rdf:type schema:DefinedTerm
    220 Na62fefdf1bfa422d87bf9001015aac6b rdf:first sg:person.01017015051.78
    221 rdf:rest rdf:nil
    222 Na9a5117fca404ae8ace826fd6f28891a schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    223 schema:name DNA Restriction-Modification Enzymes
    224 rdf:type schema:DefinedTerm
    225 Nbfa3be0b4c8043c89ecb079dda9c6242 schema:name pubmed_id
    226 schema:value 23151069
    227 rdf:type schema:PropertyValue
    228 Nc35e2412bb25477ca01fd12177157b07 schema:name dimensions_id
    229 schema:value pub.1046031735
    230 rdf:type schema:PropertyValue
    231 Neae16588c94e43798d57c790612072d1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    232 schema:name Host-Pathogen Interactions
    233 rdf:type schema:DefinedTerm
    234 Nfa01f3029d974133941bba8b15ca6c26 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    235 schema:name Virus Physiological Phenomena
    236 rdf:type schema:DefinedTerm
    237 Nfbd43cbab2524cf48679d1db49d89e1e rdf:first sg:person.01106662166.38
    238 rdf:rest Na62fefdf1bfa422d87bf9001015aac6b
    239 Nff86afdcca6c4a969c35f886b2833fe8 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    240 schema:name Bacterial Proteins
    241 rdf:type schema:DefinedTerm
    242 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    243 schema:name Biological Sciences
    244 rdf:type schema:DefinedTerm
    245 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
    246 schema:name Microbiology
    247 rdf:type schema:DefinedTerm
    248 sg:grant.2726065 http://pending.schema.org/fundedItem sg:pub.10.1186/1745-6150-7-40
    249 rdf:type schema:MonetaryGrant
    250 sg:journal.1036001 schema:issn 1745-6150
    251 schema:name Biology Direct
    252 schema:publisher Springer Nature
    253 rdf:type schema:Periodical
    254 sg:person.01017015051.78 schema:affiliation grid-institutes:grid.419234.9
    255 schema:familyName Koonin
    256 schema:givenName Eugene V
    257 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01017015051.78
    258 rdf:type schema:Person
    259 sg:person.01106662166.38 schema:affiliation grid-institutes:grid.419234.9
    260 schema:familyName Aravind
    261 schema:givenName L
    262 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01106662166.38
    263 rdf:type schema:Person
    264 sg:person.0673016603.16 schema:affiliation grid-institutes:grid.419234.9
    265 schema:familyName Anantharaman
    266 schema:givenName Vivek
    267 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0673016603.16
    268 rdf:type schema:Person
    269 sg:person.0676725351.01 schema:affiliation grid-institutes:grid.419234.9
    270 schema:familyName Makarova
    271 schema:givenName Kira S
    272 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676725351.01
    273 rdf:type schema:Person
    274 sg:pub.10.1007/978-1-4614-3567-9_16 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022742188
    275 https://doi.org/10.1007/978-1-4614-3567-9_16
    276 rdf:type schema:CreativeWork
    277 sg:pub.10.1007/s11538-010-9530-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017081866
    278 https://doi.org/10.1007/s11538-010-9530-7
    279 rdf:type schema:CreativeWork
    280 sg:pub.10.1038/nature04160 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043981198
    281 https://doi.org/10.1038/nature04160
    282 rdf:type schema:CreativeWork
    283 sg:pub.10.1038/nature10402 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003817588
    284 https://doi.org/10.1038/nature10402
    285 rdf:type schema:CreativeWork
    286 sg:pub.10.1038/nature10886 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053669571
    287 https://doi.org/10.1038/nature10886
    288 rdf:type schema:CreativeWork
    289 sg:pub.10.1038/ncomms1937 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026211758
    290 https://doi.org/10.1038/ncomms1937
    291 rdf:type schema:CreativeWork
    292 sg:pub.10.1038/nrmicro1147 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034055556
    293 https://doi.org/10.1038/nrmicro1147
    294 rdf:type schema:CreativeWork
    295 sg:pub.10.1038/nrmicro1163 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017393430
    296 https://doi.org/10.1038/nrmicro1163
    297 rdf:type schema:CreativeWork
    298 sg:pub.10.1038/nrmicro1750 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049635150
    299 https://doi.org/10.1038/nrmicro1750
    300 rdf:type schema:CreativeWork
    301 sg:pub.10.1038/nrmicro2315 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035378322
    302 https://doi.org/10.1038/nrmicro2315
    303 rdf:type schema:CreativeWork
    304 sg:pub.10.1038/nrmicro2577 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020345829
    305 https://doi.org/10.1038/nrmicro2577
    306 rdf:type schema:CreativeWork
    307 sg:pub.10.1038/nrmicro2651 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028527851
    308 https://doi.org/10.1038/nrmicro2651
    309 rdf:type schema:CreativeWork
    310 sg:pub.10.1038/srep00238 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007703661
    311 https://doi.org/10.1038/srep00238
    312 rdf:type schema:CreativeWork
    313 sg:pub.10.1186/1743-422x-7-360 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011404836
    314 https://doi.org/10.1186/1743-422x-7-360
    315 rdf:type schema:CreativeWork
    316 sg:pub.10.1186/1745-6150-1-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1011010591
    317 https://doi.org/10.1186/1745-6150-1-7
    318 rdf:type schema:CreativeWork
    319 sg:pub.10.1186/1745-6150-3-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006845773
    320 https://doi.org/10.1186/1745-6150-3-8
    321 rdf:type schema:CreativeWork
    322 sg:pub.10.1186/1745-6150-4-19 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025245856
    323 https://doi.org/10.1186/1745-6150-4-19
    324 rdf:type schema:CreativeWork
    325 sg:pub.10.1186/1745-6150-4-29 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015797830
    326 https://doi.org/10.1186/1745-6150-4-29
    327 rdf:type schema:CreativeWork
    328 sg:pub.10.1186/1745-6150-6-38 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036092892
    329 https://doi.org/10.1186/1745-6150-6-38
    330 rdf:type schema:CreativeWork
    331 sg:pub.10.1186/1745-6150-7-18 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040385591
    332 https://doi.org/10.1186/1745-6150-7-18
    333 rdf:type schema:CreativeWork
    334 sg:pub.10.1186/gb-2003-4-12-r81 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016542336
    335 https://doi.org/10.1186/gb-2003-4-12-r81
    336 rdf:type schema:CreativeWork
    337 sg:pub.10.1385/mb:23:3:225 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018624526
    338 https://doi.org/10.1385/mb:23:3:225
    339 rdf:type schema:CreativeWork
    340 grid-institutes:grid.419234.9 schema:alternateName National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
    341 schema:name National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, 20894, USA
    342 rdf:type schema:Organization
     




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


    ...