Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, ... View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2013-04-22

AUTHORS

Mircea Podar, Kira S Makarova, David E Graham, Yuri I Wolf, Eugene V Koonin, Anna-Louise Reysenbach

ABSTRACT

BACKGROUND: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. CONCLUSIONS: Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. REVIEWERS: This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia. More... »

PAGES

9-9

References to SciGraph publications

  • 2008-02-08. The RAST Server: Rapid Annotations using Subsystems Technology in BMC GENOMICS
  • 2012-12-14. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer in BIOLOGY DIRECT
  • 2011-09-18. De novo assembly of bacterial genomes from single cells in NATURE BIOTECHNOLOGY
  • 2011-05-09. Evolution and classification of the CRISPR–Cas systems in NATURE REVIEWS MICROBIOLOGY
  • 2004-09-14. Composition of the lipids of Nanoarchaeum equitans and their origin from its host Ignicoccus sp. strain KIN4/I in ARCHIVES OF MICROBIOLOGY
  • 2007-01-15. Prediction of effective genome size in metagenomic samples in GENOME BIOLOGY
  • 2005-02. Nanoarchaeum equitans creates functional tRNAs from separate genes for their 5′- and 3′-halves in NATURE
  • 2007-11-27. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea in BIOLOGY DIRECT
  • 2002-05. A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont in NATURE
  • 2008-05. Life without RNase P in NATURE
  • 2012-02-13. The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes in BIOLOGY DIRECT
  • 2012-08-14. Genomic sequencing of uncultured microorganisms from single cells in NATURE REVIEWS MICROBIOLOGY
  • 2009-09-17. Formal Proof that the Split Genes of tRNAs of Nanoarchaeum equitans Are an Ancestral Character in JOURNAL OF MOLECULAR EVOLUTION
  • 2012-07-18. RNA processing in the minimal organism Nanoarchaeum equitans in GENOME BIOLOGY
  • 2011-09-13. Functional curation of the Sulfolobus solfataricus P2 and S. acidocaldarius 98-3 complete genome sequences in EXTREMOPHILES
  • 2004-02-26. Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox in GENOME BIOLOGY
  • 2008-11-10. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans in GENOME BIOLOGY
  • 2008-07-12. Ignicoccus hospitalis and Nanoarchaeum equitans: ultrastructure, cell–cell interaction, and 3D reconstruction from serial sections of freeze-substituted cells and by electron cryotomography in ARCHIVES OF MICROBIOLOGY
  • 2008-06-14. Nanoarchaeal 16S rRNA gene sequences are widely dispersed in hyperthermophilic and mesophilic halophilic environments in EXTREMOPHILES
  • 2005-04-14. Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? in GENOME BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1745-6150-8-9

    DOI

    http://dx.doi.org/10.1186/1745-6150-8-9

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1025008134

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/23607440


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Archaeal Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Biological Evolution", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Evolution, Molecular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Archaeal", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Molecular Sequence Data", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Nanoarchaeota", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Polymerase Chain Reaction", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Homology", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sulfolobales", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Symbiosis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Wyoming", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA", 
              "id": "http://www.grid.ac/institutes/grid.411461.7", 
              "name": [
                "Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA", 
                "Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Podar", 
            "givenName": "Mircea", 
            "id": "sg:person.01334660037.45", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01334660037.45"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA", 
              "id": "http://www.grid.ac/institutes/grid.419234.9", 
              "name": [
                "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 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": "Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA", 
              "id": "http://www.grid.ac/institutes/grid.411461.7", 
              "name": [
                "Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA", 
                "Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Graham", 
            "givenName": "David E", 
            "id": "sg:person.0755636111.03", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755636111.03"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA", 
              "id": "http://www.grid.ac/institutes/grid.419234.9", 
              "name": [
                "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wolf", 
            "givenName": "Yuri I", 
            "id": "sg:person.0634453251.89", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634453251.89"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA", 
              "id": "http://www.grid.ac/institutes/grid.419234.9", 
              "name": [
                "National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 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"
          }, 
          {
            "affiliation": {
              "alternateName": "Department of Biology, Portland State University, Portland, OR, 97207, USA", 
              "id": "http://www.grid.ac/institutes/grid.262075.4", 
              "name": [
                "Department of Biology, Portland State University, Portland, OR, 97207, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Reysenbach", 
            "givenName": "Anna-Louise", 
            "id": "sg:person.01035426230.62", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035426230.62"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1186/gb-2004-5-3-r17", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028464475", 
              "https://doi.org/10.1186/gb-2004-5-3-r17"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2012-13-7-r63", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007749102", 
              "https://doi.org/10.1186/gb-2012-13-7-r63"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.1966", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013335891", 
              "https://doi.org/10.1038/nbt.1966"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature06833", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035908939", 
              "https://doi.org/10.1038/nature06833"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2008-9-11-r158", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051170330", 
              "https://doi.org/10.1186/gb-2008-9-11-r158"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00792-011-0392-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008401059", 
              "https://doi.org/10.1007/s00792-011-0392-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00203-008-0402-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013570847", 
              "https://doi.org/10.1007/s00203-008-0402-6"
            ], 
            "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.10.1038/nrmicro2857", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1025397815", 
              "https://doi.org/10.1038/nrmicro2857"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2005-6-5-r42", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024763433", 
              "https://doi.org/10.1186/gb-2005-6-5-r42"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/417063a", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012444409", 
              "https://doi.org/10.1038/417063a"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2007-8-1-r10", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044994861", 
              "https://doi.org/10.1186/gb-2007-8-1-r10"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-9-75", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013431920", 
              "https://doi.org/10.1186/1471-2164-9-75"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-2-33", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004145791", 
              "https://doi.org/10.1186/1745-6150-2-33"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00239-009-9280-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009722667", 
              "https://doi.org/10.1007/s00239-009-9280-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-7-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1052428768", 
              "https://doi.org/10.1186/1745-6150-7-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00203-004-0725-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019445933", 
              "https://doi.org/10.1007/s00203-004-0725-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature03233", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016211745", 
              "https://doi.org/10.1038/nature03233"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1745-6150-7-46", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010731156", 
              "https://doi.org/10.1186/1745-6150-7-46"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00792-008-0170-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033747107", 
              "https://doi.org/10.1007/s00792-008-0170-x"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2013-04-22", 
        "datePublishedReg": "2013-04-22", 
        "description": "BACKGROUND: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes.\nRESULTS: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales.\nCONCLUSIONS: Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships.\nREVIEWERS: This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/1745-6150-8-9", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2726032", 
            "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": "8"
          }
        ], 
        "keywords": [
          "Obsidian Pool", 
          "Yellowstone National Park", 
          "severe genome reduction", 
          "cultured marine organisms", 
          "protein encoding genes", 
          "genomic data sets", 
          "National Park", 
          "single-cell isolation", 
          "symbiotic archaea", 
          "Patrick Forterre", 
          "terrestrial lineages", 
          "streamlined genome", 
          "genome reduction", 
          "archaeal evolution", 
          "reduced genome", 
          "archaeal lineages", 
          "hyperthermophilic members", 
          "compact genome", 
          "split genes", 
          "parasitic lifestyle", 
          "ancestral characters", 
          "large genomes", 
          "common ancestor", 
          "phylogenetic analysis", 
          "ribosomal RNA", 
          "biosynthetic capabilities", 
          "encoding genes", 
          "Nanoarchaeota", 
          "protein sequences", 
          "genome", 
          "marine organisms", 
          "putative hosts", 
          "gluconeogenesis pathway", 
          "flagella proteins", 
          "NST1", 
          "molecular mechanisms", 
          "energetic metabolism", 
          "small repertoire", 
          "novel insights", 
          "genes", 
          "full complement", 
          "equitans", 
          "Sulfolobales", 
          "symbiosis", 
          "lineages", 
          "host", 
          "cell isolation", 
          "Nanoarchaeum", 
          "symbionts", 
          "archaea", 
          "archaeon", 
          "tRNA", 
          "Forterre", 
          "ancestor", 
          "parasitism", 
          "pool", 
          "unusual features", 
          "Park", 
          "RNA", 
          "organisms", 
          "protein", 
          "evolution", 
          "pathway", 
          "insights", 
          "sequence", 
          "metabolism", 
          "repertoire", 
          "isolation", 
          "members", 
          "character", 
          "Further studies", 
          "mechanism", 
          "complement", 
          "data sets", 
          "Sieber", 
          "branches", 
          "features", 
          "analysis", 
          "form", 
          "findings", 
          "lifestyle", 
          "relationship", 
          "study", 
          "comparison", 
          "set", 
          "reduction", 
          "capability", 
          "thermal features", 
          "article", 
          "single cultured marine organism", 
          "Nanoarchaeota branch", 
          "first terrestrial hyperthermophilic member", 
          "terrestrial hyperthermophilic member", 
          "new Nanoarchaeota", 
          "Nst1 genome", 
          "complete gluconeogenesis pathway", 
          "archaeal flagellum proteins", 
          "split protein encoding genes", 
          "split non-contiguous tRNAs", 
          "non-contiguous tRNAs", 
          "multiple split genes", 
          "inferred host", 
          "distinct Nanoarchaeota-host genomic data sets", 
          "Nanoarchaeota-host genomic data sets", 
          "archaeal symbiosis", 
          "Bettina Siebers", 
          "Purification Lopez-Garcia", 
          "Lopez-Garcia", 
          "nanoarchaeon", 
          "inferred crenarchaeal host", 
          "crenarchaeal host"
        ], 
        "name": "Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park", 
        "pagination": "9-9", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1025008134"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/1745-6150-8-9"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "23607440"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/1745-6150-8-9", 
          "https://app.dimensions.ai/details/publication/pub.1025008134"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2021-11-01T18:20", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20211101/entities/gbq_results/article/article_606.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/1745-6150-8-9"
      }
    ]
     

    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.10.1186/1745-6150-8-9'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-8-9'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-8-9'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1745-6150-8-9'


     

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

    344 TRIPLES      22 PREDICATES      168 URIs      140 LITERALS      19 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/1745-6150-8-9 schema:about N09224f1bd5064aa2acdbb33618c89c48
    2 N1741450187154d89a661a8b58f707a45
    3 N2c1c75c1ca7d471185f4ea42e090c9a3
    4 N2fc003e7f50b4c1a9a1ea58e81281561
    5 N37a89c8fe1974d799fa362e22d8772de
    6 N81bb5de7274d481389b312ad012b8575
    7 N86a15e185cf54c38b10c88c05e54b735
    8 N99d21096766e464e896379f936d1e98e
    9 Nc9d0dbe37e5448e9af0e32fde87c0d76
    10 Nd72edd823bd0460bb63075d8f1fe8c71
    11 Ne10fe2f513c74ef88333c5b3395f0e38
    12 Nfe85ff38a731499eb8d82c75f894501f
    13 anzsrc-for:06
    14 anzsrc-for:0604
    15 schema:author Nb5cb16f0922b4b7093e0c9918923ed76
    16 schema:citation sg:pub.10.1007/s00203-004-0725-x
    17 sg:pub.10.1007/s00203-008-0402-6
    18 sg:pub.10.1007/s00239-009-9280-z
    19 sg:pub.10.1007/s00792-008-0170-x
    20 sg:pub.10.1007/s00792-011-0392-1
    21 sg:pub.10.1038/417063a
    22 sg:pub.10.1038/nature03233
    23 sg:pub.10.1038/nature06833
    24 sg:pub.10.1038/nbt.1966
    25 sg:pub.10.1038/nrmicro2577
    26 sg:pub.10.1038/nrmicro2857
    27 sg:pub.10.1186/1471-2164-9-75
    28 sg:pub.10.1186/1745-6150-2-33
    29 sg:pub.10.1186/1745-6150-7-46
    30 sg:pub.10.1186/1745-6150-7-7
    31 sg:pub.10.1186/gb-2004-5-3-r17
    32 sg:pub.10.1186/gb-2005-6-5-r42
    33 sg:pub.10.1186/gb-2007-8-1-r10
    34 sg:pub.10.1186/gb-2008-9-11-r158
    35 sg:pub.10.1186/gb-2012-13-7-r63
    36 schema:datePublished 2013-04-22
    37 schema:datePublishedReg 2013-04-22
    38 schema:description BACKGROUND: A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS: The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. CONCLUSIONS: Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. REVIEWERS: This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia.
    39 schema:genre article
    40 schema:inLanguage en
    41 schema:isAccessibleForFree true
    42 schema:isPartOf N7acc8b51f18f45feac07295ed8ec727c
    43 Na5f4b1f4ee494a9a83e90c412255546b
    44 sg:journal.1036001
    45 schema:keywords Bettina Siebers
    46 Forterre
    47 Further studies
    48 Lopez-Garcia
    49 NST1
    50 Nanoarchaeota
    51 Nanoarchaeota branch
    52 Nanoarchaeota-host genomic data sets
    53 Nanoarchaeum
    54 National Park
    55 Nst1 genome
    56 Obsidian Pool
    57 Park
    58 Patrick Forterre
    59 Purification Lopez-Garcia
    60 RNA
    61 Sieber
    62 Sulfolobales
    63 Yellowstone National Park
    64 analysis
    65 ancestor
    66 ancestral characters
    67 archaea
    68 archaeal evolution
    69 archaeal flagellum proteins
    70 archaeal lineages
    71 archaeal symbiosis
    72 archaeon
    73 article
    74 biosynthetic capabilities
    75 branches
    76 capability
    77 cell isolation
    78 character
    79 common ancestor
    80 compact genome
    81 comparison
    82 complement
    83 complete gluconeogenesis pathway
    84 crenarchaeal host
    85 cultured marine organisms
    86 data sets
    87 distinct Nanoarchaeota-host genomic data sets
    88 encoding genes
    89 energetic metabolism
    90 equitans
    91 evolution
    92 features
    93 findings
    94 first terrestrial hyperthermophilic member
    95 flagella proteins
    96 form
    97 full complement
    98 genes
    99 genome
    100 genome reduction
    101 genomic data sets
    102 gluconeogenesis pathway
    103 host
    104 hyperthermophilic members
    105 inferred crenarchaeal host
    106 inferred host
    107 insights
    108 isolation
    109 large genomes
    110 lifestyle
    111 lineages
    112 marine organisms
    113 mechanism
    114 members
    115 metabolism
    116 molecular mechanisms
    117 multiple split genes
    118 nanoarchaeon
    119 new Nanoarchaeota
    120 non-contiguous tRNAs
    121 novel insights
    122 organisms
    123 parasitic lifestyle
    124 parasitism
    125 pathway
    126 phylogenetic analysis
    127 pool
    128 protein
    129 protein encoding genes
    130 protein sequences
    131 putative hosts
    132 reduced genome
    133 reduction
    134 relationship
    135 repertoire
    136 ribosomal RNA
    137 sequence
    138 set
    139 severe genome reduction
    140 single cultured marine organism
    141 single-cell isolation
    142 small repertoire
    143 split genes
    144 split non-contiguous tRNAs
    145 split protein encoding genes
    146 streamlined genome
    147 study
    148 symbionts
    149 symbiosis
    150 symbiotic archaea
    151 tRNA
    152 terrestrial hyperthermophilic member
    153 terrestrial lineages
    154 thermal features
    155 unusual features
    156 schema:name Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park
    157 schema:pagination 9-9
    158 schema:productId N408d001996a94118a7bb1d7e4ae51bdb
    159 N4384481cbcf1445a85eca975265660e9
    160 N4dfdc55ef38e44c0993fbd788ed08a7a
    161 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025008134
    162 https://doi.org/10.1186/1745-6150-8-9
    163 schema:sdDatePublished 2021-11-01T18:20
    164 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    165 schema:sdPublisher N1a29b9d6df0d44f68a53c08d876c7b3b
    166 schema:url https://doi.org/10.1186/1745-6150-8-9
    167 sgo:license sg:explorer/license/
    168 sgo:sdDataset articles
    169 rdf:type schema:ScholarlyArticle
    170 N02469cd7020842c180853da4f739ee04 rdf:first sg:person.01035426230.62
    171 rdf:rest rdf:nil
    172 N09224f1bd5064aa2acdbb33618c89c48 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    173 schema:name Archaeal Proteins
    174 rdf:type schema:DefinedTerm
    175 N1741450187154d89a661a8b58f707a45 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    176 schema:name Sequence Homology
    177 rdf:type schema:DefinedTerm
    178 N1a29b9d6df0d44f68a53c08d876c7b3b schema:name Springer Nature - SN SciGraph project
    179 rdf:type schema:Organization
    180 N2c1c75c1ca7d471185f4ea42e090c9a3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    181 schema:name Genome, Archaeal
    182 rdf:type schema:DefinedTerm
    183 N2fc003e7f50b4c1a9a1ea58e81281561 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    184 schema:name Polymerase Chain Reaction
    185 rdf:type schema:DefinedTerm
    186 N37a89c8fe1974d799fa362e22d8772de schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    187 schema:name Phylogeny
    188 rdf:type schema:DefinedTerm
    189 N408d001996a94118a7bb1d7e4ae51bdb schema:name pubmed_id
    190 schema:value 23607440
    191 rdf:type schema:PropertyValue
    192 N4384481cbcf1445a85eca975265660e9 schema:name doi
    193 schema:value 10.1186/1745-6150-8-9
    194 rdf:type schema:PropertyValue
    195 N4dfdc55ef38e44c0993fbd788ed08a7a schema:name dimensions_id
    196 schema:value pub.1025008134
    197 rdf:type schema:PropertyValue
    198 N5be6a29dde39499ebee96bc22839a5b7 rdf:first sg:person.01017015051.78
    199 rdf:rest N02469cd7020842c180853da4f739ee04
    200 N74e6dbe2a8684e2aa3fe36d2ce0646e4 rdf:first sg:person.0755636111.03
    201 rdf:rest N9c48031da66646989ee591fe2b48bf26
    202 N7acc8b51f18f45feac07295ed8ec727c schema:issueNumber 1
    203 rdf:type schema:PublicationIssue
    204 N81bb5de7274d481389b312ad012b8575 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    205 schema:name Symbiosis
    206 rdf:type schema:DefinedTerm
    207 N86a15e185cf54c38b10c88c05e54b735 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    208 schema:name Nanoarchaeota
    209 rdf:type schema:DefinedTerm
    210 N99d21096766e464e896379f936d1e98e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    211 schema:name Evolution, Molecular
    212 rdf:type schema:DefinedTerm
    213 N9c48031da66646989ee591fe2b48bf26 rdf:first sg:person.0634453251.89
    214 rdf:rest N5be6a29dde39499ebee96bc22839a5b7
    215 Na5f4b1f4ee494a9a83e90c412255546b schema:volumeNumber 8
    216 rdf:type schema:PublicationVolume
    217 Nb5cb16f0922b4b7093e0c9918923ed76 rdf:first sg:person.01334660037.45
    218 rdf:rest Necf1d6fdb7ef4a6f98022e69977f5c75
    219 Nc9d0dbe37e5448e9af0e32fde87c0d76 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    220 schema:name Wyoming
    221 rdf:type schema:DefinedTerm
    222 Nd72edd823bd0460bb63075d8f1fe8c71 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    223 schema:name Molecular Sequence Data
    224 rdf:type schema:DefinedTerm
    225 Ne10fe2f513c74ef88333c5b3395f0e38 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    226 schema:name Sulfolobales
    227 rdf:type schema:DefinedTerm
    228 Necf1d6fdb7ef4a6f98022e69977f5c75 rdf:first sg:person.0676725351.01
    229 rdf:rest N74e6dbe2a8684e2aa3fe36d2ce0646e4
    230 Nfe85ff38a731499eb8d82c75f894501f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    231 schema:name Biological Evolution
    232 rdf:type schema:DefinedTerm
    233 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    234 schema:name Biological Sciences
    235 rdf:type schema:DefinedTerm
    236 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    237 schema:name Genetics
    238 rdf:type schema:DefinedTerm
    239 sg:grant.2726032 http://pending.schema.org/fundedItem sg:pub.10.1186/1745-6150-8-9
    240 rdf:type schema:MonetaryGrant
    241 sg:journal.1036001 schema:issn 1745-6150
    242 schema:name Biology Direct
    243 schema:publisher Springer Nature
    244 rdf:type schema:Periodical
    245 sg:person.01017015051.78 schema:affiliation grid-institutes:grid.419234.9
    246 schema:familyName Koonin
    247 schema:givenName Eugene V
    248 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01017015051.78
    249 rdf:type schema:Person
    250 sg:person.01035426230.62 schema:affiliation grid-institutes:grid.262075.4
    251 schema:familyName Reysenbach
    252 schema:givenName Anna-Louise
    253 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035426230.62
    254 rdf:type schema:Person
    255 sg:person.01334660037.45 schema:affiliation grid-institutes:grid.411461.7
    256 schema:familyName Podar
    257 schema:givenName Mircea
    258 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01334660037.45
    259 rdf:type schema:Person
    260 sg:person.0634453251.89 schema:affiliation grid-institutes:grid.419234.9
    261 schema:familyName Wolf
    262 schema:givenName Yuri I
    263 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0634453251.89
    264 rdf:type schema:Person
    265 sg:person.0676725351.01 schema:affiliation grid-institutes:grid.419234.9
    266 schema:familyName Makarova
    267 schema:givenName Kira S
    268 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0676725351.01
    269 rdf:type schema:Person
    270 sg:person.0755636111.03 schema:affiliation grid-institutes:grid.411461.7
    271 schema:familyName Graham
    272 schema:givenName David E
    273 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0755636111.03
    274 rdf:type schema:Person
    275 sg:pub.10.1007/s00203-004-0725-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1019445933
    276 https://doi.org/10.1007/s00203-004-0725-x
    277 rdf:type schema:CreativeWork
    278 sg:pub.10.1007/s00203-008-0402-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013570847
    279 https://doi.org/10.1007/s00203-008-0402-6
    280 rdf:type schema:CreativeWork
    281 sg:pub.10.1007/s00239-009-9280-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1009722667
    282 https://doi.org/10.1007/s00239-009-9280-z
    283 rdf:type schema:CreativeWork
    284 sg:pub.10.1007/s00792-008-0170-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1033747107
    285 https://doi.org/10.1007/s00792-008-0170-x
    286 rdf:type schema:CreativeWork
    287 sg:pub.10.1007/s00792-011-0392-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008401059
    288 https://doi.org/10.1007/s00792-011-0392-1
    289 rdf:type schema:CreativeWork
    290 sg:pub.10.1038/417063a schema:sameAs https://app.dimensions.ai/details/publication/pub.1012444409
    291 https://doi.org/10.1038/417063a
    292 rdf:type schema:CreativeWork
    293 sg:pub.10.1038/nature03233 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016211745
    294 https://doi.org/10.1038/nature03233
    295 rdf:type schema:CreativeWork
    296 sg:pub.10.1038/nature06833 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035908939
    297 https://doi.org/10.1038/nature06833
    298 rdf:type schema:CreativeWork
    299 sg:pub.10.1038/nbt.1966 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013335891
    300 https://doi.org/10.1038/nbt.1966
    301 rdf:type schema:CreativeWork
    302 sg:pub.10.1038/nrmicro2577 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020345829
    303 https://doi.org/10.1038/nrmicro2577
    304 rdf:type schema:CreativeWork
    305 sg:pub.10.1038/nrmicro2857 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025397815
    306 https://doi.org/10.1038/nrmicro2857
    307 rdf:type schema:CreativeWork
    308 sg:pub.10.1186/1471-2164-9-75 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013431920
    309 https://doi.org/10.1186/1471-2164-9-75
    310 rdf:type schema:CreativeWork
    311 sg:pub.10.1186/1745-6150-2-33 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004145791
    312 https://doi.org/10.1186/1745-6150-2-33
    313 rdf:type schema:CreativeWork
    314 sg:pub.10.1186/1745-6150-7-46 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010731156
    315 https://doi.org/10.1186/1745-6150-7-46
    316 rdf:type schema:CreativeWork
    317 sg:pub.10.1186/1745-6150-7-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052428768
    318 https://doi.org/10.1186/1745-6150-7-7
    319 rdf:type schema:CreativeWork
    320 sg:pub.10.1186/gb-2004-5-3-r17 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028464475
    321 https://doi.org/10.1186/gb-2004-5-3-r17
    322 rdf:type schema:CreativeWork
    323 sg:pub.10.1186/gb-2005-6-5-r42 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024763433
    324 https://doi.org/10.1186/gb-2005-6-5-r42
    325 rdf:type schema:CreativeWork
    326 sg:pub.10.1186/gb-2007-8-1-r10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044994861
    327 https://doi.org/10.1186/gb-2007-8-1-r10
    328 rdf:type schema:CreativeWork
    329 sg:pub.10.1186/gb-2008-9-11-r158 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051170330
    330 https://doi.org/10.1186/gb-2008-9-11-r158
    331 rdf:type schema:CreativeWork
    332 sg:pub.10.1186/gb-2012-13-7-r63 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007749102
    333 https://doi.org/10.1186/gb-2012-13-7-r63
    334 rdf:type schema:CreativeWork
    335 grid-institutes:grid.262075.4 schema:alternateName Department of Biology, Portland State University, Portland, OR, 97207, USA
    336 schema:name Department of Biology, Portland State University, Portland, OR, 97207, USA
    337 rdf:type schema:Organization
    338 grid-institutes:grid.411461.7 schema:alternateName Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
    339 schema:name Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
    340 Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
    341 rdf:type schema:Organization
    342 grid-institutes:grid.419234.9 schema:alternateName National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    343 schema:name National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
    344 rdf:type schema:Organization
     




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


    ...