The metabolic network of the last bacterial common ancestor View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-03-26

AUTHORS

Joana C. Xavier, Rebecca E. Gerhards, Jessica L. E. Wimmer, Julia Brueckner, Fernando D. K. Tria, William F. Martin

ABSTRACT

Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites. Our results indicate that LBCA performed gluconeogenesis towards cell wall synthesis, and had numerous RNA modifications and multifunctional enzymes that permitted life with low gene content. In accordance with recent findings for LUCA and LACA, analyses of thousands of individual gene trees indicate that LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-CoA pathway. More... »

PAGES

413

References to SciGraph publications

  • 2014-10-15. Origins of major archaeal clades correspond to gene acquisitions from bacteria in NATURE
  • 2002-05. A non-hyperthermophilic ancestor for Bacteria in NATURE
  • 2018-04-23. Native iron reduces CO2 to intermediates and end-products of the acetyl-CoA pathway in NATURE ECOLOGY & EVOLUTION
  • 2008-01-16. The rise of atmospheric oxygen in NATURE
  • 2020-10-19. Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition in NATURE ECOLOGY & EVOLUTION
  • 2020-02-03. SciPy 1.0: fundamental algorithms for scientific computing in Python in NATURE METHODS
  • 2017-06-19. Phylogenetic rooting using minimal ancestor deviation in NATURE ECOLOGY & EVOLUTION
  • 2018-08-20. Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origin in NATURE ECOLOGY & EVOLUTION
  • 2014-02-19. The rise of oxygen in Earth’s early ocean and atmosphere in NATURE
  • 2002-03-05. Desulfotignum phosphitoxidans sp. nov., a new marine sulfate reducer that oxidizes phosphite to phosphate in ARCHIVES OF MICROBIOLOGY
  • 2016-11-21. Independent evolution of shape and motility allows evolutionary flexibility in Firmicutes bacteria in NATURE ECOLOGY & EVOLUTION
  • 2010-03-28. Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme in NATURE
  • 2017-09-28. Early trace of life from 3.95 Ga sedimentary rocks in Labrador, Canada in NATURE
  • 2000-04. Phylogenetic Depth of the Bacterial Genera Aquifex and Thermotoga Inferred from Analysis of Ribosomal Protein, Elongation Factor, and RNA Polymerase Subunit Sequences in JOURNAL OF MOLECULAR EVOLUTION
  • 2020-03-02. A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism in NATURE ECOLOGY & EVOLUTION
  • 2018-09-24. The biomass and biodiversity of the continental subsurface in NATURE GEOSCIENCE
  • 2016-06-27. Sporulation, bacterial cell envelopes and the origin of life in NATURE REVIEWS MICROBIOLOGY
  • 2019-08-21. Challenges in evidencing the earliest traces of life in NATURE
  • 2001-02. The habitat and nature of early life in NATURE
  • 2016-07-25. The physiology and habitat of the last universal common ancestor in NATURE MICROBIOLOGY
  • 2014-12-30. Concatenated alignments and the case of the disappearing tree in BMC ECOLOGY AND EVOLUTION
  • 2019-02-13. Bacteria and archaea on Earth and their abundance in biofilms in NATURE REVIEWS MICROBIOLOGY
  • 2017-08-22. Coding of Class I and II Aminoacyl-tRNA Synthetases in PROTEIN REVIEWS
  • 2020-07-13. Phylogenetic analyses with systematic taxon sampling show that mitochondria branch within Alphaproteobacteria in NATURE ECOLOGY & EVOLUTION
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/s42003-021-01918-4

    DOI

    http://dx.doi.org/10.1038/s42003-021-01918-4

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1136687799

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/33772086


    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/2008/0601", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biochemistry and Cell Biology", 
            "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"
          }, 
          {
            "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": "Bacteria", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Bacterial Proteins", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Energy Metabolism", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Evolution, Molecular", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Expression Regulation, Bacterial", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Metabolic Networks and Pathways", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany", 
              "id": "http://www.grid.ac/institutes/grid.411327.2", 
              "name": [
                "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Xavier", 
            "givenName": "Joana C.", 
            "id": "sg:person.013152151524.04", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013152151524.04"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany", 
              "id": "http://www.grid.ac/institutes/grid.411327.2", 
              "name": [
                "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Gerhards", 
            "givenName": "Rebecca E.", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany", 
              "id": "http://www.grid.ac/institutes/grid.411327.2", 
              "name": [
                "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Wimmer", 
            "givenName": "Jessica L. E.", 
            "id": "sg:person.010601101047.81", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010601101047.81"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany", 
              "id": "http://www.grid.ac/institutes/grid.411327.2", 
              "name": [
                "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Brueckner", 
            "givenName": "Julia", 
            "id": "sg:person.015415203311.94", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015415203311.94"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany", 
              "id": "http://www.grid.ac/institutes/grid.411327.2", 
              "name": [
                "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tria", 
            "givenName": "Fernando D. K.", 
            "id": "sg:person.014201620631.83", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014201620631.83"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany", 
              "id": "http://www.grid.ac/institutes/grid.411327.2", 
              "name": [
                "Institute for Molecular Evolution, Heinrich-Heine-University, 40225, D\u00fcsseldorf, Germany"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Martin", 
            "givenName": "William F.", 
            "id": "sg:person.01031250622.21", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031250622.21"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/nature13805", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1033311045", 
              "https://doi.org/10.1038/nature13805"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41559-016-0009", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034665348", 
              "https://doi.org/10.1038/s41559-016-0009"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/417244a", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1011730206", 
              "https://doi.org/10.1038/417244a"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12862-014-0266-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032240352", 
              "https://doi.org/10.1186/s12862-014-0266-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00203-002-0402-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050399420", 
              "https://doi.org/10.1007/s00203-002-0402-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41579-019-0158-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1112089780", 
              "https://doi.org/10.1038/s41579-019-0158-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature08884", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036063726", 
              "https://doi.org/10.1038/nature08884"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature24019", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091923377", 
              "https://doi.org/10.1038/nature24019"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41559-018-0542-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1103565796", 
              "https://doi.org/10.1038/s41559-018-0542-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/5584_2017_93", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091281322", 
              "https://doi.org/10.1007/5584_2017_93"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmicrobiol.2016.116", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023830860", 
              "https://doi.org/10.1038/nmicrobiol.2016.116"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/35059210", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010826689", 
              "https://doi.org/10.1038/35059210"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41561-018-0221-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1107189154", 
              "https://doi.org/10.1038/s41561-018-0221-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41559-020-1239-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1129309484", 
              "https://doi.org/10.1038/s41559-020-1239-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41592-019-0686-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1124547608", 
              "https://doi.org/10.1038/s41592-019-0686-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41559-020-1125-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1125312918", 
              "https://doi.org/10.1038/s41559-020-1125-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41559-017-0193", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1086071563", 
              "https://doi.org/10.1038/s41559-017-0193"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41559-018-0644-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1106187446", 
              "https://doi.org/10.1038/s41559-018-0644-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrmicro.2016.85", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051549007", 
              "https://doi.org/10.1038/nrmicro.2016.85"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-019-1436-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1120441678", 
              "https://doi.org/10.1038/s41586-019-1436-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature13068", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042316110", 
              "https://doi.org/10.1038/nature13068"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41559-020-01299-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1131875482", 
              "https://doi.org/10.1038/s41559-020-01299-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s002399910040", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1031825915", 
              "https://doi.org/10.1007/s002399910040"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature06587", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016805963", 
              "https://doi.org/10.1038/nature06587"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2021-03-26", 
        "datePublishedReg": "2021-03-26", 
        "description": "Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites. Our results indicate that LBCA performed gluconeogenesis towards cell wall synthesis, and\u00a0had numerous RNA modifications and multifunctional enzymes that permitted life with low gene content. In accordance with recent findings for LUCA and LACA, analyses of thousands of individual gene trees indicate that LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-CoA pathway.", 
        "genre": "article", 
        "id": "sg:pub.10.1038/s42003-021-01918-4", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.4456536", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1300829", 
            "issn": [
              "2399-3642"
            ], 
            "name": "Communications Biology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "4"
          }
        ], 
        "keywords": [
          "last bacterial common ancestor", 
          "common ancestor", 
          "widespread lateral gene transfer", 
          "metabolic networks", 
          "individual gene trees", 
          "lateral gene transfer", 
          "low gene content", 
          "cell wall synthesis", 
          "acetyl-CoA pathway", 
          "gene trees", 
          "first lineage", 
          "gene content", 
          "reference genome", 
          "protein family", 
          "RNA modifications", 
          "wall synthesis", 
          "striking diversity", 
          "multifunctional enzyme", 
          "bacterial stem", 
          "analysis of thousands", 
          "first bacteria", 
          "gene transfer", 
          "bacterial anaerobes", 
          "LbcA", 
          "metabolic capacity", 
          "universal metabolite", 
          "ancestor", 
          "recent findings", 
          "abundant cells", 
          "bacteria", 
          "genome", 
          "lineages", 
          "autotrophs", 
          "genes", 
          "diversity", 
          "enzyme", 
          "physiology", 
          "pathway", 
          "Clostridium", 
          "stem", 
          "trees", 
          "gluconeogenesis", 
          "LACA", 
          "cells", 
          "family", 
          "anaerobes", 
          "metabolites", 
          "thousands", 
          "modification", 
          "synthesis", 
          "content", 
          "analysis", 
          "transfer", 
          "network", 
          "findings", 
          "capacity", 
          "Earth", 
          "Lucas", 
          "results", 
          "core", 
          "accordance", 
          "life"
        ], 
        "name": "The metabolic network of the last bacterial common ancestor", 
        "pagination": "413", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1136687799"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1038/s42003-021-01918-4"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "33772086"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1038/s42003-021-01918-4", 
          "https://app.dimensions.ai/details/publication/pub.1136687799"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-12-01T06:41", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20221201/entities/gbq_results/article/article_873.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1038/s42003-021-01918-4"
      }
    ]
     

    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.10.1038/s42003-021-01918-4'

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

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s42003-021-01918-4'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s42003-021-01918-4'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s42003-021-01918-4'


     

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

    290 TRIPLES      21 PREDICATES      120 URIs      86 LITERALS      14 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1038/s42003-021-01918-4 schema:about N21f8c04d25d640988a6917f2357f3587
    2 N6e1437e4b18d426f919bac3ed240e06c
    3 N76b99cfef285455d9bbcbaeb16a3d6ed
    4 Nb080b3acf5974ebdb37f3d547706d7bb
    5 Ncfd39f9372b34301a57c9fb338213282
    6 Nd418a1246db847dcb6679ad6c9c8c195
    7 Nfbac98cad0b941a58fe593623eaebe20
    8 anzsrc-for:06
    9 anzsrc-for:0601
    10 anzsrc-for:0604
    11 anzsrc-for:0605
    12 schema:author N071f626e3dd844b9a460ba17e9a6f931
    13 schema:citation sg:pub.10.1007/5584_2017_93
    14 sg:pub.10.1007/s00203-002-0402-x
    15 sg:pub.10.1007/s002399910040
    16 sg:pub.10.1038/35059210
    17 sg:pub.10.1038/417244a
    18 sg:pub.10.1038/nature06587
    19 sg:pub.10.1038/nature08884
    20 sg:pub.10.1038/nature13068
    21 sg:pub.10.1038/nature13805
    22 sg:pub.10.1038/nature24019
    23 sg:pub.10.1038/nmicrobiol.2016.116
    24 sg:pub.10.1038/nrmicro.2016.85
    25 sg:pub.10.1038/s41559-016-0009
    26 sg:pub.10.1038/s41559-017-0193
    27 sg:pub.10.1038/s41559-018-0542-2
    28 sg:pub.10.1038/s41559-018-0644-x
    29 sg:pub.10.1038/s41559-020-01299-7
    30 sg:pub.10.1038/s41559-020-1125-6
    31 sg:pub.10.1038/s41559-020-1239-x
    32 sg:pub.10.1038/s41561-018-0221-6
    33 sg:pub.10.1038/s41579-019-0158-9
    34 sg:pub.10.1038/s41586-019-1436-4
    35 sg:pub.10.1038/s41592-019-0686-2
    36 sg:pub.10.1186/s12862-014-0266-0
    37 schema:datePublished 2021-03-26
    38 schema:datePublishedReg 2021-03-26
    39 schema:description Bacteria are the most abundant cells on Earth. They are generally regarded as ancient, but due to striking diversity in their metabolic capacities and widespread lateral gene transfer, the physiology of the first bacteria is unknown. From 1089 reference genomes of bacterial anaerobes, we identified 146 protein families that trace to the last bacterial common ancestor, LBCA, and form the conserved predicted core of its metabolic network, which requires only nine genes to encompass all universal metabolites. Our results indicate that LBCA performed gluconeogenesis towards cell wall synthesis, and had numerous RNA modifications and multifunctional enzymes that permitted life with low gene content. In accordance with recent findings for LUCA and LACA, analyses of thousands of individual gene trees indicate that LBCA was rod-shaped and the first lineage to diverge from the ancestral bacterial stem was most similar to modern Clostridia, followed by other autotrophs that harbor the acetyl-CoA pathway.
    40 schema:genre article
    41 schema:isAccessibleForFree true
    42 schema:isPartOf Na20adf628af9447ca20cd5262887f536
    43 Nc46bc519c51a4ec1884237ca098c33ed
    44 sg:journal.1300829
    45 schema:keywords Clostridium
    46 Earth
    47 LACA
    48 LbcA
    49 Lucas
    50 RNA modifications
    51 abundant cells
    52 accordance
    53 acetyl-CoA pathway
    54 anaerobes
    55 analysis
    56 analysis of thousands
    57 ancestor
    58 autotrophs
    59 bacteria
    60 bacterial anaerobes
    61 bacterial stem
    62 capacity
    63 cell wall synthesis
    64 cells
    65 common ancestor
    66 content
    67 core
    68 diversity
    69 enzyme
    70 family
    71 findings
    72 first bacteria
    73 first lineage
    74 gene content
    75 gene transfer
    76 gene trees
    77 genes
    78 genome
    79 gluconeogenesis
    80 individual gene trees
    81 last bacterial common ancestor
    82 lateral gene transfer
    83 life
    84 lineages
    85 low gene content
    86 metabolic capacity
    87 metabolic networks
    88 metabolites
    89 modification
    90 multifunctional enzyme
    91 network
    92 pathway
    93 physiology
    94 protein family
    95 recent findings
    96 reference genome
    97 results
    98 stem
    99 striking diversity
    100 synthesis
    101 thousands
    102 transfer
    103 trees
    104 universal metabolite
    105 wall synthesis
    106 widespread lateral gene transfer
    107 schema:name The metabolic network of the last bacterial common ancestor
    108 schema:pagination 413
    109 schema:productId N53eefabaab774ef5bf89a9822b184d86
    110 N6484b04af6054ac4bc0426130b53bea9
    111 Nc495fdc11ef341b496f301c38499f7dc
    112 schema:sameAs https://app.dimensions.ai/details/publication/pub.1136687799
    113 https://doi.org/10.1038/s42003-021-01918-4
    114 schema:sdDatePublished 2022-12-01T06:41
    115 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    116 schema:sdPublisher Nb019f57294c34023baa56e75f40f697e
    117 schema:url https://doi.org/10.1038/s42003-021-01918-4
    118 sgo:license sg:explorer/license/
    119 sgo:sdDataset articles
    120 rdf:type schema:ScholarlyArticle
    121 N071f626e3dd844b9a460ba17e9a6f931 rdf:first sg:person.013152151524.04
    122 rdf:rest N1c52b5219f5149c8966fe0e0d3e0260d
    123 N0d2d2dfb470d42c3bda1a8529c76d6ab schema:affiliation grid-institutes:grid.411327.2
    124 schema:familyName Gerhards
    125 schema:givenName Rebecca E.
    126 rdf:type schema:Person
    127 N1492969692954cacb5ad88d34ade12d8 rdf:first sg:person.01031250622.21
    128 rdf:rest rdf:nil
    129 N1c52b5219f5149c8966fe0e0d3e0260d rdf:first N0d2d2dfb470d42c3bda1a8529c76d6ab
    130 rdf:rest N992201c65a60487a9ea470a4dae356bd
    131 N21f8c04d25d640988a6917f2357f3587 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    132 schema:name Evolution, Molecular
    133 rdf:type schema:DefinedTerm
    134 N362116b1ed26461e83be6548c20e3eba rdf:first sg:person.015415203311.94
    135 rdf:rest N490b2c7bd2f34c608ada4818a0e80ab7
    136 N490b2c7bd2f34c608ada4818a0e80ab7 rdf:first sg:person.014201620631.83
    137 rdf:rest N1492969692954cacb5ad88d34ade12d8
    138 N53eefabaab774ef5bf89a9822b184d86 schema:name pubmed_id
    139 schema:value 33772086
    140 rdf:type schema:PropertyValue
    141 N6484b04af6054ac4bc0426130b53bea9 schema:name dimensions_id
    142 schema:value pub.1136687799
    143 rdf:type schema:PropertyValue
    144 N6e1437e4b18d426f919bac3ed240e06c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    145 schema:name Bacteria
    146 rdf:type schema:DefinedTerm
    147 N76b99cfef285455d9bbcbaeb16a3d6ed schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    148 schema:name Phylogeny
    149 rdf:type schema:DefinedTerm
    150 N992201c65a60487a9ea470a4dae356bd rdf:first sg:person.010601101047.81
    151 rdf:rest N362116b1ed26461e83be6548c20e3eba
    152 Na20adf628af9447ca20cd5262887f536 schema:issueNumber 1
    153 rdf:type schema:PublicationIssue
    154 Nb019f57294c34023baa56e75f40f697e schema:name Springer Nature - SN SciGraph project
    155 rdf:type schema:Organization
    156 Nb080b3acf5974ebdb37f3d547706d7bb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    157 schema:name Energy Metabolism
    158 rdf:type schema:DefinedTerm
    159 Nc46bc519c51a4ec1884237ca098c33ed schema:volumeNumber 4
    160 rdf:type schema:PublicationVolume
    161 Nc495fdc11ef341b496f301c38499f7dc schema:name doi
    162 schema:value 10.1038/s42003-021-01918-4
    163 rdf:type schema:PropertyValue
    164 Ncfd39f9372b34301a57c9fb338213282 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    165 schema:name Gene Expression Regulation, Bacterial
    166 rdf:type schema:DefinedTerm
    167 Nd418a1246db847dcb6679ad6c9c8c195 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    168 schema:name Metabolic Networks and Pathways
    169 rdf:type schema:DefinedTerm
    170 Nfbac98cad0b941a58fe593623eaebe20 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    171 schema:name Bacterial Proteins
    172 rdf:type schema:DefinedTerm
    173 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    174 schema:name Biological Sciences
    175 rdf:type schema:DefinedTerm
    176 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
    177 schema:name Biochemistry and Cell Biology
    178 rdf:type schema:DefinedTerm
    179 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    180 schema:name Genetics
    181 rdf:type schema:DefinedTerm
    182 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
    183 schema:name Microbiology
    184 rdf:type schema:DefinedTerm
    185 sg:grant.4456536 http://pending.schema.org/fundedItem sg:pub.10.1038/s42003-021-01918-4
    186 rdf:type schema:MonetaryGrant
    187 sg:journal.1300829 schema:issn 2399-3642
    188 schema:name Communications Biology
    189 schema:publisher Springer Nature
    190 rdf:type schema:Periodical
    191 sg:person.01031250622.21 schema:affiliation grid-institutes:grid.411327.2
    192 schema:familyName Martin
    193 schema:givenName William F.
    194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01031250622.21
    195 rdf:type schema:Person
    196 sg:person.010601101047.81 schema:affiliation grid-institutes:grid.411327.2
    197 schema:familyName Wimmer
    198 schema:givenName Jessica L. E.
    199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.010601101047.81
    200 rdf:type schema:Person
    201 sg:person.013152151524.04 schema:affiliation grid-institutes:grid.411327.2
    202 schema:familyName Xavier
    203 schema:givenName Joana C.
    204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013152151524.04
    205 rdf:type schema:Person
    206 sg:person.014201620631.83 schema:affiliation grid-institutes:grid.411327.2
    207 schema:familyName Tria
    208 schema:givenName Fernando D. K.
    209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014201620631.83
    210 rdf:type schema:Person
    211 sg:person.015415203311.94 schema:affiliation grid-institutes:grid.411327.2
    212 schema:familyName Brueckner
    213 schema:givenName Julia
    214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015415203311.94
    215 rdf:type schema:Person
    216 sg:pub.10.1007/5584_2017_93 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091281322
    217 https://doi.org/10.1007/5584_2017_93
    218 rdf:type schema:CreativeWork
    219 sg:pub.10.1007/s00203-002-0402-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1050399420
    220 https://doi.org/10.1007/s00203-002-0402-x
    221 rdf:type schema:CreativeWork
    222 sg:pub.10.1007/s002399910040 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031825915
    223 https://doi.org/10.1007/s002399910040
    224 rdf:type schema:CreativeWork
    225 sg:pub.10.1038/35059210 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010826689
    226 https://doi.org/10.1038/35059210
    227 rdf:type schema:CreativeWork
    228 sg:pub.10.1038/417244a schema:sameAs https://app.dimensions.ai/details/publication/pub.1011730206
    229 https://doi.org/10.1038/417244a
    230 rdf:type schema:CreativeWork
    231 sg:pub.10.1038/nature06587 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016805963
    232 https://doi.org/10.1038/nature06587
    233 rdf:type schema:CreativeWork
    234 sg:pub.10.1038/nature08884 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036063726
    235 https://doi.org/10.1038/nature08884
    236 rdf:type schema:CreativeWork
    237 sg:pub.10.1038/nature13068 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042316110
    238 https://doi.org/10.1038/nature13068
    239 rdf:type schema:CreativeWork
    240 sg:pub.10.1038/nature13805 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033311045
    241 https://doi.org/10.1038/nature13805
    242 rdf:type schema:CreativeWork
    243 sg:pub.10.1038/nature24019 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091923377
    244 https://doi.org/10.1038/nature24019
    245 rdf:type schema:CreativeWork
    246 sg:pub.10.1038/nmicrobiol.2016.116 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023830860
    247 https://doi.org/10.1038/nmicrobiol.2016.116
    248 rdf:type schema:CreativeWork
    249 sg:pub.10.1038/nrmicro.2016.85 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051549007
    250 https://doi.org/10.1038/nrmicro.2016.85
    251 rdf:type schema:CreativeWork
    252 sg:pub.10.1038/s41559-016-0009 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034665348
    253 https://doi.org/10.1038/s41559-016-0009
    254 rdf:type schema:CreativeWork
    255 sg:pub.10.1038/s41559-017-0193 schema:sameAs https://app.dimensions.ai/details/publication/pub.1086071563
    256 https://doi.org/10.1038/s41559-017-0193
    257 rdf:type schema:CreativeWork
    258 sg:pub.10.1038/s41559-018-0542-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1103565796
    259 https://doi.org/10.1038/s41559-018-0542-2
    260 rdf:type schema:CreativeWork
    261 sg:pub.10.1038/s41559-018-0644-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1106187446
    262 https://doi.org/10.1038/s41559-018-0644-x
    263 rdf:type schema:CreativeWork
    264 sg:pub.10.1038/s41559-020-01299-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1131875482
    265 https://doi.org/10.1038/s41559-020-01299-7
    266 rdf:type schema:CreativeWork
    267 sg:pub.10.1038/s41559-020-1125-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1125312918
    268 https://doi.org/10.1038/s41559-020-1125-6
    269 rdf:type schema:CreativeWork
    270 sg:pub.10.1038/s41559-020-1239-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1129309484
    271 https://doi.org/10.1038/s41559-020-1239-x
    272 rdf:type schema:CreativeWork
    273 sg:pub.10.1038/s41561-018-0221-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1107189154
    274 https://doi.org/10.1038/s41561-018-0221-6
    275 rdf:type schema:CreativeWork
    276 sg:pub.10.1038/s41579-019-0158-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112089780
    277 https://doi.org/10.1038/s41579-019-0158-9
    278 rdf:type schema:CreativeWork
    279 sg:pub.10.1038/s41586-019-1436-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1120441678
    280 https://doi.org/10.1038/s41586-019-1436-4
    281 rdf:type schema:CreativeWork
    282 sg:pub.10.1038/s41592-019-0686-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1124547608
    283 https://doi.org/10.1038/s41592-019-0686-2
    284 rdf:type schema:CreativeWork
    285 sg:pub.10.1186/s12862-014-0266-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032240352
    286 https://doi.org/10.1186/s12862-014-0266-0
    287 rdf:type schema:CreativeWork
    288 grid-institutes:grid.411327.2 schema:alternateName Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
    289 schema:name Institute for Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany
    290 rdf:type schema:Organization
     




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


    ...