Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-09-23

AUTHORS

Nicolas Gallois, Béatrice Alpha-Bazin, Nicolas Bremond, Philippe Ortet, Mohamed Barakat, Laurie Piette, Abbas Mohamad Ali, David Lemaire, Pierre Legrand, Nicolas Theodorakopoulos, Magali Floriani, Laureline Février, Christophe Den Auwer, Pascal Arnoux, Catherine Berthomieu, Jean Armengaud, Virginie Chapon

ABSTRACT

Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39–47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance. More... »

PAGES

705-716

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/s41396-021-01113-7

DOI

http://dx.doi.org/10.1038/s41396-021-01113-7

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1141322181

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/34556817


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"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Bacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Iron", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Iron-Binding Proteins", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Soil", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Uranium", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gallois", 
        "givenName": "Nicolas", 
        "id": "sg:person.01035253041.37", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035253041.37"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "D\u00e9partement M\u00e9dicaments et Technologies pour la Sant\u00e9 (DMTS), Universit\u00e9 Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-C\u00e8ze, France", 
          "id": "http://www.grid.ac/institutes/grid.460789.4", 
          "name": [
            "D\u00e9partement M\u00e9dicaments et Technologies pour la Sant\u00e9 (DMTS), Universit\u00e9 Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-C\u00e8ze, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Alpha-Bazin", 
        "givenName": "B\u00e9atrice", 
        "id": "sg:person.01351173115.98", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01351173115.98"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Bremond", 
        "givenName": "Nicolas", 
        "id": "sg:person.01134623657.91", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01134623657.91"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ortet", 
        "givenName": "Philippe", 
        "id": "sg:person.0637520660.45", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0637520660.45"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Barakat", 
        "givenName": "Mohamed", 
        "id": "sg:person.0673264122.96", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0673264122.96"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Piette", 
        "givenName": "Laurie", 
        "id": "sg:person.0745763400.82", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0745763400.82"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Mohamad Ali", 
        "givenName": "Abbas", 
        "id": "sg:person.013452635034.89", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013452635034.89"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lemaire", 
        "givenName": "David", 
        "id": "sg:person.01250262144.30", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01250262144.30"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Synchrotron SOLEIL. L\u2019Orme des Merisiers Saint-Aubin. BP 48, 91192, Gif-sur-Yvette, France", 
          "id": "http://www.grid.ac/institutes/grid.426328.9", 
          "name": [
            "Synchrotron SOLEIL. L\u2019Orme des Merisiers Saint-Aubin. BP 48, 91192, Gif-sur-Yvette, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Legrand", 
        "givenName": "Pierre", 
        "id": "sg:person.01064572753.71", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064572753.71"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France", 
          "id": "http://www.grid.ac/institutes/grid.418735.c", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
            "IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Theodorakopoulos", 
        "givenName": "Nicolas", 
        "id": "sg:person.0743260041.15", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0743260041.15"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France", 
          "id": "http://www.grid.ac/institutes/grid.418735.c", 
          "name": [
            "IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Floriani", 
        "givenName": "Magali", 
        "id": "sg:person.01350015161.78", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01350015161.78"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France", 
          "id": "http://www.grid.ac/institutes/grid.418735.c", 
          "name": [
            "IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "F\u00e9vrier", 
        "givenName": "Laureline", 
        "id": "sg:person.01171005174.14", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01171005174.14"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, ICN, 06108, Nice, France", 
          "id": "http://www.grid.ac/institutes/grid.462124.7", 
          "name": [
            "Universit\u00e9 C\u00f4te d\u2019Azur, CNRS, ICN, 06108, Nice, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Den Auwer", 
        "givenName": "Christophe", 
        "id": "sg:person.01246623543.06", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01246623543.06"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Arnoux", 
        "givenName": "Pascal", 
        "id": "sg:person.01260473513.43", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01260473513.43"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Berthomieu", 
        "givenName": "Catherine", 
        "id": "sg:person.0641716334.91", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0641716334.91"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "D\u00e9partement M\u00e9dicaments et Technologies pour la Sant\u00e9 (DMTS), Universit\u00e9 Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-C\u00e8ze, France", 
          "id": "http://www.grid.ac/institutes/grid.460789.4", 
          "name": [
            "D\u00e9partement M\u00e9dicaments et Technologies pour la Sant\u00e9 (DMTS), Universit\u00e9 Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-C\u00e8ze, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Armengaud", 
        "givenName": "Jean", 
        "id": "sg:person.01203622627.36", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01203622627.36"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France", 
          "id": "http://www.grid.ac/institutes/grid.5399.6", 
          "name": [
            "Aix Marseille Universit\u00e9, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Chapon", 
        "givenName": "Virginie", 
        "id": "sg:person.0647637040.68", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0647637040.68"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1016/j.jasms.2010.01.021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1014526261", 
          "https://doi.org/10.1016/j.jasms.2010.01.021"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nprot.2008.91", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003221462", 
          "https://doi.org/10.1038/nprot.2008.91"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11270-013-1748-1", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024209844", 
          "https://doi.org/10.1007/s11270-013-1748-1"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00203-008-0385-3", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053375599", 
          "https://doi.org/10.1007/s00203-008-0385-3"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s11120-005-0637-x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028766314", 
          "https://doi.org/10.1007/s11120-005-0637-x"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nrmicro.2017.15", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1084129748", 
          "https://doi.org/10.1038/nrmicro.2017.15"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/978-1-4939-7033-9_10", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1090322470", 
          "https://doi.org/10.1007/978-1-4939-7033-9_10"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00248-017-1102-z", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1092649237", 
          "https://doi.org/10.1007/s00248-017-1102-z"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/s41587-020-0501-8", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1127149209", 
          "https://doi.org/10.1038/s41587-020-0501-8"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s00253-016-7945-2", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024966110", 
          "https://doi.org/10.1007/s00253-016-7945-2"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2021-09-23", 
    "datePublishedReg": "2021-09-23", 
    "description": "Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39\u201347% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.", 
    "genre": "article", 
    "id": "sg:pub.10.1038/s41396-021-01113-7", 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1038436", 
        "issn": [
          "1751-7362", 
          "1751-7370"
        ], 
        "name": "The ISME Journal: Multidisciplinary Journal of Microbial Ecology", 
        "publisher": "Springer Nature", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "3", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "16"
      }
    ], 
    "keywords": [
      "uranium tolerance", 
      "C-terminal soluble domain", 
      "single-pass transmembrane protein", 
      "Comparative Proteogenomics", 
      "uranyl exposure", 
      "tolerance phenotype", 
      "transmembrane protein", 
      "soluble domain", 
      "membrane proteins", 
      "soil bacteria", 
      "actinobacterial strain", 
      "apo state", 
      "molecular mechanisms", 
      "unknown function", 
      "cellular responses", 
      "uranium exposure", 
      "protein", 
      "metal binding", 
      "iron metabolism", 
      "nanomolar binding affinity", 
      "binding affinities", 
      "bacteria", 
      "tolerance", 
      "proteogenomics", 
      "human activities", 
      "non-human biota", 
      "total protein", 
      "biota", 
      "domain", 
      "strains", 
      "crystal structure", 
      "phenotype", 
      "residues", 
      "comparative analysis", 
      "binding", 
      "PEPSY", 
      "metabolism", 
      "discovery", 
      "affinity", 
      "soil", 
      "dimers", 
      "humans", 
      "mechanism", 
      "exposure", 
      "tandem", 
      "characterization", 
      "activity", 
      "function", 
      "phosphate", 
      "carboxylate groups", 
      "response", 
      "XAS spectroscopy", 
      "redistribution", 
      "importance", 
      "structure", 
      "environmental concerns", 
      "mono", 
      "analysis", 
      "display", 
      "effect", 
      "adverse effects", 
      "bidentate carboxylate groups", 
      "metals", 
      "impact", 
      "set", 
      "group", 
      "approach", 
      "state", 
      "work", 
      "concern", 
      "face", 
      "uranium", 
      "radionuclides", 
      "ATR-FTIR", 
      "UO22"
    ], 
    "name": "Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria", 
    "pagination": "705-716", 
    "productId": [
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1141322181"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1038/s41396-021-01113-7"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "34556817"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1038/s41396-021-01113-7", 
      "https://app.dimensions.ai/details/publication/pub.1141322181"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2022-12-01T06:42", 
    "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_879.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://doi.org/10.1038/s41396-021-01113-7"
  }
]
 

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/s41396-021-01113-7'

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/s41396-021-01113-7'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41396-021-01113-7'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41396-021-01113-7'


 

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

323 TRIPLES      21 PREDICATES      115 URIs      97 LITERALS      12 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1038/s41396-021-01113-7 schema:about N12c273e1b65e45fb8f9e2a51556221ed
2 N39cc24b55ff44d0488efbef60b792a4e
3 N76638de2c32f484ab6732d2859ddf8a1
4 Na8a5e0516ff042528258b82d122fb536
5 Ne3324bba5d50415cb628267db1664894
6 anzsrc-for:06
7 anzsrc-for:0601
8 schema:author Ndd6580d001a84079a3545e53703c34cf
9 schema:citation sg:pub.10.1007/978-1-4939-7033-9_10
10 sg:pub.10.1007/s00203-008-0385-3
11 sg:pub.10.1007/s00248-017-1102-z
12 sg:pub.10.1007/s00253-016-7945-2
13 sg:pub.10.1007/s11120-005-0637-x
14 sg:pub.10.1007/s11270-013-1748-1
15 sg:pub.10.1016/j.jasms.2010.01.021
16 sg:pub.10.1038/nprot.2008.91
17 sg:pub.10.1038/nrmicro.2017.15
18 sg:pub.10.1038/s41587-020-0501-8
19 schema:datePublished 2021-09-23
20 schema:datePublishedReg 2021-09-23
21 schema:description Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carried out a comparative analysis of four actinobacterial strains isolated from metal and radionuclide-rich soils that display contrasted uranium tolerance phenotypes. Comparative proteogenomics showed that uranyl exposure affects 39–47% of the total proteins, with an impact on phosphate and iron metabolisms and membrane proteins. This approach highlighted a protein of unknown function, named UipA, that is specific to the uranium-tolerant strains and that had the highest positive fold-change upon uranium exposure. UipA is a single-pass transmembrane protein and its large C-terminal soluble domain displayed a specific, nanomolar binding affinity for UO22+ and Fe3+. ATR-FTIR and XAS-spectroscopy showed that mono and bidentate carboxylate groups of the protein coordinated both metals. The crystal structure of UipA, solved in its apo state and bound to uranium, revealed a tandem of PepSY domains in a swapped dimer, with a negatively charged face where uranium is bound through a set of conserved residues. This work reveals the importance of UipA and its PepSY domains in metal binding and radionuclide tolerance.
22 schema:genre article
23 schema:isAccessibleForFree true
24 schema:isPartOf Nb548b8b910534fbea25829f2b0f00072
25 Necd334aa03fd4d0d9826ffa5862a402d
26 sg:journal.1038436
27 schema:keywords ATR-FTIR
28 C-terminal soluble domain
29 Comparative Proteogenomics
30 PEPSY
31 UO22
32 XAS spectroscopy
33 actinobacterial strain
34 activity
35 adverse effects
36 affinity
37 analysis
38 apo state
39 approach
40 bacteria
41 bidentate carboxylate groups
42 binding
43 binding affinities
44 biota
45 carboxylate groups
46 cellular responses
47 characterization
48 comparative analysis
49 concern
50 crystal structure
51 dimers
52 discovery
53 display
54 domain
55 effect
56 environmental concerns
57 exposure
58 face
59 function
60 group
61 human activities
62 humans
63 impact
64 importance
65 iron metabolism
66 mechanism
67 membrane proteins
68 metabolism
69 metal binding
70 metals
71 molecular mechanisms
72 mono
73 nanomolar binding affinity
74 non-human biota
75 phenotype
76 phosphate
77 protein
78 proteogenomics
79 radionuclides
80 redistribution
81 residues
82 response
83 set
84 single-pass transmembrane protein
85 soil
86 soil bacteria
87 soluble domain
88 state
89 strains
90 structure
91 tandem
92 tolerance
93 tolerance phenotype
94 total protein
95 transmembrane protein
96 unknown function
97 uranium
98 uranium exposure
99 uranium tolerance
100 uranyl exposure
101 work
102 schema:name Discovery and characterization of UipA, a uranium- and iron-binding PepSY protein involved in uranium tolerance by soil bacteria
103 schema:pagination 705-716
104 schema:productId N3aa96f4cd19d416faab50a0d34a581c0
105 N88db293e7e0b440f9d0f44ca432b140c
106 Nc281af9b6fb5472da0073908af363f1f
107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1141322181
108 https://doi.org/10.1038/s41396-021-01113-7
109 schema:sdDatePublished 2022-12-01T06:42
110 schema:sdLicense https://scigraph.springernature.com/explorer/license/
111 schema:sdPublisher N77146cede2a44cd8a55074caa410b8b7
112 schema:url https://doi.org/10.1038/s41396-021-01113-7
113 sgo:license sg:explorer/license/
114 sgo:sdDataset articles
115 rdf:type schema:ScholarlyArticle
116 N019b2c3cb54d4c35872f1219ee4da2bb rdf:first sg:person.0743260041.15
117 rdf:rest N92d463db19984e9c9802bbe0e92d6b75
118 N12c273e1b65e45fb8f9e2a51556221ed schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
119 schema:name Soil
120 rdf:type schema:DefinedTerm
121 N36d346ee446545aeb6a9d5534890647d rdf:first sg:person.01351173115.98
122 rdf:rest Nb69b066e6675436d99e7332eca743f71
123 N39cc24b55ff44d0488efbef60b792a4e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
124 schema:name Iron-Binding Proteins
125 rdf:type schema:DefinedTerm
126 N3aa96f4cd19d416faab50a0d34a581c0 schema:name doi
127 schema:value 10.1038/s41396-021-01113-7
128 rdf:type schema:PropertyValue
129 N41e4caae58074669b3de6ccb33c4fa6e rdf:first sg:person.01260473513.43
130 rdf:rest N4f45e983833c42d28cdb8013f6773cfa
131 N4502df44007743bfa1bfe54f01e04a44 rdf:first sg:person.01171005174.14
132 rdf:rest Ndb2165433ca94200b5e8a34f7f109ccf
133 N4f45e983833c42d28cdb8013f6773cfa rdf:first sg:person.0641716334.91
134 rdf:rest N5e6917061e014ae0a5cbb5a485a62e93
135 N55a6fd2f359c404aa64a3123e495b9b1 rdf:first sg:person.0745763400.82
136 rdf:rest N90d6c0901d8143a49b9cb1de84304481
137 N5e6917061e014ae0a5cbb5a485a62e93 rdf:first sg:person.01203622627.36
138 rdf:rest N7cf7b7eb45a746c58f5fde57e3750230
139 N71bdd026e43844f9a95143b8f8dc6c67 rdf:first sg:person.0673264122.96
140 rdf:rest N55a6fd2f359c404aa64a3123e495b9b1
141 N76638de2c32f484ab6732d2859ddf8a1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
142 schema:name Uranium
143 rdf:type schema:DefinedTerm
144 N77146cede2a44cd8a55074caa410b8b7 schema:name Springer Nature - SN SciGraph project
145 rdf:type schema:Organization
146 N7cf7b7eb45a746c58f5fde57e3750230 rdf:first sg:person.0647637040.68
147 rdf:rest rdf:nil
148 N88db293e7e0b440f9d0f44ca432b140c schema:name dimensions_id
149 schema:value pub.1141322181
150 rdf:type schema:PropertyValue
151 N90d6c0901d8143a49b9cb1de84304481 rdf:first sg:person.013452635034.89
152 rdf:rest Nfa3691a6c0214706889816d00f938ca2
153 N92d463db19984e9c9802bbe0e92d6b75 rdf:first sg:person.01350015161.78
154 rdf:rest N4502df44007743bfa1bfe54f01e04a44
155 N99139159491545c599ccf2fe73ac853a rdf:first sg:person.01064572753.71
156 rdf:rest N019b2c3cb54d4c35872f1219ee4da2bb
157 Na8a5e0516ff042528258b82d122fb536 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
158 schema:name Bacteria
159 rdf:type schema:DefinedTerm
160 Nb548b8b910534fbea25829f2b0f00072 schema:volumeNumber 16
161 rdf:type schema:PublicationVolume
162 Nb69b066e6675436d99e7332eca743f71 rdf:first sg:person.01134623657.91
163 rdf:rest Ndb07a738c7ff4e5b85088515b543a1ef
164 Nc281af9b6fb5472da0073908af363f1f schema:name pubmed_id
165 schema:value 34556817
166 rdf:type schema:PropertyValue
167 Ndb07a738c7ff4e5b85088515b543a1ef rdf:first sg:person.0637520660.45
168 rdf:rest N71bdd026e43844f9a95143b8f8dc6c67
169 Ndb2165433ca94200b5e8a34f7f109ccf rdf:first sg:person.01246623543.06
170 rdf:rest N41e4caae58074669b3de6ccb33c4fa6e
171 Ndd6580d001a84079a3545e53703c34cf rdf:first sg:person.01035253041.37
172 rdf:rest N36d346ee446545aeb6a9d5534890647d
173 Ne3324bba5d50415cb628267db1664894 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
174 schema:name Iron
175 rdf:type schema:DefinedTerm
176 Necd334aa03fd4d0d9826ffa5862a402d schema:issueNumber 3
177 rdf:type schema:PublicationIssue
178 Nfa3691a6c0214706889816d00f938ca2 rdf:first sg:person.01250262144.30
179 rdf:rest N99139159491545c599ccf2fe73ac853a
180 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
181 schema:name Biological Sciences
182 rdf:type schema:DefinedTerm
183 anzsrc-for:0601 schema:inDefinedTermSet anzsrc-for:
184 schema:name Biochemistry and Cell Biology
185 rdf:type schema:DefinedTerm
186 sg:journal.1038436 schema:issn 1751-7362
187 1751-7370
188 schema:name The ISME Journal: Multidisciplinary Journal of Microbial Ecology
189 schema:publisher Springer Nature
190 rdf:type schema:Periodical
191 sg:person.01035253041.37 schema:affiliation grid-institutes:grid.5399.6
192 schema:familyName Gallois
193 schema:givenName Nicolas
194 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01035253041.37
195 rdf:type schema:Person
196 sg:person.01064572753.71 schema:affiliation grid-institutes:grid.426328.9
197 schema:familyName Legrand
198 schema:givenName Pierre
199 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01064572753.71
200 rdf:type schema:Person
201 sg:person.01134623657.91 schema:affiliation grid-institutes:grid.5399.6
202 schema:familyName Bremond
203 schema:givenName Nicolas
204 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01134623657.91
205 rdf:type schema:Person
206 sg:person.01171005174.14 schema:affiliation grid-institutes:grid.418735.c
207 schema:familyName Février
208 schema:givenName Laureline
209 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01171005174.14
210 rdf:type schema:Person
211 sg:person.01203622627.36 schema:affiliation grid-institutes:grid.460789.4
212 schema:familyName Armengaud
213 schema:givenName Jean
214 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01203622627.36
215 rdf:type schema:Person
216 sg:person.01246623543.06 schema:affiliation grid-institutes:grid.462124.7
217 schema:familyName Den Auwer
218 schema:givenName Christophe
219 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01246623543.06
220 rdf:type schema:Person
221 sg:person.01250262144.30 schema:affiliation grid-institutes:grid.5399.6
222 schema:familyName Lemaire
223 schema:givenName David
224 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01250262144.30
225 rdf:type schema:Person
226 sg:person.01260473513.43 schema:affiliation grid-institutes:grid.5399.6
227 schema:familyName Arnoux
228 schema:givenName Pascal
229 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01260473513.43
230 rdf:type schema:Person
231 sg:person.013452635034.89 schema:affiliation grid-institutes:grid.5399.6
232 schema:familyName Mohamad Ali
233 schema:givenName Abbas
234 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013452635034.89
235 rdf:type schema:Person
236 sg:person.01350015161.78 schema:affiliation grid-institutes:grid.418735.c
237 schema:familyName Floriani
238 schema:givenName Magali
239 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01350015161.78
240 rdf:type schema:Person
241 sg:person.01351173115.98 schema:affiliation grid-institutes:grid.460789.4
242 schema:familyName Alpha-Bazin
243 schema:givenName Béatrice
244 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01351173115.98
245 rdf:type schema:Person
246 sg:person.0637520660.45 schema:affiliation grid-institutes:grid.5399.6
247 schema:familyName Ortet
248 schema:givenName Philippe
249 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0637520660.45
250 rdf:type schema:Person
251 sg:person.0641716334.91 schema:affiliation grid-institutes:grid.5399.6
252 schema:familyName Berthomieu
253 schema:givenName Catherine
254 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0641716334.91
255 rdf:type schema:Person
256 sg:person.0647637040.68 schema:affiliation grid-institutes:grid.5399.6
257 schema:familyName Chapon
258 schema:givenName Virginie
259 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0647637040.68
260 rdf:type schema:Person
261 sg:person.0673264122.96 schema:affiliation grid-institutes:grid.5399.6
262 schema:familyName Barakat
263 schema:givenName Mohamed
264 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0673264122.96
265 rdf:type schema:Person
266 sg:person.0743260041.15 schema:affiliation grid-institutes:grid.418735.c
267 schema:familyName Theodorakopoulos
268 schema:givenName Nicolas
269 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0743260041.15
270 rdf:type schema:Person
271 sg:person.0745763400.82 schema:affiliation grid-institutes:grid.5399.6
272 schema:familyName Piette
273 schema:givenName Laurie
274 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0745763400.82
275 rdf:type schema:Person
276 sg:pub.10.1007/978-1-4939-7033-9_10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1090322470
277 https://doi.org/10.1007/978-1-4939-7033-9_10
278 rdf:type schema:CreativeWork
279 sg:pub.10.1007/s00203-008-0385-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053375599
280 https://doi.org/10.1007/s00203-008-0385-3
281 rdf:type schema:CreativeWork
282 sg:pub.10.1007/s00248-017-1102-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1092649237
283 https://doi.org/10.1007/s00248-017-1102-z
284 rdf:type schema:CreativeWork
285 sg:pub.10.1007/s00253-016-7945-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024966110
286 https://doi.org/10.1007/s00253-016-7945-2
287 rdf:type schema:CreativeWork
288 sg:pub.10.1007/s11120-005-0637-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1028766314
289 https://doi.org/10.1007/s11120-005-0637-x
290 rdf:type schema:CreativeWork
291 sg:pub.10.1007/s11270-013-1748-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024209844
292 https://doi.org/10.1007/s11270-013-1748-1
293 rdf:type schema:CreativeWork
294 sg:pub.10.1016/j.jasms.2010.01.021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014526261
295 https://doi.org/10.1016/j.jasms.2010.01.021
296 rdf:type schema:CreativeWork
297 sg:pub.10.1038/nprot.2008.91 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003221462
298 https://doi.org/10.1038/nprot.2008.91
299 rdf:type schema:CreativeWork
300 sg:pub.10.1038/nrmicro.2017.15 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084129748
301 https://doi.org/10.1038/nrmicro.2017.15
302 rdf:type schema:CreativeWork
303 sg:pub.10.1038/s41587-020-0501-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1127149209
304 https://doi.org/10.1038/s41587-020-0501-8
305 rdf:type schema:CreativeWork
306 grid-institutes:grid.418735.c schema:alternateName IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France
307 IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France
308 schema:name Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
309 IRSN, PSE-ENV/SRTE/LECO, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France
310 IRSN, PSE-ENV/SRTE/LR2T, B.P. 3, 13115, Saint Paul-lez-Durance, Cedex, France
311 rdf:type schema:Organization
312 grid-institutes:grid.426328.9 schema:alternateName Synchrotron SOLEIL. L’Orme des Merisiers Saint-Aubin. BP 48, 91192, Gif-sur-Yvette, France
313 schema:name Synchrotron SOLEIL. L’Orme des Merisiers Saint-Aubin. BP 48, 91192, Gif-sur-Yvette, France
314 rdf:type schema:Organization
315 grid-institutes:grid.460789.4 schema:alternateName Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
316 schema:name Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
317 rdf:type schema:Organization
318 grid-institutes:grid.462124.7 schema:alternateName Université Côte d’Azur, CNRS, ICN, 06108, Nice, France
319 schema:name Université Côte d’Azur, CNRS, ICN, 06108, Nice, France
320 rdf:type schema:Organization
321 grid-institutes:grid.5399.6 schema:alternateName Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
322 schema:name Aix Marseille Université, CEA, CNRS, BIAM, 13108, Saint Paul-Lez-Durance, France
323 rdf:type schema:Organization
 




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


...