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Bacterial Interactomes: Interacting Protein Partners Share Similar Function and Are Validated in Independent Assays More Frequently Than Previously Reported.
Shatsky, Maxim; Allen, Simon; Gold, Barbara L; Liu, Nancy L; Juba, Thomas R; Reveco, Sonia A; Elias, Dwayne A; Prathapam, Ramadevi; He, Jennifer; Yang, Wenhong; Szakal, Evelin D; Liu, Haichuan; Singer, Mary E; Geller, Jil T; Lam, Bonita R; Saini, Avneesh; Trotter, Valentine V; Hall, Steven C; Fisher, Susan J; Brenner, Steven E; Chhabra, Swapnil R; Hazen, Terry C; Wall, Judy D; Witkowska, H Ewa; Biggin, Mark D; Chandonia, John-Marc; Butland, Gareth.
Afiliação
  • Shatsky M; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Allen S; the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
  • Gold BL; the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Liu NL; the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Juba TR; the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211;
  • Reveco SA; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Elias DA; the Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37831;
  • Prathapam R; the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • He J; the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Yang W; the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Szakal ED; the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
  • Liu H; the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
  • Singer ME; the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Geller JT; the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Lam BR; the Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Saini A; the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Trotter VV; the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Hall SC; the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
  • Fisher SJ; the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
  • Brenner SE; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; the Department of Plant and Microbial Biology, University of California at Berkeley, Berkeley, California, 94720;
  • Chhabra SR; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720;
  • Hazen TC; the Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, 37996; and.
  • Wall JD; the Departments of Biochemistry and of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri, 65211;
  • Witkowska HE; the Department of Obstetrics, Gynecology and Reproductive Sciences and Sandler-Moore Mass Spectrometry Core Facility, University of California at San Francisco, San Francisco, California, 94143;
  • Biggin MD; the Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720.
  • Chandonia JM; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; gpbutland@lbl.gov jmchandonia@lbl.gov.
  • Butland G; the Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; From the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720; gpbutland@lbl.gov jmchandonia@lbl.gov.
Mol Cell Proteomics ; 15(5): 1539-55, 2016 05.
Article em En | MEDLINE | ID: mdl-26873250
ABSTRACT
Numerous affinity purification-mass spectrometry (AP-MS) and yeast two-hybrid screens have each defined thousands of pairwise protein-protein interactions (PPIs), most of which are between functionally unrelated proteins. The accuracy of these networks, however, is under debate. Here, we present an AP-MS survey of the bacterium Desulfovibrio vulgaris together with a critical reanalysis of nine published bacterial yeast two-hybrid and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli Compared with the nine published interactomes, our two networks are smaller, are much less highly connected, and have significantly lower false discovery rates. In addition, our interactomes are much more enriched in protein pairs that are encoded in the same operon, have similar functions, and are reproducibly detected in other physical interaction assays than the pairs reported in prior studies. Our work establishes more stringent benchmarks for the properties of protein interactomes and suggests that bona fide PPIs much more frequently involve protein partners that are annotated with similar functions or that can be validated in independent assays than earlier studies suggested.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Proteínas de Bactérias / Desulfovibrio vulgaris / Biologia Computacional / Escherichia coli Idioma: En Ano de publicação: 2016 Tipo de documento: Article
Texto completo
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Proteínas de Bactérias / Desulfovibrio vulgaris / Biologia Computacional / Escherichia coli Idioma: En Ano de publicação: 2016 Tipo de documento: Article