skip to main content

DOE PAGESDOE PAGES

This content will become publicly available on May 1, 2017

Title: Bacterial interactomes: Interacting protein partners share similar function and are validated in independent assays more frequently than previously reported.

Numerous affinity purification – mass-spectrometry (AP-MS) and yeast two hybrid (Y2H) screens have each defined thousands of pairwise protein-protein interactions (PPIs), most 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 Y2H and AP-MS screens. We have identified 459 high confidence PPIs from D. vulgaris and 391 from Escherichia coli. Compared to the nine published interactomes, our two networks are smaller; are much less highly connected; have significantly lower false discovery rates; and 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. Lastly, 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.
Authors:
 [1] ;  [2] ;  [3] ;  [3] ;  [4] ;  [5] ;  [1] ;  [3] ;  [3] ;  [3] ;  [2] ;  [2] ;  [6] ;  [6] ;  [6] ;  [3] ;  [3] ;  [2] ;  [2] ;  [7] more »;  [1] ;  [8] ;  [9] ;  [2] ;  [10] ;  [1] ;  [11] « less
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
  2. Univ. of California, San Francisco, CA (United States). Dept. of Obstetrics, Gynecology and Reproductive Sciences
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division
  4. Univ. of Missouri, Columbia, MO (United States). Dept. of Biochemistry and of Molecular Microbiology & Immunology
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division
  7. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
  8. Univ. of Tennessee, Knoxville, TN (United States). Dept. of Civil and Environmental Engineering
  9. Univ. of Missouri, Columbia, MO (United States). Dept. of Biochemistry and of Molecular Microbiology and Immunology
  10. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
  11. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
Publication Date:
OSTI Identifier:
1261350
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231; P30 CA08210
Type:
Accepted Manuscript
Journal Name:
Molecular and Cellular Proteomics
Additional Journal Information:
Journal Volume: 15; Journal Issue: 5; Journal ID: ISSN 1535-9476
Publisher:
American Society for Biochemistry and Molecular Biology
Research Org:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Inst. of Health (NIH)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES