skip to main content

DOE PAGESDOE PAGES

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:
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
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 Lab. (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); National Institutes of Health (NIH)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1261350
Alternate Identifier(s):
OSTI ID: 1379316

Shatsky, Maxim, Allen, Simon, Gold, Barbara, Liu, Nancy L., Juba, Thomas R., Elias, Dwayne A, Reveco, Sonia 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, Hazen, Terry C., Wall, Judy D., Witkowska, Ewa, Biggin, Mark D., Chandonia, John-Marc, and Butland, Gareth. Bacterial interactomes: Interacting protein partners share similar function and are validated in independent assays more frequently than previously reported.. United States: N. p., Web. doi:10.1074/mcp.M115.054692.
Shatsky, Maxim, Allen, Simon, Gold, Barbara, Liu, Nancy L., Juba, Thomas R., Elias, Dwayne A, Reveco, Sonia 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, Hazen, Terry C., Wall, Judy D., Witkowska, Ewa, Biggin, Mark D., Chandonia, John-Marc, & Butland, Gareth. Bacterial interactomes: Interacting protein partners share similar function and are validated in independent assays more frequently than previously reported.. United States. doi:10.1074/mcp.M115.054692.
Shatsky, Maxim, Allen, Simon, Gold, Barbara, Liu, Nancy L., Juba, Thomas R., Elias, Dwayne A, Reveco, Sonia 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, Hazen, Terry C., Wall, Judy D., Witkowska, Ewa, Biggin, Mark D., Chandonia, John-Marc, and Butland, Gareth. 2016. "Bacterial interactomes: Interacting protein partners share similar function and are validated in independent assays more frequently than previously reported.". United States. doi:10.1074/mcp.M115.054692. https://www.osti.gov/servlets/purl/1261350.
@article{osti_1261350,
title = {Bacterial interactomes: Interacting protein partners share similar function and are validated in independent assays more frequently than previously reported.},
author = {Shatsky, Maxim and Allen, Simon and Gold, Barbara and Liu, Nancy L. and Juba, Thomas R. and Elias, Dwayne A and Reveco, Sonia A. and Prathapam, Ramadevi and He, Jennifer and Yang, Wenhong and Szakal, Evelin D. and Liu, Haichuan and Singer, Mary E. and Geller, Jil T. and Lam, Bonita R. and Saini, Avneesh and Trotter, Valentine V. and Hall, Steven C. and Fisher, Susan J. and Brenner, Steven E. and Chhabra, Swapnil and Hazen, Terry C. and Wall, Judy D. and Witkowska, Ewa and Biggin, Mark D. and Chandonia, John-Marc and Butland, Gareth},
abstractNote = {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.},
doi = {10.1074/mcp.M115.054692},
journal = {Molecular and Cellular Proteomics},
number = 5,
volume = 15,
place = {United States},
year = {2016},
month = {5}
}

Works referenced in this record:

MicrobesOnline: an integrated portal for comparative and functional genomics
journal, November 2009
  • Dehal, P. S.; Joachimiak, M. P.; Price, M. N.
  • Nucleic Acids Research, Vol. 38, Issue suppl_1, p. D396-D400
  • DOI: 10.1093/nar/gkp919