Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli

Research output: Contribution to journalArticle

Authors

  • Mohan Babu
  • Cedoljub Bundalovic-Torma
  • Alla Gagarinova
  • Keith S Wong
  • Ashwani Kumar
  • Geordie Stewart
  • Bahram Samanfar
  • Hiroyuki Aoki
  • Omar Wagih
  • James Vlasblom
  • Sadhna Phanse
  • Krunal Lad
  • Angela Yeou Hsiung Yu
  • Christopher Graham
  • Ke Jin
  • Eric Brown
  • Ashkan Golshani
  • Philip Kim
  • Gabriel Moreno-Hagelsieb
  • Jack Greenblatt
  • Walid A Houry
  • John Parkinson
  • Andrew Emili

Colleges, School and Institutes

Abstract

Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways and processes. Conversely, genetic interaction (GI) screens can provide insights into the biological role(s) of individual gene and higher order associations. Combining the information from both approaches should elucidate how complexes and pathways intersect functionally at a systems level. However, such integrative analysis has been hindered due to the lack of relevant GI data. Here we present a systematic, unbiased, and quantitative synthetic genetic array screen in E. coli describing the genetic dependencies and functional cross-talk among over 600,000 digenic mutant combinations. Combining this epistasis information with putative functional modules derived from previous proteomic data and genomic context-based methods revealed unexpected associations, including new components required for the biogenesis of iron-sulphur and ribosome integrity, and the interplay between molecular chaperones and proteases. We find that functionally-linked genes co-conserved among γ-proteobacteria are far more likely to have correlated GI profiles than genes with divergent patterns of evolution. Overall, examining bacterial GIs in the context of protein complexes provides avenues for a deeper mechanistic understanding of core microbial systems.

Details

Original languageEnglish
Article numbere1004120
JournalPLoS Genetics
Volume10
Issue number2
Publication statusPublished - 20 Feb 2014

Keywords

  • Cytoplasm, Epistasis, Genetic, Escherichia coli, Genome, Bacterial, Humans, Molecular Chaperones, Multiprotein Complexes, Mutation, Oligonucleotide Array Sequence Analysis, Protein Interaction Maps, Proteomics, Journal Article, Research Support, Non-U.S. Gov't