The binary protein-protein interaction landscape of Escherichia coli

Research output: Contribution to journalArticle


  • Seesandra V. Rajagopala
  • Patricia Sikorski
  • Ashwani Kumar
  • Roberto Mosca
  • James Vlasblom
  • Jonathan Franca-Koh
  • Suman B. Pakala
  • Sadhna Phanse
  • Arnaud Ceol
  • Roman Häuser
  • Gabriella Siszler
  • Stefan Wuchty
  • Andrew Emili
  • Mohan Babu
  • Patrick Aloy
  • Rembert Pieper
  • Peter Uetz

Colleges, School and Institutes

External organisations

  • J. Craig Venter Institute
  • University of Regina
  • Institute for Research in Biomedicine (IRB Barcelona)
  • German Cancer Research Center (Deutsches Krebsforschungszentrum)
  • National Center of Biotechnology Information
  • University of Toronto
  • Virginia Commonwealth University


Efforts to map the Escherichia coli interactome have identified several hundred macromolecular complexes, but direct binary protein-protein interactions (PPIs) have not been surveyed on a large scale. Here we performed yeast two-hybrid screens of 3,305 baits against 3,606 preys (∼70% of the E. coli proteome) in duplicate to generate a map of 2,234 interactions, which approximately doubles the number of known binary PPIs in E. coli. Integration of binary PPI and genetic-interaction data revealed functional dependencies among components involved in cellular processes, including envelope integrity, flagellum assembly and protein quality control. Many of the binary interactions that we could map in multiprotein complexes were informative regarding internal topology of complexes and indicated that interactions in complexes are substantially more conserved than those interactions connecting different complexes. This resource will be useful for inferring bacterial gene function and provides a draft reference of the basic physical wiring network of this evolutionarily important model microbe.


Original languageEnglish
Pages (from-to)285-290
Number of pages6
JournalNature Biotechnology
Issue number3
Publication statusPublished - 23 Feb 2014


  • Escherichia coli Proteins, Protein Interaction Mapping, Protein Interaction Maps, Proteomics, Two-Hybrid System Techniques, Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't