title: The binary protein-protein interaction landscape of Escherichia coli.
abstract: 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.
authors.affiliation: J Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Seesandra V
authors.initials: SV
authors.lastname: Rajagopala
authors.affiliation: J Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Patricia
authors.initials: P
authors.lastname: Sikorski
authors.affiliation: Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada.
authors.forename: Ashwani
authors.initials: A
authors.lastname: Kumar
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
authors.forename: Roberto
authors.initials: R
authors.lastname: Mosca
authors.affiliation: Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada.
authors.forename: James
authors.initials: J
authors.lastname: Vlasblom
authors.affiliation: The Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Roland
authors.initials: R
authors.lastname: Arnold
authors.affiliation: J Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Franca-Koh
authors.affiliation: J Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Suman B
authors.initials: SB
authors.lastname: Pakala
authors.affiliation: Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada.
authors.forename: Sadhna
authors.initials: S
authors.lastname: Phanse
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Ceol
authors.affiliation: German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Roman
authors.initials: R
authors.lastname: Häuser
authors.affiliation: German Cancer Research Center (DKFZ), Heidelberg, Germany.
authors.forename: Gabriella
authors.initials: G
authors.lastname: Siszler
authors.affiliation: National Center of Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
authors.forename: Stefan
authors.initials: S
authors.lastname: Wuchty
authors.affiliation: The Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Andrew
authors.initials: A
authors.lastname: Emili
authors.affiliation: Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada.
authors.forename: Mohan
authors.initials: M
authors.lastname: Babu
authors.affiliation: Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain.|Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
authors.forename: Patrick
authors.initials: P
authors.lastname: Aloy
authors.affiliation: J Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Rembert
authors.initials: R
authors.lastname: Pieper
authors.affiliation: Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Uetz
mesh_terms: D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps / Q000502:physiology*; D040901:Proteomics / Q000379:methods*; D020798:Two-Hybrid System Techniques
chemical_list: D029968:Escherichia coli Proteins