The binary protein-protein interaction landscape of Escherichia coli

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...

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Bibliographic Details
Published in:Nature biotechnology 2014-03, Vol.32 (3), p.285-290
Main Authors: Rajagopala, Seesandra V, Sikorski, Patricia, Kumar, Ashwani, Mosca, Roberto, Vlasblom, James, Arnold, Roland, Franca-Koh, Jonathan, Pakala, Suman B, Phanse, Sadhna, Ceol, Arnaud, Häuser, Roman, Siszler, Gabriella, Wuchty, Stefan, Emili, Andrew, Babu, Mohan, Aloy, Patrick, Pieper, Rembert, Uetz, Peter
Format: Article
Language:English
Subjects:
Bacterial genetics
Bacterial proteins
Bacteriology
E coli
Escherichia coli
Escherichia coli Proteins - chemistry
Escherichia coli Proteins - genetics
Escherichia coli Proteins - metabolism
Genes
Genomics
Interactomes
Physiological aspects
Protein Interaction Mapping - methods
Protein Interaction Maps - physiology
Protein research
Protein-protein interactions
Proteins
Proteomics
Proteomics - methods
Surveys
Two-Hybrid System Techniques
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Summary: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.
ISSN:1087-0156
1546-1696
DOI:10.1038/nbt.2831