The binary protein-protein interaction landscape of Escherichia coli

By S. Rajagopala, Patricia M. Sikorski, Ashwani Kumar, Roberto Mosca, James Vlasblom, Roland Arnold, Jonathan Franca-Koh, S. Pakala, S. Phanse, Arnaud Céol and 8 more. 2014

250 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Sequence co-evolution gives 3D contacts and structures of protein complexes (2014, methodology): “Selection of interacting protein pairs for co-evolution calculation The candidate set of complexes for testing and de novo prediction was derived starting from a dataset of binary protein-protein interactions in E. coli including yeast two-hybrid experiments, literature-curated interactions and 3D c”
Inferring interaction partners from protein sequences using mutual information (2018, background): “High-throughput experiments have recently elucidated a substantial fraction 5 of protein-protein interactions in a few model organisms [1], but such experiments remain chal- 6 lenging.”
Inferring interaction partners from protein sequences (2016, background): “High-throughput experiments have recently elucidated a substantial fraction of protein-protein interactions in a few model organisms [1], but such experiments remain challenging.”
The BioGRID interaction database: 2015 update (2014, background): “The systematic experimental identification and characterization of protein and genetic interaction networks in major model organism species and humans has continued to grow in pace and scale (21,23,29–35).”