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The binary protein-protein interaction landscape of Escherichia coli

Nature Biotechnology volume 32, pages 285–290 (2014)Cite this article

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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.

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Figure 1: Systematic identification of binary PPIs in E. coli.
Figure 2: Quality assessment and comparison of Y2H interactions with data from the literature.
Figure 3: Structural analysis of the E. coli binary interactome.
Figure 4: Comparison of the properties of binary and AP-MS interaction networks.
Figure 5: Integrative analyses on the PPI and GI data.
Figure 6: Conservation of physical interactions between and within protein complexes.

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Acknowledgements

S.V.R. and P.U. were supported by US National Institutes of Health grant GM079710. P.U., R.H. and P.A. were supported by the Seventh Research Framework Programme of the European Union (AntiPathoGN; EU grant HEALTH-F3-2009-223101). M.B. was supported by the Discovery Grant from the Natural Sciences and Engineering Research Council (DG-20234). We thank X. De Bolle (University of Namur, Belgium) for providing pRH016 and pRH018 vectors.

Author information

Author notes

  1. Stefan Wuchty

    Present address: Present address: Department of Computer Science, University of Miami, Coral Gables, Florida, USA.,

  2. Patricia Sikorski, Ashwani Kumar and Roberto Mosca: These authors contributed equally to this work.

Authors and Affiliations

  1. J. Craig Venter Institute, Rockville, Maryland, USA

    Seesandra V Rajagopala, Patricia Sikorski, Jonathan Franca-Koh, Suman B Pakala & Rembert Pieper

  2. Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, Saskatchewan, Canada

    Ashwani Kumar, James Vlasblom, Sadhna Phanse & Mohan Babu

  3. Joint IRB-BSC Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain

    Roberto Mosca, Arnaud Ceol & Patrick Aloy

  4. The Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada

    Roland Arnold & Andrew Emili

  5. German Cancer Research Center (Deutsches Krebsforschungszentrum), Heidelberg, Germany

    Roman Häuser & Gabriella Siszler

  6. National Center of Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA

    Stefan Wuchty

  7. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain

    Patrick Aloy

  8. Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA

    Peter Uetz

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Contributions

The project was conceived by S.V.R. and P.U. and directed by S.V.R. and R.P.; P.S., J.F.-K., R.H., G.S. and S.V.R. performed the experiments; S.V.R., A.K., R.M., S.B.P., J.V., R.A., S.P., A.C., S.W., P.A. and M.B. performed computational analysis; and A.E. provided support for computational analysis tools. S.V.R., P.A. and M.B. wrote the manuscript, with input from P.U.

Corresponding authors

Correspondence to Seesandra V Rajagopala or Mohan Babu.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Figures 1–9, Supplementary Tables 3–4 and 8, Supplementary Note (PDF 14094 kb)

Supplementary Table 1

Literature curated E. coli binary PPIs supported by multiple publications or methods. (XLS 158 kb)

Supplementary Table 2

Escherichia coli protein-protein interactions indentified by Y2H screening. (XLS 248 kb)

Supplementary Table 5

Escherichia coli combined binary PPIs (obtained by combining Y2H data from this study with the manually curated literature binary interactions) (XLS 443 kb)

Supplementary Table 6

Literature binary interactions used for the mapping of the internal topology of complexes of 3+ components from (Hu et al.) (XLS 228 kb)

Supplementary Table 7

List of Y2H PPIs and their corresponding GI scores (XLS 49 kb)

Supplementary Table 9

Predicted protein complexes from Hu et al. (XLS 62 kb)

Supplementary Table 10

EcoCyc protein complexes (XLS 78 kb)

Supplementary Table 11

Ecoli interactions observed in experimental structures from the Protein Data Bank (XLS 1994 kb)

Supplementary Table 12

E. coli interactions from AP/MS studies with Socio-affinity score higher than 10 (XLS 34 kb)

Supplementary Table 13

Conserved PPIs experimentally characterized in other bacteria (interologs) (XLS 211 kb)

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Rajagopala, S., Sikorski, P., Kumar, A. et al. The binary protein-protein interaction landscape of Escherichia coli. Nat Biotechnol 32, 285–290 (2014). https://doi.org/10.1038/nbt.2831

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