Interaction network containing conserved and essential protein complexes in Escherichia coli (original) (raw)

Nature volume 433, pages 531–537 (2005)Cite this article

Abstract

Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism1, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (∼ 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data2. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.

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Acknowledgements

The authors wish to thank C. J. Ingles and M. Shales for comments on the manuscript. This work was supported by funds from the Ontario Research and Development Challenge Fund and Genome Canada to A.E. and J.G. G.B. was a recipient of a Charles H. Best Post-Doctoral Fellowship. J.M.P.-A. acknowledges support from the Hospital for Sick Children (Toronto, Ontario, Canada) Research Training Centre. Computer analyses were undertaken at the Centre for Computational Biology, Hospital for Sick Children.Authors’ contributions Informatics studies were performed and analysed by J.M.P.-A. and J.P. Experimental design and data analysis were coordinated by G.B. Tagging and purification experiments were performed by W.Y., X.Y., J.L. and G.B. V.C., A.S., D.R., B.B., N.J.K. and M.D. performed and assisted with mass spectrometry analysis. The manuscript was jointly drafted by G.B., A.E., J.G., J.M.P.-A. and J.P. The project was conceived and designed by J.G. and was directed by A.E.

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Authors and Affiliations

  1. Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Ontario, M5G 1L6, Toronto, Canada
    Gareth Butland, Joyce Li, Wehong Yang, Xiaochun Yang, Andrei Starostine, Nevan Krogan, Michael Davey, Jack Greenblatt & Andrew Emili
  2. Hospital for Sick Children, 555 University Avenue, Ontario, M4K 1X8, Toronto, Canada
    José Manuel Peregrín-Alvarez & John Parkinson
  3. Affinium Pharmaceuticals, 100 University Avenue, Ontario, M5J 1V6, Toronto, Canada
    Veronica Canadien, Dawn Richards, Bryan Beattie & Jack Greenblatt
  4. Department of Biochemistry,
    John Parkinson
  5. Department of Medical Genetics and Microbiology, University of Toronto, Medical Sciences Building, 1 King's College Circle, Ontario, M5S 1A8, Toronto, Canada
    John Parkinson, Jack Greenblatt & Andrew Emili

Authors

  1. Gareth Butland
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  2. José Manuel Peregrín-Alvarez
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  3. Joyce Li
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  4. Wehong Yang
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  5. Xiaochun Yang
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  6. Veronica Canadien
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  7. Andrei Starostine
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  8. Dawn Richards
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  9. Bryan Beattie
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  10. Nevan Krogan
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  11. Michael Davey
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  12. John Parkinson
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  13. Jack Greenblatt
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  14. Andrew Emili
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Correspondence toAndrew Emili.

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Supplementary information

Supplementary Notes 1

This contains the Supplementary Discussion, Supplementary Methods and legends to accompany the Supplementary Figures (S1-S6) and Supplementary Tables (S1-7). (DOC 69 kb)

Supplementary Notes 2

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Supplementary Figures S1-6

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Supplementary Tables S1-S7

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Butland, G., Peregrín-Alvarez, J., Li, J. et al. Interaction network containing conserved and essential protein complexes in Escherichia coli.Nature 433, 531–537 (2005). https://doi.org/10.1038/nature03239

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Editorial Summary

Essence of E. coli

Proteomic analysis of native protein–protein interactions in E. coli combined with protein mass spectrometry has revealed an interaction network consisting of the proteins essential to bacterial life. The network is highly conserved, providing insight into core bacterial processes, the nature of evolutionary constraints, and suitable new antimicrobial drug targets.