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Interaction network containing conserved and essential protein complexes in Escherichia coli

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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Figure 1: Systematic identification and validation of protein complexes in E. coli.
Figure 2: Analysis of affinity-purified protein complexes.
Figure 3: Network properties of bacterial protein–protein interactions.
Figure 4: Bioinformatic analyses of interacting protein modules.

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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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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)

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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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