Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Interaction network containing conserved and essential protein complexes in Escherichia coli


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.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

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.


  1. Neidhardt, F. (ed.) Escherichia coli and Salmonella: Cellular and Molecular Biology (ASM Press, Washington DC, 1996)

  2. Serres, M. H. et al. A functional update of the Escherichia coli K-12 genome. Genome Biol. 2, research0035.1–0035.7 (2001)

    Article  Google Scholar 

  3. Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147 (2002)

    ADS  CAS  Article  Google Scholar 

  4. Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000)

    ADS  CAS  Article  Google Scholar 

  5. Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli . Proc. Natl Acad. Sci. USA 97, 5978–5983 (2000)

    ADS  CAS  Article  Google Scholar 

  6. Zeghouf, M. et al. Sequential Peptide Affinity (SPA) system for the identification of mammalian and bacterial protein complexes. J. Proteome Res. 3, 463–468 (2004)

    CAS  Article  Google Scholar 

  7. Stukenberg, P. T. & O'Donnell, M. Assembly of a chromosomal replication machine: two DNA polymerases, a clamp loader, and sliding clamps in one holoenzyme particle. V. Four different polymerase-clamp complexes on DNA. J. Biol. Chem. 270, 13384–13391 (1995)

    CAS  Article  Google Scholar 

  8. Harmon, F. G., Brockman, J. P. & Kowalczykowski, S. C. RecQ helicase stimulates both DNA catenation and changes in DNA topology by topoisomerase III. J. Biol. Chem. 278, 42668–42678 (2003)

    CAS  Article  Google Scholar 

  9. Witte, G., Urbanke, C. & Curth, U. DNA polymerase III chi subunit ties single-stranded DNA binding protein to the bacterial replication machinery. Nucleic Acids Res. 31, 4434–4440 (2003)

    CAS  Article  Google Scholar 

  10. Nakayama, H. RecQ family helicases: roles as tumor suppressor proteins. Oncogene 21, 9008–9021 (2002)

    CAS  Article  Google Scholar 

  11. von Mering, C. et al. Comparative assessment of large-scale data sets of protein–protein interactions. Nature 417, 399–403 (2002)

    ADS  CAS  Article  Google Scholar 

  12. Salwinski, L. et al. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 32 (Database issue), D449–D451 (2004)

    CAS  Article  Google Scholar 

  13. Bader, G. D., Betel, D. & Hogue, C. W. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248–250 (2003)

    CAS  Article  Google Scholar 

  14. von Mering, C. et al. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31, 258–261 (2003)

    CAS  Article  Google Scholar 

  15. Bowers, P. et al. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 5, R35 (2004)

    Article  Google Scholar 

  16. Rain, J. C. et al. The protein–protein interaction map of Helicobacter pylori . Nature 409, 211–215 (2001)

    ADS  CAS  Article  Google Scholar 

  17. Gully, D., Moinier, D., Loiseau, L. & Bouveret, E. New partners of acyl carrier protein detected in Escherichia coli by tandem affinity purification. FEBS Lett. 548, 90–96 (2003)

    CAS  Article  Google Scholar 

  18. Wuchty, S., Oltvai, Z. N. & Barabasi, A. L. Evolutionary conservation of motif constituents in the yeast protein interaction network. Nature Genet. 35, 176–179 (2003)

    CAS  Article  Google Scholar 

  19. Jordan, I. K., Wolf, Y. I. & Koonin, E. V. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3, 1 (2003)

    Article  Google Scholar 

  20. Fraser, H. B., Wall, D. P. & Hirsh, A. E. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol. Biol. 3, 11 (2003)

    Article  Google Scholar 

  21. Peregrin-Alvarez, J. M., Tsoka, S. & Ouzounis, C. A. The phylogenetic extent of metabolic enzymes and pathways. Genome Res. 13, 422–427 (2003)

    CAS  Article  Google Scholar 

  22. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631–637 (1997)

    ADS  CAS  Article  Google Scholar 

  23. Wu, J., Kasif, S. & DeLisi, C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19, 1524–1530 (2003)

    CAS  Article  Google Scholar 

  24. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D. & Yeates, T. O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA 96, 4285–4288 (1999)

    ADS  CAS  Article  Google Scholar 

  25. Date, S. V. & Marcotte, E. M. Discovery of uncharacterized cellular systems by genome-wide analysis of functional linkages. Nature Biotechnol. 21, 1055–1062 (2003)

    CAS  Article  Google Scholar 

  26. Yu, H. et al. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 14, 1107–1118 (2004)

    MathSciNet  CAS  Article  Google Scholar 

  27. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D. & Maltsev, N. The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA 96, 2896–2901 (1999)

    ADS  CAS  Article  Google Scholar 

  28. Haselbeck, R. et al. Comprehensive essential gene identification as a platform for novel anti-infective drug discovery. Curr. Pharm. Des. 8, 1155–1172 (2002)

    CAS  Article  Google Scholar 

  29. Krogan, N. J. et al. High-definition macromolecular composition of yeast RNA-processing complexes. Mol. Cell 13, 225–239 (2004)

    CAS  Article  Google Scholar 

  30. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997)

    CAS  Article  Google Scholar 

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Andrew Emili.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

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

This contains a brief description for each of the Supplementary Figures and Supplementary Tables. (DOC 23 kb)

Supplementary Figures S1-6

This file contains Supplementary Figures S1-S6. (PDF 1878 kb)

Supplementary Tables S1-S7

This file contains Supplementary Tables S1-S7. (PDF 772 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

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).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing