Interaction network containing conserved and essential protein complexes in Escherichia coli

Nature

Volumn 433, Issue 7025, 2005, Pages 531-537

  Butland, Gareth ^a   Peregrin Alvarez, José Manuel ^b   Li, Joyce ^a   Yang, Wehong ^a   Yang, Xiaochun ^a   Canadien, Veronica ^c   Starostine, Andrei ^a   Richards, Dawn ^c   Beattie, Bryan ^c   Krogan, Nevan ^a   Davey, Michael ^a   Parkinson, John ^b,d   Greenblatt, Jack ^a,c,d   Emili, Andrew ^a,d  

^a UNIVERSITY OF TORONTO   (Canada)

^b HOSPITAL FOR SICK CHILDREN   (Canada)

^c Affinium Pharmaceuticals   (Canada)

^d UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CHROMOSOMES; DNA; ESCHERICHIA COLI; GENES;

MULTI-SUBUNIT COMPLEXES; PROKARYOTA;

PROTEINS;

DNA; PROTEIN;

BACTERIUM; PROTEIN;

ALLELE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHROMOSOME; COMPLEX FORMATION; ESCHERICHIA COLI; GENE CASSETTE; GENETIC CONSERVATION; MASS SPECTROMETRY; NONHUMAN; OPEN READING FRAME; PHENOTYPE; PRIORITY JOURNAL; PROKARYOTE; PROTEIN FUNCTION; PROTEIN INTERACTION; VALIDATION PROCESS;

ESCHERICHIA COLI;

EID: 13444283630     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature03239     Document Type: Article

References (30)

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).
3. Gavin, A. C. et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141-147 (2002).
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).
5. Yu, D. et al. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl Acad. Sci. USA 97, 5973-5983 (2000).
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).
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).
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).
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).
10. Nakayama, H. RecQ family helicases: roles as tumor suppressor proteins. Oncogene 21, 9008-9021 (2002).
11. von Mering, C. et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403 (2002).
12. Salwinski, L. et al. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 32 (Database issue), D449-D451 (2004).
13. Bader, G. D., Betel, D. & Hogue, C. W. BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res. 31, 248-250 (2003).
14. von Mering, C. et al. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31, 258-261 (2003).
15. Bowers, P. et al. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 5, R35 (2004).
16. Rain, J. C. et al. The protein-protein interaction map of Helicobacter pylori Nature 409, 211-215 (2001).
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).
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).
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).
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).
21. Peregrin-Alvarez, J. M., Tsoka, S. & Ouzounis, C. A. The phylogenetic extent of metabolic enzymes and pathways. Genome Res. 13, 422-427 (2003).
22. Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631-637 (1997).
23. Wu, J., Kasif, S. & DeLisi, C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19, 1524-1530 (2003).
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).
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).
26. Yu, H. et al. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res. 14, 1107-1118 (2004).
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).
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).
29. Krogan, N. J. et al. High-definition macromolecular composition of yeast RNA-processing complexes. Mol. Cell 13, 225-239 (2004).
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).