Large-scale identification of protein-protein interaction of Escherichia coli K-12

Genome Research

Volumn 16, Issue 5, 2006, Pages 686-691

  Arifuzzaman, Mohammad ^a,b,h   Maeda, Maki ^a,c   Itoh, Aya ^d   Nishikata, Kensaku ^a   Takita, Chiharu ^c   Saito, Rintaro ^d   Ara, Takeshi ^d   Nakahigashi, Kenji ^d   Huang, Hsuan Cheng ^e   Hirai, Aki ^c   Tsuzuki, Kohei ^d   Nakamura, Seira ^d   Altaf Ul Amin, Mohammad ^a   Oshima, Taku ^a   Baba, Tomoya ^a,d   Yamamoto, Natsuko ^a,b   Kawamura, Tomoyo ^c   Ioka Nakamichi, Tomoko ^c   Kitagawa, Masanari ^a,g   Tomita, Masaru ^d   Kanaya, Shigehiko ^a   Wada, Chieko ^f   Mori, Hirotada ^a,d   more..

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b KYOWA HAKKO KOGYO CO LTD   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d KEIO UNIVERSITY   (Japan)

^e NATIONAL YANG MING UNIVERSITY   (Taiwan)

^f KYOTO UNIVERSITY   (Japan)

^g TAKARA BIO INC   (Japan)

^h BGC Trust Medical College   (Bangladesh)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; HISTIDINE; PROTEOME;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; ESCHERICHIA COLI K 12; GENE LIBRARY; MASS SPECTROMETRY; METABOLISM; OPEN READING FRAME; PROTEOMICS;

ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; GENE LIBRARY; HISTIDINE; MODELS, BIOLOGICAL; OPEN READING FRAMES; PROTEOME; PROTEOMICS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 33745160404     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.4527806     Document Type: Article

References (42)

1. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., and Mori, H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knock-out mutants - the Keio collection. Mol. Syst. Biol. http://www.nature.com/msb/journal/v2/n1/full/ msb4100050.html
2. Bader, G.D. and Hogue, C.W. 2002. Analyzing yeast protein-protein interaction data obtained from different sources. Nat. Biotechnol. 20: 991-997.
3. Barabasi, A.L. and Albert, R. 1999. Emergence of scaling in random networks. Science 286: 509-512.
4. Bell, P.J., Andrews, S.C., Sivak, M.N., and Guest, J.R. 1989. Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12. J. Bacteriol. 171: 3494-3503. (Pubitemid 19145706)
5. Brandi, A., Pon, C.L., and Gualerzi, C.O. 1994. Interaction of the main cold shock protein CS7.4 (CspA) of Escherichia coli with the promoter region of hns. Biochimie 76: 1090-1098.
6. Buck, D., Spencer, M.E., and Guest, J.R. 1985. Primary structure of the succinyl-CoA synthetase of Escherichia coli. Biochemistry 24: 6245-6252.
7. Butland, G., Peregrin-Alvarez, J.M., Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., et al. 2005. Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-537. (Pubitemid 40204311)
8. Cheng, Z.F., Zuo, Y., Li, Z., Rudd, K.E., and Deutscher, M.P. 1998. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 273: 14077-14080. (Pubitemid 28319112)
9. Deuerling, E., Patzelt, H., Vorderwulbecke, S., Rauch, T., Kramer, G., Schaffitzel, E., Mogk, A., Schulze-Specking, A., Langen, H., and Bukau, B. 2003. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities. Mol. Microbiol. 47: 1317-1328. (Pubitemid 36307854)
10. Fields, S. and Song, O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340: 245-246. (Pubitemid 19171591)
11. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147. (Pubitemid 34059510)
12. Glover, J.R. and Lindquist, S. 1998. Hsp104, Hsp70, and Hsp40: A novel chaperone system that rescues previously aggregated proteins. Cell 94: 73-82. (Pubitemid 28347471)
13. Goloubinoff, P., Mogk, A., Zvi, A.P., Tomoyasu, T., and Bukau, B. 1999. Sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network. Proc. Natl. Acad. Sci. 96: 13732-13737.
14. Guest, J.R. 1992. Oxygen-regulated gene expression in Escherichia coli. The 1992 Marjory Stephenson Prize Lecture. J. Gen. Microbiol. 138: 2253-2263.
15. Guest, J.R. and Russell, G.C. 1992. Complexes and complexities of the citric acid cycle in Escherichia coli. Curr. Top. Cell. Regul. 33: 231-247.
16. Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., et al. 2002. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183. (Pubitemid 34059520)
17. Houry, W.A., Frishman, D., Eckerskorn, C., Lottspeich, F., and Hartl, F.U. 1999. Identification of in vivo substrates of the chaperonin GroEL. Nature 402: 147-154.
18. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. 98: 4569-4574. (Pubitemid 32295017)
19. Ito, T., Ota, K., Kubota, H., Yamaguchi, Y., Chiba, T., Sakuraba, K., and Yoshida, M. 2002. Roles for the two-hybrid system in exploration of the yeast protein interactome. Mol. Cell. Proteomics 1: 561-566.
20. Kainz, M. and Gourse, R.L. 1998. The C-terminal domain of the α subunit of Escherichia coli RNA polymerase is required for efficient ρ-dependent transcription termination. J. Mol. Biol. 284: 1379-1390. (Pubitemid 28566074)
21. Kanehisa, M., Goto, S., Kawashima, S., and Nakaya, A. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res. 30: 42-46.
22. Kimura, M. and Ishihama, A. 1996. Subunit assembly in vivo of Escherichia coli RNA polymerase: Role of the amino-terminal assembly domain of α subunit. Genes Cells 1: 517-528. (Pubitemid 126673146)
23. Kitagawa, M., Ara, T., Arifuzzaman, M., Ioka-Nakamichi, T., Inamoto, E., Toyonaga, H., and Mori, H. 2005. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): Unique resources for biological research. DNA Res. 12: 291-299.
24. Kitano, H. 2002. Systems biology: A brief overview. Science 295: 1662-1664.
25. Lau, L.F., Roberts, J.W., and Wu, R. 1983. RNA polymerase pausing and transcript release at the λ tR1 terminator in vitro. J. Biol. Chem. 258: 9391-9397.
26. Li, Z., Pandit, S., and Deutscher, M.P. 1998. Polyadenylation of stable RNA precursors in vivo. Proc. Natl. Acad. Sci. 95: 12158-12162. (Pubitemid 28483735)
27. Mogk, A., Tomoyasu, T., Goloubinoff, P., Rudiger, S., Roder, D., Langen, H., and Bukau, B. 1999. Identification of thermolabile Escherichia coli proteins: Prevention and reversion of aggregation by DnaK and ClpB. EMBO J. 18: 6934-6949. (Pubitemid 30000447)
28. Motohashi, K., Watanabe, Y., Yohda, M., and Yoshida, M. 1999. Heat-inactivated proteins are rescued by the DnaK.J-GrpE set and ClpB chaperones. Proc. Natl. Acad. Sci. 96: 7184-7189. (Pubitemid 29299636)
29. Nehrke, K.W., Zalatan, F., and Platt, T. 1993. NusG alters ρ-dependent termination of transcription in vitro independent of kinetic coupling. Gene Expr. 3: 119-133.
30. Quail, M.A., Haydon, D.J., and Guest, J.R. 1994. The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex. Mol. Microbiol. 12: 95-104. (Pubitemid 24197447)
31. Riley, M., Abe, T., Arnaud, M.B., Berlyn, M.K., Blattner, F.R., Chaudhuri, R.R., Glasner, J.D., Mori, G., Horiuchi, T., Keseler, I.M., et al. 2006. Escherichia coli K-12: A cooperatively developed annotation snapshot - 2005. Nucleic Acids Res. 34: 1-9. (Pubitemid 43160031)
32. Salgado, H., Moreno-Hagelsieb, G., Smith, T.F., and Collado-Vides, J. 2000. Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci. 97: 6652-6657. (Pubitemid 30412769)
33. Sigmund, C.D. and Morgan, E.A. 1988. Nus A protein affects transcriptional pausing and termination in vitro by binding to different sites on the transcription complex. Biochemistry 27: 5622-5627.
34. Silver, P. and Way, J. 2004. Cells by design. Scientist 18: 30-31.
35. Sommerville, J. and Ladomery, M. 1996. Masking of mRNA by Y-box proteins. FASEB J. 10: 435-443.
36. Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403: 623-627.
37. Wolffe, A.P. 1994. Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins. Bioessays 16: 245-251. (Pubitemid 2073505)
38. Xenarios, I., Rice, D.W., Salwinski, L., Baron, M.K., Marcotte, E.M., and Eisenberg, D. 2000. DIP: The database of interacting proteins. Nucleic Acids Res. 28: 289-291.
39. Yamanaka, K., Fang, L., and Inouye, M. 1998. The CspA family in Escherichia coli: Multiple gene duplication for stress adaptation. Mol. Microbiol. 27: 247-255. (Pubitemid 28035250)
40. Yu, H., Greenbaum, D., Xin Lu, H., Zhu, X., and Gerstein, M. 2004. Genomic analysis of essentiality within protein networks. Trends Genet. 20: 227-231. (Pubitemid 38625679)
41. Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., Lan, N., Jansen, R., Bidlingmaier, S., Houfek, T., et al. 2001. Global analysis of protein activities using proteome chips. Science 293: 2101-2105. (Pubitemid 32848060)
42. Zolkiewski, M. 1999. ClpB cooperates with DnaK, DnaJ, and GrpE in suppressing protein aggregation. A novel multi-chaperone system from Escherichia coli. J. Biol. Chem. 274: 28083-28086. (Pubitemid 129504666)