Multiple high-throughput analyses monitor the response of E. coli to perturbations

Science

Volumn 316, Issue 5824, 2007, Pages 593-597

  Ishii, Nobuyoshi ^a   Nakahigashi, Kenji ^a   Baba, Tomoya ^a,b   Robert, Martin ^a   Soga, Tomoyoshi ^a,e   Kanai, Akio ^a   Hirasawa, Takashi ^a   Naba, Miki ^a   Hirai, Kenta ^a   Hoque, Aminul ^a   Ho, Pei Yee ^d   Kakazu, Yuji ^a   Sugawara, Kaori ^a   Igarashi, Saori ^a   Harada, Satoshi ^a   Masuda, Takeshi ^a   Sugiyama, Naoyuki ^e   Togashi, Takashi ^a   Hasegawa, Miki ^a   Takai, Yuki ^a   Yugi, Katsuyuki ^a   Arakawa, Kazuharu ^a   Iwata, Nayuta ^a   Toya, Yoshihiro ^a   Nakayama, Yoichi ^a   Nishioka, Takaaki ^a,c   Shimizu, Kazuyuki ^a,d   Mori, Hirotada ^a,b   Tomita, Masaru ^a,e   more..

^a KEIO UNIVERSITY   (Japan)

^b NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

^d KYUSHU INSTITUTE OF TECHNOLOGY   (Japan)

^e Keio University and Human Metabolome Technologies Inc   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME; MESSENGER RNA;

BIOASSAY; COLIFORM BACTERIUM; ENVIRONMENTAL STRESS; ENZYME ACTIVITY; GROWTH RATE; METABOLISM; PHYSIOLOGICAL RESPONSE; PROTEIN; RNA;

ARTICLE; BACTERIAL CELL; BACTERIAL GROWTH; BACTERIAL METABOLISM; ESCHERICHIA COLI; GENE DISRUPTION; GROWTH RATE; HIGH THROUGHPUT SCREENING; METABOLITE; MONITORING; NONHUMAN; PRIORITY JOURNAL; REGULATORY MECHANISM;

CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; ELECTROPHORESIS, CAPILLARY; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ENZYME INDUCTION; ENZYME REPRESSION; ENZYMES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION; GENES, BACTERIAL; MASS SPECTROMETRY; METABOLIC NETWORKS AND PATHWAYS; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEOME; RNA, MESSENGER; SYSTEMS BIOLOGY; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 34247612307     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.1132067     Document Type: Article

References (22)

1. A. R. Joyce, B. O. Palsson, Nat. Rev. Mol. Cell Biol. 7, 198 (2006).
2. S. S. Fong, A. Nanchen, B. O. Palsson, U. Sauer, J. Biol. Chem. 281, 8024 (2006).
3. G. N. Vemuri, A. A. Aristidou, Microbiol. Mol. Biol. Rev. 69, 197 (2005).
4. A. Mukhopadhyay et al., J. Bacteriol. 188, 4068 (2006).
5. M. Y. Hirai et al., Proc. Natl. Acad. Sci. U.S.A. 101, 10205 (2004).
6. H. Ge, A. J. Walhout, M. Vidal, Trends Genet. 19, 551 (2003).
7. T. Toyoda, A. Wada, Bioinformatics 20, 1759 (2004).
8. T. Ideker et al., Science 292, 929 (2001).
9. R. Marouga, S. David, E. Hawkins, Anal. Bioanal. Chem. 382, 669 (2005).
10. T. Soga et al., J. Proteome Res. 2, 488 (2003).
11. T. Soga et al., J. Biol. Chem. 281, 16768 (2006).
12. Materials and Methods are available as supporting material on Science Online.
13. T. Baba et al., Mol. Syst. Biol. 2, published online 21 February 2006 (10.1038/msb4100050).
14. P. A. Hoskisson, G. Hobbs, Microbiology 151, 3153 (2005).
15. A. J. Skinner, R. A. Cooper, J. Bacteriol. 118, 1183 (1974).
16. F. Daldal, J. Mol. Biol. 168, 285 (1983).
17. Z. Gu et al., Nature 421, 63 (2003).
18. J. Stelling, S. Klamt, K. Bettenbrock, S. Schuster, E. D. Gilles, Nature 420, 190 (2002).
19. H. Kitano, Nat. Rev. Genet. 5, 826 (2004).
20. D. Becker et al., Nature 440, 303 (2006).
21. http://ecoli.iab.keio.ac.jp
22. The authors thank M. Li and M. J. Arauzo-Bravo for help with the metabolic flux calculations; Y. Ishihama for proofreading the manuscript and for advice about LC-MS/MS absolute quantification of proteins; and T. Ogawa, Y. Suga, A. Hagiya, and M. Yoshino for experimental support for protein analyses. This study was carried out as part of a grant from the New Energy and Industrial Technology Development Organization (NEDO) of the Ministry of Economy, Trade, and Industry of Japan (METI) (Development of a Technological Infrastructure for Industrial Bioprocess Project). The work was also supported by a grant from Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST) (Development of Modeling/Simulation Environment for Systems Biology); a grant from Japan Society for the Promotion of Science (JSPS); and "grant-in-aid" research grants from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) for the 21st Century Centre of Excellence (COE) Program (Understanding and Control of Life's Function via Systems Biology), Scientific Research on Priority Areas "Systems Genomics," and Scientific Research on Priority Areas " Lifesurveyor"; as well as funds from the Yamagata Prefectural Government and Tsuruoka City. We thank the faculty and students of the Systems Biology Program at Keio University for useful discussions, as well as members of the International E. coli Alliance (IECA).