The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12

Methods in Molecular Biology

Volumn 416, Issue , 2007, Pages 183-194

  Baba, Tomoya ^a   Huan, Hsuan Cheng ^a   Datsenko, Kirill ^a   Wanner, Barry L ^a   Mori, Hirotada ^a  

^a NONE

Author keywords

Escherichia coli K 12; Essential genes; Keio collection

Indexed keywords

ESCHERICHIA COLI PROTEIN;

ARTICLE; BACTERIAL GENOME; ESCHERICHIA COLI K 12; GENE DELETION; GENETICS; NOMENCLATURE; ORGANIZATION; TRANSGENIC ORGANISM;

CONGRESSES AS TOPIC; ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; GENE DELETION; GENOME, BACTERIAL; ORGANISMS, GENETICALLY MODIFIED; TERMINOLOGY AS TOPIC;

ESCHERICHIA COLI K12;

EID: 40549102134     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article

References (38)

1. Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., et al. (1.997) The complete genome sequence of Escherichia coli K-1.2. Science 277, 1453-1474.
2. Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., et al. (2006) Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol. Syst. Biol.
3. Riley, M., Abe, T., Arnaud, M. B., Berlyn, M. K., Blattner, F. R., Chaudhuri, R. et al. (2006) Escherichia coli K-1.2: a cooperatively developed annotation snapshot-2005. Nucleic Acids Res. 34, 1-9.
4. Baba, T., Ara, T., Ilasegawa, M., Takai, Y., Okumura, Y., Baba, M., et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knock-out mutants-the Keio collection, Mol. Syst. Biol.
5. Gerdes, S. Y., Scholle, M. D., Campbell, J. W., Balazsi, G., Ravasz, E., Daugherty, M. D., et: al. (2003) Experimental determination and system, level analysis of essential genes in Escherichia coli MG1655. J. Bacteriol. 185, 5673-5684.
6. Hashimoto, M., Ichimura, T., Mizoguchi, H., Tanaka, K., Fujimitsu, K., Keyamura, K., et al. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol. Microbiol. 55, 137-149.
7. Kang, Y., Durfee, T., Glasner, J. D., Qiu, Y., Frisch, D., Winterberg, K. M. and Blattner, F. R. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186, 4921.-4930.
8. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1.997) A genomic perspective on protein families. Science 278, 631-637.
9. Uchiyama, I. (2003) MBGD: microbial genome database for comparative analysis. Nucleic Acids Res. 31, 58-62.
10. Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Kobayashi, Y., and Tomita, M. (2003) G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 19, 305-306.
11. Tatusov, R. L., Natale, D. A., Garkavtsev, I. V., Tatusova, T. A., Shankavaram, U. T., Rao, B. S., et al. (2001.) The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29, 22-28.
12. Hiratsu, K., Amemura, M., Nashimoto, H., Shinagawa, H., and Makino, K. (1995) The rpoE gene of Escherichia coli, which encodes sigma E, is essential, for bacterial growth at high temperature. J. Bacteriol. 177, 2918-2922.
13. Zhou, Y. N., Kusukawa, N., Erickson, J. W., Gross, C. A., and Yura, T. (1988) Isolation and characterization of Escherichia coli mutants that lack the heat shock sigma factor sigma 32. J. Bacteriol, 170, 3640-3649.
14. Dabbs, E. R. (1991) Mutants lacking individual ribosomal proteins as a tool to investigate ribosomal properties. Biochimie 73, 639-645.
15. Tong, X., Campbell, J. W., Balazsi, G., Kay, K. A., Wanner, B. L., Gerdes, S. Y., and Oltvai, Z. N. (2004) Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays. Biochem. Biophys. Res. Commun. 322, 347-354.
16. Kobayashi, K., Ehrlich, S. D., Albertini, A., Amati, G., Andersen, K. K., Arnaud, M., et al. (2003) Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. U.S.A. 100, 4678-4683.
17. Neidhardt, F. C., Bloch, P. L. and Smith, D. F. (1.974) Culture medium for enterobacteria. J. Bacteriol., 119, 736-747.
18. Yook, S. H., Oltvai, Z. N., and Barabasi, A. L. (2004) Functional and topological characterization of protein interaction networks. Proteomics 4, 928-942.
19. Barabasi, A. L., and Oltvai, Z. N. (2004) Network biology: understanding the cell's functional organization, Nat. Rev. Genet. 5, 101.-113.
20. Jeong, H., Mason, S. P., Barabasi, A., L., and Oltvai, Z. N. (2001) Lethality and centrality in protein networks. Nature 411, 41.-42.
21. 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.
22. Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16, 686-691.
23. Melnick, J., Lis, E., Park, J. H., Kinsland, C., Mori, H., Baba, T., et al. (2004) Identification of the two missing bacterial genes involved in thiamine salvage: thiamine pyrophosphokinase and thiamine kinase. J. Bacteriol. 186, 3660-3662.
24. Yang, C., Hua, Q., Baba, T., Mori, H., and Shimizu, K. (2003) Analysis of Escherichia coli anaplerotic metabolism and its regulation mechanisms from the metabolic responses to altered dilution rates andphosphoenolpyruvate carboxykinase knockout. Biotechnol. Bioeng. 84, 1.29-144.
25. Hua, Q., Yang, C., Baba, T., Mori, H., and Shimizu, K., (2003) Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J. Bacteriol, 185, 7053-7067.
26. Hua, Q., Yang, C., Oshima, T., Mori, H., and Shimizu, K., (2004) Analysis of gene expression in Escherichia coli in response to changes of growtli-limiting nutrient in chemostat cultures. Appl. Environ. Microbiol. 70, 2354-2366.
27. Jiao, Z., Baba, T., Mori, H., and Shimizu, K. (2003) Analysis of metabolic and physiological responses to gnd knockout in Escherichia coli by using C-1.3 tracer experiment and enzyme activity measurement. FEMS Microbiol. Lett. 220, 295-301.
28. Zhao, J., Baba, T., Mori, H., and Shimizu, K. (2004) Effect of zwf gene knockout on the metabolism of Escherichia coli grown on glucose or acetate. Metab. Eng. 6, 164-174.
29. Zhao, J., Baba, T., Mori, H., and Shimizu, K. (2004) Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on 13C-labeling experiments and the measurement of enzyme activities. Appl. Microbiol. Biotechnol. 64, 91-98.
30. Perrenoud, A., and Sauer, U. (2005) Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli J. Bacteriol, 187, 3171.-3179.
31. Tenorio, E., Saeki, T., Fujita, K., Kitakawa, M., Baba, T., Mori, H., and Isono, K. (2003) Systematic characterization of Escherichia coli genes/ORFs affecting biofilm, formation. FEMS Microbiol. Lett. 225, 107-114.
32. Itoh, A., Ohashi, Y., Soga, T., Mori, H., Nishioka, T., and Tomita, M. (2004) Application of capillary electrophoresis-mass spectrometry to synthetic in vitro glycolysis studies. Electrophoresis 25, 1996-2002.
33. Nakatogawa, H., Murakami, A., Mori, H., and Ito, K. (2005) SecM facilitates translocase function of SecA by localizing its biosynthesis. Genes Dev. 19, 436-444.
34. Murakami, A., Nakatogawa, H., and Ito, K. (2004) Translation arrest of SecM is essential for the basal and regulated expression of SecA. Proc. Natl. Acad. Sci. U.S.A. 101, 12330-12335.
35. Kruse, T., Moller-Jensen, J., Lobner-Olesen, A., and Gerdes, K. (2003) Dysfunctional MreB inhibits chromosome segregation in Escherichia coli. EMBO J. 22, 5283-5292.
36. Kruse, T., Bork-Jensen, J., and Gerdes, K. (2005) The morphogenetic MreBCD proteins of Escherichia coli form an essential membrane-bound complex. Mol. Microbiol. 55, 78-89.
37. Anderson, R. P., and Roth, J. R. (1978) Tandem genetic duplications in Salmonella typhimurium: amplification of the histidine operon. J. Mol. Biol. 126, 53-71.
38. Giaever, G., Chu, A. M., Ni, L., Connelly, C., Riles, L., Veronneau, S., et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418, 387-391.