Functional genomics of Escherichia coli in Japan

Research in Microbiology

Volumn 151, Issue 2, 2000, Pages 121-128

  Mori, Hirotada ^a   Isono, Katsumi ^b   Horiuchi, Takashi ^c   Miki, Takeyoshi ^d  

^a Nara Inst Sci T   (Japan)

^b KOBE UNIVERSITY   (Japan)

^c NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^d KYUSHU UNIVERSITY   (Japan)

Author keywords

Database; Escherichia coli; Functional genomics

Indexed keywords

BACTERIAL GENE; CODON; DNA DETERMINATION; ESCHERICHIA COLI; GENE SEQUENCE; JAPAN; MOLECULAR CLONING; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; REVIEW;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0034129918     PISSN: 09232508     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0923-2508(00)00119-4     Document Type: Review

References (20)

1. Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., IKasai H., Kashimoto K., Kimura S., Kitagawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y., Nashimoto H., Nishino Y., Oshima T., Saito S., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T. A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map. DNA Res. 3:1996;363-377.
2. Blattner F.R., Plunkett G., Bloch C.A., Perna N.T., Buriand V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau M., Shao Y. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1462.
3. Fujita N., Mori H., Yura T., Ishihama A. Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110, 917-193, 643 bp) region. Nucleic Acids Res. 22:1994;1637-1639.
4. Green P., Lipman D., Hillier L., Waterston R., States D., Claverie J.M. Ancient conserved regions in new gene sequences and the protein databases. Science. 259:1993;1711-1716.
5. Ito Y., Suzuki M., Husimi Y. A novel mutant of green fluorescent protein with enhanced sensitivity for microanalysis at 488 nm excitation. Biochem. Biophys. Res. Commun. 264:1999;556-560.
6. Itoh T., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Kasai H., Kimura S., Kitagawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S., Nakamura Y., Hashimoto H., Nishino Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Wada C., Yamamoto Y., Horiuchi T. A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1-50.0 min region on the linkage map. DNA Res. 3:1996;379-392.
7. Kanaya S., Kudo Y., Nakamura Y., Ikemura T. Detection of genes in Escherichia coli sequences determined by genome projects and prediction of protein production levels, based on multivariate diversity in codon usage. Comput. Appl. Biosci. 12:1996;213-225.
8. Kanaya S., Yamada Y., Kudo Y., Ikemura T. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. Gene. 238:1999;143-155.
9. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 50:1987;495-508.
10. Kohonen T., Oja E., Simula O., Visa A., Kangas J. Engineering applications of the self-organizing map. Proc. IEEE. 84:1996;1358-1384.
11. Koonin E.V., Tatusov R.L., Rudd K.E. Sequence similarity analysis of Escherichia coli proteins: Functional and evolutionary implications. Proc. Natl. Acad. Sci. USA. 92:1995;11921-11925.
12. Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishino Y., Saito N., Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., Horiuchi T. A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-28.0 min region on the linkage map. DNA Res. 3:1996;137-155.
13. Riley M., Labeda B. Protein evolution viewed through Escherichia coli protein sequences: Introducing the notion of a structural segment of homology, the module. J. Mol. Biol. 268:1997;857-868.
14. Schena M., Shalon D., Davis R.W., Brown P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270:1995;467-470.
15. Tamura T., Mori H., Sugawara H. Genome information broker for large and small genomes. Trends Genet. 13:1997;498.
16. Tatusov R.L., Koonin E.V., Lipman D.J. A genomic perspective on protein families. Science. 278:1997;631-637.
17. Wada A. Analysis of Escherichia coli ribosomal proteins by an improved two dimensional gel electrophoresis. I. Detection of new proteins. J. Biochem. 100:1986;1583-1594.
18. Way J.C., Davis M.A., Morisato D., Roberts D.E., Kleckner N. New Tn10 derivatives for transposon mutagenesis and for construction of lacZ operon fusions by transposition. Gene. 32:1984;369-379.
19. Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. Construction of a contiguous 874-kb sequence of the Escherichia coli K-12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features. DNA Res. 4:1997;91-113.
20. Yura T., Mori H., Nagai H., Nagata T., Ishihama A., Fujita N., Isono K., Mizobuchi K., Nakata A. Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region. Nucleic Acids Res. 20:1992;3305-3308.