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 Research

Volumn 12, Issue 5, 2005, Pages 291-299

  Kitagawa, Masanari ^a,d   Ara, Takeshi ^b   Arifuzzaman, Mohammad ^a   Ioka Nakamichi, Tomoko ^c   Inamoto, Eiji ^c   Toyonaga, Hiromi ^c   Mori, Hirotada ^a,b,c  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b KEIO UNIVERSITY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^d TAKARA BIO INC   (Japan)

Author keywords

Bacterial functional genomics; Escherichia coli; ORF clone; Resource

Indexed keywords

AMINO ACID; GENE PRODUCT; GREEN FLUORESCENT PROTEIN; HISTIDINE; ISOPROPYL THIOGALACTOSIDE; PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BACTERIAL GENOME; CARBOXY TERMINAL SEQUENCE; DNA MICROARRAY; ESCHERICHIA COLI K 12; FUNCTIONAL GENOMICS; GENE LIBRARY; GENE SEQUENCE; MOLECULAR CLONING; NONHUMAN; OPEN READING FRAME; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN SYNTHESIS; REPRESSOR GENE; RESTRICTION SITE;

ESCHERICHIA COLI K12; ESCHERICHIA COLI PROTEINS; GENE LIBRARY; GREEN FLUORESCENT PROTEINS; HISTIDINE; OPEN READING FRAMES; PROMOTER REGIONS (GENETICS); RECOMBINANT FUSION PROTEINS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; ESCHERICHIA COLI K12;

EID: 33646568438     PISSN: 13402838     EISSN: 13402838     Source Type: Journal    
DOI: 10.1093/dnares/dsi012     Document Type: Article

References (43)

1. Janssen, P., Audit, B., Cases, I., et al. 2003, Beyond 100 genomes, Genome Biol., 4, 402.
2. Kunst, F., Ogasawara, N., Moszer, I., et al. 1997, The complete genome sequence of the gram-positive bacterium Bacillus subtilis, Nature, 390, 249-256.
3. Blattner, F. R., Plunkett, G.,III, Bloch, C. A., et al. 1997, The complete genome sequence of Escherichia coli K-12, Science, 277, 1453-1474.
4. Mewes, H. W., Albermann, K., Bahr, M., et al. 1997, Overview of the yeast genome, Nature, 387, 7-65.
5. Storms, R. K., Wang, Y., Fortin, N., et al. 1997, Analysis of a 103 kb cluster homology region from the left end of Saccharomyces cerevisiae chromosome I, Genome, 40, 151-164.
6. Galperin, M. Y and Koonin, E. V. 1999, Functional genomics and enzyme evolution. Homologous and analogous enzymes encoded in microbial genomes, Genetica, 106, 159-170.
7. Labedan, B. and Riley, M. 1995, Gene products of Escherichia coli: sequence comparisons and common ancestries, Mol. Biol. Evol., 12, 980-987.
8. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. 1997, A genomic perspective on protein families, Science, 278, 631-637.
9. Riley, M. and Labedan, B. 1997, Protein evolution viewed through Escherichia coli protein sequences: introducing the notion of a structural segment of homology, the module, J. Mol. Biol., 268, 857-868.
10. Zipkas, D. and Riley, M. 1975, Proposal concerning mechanism of evolution of the genome of Escherichia coli, Proc. Natl Acad. Sci. USA, 72, 1354-1358.
11. Overbeek, R., Fonstein, M., D'Souza, M., et al. 1999, The use of gene clusters to infer functional coupling, Proc. Natl Acad. Sci. USA, 96, 2896-2901.
12. Uchiyama, I. 2003, MBGD: microbial genome database for comparative analysis, Nucleic Acids Res., 31, 58-62.
13. Riley, M. 1993, Functions of the gene products of Escherichia coli, Microbiol. Rev., 57, 862-952.
14. Hutchison, C. A., Peterson, S. N., Gill, S. R., et al. 1999, Global transposon mutagenesis and a minimal Mycoplasma genome, Science, 286, 2165-2169.
15. Kobayashi, K., Ehrlich, S. D., Albertini, A., et al. 2003, Essential Bacillus subtilis genes, Proc. Natl Acad. Sci. USA, 100, 4678-4683.
16. Winzeler, E. A., Shoemaker, D. D., Astrornoff, A., et al. 1999, Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis, Science, 285, 901-906.
17. Vidan, S. and Snyder, M. 2001, Large-scale mutagenesis: yeast genetics in the genome era, Curr. Opin. Biotechnol., 12, 28-34.
18. Nishimura, A., Akiyama, K., Kohara, Y., et al. 1992, Correlation of a subset of the pLC plasmids to the physical map of Escherichia coli K-12, Microbiol. Rev., 56, 137-151.
19. Tabata, S., Higashitani, A., Takanami, M., et al. 1989, Construction of an ordered cosmid collection of the Escherichia coli K-12 W3110 chromosome, J. Bacteriol., 171, 1214-1218.
20. Knott, V., Blake, D. J., and Brownlee, G. G. 1989, Completion of the detailed restriction map of the E. coli genome by the isolation of overlapping cosmid clones, Nucleic Acids Res., 17, 5901-5912.
21. Birkenbihl, R. P. and Vielmetter, W. 1989, Cosmid-derived map of E. coli strain BHB2600 in comparison to the map of strain W3110, Nucleic Acids Res., 17, 5057-5069.
22. Kohara, Y., Akiyama, K., and Isono, K. 1987, 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, 495-508.
23. Daniels, D. L. and Blattner, F. R. 1987, Mapping using gene encyclopaedias, Nature, 325, 831-832.
24. Jeffery, C. J. 1999, Moonlighting proteins, Trends Biochem. Sci., 24, 8-11.
25. Nishioka, M., Mizuguchi, H., Fujiwara, S., et al. 2001, Long and accurate PCR with a mixture of KOD DNA polymerase and its exonuclease deficient mutant enzyme, J. Biotechnol., 88, 141-149.
26. Takagi, M., Nishioka, M., Kakihara, H., et al. 1997, Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR, Appl. Environ. Microbiol., 63, 4504-4510.
27. Sambrook, J., Fritsch, E. F., and Maniatis, T. 1998, Molecular Cloning: A Laboratory Manual. 2nd Ed.. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York.
28. Ito, Y., Suzuki, M., and Husimi, Y. 1999, A novel mutant of green fluorescent protein with enhanced sensitivity for microanalysis at 488 nm excitation, Biochem. Biophys. Res. Commun., 264, 556-560.
29. Nahvi, A., Sudarsan, N., Ebert, M. S., et al. 2002, Genetic control by a metabolite binding mRNA, Chem. Biol., 9, 1043.
30. Oshima, T., Aiba, H., Masuda, Y., et al. 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12, Mol. Microbiol., 46, 281-291.
31. Oshima, T., Wada, C., Kawagoe, Y., et al. 2002, Genome-wide analysis of deoxyadenosine methyltransferase-mediated control of gene expression in Escherichia coli, Mol. Microbiol., 45, 673-695.
32. Nakahigashi, K., Kubo, N., Narita, S., et al. 2002, HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination, Proc. Natl Acad. Sci. USA, 99, 1473-1478.
33. Kodama, K., Kobayashi, T., Niki, H., et al. 2002, Amplification of Hot DNA segments in Escherichia coli, Mol. Microbiol., 45, 1575-1588.
34. 2+ stimulon of Escherichia coli, J. Bacteriol., 185, 3696-3702.
35. Kawano, M., Oshima, T., Kasai, H., et al. 2002, Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli, Mol. Microbiol., 45, 333-349.
36. Awano, N., Wada, M., Mori, H., et al. 2005, Identification and functional analysis of Escherichia coli cysteine desulfhydrases, Appl. Environ. Microbiol., 71, 4149-4152.
37. Melnick, J., Lis, E., Park, J. H., et al. 2004, Identification of the two missing bacterial genes involved in thiamine salvage: thiamine pyrophosphokinase and thiamine kinase, J. Bacteriol., 186, 3660-3662.
38. Proudfoot, M., Kuznetsova, E., Brown, G., et al. 2004, General enzymatic screens identify three new nucleotidases in Escherichia coli. Biochemical characterization of SurE, YfbR, and YjjG, J. Biol. Chem., 279, 54687-54694.
39. Kimata, Y., Iwaki, M., Lim, C. R., et al. 1997, A novel mutation which enhances the fluorescence of green fluorescent protein at high temperatures, Biochem. Biophys. Res. Commun., 232, 69-73.
40. Takeshita, S., Sato, M., Toba, M., et al. 1987, High-copy-number and low-copy-number plasmid vectors for lacZ alpha-complementation and chloramphenicol- or kanamycin-resistance selection, Gene, 61, 63-74.
41. Smith, D. B. and Johnson, K. S. 1988, Single-step purification of polypeptides expressed in Escherichia coli as fusions with glutathione S-transferase, Gene, 67, 31-40.
42. Kleckner, N., Bender, J., and Gottesman, S. 1991, Uses of transposons with emphasis on Tn10, Methods Enzymol., 204, 139-180.
43. Ma, X., Ehrhardt, D. W., and Margolin, W. 1996, Colocalization of cell division proteins FtsZ and FtsA to cytoskeletal structures in living Escherichia coli cells by using green fluorescent protein,, Proc. Natl Acad. Sci. USA, 93, 12998-13003.