Novel intergenic repeats of Escherichia coli K-12

Research in Microbiology

Volumn 150, Issue 9-10, 1999, Pages 653-664

  Rudd, Kenneth E ^a  

^a UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

Author keywords

Database; Genome, bacterial; Repetitive sequence

Indexed keywords

REPETITIVE DNA;

DNA SEQUENCE; ESCHERICHIA COLI; GENETIC ANALYSIS; GENOME; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS;

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

EID: 0033386645     PISSN: 09232508     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0923-2508(99)00126-6     Document Type: Article

References (43)

1. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:1997;3389-3402.
2. Bachellier S. Les BIMES: un example de sequences repetées chez les enterobactéries. Bull. Inst. Pasteur. 93:1995;97-152.
3. Bachellier S., Gilson E., Hofnung M., Hill C.W. Neidhardt F.C, Curtiss R, Ingraham J.L, Lin E.C.C, Low K.B, Magasanik B, Reznikoff W.S, Riley M, Schaechter M, Umbarger H.E. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;2012-2040 ASM Press, Washington DC.
4. Bedwell D., Davis G., Gosink M., Post L., Nomura M., Kestler H., Zengel J.M., Lindahl L. Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli. Nucleic Acids Res. 13:1985;3891-3903.
5. Berlyn M.B., Low K.B., Rudd K.E. Neidhardt F.C, Curtiss R, Ingraham J.L, Lin E.C.C, Low K.B, Magasanik B, Reznikoff W.S, Riley M, Schaechter M, Umbarger H.E. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;1715-1902 ASM Press, Washington DC.
6. Berlyn M.K.B. Linkage map of Escherichia coli K-12, edition 10: the traditional map. Microbiol. Mol. Biol. Rev. 62:1998;814-984.
7. Blaisdell B.E., Rudd K.E., Matin A., Karlin S. Significant dispersed recurrent DNA sequences in the Escherichia coli genome. Several new groups. J. Mol. Biol. 229:1993;833-848.
8. Blattner F.R., Plunkett G., Bloch C.A., Perna N.T., Burland 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 B., Shao Y. The complete genome sequence of Escherichia coli K-12. Science. 277:1997;1453-1462.
9. Bosl M., Kersten H. A novel RNA product of the tyrT operon of Escherichia coli. Nucleic Acids Res. 19:1991;5863-5870.
10. Campbell A.M. Neidhardt F.C, Curtiss R, Ingraham J.L, Lin E.C.C, Low K.B, Magasanik B, Reznikoff W.S, Riley M, Schaechter M, Umbarger H.E. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;2041-2046 ASM Press, Washington DC.
11. Deonier R.C. Neidhardt F.C, Curtiss R, Ingraham J.L, Lin E.C.C, Low K.B, Magasanik B, Reznikoff W.S, Riley M, Schaechter M, Umbarger H.E. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;2000-2011 ASM Press, Washington DC.
12. Dimri G.P., Rudd K.E., Morgan M.K., Bayat H., Ames G.F. Physical mapping of repetitive extragenic palindromic sequences in Escherichia coli and phylogenetic distribution among Escherichia coli strains and other enteric bacteria. J. Bacteriol. 174:1992;4583-4593.
13. Doolittle R.F. Convergent evolution: the need to be explicit. Trends. Biochem. Sci. 19:1994;15-18.
14. Dorman C.J., Higgins C.F. Fimbrial phase variation in Escherichia coli: dependence on integration host factor and homologies with other site-specific recombinases. J. Bacteriol. 169:1987;3840-3843.
15. Egan J., Landy A. Structural analysis of the tRNA1Tyr gene of Escherichia coli. A 178 base pair sequence that is repeated 3. 14 times. J. Biol. Chem. 253:1978;3607-3622.
16. Hacker J., Blum-Oehler G., Muhldorfer I., Tschape H. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23:1997;1089-1097.
17. Hama H., Kayahara T., Ogawa W., Tsuda M., Tsuchiya T. Enhancement of serine-sensitivity by a gene encoding rhodanese-like protein in Escherichia coli. J. Biochem. (Tokyo). 115:1994;1135-1140.
18. Hill T.M. Neidhardt F.C, Curtiss R, Ingraham J.L, Lin E.C.C, Low K.B, Magasanik B, Reznikoff W.S, Riley M, Schaechter M, Umbarger H.E. Escherichia coliandSalmonellaCellular and Molecular Biology. 1996;1602-1614 ASM Press, Washington DC.
19. Hobbs M., Reeves P.R. The JUMPstart sequence: a 39 bp element common to several polysaccharide gene clusters [letter]. Mol. Microbiol. 12:1994;855-856.
20. Jackowski S., Jackson P.D., Rock C.O. Sequence and function of the aas gene in Escherichia coli. J. Biol. Chem. 269:1994;2921-2928.
21. Kao C., Snyder L. The lit gene product which blocks bacteriophage T4 late gene expression is a membrane protein encoded by a cryptic DNA element, e14. J. Bacteriol. 170:1988;2056-2062.
22. Kirby J.E., Trempy J.E., Gottesman S. Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli. J. Bacteriol. 176:1994;2068-2081.
23. Komine Y., Adachi T., Inokuchi H., Ozeki H. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J. Mol. Biol. 212:1990;579-598.
24. Lawrence J.G., Ochman H. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA. 95:1998;9413-9417.
25. Leeds J.A., Welch R.A. Enhancing transcription through the Escherichia coli hemolysin operon, hlyCABD: RfaH and upstream jumpstart DNA sequences function together via a postinitiation mechanism. J. Bacteriol. 179:1997;3519-3527.
26. Lindahl L., Sor F., Archer R.H., Nomura M., Zengel J.M. Transcriptional organization of the S10, spc and alpha operons of Escherichia coli. Biochim. Biophys. Acta. 1050:1990;337-342.
27. Madden K.A., Landy A. Rho-dependent transcription termination in the tyrT operon of Escherichia coli. Gene. 76:1989;271-280.
28. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;911-940.
29. Medigue C., Viari A., Henaut A., Danchin A. Colibri: a functional data base for the Escherichia coli genome. Microbiol. Rev. 57:1993;623-654.
30. Nakata A., Amemura M., Makino K. Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J. Bacteriol. 171:1989;3553-3556.
31. Oppenheim A.B., Rudd K.E., Mendelson I., Teff D. Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli. Mol. Microbiol. 10:1993;113-122.
32. 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., Nishio Y., Saito N., Horiuchi T., et al. 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.
33. Pearson W.R., Lipman D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA. 85:1988;2444-2448.
34. Phadtare S., Inouye M. Sequence-selective interactions with RNA by CspB, CspC and CspE, members of the CspA family of Escherichia coli. Mol. Microbiol. 33:1999;1004-1014.
35. Pierson L.S., Kahn M.L. Integration of satellite bacteriophage P4 in Escherichia coli. DNA sequences of the phage and host regions involved in site-specific recombination. J. Mol. Biol. 196:1987;487-496.
36. Reed R.E.A.L.T.M.A.N.S. Repeated sequences and open reading frames in the 3' flanking region of the gene for the RNA subunit of Escherichia coli ribonuclease P. Proc. Natl. Acad. Sci. USA. 80:1983;5359-5363.
37. Rudd K.E. Linkage map of Escherichia coli K-12, edition 10: the physical map. Microbiol. Mol. Biol. Rev. 62:1998;985-1019.
38. Rudd K.E., Humphery-Smith I., Wasinger V.C., Bairoch A. Low molecular weight proteins: a challenge for post-genomic research. Electrophoresis. 19:1998;536-544.
39. Saurin W. Repetitive palindromic sequences in Escherichia coli. Detection and characterization with a new computer program. Comput. Appl. Biosci. 3:1987;121-127.
40. Stevens M.P., Clarke B.R., Roberts I.S. Regulation of the Escherichia coli K5 capsule gene cluster by transcription antitermination. Mol. Microbiol. 24:1997;1001-1012.
41. Wang M.X., Church G.M. A whole genome approach to in vivo DNA-protein interactions in E. coli. Nature. 360:1992;606-610.
42. Weickert M.J., Adhya S. Control of transcription of gal repressor and isorepressor genes in Escherichia coli. J. Bacteriol. 175:1993;251-258.
43. Wright J.J., Kumar A., Hayward R.S. Hypersymmetry in a transcriptional terminator of Escherichia coli confers increased efficiency as well as bidirectionality. EMBO J. 11:1992;1957-1964.