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Volumn 9, Issue 1, 2002, Pages 1-10

Distribution of repetitive sequences on the leading and lagging strands of the Escherichia coli genome: Comparative study of long direct repeat (LDR) sequences

Author keywords

Codon usage; Escherichia coli K 12 (W3110); LDR; Leading and lagging strand; Repetitive sequence

Indexed keywords

PALINDROMIC DNA;

EID: 0036932524     PISSN: 13402838     EISSN: None     Source Type: Journal    
DOI: 10.1093/dnares/9.1.1     Document Type: Article
Times cited : (7)

References (42)
  • 1
    • 0017729265 scopus 로고
    • Genetics of bacterial ribosomes
    • Nomura, M. and Morga, E. A. 1977, Genetics of bacterial ribosomes, Annu. Rev. Genet., 11, 297-347.
    • (1977) Annu. Rev. Genet. , vol.11 , pp. 297-347
    • Nomura, M.1    Morga, E.A.2
  • 2
    • 0032882170 scopus 로고    scopus 로고
    • 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
    • Kanaya, S., Yamada, Y., Kudo, Y., and Ikemura, T. 1999, 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, 145-155.
    • (1999) Gene , vol.238 , pp. 145-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 3
    • 0017712626 scopus 로고
    • Tandem duplications resulting from recombination between ribosomal RNA genes in Escherichia coli
    • Hill, C. W., Grafstrom, R. H., Harnish, B. W., and Hillman, B. S. 1977, Tandem duplications resulting from recombination between ribosomal RNA genes in Escherichia coli, J. Mol. Biol., 116, 407-428.
    • (1977) J. Mol. Biol. , vol.116 , pp. 407-428
    • Hill, C.W.1    Grafstrom, R.H.2    Harnish, B.W.3    Hillman, B.S.4
  • 4
    • 0019348834 scopus 로고
    • Evolutionary significance of accessory DNA elements in bacteria
    • Campbell, A. M. 1981, Evolutionary significance of accessory DNA elements in bacteria, Annu. Rev. Microbiol., 35, 55-83.
    • (1981) Annu. Rev. Microbiol. , vol.35 , pp. 55-83
    • Campbell, A.M.1
  • 6
    • 0017333825 scopus 로고
    • Tandem genetic duplications in phage and bacteria
    • Anderson, R. P. and Roth, J. R. 1977, Tandem genetic duplications in phage and bacteria, Annu. Rev. Microbiol., 31, 473-505.
    • (1977) Annu. Rev. Microbiol. , vol.31 , pp. 473-505
    • Anderson, R.P.1    Roth, J.R.2
  • 7
    • 0017794180 scopus 로고
    • Evolution of the bacterial genome
    • Riley, M. and Anilionis, A. 1987, Evolution of the bacterial genome, Annu. Rev. Microbiol., 32, 519-560.
    • (1987) Annu. Rev. Microbiol. , vol.32 , pp. 519-560
    • Riley, M.1    Anilionis, A.2
  • 8
    • 0023413620 scopus 로고
    • Histonelike proteins of bacteria
    • Drlica, K. and Rouviere-Yaniv, J. 1987, Histonelike proteins of bacteria, Microbiol. Rev., 51, 301-319.
    • (1987) Microbiol. Rev. , vol.51 , pp. 301-319
    • Drlica, K.1    Rouviere-Yaniv, J.2
  • 9
    • 0024262193 scopus 로고
    • Recombination between repeated sequences in microoriganisms
    • Petes, T. D. and Hill, C. W. 1988, Recombination between repeated sequences in microoriganisms, Annu. Rev. Genet., 22, 147-168.
    • (1988) Annu. Rev. Genet. , vol.22 , pp. 147-168
    • Petes, T.D.1    Hill, C.W.2
  • 10
    • 0025245767 scopus 로고
    • Organization of the bacterial chromosome
    • Krawiec, S. and Riley, M. 1990, Organization of the bacterial chromosome, Microbiol. Rev., 54, 502-539.
    • (1990) Microbiol. Rev. , vol.54 , pp. 502-539
    • Krawiec, S.1    Riley, M.2
  • 11
    • 0343114274 scopus 로고    scopus 로고
    • Short palindromic repetitive DNA elements in enterobacteria: A survey
    • Bachellier, S., Clement, J. M., and Hofnung, M. 1999, Short palindromic repetitive DNA elements in enterobacteria: a survey, Res. Microbiol., 150, 627-639.
    • (1999) Res. Microbiol. , vol.150 , pp. 627-639
    • Bachellier, S.1    Clement, J.M.2    Hofnung, M.3
  • 12
    • 0027210404 scopus 로고
    • DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: Organization symmetry around the origin of replication
    • Burland, V., Plunkett III, G., Daniels, D. L., and Blattner, F. R. 1993, DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organization symmetry around the origin of replication, Genomics, 16, 551-561.
    • (1993) Genomics , vol.16 , pp. 551-561
    • Burland, V.1    Plunkett G. III2    Daniels, D.L.3    Blattner, F.R.4
  • 13
    • 0035925404 scopus 로고    scopus 로고
    • Promotion of evolution by intracellular coexistence of mutator and normal DNA polymerases
    • Aoki, K. and Furusawa, M. 2001, Promotion of evolution by intracellular coexistence of mutator and normal DNA polymerases, J. Theor. Biol., 209, 213-222.
    • (2001) J. Theor. Biol. , vol.209 , pp. 213-222
    • Aoki, K.1    Furusawa, M.2
  • 15
    • 0000117110 scopus 로고    scopus 로고
    • Neidhardt F. C., Curtiss, R., Ingraham, J. L. et al. (eds) ASM Press, Washington DC
    • Hill, T. M. 1996, In: Neidhardt, F. C., Curtiss, R., Ingraham, J. L. et al. (eds) Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington DC, pp. 2012-2040.
    • (1996) Escherichia coli and Salmonella: Cellular and Molecular Biology , pp. 2012-2040
    • Hill, T.M.1
  • 16
    • 0021720088 scopus 로고
    • The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites
    • Fuller, R. S., Funnell, B. E., and Kornberg, A. 1984, The dnaA protein complex with the E. coli chromosomal replication origin (oriC) and other DNA sites, Cell, 38, 889-900.
    • (1984) Cell , vol.38 , pp. 889-900
    • Fuller, R.S.1    Funnell, B.E.2    Kornberg, A.3
  • 17
    • 0021443498 scopus 로고
    • A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli
    • Giison, E., Clement, J. M., Brutlag, D., and Hofnung, M. 1984, A family of dispersed repetitive extragenic palindromic DNA sequences in E. coli, EMBO J., 3, 1417-1421.
    • (1984) EMBO J. , vol.3 , pp. 1417-1421
    • Giison, E.1    Clement, J.M.2    Brutlag, D.3    Hofnung, M.4
  • 18
    • 0021669070 scopus 로고
    • Repetitive extragenic palindromic sequences: A major component of the bacterial genome
    • Stern, M. J., Ames, G. F., Smith, N. H., Robinson, E. C., and Higgins, C. F. 1984, Repetitive extragenic palindromic sequences: a major component of the bacterial genome, Cell, 37, 1015-1026.
    • (1984) Cell , vol.37 , pp. 1015-1026
    • Stern, M.J.1    Ames, G.F.2    Smith, N.H.3    Robinson, E.C.4    Higgins, C.F.5
  • 19
    • 0024999660 scopus 로고
    • A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes
    • Sharples, G. J. and Lloyd, R. G. 1990, A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes, Nucleic Acids Res., 18, 6503-6508.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6503-6508
    • Sharples, G.J.1    Lloyd, R.G.2
  • 20
    • 0025761156 scopus 로고
    • ERIC sequences: A novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria
    • Hulton, C. S., Higgins, C. F., and Sharp, P. M. 1991, ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria, Mol. Microbiol., 5, 825-834.
    • (1991) Mol. Microbiol. , vol.5 , pp. 825-834
    • Hulton, C.S.1    Higgins, C.F.2    Sharp, P.M.3
  • 21
    • 0026713759 scopus 로고
    • Sequences of the envM gene and of two mutated alleles in Escherichia coli
    • Bergler, H., Hogenauer, G., and Turnowsky, F. 1992, Sequences of the envM gene and of two mutated alleles in Escherichia coli, J. Gen. Microbiol., 138, 2093-2100.
    • (1992) J. Gen. Microbiol. , vol.138 , pp. 2093-2100
    • Bergler, H.1    Hogenauer, G.2    Turnowsky, F.3
  • 22
    • 0033386645 scopus 로고    scopus 로고
    • Novel intergenic repeats of Escherichia coli K-12
    • Rudd, K. E. 1999, Novel intergenic repeats of Escherichia coli K-12, Res. Microbiol., 150, 542-664.
    • (1999) Res. Microbiol. , vol.150 , pp. 542-664
    • Rudd, K.E.1
  • 24
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin, S. and Altschul, S. F. 1990, Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes, Proc. Natl. Acad. Sci. USA, 87, 2264-2268.
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 25
    • 0027175241 scopus 로고
    • Applications and statistics for multiple high-scoring segments in molecular sequences
    • Karlin, S. and Altschul, S. F. 1993, Applications and statistics for multiple high-scoring segments in molecular sequences, Proc. Natl. Acad. Sci. USA, 90, 5873-5877.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 5873-5877
    • Karlin, S.1    Altschul, S.F.2
  • 26
    • 0029985398 scopus 로고    scopus 로고
    • Asymmetric substitution patterns in the two DNA strands of bacteria
    • Lobry, J. R. 1996, Asymmetric substitution patterns in the two DNA strands of bacteria, Mol. Biol. Evol., 13, 660-665.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 660-665
    • Lobry, J.R.1
  • 27
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • Blattner, F. R., Plunkett III, G., Bloch, C. A. et al. 1997, The complete genome sequence of Escherichia coli K-12, Science, 277, 1553-1462.
    • (1997) Science , vol.277 , pp. 1553-1462
    • Blattner, F.R.1    Plunkett G. III2    Bloch, C.A.3
  • 28
    • 0034707195 scopus 로고    scopus 로고
    • The orientation bias of Chi sequences is a general tendency of G-rich oligomers
    • Uno, R., Nakayama, Y., Arakawa, K., and Tomita, M. 2000, The orientation bias of Chi sequences is a general tendency of G-rich oligomers, Gene, 259, 207-215.
    • (2000) Gene , vol.259 , pp. 207-215
    • Uno, R.1    Nakayama, Y.2    Arakawa, K.3    Tomita, M.4
  • 29
    • 0025728069 scopus 로고
    • Palindromic units are part of a new bacterial interspersed mosaic element (BIME)
    • Gilson, E., Saurin, W., Perrin, D., Bachellier, S., and Hofnung, M. 1991, Palindromic units are part of a new bacterial interspersed mosaic element (BIME), Nucleic Acids Res., 19, 1375-1383.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 1375-1383
    • Gilson, E.1    Saurin, W.2    Perrin, D.3    Bachellier, S.4    Hofnung, M.5
  • 30
    • 0023088022 scopus 로고
    • Species specificity of bacterial palindromic units
    • Gilson, E., Perrin, D., Saurin, W., and Hofnung, M. 1987, Species specificity of bacterial palindromic units, J. Mol. Evol., 25, 371-373.
    • (1987) J. Mol. Evol. , vol.25 , pp. 371-373
    • Gilson, E.1    Perrin, D.2    Saurin, W.3    Hofnung, M.4
  • 31
    • 0025020281 scopus 로고
    • Tandem chromosomal duplications: Role of REP sequences in the recombination event at the join-point
    • Shyamala, V., Schneider, E., and Ames, G. F. 1990, Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point, EMBO J., 9, 939-946.
    • (1990) EMBO J. , vol.9 , pp. 939-946
    • Shyamala, V.1    Schneider, E.2    Ames, G.F.3
  • 33
    • 0023667782 scopus 로고
    • Stabilization of translationally active mRNA by prokaryotic REP sequences
    • Newbury, S. F., Smith, N. H., Robinson, E. C., Hiles, I. D., and Higgins, C. F. 1987, Stabilization of translationally active mRNA by prokaryotic REP sequences, Cell, 48, 297-310.
    • (1987) Cell , vol.48 , pp. 297-310
    • Newbury, S.F.1    Smith, N.H.2    Robinson, E.C.3    Hiles, I.D.4    Higgins, C.F.5
  • 34
    • 0023043456 scopus 로고
    • Palindromic units from E. coli as binding sites for a chromoid-associated protein
    • Gilson, E., Perrin, D., Clement, J. M., Szmelcman, S., Dassa, E., and Hofnung, M. 1986, Palindromic units from E. coli as binding sites for a chromoid-associated protein, FEBS Lett., 206, 323-328.
    • (1986) FEBS Lett. , vol.206 , pp. 323-328
    • Gilson, E.1    Perrin, D.2    Clement, J.M.3    Szmelcman, S.4    Dassa, E.5    Hofnung, M.6
  • 35
    • 0027441932 scopus 로고
    • Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3′ end of transcription units
    • Boccard, F. and Prentki, P. 1993, Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3′ end of transcription units, EMBO J., 12, 5019-5027.
    • (1993) EMBO J. , vol.12 , pp. 5019-5027
    • Boccard, F.1    Prentki, P.2
  • 36
    • 0026199536 scopus 로고
    • Identification of regulatory building blocks in the Escherichia coli genome
    • Kunisawa, T. and Nakamura, M. 1991, Identification of regulatory building blocks in the Escherichia coli genome, Protein Sequence Data Anal., 4, 43-47.
    • (1991) Protein Sequence Data Anal. , vol.4 , pp. 43-47
    • Kunisawa, T.1    Nakamura, M.2
  • 37
    • 0035395606 scopus 로고    scopus 로고
    • Identification of novel small RNAs using comparative genomic and microarrays
    • Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G., and Gottesman, S. 2001, Identification of novel small RNAs using comparative genomic and microarrays, Genes Dev., 15, 1637-1651.
    • (2001) Genes Dev. , vol.15 , pp. 1637-1651
    • Wassarman, K.M.1    Repoila, F.2    Rosenow, C.3    Storz, G.4    Gottesman, S.5
  • 38
    • 0030606602 scopus 로고    scopus 로고
    • A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-29.0 min region on the linkage map
    • Oshima, T., Aiba, H., Baba, T. et al. 1996, A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7-29.0 min region on the linkage map, DNA Res., 3, 137-155.
    • (1996) DNA Res. , vol.3 , pp. 137-155
    • Oshima, T.1    Aiba, H.2    Baba, T.3
  • 39
    • 0032519353 scopus 로고    scopus 로고
    • GeneMark.hmm: New solutions for gene finding
    • Lukashin, A. V. and Borodovsky, M. 1998, GeneMark.hmm: new solutions for gene finding, Nucleic Acids Res., 26, 1107-1115.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1107-1115
    • Lukashin, A.V.1    Borodovsky, M.2
  • 41
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura, T. 1985, Codon usage and tRNA content in unicellular and multicellular organisms, Mol. Biol. Evol., 2, 13-34.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 42
    • 0002194749 scopus 로고    scopus 로고
    • Systematization of species-specific diversity of genes in codon usage: Comparison of the diversity among bacteria and prediction of the protein production levels in cells
    • Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S., and Nakai, K. (eds)
    • Kanaya, S., Kudo, Y., Suzuki, S., and Ikemura, T. 1996, Systematization of species-specific diversity of genes in codon usage: Comparison of the diversity among bacteria and prediction of the protein production levels in cells, In: Akutsu, T., Asai, K., Hagiya, M., Kuhara, S., Miyano, S., and Nakai, K. (eds) Genome Informatics Series, No. 7, pp. 61-71.
    • (1996) Genome Informatics Series , vol.7 , pp. 61-71
    • Kanaya, S.1    Kudo, Y.2    Suzuki, S.3    Ikemura, T.4


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