메뉴 건너뛰기




Volumn 13, Issue 6 A, 2003, Pages 1123-1132

An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: From duplications to genome reduction

Author keywords

[No Author keywords available]

Indexed keywords

SPACER DNA;

EID: 0037803483     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.966203     Document Type: Article
Times cited : (57)

References (54)
  • 1
    • 0035211889 scopus 로고    scopus 로고
    • Study of intrachromosomal duplications among the eukaryote genomes
    • Achaz, G., Netter, P., and Coissac, E. 2001. Study of intrachromosomal duplications among the eukaryote genomes. Mol. Biol. Evol. 18: 2280-2288.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2280-2288
    • Achaz, G.1    Netter, P.2    Coissac, E.3
  • 3
    • 0019996193 scopus 로고
    • On the formation of spontaneous deletions: The importance of short sequence homologies in the generation of large deletions
    • Albertini, A.M., Hofer, M., Calos, M.P., and Miller, J.H. 1982. On the formation of spontaneous deletions: The importance of short sequence homologies in the generation of large deletions. Cell 29: 319-328.
    • (1982) Cell , vol.29 , pp. 319-328
    • Albertini, A.M.1    Hofer, M.2    Calos, M.P.3    Miller, J.H.4
  • 4
    • 0035029472 scopus 로고    scopus 로고
    • Pseudogenes, junk DNA and the dynamics of Rickettsia genomes
    • Andersson, J.O. and Andersson, S.G. 2001. Pseudogenes, junk DNA and the dynamics of Rickettsia genomes. Mol. Biol. Evol. 18: 829-839.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 829-839
    • Andersson, J.O.1    Andersson, S.G.2
  • 5
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: A program to analyze DNA sequences
    • Benson, G. 1999. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 27: 573-580.
    • (1999) Nucleic Acids Res. , vol.27 , pp. 573-580
    • Benson, G.1
  • 6
    • 0029877516 scopus 로고    scopus 로고
    • A replication model for DNA recombination between direct repeats
    • Bi, X. and Liu, L.F. 1996. A replication model for DNA recombination between direct repeats. J. Mol. Biol. 256: 849-858.
    • (1996) J. Mol. Biol. , vol.256 , pp. 849-858
    • Bi, X.1    Liu, L.F.2
  • 7
    • 0035902443 scopus 로고    scopus 로고
    • Instability of repetitive DNA sequences: The role of replication in multiple mechanisms
    • Bzymek, M. and Lovett, S.T. 2001. Instability of repetitive DNA sequences: The role of replication in multiple mechanisms. Proc. Natl. Acad. Sci. 98: 8319-8325.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 8319-8325
    • Bzymek, M.1    Lovett, S.T.2
  • 8
    • 0028307745 scopus 로고
    • Frequency of deletion formation decreases exponentially with distance between short direct repeats
    • Chédin, F., Dervyn, E., Ehrlich, S.D., and Noirot, P. 1994. Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol. Microbiol. 12: 561-569.
    • (1994) Mol. Microbiol. , vol.12 , pp. 561-569
    • Chédin, F.1    Dervyn, E.2    Ehrlich, S.D.3    Noirot, P.4
  • 9
    • 0033972220 scopus 로고    scopus 로고
    • The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases
    • De Bolle, X., Bayliss, C.D., Field, D., van de Ven, T., Saunders, N.J., Hood, D.W., and Moxon, E.R. 2000. The length of a tetranucleotide repeat tract in Haemophilus influenzae determines the phase variation rate of a gene with homology to type III DNA methyltransferases. Mol. Microbiol. 35: 211-222.
    • (2000) Mol. Microbiol. , vol.35 , pp. 211-222
    • De Bolle, X.1    Bayliss, C.D.2    Field, D.3    van de Ven, T.4    Saunders, N.J.5    Hood, D.W.6    Moxon, E.R.7
  • 10
    • 2642654225 scopus 로고    scopus 로고
    • Shared themes of antigenic variation and virulence in bacterial, protozoal and fungal infections
    • Deitsch, K.W., Moxon, E.R., and Wellems, T.E. 1997. Shared themes of antigenic variation and virulence in bacterial, protozoal and fungal infections. Microbiol. Mol. Biol. Rev. 61: 281-293.
    • (1997) Microbiol. Mol. Biol. Rev. , vol.61 , pp. 281-293
    • Deitsch, K.W.1    Moxon, E.R.2    Wellems, T.E.3
  • 11
    • 0031438685 scopus 로고    scopus 로고
    • Searching for patterns in genomic data
    • Dsouza, M., Larsen, N., and Overbeek, R. 1997. Searching for patterns in genomic data. Trends Genet. 13: 497-498.
    • (1997) Trends Genet. , vol.13 , pp. 497-498
    • Dsouza, M.1    Larsen, N.2    Overbeek, R.3
  • 12
    • 0034661615 scopus 로고    scopus 로고
    • Mutational analyses of dinucleotide and tetranucleotide microsatellites in Escherichia coli: Influence of sequence on expansion mutagenesis
    • Eckert, K.A. and Yan, G. 2000. Mutational analyses of dinucleotide and tetranucleotide microsatellites in Escherichia coli: Influence of sequence on expansion mutagenesis. Nucleic Acids Res. 28: 2831-2838.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2831-2838
    • Eckert, K.A.1    Yan, G.2
  • 13
    • 0028118638 scopus 로고
    • SIMPLE34: An improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences
    • Hancock, J.M. and Armstrong, J.S. 1994. SIMPLE34: An improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences. Comput. Appl. Biosci. 10: 67-70.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 67-70
    • Hancock, J.M.1    Armstrong, J.S.2
  • 14
    • 0028881922 scopus 로고
    • The stabilization of repetitive tracts of DNA by variant repeats requires a functional DNA mismatch repair system
    • Heale, S.M. and Petes, T.D. 1995. The stabilization of repetitive tracts of DNA by variant repeats requires a functional DNA mismatch repair system. Cell 83: 539-545.
    • (1995) Cell , vol.83 , pp. 539-545
    • Heale, S.M.1    Petes, T.D.2
  • 15
    • 0024060034 scopus 로고
    • Effects of chromosomal inversion on cell fitness in Escherichia coli K-12
    • Hill, C.W. and Gray, J.A. 1988. Effects of chromosomal inversion on cell fitness in Escherichia coli K-12. Genetics 119: 771-778.
    • (1988) Genetics , vol.119 , pp. 771-778
    • Hill, C.W.1    Gray, J.A.2
  • 16
    • 0000657507 scopus 로고    scopus 로고
    • Impact of homologous recombination on genome organization and stability
    • (ed. R.L. Charlebois), ASM Press, Washington DC
    • Hughes, D. 1999. Impact of homologous recombination on genome organization and stability. In Organization of the prokaryotic genome (ed. R.L. Charlebois), pp. 109-128. ASM Press, Washington DC.
    • (1999) Organization of the Prokaryotic Genome , pp. 109-128
    • Hughes, D.1
  • 17
    • 0036408356 scopus 로고    scopus 로고
    • Identification of a novel family of sequence repeats among prokaryotes
    • Jansen, R., van Embden, J.D., Gaastra, W., and Schouls, L.M. 2002. Identification of a novel family of sequence repeats among prokaryotes. OMICS 6: 23-33.
    • (2002) OMICS , vol.6 , pp. 23-33
    • Jansen, R.1    van Embden, J.D.2    Gaastra, W.3    Schouls, L.M.4
  • 18
    • 0000821054 scopus 로고
    • Maximal segmental match length among random sequences from a finite alphabet
    • (eds L.M.L. Cam and R.A. Olshen), Wadsworth, Belmont, CA
    • Karlin, S. and Ost, F. 1985. Maximal segmental match length among random sequences from a finite alphabet. In Proceedings of the Berkeley Conference in honor of Jerzy Neyman and Jack Kiefer (eds L.M.L. Cam and R.A. Olshen), pp. 225-243. Wadsworth, Belmont, CA.
    • (1985) Proceedings of the Berkeley Conference in Honor of Jerzy Neyman and Jack Kiefer , pp. 225-243
    • Karlin, S.1    Ost, F.2
  • 20
    • 1842332701 scopus 로고    scopus 로고
    • Compositional biases of bacterial genomes and evolutionary implications
    • Karlin, S., Mrazek, J., and Campbell, A.M. 1997. Compositional biases of bacterial genomes and evolutionary implications. J. Bacteriol. 179: 3899-3913.
    • (1997) J. Bacteriol. , vol.179 , pp. 3899-3913
    • Karlin, S.1    Mrazek, J.2    Campbell, A.M.3
  • 21
    • 0022624675 scopus 로고
    • Role of homology and pathway specificity for recombination between plasmids and bacteriophage λ
    • King, S.R. and Richardson, J.P. 1986. Role of homology and pathway specificity for recombination between plasmids and bacteriophage λ. Mol. Gen. Genet. 204: 141-147.
    • (1986) Mol. Gen. Genet. , vol.204 , pp. 141-147
    • King, S.R.1    Richardson, J.P.2
  • 22
    • 0033066718 scopus 로고    scopus 로고
    • REPuter: Fast computation of maximal repeats in complete genomes
    • Kurtz, S. and Schleiermacher, C. 1999. REPuter: Fast computation of maximal repeats in complete genomes. BioInformatics 15: 426-427.
    • (1999) BioInformatics , vol.15 , pp. 426-427
    • Kurtz, S.1    Schleiermacher, C.2
  • 23
    • 0035902579 scopus 로고    scopus 로고
    • DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination
    • Kuzminov, A. 2001. DNA replication meets genetic exchange: Chromosomal damage and its repair by homologous recombination. Proc. Natl. Acad. Sci. 98: 8461-8468.
    • (2001) Proc. Natl. Acad. Sci. , vol.98 , pp. 8461-8468
    • Kuzminov, A.1
  • 24
  • 25
    • 0023256559 scopus 로고
    • Slipped-strand mispairing: A major mechanism for DNA sequence evolution
    • Levinson, G. and Gutman, G.A. 1987. Slipped-strand mispairing: A major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4: 203-221.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 203-221
    • Levinson, G.1    Gutman, G.A.2
  • 26
    • 0028088757 scopus 로고
    • Recombination between repeats in E. coli by a recA-independent, proximity-sensitive mechanism
    • Lovett, S.T., Gluckman, T.J., Simon, P.J., Sutera, V.A., and Drapkin, P.T. 1994. Recombination between repeats in E. coli by a recA-independent, proximity-sensitive mechanism. Mol. Gen. Genet. 245: 294-300.
    • (1994) Mol. Gen. Genet. , vol.245 , pp. 294-300
    • Lovett, S.T.1    Gluckman, T.J.2    Simon, P.J.3    Sutera, V.A.4    Drapkin, P.T.5
  • 27
    • 0002767358 scopus 로고    scopus 로고
    • Illegitimate recombination in bacteria
    • (ed. R.L. Charlebois), ASM Press, Washington DC
    • Michel, B. 1999. Illegitimate recombination in bacteria. In Organization of the prokaryotic genome (ed. R.L. Charlebois), pp. 129-150. ASM Press, Washington DC.
    • (1999) Organization of the Prokaryotic Genome , pp. 129-150
    • Michel, B.1
  • 28
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial
    • Mira, A., Ochman, H., and Moran, N.A. 2001. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17: 589-596.
    • (2001) Genomes Trends Genet. , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 29
    • 0028065674 scopus 로고
    • Adaptive evolution of highly mutable loci in pathogenic bacteria
    • Moxon, E.R., Rainey, P.B., Nowak, M.A., and Lenski, R.E. 1994. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4: 24-33.
    • (1994) Curr. Biol. , vol.4 , pp. 24-33
    • Moxon, E.R.1    Rainey, P.B.2    Nowak, M.A.3    Lenski, R.E.4
  • 30
    • 0024362982 scopus 로고
    • Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome
    • Nakata, A., Amemura, M., and Makino, K. 1989. Unusual nucleotide arrangement with repeated sequences in the Escherichia coli K-12 chromosome. J. Bacteriol. 171: 3553-3556.
    • (1989) J. Bacteriol. , vol.171 , pp. 3553-3556
    • Nakata, A.1    Amemura, M.2    Makino, K.3
  • 31
    • 0034671796 scopus 로고    scopus 로고
    • Evolutionary dynamics of full genome content in Escherichia coli
    • Ochman, H. and Jones, I.B. 2000. Evolutionary dynamics of full genome content in Escherichia coli. EMBO J. 19: 6637-6643.
    • (2000) EMBO J. , vol.19 , pp. 6637-6643
    • Ochman, H.1    Jones, I.B.2
  • 32
    • 0035843908 scopus 로고    scopus 로고
    • Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis
    • Ochman, H. and Moran, N.A. 2001. Genes lost and genes found: Evolution of bacterial pathogenesis and symbiosis. Science 292: 1096-1099.
    • (2001) Science , vol.292 , pp. 1096-1099
    • Ochman, H.1    Moran, N.A.2
  • 33
    • 0036274037 scopus 로고    scopus 로고
    • The Mismatch Repair System (mutS, mutL, and uvrD genes) in Pseudomonas aeruginosa: Molecular characterization of naturally occurring mutants
    • Oliver, A., Baquero, F., and Blázquez, J. 2002. The Mismatch Repair System (mutS, mutL, and uvrD genes) in Pseudomonas aeruginosa: Molecular characterization of naturally occurring mutants. Mol. Microbiol. 43: 1641-1650.
    • (2002) Mol. Microbiol. , vol.43 , pp. 1641-1650
    • Oliver, A.1    Baquero, F.2    Blázquez, J.3
  • 34
    • 0023899705 scopus 로고
    • Structural plasmid instability in Bacillus subtilis: Effect of direct and inverted repeats
    • Peeters, B.P., de Boer, J.H., Bron, S., and Venema, G. 1988. Structural plasmid instability in Bacillus subtilis: Effect of direct and inverted repeats. Mol. Gen. Genet. 212: 450-458.
    • (1988) Mol. Gen. Genet. , vol.212 , pp. 450-458
    • Peeters, B.P.1    de Boer, J.H.2    Bron, S.3    Venema, G.4
  • 35
    • 0036334551 scopus 로고    scopus 로고
    • Short-sequence tandem and nontandem DNA repeats and endogenous hydrogen peroxide production contribute to genetic instability of Streptococcus pneumoniae
    • Pericone, C.D., Bae, D., Shchepetov, M., McCool, T., and Weiser, J.N. 2002. Short-sequence tandem and nontandem DNA repeats and endogenous hydrogen peroxide production contribute to genetic instability of Streptococcus pneumoniae. J. Bacteriol. 184: 4392-4399.
    • (2002) J. Bacteriol. , vol.184 , pp. 4392-4399
    • Pericone, C.D.1    Bae, D.2    Shchepetov, M.3    McCool, T.4    Weiser, J.N.5
  • 36
    • 0025862207 scopus 로고
    • The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7
    • Pierce, J.C., Kong, D., and Masker, W. 1991. The effect of the length of direct repeats and the presence of palindromes on deletion between directly repeated DNA sequences in bacteriophage T7. Nucleic Acids Res. 19: 3901-3905.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 3901-3905
    • Pierce, J.C.1    Kong, D.2    Masker, W.3
  • 37
    • 0024469392 scopus 로고
    • The barrier to recombination between E. coli and S. typhimurium is disrupted in mismatch-repair mutants
    • Rayssiguier, C., Thaler, D.S., and Radman, M. 1989. The barrier to recombination between E. coli and S. typhimurium is disrupted in mismatch-repair mutants. Nature 342: 396-401.
    • (1989) Nature , vol.342 , pp. 396-401
    • Rayssiguier, C.1    Thaler, D.S.2    Radman, M.3
  • 38
    • 0030935318 scopus 로고    scopus 로고
    • Detection of significant patterns by compression algorithms: The case of approximate tandem repeats in DNA sequences
    • Rivals, E., Delgrange, O., Delahaye, J.P., Dauchet, M., Delorme, M.O., Henaut, A., and Ollivier, E. 1997. Detection of significant patterns by compression algorithms: The case of approximate tandem repeats in DNA sequences. Comput. Appl. Biosci. 13: 131-136.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 131-136
    • Rivals, E.1    Delgrange, O.2    Delahaye, J.P.3    Dauchet, M.4    Delorme, M.O.5    Henaut, A.6    Ollivier, E.7
  • 39
    • 0036567258 scopus 로고    scopus 로고
    • Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution
    • Rocha, E.P.C. and Blanchard, A. 2002. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution. Nucleic Acids Res. 30: 2031-2042.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 2031-2042
    • Rocha, E.P.C.1    Blanchard, A.2
  • 40
    • 0032843459 scopus 로고    scopus 로고
    • Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes
    • Rocha, E.P.C., Danchin, A., and Viari, A. 1999. Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes. Mol. Biol. Evol. 16: 1219-1230.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1219-1230
    • Rocha, E.P.C.1    Danchin, A.2    Viari, A.3
  • 41
    • 0036567071 scopus 로고    scopus 로고
    • Over-representation of close repeats in stress response genes: A strategy to increase versatility under stressful conditions?
    • Rocha, E.P.C., Matic, I., and Taddei, F. 2002. Over-representation of close repeats in stress response genes: A strategy to increase versatility under stressful conditions? Nucleic Acids Res. 30: 1886-1894.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1886-1894
    • Rocha, E.P.C.1    Matic, I.2    Taddei, F.3
  • 42
    • 0031468083 scopus 로고    scopus 로고
    • Gene amplification and genomic plasticity in prokaryotes
    • Romero, D. and Palacios, R. 1997. Gene amplification and genomic plasticity in prokaryotes. Annu. Rev. Genet. 31: 91-111.
    • (1997) Annu. Rev. Genet. , vol.31 , pp. 91-111
    • Romero, D.1    Palacios, R.2
  • 43
    • 0031752310 scopus 로고    scopus 로고
    • Identifying satellites and periodic repetitions in biological sequences
    • Sagot, M.F. and Myers, E.W. 1998. Identifying satellites and periodic repetitions in biological sequences. J. Comput. Biol. 5: 539-553.
    • (1998) J. Comput. Biol. , vol.5 , pp. 539-553
    • Sagot, M.F.1    Myers, E.W.2
  • 44
    • 0031931361 scopus 로고    scopus 로고
    • Simple sequence repeats in the Helicobacter pylori genome
    • Saunders, N.J., Peden, J.F., Hood, D.W., and Moxon, E.R. 1998. Simple sequence repeats in the Helicobacter pylori genome. Mol. Microbiol. 27: 1091-1098.
    • (1998) Mol. Microbiol. , vol.27 , pp. 1091-1098
    • Saunders, N.J.1    Peden, J.F.2    Hood, D.W.3    Moxon, E.R.4
  • 45
    • 0030902447 scopus 로고    scopus 로고
    • Enhanced deletion formation by aberrant DNA replication in Escherichia coli
    • Saveson, C.J. and Lovett, S.T. 1997. Enhanced deletion formation by aberrant DNA replication in Escherichia coli. Genetics 146: 457-470.
    • (1997) Genetics , vol.146 , pp. 457-470
    • Saveson, C.J.1    Lovett, S.T.2
  • 46
    • 0034618559 scopus 로고    scopus 로고
    • Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS
    • Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y., and Ishikawa, H. 2000. Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature 407: 81-86.
    • (2000) Nature , vol.407 , pp. 81-86
    • Shigenobu, S.1    Watanabe, H.2    Hattori, M.3    Sakaki, Y.4    Ishikawa, H.5
  • 47
    • 0035500843 scopus 로고    scopus 로고
    • Genome size reduction through multiple events of gene disintegration in Buchnera APS
    • Silva, F.J., Latorre, A., and Moya, A. 2001. Genome size reduction through multiple events of gene disintegration in Buchnera APS. Trends Genet. 17: 615-618.
    • (2001) Trends Genet. , vol.17 , pp. 615-618
    • Silva, F.J.1    Latorre, A.2    Moya, A.3
  • 48
    • 0024292941 scopus 로고
    • Deletion formation in bacteriophage T4
    • Singer, B.S. and Westlye, J. 1988. Deletion formation in bacteriophage T4. J. Mol. Biol. 202: 233-243.
    • (1988) J. Mol. Biol. , vol.202 , pp. 233-243
    • Singer, B.S.1    Westlye, J.2
  • 49
    • 0023976653 scopus 로고
    • Homologous recombination in prokaryotes
    • Smith, G.R. 1988. Homologous recombination in prokaryotes. Microbiol. Rev. 52: 1-28.
    • (1988) Microbiol. Rev. , vol.52 , pp. 1-28
    • Smith, G.R.1
  • 51
    • 0022533981 scopus 로고
    • Cryptic simplicity in DNA is a major source of genetic variation
    • Tautz, D., Trick, M., and Dover, G.A. 1986. Cryptic simplicity in DNA is a major source of genetic variation. Nature 322: 652-656.
    • (1986) Nature , vol.322 , pp. 652-656
    • Tautz, D.1    Trick, M.2    Dover, G.A.3
  • 52
    • 0026419949 scopus 로고
    • Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli
    • Trinh, T.Q. and Sinden, R.R. 1991. Preferential DNA secondary structure mutagenesis in the lagging strand of replication in E. coli. Nature 352: 544-547.
    • (1991) Nature , vol.352 , pp. 544-547
    • Trinh, T.Q.1    Sinden, R.R.2
  • 54
    • 0004252445 scopus 로고    scopus 로고
    • Chapters 13 and 25. Prentice Hall, NJ
    • Zar, J.H. 1996. Biostatistical analysis. Chapters 13 and 25. Prentice Hall, NJ.
    • (1996) Biostatistical Analysis
    • Zar, J.H.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.