Gene conversion and concerted evolution in bacterial genomes

FEMS Microbiology Reviews

Volumn 29, Issue 2, 2005, Pages 169-183

  Santoyo, Gustavo ^a   Romero, David ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

Author keywords

Antigenic variation; Concerted evolution; Gene conversion; Homologous recombination

Indexed keywords

DNA; DNA POLYMERASE; RIBOSOME RNA;

ANTIGENICITY; BACTERIAL GENOME; BACTERIAL VIRULENCE; CHROMOSOME ANALYSIS; DNA SYNTHESIS; EVOLUTION; GENE CONVERSION; GENE IDENTIFICATION; GENE INTERACTION; GENE MUTATION; GENE SEQUENCE; GENE TRANSFER; GENETIC ANALYSIS; HOMOLOGOUS RECOMBINATION; IMMUNE SYSTEM; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; MOLECULAR MODEL; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; REVIEW; SEQUENCE HOMOLOGY;

EID: 15944412560     PISSN: 01686445     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.femsre.2004.10.004     Document Type: Review

References (114)

1. K.J. Marians Mechanisms of replication fork restart in Escherichia coli Philos. Trans. R. Soc. Lond. B 29 2004 71 77
2. A. Kuzminov DNA replication meets genetic exchange: chromosomal damage and its repair by homologous recombination Proc. Natl. Acad. Sci. USA 98 2001 8461 8468
3. B. Michel, M.-J. Flores, E. Viguera, G. Grompone, M. Seigneur, and V. Bidnenko Rescue of arrested replication forks by homologous recombination Proc. Natl. Acad. Sci. USA 98 2001 8181 8188
4. E.P. Rocha, A. Danchin, and A. Viari Functional and evolutionary roles of long repeats in prokaryotes Res. Microbiol. 150 1999 725 733
5. E.P. Rocha, A. Danchin, and A. Viari Analysis of long repeats in bacterial genomes reveals alternative evolutionary mechanisms in Bacillus subtilis and other competent prokaryotes Mol. Biol. Evol. 16 1999 1219 1230
6. D. Romero, J. MartIÍnez-Salazar, E. Ortiz, C. RodrIÍguez, and E. Valencia-Morales Repeated sequences in bacterial chromosomes and plasmids: a glimpse from sequenced genomes Res. Microbiol. 150 1999 735 743
7. D. Romero, and R. Palacios Gene amplification and genomic plasticity in prokaryotes Annu. Rev. Genet. 31 1997 91 111
8. D. Hughes Evaluating genome dynamics: the constraints on rearrangements within bacterial genomes Genome Biol. 1 2000 reviews 0006.1-0006.8
9. M. Flores, P. Mavingui, X. Perret, W.J. Broughton, D. Romero, G. Hernández, G. Dávila, and R. Palacios Prediction, identification, and artificial selection of DNA rearrangements in Rhizobium: toward a natural genomic design Proc. Natl. Acad. Sci. USA 97 2000 9138 9143
10. K.W. Deitsch, E.R. Moxon, and T.E. Wellems Shared themes of antigenic variation and virulence in bacterial, protozoal, and fungal infections Microbiol. Mol. Biol. Rev. 61 1997 281 293
11. K.A. Brayton, G.H. Palmer, A. Lundgren, J. Yi, and A.F. Barbet Antigenic variation of Anaplasma marginale msp2 occurs by combinatorial gene conversion Mol. Microbiol. 43 2002 1151 1159
12. A.F. Barbet, A. Lundgren, J. Yi, F.R. Rurangirwa, and G.H. Palmer Antigenic variation of Anaplasma marginale by expression of MSP2 mosaics Infect. Immun. 68 2000 6133 6138
13. B. Howell-Adams, and H.S. Seifert Molecular models accounting for the gene conversion reactions mediating gonococcal pilin antigenic variation Mol. Microbiol. 37 2000 1146 1158
14. G. Dover Molecular drive Trends Genet. 18 2002 587 589
15. A. Belle, M. Landthaler, and D.A. Shub Intronless homing: site-specific endonuclease Seg F of bacteriophage T4 mediates localized marker exclusion analogous to homing endonucleases of group I introns Genes Dev. 16 2002 351 362
16. Q. Liu, A. Belle, D.A. Shub, M. Belfort, and D.R. Edgell SegG endonuclease promotes marker exclusion and mediates co-conversion from a distant cleavage site J. Mol. Biol. 334 2003 13 23
17. M. Landthaler, M.C. Lau, and D.A. Shub Group I intron homing in Bacillus phages SPO1 and SP82: a gene conversion event initiated by a nicking homing endonuclease J. Bacteriol. 186 2004 4307 4314
18. F.W. Stahl Genetic Recombination: Thinking About it in Phage and Fungi 1979 Freeman New York 333 pp.
19. D.R.F. Leach Genetic Recombination 1996 Blackwell Science London 192pp
20. R. Holliday A mechanism for gene conversion Genet. Res. 5 1964 282 304
21. F. Stahl The Holliday junction on its thirtieth anniversary Genetics 138 1994 241 246
22. M.S. Meselson, and C.M. Radding A general model for genetic recombination Proc. Natl. Acad. Sci. USA 72 1975 358 361
23. E. Alani, R.A. Reenan, and R.D. Kolodner Interaction between mismatch repair and genetic recombination in Saccharomyces cerevisiae Genetics 137 1994 19 39
24. J. Szostak, T. Orr-Weaver, R. Rothstein, and F. Stahl The double-strand-break repair model for recombination Cell 33 1983 25 35
25. F. Stahl Meiotic recombination in yeast: coronation of the double-strand-break repair model Cell 87 1996 965 968
26. T.D. Petes Meiotic recombination hotspots and coldspots Nat Rev. Gen. 2 2001 360 369
27. A. Koren, S. Ben-Aroya, and M. Kupiec Control of meiotic recombination initiation: a role for the enviroment? Curr. Genet. 42 2002 129 139
28. H. Wolf-Dietrich Recombination: Holliday junction resolution and crossover formation Curr. Biol. 14 2004 R56 R58
29. D. Bishop, and D. Zickler Early decision: meiotic crossover interference prior to stable strand exchange and synapsis Cell 117 2004 9 15
30. A. Aguilera, S. Chavez, and F. Malagón Mitotic recombination in yeast: elements controlling its incidence Yeast 16 2000 731 754
31. F. Prado, F. Cortes-Ledesma, P. Huertas, and A. Aguilera Mitotic recombination in Saccharomyces cerevisiae Curr. Genet. 42 2003 185 198
32. G. Ira, A. Malkova, G. Liberi, M. Foiani, and J.E. Haber Src2 and Sgs1-Top3 suppress crossovers during double-strand break repair in yeast Cell 115 2003 401 411
33. T. Allers, and M. Lichten Differential timing and control of noncrossover and crossover recombination during meiosis Cell 106 2001 47 57
34. S.C. West Molecular views of recombination proteins and their control Nat. Rev. Mol. Cell Biol. 4 2003 435 445
35. G.A. Cromie, J.C. Connelly, and D.R. Leach Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans Mol. Cell 8 2001 1163 1174
36. S.C. Kowalczykowski, D.A. Dixon, A.K. Eggleston, S.D. Lauder, and W.M. Rehrauer Biochemistry of homologous recombination in Escherichia coli Microbiol. Rev. 58 1994 401 465
37. N. Takahashi, and I. Kobayashi Evidence for the double-strand break repair model of bacteriophage lambda recombination Proc. Natl. Acad. Sci. USA 87 1990 2790 2794
38. I. Kobayashi, and N. Takahashi Double-stranded gap repair of DNA by gene conversion in Escherichia coli Genetics 119 1988 751 757
39. N.K. Takahashi, K. Kusano, T. Yokochi, Y. Kitamura, H. Yoshikura, and I. Kobayashi Genetic analysis of double-strand break repair in Escherichia coli J. Bacteriol. 175 1993 5176 5185
40. T. Yokochi, K. Kusano, and I. Kobayashi Evidence for conservative (two-progeny) DNA double-strand break repair Genetics 139 1995 5 17
41. N. Handa, and I. Kobayashi Accumulation of large non-circular forms of the chromosome in recombination-defective mutants of Escherichia coli BMC Mol. Biol. 4 2003 5
42. A. Kuzminov Single-strand interruptions in replicating chromosomes cause double-strand breaks Proc. Natl. Acad. Sci. USA 98 2001 8241 8246
43. A.M. Segall, and J.R. Roth Approaches to half-tetrad analysis in bacteria: recombination between repeated, inverse-order chromosomal sequences Genetics 136 1994 27 39
44. + strain is explained by multiple rounds of reciprocal crossing-over Mol. Gen. Genet. 212 1988 393 404
45. A.J. Clark rec Genes and homologous recombination proteins in Escherichia coli Biochimie 73 1991 523 532
46. K. Yamamoto, K. Kusano, N.K. Takahashi, H. Yoshikura, and I. Kobayashi Gene conversion in the Escherichia coli RecF pathway: a successive half crossing-over model Mol. Gen. Genet. 234 1992 1 13
47. I. Kobayashi Mechanisms for gene conversion and homologous recombination: the double-strand and break repair model and the succesive half crossing-over model Adv. Biophys. 28 1992 81 133
48. N.K. Takahashi, K. Yamamoto, Y. Kitamura, S.Q. Luo, H. Yoshikura, and I. Kobayashi Nonconservative recombination in Escherichia coli Proc. Natl. Acad. Sci. USA 89 1992 5912 5916
49. K. Yamamoto, N. Takahashi, Y. Fujitani, H. Yoshikura, and I. Kobayashi Orientation dependence in homologous recombination Genetics 143 1996 27 36
50. M.J. Mahan, and J.R. Roth Reciprocality of recombination events that rearrange the chromosome Genetics 120 1988 23 35
51. M.J. Mahan, and J.R. Roth Role of recBC function in formation of chromosomal rearrangements: a two-step model for recombination Genetics 121 1989 433 443
52. S.T. Lovett, R.L. Hurley, V.A. Sutera Jr., R.H. Aubuchon, and M.A. Lebedeva Crossing over between regions of limited homology in Escherichia coli: RecA-dependent and RecA-independent pathways Genetics 160 2002 851 859
53. F. Abdulkarim, and D. Hughes Homologous recombination between the tuf genes of Salmonella typhimurium J. Mol. Biol. 260 1996 506 522
54. D. Hughes Co-evolution of the tuf genes links gene conversion with the generation of chromosomal inversions J. Mol. Biol. 297 2000 355 364
55. O. Arwidsson, and D. Hughes Evidence against reciprocal recombination as the basis for tuf gene conversion in Salmonella enterica serovar typhimurium J. Mol. Biol. 338 2004 463 467
56. T. Prammananan, P. Sander, B. Springer, and E.C. Bottger RecA-mediated gene conversion and aminoglycoside resistance in strains heterozygous for rRNA Antimicrob. Agents Chemother. 43 1999 447 453
57. D.T. Pride, and M.J. Blaser Concerted evolution between duplicated genetic elements in Helicobacter pylori J. Mol. Biol. 316 2002 629 642
58. M. Flores, V. González, S. Brom, E. MartIÍnez, D. Piñero, D. Romero, G. Dávila, and R. Palacios Reiterated DNA sequences in Rhizobium and Agrobacterium spp J. Bacteriol. 169 1987 5782 5788
59. C. Quinto, H. de la Vega, M. Flores, L. Fernández, T. Ballado, G. Soberón, and R. Palacios Reiteration of nitrogen fixation gene sequences in Rhizobium phaseoli Nature 299 1982 724 726
60. C. Quinto, H. de la Vega, M. Flores, J. Leemans, M.A. Cevallos, M.A. Pardo, R. Azpiroz, M.L. Girard, E. Calva, and R. Palacios Nitrogenase reductase: a functional multigene family in Rhizobium phaseoli Proc. Natl. Acad. Sci. USA 82 1985 1170 1174
61. C. RodrIÍguez, and D. Romero Multiple recombination events maintain sequence identity among members of the nitrogenase multigene family in Rhizobium etli Genetics 149 1998 785 794
62. L.A. Gregg-Jolly, and L.N. Ornston Properties of Acinetobacter calcoaceticus recA and its contribution to intracellular gene conversion Mol. Microbiol. 12 1994 985 992
63. G.A. Kowalchuk, L.A. Gregg-Jolly, and L.N. Ornston Nucleotide sequences transferred by gene conversion in the bacterium Acinetobacter calcoaceticus Gene 153 1995 111 115
64. R.C. Doten, L.A. Gregg, and L.N. Ornston Influence of the catBCE sequence on the phenotypic reversion of a pcaE mutation in Acinetobacter calcoaceticus J. Bacteriol. 169 1987 3175 3180
65. S. Sawyer Statistical tests for detecting gene conversion Mol. Biol. Evol. 6 1989 526 538
66. G. Drouin, F. Prat, M. Ell, and G.D. Clarke Detecting and characterizing gene conversions between multigene family members Mol. Biol. Evol. 16 1999 1369 1390
67. P. Awadalla The evolutionary genomics of pathogen recombination Nat. Rev. Genet. 4 2003 50 60
68. I.K. Jordan, K.S. Makarova, Y.I. Wolf, and E.V. Koonin Gene conversions in genes encoding outer-membrane proteins in H. pylori and C. pneumoniae Trends Genet. 17 2001 7 10
69. J.P. Gogarten, and L. Olendzenski Orthologs, paralogs and genome comparisons Curr. Opin. Genet. Dev. 9 1999 630 636
70. C.F. Higgins, R.S. McLaren, and S.F. Newbury Repetitive extragenic palindromic sequences, mRNA stability and gene expression: evolution by gene conversion? A review Gene 72 1988 3 14
71. D. Liao Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea J. Mol. Evol. 51 2000 305 317
72. W.C. Lathe III, and P. Bork Evolution of tuf genes: ancient duplication, differential loss and gene conversion FEBS Lett. 502 2001 113 116
73. J.V. Solnick, L.M. Hansen, N.R. Salama, J.K. Boonjakuakul, and M. Syvanen Modification of Helicobacter pylori outer membrane protein expression during experimental infection of rhesus macaques Proc. Natl. Acad. Sci. USA 101 2004 2106 2111
74. R.J. Meinersmann, and K.L. Hiett Concerted evolution of duplicate fla genes in Campylobacter Microbiology 146 2000 2283 2290
75. N.R. Mattatall, and K.E. Sanderson Salmonella typhimurium LT2 possesses three distinct 23S rRNA intervening sequences J. Bacteriol. 178 1996 2272 2278
76. L.M. Pronk, and K.E. Sanderson Intervening sequences in rrl genes and fragmentation of 23S rRNA in genera of the family Enterobacteriaceae J. Bacteriol. 183 2001 5782 5787
77. M. Skurnik, and P. Toivanen Intervening sequences (IVSs), in the 23S ribosomal RNA genes of pathogenic Yersinia enterocolitica strains. The IVSs in Y. enterocolitica and Salmonella typhimurium have a common origin Mol. Microbiol. 5 1991 585 593
78. N.R. Mattatall, D.A. Daines, S.-L. Liu, and K.E. Sanderson Salmonella typhi contains identical intervening sequences in all seven rrl genes J. Bacteriol. 178 1996 5323 5326
79. Q.Y. Zhang, D. De Ryckere, P. Lauer, and M. Koomey Gene conversion in Neisseria gonorrhoeae: evidence for its role in pilus antigenic variation Proc. Natl. Acad. Sci. USA 89 1992 5366 5370
80. A.H. Noormohammadi, P.F. Markham, A. Kanci, K.G. Whithear, and G.F. Browning A novel mechanism for control of antigenic variation in the haemagglutinin gene family of Mycoplasma synoviae Mol. Microbiol. 35 2000 911 923
81. J.R. Zhang, and S.J. Norris Genetic variation of the Borrelia burgdorferi gene vlsE involves cassette-specific segmental gene conversion Infect. Immun. 66 1998 3698 3704
82. B.I. Restrepo, and A.G. Barbour Antigenic diversity in the bacterium B. hermsii through "somatic" mutations in rearranged vmp genes Cell 78 1994 867 876
83. C.S. Harrington, F.M. Thomson-Carter, and P.E. Carter Evidence for recombination in the flagellin locus of Campylobacter jejuni: implications for the flagellin gene typing scheme J. Clin. Microbiol. 35 1997 2386 2392
84. K.A. Kline, E.V. Sechman, E.P. Skaar, and H.S. Seifert Recombination, repair and replication in the pathogenic Neisseriae: the 3 R's of molecular genetics of two human-specific bacterial pathogens Mol. Microbiol. 50 2003 3 13
85. R. Haas, and T.F. Meyer The repertoire of silent pilus genes in Neisseria gonorrhoeae: evidence for gene conversion Cell 44 1986 107 115
86. R. Haas, S. Veit, and T.F. Meyer Silent pilin genes of Neisseria gonorrhoeae MS11 and the occurrence of related hypervariant sequences among other gonococcal isolates Mol. Microbiol. 6 1992 197 208
87. T.S. Hamrick, J.A. Dempsey, M.S. Cohen, and J.G. Cannon Antigenic variation of gonococcal pilin expression in vivo: analysis of the strain FA1090 pilin repertoire and identification of the pilS gene copies recombining with pilE during experimental human infection Microbiology 147 2001 839 849
88. C.D. Serkin, and H.S. Seifert Frequency of pilin antigenic variation in Neisseria gonorrhoeae J. Bacteriol. 180 1998 1955 1958
89. C.D. Serkin, and H.S. Seifert Iron availability regulates DNA recombination in Neisseria gonorrhoeae Mol. Microbiol. 37 2000 1075 1086
90. M. Koomey, E.C. Gotschlich, K. Robbins, S. Bergstrom, and J. Swanson Effects of recA mutations on pilus antigenic variation and phase transitions in Neisseria gonorrhoeae Genetics 117 1987 391 398
91. E.A. Stohl, and H.S. Seifert The recX gene potentiates homologous recombination in Neisseria gonorrhoeae Mol. Microbiol. 40 2001 1301 1310
92. I.J. Mehr, and H.S. Seifert Differential roles of homologous recombination pathways in Neisseria gonorrhoeae pilin antigenic variation, DNA transformation and DNA repair Mol. Microbiol. 30 1998 697 710
93. E.P. Skaar, M.P. Lazio, and H.S. Seifert Roles of the recJ and recN genes in homologous recombination and DNA repair pathways of Neisseria gonorrhoeae J. Bacteriol. 184 2002 919 927
94. M.S. Chaussee, J. Wilson, and S.A. Hill Characterization of the recD gene of Neisseria gonorrhoeae MS11 and the effect of recD inactivation on pilin variation and DNA transformation Microbiology 145 1999 389 400
95. P. Salvatore Phenotypes of a naturally defective recB allele in Neisseria meningitidis clinical isolates Infect. Immun. 70 2002 4185 4195
96. J.R. Zhang, J.M. Hardham, A.G. Barbour, and S.J. Norris Antigenic variation in Lyme disease borreliae by promiscuous recombination of VMP-like sequence cassettes Cell 89 1997 275 285
97. J.E. Donelson Mechanisms of antigenic variation in Borrelia hermsii and african trypanosomes J. Biol. Chem. 270 1995 7783 7786
98. J.S. Dumler, and J.S. Bakken Human ehrlichioses: newly recognized infections transmitted by ticks Annu. Rev. Med. 49 1998 201 213
99. K.A. Brayton, D.P. Knowles, T.C. McGuire, and G.H. Palmer Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens Proc. Natl. Acad. Sci. USA 98 2001 4130 4135
100. D.M. French, W.C. Brown, and G.H. Palmer Emergence of Anaplasma marginale antigenic variants during persistent rickettsemia Infect. Immun. 67 1999 5834 5840
101. A.H. Noormohammadi, P.F. Markham, K.G. Whithear, I.D. Walker, V.A. Gurevich, D.H. Ley, and G.F. Browning Mycoplasma synoviae has two distinct phase-variable major membrane antigens, one of which is a putative hemagglutinin Infect. Immun. 65 1997 2542 2547
102. A.H. Noormohammadi, P.F. Markham, M.F. Duffy, K.G. Whithear, and G.F. Browning Multigene families encoding the major hemagglutinins in phylogenetically distinct mycoplasmas Infect. Immun. 66 1998 3470 3745
103. A. Centurion-Lara, R.E. LaFond, K. Hevner, C. Godornes, B.J. Molini, W.C. Van Hoorhis, and S.A. Lukehart Gene conversion: a mechanism for generation of heterogeneity in the tprK gene of Treponema pallidum during infection Mol. Microbiol. 52 2004 1579 1596
104. G.R. Smith Homologous recombination near and far from DNA breaks: alternative roles and contrasting views Annu. Rev. Genet. 35 2001 243 274
105. L. Worth Jr., S. Clark, M. Radman, and P. Modrich Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs Proc. Natl. Acad. Sci. USA 91 1994 3238 3241
106. T.C. Zahrt, G.C. Mora, and S. Maloy Inactivation of mismatch repair overcomes the barrier to transduction between Salmonella typhimurium and Salmonella typhi J. Bacteriol. 176 1994 1527 1529
107. J.E. LeClerc, B. Li, W.L. Payne, and T.A. Cebula High mutation frequencies among Escherichia coli and Salmonella pathogens Science 274 1996 1208 1211
108. I. Matic, M. Radman, F. Taddei, B. Picard, C. Doit, E. Bingen, E. Denamur, and J. Elion Highly variable mutation rates in commensal and pathogenic Escherichia coli Science 277 1997 1833 1834
109. A. Oliver, R. Cantón, P. Campo, F. Baquero, and J. Blázquez High frequency of hypermutable Pseudomonas aeruginosa in cystic fibrosis lung infection Science 288 2000 1251 1253
110. A.L. Prunier, B. Malbruny, M. Laurans, J. Brouard, J.F. Duhamel, and R. Leclercq High rate of macrolide resistance in Staphylococcus aureus strains from patients with cystic fibrosis reveals high proportions of hypermutable strains J. Infect. Dis. 187 2003 1709 1716
111. F. Taddei, M. Radman, J. Maynard-Smith, B. Toupance, P.H. Gouyon, and B. Godell Role of mutator alleles in adaptive evolution Nature 387 1997 700 702
112. A. Giraud, I. Matic, O. Tenaillon, A. Clara, M. Radman, M. Fons, and F. Taddei Costs and benefits of high mutation rates: adaptive evolution of bacteria in the mouse gut Science 291 2001 2606 2608
113. J.P. Townsend, K.M. Nielsen, D.S. Fisher, and D.L. Hartl Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes Genetics 164 2003 13 21
114. I. Matic, A. Babic, and M. Radman 2-aminopurine allows interspecies recombination by a reversible inactivation of the Escherichia coli mismatch repair system J. Bacteriol. 185 2003 1459 1461