1887

Chapter 7 : Impact of Homologous Recombination on Genome Organization and Stability

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

Impact of Homologous Recombination on Genome Organization and Stability, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818180/9781555811518_Chap07-1.gif /docserver/preview/fulltext/10.1128/9781555818180/9781555811518_Chap07-2.gif

Abstract:

This chapter talks about bacterial genomes, primarily those of and (proper name, serovar Typhimurium). For these bacteria, abundant information is available on evolutionary relationships, high-quality genetic maps exist ( is completely sequenced), and there is extensive knowledge of mechanisms of recombination. Comparing the genomes of and is therefore a natural starting point for discussing the forces which determine genome organization and stability in general. The degree to which ectopic exchanges between directly repeated sequences are RecA dependent varies with size and distance. Large chromosomal duplications are genetically unstable but are stabilized by mutations, implicating homologous recombination in their formation and loss. Genes expressed at high levels are generally located in the origin-proximal half of the chromosome, presumably because closeness to the origin of DNA replication gives a gene dosage effect. Tandem duplications, and their associated deletions and translocations, create novel sequence join points which potentially have selective value for the cell. Recombination between directly oriented repeat sequences can create a DNA fragment (linear or circular, depending on the mechanism of recombination) which can recombine with the chromosome. Inversions can occur between homologous short and long sequences. Most inversions isolated in and are reported as having no significant effects on growth rate, but the few translocations made and tested in are associated with decreases in growth rate of up to a few percent.

Citation: Hughes D. 1999. Impact of Homologous Recombination on Genome Organization and Stability, p 109-128. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch7

Key Concept Ranking

Gene Expression and Regulation
0.7530242
DNA Polymerase III
0.50526315
0.7530242
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

The circular chromosome of and , showing the orientations and positions of the operons and the genes relative to the origin and terminus of DNA replication. The region around the terminus which is inverted in relative to that in is also indicated.

Citation: Hughes D. 1999. Impact of Homologous Recombination on Genome Organization and Stability, p 109-128. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

Linear map of the chromosome opened at the origin of DNA replication. map positions (approximately equivalent in are shown above the line, and the positions of sites (E, D, A, C, B, F, and G) and are shown on the line and labeled below. The bars above the line indicate the nondivisible zones for inversion endpoints based on the data in reference . The operon position is shown on the line to facilitate comparison with the results from shown below the line. The solid bars indicate permissive inversion intervals, and the dashed lines indicate nonpermissive inversion intervals for . This is a representative sample of the data from reference . Note that there is currently no experimental evidence that has the same organization of and sites as .

Citation: Hughes D. 1999. Impact of Homologous Recombination on Genome Organization and Stability, p 109-128. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Chromosome map of showing the relative positions of the TRZ, the site-specific recombination site, and the sites. The region that is inverted relative to that in is indicated and bracketed.

Citation: Hughes D. 1999. Impact of Homologous Recombination on Genome Organization and Stability, p 109-128. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch7
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818180.chap7
1. Abdulkarim, F.,, and D. Hughes. 1996. Homologous recombination between the tuf genes of Salmonella typhimurium . J. Mol Biol. 260: 506522.
2. Albertini, A. M.,, M. Hofer,, M. P. Calos,, and J. H. Miller. 1982. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell 29:319328.
3. Ames, G. F.,, D. P. Biek,, and E. N. Spudich. 1978. Duplications of histidine transport genes in Salmonella typhimurium and their use for the selection of deletion mutants. J. Bacteriol 136: 10941108.
4. Anderson, R. P.,, and J. R. Roth. 1978. Tandem chromosomal duplications in Salmonella typhimurium: fusion of histidine genes to novel promoters. J. Mol Biol 119:147166.
5. Anderson, R. P.,, and J. R. Roth. 1978. Tandem genetic duplications in Salmonella typhimurium: amplification of the histidine operon. J. Mol Biol 126:5371.
6. Anderson, R. P.,, and J. R. Roth. 1981. Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons. Proc. Natl Acad. Sci. USA 78:31133117.
7. Anderson, R. P.,, C. G. Miller,, and J. R. Roth. 1976. Tandem duplications of the histidine operon observed following generalized transduction in Salmonella typhimurium . J. Mol Biol 105:201218.
8. Andersson, D. I.,, E. S. Schlecta,, and J. R. Roth. 1998. Evidence that gene amplification underlies adaptive mutability of the bacterial lac operon. Science 282:11331135.
9. Arthur, H. M.,, and R. G. Lloyd. 1980. Hyperrecombination in uvrD mutants of Escherichia coli K-12. Mol Gen. Genet. 180:185191.
10. Asai, T.,, S. Sommer,, A. Bailone,, and T. Kogoma. 1993. Homologous recombination-dependent initiation of DNA replication from DNA damage-inducible origins in Escherichia coli . EMBO J. 12:32873295.
11. Asai, T.,, D. B. Bates,, and T. Kogoma. 1994. DNA replication triggered by double-stranded breaks in E. coli: dependence on homologous recombination functions. Cell 78:10511061.
12. Baker, T. A. 1991. ... and then there were two. Nature 353:794795.
13. Bender, R. A.,, A. Macaluso,, and B. Magasanik. 1976. Glutamate dehydrogenase: genetic mapping and isolation of regulatory mutants of Klebsiella aerogenes . J. Bacteriol. 127:141148.
14. Berg, O. G. 1999. Synonymous nucleotide divergence and saturation: effects of site-specific variations in codon bias and mutation rates. J. Mol Evol. 48:398407.
15. Bergthorsson, U.,, and H. Ochman. 1995. Heterogeneity of genome sizes among natural isolates of Escherichia coli . J. Bacteriol 177:57845789.
16. Berlyn, M. K. B.,, K. B. Low,, K. E. Rudd,, and M. Singer,. 1996. Linkage map of Escherichia coli K-12, edition 9, p. 17151902. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology , 2nd ed., vol. 2. American Society for Microbiology, Washington, D.C.
17. Bi, X.,, and L. F. Liu. 1994. recA -independent and recA -dependent intramolecular plasmid recombination. Differential homology requirement and distance effect. J. Mol Biol. 235:414423.
18. Björkman, J.,, D. Hughes,, and D. I. Andersson. 1998. Virulence of antibiotic-resistant Salmonella typhimurium . Proc. Natl Acad. Sci. USA 95:39493953.
19. Björkman, J.,, P. Samuelsson,, D. I. Andersson,, and D. Hughes. 1999. Novel mutations affecting translational accuracy, antibiotic resistance and virulence of Salmonella typhimurium . Mol Microbiol. 31:5358.
20. Blakely, G.,, S. Colloms,, G. May,, M. Burke,, and D. Sherratt. 1991. Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol. 3:789798.
21. Blakely, G.,, G. May,, R. McCuUoch,, L. K. Arciszewska,, M. Burke,, S. T. Lovett,, and D. J. Sherratt. 1993. Two related recombinases are required for site-specific recombination at dif and cer in E. coli . Cell 75:351361.
22. Blattner, F. R.,, G. Plunkett III,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Ruey,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D. J. Rose,, B. Mau,, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:14531474.
23. Brewer, B. J.,, and W. L. Fangman. 1988. A replication fork barrier at the 3' end of yeast ribosomal RNA genes. Cell 55:637643.
24. Burland, V.,, G. Plunkett III,, D. L. Daniels,, and F. R. Blattner. 1993. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16:551561.
25. Casse, F.,, M.-C. Pascal,, and M. Chippaux. 1973. Comparison between the chromosomal maps of Escherichia coli and Salmonella typhimurium. Length of the inverted segment in the trp region. Mol Gen. Genet. 124:253257.
26. Charlebois, R. L.,, and A. St. Jean. 1995. Supercoiling and map stability in the bacterial chromosome. J. Mol Evol. 41:1523.
27. Clugston, C. K.,, and A. P. Jessop. 1991. A bacterial position effect: when the F factor in E. coli K-12 is integrated in cis to a chromosomal gene that is flanked by IS1 repeats the elements are activated so that amplification and other regulatory changes that affect the gene can occur. Mutat. Res. 248:115.
28. Cornet, F.,, J. Lou am,, J. Patte,, and J.-M. Louarn. 1996. Restriction of the activity of the recombination site dif to a small zone of the Escherichia coli chromosome. Genes Dev. 10: 11521161.
29. Corre, J.,, F. Cornet,, J. Patte,, and J.-M. Louarn. 1997. Unraveling a region-specific hyperrecombination phenomenon: genetic control and modalities of terminal recombination in Escherichia coli . Genetics 147:979989.
30. de Massey, B.,, S. Bejar,, J. Louarn,, J.-M. Louarn,, and J. P. Bouche. 1987. Inhibition of replication forks exiting the terminus region of the Escherichia coli chromosome occurs at two loci separated by 5 min. Proc. Natl. Acad. Sci. USA 84:17591763.
31. Drake, J. W. 1991. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl Acad. Sci. USA 88:71607164.
32. Edlund, T.,, and S. Normark. 1981. Recombination between short DNA homologies causes tandem duplication. Nature 292:269271.
33. Edlund, T.,, T. Grundström,, and S. Normark. 1979. Isolation and characterization of DNA repetitions carrying the chromosomal beta-lactamase gene of Escherichia coli K-12. Mol Gen. Genet. 173:115125.
34. Folk, W. R.,, and P. Berg. 1971. Duplication of the structural gene for glycyl-transfer RNA synthetase in Escherichia coli . J. Mol Biol. 58: 595610.
35. François, V.,, J. Louarn,, and J.-M. Louarn. 1989. The terminus of the Escherichia coli chromosome is flanked by several polar replication pause sites. Mol Microbiol. 3:9951002.
36. François, V.,, J. Louarn,, J. Patte,, J. E. Rebollo,, and J.-M. Louarn. 1990. Constraints in chromosomal inversions in Escherichia coli are not explained by replication pausing at inverted terminator-like sequences. Mol Microbiol. 4:537542.
37. Fulcher, C. A.,, and R. Bauerle. 1978. Reinitiation of tryptophan operon expression in a promoter deletion strain of Salmonella typhimurium . Mol Gen. Genet. 158:239250.
38. Galitski, T.,, and J. R. Roth. 1995. Evidence that F plasmid transfer replication underlies apparent adaptive mutations. Science 268:421423.
39. Galitski, T.,, and J. R. Roth. 1997. Pathways for homologous recombination between chromosomal direct repeats in Salmonella typhimurium . Genetics 146:751767.
40. Haack, K. R.,, and J. R. Roth. 1995. Recombination between chromosomal IS200 elements supports frequent duplication formation in Salmonella typhimurium . Genetics 141:12451252.
41. Higgins, C. F.,, G. F.-L. Ames,, W. M. Barnes,, J. M. Clement,, and M. Hofhung. 1982. A novel intercistronic regulatory element of prokaryotic operons. Nature 298:760762.
42. Hill, C. W.,, and J. A. Gray. 1988. Effects of chromosomal inversion on cell fitness in Escherichia coli K-12. Genetics 119:771778.
43. Hill, C. W.,, and B. W. Harnish. 1981. Inversions between ribosomal RNA genes of Escherichia coli . Proc. Natl Acad. Sci. USA 78: 70697072.
44. Hill, C. W.,, and B. W. Harnish. 1982. Transposition of a chromosomal segment bounded by redundant rRNA genes into other rRNA genes in Escherichia coli . J. Bacteriol. 149:449457.
45. Hill, C. W.,, J. Foulds,, L. Soil,, and P. Berg. 1969. Instability of a missense suppressor resulting from a duplication of genetic material. J. Mol Biol 39:563581.
46. Hill, T. M., 1996. Features of the chromosome terminus region, p. 16021614. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology , 2nd ed., vol. 2. American Society for Microbiology, Washington, D.C.
47. Hill, T. M.,, and K. J. Marinus. 1990. Escherichia coli Tus protein acts to arrest the progression of DNA replication forks in vitro . Proc. Natl. Acad. Sci. USA 87:24812485.
48. Hoffinann, G. R.,, R. W. Morgan,, and R. C. Harvey. 1978. Effects of chemical and physical mutagens on the frequency of a large genetic duplication in Salmonella typhimurium. I. Induction of duplications. Mutat. Res. 52:7380.
49. Hoffinann, G. R.,, R. W. Morgan,, and R. Kirven. 1978. Effects of chemical and physical mutagens on the frequency of a large genetic duplication in Salmonella typhimurium. II. Stimulation of duplication-loss from merodiploids. Mutat. Res. 52:8186
50. Hofrmann, G. R.,, M. J. Walkowicz,, J. M. Mason,, and J. F. Atkins. 1983. Genetic instability associated with the aroC321 allele in Salmonella typhimurium involves genetic duplication. Mol. Gen. Genet. 190:183188.
51. Holliday, R. 1964. A mechanism for gene conversion in fungi. Genet. Res. 5:282304.
52. Horiuchi, T.,, and Y. Fujimura. 1995. Recombinational rescue of the stalled DNA replication fork: a model based on analysis of an Escherichia coli strain with a chromosome region difficult to replicate. J. Bacteriol. 177:783791.
53. Horiuchi, T.,, Y. Fujimura,, H. Nishitani,, Y. Kobayashi,, and M. Hidaka. 1994. The DNA replication fork blocked at the Ter site may be an entrance for the RecBCD enzyme into duplex DNA. J. Bacteriol. 176:46564663.
54. Horiuchi, T.,, H. Nishitani,, and T. Kobayashi. 1995. A new type of E. coli recombinational hotspot which requires for activity both DNA replication termination events and the Chi sequence. Adv. Biophys. 31:133147.
55. Jessop, A. P.,, and C. Clugston. 1985. Amplification of the ArgF region in strain HfrP4X of E. coli K-12. Mol. Gen. Genet. 201:347350.
56. Jones, I. M.,, S. B. Primrose,, and S. D. Erlich. 1982. Recombination between short direct repeats in a RecA host. Mol. Gen. Genet. 188: 486489.
57. Kleckner, N.,, K. Reichardt,, and D. Botstein. 1979. Inversions and deletions of the Salmonella chromosome generated by the translocatable tetracycline resistance element Tn10. J. Mol. Biol. 127:89115.
58. Kogoma, T. 1997. Stable DNA replication: the interplay between DNA replication, homologous recombination, and transcription. Microbiol. Mol. Biol. Rev. 61:212238.
59. Kogoma, T.,, G. W. Cadwell,, K. G. Barnard,, and T. Asai. 1996. The DNA replication priming protein, PriA, is required for homologous recombination and double-strand break repair. J. Bacteriol. 178:12581264.
60. Konrad, E. B. 1977. Method for the isolation of Escherichia coli mutants with enhanced recombination between chromosomal duplications. J. Bacteriol. 130:167172.
61. Krug, P. J.,, A. Z. Gileski,, R. J. Code,, A. Torjussen,, and M. B. Schmid. 1994. Endpoint bias in large Tn10 -catalyzed inversions in Salmonella typhimurium . Genetics 136:747756.
62. Kuempel, P.,, A. Hogaard,, M. Nielsen,, O. Nagappan,, and M. Tecklenburg. 1996. Use of a transposon (Tndif) to obtain suppressing and nonsuppressing insertions of the dij resolvase site of Escherichia coli . Genes Dev. 10:11621171.
63. Kuempel, P. L.,, S. A. Duerr,, and N. R. Seeley. 1977. Terminus region of the chromosome in Escherichia coli inhibits replication forks. Proc. Natl. Acad. Sci. USA 74:39273931.
64. Kuempel, P. L.,, J. M. Henson,, L. Dircks,, M. Tecklenburg,, and D. F. Lim. 1991. dif, a recA -independent recombination site in the terminus region of Escherichia coli . New Biol. 3:799811.
65. Kuzminov, A. 1995. Instability of inhibited replication forks in E. coli . Bioessays 17:733741.
66. Kuzminov, A. 1995. Collapse and repair of replication forks in Escherichia coli . Mol. Microbiol. 16: 373384.
67. Kuzminov, A.,, E. Schabtach,, and F. W. Stahl. 1994. χ sites in combination with RecA protein increase the survival of linear DNA in Escherichia coli by inactivating exoV activity of RecBCD nuclease. EMBO J. 13:27642776.
68. Lee, E. H.,, A. Kornberg,, M. Hikada,, T. Kobayashi,, and T. Horiuchi. 1989. Escherichia coli replication termination protein impedes the action of helicases. Proc. Natl. Acad. Sci. USA 86: 91049108.
69. Lehner, A. F.,, and C. W. Hill. 1980. Involvement of ribosomal ribonucleic acid operons in Salmonella typhimurium chromosomal rearrangements. J. Bacteriol. 143:492498.
70. Leslie, N. R.,, and D. J. Sherratt. 1995. Site-specific recombination in the replication terminus of Escherichia coli: functional replacement of dif . EMBO J. 14:15611570.
71. Lin, R. J.,, M. Capage,, and C. W. Hill. 1984. A repetitive DNA sequence, rhs, responsible for duplications within the Escherichia coli K-12 chromosome. J. Mol. Biol. 177:118.
72. Lindegren, C. C. 1953. Gene conversion in Saccharomyces . J. Genet. 51:625637.
73. Liu, B.,, and B. M. Alberts. 1995. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science 267:11311136.
74. Liu, S.-L.,, and K. E. Sanderson. 1995. Rearrangements in the genome of the bacterium Salmonella typhi . Proc. Natl. Acad. Sci. USA 92: 10181022.
75. Liu, S.-L.,, and K. E. Sanderson. 1995. I-Ceu I reveals conservation of the genome of independent strains of Salmonella typhimurium . J. Bacteriol. 177:33553357.
76. Liu, S.-L.,, and K. E. Sanderson. 1995. The chromosome of Salmonella paratyphi A is inverted by recombination between rrnH and rrnG . J. Bacteriol. 177:65856592.
77. Liu, S.-L.,, and K. E. Sanderson. 1996. Highly plastic chromosomal organization in Salmonella typhi . Proc. Natl. Acad. Sci. USA 93:1030310308.
78. Liu, S.-L.,, A. Hessel,, and K. E. Sanderson. 1993. The Xba I-Bln I-Ceu I genomic cleavage map of Salmonella enteritidis shows an inversion relative to Salmonella typhimurium LT2. Mol. Microbiol. 10:655664.
79. Louarn, J.,, J. Patte, andj. M. Louarn. 1977. Evidence for a fixed termination site of chromosome replication in Escherichia coli K12. J. Mol. Biol. 115:295314.
80. Louarn, J.,, F. Cornet,, V. François,, J. Patte,, and J.-M. Louarn. 1994. Hyperrecombination in the terminus region of the E. coli chromosome: possible relation to nucleoid organization. J. Bacteriol. 176:75247531.
81. Louarn, J.-M.,, J. Louarn,, V. François,, and J. Patte. 1991. Analysis and possible role of hyperrecombination in the termination region of the Escherichia coli chromosome. J. Bacteriol. 173:50975104.
82. Lovett, S. T.,, P. T. Drapkin,, V. A. Sutura, Jr.,, and T. J. Gluckman. 1993. A sister-strand exchange mechanism for recA -independent deletion of repeated DNA sequences in Escherichia coli . Genetics 135:631642.
83. Lovett, S. T.,, T. J. Gluckman,, P. J. Simon,, V. A. Sutera, Jr.,, and P. T. Drapkin. 1994. Recombination between repeats in Escherichia coli by a recA -independent, proximity-sensitive mechanism. Mol. Gen. Genet. 245:294300.
84. Mahan, M. J.,, and J. R. Roth. 1988. Reciprocality of recombination events that rearrange the chromosome. Genetics 120:2335.
85. Mahan, M. J., andj. R. Roth. 1989. Role of recBC function in formation of chromosomal rearrangements: a two-step model for recombination. Genetics 121:433443.
86. Marinus, M. G.,, and E. B. Konrad. 1976. Hyperrecombination in dam mutants of Escherichia coli K-12. Mol. Gen. Genet. 149:273277.
87. Marvo, S. L.,, R. S. King,, and S. R. Jaskunas. 1983. Role of short regions of homology in intermolecular illegitimate recombination events. Proc. Natl. Acad. Sci. USA 80:24522456.
88. Masai, H.,, T. Asai,, Y. Kubota,, K. Arai,, and T. Kogoma. 1994. Escherichia coli PriA protein is essential for inducible and constitutive stable DNA replication. EMBO J. 13:53385346.
89. Matfield, M.,, R. Badawi,, and W. J. Brammar. 1985. Rec-dependent and rec-independent recombination of plasmid-borne duplications in Escherichia coli K12. Mol. Gen. Genet. 199:518523.
90. Mazin, A. V.,, A. V. Kuzminov,, G. L. Dianov,, and R. I. Salganik. 1991. Molecular mechanisms of deletion formation in Escherichia coli plasmids. II. Deletion formation mediated by short direct repeats. Mol. Gen. Genet. 228: 209214.
91. McGlynn, P.,, A. A. Al-Deib,, J. Lui,, K. J. Marians,, and R. G. Lloyd. 1997. The DNA replication protein PriA and the recombination protein RecG bind D-loops. J. Mol. Biol. 270: 212221.
92. Médigue, C.,, A. Viari,, A. Henaut,, and A. Danchin. 1993. Colibri: a functional database for the Escherichia coli genome. Microbiol. Rev. 57:623654.
93. Michel, B.,, S. D. Erlich,, and M. Uzest. 1997. DNA double-strand breaks caused by replication arrest. EMBO J. 16:430438.
94. Miesel, L.,, A. Segall, andj. R. Roth. 1994. Construction of chromosomal rearrangements in Salmonella by transduction: inversions of non-permissive segments are not lethal. Genetics 137: 919932.
95. Mills, D. M.,, V. Bajaj,, and C. A. Lee. 1995. A 40 kb chromosomal fragment encoding Salmonella typhimurium invasion genes is absent from the corresponding region of the Escherichia coli K-12 genome. Mol. Microbiol. 15:749759.
96. Mitchell, M. B. 1955. Aberrant recombination of pyroxidine mutants of Neurospora . Proc. Natl. Acad. Sci. USA 41:215220.
97. Mitchell, M. B. 1955. Further evidence of aberrant recombination in Neurospora . Proc. Natl. Acad. Sci. USA 41:935937.
98. Myers, R. S.,, and F. W. Stahl. 1994. χ and the RecBCD enzyme of Escherichia coli . Annu. Rev. Genet. 28:4970.
99. Ochman, H.,, and E. A. Groisman. 1994. The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium. EXS 69:479493.
100. Ochman, H.,, and A. C. Wilson. 1987. Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J. Mol. Evol. 26:7486.
101. Olive, S. 1959. Aberrant tetrads in S. fimicola . Proc. Natl. Acad. Sci. USA 45:727732.
102. Payne, G. M.,, E. N. Spudich,, and G. F. Ames. 1985. A mutational hot-spot in the hisM gene of the histidine transport operon in Salmonella typhimurium is due to deletion of repeated sequences and results in an altered specificity of transport. Mol. Gen. Genet. 200:493496.
103. Petit, M.-A.,, J. M. Mesas,, P. Noiret,, F. Morel-Deville,, and S. D. Erlich. 1992. Induction of DNA amplification in the Bacillus subtilis chromosome. EMBO J. 11:13171326.
104. Rayssiguier, C.,, D. S. Thaler,, and M. Radman. 1989. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature 342:396401.
105. Rebello, J.-E.,, V. François,, and J.-M. Louarn. 1988. Detection and possible role of two large nondivisible zones on the Escherichia coli chromosome. Proc. Natl. Acad. Sci. USA 85: 93919395.
106. Riley, M.,, and S. Krawiec,. 1987. Genome organization, p. 967981. In F. C. Neidhardt,, J. L. Ingraham,, K. B. Low,, B. Magasanik,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology . American Society for Microbiology, Washington, D.C.
107. Roth, J. R.,, N. Benson,, T. Galitski,, K. Haack,, J. G. Lawrence,, and L. Miesel,. 1996. Rearrangements of the bacterial chromosome: formation and applications, p. 22562276. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 2. American Society for Microbiology, Washington, D.C.
108. Sanderson, K. E.,, and C. A. Hall. 1968. F-prime factors of Salmonella typhimurium and an inversion between S. typhimurium and E. coli . Genetics 64:215228.
109. Sanderson, K. E.,, A. Hessel,, S.-L. Liu,, and K. E. Rudd,. 1996. The genetic map of Salmonella typhimurium, edition VIII, p. 19031999. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 2. American Society for Microbiology, Washington, D.C.
110. Sandier, S. J.,, S. Samra,, and A. J. Clark. 1996. Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC . Genetics 143:513.
111. Savageau, M. A. 1983. Escherichia coli: habitats, cell types, and molecular mechanisms of gene control. Am. Nat. 122:732744.
112. Saveson, C. J.,, and S. T. Lovett. 1997. Enhanced deletion formation by aberrant DNA replication in Escherichia coli . Genetics 146:457470.
113. Schmid, M. B.,, and J. R. Roth. 1983. Genetic methods for analysis and manipulation of inversion mutations in bacteria. Genetics 105: 517537.
114. Schmid, M. B.,, and J. R. Roth. 1983. Selection and endpoint distribution of bacterial inversion mutations. Genetics 105:539557.
115. Schmid, M. B.,, and J. R. Roth. 1987. Gene location affects expression level in Salmonella typhimurium . J. Bacteriol. 169:28722875.
116. Schofield, M. A.,, R. Agbunag,, and J. H. Miller. 1992. DNA inversions between short inverted repeats in Escherichia coli . Genetics 132: 295302.
117. Sclafani, R. A.,, and J. A. Wechsler. 1981. High frequency of genetic duplications in the dnaB region of the Escherichia coli K12 chromosome. Genetics 98:677690.
118. Segall A. M.,, and J. R. Roth. 1989. Recombination between homologies in direct and inverse orientation in the chromosome of Salmonella: intervals which are nonpermissive for inversion formation. Genetics 122:737747.
119. Segall, A. M.,, and J. R. Roth. 1994. Approaches to half-tetrad analysis in bacteria: recombination between repeated, inverse-order chromosomal sequences. Genetics 136:2739.
120. Segall, A. M.,, M. J. Mahan,, and J. R. Roth. 1988. Rearrangement of the bacterial chromosome: forbidden inversions. Science 241:13141318.
121. Seigneur, M.,, V. Bidnenko,, S. D. Erlich,, and B. Michel. 1998. RuvAB acts at arrested replication forks. Cell 95:419430.
122. Sharp, P. M. 1991. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J. Mol. Evol. 33:2333.
123. Shen, P.,, and H. V. Huang. 1986. Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics 112:441457.
124. Shen, P.,, and H. V. Huang. 1989. Effect of base pair mismatches on recombination via the RecBCD pathway. Mol. Gen. Genet. 218:358360.
125. Shyamala, V.,, E. Schneider,, and G. F. Ames. 1990. Tandem chromosomal duplications: role of REP sequences in the recombination event at the joint-point. EMBO J. 9: 939946.
126. Smith, G. R. 1991. Conjugational recombination in E. coli: myths and mechanisms. Cell 64:1927.
127. Sonti, R. V.,, and J. R. Roth. 1989. Role of gene duplications in the adaptation of Salmonella typhimurium to growth on limiting carbon sources. Genetics 123:1928.
128. Sousa, C.,, V. de Lorenza,, and A. Cebolla. 1997. Modulation of gene expression through chromosomal positioning in Escherichia coli . Microbiology 143:20712078.
129. Straus, D. S. 1975. Selection for a large genetic duplication in Salmonella typhimurium . Genetics 80:227237.
130. Straus, D. S.,, and L. D. Straus. 1976. Large overlapping duplications in Salmonella typhimurium . J. Mol Biol. 103:143153.
131. Streissinger, G. 1985. Mechanisms of spontaneous and induced frameshift mutations. Genetics 109:633659.
132. Szostak, J. W.,, T. Orr-Weaver,, R. J. Rothstein,, and F. W. Stahl. 1983. The double-strand-break repair model for recombination. Cell 33:2535.
133. Tecklenburg, M.,, A. Naumer,, A. Nagappan,, and P. Kuempel. 1995. The difresolvase locus of the Escherichia coli chromosome can be replaced by a 33-bp sequence, but function depends on location. Proc. Natl. Acad. Sci. USA 92:13521356.
134. Tlsty, T. D.,, A. M. Albertini,, and J. H. Miller. 1984. Gene amplification in the lac region of E. coli . Cell 37:217224.
135. Trinh, T. Q.,, and R. R. Sinden. 1993. The influence of primary and secondary DNA structure in deletion and duplication between direct repeats in Escherichia coli . Genetics 134:409422.
136. Watt, V. M.,, C. J. Ingles,, M. S. Urdea,, and W. J. Rutter. 1985. Homology requirements for recombination in Escherichia coli . Proc. Natl. Acad. Sci. USA 82:47684772.
137. Whoriskey, S. K.,, V. H. Nghiem,, P. M. Leong,, J. M. Masson,, and J. H. Miller. 1987. Genetic rearrangements and gene amplification in Escherichia coli: DNA sequences at the junctures of amplified gene fusions. Genes Dev. 1:227237.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error