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

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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
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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
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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
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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
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