Impact of Homologous Recombination on Genome Organization and Stability

Diarmaid Hughes

doi:10.1128/9781555818180.ch7

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

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Affiliations: 1: Department of Molecular Biology, Box 590, The Biomédical Center, Uppsala University, S-751 24 Uppsala, Sweden

Content Type: Monograph

Publication Year: 1999

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555818180

Chapter DOI: 10.1128/9781555818180.ch7

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Abstract:

This chapter talks about bacterial genomes, primarily those of Escherichia coli and Salmonella typhimurium (proper name, Salmonella enterica serovar Typhimurium). For these bacteria, abundant information is available on evolutionary relationships, high-quality genetic maps exist (E. coli is completely sequenced), and there is extensive knowledge of mechanisms of recombination. Comparing the genomes of E. coli and S. typhimurium 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 recA 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 E. coli and S. typhimurium are reported as having no significant effects on growth rate, but the few translocations made and tested in E. coli 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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Impact of Homologous Recombination on Genome Organization and Stability

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FIGURE 1

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

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FIGURE 1

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FIGURE 2

Linear map of the E. coli chromosome opened at the origin of DNA replication. E. coli map positions (approximately equivalent in S. typhimurium) are shown above the line, and the positions of Ter sites (E, D, A, C, B, F, and G) and dif 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 105 . The his operon position is shown on the line to facilitate comparison with the results from S. typhimurium shown below the line. The solid bars indicate permissive inversion intervals, and the dashed lines indicate nonpermissive inversion intervals for S. typhimurium. This is a representative sample of the data from reference 120 . Note that there is currently no experimental evidence that S. typhimurium has the same organization of dif and Ter sites as E. coli.

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FIGURE 2

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FIGURE 3

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

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FIGURE 3

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