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Chapter 12 : Genome Architecture and Evolution of Bacterial Pathogens

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Abstract:

Bacterial genomes are usually packed with genes occupying around 90% of their DNA, and no structures resembling isochores or telomeres have been identified. A second source of heterogeneity could come from structural domains in the genome, which would make some areas of the chromosome more accessible than others to foreign DNA sequences and influence intrachromosomal recombination. With the advent of genomic data and the improvement of methods for replication origin and terminus detection, it is now possible to review the genome balance hypothesis. The mutation probability has been proposed to vary within a bacterial chromosome for genes located at different positions relative to the replication origin. Electron micrographs of the Escherichia coli chromosome displayed a rossette-like organization with loops of supercoiled DNA distributed around a central node. Species such as Staphylococcus aureus and E. coli display an increase in horizontally acquired genes closer to the terminus, whereas transposable elements seem unaffected. Sequence repeats, in all their variants, are one of the main evolutionary tools to generate variability, this being structural (rearrangements) or functional (generation of new genes). The plethora of genomic data has unexpectedly suggested that the traditional view of IS Elements (ISs) as detrimental selfish elements is probably an oversimplification. In relation to bacterial pathogens, the data suggest that their genomes are more flexible than related nonpathogenic species, as if their need for fast adaptation and plasticity had relaxed organizational constraints.

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12
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Figures

Image of Figure 1.
Figure 1.

Expression and location. Putative expression level, measured as the Codon Adaptation Index (Sharp and Li, 1987) and chromosomal location of E. coli O157 genes. Many genes of predicted high and low expression levels appear clustered in some areas or domains.

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12
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Image of Figure 2.
Figure 2.

Location of paralogous sequences. (a) Distance between paralogous genes in Clostridium acetubutylicum. Gene pairs with high sequence similarity are closely located. (b) Genomic distance of paralogous genes in Mycoplasma gallisepticum. Vertical patterns appear, showing gradients of sequence similarity among clustered genes.

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12
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Tables

Generic image for table
Table 1.

Genome balance across bacterial taxa

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12
Generic image for table
Table 2.

Density of antibiotic-resistance genes in chromosomes and plasmids c

Citation: Mira A, Pushker R. 2008. Genome Architecture and Evolution of Bacterial Pathogens, p 115-127. In Baquero F, Nombela C, Cassell G, Gutiérrez-Fuentes J (ed), Evolutionary Biology of Bacterial and Fungal Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555815639.ch12

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