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Chapter 3 : Bacterial Genomes—All Shapes and Sizes

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Abstract:

This chapter summarizes the recent findings of bacterial genomics and comments on the themes and trends which are emerging. A variety of techniques and methods are available to construct physical maps, and those most commonly employed involve pulsed field gel electrophoresis (PFGE) of macrorestriction fragments generated by digesting intact genomic DNA, immobilized in agarose plugs, with rare-cutting enzymes. Hybridization techniques are often used to construct a map and to deduce the positions of genetic markers. In recent years significant effort has been devoted to developing direct-mapping techniques for large DNA molecules that do not require gel electrophoresis. Among the more promising of these are two new methods known as DNA combing and optical mapping, both of which make use of fluorescence microscopy and image analysis to visualize single DNA molecules. Overall, bacterial genomes range in size from about 0.6 to 9.4 Mb. In a recent review, it was suggested that there may be a relationship between the genome sizes and the lifestyles of bacteria. The genome size of strains varies from 5.5 to 6.3 Mb, and great diversity is seen in the number and organization of the chromosomes. Higher levels of gene expression might result from altered topological constraints acting on the DNA or from a more favorable location with respect to the origin of replication, leading to an increase in gene dosage.

Citation: Cole S, Saint-Girons I. 1999. Bacterial Genomes—All Shapes and Sizes, p 35-62. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch3

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Tables

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TABLE 1

Physical and genetic maps from purple bacteria

Citation: Cole S, Saint-Girons I. 1999. Bacterial Genomes—All Shapes and Sizes, p 35-62. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch3
Generic image for table
TABLE 2

Physical and genetic maps from gram-positive bacteria

Citation: Cole S, Saint-Girons I. 1999. Bacterial Genomes—All Shapes and Sizes, p 35-62. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch3
Generic image for table
TABLE 3

Physical and genetic maps from other bacteria: chlamydia, cyanobacteria, green sulfur bacteria, planctomycetes, and spirochetes

Citation: Cole S, Saint-Girons I. 1999. Bacterial Genomes—All Shapes and Sizes, p 35-62. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch3
Generic image for table
TABLE 4

TABLE 4 Physical and genetic maps from archaea

Citation: Cole S, Sain