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Chapter 1 : Where's the Beef? Looking for Information in Bacterial Chromosomes

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Abstract:

The challenge to those trying to explain chromosome behavior is to identify the critical sequence elements. One might expect that a genome would be under constant selective pressure to expand, adding new genes that broaden the capabilities of the organism. Three aspects of population biology and lifestyle limit this expansion: mutation rate, population size, and recombination frequency. First, if all other factors remain constant, mutation rate limits genome size; beyond a critical point, the genome can expand only if the mutation rate drops. Second, larger populations allow genome expansion because selection is more effective and genes with a smaller fitness contribution can be maintained. Third, sexual recombination allows genome expansion by permitting assembly of intact information sets from those damaged by mutation. Selfish mechanisms used by phage, transposons, and plasmids can also contribute to maintenance of genes that are respectable chromosome residents. The chapter describes some genome features that depend to varying extents on their selfish behavior for their maintenance in the genome. These assumptions can be used in reverse to draw conclusions regarding the fitness contribution of genes based on their genomic position. Two short sequence elements have been extensively studied with regard to their effects on chromosome replication (Ter) and recombination (Chi). In and , the positions and orientation of seven repeated rRNA operons are conserved. Several small sequence elements are found in the genome of .

Citation: Roth J. 2005. Where's the Beef? Looking for Information in Bacterial Chromosomes, p 3-18. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch1

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Gene Expression and Regulation
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Genetic Elements
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Horizontal Gene Transfer
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Figures

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Figure 1.

A proposal for the role of Chi and Ter sites in managing recombinational replication. (Left) Diagram of a double-strand break and the positions of nearby Chi sequences in their predominant orientation. The left end is likely to be promptly activated for recombination and lead to a fork moving toward the terminus. The right end is likely to be extensively degraded before engaging in recombination and could form a fork moving toward the origin. (Right) Diagram of the possible outcomes if the two broken ends establish independent recombinational forks. Depending on the timing of fork initiation, the two forks may diverge, or converge, or one end may be destroyed, leaving a single fork. Forks bound toward the origin might be terminated at Ter sites before converging with approaching replication forks. The concerted action of Chi and Ter might act to minimize fork collision and preferentially direct all recombinational replication toward the terminus.

Citation: Roth J. 2005. Where's the Beef? Looking for Information in Bacterial Chromosomes, p 3-18. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch1
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Tables

Generic image for table
Table 1.

Genetic elements listed in order of decreasing fitness contribution (and increasing selfish behavior)

Citation: Roth J. 2005. Where's the Beef? Looking for Information in Bacterial Chromosomes, p 3-18. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch1

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