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Chapter 5 : Mechanisms of Genome Stability and Evolution

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Abstract:

This chapter examines the ‘’natural genetics’’ of methanogenic, halophilic, and thermophilic archaea, progressing from the molecular scale to cells and finally to populations. The simplest reconciliation of observations would seem to be that the thermophilic and hyperthermophilic archaea have alternative molecular strategies that assume the function of classical MMR and NER systems but do not involve homologous proteins. In its most general sense, genetic recombination means the creation of new DNA sequences from existing sequences by processes involving strand exchange rather than error-prone synthesis. ‘’Illegitimate’’ recombination breaks and joins DNA sequences with negligible influence of the sequences involved. Limited migration elevates the importance of mutation and recombination in the evolution of natural populations. Testing hypothesis that archaea, or major archaeal groups will involve measuring molecular processes central to the survival, reproduction, and evolution of archaea and to the development of experimental tools for establishing gene function at the molecular level. Compared with bacteria and unicellular eucarya, archaea that have been analyzed in genetic terms have rather low rates of neutral mutation and high rates of recombination. This combination of properties would seem ideal for evolutionary adaptation. Combining computational genetic analyses of natural populations with experimental analyses of cultured archaea will help clarify how molecular mechanisms of archaea determine genetic properties and how genetic properties of archaea affect genome stability and evolution.

Citation: Grogan D. 2007. Mechanisms of Genome Stability and Evolution , p 120-138. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch5

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Bacteria and Archaea
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Genetic Recombination
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DNA Synthesis
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Genetic Elements
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Holliday Junction Resolvase
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Figures

Image of Figure 1.
Figure 1.

The five processes that drive genetic change in natural populations. Each horizontal line represents a distinct genotype (i.e., genome sequence) present in a hypothetical population of a microbial species as a function of time. New genotypes arise in this population by mutation, immigration from other populations, and recombination. Conversely, genotypes are eliminated randomly by drift, or according to functional properties determined by particular alleles, by selection. As a result of these natural processes, the genetic composition of the population changes irreversibly over time. For a comprehensive discussion, see Ridley ( ).

Citation: Grogan D. 2007. Mechanisms of Genome Stability and Evolution , p 120-138. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch5
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Image of Figure 2.
Figure 2.

Molecular strategies for coping with DNA damage. Schematic summary of the molecular events associated with damage reversal, damage excision, and damage tolerance. Abbreviations: AT, alkyl transfer; PR, photoreactivation; BER, base excision repair; NER, nucleotide excision repair; MMR, mismatch repair; TLS, -lesion synthesis; HR, homologous recombination. Some of the processes (HR, in particular) are shown greatly simplified; for comprehensive review, see Friedberg et al. ( ).

Citation: Grogan D. 2007. Mechanisms of Genome Stability and Evolution , p 120-138. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch5
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Tables

Generic image for table
Table 1.

Comparison of mutational spectra across the three domains

Citation: Grogan D. 2007. Mechanisms of Genome Stability and Evolution , p 120-138. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch5
Generic image for table
Table 2.

Representation of major DNA repair pathways in microbial genomes

Citation: Grogan D. 2007. Mechanisms of Genome Stability and Evolution , p 120-138. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch5
Generic image for table
Table 3.

Distinct types of genetic recombination

Citation: Grogan D. 2007. Mechanisms of Genome Stability and Evolution , p 120-138. In Cavicchioli R (ed), Archaea. ASM Press, Washington, DC. doi: 10.1128/9781555815516.ch5

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