Chapter category: Evolution
Early Evolution of DNA Repair Mechanisms
The Genetic Code and the Origin of Life
Edited by: Lluis Ribas de PouplanaISBN: 0-306-47843-9
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Chapter authors:
Jocelyne DiRuggiero and Frank T. Robb
DNA repair is critical for the maintenance of genome integrity and replication fidelity in all cells, and therefore was arguably of major importance in the Last Universal Cellular Ancestor (LUCA) as well. Archaea, and hyperthermophiles in particular, are well suited for studying early DNA repair mechanisms from two perspectives. First, these prokaryotes embody a mix of bacterial and eukaryal molecular features. Second, DNA in many archaea is subject to ongoing damage during normal growth under extreme conditions such as high temperature or low pH. Third, recent work suggests that the mutation rates of model hyperthermophiles are quite close to norms for bacteria, indicating that their replication/repair processes are operating with high fidelity at elevated temperatures. The Archaea also have minimal sets of genes involved in all of the major cellular information transfer processes, compared with Eukarya, which have highly paralogous and redundant sets of genes for DNA replication, repair and recombination. Repair activities have been demonstrated for several hyperthermophiles including our studies with Pyrococcus furiosus, an archaeon growing optimally at 100°C. In addition, using comparative genomic analysis and the genome sequence of several hyperthermophilic archaea, homologs of conserved eukaryotic and bacterial DNA repair proteins have been identified. Although close to 100 microbial genome sequences have been analyzed, including 16 from the Archaea, so far many highly conserved repair genes are missing in some or in all of the archaeal genomes. This may be the result of low sequence conservation across the three domains of life, preventing identification using sequence similarity searches. It is possible, and proven in some instances, that Archaea have novel versions of repair proteins. Here we argue that the commonality of mechanisms and protein sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflects diversification from a minimal set of genes. However, for several pathways, the close similarity between components of eukaryal and archaeal repair pathways suggests that those specific processes likely evolved independently in the bacterial and archaeal/eukaryal lineages.
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