posted 24. March 2004 12:19                   

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Abstract:
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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A detailed analysis of protein domains involved in DNA repair was performed by comparing the sequences of the repair proteins from two well-studied model organisms, the bacterium Escherichia coli and yeast Saccharomyces cerevisiae, to the entire sets of protein sequences encoded in completely sequenced genomes of bacteria, archaea and eukaryotes. Previously uncharacterized conserved domains involved in repair were identified, namely four families of nucleases and a family of eukaryotic repair proteins related to the proliferating cell nuclear antigen. In addition, a number of previously undetected occurrences of known conserved domains were detected; for example, a modified helix-hairpin-helix nucleic acid-binding domain in archaeal and eukaryotic RecA homologs. There is a limited repertoire of conserved domains, primarily ATPases and nucleases, nucleic acid-binding domains and adaptor (protein-protein interaction) domains that comprise the repair machinery in all cells, but very few of the repair proteins are represented by orthologs with conserved domain architecture across the three superkingdoms of life. Both the external environment of an organism and the internal environment of the cell, such as the chromatin superstructure in eukaryotes, seem to have a profound effect on the layout of the repair systems. Another factor that apparently has made a major contribution to the composition of the repair machinery is horizontal gene transfer, particularly the invasion of eukaryotic genomes by organellar genes, but also a number of likely transfer events between bacteria and archaea. Several additional general trends in the evolution of repair proteins were noticed; in particular, multiple, independent fusions of helicase and nuclease domains, and independent inactivation of enzymatic domains that apparently retain adaptor or regulatory functions.

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Abstract
It is now generally accepted that the Archaea share many similarities in their information-processing pathways with eukarya. Archaeal and eukaryal DNA replication and transcriptional machineries show particularly striking similarities, and the archaeal processes have been used extensively as simpler models
of the much more complex eukaryal ones. Archaeal DNA-repair pathways are not yet well characterized, and their relationship with repair pathways in bacteria and eukarya are still open to question. There are also strong distinctions between the major subdivisions crenarchaea and euryarchaea within the archaeal domain. This review highlights some of these similarities and differences using specific examples arising from our studies of the double-stranded and single-stranded DNA-binding proteins and the repair endonuclease XPF in the crenarchaeote Sulfolobus solfataricus.

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Ionizing radiation, chemicals, and other agents can result in genetic damage, which, if not repaired, can lead to diseases such as cancer. Fortunately, a system of genes directs the production of sensitive DNA repair enzymes, which monitor for genetic damage and fix most errors. The role of DNA repair processes in fixing genetic damage, as well as the role of genetically impaired repair mechanisms in cancer, were first discovered by investigators funded by predecessors to the Office of Science in the 1960s. More recently at Lawrence Livermore, Los Alamos, and Lawrence Berkeley national laboratories, researchers have cloned and studied a number of crucial DNA repair genes. A clear picture is emerging that unrepaired DNA damage is the culprit in the long-term consequences of radiation exposure. Scientists now see that X-rays, ultraviolet light, and cancer-causing chemicals work in similar ways in disabling the natural DNA repair mechanisms. A team at Lawrence Berkeley demonstrated a strong correlation between the inability to repair oxidative damage to DNA and severe developmental failure and early death in a hereditary condition called Cockayne's syndrome.

Scientific Impact: Research on DNA repair helps scientists better understand biological processes, from the microscale (e.g., cell death) to the macroscale (e.g., evolution). So central is the role of DNA repair that in 1994, Science magazine designated the entire class of DNA repair enzymes as "Molecule of the Year."

Social Impact: By explaining how DNA repair processes can go awry, scientists contribute to sound policymaking on environmental hazards. This research also could lead to medical and pharmaceutical treatments for repair-deficiency disorders, implicated in conditions ranging from cancer to aging.

Reference: R.D. Wood, M. Mitchell, J. Sgouros, T. Lindahl, "Human DNA Repair Genes," Science 291 (2001) 1284-1289.

L.H. Thompson, D. Schild, "The contribution of homologous recombination in preserving genome integrity in mammalian cells," Biochimie (1999) 87-105.

M. Takata, M.S. Sasaki, S. Tachiiri, T. Fukushima, E. Sonoda, D. Schild, L.H. Thompson, S. Takeda, "Chromosome instability and defective recombinational repair in knockout mutants of the five Rad51 paralogs," Mol. Cell. Biol. 21 (2001) 2858-2866.

Le Page, F., Kwoh, E.E., Avrutskaya, A., Gentil, A., Leadon, S.A., Sarasin, A., and Cooper, P.K. "Transcription-Coupled Repair of 8-oxoGuanine: Requirement for XPG, TFIIH, and CSB and Implications for Cockayne Syndrome," Cell 101, 159-171 (2000).

Brenneman, M. A., A. E. Weiss, J. A. Nickoloff and D. J. Chen, "XRCC3 is Required for efficient repair of chromosome break by homologous recombination," DNA Repair Mutat Res 20;459(2):89-97 (2000).

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