DNA repair systems in Archaea: Mementos from the last universal common ancestor?

DNA repair in the Archaea is relevant to the consideration of genome mainte nance and replication fidelity in the last universal common ancestor (LUCA) from two perspectives. First, these prokaryotes embody a mix of bacterial and eukaryal molecular features. Second, DNA repair proteins would have bee n essential in LUCA to maintain genome integrity, regardless of the environ mental temperature. Yet we know very little of the basic molecular mechanis ms of DNA damage and repair in the Archaea in general. Many studies on DNA repair in archaea have been conducted with hyperthermophiles because of the additional stress imposed on their macromolecules by high temperatures. In addition, of the six complete archaeal genome sequences published so far, five are thermophilic archaea. We have recently shown that the hyperthermop hile Pyrococcus furiosus has an extraordinarily high capacity for repair of radiation-induced double-strand breaks and we have identified and sequence d several genes involved in DNA repair in P. furiosus. At the sequence leve l, only a few genes share homology with known bacterial repair genes. For i nstance, our phylogenetic analysis indicates that archaeal recombinases occ ur in two paralogous gene families, one of which is very deeply branched, a nd both recombinases are more closely related to the eukaryotic RAD51 and D mc1 gene families than to the Escherichia a repair endo/exonuclease in the genomes of several Archaea. The archaeal sequences are highly homologous to those of the eukaryotic Rad:! family and they cluster with genes of the FE N-1 subfamily, which are known to be involved in DNA replication and repair in eukaryotes. We argue that there is a commonality of mechanisms and prot ein sequences, shared between prokaryotes and eukaryotes for several modes of DNA repair, reflecting diversification from a minimal set of genes thoug ht to represent the genome of the LUCA.