Diversity of <i>radA</i> Genes from Cultured and Uncultured <i>Archaea</i> : Comparative Analysis of Putative RadA Proteins and Their Use as a Phylogenetic Marker

<jats:title>ABSTRACT</jats:title> <jats:p> <jats:italic>Archaea</jats:italic> -specific <jats:italic>radA</jats:italic> primers were used with PCR to amplify fragments of <jats:italic>radA</jats:italic> genes from 11 cultivated archaeal species and one marine sponge tissue sample that contained essentially an archaeal monoculture. The amino acid sequences encoded by the PCR fragments, three RadA protein sequences previously published (21), and two new complete RadA sequences were aligned with representative bacterial RecA proteins and eucaryal Rad51 and Dmc1 proteins. The alignment supported the existence of four insertions and one deletion in the archaeal and eucaryal sequences relative to the bacterial sequences. The sizes of three of the insertions were found to have taxonomic and phylogenetic significance. Comparative analysis of the RadA sequences, omitting amino acids in the insertions and deletions, shows a cladal distribution of species which mimics to a large extent that obtained by a similar analysis of archaeal 16S rRNA sequences. The PCR technique also was used to amplify fragments of 15 <jats:italic>radA</jats:italic> genes from uncultured natural sources. Phylogenetic analysis of the amino acid sequences encoded by these fragments reveals several clades with affinity, sometimes only distant, to the putative RadA proteins of several species of <jats:italic>Crenarcheota</jats:italic> . The two most deeply branching archaeal <jats:italic>radA</jats:italic> genes found had some amino acid deletion and insertion patterns characteristic of bacterial <jats:italic>recA</jats:italic> genes. Possible explanations are discussed. Finally, signature codons are presented to distinguish among RecA protein family members. </jats:p>