ORIGINAL PAPER Abstract In eubacteria, the recA gene has long been rec- ognized as essential for homologous recombination and DNA repair. Recent work has identified recA homologs in archaebacteria and eukaryotes, thus emphasizing the uni- versal role this gene plays in DNA metabolism. We have isolated and characterized two new recA homologs, one from the basidiomycete Coprinus cinereus and the other from the angiosperm Lycopersicon esculentum. Like the RAD51 gene of Saccharomyces cerevisiae, the Coprinus gene is highly induced by gamma irradiation and during meiosis. Phylogenetic analyses of eukarotic recA homo- logs reveal a gene duplication early in eukaryotic evolu- tion which gave rise to two putatively monophyletic groups of recA-like genes. One group of 11 characterized genes, designated the rad51 group, is orthologous to the Saccha- romyces RAD51 gene and also contains the Coprinus and Lycopersicon genes. The other group of seven genes, des- ignated the dmc1 group, is orthologous to the Saccharo- myces DMC1 gene. Sequence comparisons and phyloge- netic analysis reveal extensive lineage- and gene-specific differences in rates of RecA protein evolution. Dmc1 con- sistently evolves faster than Rad51, and fungal proteins of both types, especially those of Saccharomyces, change rap- idly, particularly in comparison to the slowly evolving ver- tebrate proteins. The Drosophila Rad51 protein has under- gone remarkably rapid sequence divergence. Key words Coprinus cinereus · Lycopersicon esculentum · RAD51 homologs · Gene duplication · Unequal evolutionary rates · Molecular phylogeny Introduction The recA gene of Escherichia coli is necessary for homol- ogous recombination and DNA repair (West 1992; Clark and Sandler 1994; Camerini-Otero and Hsieh 1995). Bio- chemical studies have shown that the RecA protein pro- motes identification and exchange of regions of homology (for reviews see Roca and Cox 1990; Kowalczykowski 1991; Clark and Sandler 1994; Camerini-Otero and Hsieh 1995), and the RecA protein is also central to the bacterial recombinational DNA-repair system, which responds to DNA damage (Cox 1993). recA genes have been isolated and studied from a large number (>65) of diverse eubac- teria (Eisen 1995) and, recently, from three diverse archae- bacteria (Sandler et al. 1996). In the last few years, multi- ple recA-like genes have been sequenced from several an- imals, fungi, and plants (for references, see Materials and methods). In Saccharomyces cerevisiae four recA homology have been identified. Three of these genes, RAD51, RAD55 and RAD57, belong to the RAD52 epistasis group for DNA re- pair. All three of these genes are involved in recombina- tion and recombinational repair (Game 1993); mutants in these genes are sensitive to DNA-damaging agents such as methyl methanesulfonate and ionizing radiation, and are defective in meiosis. The fourth recA homolog of Saccha- romyces, DMC1, is required for meiosis, but does not ap- pear to be involved in DNA repair (Bishop et al. 1992). The Rad51 protein can form a helical filament on both sin- gle- and double-stranded DNA, although the polarity of this filament is opposite to that formed by recA (Ogawa et al. 1993a; Sung and Robberson 1995). Also, like RecA, the Rad51 protein can catalyze homologous DNA pairing and strand exchange in an ATP-dependent manner (Sung 1994). The RAD51 transcript is inducible during meiosis Curr Genet (1997) 31: 144–157 © Springer-Verlag 1997 Received: 20 July / 25 October 1996 Natalie Yeager Stassen · John M. Logsdon Jr Gaurav J. Vora · Hildo H. Offenberg Jeffrey D. Palmer · Miriam E. Zolan Isolation and characterization of rad51 orthologs from Coprinus cinereus and Lycopersicon esculentum, and phylogenetic analysis of eukaryotic recA homologs ORIGINAL PAPER N. Y. Stassen · J. M. Logsdon Jr. 1 · G. J. Vora 2 · J. D. Palmer M. E. Zolan () Department of Biology, Indiana University, Bloomington, IN 47405, USA H. H. Offenberg Department of Genetics, Agricultural University, Wageningen, The Netherlands Present addresses: 1 Department of Biochemistry, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada 2 Department of Microbiology, University of Massachussetts, Am- herst, MA 01003, USA Communicated by B. G. Turgeon