Evolution of Eukaryotic Specific DNA Binding Sites in Asgard Archaeal RecA Recombinases

RecA-type recombinases are essential for genome maintenance in all domains of life, promoting homologous recombination (HR). While the general reaction catalyzed by recombinases is the same in all domains, key differences at the amino acid level can lead to the specialization of this family of proteins. A key example of this is in the domain of Eukarya, which can utilize two different RecA homologs depending on the life cycle stage of the organism, with the activity of Rad51 utilized during mitotic growth and the activity of Dmc1 used during meiosis. Why most eukaryotes utilize two RecA homologs is an open question. A missing piece of information in this story is the identity of RecA homologs before the divergence of Rad51 and Dmc1, which occurred in early eukaryotes. We analyzed sequence data from the Archaeal homolog, RadA, in the Asgard Archaea superphyla. Our findings include evidence for the evolution of a eukaryotic-specific DNA binding site II within the Asgard lineage. We also identify sequence variants within DNA binding loops L1 and L2, part of binding site I, that imply higher mismatch tolerance within the Asgard and DPANN superphylum. These loops are also observed in the meiosis-specific recombinase Dmc1 within Eukarya. Our phylogenetic analysis suggests the last Archaeal ancestor of Rad51 and Dmc1 was more Dmc1-like in character and likely of lower fidelity.