A feature of all homologous recombination reactions is the requirement for a ssDNA intermediate to base pair with the complementary strand in the process. In oligo recombination the donor molecule is introduced in the single-stranded form and obviates the requirement for initial processing to expose single-stranded regions. The involvement of DNA replication is suggested by the result that oligos matching the lagging strand of replicated DNA recombine at a higher frequency than oligos matching the leading strand. This strand bias was observed in both P. syringae and E. coli (also in S. typhimurium and S. flexneri, data not shown). One hypothesis is that the transformed oligos are able to hybridize with single-stranded regions made accessible during DNA replication. Because of the conservation of the DNA replication process it would not be surprising if oligos could find access to ssDNA using the same mechanism in other organisms. Consistent with this idea, we found that oligo recombination could be detected in all four of the species tested here.
There is evidence that oligo recombination exists in organisms beyond bacteria. In the late 1980s, Fred Sherman and co-workers found that recombinants could be generated in Saccharomyces cerevisiae transformed with synthetic oligos encoding point mutations that confer a selectable phenotype (Moerschell et al., 1988). This discovery prompted the authors to consider that it would be interesting to investigate whether prokaryotes also had the capability to undergo recombination with synthetic oligos introduced directly by transformation. There are several striking similarities in the details of yeast and bacterial oligo recombination. First, in yeast, carrier DNA also increased the frequency of recombination (Yamamoto et al., 1992a). The authors speculated that carrier enhanced recombination rates by saturating endogenous nucleases. This explanation is also plausible in bacteria, where deletion of genes encoding ssDNA nucleases xonA and recJ boost oligo recombination rates in E. coli (Dutra et al., 2007). Furthermore, the addition of carrier DNA can also enhance the frequency of lambda Red-catalysed oligo recombination in E. coli (J.A. Sawitzke, N. Costantino, X.T. Li and D.L. Court, in preparation). Deletion of exonuclease genes also increases recombination and, consistent with its role in titrating exonucleases, carrier does not further increase the recombination frequency in exonuclease-deficient strains (J.A. Sawitzke, N. Costantino, X.T. Li and D.L. Court, in preparation). Second, in yeast, the number of mismatches and the specific mismatches in oligos encoding di-nucleotide changes affected the recombination rates (Yamamoto et al., 1992a). This is reminiscent of our observations of oligo recombination in bacteria where the ability of the MMR system to recognize specific mismatches influences the recombination rates of oligos with different sequences (Table 3). Third, the strand bias was also present in yeast, with one strand consistently generating more recombinants than its complement. At the time, the authors proposed that this was likely due to differences in the preference for leading or lagging strand oligos to incorporate during DNA replication (Yamamoto et al., 1992b). Finally in both yeast and bacteria an endogenous recombinase that directly facilitates oligo recombination has not been identified. S. cerevisiae encodes a Beta-like protein, Rad52, but it was found not to affect oligo recombination (Yamamoto et al., 1992a). Since the initial discovery of oligo recombination in yeast, similar evidence for oligo recombination in archaea (Grogan and Stengel, 2008) and mammalian cells (Campbell et al., 1989) has also been obtained. Even though the mechanistic details of oligo recombination in eukaryotes, archaea and bacteria have not been elucidated these similarities prompt us to speculate that this process is evolutionarily conserved across biological kingdoms.