Recombination and modular exchange in the genesis of new lambdoid phages

Comparison of the nucleotide sequence of the integrase genes of lambdoid phages 21 and 434 with the published sequences of phages HK022 and lambda shows that lambda and 434 are very closely related (98% base sequence identity), whereas HK022 and 21 respectively show 73% and 48% identity to lambda. It is likely that several homologous recombination events occurred in the int gene and flanking DNA among the progenitors of these phages. Sequence divergence to different alternative sequences at a common site (tL4) suggests that tL4 has been repeatedly used as a recombination site, despite the very limited homology it provides. A minor constitutive transcript that terminates at tL4 of lambda has been identified. We propose that the principal selective force acting to conserve tL4 is for terminator function, but that the use of tL4 as a recombination site has allowed the formation of selectively favored recombinants. By extension, we suggest that conservation of microhomologies at functional sites serves to keep lambdoid phages within a common gene pool despite extensive drift and divergence.