Orientation specificity of the Lactococcus lactis Chi site

Background: In Escherichia coli, the Chi sequence modulates the activity of RecBCD, a powerful double-stranded (ds) DNA exonuclease/helicase. Chi attenuates RecBCD exonuclease activity and stimulates homologous recombination in an orientation-dependent manner. Chi(Ec) is frequent and overrepresented on its genome, which is thought to be related to its role in dsDNA break repair. We previously identified a Chi-like sequence (referred to as Chi(L1)) and an exonuclease/helicase in the Grampositive bacterium Lactococcus lactis. Chi(L1) and RexAB are functional analogues of Chi(Ec) and RecBCD. Results: We report that Chi(L1) attenuates RexAB exonuclease activity and stimulates homologous recombination in an orientation-dependent manner. Analysis of Chi(L1) distribution on the L. lactis chromosome reveals that Chi(L1) is frequent, highly over-represented, and oriented with respect to the direction of replication. Conclusion: Our results show that a single orientation of Chi(L1) interacts with RexAB. The active orientation is preferentially found on the replication leading strand of the L. lactis genome, consistent with a primary role of Chi(L1) in repair of dsDNA breaks at the replication fork. We propose that orientation-dependence of Chi activity and overrepresentation of Chi sequences on bacterial genomes may be conserved properties of exonuclease/helicase-Chi couples. Other properties of the Chi sequence distribution on the genomes might reflect more specific characteristics of each couple and of the host.