Mobile element integration reveals a chromosome dimer resolution system in Legionellales

Abstract

In bacteria, the mechanisms used to repair DNA lesions during genome replication include homologous recombination between sister chromosomes. This can lead to the formation of chromosome dimers if an odd number of crossover events occurs. The concatenated DNA must be resolved before cell separation to ensure genomic stability and cell viability. The broadly conserved dif/Xer system counteracts the formation of dimers by catalyzing one additional crossover event immediately prior to cell separation. While dif/Xer systems have been characterized or predicted in the vast majority of proteobacteria, no homologs to dif or xer have been identified in the order Legionellales. Here we report the discovery of a distinct dif/Xer system in the intracellular pathogen Legionella pneumophila. The dif site was uncovered by our analysis of Legionella mobile element-1 (LME-1), which harbors a dif site-mimic and integrates into the L. pneumophila genome via site-specific recombination. We demonstrate that lpg1867 (herein named xerL) encodes a tyrosine recombinase that is necessary and sufficient for catalyzing recombination at the dif site, and that deletion of dif or xerL causes filamentation and slow growth phenotypes. In addition, our data show that LME-1 can be classified as an integrative mobile element exploiting Xer (IMEX). The identification of LME-1 as an IMEX of Legionella's atypical dif/Xer system further highlights the extent to which diverse mobile elements have independently evolved to exploit this critical cellular machinery.