Abstract
Homologous recombination events between circular chromosomes, occurring during or after replication, can generate dimers that need to be converted to monomers prior to their segregation at cell division. In Escherichia coli, chromosome dimers are converted to monomers by two paralogous site-specific tyrosine recombinases of the Xer family (XerC/D). The Xer recombinases act at a specific dif site located in the replication termination region, assisted by the cell division protein FtsK. This chromosome resolution system has been predicted in most Bacteria and further characterized for some species. Archaea have circular chromosomes and an active homologous recombination system and should therefore resolve chromosome dimers. Most archaea harbour a single homologue of bacterial XerC/D proteins (XerA), but not of FtsK. Therefore, the role of XerA in chromosome resolution was unclear. Here, we have identified dif-like sites in archaeal genomes by using a combination of modeling and comparative genomics approaches. These sites are systematically located in replication termination regions. We validated our in silico prediction by showing that the XerA protein of Pyrococcus abyssi specifically recombines plasmids containing the predicted dif site in vitro. In contrast to the bacterial system, XerA can recombine dif sites in the absence of protein partners. Whereas Archaea and Bacteria use a completely different set of proteins for chromosome replication, our data strongly suggest that XerA is most likely used for chromosome resolution in Archaea.
Highlights
In Bacteria, homologous recombination is essential during DNA replication to resume stalled replication forks and to repair DNA double and single strand breaks
Homologues of XerCD are widespread in the bacterial domain, and dif sites have been characterized in several Proteobacteria and Firmicutes [5,6,7,8,9,10]. dif sites are semi-conservative inverted repeats formed by two arms (Xer protein binding sites) of 11 base pairs [11], separated by a spacer of 6 bp and are fairly conserved among Bacteria [5]
The recombination event is tightly regulated by the chromosome translocase FtsK. This chromosome resolution system has been predicted in most bacteria and further characterized for some species
Summary
In Bacteria, homologous recombination is essential during DNA replication to resume stalled replication forks and to repair DNA double and single strand breaks. In several Lactococcus and Streptococcus strains, the canonical bacterial XerCD-dif system has been replaced by a single tyrosine recombinase, XerS (distantly related to XerCD) whose gene is located next to its specific dif-like site and localized at the terminus of replication [22]. This XerS-dif-like system still depends on the KOPS-oriented FtsK activity to form the synaptic complex for recombination [22]
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