Evidence for a Xer/dif system for chromosome resolution in archaea.
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.
Cortez
Diego
D
Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Paris, France.
Quevillon-Cheruel
Sophie
S
Gribaldo
Simonetta
S
Desnoues
Nicole
N
Sezonov
Guennadi
G
Forterre
Patrick
P
Serre
Marie-Claude
MC
D000595:Amino Acid Sequence; D001105:Archaea / Q000201:enzymology / Q000235:genetics*; D019843:Archaeal Proteins / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D019847:Chromosomes, Archaeal / Q000235:genetics*; D003001:Cloning, Molecular; D004254:DNA Nucleotidyltransferases / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D004261:DNA Replication; D019641:DNA, Archaeal / Q000235:genetics / Q000378:metabolism; D004270:DNA, Circular / Q000235:genetics / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D008969:Molecular Sequence Data; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics; D011485:Protein Binding; D043903:Pyrococcus abyssi / Q000201:enzymology / Q000235:genetics; D011995:Recombination, Genetic; D017386:Sequence Homology, Amino Acid
D019843:Archaeal Proteins; D019641:DNA, Archaeal; D004270:DNA, Circular; D004254:DNA Nucleotidyltransferases; C077570:Site-specific recombinase