Distribution of Centromere-LikeparSSites in Bacteria: Insights from Comparative Genomics

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Abstract
Partitioning of low-copy-number plasmids to daughter cells often depends on ParA and ParB proteins acting on centromere-likeparSsites. Similar chromosome-encodedparloci likely also contribute to chromosome segregation. Here, we used bioinformatic approaches to search for chromosomalparSsites in 400 prokaryotic genomes. Although the consensus sequence matrix used to search forparSsites was derived from two gram-positive species, putativeparSsites were identified on the chromosomes of 69% of strains from all branches of bacteria. Strains that were not found to containparSsites clustered among relatively few branches of the prokaryotic evolutionary tree. In the vast majority of cases,parSsites were identified in origin-proximal regions of chromosomes. The widespread conservation ofparSsites across diverse bacteria suggests thatparloci evolved very early in the evolution of bacterial chromosomes and that the absence ofparS,parA, and/orparBin certain strains likely reflects the loss of one of more of these loci much later in evolution. Moreover, the highly conserved origin-proximal position ofparSsuggestsparloci are primarily devoted to regulating processes that involve the origin region of bacterial chromosomes. In species containing multiple chromosomes, theparSsites found on secondary chromosomes diverge significantly from those found on their primary chromosomes, suggesting that chromosome segregation of multipartite genomes requires distinct replicon-specificparloci. Furthermore,parSsites on secondary chromosomes are not well conserved among different species, suggesting that the evolutionary histories of secondary chromosomes are more diverse than those of primary chromosomes.