Abstract
BackgroundThe annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori). Identifying the ori of these bacteria and related alpha-Proteobacteria as well as their patterns of sequence evolution will aid studies of cell replication and cell density, as well as the potential genetic manipulation of these widespread intracellular bacteria.ResultsUsing features that have been previously experimentally verified in the alpha-Proteobacterium Caulobacter crescentus, the origin of DNA replication (ori) regions were identified in silico for Wolbachia strains and eleven other related bacteria belonging to Ehrlichia, Anaplasma, and Rickettsia genera. These features include DnaA-, CtrA- and IHF-binding sites as well as the flanking genes in C. crescentus. The Wolbachia ori boundary genes were found to be hemE and COG1253 protein (CBS domain protein). Comparisons of the putative ori region among related Wolbachia strains showed higher conservation of bases within binding sites.ConclusionThe sequences of the ori regions described here are only similar among closely related bacteria while fundamental characteristics like presence of DnaA and IHF binding sites as well as the boundary genes are more widely conserved. The relative paucity of CtrA binding sites in the ori regions, as well as the absence of key enzymes associated with DNA replication in the respective genomes, suggest that several of these obligate intracellular bacteria may have altered replication mechanisms. Based on these analyses, criteria are set forth for identifying the ori region in genome sequencing projects.
Highlights
The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication
Our approach was based on four criteria: (a) position near either hemE or COG1806 orthologs; (b) an intergenic region containing an appropriate number of binding sites for the DnaA, CtrA and IHF factors; (c) genome-wide searches confirming that no other appropriately sized intergenic region (>300 bp) contains a significant number of these three characteristic binding sites and (d) the AT-content of the predicted origins that is higher than the average for the respective genome
We provide in silico evidence for the location of the origin of replication in Wolbachia and its close relatives: Ehrlichia, Anaplasma, Rickettsia and Neorickettsia
Summary
The annotated genomes of two closely related strains of the intracellular bacterium Wolbachia pipientis have been reported without the identifications of the putative origin of replication (ori). The unique biology of Wolbachia has attracted a growing number of researchers interested in questions ranging from the evolutionary implications of infection to the use of this agent for pest and disease control [5,6,7,8,9]. These endosymbiotic bacteria are typically transmitted through the eggs of their hosts and their replication rate is regulated to avoid overgrowth prior to host reproduction [2,3,4]. Neither of these studies identified the putative origin of replication (ori) for Wolbachia
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