BACKGROUND: 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). 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.
RESULTS: Using 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.
CONCLUSION: The 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.