Caulobacter crescentus (CB15) initiates chromosome replication only in stalked 
cells and not in swarmers. To better understand this dimorphic control of 
chromosome replication, we isolated replication origins (oris) from freshwater 
Caulobacter (FWC) and marine Caulobacter (MCS) species. Previous studies 
implicated integration host factor (IHF) and CcrM DNA methylation sites in 
replication control. However, ori IHF and CcrM sites identified in the model FWC 
CB15 were only conserved among closely related FWCs. DnaA boxes and CtrA binding 
sites are established CB15 ori components. CtrA is a two-component regulator 
that blocks chromosome replication selectively in CB15 swarmers. DnaA boxes and 
CtrA sites were found in five FWC and three MCS oris. Usually, a DnaA box and a 
CtrA site were paired, suggesting that CtrA binding regulates DnaA activity. We 
tested this hypothesis by site-directed mutagenesis of an MCS10 ori which 
contains only one CtrA binding site overlapping a critical DnaA box. This 
overlapping site is unique in the whole MCS10 genome. Selective DnaA box 
mutations decreased replication, while selective CtrA binding site mutations 
increased replication of MCS10 ori plasmids. Therefore, both FWC and MCS oris 
use CtrA to repress replication. Despite this similarity, phylogenetic analysis 
unexpectedly shows that CtrA usage evolved separately among these Caulobacter 
oris. We discuss consensus oris and convergent ori evolution in differentiating 
bacteria.