Comparative analysis of Caulobacter chromosome replication origins

Microbiology (Reading). 2009 Apr;155(Pt 4):1215-1225. doi: 10.1099/mic.0.025528-0.

Abstract

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.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Base Sequence
  • Binding Sites / genetics
  • Caulobacter / genetics*
  • Caulobacter / isolation & purification
  • DNA Replication*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Electroporation
  • Evolution, Molecular*
  • Fresh Water / microbiology*
  • Gene Expression Regulation, Bacterial
  • Integration Host Factors
  • Molecular Sequence Data
  • Mutation
  • Phylogeny
  • Replication Origin / genetics*
  • Replication Origin / physiology
  • Seawater / microbiology*
  • Sequence Analysis, DNA
  • Transcription Factors / chemistry
  • Transcription Factors / genetics
  • Transcription Factors / metabolism

Substances

  • Bacterial Proteins
  • CtrA protein, Caulobacter
  • DNA-Binding Proteins
  • DnaA protein, Bacteria
  • Integration Host Factors
  • Transcription Factors

Associated data

  • GENBANK/EU327255
  • GENBANK/EU327256
  • GENBANK/EU327257
  • GENBANK/EU327258