RNA-seq gene expression profiling comparing WT (NA1000) and isogenic ?scmA Caulobacter crescentus cells

The precise biological function of solitary cytosine MTases in bacteria remains mostly elusive. In this study, we dissected the potential influence of the solitary cytosine MTase CCNA_01085 (named ScmA), in the Caulobacter crescentus Alphaproteobacterial model. We constructed a ?scmA mutant and used it to study the impact of ScmA-dependent methylation on C. crescentus phenotypes, on its fitness and on its transcriptome. These analyses revealed that DNA damaging events often take place in ?scmA cells. Interestingly, these were shown to be dependent on the presence of the CCNA_2930 Vsr-like repair endonuclease naturally expressed in WT C. crescentus cells (named VsrA). Thus, we hypothesize that DNA damage can be induced by VsrA during DNA repair anomalies. Consequently, scmA+ cells largely outcompete ?scmA cells during standard growth conditions. Interestingly, the vsrA gene is not genetically linked with the scmA gene on the C. crescentus chromosome despite the functional link that we discovered, revealing an original gene positioning architecture compared to previously characterized systems where Vsr-like repair endonucleases are usually encoded by genes located right next to MTase genes. Overall design: To investigate the impact of DNA methylation by ScmA (CCNA_01085) on the transcriptome of Caulobacter crescentus NA1000, we constructed a ?scmA mutant. We then performed gene expression profiling analyses using data obtained from RNA-seq of WT/?scmA cells grown exponentially (OD660=~0.4) in M2G medium.