DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria

Several regulators are involved in the control of cell cycle progression in the bacterial model system caulobacter crescentus,which divides asymmetrically into a vegetative g1-phase (swarmer) cell and a replicative s-phase (stalked) cell. here we report a novel functional interaction between the enigmatic cell cycle regulator gcra and the n6-adenosine methyltransferase ccrm,both highly conserved proteins among alphaproteobacteria,that are activated early and at the end of s-phase,respectively. as no direct biochemical and regulatory relationship between gcra and ccrm were known,we used a combination of chip (chromatin-immunoprecipitation),biochemical and biophysical experimentation,and genetics to show that gcra is a dimeric dna-binding protein that preferentially targets promoters harbouring ccrm methylation sites. after tracing ccrm-dependent n6-methyl-adenosine promoter marks at a genome-wide scale,we show that these marks recruit gcra in vitro and in vivo. moreover,we found that,in the presence of a methylated target,gcra recruits the rna polymerase to the promoter,consistent with its role in transcriptional activation. since methylation-dependent dna binding is also observed with gcra orthologs from other alphaproteobacteria,we conclude that gcra is the founding member of a new and conserved class of transcriptional regulators that function as molecular effectors of a methylation-dependent (non-heritable) epigenetic switch that regulates gene expression during the cell cycle. © 2013 fioravanti et al.