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

Antonella Fioravanti (1) , Coralie Fumeaux (2) , Saswat S Mohapatra (1) , Coralie Bompard (1) , Matteo Brilli (3) , Antonio Frandi (2) , Vincent Castric (4) , Vincent Villeret (1) , Patrick H. Viollier (2) , Emanuele G Biondi (1)

1 IRI - Institut de Recherche Interdisciplinaire [Villeneuve d'Ascq]
2 UNIGE - Université de Genève = University of Geneva
3 BPGE - Bioinformatique, phylogénie et génomique évolutive
4 GEPV - Laboratoire de Génétique et Evolution des Populations Végétales

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. Citation: Fioravanti A, Fumeaux C, Mohapatra SS, Bompard C, Brilli M, et al. (2013) DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria. PLoS Genet 9(5): e1003541.

Domaines: Génétique des populations [q-bio.PE]

Antonella Fioravanti, Coralie Fumeaux, Saswat S Mohapatra, Coralie Bompard, Matteo Brilli, et al.. DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria. PLoS Genetics, 2013, 9, pp.e1003541. ⟨10.1371/journal.pgen.1003541⟩. ⟨hal-01110809⟩