Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. It was shown that the DdrO and IrrE proteins play a major role in regulating the expression of approximately twenty genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. At present, many questions remain, such as the number of genes regulated by DdrO. Here, we present the first ChIP-seq analysis performed at the genome level in Deinococcus species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of D. radiodurans R1 ATCC 13939 to obtain an accurate reference for read alignments and gene expression quantifications. We highlighted genes that are directly under the control of this transcriptional repressor and showed that the DdrO regulon in D. radiodurans includes numerous other genes than those previously described, including DNA and RNA metabolism proteins. These results thus pave the way to better understand the radioresistance pathways encoded by this bacterium and to compare the stress-induced responses mediated by this pair of proteins in diverse bacteria.

Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. The DdrO and IrrE proteins play a major role in regulating the expression of approximately predicted twenty of these genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. Bioinformatic analyzes showed that this mechanism seems to be conserved in several species of Deinococcus , but many questions remain as such the number of genes regulated by DdrO. Here, by RNA-seq and CHiP-seq assays performed at a genome-wide scale coupled with bioinformatic analyses, we show that, the DdrO regulon in D. radiodurans includes many other genes than those previously described. These results thus pave the way to better understand the radioresistance mechanisms encoded by this bacterium. Author Summary: The main response pathway to genotoxic conditions in the radioresistant bacterium Deinococcus radiodurans is regulated by the constitutively expressed metalloprotease IrrE that cleaves the transcriptional repressor DdrO, leading to the expression of the genes repressed by DdrO. One of the major goals to better understand how pathways involved in radioresistance are coordinated into this fascinating bacterium is to highlight genes regulated by DdrO. In this study, we mapped in vivo the DdrO regulon in D. radiodurans by using two genome-scale approaches, ChIP-seq and RNA-seq analyses, coupled with bioinformatic analyses. As homologs of these two proteins are also found in many other bacteria, these results also pave the way to compare the stress-induced responses mediated by this couple of proteins in diverse bacteria.

La bactérie Deinococcus radiodurans est l’un des organismes les plus radiorésistants connus à ce jour. Cette tolérance aux conditions responsables de sévères dommages à l’ADN telles l’exposition à d’importantes doses de rayonnements γ, UV ou encore à une dessiccation prolongée est la résultante d’une synergie entre un ensemble de mécanismes finement régulés au sein des cellules.Le répresseur transcriptionnel DdrO (DNA damage response) et la métalloprotéase IrrE jouent un rôle clé dans la régulation de la réponse aux radiations et à la dessiccation. Lors de conditions engendrant des dommages à l’ADN, IrrE clive et inactive DdrO, abolissant son rôle de répresseur. Appartenant à famille de répresseur XRE, la structure de DdrO présente un domaine de fixation à l’ADN de type Hélice-Tour-Hélice et une région en C-terminale nécessaire à la capacité de DdrO à s’oligomériser afin de former un répresseur fonctionnel.L’ensemble des gènes dont l’expression est sous le contôle de DdrO appartiennent au régulon RDR (Radiation Desiccation Response). Par l’association d’approches génomiques, nous présentons la première cartographie in vivo des cibles de DdrO chez D. radiodurans. Cette nouvelle définition du régulon RDR comprend les nombreux gènes initialement mis en évidence comme étant impliqués dans les mécanismes de réparation des dommages à l’ADN ainsi que de nouvelles cibles associées au métabolisme de l’ADN ou de fonctions inconnues.Le répresseur DdrO est essentiel pour la viabilité cellulaire et sa déplétion prolongée entraine des modifications morphologiques des cellules évocatrices d'une réponse apoptotique bactérienne (formation de vésicules membranaires, nanotubes, défaut de division cellulaire, fragmentation de l'ADN, nanotubes). Les données transcriptomiques obtenues lors de ce phénomène mettent en évidence un phénomène complexe lié indirectement au régulon RDR. La forte répression d’une endopeptidase NlpC/P60 semble impliquée dans la mise en place des phénotypes de modification de la membrane.