Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses

Abstract

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.

Spatial chromosome organization and adaptation of the radiation-resistant extremophileDeinococcus radiodurans

“…The PprI/DdrO-mediated regulatory system has been recognized as a unique transcriptional inhibition and removal system of D. radiodurans in response to DNA damage. Under environmental stress conditions, PprI, a metal-dependent protease, is activated to specifically cleave the C-terminal region of the DdrO, abolishing its DNA binding activity, and resulting in the expression of DNA damage repair genes that are inhibited by the DdrO (48). Enrichment analysis of the downregulated genes in the mutant reveal their involvement in vital cellular processes closely related to respiration, translation, RNA metabolism, and electron transfer ( Fig.…”

Structural and functional insights into the activation of the dual incision activity of UvrC, a key player in bacterial NER

“…In this scenario, UvrC is more likely to be recruited as a binary complex with UvrB to sites of DNA damage. In D. radiodurans , although the uvrC gene is not part of the conserved radiation/desiccation response (RDR) regulon ( 83 , 84 ), its expression has been reported to be upregulated in response to ionizing radiation, but to a lesser extent than the uvrA , uvrB and uvrD genes ( 85 ), suggesting that the relative abundance of the UvrABC machinery during the response to DNA damage may be different to that observed in E. coli and some UvrC may remain unbound. In this case, UvrC may be recruited directly to UvrB-DNA pre-incision complexes aided by its relatively strong binding affinity for damaged DNA.…”

Active Transposition of Insertion Sequences in Prokaryotes: Insights from the Response of Deinococcus geothermalis to Oxidative Stress

“…IrrE is a metalloprotease that cleaves the dimeric form of DdrO bound to the RDRM motif of the RDR regulon. By inactivating the repressor DdrO, gene expression mediated by the RDR regulon is activated [75,78]. We expect this is an example of a defined redox-sensing pathway.…”

“…Very recently, chromatin immunoprecipitation sequencing (ChIP-Seq) analysis and RNA sequencing (RNA-Seq) analysis showed that the radiation/desiccation response (RDR) regulon operated through the cis-acting sequence RDRM (Radiation Desiccation Response Motif), the trans-acting repressor DdrO and the protease IrrE possibly controlled a unique IS family [75]. The authors performed a systematic and comprehensive sequence analysis for the RDR motif and newly found the DdrO target genes, which involved two Tpase that included the IS5 and Tn3 families.…”