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Characterization of the Radiation Desiccation Response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses.

ABSTRACT: Characterization of the Radiation Desiccation Response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses.

PROVIDER: PRJNA734175 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14698434_1.fastq.gz	Fastqsanger.gz
	SRR14698434_2.fastq.gz	Fastqsanger.gz
	SRR14698435_1.fastq.gz	Fastqsanger.gz
	SRR14698435_2.fastq.gz	Fastqsanger.gz
	SRR14698436_1.fastq.gz	Fastqsanger.gz

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Characterization of the Radiation Desiccation Response regulon of the radioresistant bacterium Deinococcus radiodurans by integrative genomic analyses.

Project description:In this study, we mapped the DdrO regulon in Deinococcus radiodurans by using two genome-scale approaches, ChIP-seq and RNA-seq analyses. These approaches were performed to find additional DdrO targets sites that were not predicted by previous in silico analyses. To our knowledge, we present here the first ChIP-seq analysis performed at the genome level in D. radiodurans. Alignments of DNA sequences extracted from ChIP-seq analysis were also performed to compare the consensus motif found to the predicted DdrO-binding motif. Our results show that the RDR regulon in D. radiodurans is more complex than previously thought and is composed of at least 35 genes, including such DNA and RNA metabolism proteins as RecG and HelD helicases, and the prokaryotic replicative DNA ligase LigA, but also new genes associated with different metabolic pathways, involved in translation or encoding proteins of unknown function.

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Deinococcus radiodurans R1 Cells: Control vs. bphPR deletion mutant

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Project description:Transcriptional profiling of Deinococcus radiodurans comparing control wild type cells with bphPR deletion mutant Two-condition experiment, R1 vs. bphPR deletion cell. Biological replicates: 3 control replicates, 3 bphPR deletion mutant replicates.

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Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria

Project description:The extreme radiation resistance of Deinococcus bacteria requires the radiation-stimulated cleavage of protein DdrO by a specific metalloprotease called IrrE. DdrO is the repressor of a predicted radiation/desiccation response (RDR) regulon, composed of radiation-induced genes having a conserved DNA motif (RDRM) in their promoter regions. Here, we showed that addition of zinc ions to purified apo-IrrE, and short exposure of Deinococcus cells to zinc ions, resulted in cleavage of DdrO in vitro and in vivo, respectively. Binding of IrrE to RDRM-containing DNA or interaction of IrrE with DNA-bound DdrO was not observed. The data are in line with IrrE being a zinc peptidase, and indicate that increased zinc availability, caused by oxidative stress, triggers the in vivo cleavage of DdrO unbound to DNA. Transcriptomics and proteomics of Deinococcus deserti confirmed the IrrE-dependent regulation of predicted RDR regulon genes and also revealed additional members of this regulon. Comparative analysis showed that the RDR regulon is largely well conserved in Deinococcus species, but also showed diversity in the regulon composition. Notably, several RDR genes with an important role in radiation resistance in Deinococcus radiodurans, for example pprA, are not conserved in some other radiation-resistant Deinococcus species.

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Succinylome analysis reveals the involvement of lysine succinylation in extreme resistance of Deinococcus radiodurans

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2021-04-26 | PXD012149 | Pride

Characterization of a novel N4 -methylcytosine restriction-modification system in Deinococcus radiodurans

Project description:Deinococcus radiodurans is an extremophilic microorganism that possesses a unique DNA damage repair system, conferring strong resistance to radiation, desiccation, oxidative stress, and chemical damage. Recently, we discovered that D. radiodurans possesses a N4-methylation (m4C) methyltransferase called M.DraR1, which recognizes the 5'-CCGCGG-3' sequence and methylates the second cytosine. Here, we revealed its cognate restriction endonuclease R.DraR1 and recognized that it is the only endonuclease specially for non-4C-methylated 5'-CCGCGG-3' sequence so far. We designated the particular m4C R.DraR1-M.DraR1 as DraI R-M system. Bioinformatics searches displayed the rarity of the DraI R-M homologues system. Meanwhile, recombination and transformation efficiency experiments demonstrated the important role of the DraI R-M system in response to oxidative stress. Besides, in vitro activity experiments showed that R.DraR1 could exceptionally cleave DNA substrates with m5C-methlated 5'-CCGCGG-3' sequence besides its routine activity, suggesting that this particular R-M component possesses a broader substrate choice. Furthermore, an imbalance of the DraI R-M system led to cell death through regulating genes involved in the maintenance of cell survival such as genome stability, transporter, energy production. Thus, our research revealed a novel m4C R-M system that plays key roles in maintaining cell viability and defending foreign DNA in D. radiodurans.

2024-02-14 | GSE251690 | GEO

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

Project description: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.

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