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

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...

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Autores principales: Eugénie, Nicolas, Zivanovic, Yvan, Lelandais, Gaelle, Coste, Geneviève, Bouthier de la Tour, Claire, Bentchikou, Esma, Servant, Pascale, Confalonieri, Fabrice
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8533742/
https://www.ncbi.nlm.nih.gov/pubmed/34685516
http://dx.doi.org/10.3390/cells10102536
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author Eugénie, Nicolas
Zivanovic, Yvan
Lelandais, Gaelle
Coste, Geneviève
Bouthier de la Tour, Claire
Bentchikou, Esma
Servant, Pascale
Confalonieri, Fabrice
author_facet Eugénie, Nicolas
Zivanovic, Yvan
Lelandais, Gaelle
Coste, Geneviève
Bouthier de la Tour, Claire
Bentchikou, Esma
Servant, Pascale
Confalonieri, Fabrice
author_sort Eugénie, Nicolas
collection PubMed
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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spelling pubmed-85337422021-10-23 Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses Eugénie, Nicolas Zivanovic, Yvan Lelandais, Gaelle Coste, Geneviève Bouthier de la Tour, Claire Bentchikou, Esma Servant, Pascale Confalonieri, Fabrice Cells Article 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. MDPI 2021-09-25 /pmc/articles/PMC8533742/ /pubmed/34685516 http://dx.doi.org/10.3390/cells10102536 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Eugénie, Nicolas
Zivanovic, Yvan
Lelandais, Gaelle
Coste, Geneviève
Bouthier de la Tour, Claire
Bentchikou, Esma
Servant, Pascale
Confalonieri, Fabrice
Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses
title Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses
title_full Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses
title_fullStr Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses
title_full_unstemmed Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses
title_short Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses
title_sort characterization of the radiation desiccation response regulon of the radioresistant bacterium deinococcus radiodurans by integrative genomic analyses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8533742/
https://www.ncbi.nlm.nih.gov/pubmed/34685516
http://dx.doi.org/10.3390/cells10102536
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