Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium <i>Deinococcus radiodurans</i> by Integrative Genomic Analyses
Numerous genes are overexpressed in the radioresistant bacterium <i>Deinococcus radiodurans</i> 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 transcripti...
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MDPI AG
2021-09-01
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| author | Nicolas Eugénie Yvan Zivanovic Gaelle Lelandais Geneviève Coste Claire Bouthier de la Tour Esma Bentchikou Pascale Servant Fabrice Confalonieri |
| author_facet | Nicolas Eugénie Yvan Zivanovic Gaelle Lelandais Geneviève Coste Claire Bouthier de la Tour Esma Bentchikou Pascale Servant Fabrice Confalonieri |
| author_sort | Nicolas Eugénie |
| collection | DOAJ |
| description | Numerous genes are overexpressed in the radioresistant bacterium <i>Deinococcus radiodurans</i> 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 <i>Deinococcus</i> species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of <i>D. radiodurans</i> 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 <i>D. radiodurans</i> 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. |
| first_indexed | 2024-03-10T06:39:13Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-10T06:39:13Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-1a59b173fec543a981d2f30b67a43d8f2023-11-22T17:45:12ZengMDPI AGCells2073-44092021-09-011010253610.3390/cells10102536Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium <i>Deinococcus radiodurans</i> by Integrative Genomic AnalysesNicolas Eugénie0Yvan Zivanovic1Gaelle Lelandais2Geneviève Coste3Claire Bouthier de la Tour4Esma Bentchikou5Pascale Servant6Fabrice Confalonieri7Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, FranceUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, FranceUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, FranceUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, FranceUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, FranceUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, FranceUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, FranceUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, FranceNumerous genes are overexpressed in the radioresistant bacterium <i>Deinococcus radiodurans</i> 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 <i>Deinococcus</i> species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of <i>D. radiodurans</i> 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 <i>D. radiodurans</i> 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.https://www.mdpi.com/2073-4409/10/10/2536radioresistance/desiccationtranscriptional regulator<i>Deinococcus radiodurans</i>ChIP-seqRNA-seqbioinformatic analyses |
| spellingShingle | Nicolas Eugénie Yvan Zivanovic Gaelle Lelandais Geneviève Coste Claire Bouthier de la Tour Esma Bentchikou Pascale Servant Fabrice Confalonieri Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium <i>Deinococcus radiodurans</i> by Integrative Genomic Analyses Cells radioresistance/desiccation transcriptional regulator <i>Deinococcus radiodurans</i> ChIP-seq RNA-seq bioinformatic analyses |
| title | Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium <i>Deinococcus radiodurans</i> by Integrative Genomic Analyses |
| title_full | Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium <i>Deinococcus radiodurans</i> by Integrative Genomic Analyses |
| title_fullStr | Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium <i>Deinococcus radiodurans</i> by Integrative Genomic Analyses |
| title_full_unstemmed | Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium <i>Deinococcus radiodurans</i> by Integrative Genomic Analyses |
| title_short | Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium <i>Deinococcus radiodurans</i> by Integrative Genomic Analyses |
| title_sort | characterization of the radiation desiccation response regulon of the radioresistant bacterium i deinococcus radiodurans i by integrative genomic analyses |
| topic | radioresistance/desiccation transcriptional regulator <i>Deinococcus radiodurans</i> ChIP-seq RNA-seq bioinformatic analyses |
| url | https://www.mdpi.com/2073-4409/10/10/2536 |
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