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| Status |
Public on Apr 03, 2017 |
| Title |
Conservation and diversity of the IrrE/DdrO-controlled radiation response in radiation-resistant Deinococcus bacteria |
| Organism |
Deinococcus deserti |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
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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| Overall design |
Using Illumina HiSeq 2000, RNA-Seq was performed to explore the transcriptome in non-irradiated and irradiated Deinococcus deserti strains lacking gene irrE or ddrOc.
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| Contributor(s) |
de Groot A, Blanchard L |
| Citation(s) |
28397370 |
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| Submission date |
Mar 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Arjan de Groot |
| E-mail(s) |
[email protected]
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| Organization name |
CEA
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| Department |
BIAM-SBVME
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| Lab |
LBC
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| Street address |
CEA Cadarache
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| City |
Saint Paul lez Durance |
| ZIP/Postal code |
13108 |
| Country |
France |
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| Platforms (1) |
| GPL18445 |
Illumina HiSeq 2000 (Deinococcus deserti) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA377853 |
| SRA |
SRP101333 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE95658_differentialExpression_RD42.txt.gz |
180.8 Kb |
(ftp)(http) |
TXT |
| GSE95658_differentialExpression_RD62.txt.gz |
181.6 Kb |
(ftp)(http) |
TXT |
| GSE95658_readCountGenes_RD42_RD62.txt.gz |
139.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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