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Radiation resistance strategies in Deinococcus swuensis.

ABSTRACT: Search for UV radiation resistance strategies in Deinococcus swuensis isolated from Paramo.

PROVIDER: PRJEB33086 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3597220_1.fastq.gz	Fastqsanger.gz
	ERR3597220_2.fastq.gz	Fastqsanger.gz
	ERR3597221_1.fastq.gz	Fastqsanger.gz
	ERR3597221_2.fastq.gz	Fastqsanger.gz
	ERR3597222_1.fastq.gz	Fastqsanger.gz

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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.

2017-04-03 | GSE95658 | GEO

Transcription profiling by array of Arabidopsis thaliana Ler and uvr8-2 genotypes exposed to solar ultraviolet radiation

Project description:The experiment was performed to search for genes regulated by the UV RESISTANT LOCUS (UVR8) under solar ultraviolet radiation (UV).

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A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation

Project description:This study tracks the proteome during recovery from 10 kGy acute ionizing radiation (IR) in Deinococcus radiodurans R1 (WT). After 1 hour of recovery post-IR exposure, we observed 37 proteins significantly differentially expressed, including several within the Radiation and Dessication Response (RDR) pathway. Additionally, we also explored the regulatory network of a sRNA named PprS (previously Dsr2) in Deinococcus radiodurans by comparing the proteome of a sRNA knockdown strain (PprSKD, which demonstrates a ~2-fold decrease in PprS expression) to WT D. radiodurans during unirradiated conditions at late-exponential phase. Comparison between these two strains demonstrated decreased levels of one of PprS's targets, PprM, in the PprSKD strain which validated the activation mechanism we propose for PprS on pprM.

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RNA-seq and Proteogenomics Reveal the Importance of Leaderless mRNAs in the Radiation-tolerant Bacterium Deinococcus deserti

Project description:Deinococcus deserti is a desiccation- and radiation-tolerant desert bacterium. Differential RNA sequencing was performed to explore the specificities of its transcriptome. Strikingly, for 1174 (60%) mRNAs the transcription start site was found exactly at (916 cases, 47%) or very close to the translation initiation codon AUG or GUG. Such proportion of leaderless mRNAs, which may resemble ancestral mRNAs, is unprecedented for a bacterial species. Proteomics showed that leaderless mRNAs are efficiently translated in D. deserti. Interestingly, we also found 173 additional transcripts with a 5’-AUG or 5’-GUG that would make them competent for ribosome binding and translation into novel small polypeptides. Fourteen of these are predicted to be leader peptides involved in transcription attenuation. Another 30 correlated with new gene predictions and/or showed conservation with annotated and non-annotated genes in other Deinococcus species, and five of these novel polypeptides were indeed detected by mass spectrometry. The data also allowed re-annotation of the start codon position of 257 genes, including several DNA repair genes. Moreover, several novel highly radiation-induced genes were found and their potential roles are discussed. Based on our RNA sequencing and proteogenomics data, we propose that translation of many of the novel leaderless transcripts, which may have resulted from single nucleotide changes and maintained by selective pressure, provides a new explanation for the generation of a cellular pool of small peptides important for protection of proteins against oxidation and thus for radiation/desiccation tolerance and adaptation to harsh environmental conditions.

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Project description:Radiation-resistant Deinococcus radiodurans is an extreme microorganism capable of withstanding high levels of ionizing radiation and chemical mutagens. It possesses remarkable DNA repair capabilities and serves as a model organism for studying stress resistance mechanisms. However, our understanding of the relationship between the biological characteristics of this species and its chromosomal 3D structure remains limited. In this study, we employed chromosome conformation capture and sequencing (3C-seq) technology to determine the 3D genome structure of D. radiodurans and to further investigate the changes of chromosome conformation induced by ultraviolet irradiation. We observed that the overall chromatin folding structure of the cells became much looser after UV irradiation, with smaller chromosomal interaction domains (CIDs) merging to form larger CIDs. Integrating transcriptomic data analysis, we found that the majority of upregulated differentially expressed genes were significantly enriched near specific CID boundaries. Additionally, we comprehensively elucidated that Dr_ebfC as a nuclear-associated protein, serves as a global regulatory factor in gene expression processes and may modulate transcriptional regulation by altering chromosomal structure, thereby influencing the physiological state of the bacterium. Overall, our study provides insights into the chromosomal conformational changes of D. radiodurans under different conditions, offering valuable resources for further understanding the molecular mechanisms underlying its extreme resistance.

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iTRAQ-based proteomic analysis of Deinococcus radiodurans in response to 12C6+ heavy ions irradiation

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Deinococcus deserti

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

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