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Deinococcus deserti

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

PROVIDER: PRJNA377853 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5311140.fastq.gz	Fastqsanger.gz
	SRR5311141.fastq.gz	Fastqsanger.gz
	SRR5311138.fastq.gz	Fastqsanger.gz
	SRR5311139.fastq.gz	Fastqsanger.gz

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Similar Datasets

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

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.

2014-04-08 | GSE56058 | GEO

Deinococcus deserti

Project description:Radiation-resistant desert sand bacterium

| PRJNA35881 | ENA

Deinococcus deserti VCD115

Project description:Radiation-resistant desert sand bacterium

| PRJNA16691 | ENA

Deinococcus deserti

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

| PRJNA242313 | ENA

Proteogenomics of the Sahara bacterium Deinococcus deserti

Project description:Reannotation of Deinococcus deserti genome

2010-04-30 | PRD000139 | Pride

Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock

2010-07-29 | GSE17465 | GEO

Deinococcus peraridilitoris

Project description:Radiation resistant bacterium

| PRJNA61313 | ENA

Deinococcus radiodurans

Project description:Radiation-resistant bacterium

| PRJNA35079 | ENA

Transcriptional profile of Escherichia coli K12 strain JM109 harboring pMG1 and pMG1-IrrE under 1M NaCl shock

Project description:IrrE is a unique gene in Deinococcus, which is the switch of DNA repair and celluar surival network. Expressing IrrE enhanced the salt tolence in E. coli. To understand the effect of IrrE to E. coli during salt shock, we constructed the IrrE-expressing plasmid pMG1-IrrE. And pMG1 is the empty vector used as a control. The GroESL promoter was amplified from D. radiodurans R1 genomic DNA by PCR with proper primers. The PCR product was ligated into the T-cloning site of T-vector pMD18T, generating the plasmid pMG1. RNA extracted from cells of E. coli K-12 JM109 cells with pMG1 after 4 h of growth to OD 600 achieve 0.4, or cells with pMG1 after 1mol/L NaCl shock for 10 min (and 60 min) when their OD600 achieved 0.4. RNA extracted from cells of E. coli K-12 JM109 cells with pMG1-IrrE after 4 h of growth to OD 600 achieve 0.4, or cells with pMG1-IrrE after 1mol/L NaCl shock for 10 min (and 60 min)when their OD600 achieved 0.4. pMG1 and pMG1-IrrE datasets normalized separately.

2010-07-29 | E-GEOD-17465 | biostudies-arrayexpress

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