GEO DataSets

(Submitter supplied) This bacterial genome encodes pyrroloquinoline quinone (PQQ) synthase enzyme required for the synthesis of PQQ in bacteria. The gene pqqE encoding PQQ synthase was annotated in Deinococcus radiodurans R1 genome and synthesis of PQQ was shown in this bacterium. PQQ roles as an antioxidant and as an inducer of protein kinase in bacterial system was shown. The pqqE disuption mutant showed several folds decrease in gamma radiation tolerance of wild type cells and strong impairment of DSB repair. more...

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539; Deinococcus radiodurans

Type:

Expression profiling by array

Platform:

GPL8947

2 Samples

Download data: GPR

(Submitter supplied) Bacterial cells lacking pyrroloquinoline quinone (PQQ) were sensitive to gamma radiation as compared to wild type cells. Deinococcus radiodurans genome encode for five putative PQQ binding STK domain-containing proteins. The comparison of gamma radiation response of all five-deletion mutants with wild type suggested that dr2518 mutant was hypersensitive to gamma radiation as compared to wild type and other mutants. more...

Organism:

Deinococcus radiodurans; Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL8947

2 Samples

Download data: GPR

(Submitter supplied) Deinococcus radiodurans exposed to higher doses of gamma radiation showed induced levels of DRB0091 polypeptide annotated as a putative response regulator in an operon expressing upstream to DRB0090, histidine kinase. Deletion of drB0090 generated, showed decreased tolerance to DNA damage and impairment in DSB repair. Recombinant DR0090 protein showed phosphotransferase activity on its cognate response regulator, DRB0091. more...

Organism:

Deinococcus radiodurans; Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by array

Platform:

GPL8947

2 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of comparing wildtype strains with DR1790-deletion strains under normal growth contidions. Keywords: Genetic modification

Organism:

Deinococcus radiodurans

Type:

Expression profiling by array

Platform:

GPL9466

1 Sample

Download data: GPR

(Submitter supplied) In this study, we mapped the DdrO regulon in Deinococcus radiodurans by using two genome-scale approaches, ChIP-seq and RNA-seq analyses. These approaches were performed to find additional DdrO targets sites that were not predicted by previous in silico analyses. To our knowledge, we present here the first ChIP-seq analysis performed at the genome level in D. radiodurans. Alignments of DNA sequences extracted from ChIP-seq analysis were also performed to compare the consensus motif found to the predicted DdrO-binding motif. more...

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30214

41 Samples

Download data: TXT

(Submitter supplied) This study explores the regulatory network of a sRNA named PprS (previously Dsr2) in Deinococcus radiodurans R1. We compared the transcriptomes of two strains with and without exposure to 10 kGy acute ionizing radiation (IR): D. radiodurans R1 (wild-type) and a PprS knockdown mutant (PprSKD) that expresses ~2-fold less PprS compared to WT levels. Analysis of this RNAseq dataset demonstrated significant differential expression of several transcripts in both WT (34) and PprSKD (61) strains during recovery from IR. more...

Organism:

Deinococcus radiodurans

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30231

18 Samples

Download data: GFF

(Submitter supplied) 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. more...

Organism:

Deinococcus deserti

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18445

4 Samples

Download data: TXT

(Submitter supplied) In this study, we identified potential sRNA candidates in D. radiodurans by a whole transcriptome deep sequencing analysis, and confirm the expression of 31 sRNAs in D. radiodurans with Northern blotting analysis and RT-PCR. A total of 8 confirmed sRNAs showed differential expression during recovery after acute ionizing radiation (15 kGy).

Organism:

Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19650

2 Samples

Download data: TXT

(Submitter supplied) Deinococcus radiodurans is an extremophilic microorganism that possesses a unique DNA damage repair system, conferring strong resistance to radiation, desiccation, oxidative stress, and chemical damage. Recently, we discovered that D. radiodurans possesses a N4-methylation (m4C) methyltransferase called M.DraR1, which recognizes the 5'-CCGCGG-3' sequence and methylates the second cytosine. Here, we revealed its cognate restriction endonuclease R.DraR1 and recognized that it is the only endonuclease specially for non-4C-methylated 5'-CCGCGG-3' sequence so far. more...

Organism:

Deinococcus radiodurans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31018

4 Samples

Download data: TXT

(Submitter supplied) We report genome-wide transcriptional UV response in Deincoccus gobiensis

Organism:

Deinococcus gobiensis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13495

2 Samples

Download data: TXT

(Submitter supplied) 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. more...

Organism:

Deinococcus deserti

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18445

4 Samples

Download data: TXT

(Submitter supplied) RNA-seq analysis of Deinococcus metallilatus of wild type and mutant No. 6 at exponential phase (24 h)

Organism:

Deinococcus metallilatus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26584

2 Samples

Download data: TXT

(Submitter supplied) Purpose: DNA methylation has a global impact on gene expression Methods: Gene expression profiles of D. radiodurans R1 wild type and ΔM.DraR1 strains were generated by deep sequencing using Illumina HiSeqTM2500. Results: RNA-seq was used for differential expression gene analysis between wild-type and ΔM.DraR1 strains. A total of 1158 genes (766 upregulated genes and 392 downregulated genes) were differentially expressed in ΔM.DraR1 strain. more...

Organism:

Deinococcus radiodurans

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26971

4 Samples

Download data: XLSX

(Submitter supplied) Nine Curtobacterium strains (three from three clades) were subjected to a lab desiccation experiment with no access to moisture or nutrients to compare between clades. RNA was extracted at days 0, 1, and 32 and sequenced

Organism:

Curtobacterium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33356

81 Samples

Download data: CSV, SF