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Transcriptional Analysis of Deinococcus radiodurans for Novel sRNAs expression that are Differentially Expressed under Ionizing Radiation

ABSTRACT: 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(S): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

PROVIDER: GSE64952 | GEO | 2015/01/22

SECONDARY ACCESSION(S): PRJNA272579

REPOSITORIES: GEO

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Transcriptional Analysis of Deinococcus radiodurans for Novel sRNAs expression that are Differentially Expressed under Ionizing Radiation

Project description:In this study, we identified potential sRNA candidates inÂ 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). Two samples (sham and 15kGy irradiated) were sequenced.

2015-01-22 | E-GEOD-64952 | biostudies-arrayexpress

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.

2021-06-25 | PXD026633 | Pride

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

Project description: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. However, we did not observe any significantly differentially expressed transcripts between the two strains during recovery from IR. 31 transcripts were signficantly differentially expressed when comparing the two strains under unirradiated conditions. To determine the regulatory network that this sRNA, PprS could regulate we performed a MAPS (MS2-affinity purification followed by RNAsequencing) experiment in which a MS2-binding domain tagged PprS was expressed from a constutive promoter from a plasmid (pRADgro) in D. radiodurans R1. A control plasmid (containing only the MS2-binding domain) was also expressed and differential enrichment was compared to this control. MAPS suggested ~130 potential interacting transcripts with PprS and we were able to validate the binding and stabilization of one specific transcript, pprM, for PprS.

2021-06-18 | GSE176207 | GEO

Deinococcus radiodurans R1

Project description:Transcriptional Analysis of Deinococcus radiodurans for Novel sRNAs expression that are Differentially Expressed under Ionizing Radiation

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Deinococcus radiodurans R1: wildtype strains vs. oxyR disruption strains

Project description:In Deinococcus radiodurans, a previously unreported special characteristic of DrOxyR (DR0615) is found with only one conserved cysteine. dr0615 gene mutant is hypersensitive to H2O2, but a little to ionizing radiation. Site-directed mutagenesis and subsequent in vivo functional analyses revealed that the conserved cysteine (C210) is necessary for sensing H2O2, but its mutation did not alter the binding characteristics of OxyR on DNA. Under oxidant stress, DrOxyR is oxidized to sulfenic acid form, which can be reduced by reducing reagents. In addition, quantitative real-time PCR and global transcription profile results showed that OxyR is not only a transcriptional activator (e.g., katE, drb0125), but also a transcriptional repressor (e.g., dps, mntH). Transcriptional profiling of comparing wildtype strains with oxyR disruption strains under normal growth conditions. Keywords: Genetic modification

2008-02-01 | GSE9636 | GEO

Deinococcus radiodurans R1 Cells: Control vs. bphPR deletion mutant

Project description:Transcriptional profiling of Deinococcus radiodurans comparing control wild type cells with bphPR deletion mutant

2014-07-07 | GSE59135 | GEO

Signal Recognition Particle RNA Contributes to Oxidative Stress Response in Deinococcus radiodurans by Modulating Catalase Localization

Project description:The proper functioning of many proteins requires their transport to the correct cellular compartment or their secretion. Signal recognition particle (SRP) is a major protein transport pathway responsible for the co-translational movement of integral membrane proteins as well as periplasmic proteins. Deinococcus radiodurans is a ubiquitous bacterium that expresses a complex phenotype of extreme oxidative stress resistance, which is mediated by proteins involved in DNA repair, metabolism, gene regulation and antioxidant defence. These proteins are located either extracellularly or subcellularly, but the molecular mechanism of protein localization in D. radiodurans to manage oxidative stress response remains unexplored. In this study, we characterized the SRP complex in D. radiodurans R1 and showed that the knockdown of the SRP RNA (Qpr6) reduced bacterial survival under hydrogen peroxide (H2O2) and growth under chronic ionizing radiation (CIR). Through LC-MS/MS analysis, we detected 162 proteins in the periplasm of wild-type D. radiodurans, of which the transport of 65 of these proteins to the periplasm was significantly reduced in the Qpr6 knockdown strain. Through Western blotting, we further demonstrated the localization of the catalases in D. radiodurans, DR_1998 (KatE1) and DR_A0259 (KatE2), in both the cytoplasm and periplasm, and showed that the accumulation of KatE1 and KatE2 in the periplasm was reduced in the SRP-defective (Qpr6 knockdown) strain.

2023-03-11 | PXD022570 | Pride

High-throughput sequencing of Lactobacillus casei BL23 sRNAs

Project description:In the present study we characterized the sRNA profile of Lactobacillus casei BL23 using conventional and mDOT-seq approaches. In total 307 potential sRNAs were identified, 28 of which were validated by Northern hybridization. As a major portion of predicted sRNAs were shown to be conserved among the related species of Lactobacillus casei group (LCG), the results obtained in this study could serve as a valuable resource for achieving a better understanding of LCG physiology or even improving their applications in industry and medicine.

2021-05-20 | GSE166930 | GEO

Deinococcus radiodurans R1 Cells: Control vs. bphPR deletion mutant

Project description:Transcriptional profiling of Deinococcus radiodurans comparing control wild type cells with bphPR deletion mutant Two-condition experiment, R1 vs. bphPR deletion cell. Biological replicates: 3 control replicates, 3 bphPR deletion mutant replicates.

2014-07-07 | E-GEOD-59135 | biostudies-arrayexpress

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Project description:Deinococcus radiodurans R1: wildtype strains vs. oxyR disruption strains

| PRJNA103493 | ENA