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RNA-Seq analysis among dps-disrupted mutants in Deinococcus geothermalis

ABSTRACT: RNA-Seq analysis among dps-disrupted mutants in Deinococcus geothermalis

PROVIDER: PRJNA1197403 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31695500_1.fastq.gz	Fastqsanger.gz
	SRR31695500_2.fastq.gz	Fastqsanger.gz
	SRR31695501_1.fastq.gz	Fastqsanger.gz
	SRR31695501_2.fastq.gz	Fastqsanger.gz
	SRR31695502_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

RNA-Seq analysis among dps-disrupted mutants in Deinococcus geothermalis

Project description:Transcriptomic analysis was performed in Deinococcus geothermalis wild-type and three mutants including dgeo_0257, dgeo_0281, and double knockout (DK) mutants. dgeo_0281 is a major Dps-coding gene and dgeo_0257 is a novel Dps candidate. Thus, to detecte physiological functions of both Dps-encoded genes, each gene-disrupted mutant and DK mutant was constructed and performed RNA-Seq analysis. This result support better understanding for Dps roles in radiation resistant bacterium through up-regulated and down-regulated genes profile.

2025-04-30 | GSE284126 | GEO

Transcriptomic analysis of a putative LysR family regulator, a putative Dps, and a cystine importer disrupted mutants in radiation resistant bacterium Deinococcus geothermalis

Project description:Here, we compared gene expression level by RNA-Seq analysis among a wild-type (WT) Deinococcus geothermalis strain, a dgeo_2840 of LysR family member gene (Δdgeo_2840), a putative Dps dgeo_0257 (Δdgeo_0257), and a cystine importer dgeo_1986-1987 gene disrupted strain (Δdgeo_1986-1987). From this transcriptomic data, we detected dgeo_2840, dgeo_0257, and dgeo_1986-1987 controlling genes which were somehow up-regulated and/or down-regulated. In particular, Deinococcus geothermalis has a total of 73 insertion sequences (ISs) in genomes, and some of them are actively transposed to other loci with replicative mode by the oxidative stress of hydrogen peroxide treatment.

2020-06-06 | GSE151903 | GEO

Deinococcus geothermalis

Project description:Deinococcus geothermalis overview

| PRJNA35515 | ENA

Transcriptomic analysis of a putative LysR family regulator, a putative Dps, and a cystine importer disrupted mutants in radiation resistant bacterium Deinococcus geothermalis

Project description:Transcriptomic analysis of a putative LysR family regulator, a putative Dps, and a cystine importer disrupted mutants in radiation resistant bacterium Deinococcus geothermalis

| PRJNA637617 | ENA

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

Methylococcus geothermalis strain:IM1

Project description:Methylococcus geothermalis strain:IM1 Genome sequencing

| PRJNA592014 | ENA

The Transposition of Insertion Sequences in Sigma-Factor- and LysR-Deficient Mutants of <i>Deinococcus geothermalis</i>.

Project description:Some insertion sequence (IS) elements were actively transposed using oxidative stress conditions, including gamma irradiation and hydrogen peroxide treatment, in Deinococcus geothermalis, a radiation-resistant bacterium. D. geothermalis wild-type (WT), sigma factor gene-disrupted (∆dgeo_0606), and LysR gene-disrupted (∆dgeo_1692) mutants were examined for IS induction that resulted in non-pigmented colonies after gamma irradiation (5 kGy) exposure. The loss of pigmentation occurred because dgeo_0524, which encodes a phytoene desaturase in the carotenoid pathway, was disrupted by the transposition of IS elements. The types and loci of the IS elements were identified as ISDge2 and ISDge6 in the ∆dgeo_0606 mutant and ISDge5 and ISDge7 in the ∆dgeo_1692 mutant, but were not identified in the WT strain. Furthermore, 80 and 100 mM H2O2 treatments induced different transpositions of IS elements in ∆dgeo_0606 (ISDge5, ISDge6, and ISDge7) and WT (ISDge6). However, no IS transposition was observed in the ∆dgeo_1692 mutant. The complementary strain of the ∆dgeo_0606 mutation showed recovery effects in the viability assay; however, the growth-delayed curve did not return because the neighboring gene dgeo_0607 was overexpressed, probably acting as an anti-sigma factor. The expression levels of certain transposases, recognized as pivotal contributors to IS transposition, did not precisely correlate with active transposition in varying oxidation environments. Nevertheless, these findings suggest that specific IS elements integrated into dgeo_0524 in a target-gene-deficient and oxidation-source-dependent manner.

| S-EPMC10892881 | biostudies-literature

RecA proteins from Deinococcus geothermalis and Deinococcus murrayi--cloning, purification and biochemical characterisation.

Project description:BackgroundEscherichia coli RecA plays a crucial role in recombinational processes, the induction of SOS responses and mutagenic lesion bypasses. It has also been demonstrated that RecA protein is indispensable when it comes to the reassembly of shattered chromosomes in γ-irradiated Deinococcus radiodurans, one of the most radiation-resistant organisms known. Moreover, some functional differences between E. coli and D. radiodurans RecA proteins have also been shown.ResultsIn this study, recA genes from Deinococcus geothermalis and Deinococcus murrayi, bacteria that are slightly thermophilic and extremely γ-radiation resistant, were isolated, cloned and expressed in E. coli. After production and purification, the biochemical properties of DgeRecA and DmuRecA proteins were determined. Both proteins continued to exist in the solutions as heterogenous populations of oligomeric forms. The DNA binding by DgeRecA and DmuRecA proteins is stimulated by Mg2+ ions. Furthermore, both proteins bind more readily to ssDNA when ssDNA and dsDNA are in the same reaction mixture. Both proteins are slightly thermostable and were completely inactivated in 10 s at 80°C. Both proteins hydrolyze ATP and dATP in the presence of ssDNA or complementary ssDNA and dsDNA, but not in the absence of DNA or in the presence of dsDNA only, and dATP was hydrolyzed more rapidly than ATP. They were also able to promote DNA strand exchange reactions by a pathway common for other RecA proteins. However, we did not obtain DNA strand exchange products when reactions were performed on an inverse pathway, characteristic for RecA of D. radiodurans.ConclusionsThe characterization of DgeRecA and DmuRecA proteins made in this study indicates that the unique properties of D. radiodurans RecA are probably not common among RecA proteins from Deinococcus sp.

| S-EPMC3103430 | biostudies-literature

exoRNA-mediated Cell-to-cell Communications in E. coli are Supported by Dps Mobility

Project description:Being a ferroxidase and a structural factor of the Escherichia coli nucleoid, Dps protein was recently encountered in the outer membrane and attracted attention as a potential partner for bacterial RNAs. Here, we show the first images visualizing Dps on the surface of bacteria and demonstrate that Dps produced by E. coli K-12 MG1655 or BL21(DE3) cells can cross bacteria-impermeable membrane and attach to the cell surface of a dps-null mutant. Using RNAseq and pull-down assays, we identified RNAs with specifically reduced secretion in the mutant and witnessed preferential interaction of Dps with tRNA and sRNA fragments. Upon analysis of their deviations from the genomic sequences, we selected one circular and six linear oligonucleotides with different folding as model RNAs and showed their ability to affect the growth of bacteria via Dps-dependent internalization by cells. This assumes Dps involvement in intercellular signal transduction within a bacterial population through participation in RNA secretion

2023-08-30 | GSE221667 | GEO

RNA-seq analysis of Deinococcus metallilatus

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

2019-04-27 | GSE130360 | GEO