Characterize the regulon of 6C sRNA in Mycobacteria smegmatis
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ABSTRACT:
PROVIDER: PRJNA488900 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7777471_1.fastq.gz | Fastqsanger.gz | |||
| SRR7777471_2.fastq.gz | Fastqsanger.gz | |||
| SRR7777472_1.fastq.gz | Fastqsanger.gz | |||
| SRR7777472_2.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: The goals of this study are to identify the putative mRNA targets that are regulated by the 6C sRNA. We constuct an inducible vector to transiently overexpressed the 6C sRNA in M. smegmatis, and then we perform RNA-Seq to look for genes that are differicently expressed upon the over-expression of 6C sRNA, which we think these genes are the potential targets of the 6C sRNA.
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Project description:DosR is the regulator of a two-component system in mycobacteria that senses oxygen concentration and the redox state of the cells. To determine the DosR regulon, the transcriptomes of M. smegmatis mc2155 and the M-NM-^TdosR cells were compared by microarray at 10 hours following induction of oxygen-limitation in serum vials. 4 biological replicates incl. 2 dye swaps. 3 technical replicates per array
2014-07-10 | E-GEOD-56083 | biostudies-arrayexpress
Project description:Mycobacterium smegmatis SigF is a group III sigma factor. Its ortholog in M. tuberculosis is reported to have role in regulation and function of cell wall components. In present study we have created an M. smegmatis ΔsigF mutant by allele exchange method. M. smegmatis sigF mutant shows non pigmented phenotype and is more sensitive to hydrogen peroxide generated oxidative stress. DNA microarray analysis of M. smegmatis wild type and ΔsigF mutant suggests that SigF in this species controls the expression of several energy and central intermediary metabolism genes along with regulation of carotenoid biosynthesis.
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Project description:The naive CD4 T cell compartment is heterogeneous. Ly-6C- and Ly-6C+ Naive CD4 T cells were compare by microarrays.
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Project description:The naive CD4 T cell compartment is heterogeneous. Ly-6C- and Ly-6C+ Naive CD4 T cells were compare by microarrays. Ly-6C- and Ly-6C+ Naive CD4 T cells were purified for RNA extraction and hybridization on Affymetrix microarrays.
2013-03-01 | E-GEOD-37336 | biostudies-arrayexpress
Project description:Rhodopirellula europaea 6C strain:6C Genome sequencing and assembly
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Project description:DosR is the regulator of a two-component system in mycobacteria that senses oxygen concentration and the redox state of the cells.
2014-07-10 | GSE56083 | GEO
Project description:BACKGROUND: Nitrogen is an essential element for bacterial growth and an important component of biological macromolecules. Consequently, responding to nitrogen limitation is critical for bacterial survival and involves the interplay of signalling pathways and transcriptional regulation of nitrogen assimilation and scavenging genes. In the soil dwelling saprophyte Mycobacterium smegmatis the OmpR-type response regulator GlnR is thought to mediate the transcriptomic response to nitrogen limitation. However, to date only ten genes have been shown to be in the GlnR regulon, a vastly reduced number compared to other organisms. RESULTS: We investigated the role of GlnR in the nitrogen limitation response and determined the entire GlnR regulon, by combining expression profiling of M. smegmatis wild type and glnR deletion mutant, with GlnR-specific chromatin immunoprecipitation and high throughput sequencing. We identify 53 GlnR binding sites during nitrogen limitation that control the expression of over 100 genes, demonstrating that GlnR is the regulator controlling the assimilation and utilisation of nitrogen. We also determine a consensus GlnR binding motif and identify key residues within the motif that are required for specific GlnR binding. CONCLUSIONS: We have demonstrated that GlnR is the global nitrogen response regulator in M. smegmatis, directly regulating the expression of more than 100 genes. GlnR controls key nitrogen stress survival processes including primary nitrogen metabolism pathways, the ability to utilise nitrate and urea as alternative nitrogen sources, and the potential to use cellular components to provide a source of ammonium. These studies further our understanding of how mycobacteria survive nutrient limiting conditions. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-143]
2013-04-24 | E-BUGS-143 | biostudies-arrayexpress
Project description:Mycobacterium smegmatis SigF is a group III sigma factor. Its ortholog in M. tuberculosis is reported to have role in regulation and function of cell wall components. In present study we have created an M. smegmatis M-NM-^TsigF mutant by allele exchange method. M. smegmatis sigF mutant shows non pigmented phenotype and is more sensitive to hydrogen peroxide generated oxidative stress. DNA microarray analysis of M. smegmatis wild type and M-NM-^TsigF mutant suggests that SigF in this species controls the expression of several energy and central intermediary metabolism genes along with regulation of carotenoid biosynthesis. Gene expression patterns of M.smegmatis wild type and M-NM-^TsigF mutant strains were compared at two growth stages i.e. log (OD600 ~1.4) and stationary (OD600 ~3.0). M. smegmatis strains were grown in DifcoTM MiddleBrook 7H9 broth base (BD Biosciences, Sparks, MD, USA) with 0.2% glycerol (v/v) and 0.05% Tween-80 (Sigma-Aldrich, St Louis, MO, USA) supplemented with 10% albumen dextrose catalase (BD Biosciences) (v/v) at 37 0C with continuous shaking. Total RNA was isolated using Trizole (Invitrogen) method and labelled with cyanine 3 (Cy3) as per Agilent 1-color labelling protocol (Version 5.5, February 2007). Six hundred nanograms of each Cy3 labelled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were performed using Gene Expression Hybridization kit (Agilent Technologies). Hybridization was carried out in AgilentM-bM-^@M-^Ys Surehyb Chambers at 65 0C for 16 h. The hybridized slides were washed using Agilent Gene Expression wash buffers and scanned using the Agilent Microarray Scanner G Model G2565BA at 5 micron resolution. Feature extracted data was analysed using GeneSpring GX v 7.3.1 software from Agilent. Normalization of the data was done in GeneSpring GX using the recommended one color Per Chip and Per Gene Data Transformation. Set measurements less than 0.01 to 0.01 per chip, normalize to 50th percentile per gene, and normalize to specific samples.
2010-08-20 | E-GEOD-19774 | biostudies-arrayexpress