Ribosome profiling of Mycobacterium tuberculosis under nutrient starvation
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ABSTRACT:
PROVIDER: PRJEB37021 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We have performed parallel ribosome profiling and RNA sequencing to determine which mRNAs are being translated during exponential growth and following 24 hours of nutrient starvation in the human pathogen Mycobacterium tuberculosis.
2021-02-02 | E-MTAB-8835 | biostudies-arrayexpress
Project description:Transcriptional profiling of Mycobacterium tuberculosis H37Rv and Mycobacterium bovis Ravenel before (i.e., log-phase control) and at 24h and 96h after nutrient starvation. The transcriptional profile of the two strains were compared at log phase, and after 24h and 96h of starvation. In addition, the response of each strain to starvation was examined after 24h and 96h of starvation.
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Project description:UASB anammox nutrient starvation Metagenome
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Project description:Iron restriction is a growth limiting condition encountered by M. tuberculosis in the host. In this study we examined the survival and physiology of iron depleted M. tuberculosis. We found that iron depleted M. tuberculosis survive for long time with little or no replication and is able to resume normal growth when iron becomes available. To understand the mechanism used by M. tuberculosis to survive under iron starvation we examine the transcriptional profile of iron-starving in comparison to that of iron-sufficient M. tuberculosis.
2017-09-15 | GSE84554 | GEO
Project description:Mycobacterium tuberculosis was grown in Middlebrook 7H9 medium supplemented with 0.4% glycerol, 0.085% NaCL, 0.5% BSA and 0.05% Tyloxapol in roller bottle culture (2 rpm at 37°C). To induce starvation, exponentially growing bacteria were washed and resuspended in PBS supplemented with 0.025% Tyloxapol. Cultures were harvested at 0h, 12h and 24h after starvation induction. After harvesting and lysis, proteins were extracted, reduced, alkylated, and digested using trypsin. The peptides were analysed in DDA mode on a Thermo LTQ Orbitrap XL. Data analysis: Thermo raw files were converted into mzXML format using ProteoWizard. The acquired MS2 spectra were searched with OMSSA (2.1.9), X!Tandem (CYCLONE, 2010.12.01.1), and MyriMatch (2.1.114) against an Mtb H37Rv protein database (TubercuList v2.3, April 2011) additionally containing reversed sequences of all proteins in the database. Search parameters were as follows: semi-tryptic peptides (proteolytic cleavage after lysine and arginine unless followed by proline) and up to two missed cleavages were allowed, mass tolerance of the precursor ions was set to 20 ppm. Carbamidomethylation at cysteines was set as a fixed modification and oxidation at methionines as a variable modification. The output of the search engine was processed using PeptideProphet and iProphet. Only peptides at a false discovery rate of less than 1% were taken into consideration for further analysis. For MS1 based label-free quantification the openMS v1.8 framework was used as described by (Weisser et al., 2013). Signals were normalised on peptide feature level such that the median signal in each sample is the same. Abundances of the three most intense peptides were averaged to get a protein abundance value. The same peptides were used for protein quantification across all samples and proteins with less than three peptides were included. Associated RNA-seq data have been deposited to EBI ArrayExpress with accession number E-MTAB-1616.
2013-11-22 | PXD000483 | Pride
Project description:Mycobacteria are known to be non-spore forming but very hardy: the bacilli can for instance survive starvation in zero-nutrient saline in a non-replicating state. Recently we reported that mycobacteria in fact can undergo cellular differentiation when exposed to different starvation conditions. The presence of traces of nutrients triggers the development of a new, ‘small resting cell’ form (SMRCs). Saline shock-starved large resting cells (LARCs), which did not show cell size or surface changes when observed by scanning electron microscopy, remodeled their internal structure to the septated, multi-nucleoided cells seen during differentiation to SMRCs. Here we conduct RNA-seq to gain greater insights into whether starvation elicited a distinct developmental pathway. Comparative transcriptome analysis of SMRC and LARC development revealed largely overlapping sets of differentially expressed regulatory and metabolic genes. These transcriptome data are consistent with a mycobacterial starvation-induced differentiation program in which at first septated, multi-nuceloided cells are generated. Under zero-nutrient conditions bacteria terminate development at this stage as LARCs. In the presence of traces of a carbon source, these multi-nucleoided cells continue differentiation into mono-nuleoided SMRCs.
2016-10-10 | GSE69983 | GEO
Project description:Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔmetA during methionine starvation
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Project description:The development of antibiotic tolerance is believed to be a major factor in the lengthy duration of current tuberculosis therapies. In the current study, we have modeled antibiotic tolerance in vitro by exposing Mycobacterium tuberculosis to two distinct stress conditions: progressive hypoxia and nutrient starvation [phosphate-buffered saline (PBS)]. We then studied the bacterial transcriptional response using RNA-seq and employed a bioinformatics approach to identify important transcriptional regulators, which was facilitated by a novel Regulon Enrichment Test (RET). A total of 17 transcription factor (TF) regulons were enriched in the hypoxia gene set and 16 regulons were enriched in the nutrient starvation, with 12 regulons enriched in both conditions. Using the same approach to analyze previously published gene expression datasets, we found that three M. tuberculosis regulons (Rv0023, SigH, and Crp) were commonly induced in both stress conditions and were also among the regulons enriched in our data. These regulators are worthy of further study to determine their potential role in the development and maintenance of antibiotic tolerance in M. tuberculosis following stress exposure.
2018-04-03 | GSE104599 | GEO
Project description:Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔthrA during methionine starvation
2018-08-29 | GSE119105 | GEO