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Omics score: 1000

RNA-seq analysis of Mycobacterium tuberculosis response to threonine auxotrophic starvation

ABSTRACT: RNA-seq analysis of Mycobacterium tuberculosis response to threonine auxotrophic starvation

PROVIDER: PRJNA488113 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7759900.fastq.gz	Fastqsanger.gz
	SRR7759901.fastq.gz	Fastqsanger.gz
	SRR7759902.fastq.gz	Fastqsanger.gz
	SRR7759903.fastq.gz	Fastqsanger.gz
	SRR7759904.fastq.gz	Fastqsanger.gz

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Publications

Derailing the aspartate pathway of Mycobacterium tuberculosis to eradicate persistent infection.

Hasenoehrl Erik J EJ Rae Sajorda Dannah D Berney-Meyer Linda L Johnson Samantha S Tufariello JoAnn M JM Fuhrer Tobias T Cook Gregory M GM Jacobs William R WR Berney Michael M

Nature communications 20190916 1

A major constraint for developing new anti-tuberculosis drugs is the limited number of validated targets that allow eradication of persistent infections. Here, we uncover a vulnerable component of Mycobacterium tuberculosis (Mtb) persistence metabolism, the aspartate pathway. Rapid death of threonine and homoserine auxotrophs points to a distinct susceptibility of Mtb to inhibition of this pathway. Combinatorial metabolomic and transcriptomic analysis reveals that inability to produce threonine ...[more]

PMID: 31527595

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RNA-seq analysis of Mycobacterium tuberculosis response to threonine auxotrophic starvation

Project description:Time-course transcriptional profiling of the methionine auxotroph M. tuberculosis H37Rv ΔthrB during threonine starvation Overall design: RNA-Seq analysis of H37Rv∆thrB transcriptomic response during threonine starvation. Total RNA samples collected for extraction and analysis before starvation and at 1 and 2 days post starvation initiation.

2018-08-29 | GSE119106 | GEO

Arginine starvation response of Mycobacterium tuberculosis H37Rv ΔargB and ΔargF

Project description:Time -course transcriptional profiling of arginine starved Mycobacterium tuberculosis H37Rv ΔargB or ΔargF realtive to day 0 of starvation Overall design: Two-condition experiment, before starvation vs. either 1 day, 3 days or 6 days after starvation. Biological replicates: 3, one dye flip

2018-08-31 | GSE98821 | GEO

Microarry and RNA-seq analysis of M. tuberculosis response to threonine auxotrophic starvation

Project description:Microarry and RNA-seq analysis of M. tuberculosis response to threonine auxotrophic starvation

| PRJNA488112 | ENA

Mycobacterium tuberculosis Serine/Threonine Protein Kinases.

Project description:The Mycobacterium tuberculosis genome encodes 11 serine/threonine protein kinases (STPKs). A similar number of two-component systems are also present, indicating that these two signal transduction mechanisms are both important in the adaptation of this bacterial pathogen to its environment. The M. tuberculosis phosphoproteome includes hundreds of Ser- and Thr-phosphorylated proteins that participate in all aspects of M. tuberculosis biology, supporting a critical role for the STPKs in regulating M. tuberculosis physiology. Nine of the STPKs are receptor type kinases, with an extracytoplasmic sensor domain and an intracellular kinase domain, indicating that these kinases transduce external signals. Two other STPKs are cytoplasmic and have regulatory domains that sense changes within the cell. Structural analysis of some of the STPKs has led to advances in our understanding of the mechanisms by which these STPKs are activated and regulated. Functional analysis has provided insights into the effects of phosphorylation on the activity of several proteins, but for most phosphoproteins the role of phosphorylation in regulating function is unknown. Major future challenges include characterizing the functional effects of phosphorylation for this large number of phosphoproteins, identifying the cognate STPKs for these phosphoproteins, and determining the signals that the STPKs sense. Ultimately, combining these STPK-regulated processes into larger, integrated regulatory networks will provide deeper insight into M. tuberculosis adaptive mechanisms that contribute to tuberculosis pathogenesis. Finally, the STPKs offer attractive targets for inhibitor development that may lead to new therapies for drug-susceptible and drug-resistant tuberculosis.

2014-01-01 | S-EPMC4242435 | BioStudies

Ribosome profiling of Mycobacterium tuberculosis under nutrient starvation

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 | ArrayExpress

Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response.

Project description:The bacterial leucine-responsive regulatory protein (Lrp) is a global transcriptional regulator that controls the expression of many genes during starvation and the transition to stationary phase. The Mycobacterium tuberculosis gene Rv3291c encodes a 150-amino acid protein (designated here as Mtb LrpA) with homology with Escherichia coli Lrp. The crystal structure of the native form of Mtb LrpA was solved at 2.1 A. The Mtb LrpA structure shows an N-terminal DNA-binding domain with a helix-turn-helix (HTH) motif, and a C-terminal regulatory domain. In comparison to the complex of E. coli AsnC with asparagine, the effector-binding pocket (including loop 100-106) in LrpA appears to be largely preserved, with hydrophobic substitutions consistent with its specificity for leucine. The effector-binding pocket is formed at the interface between adjacent dimers, with an opening to the core of the octamer as in AsnC, and an additional substrate-access channel opening to the outer surface of the octamer. Using electrophoretic mobility shift assays, purified Mtb LrpA protein was shown to form a protein-DNA complex with the lat promoter, demonstrating that the lat operon is a direct target of LrpA. Using computational analysis, a putative motif is identified in this region that is also present upstream of other operons differentially regulated under starvation. This study provides insights into the potential role of LrpA as a global regulator in the transition of M. tuberculosis to a persistent state.

2008-01-01 | S-EPMC2144582 | BioStudies

Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases.

Project description:The Mycobacterium tuberculosis genome encodes 11 serine/threonine protein kinases (STPKs) that are structurally related to eukaryotic kinases. To gain insight into the role of Ser/Thr phosphorylation in this major global pathogen, we used a phosphoproteomic approach to carry out an extensive analysis of protein phosphorylation in M. tuberculosis. We identified more than 500 phosphorylation events in 301 proteins that are involved in a broad range of functions. Bioinformatic analysis of quantitative in vitro kinase assays on peptides containing a subset of these phosphorylation sites revealed a dominant motif shared by six of the M. tuberculosis STPKs. Kinase assays on a second set of peptides incorporating targeted substitutions surrounding the phosphoacceptor validated this motif and identified additional residues preferred by individual kinases. Our data provide insight into processes regulated by STPKs in M. tuberculosis and create a resource for understanding how specific phosphorylation events modulate protein activity. The results further provide the potential to predict likely cognate STPKs for newly identified phosphoproteins.

2010-01-01 | S-EPMC2867705 | BioStudies

Comparison of the responses of Mycobacterium tuberculosis and Mycobacterium bovis to nutrient starvation

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. Overall design: For examination of the responses of each of the two strains to starvation 6 biological replicates were used and each log phase control (i.e., 6 for each strain) was compared to the starvation samples (i.e., at both 24h and 96h after starvation). This resulted in 24 comparisons (i.e., 12 for each strain). For comparison of the two strains at each of the 3 time points (i.e., at log-phase, 24h and 96h after starvation) 4 biological replicates of one strain (M.tuberculosis H37Rv) were compared to 6 biological replicates of the other strain (M. bovis Ravenel). This involved a first experiment in which samples from 2 independent cultures of H37Rv were compared to 4 independent cultures of Ravenel (i.e., each H37Rv replicate was compared to each of 2 Ravenel replicates), followed by a 2nd experiment in which 2 independent cultures of H37Rv were compared to 2 independent cultures of Ravenel. This resulted in 18 total comparisons.

2018-04-02 | GSE17835 | GEO

Association between intrinsic disorder and serine/threonine phosphorylation in Mycobacterium tuberculosis.

Project description:Serine/threonine phosphorylation is an important mechanism that is involved in the regulation of protein function. In eukaryotes, phosphorylation occurs predominantly in intrinsically disordered regions of proteins. Though serine/threonine phosphorylation and protein disorder are much less prevalent in prokaryotes, some bacteria have high levels of serine/threonine phosphorylation and disorder, including the medically important M. tuberculosis. Here I show that serine/threonine phosphorylation sites in M. tuberculosis are highly enriched in intrinsically disordered regions, indicating similarity in the substrate recognition mechanisms of eukaryotic and M. tuberculosis kinases. Serine/threonine phosphorylation has been linked to the pathogenicity and survival of M. tuberculosis. Thus, a better understanding of how its kinases recognize their substrates could have important implications in understanding and controlling the biology of this deadly pathogen. These results also indicate that the association between serine/threonine phosphorylation and disorder is not a feature restricted to eukaryotes.

2015-01-01 | S-EPMC4304846 | BioStudies

Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems.

Project description:In order to successfully enter the latent stage, Mycobacterium tuberculosis must adapt to conditions such as nutrient limitation and hypoxia. In vitro models that mimic latent infection are valuable tools for describing the changes in metabolism that occur when the bacterium exists in a non-growing form. We used two complementary proteomic approaches, label-free LC-MS/MS analysis and two-dimensional difference gel electrophoresis, to determine the proteome profile of extracellular proteins from M. tuberculosis cultured under nutrient starvation. Through the label-free LC-MS/MS analysis of fractionated samples, 1176 proteins were identified from culture filtrates of log phase and nutrient-starved cultures, and the protein levels of 230 proteins were increased in nutrient-starved culture filtrates, whereas those of 208 proteins were decreased. By means of Gene Ontology clustering analysis, significant differences in the overall metabolism during nutrient starvation were detected. Notably, members of the toxin-antitoxin systems were present in larger quantities in nutrient-starved cultures, supporting a role for these global modules as M. tuberculosis switches its metabolism into dormancy. Decreased abundance of proteins involved in amino acid and protein synthesis was apparent, as well as changes in the lipid metabolism. Further analysis of the dataset identified increased abundance of lipoproteins and decreased abundance of ESAT-6 family proteins. Results from the two-dimensional difference gel electrophoresis proteomics demonstrated overall agreement with the LC-MS/MS data and added complementary insights about protein degradation and modification.

2013-01-01 | S-EPMC3650330 | BioStudies

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