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Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress

ABSTRACT: Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress

PROVIDER: PRJEB6175 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR489744.fastq.gz	Fastqsanger.gz
	ERR489745.fastq.gz	Fastqsanger.gz
	ERR489746.fastq.gz	Fastqsanger.gz
	ERR489747.fastq.gz	Fastqsanger.gz

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Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress

Project description:The aim of this study was to extend our analysis to the obligate human pathogen M. tuberculosis, which has to deal with a more restricted set of environmental variables in terms of nitrogen sources, and to delineate the GlnR regulon, by peforming global analysis of GlnR-DNA interactions by Chromatin Immunoprecipitation and high-throughput sequencing (ChIP-seq) over nitrogen run-out.

2014-12-01 | E-MTAB-2492 | biostudies-arrayexpress

Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress.

Project description:A key component to the success of Mycobacterium tuberculosis as a pathogen is the ability to sense and adapt metabolically to the diverse range of conditions encountered in vivo, such as oxygen tension, environmental pH and nutrient availability. Although nitrogen is an essential nutrient for every organism, little is known about the genes and pathways responsible for nitrogen assimilation in M. tuberculosis. In this study we have used transcriptomics and chromatin immunoprecipitation and high-throughput sequencing to address this. In response to nitrogen starvation, a total of 185 genes were significantly differentially expressed (96 up-regulated and 89 down regulated; 5% genome) highlighting several significant areas of metabolic change during nitrogen limitation such as nitrate/nitrite metabolism, aspartate metabolism and changes in cell wall biosynthesis. We identify GlnR as a regulator involved in the nitrogen response, controlling the expression of at least 33 genes in response to nitrogen limitation. We identify a consensus GlnR binding site and relate its location to known transcriptional start sites. We also show that the GlnR response regulator plays a very different role in M. tuberculosis to that in non-pathogenic mycobacteria, controlling genes involved in nitric oxide detoxification and intracellular survival instead of genes involved in nitrogen scavenging.

| S-EPMC4950008 | biostudies-other

Transcription profiling by array of Mycobacterium smegmatis response to nitrogen stress using bipartite active modules

Project description:BACKGROUND: The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. RESULTS: A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. CONCLUSIONS: Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-140]

2013-06-10 | E-BUGS-140 | biostudies-arrayexpress

Comprehensive Proteomic Analysis of Nitrogen Starved Mycobacterium smegmatis Δpup Reveals the Impact of Pupylation on Nitrogen Stress Response

Project description:Mycobacterium smegmatis is a soil bacterium exposed to continuously environmental changes of nitrogen availability. As member of Actinobacteria, it possesses an ubiquitin-like post-translational modification pathway called pupylation. The pathway starts when a small protein called Pup is attached to a lysine of a specific cellular target. Then the Pup-modified protein is degraded by the proteasome, as it was shown that Pup acts as degradation signal. Recent studies showed the role of pupylation in Mycobacterium smegmatis for survival under nitrogen starvation by supplying recycled amino acids. The present study is an investigation of the influence of Mycobacterium smegmatis Pup protein on the whole proteome in absence of nitrogen sources. Therefore a pup deletion mutant was generated. Applying stable isotope dimethyl labelling, low impact of the pupylation on proteome was revealed immediately after exposure to growth medium lacking nitrogen. In contrast, post 24 h of nitrogen starvation, Msm pup deletion strain showed several proteins with significant changes in abundance. Noteworthy, key proteins involved in nitrogen assimilation were significantly affected in Msm Δpup. Furthermore, we label-free quantified pupylated proteins of nitrogen starved Msm for a more extensive understanding of pupylation role in surviving and overcoming the lack of nitrogen.

2016-08-11 | PXD003229 | Pride

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection (expression)

Project description:Identification of genetic polymorphisms associated with inter-individual variation in immune response to Mycobacterium tuberculosis infection.

2011-12-06 | GSE34151 | GEO

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection (genotype)

Project description:Identification of genetic polymorphisms associated with inter-individual variation in immune response to Mycobacterium tuberculosis infection.

2011-12-30 | GSE34588 | GEO

Aspartate aminotransferase Rv3722c governs aspartate-dependent nitrogen metabolism in Mycobacterium tuberculosis

Project description:<p>Gene rv3722c of Mycobacterium tuberculosis is essential for in vitro growth, and encodes a putative pyridoxal phosphate-binding protein of unknown function. Here we use metabolomic, genetic and structural approaches to show that Rv3722c is the primary aspartate aminotransferase of M. tuberculosis, and mediates an essential but underrecognized role in metabolism: nitrogen distribution. Rv3722c deficiency leads to virulence attenuation in macrophages and mice. Our results identify aspartate biosynthesis and nitrogen distribution as potential species-selective drug targets in M. tuberculosis.</p>

2020-05-01 | MTBLS1559 | MetaboLights

Transcription profiling by array of adenylylation of mycobacterial Glnk (PII) protein induced by nitrogen limitation

Project description:PII proteins are pivotal regulators of nitrogen metabolism in most prokaryotes, controlling the activities of many targets, including nitrogen assimilation enzymes, two component regulatory systems and ammonium transport proteins. Escherichia coli contains two PII-like proteins, PII (product of glnB) and GlnK, both of which are uridylylated under nitrogen limitation at a conserved Tyrosine-51 residue by GlnD (a uridylyl transferase). PII-uridylylation in E. coli controls glutamine synthetase (GS) adenylylation by GlnE and mediates the NtrB/C transcriptomic response. Mycobacteria contain only one PII protein (GlnK) which in environmental Actinomycetales is adenylylated by GlnD under nitrogen limitation. However in mycobacteria, neither the type of GlnK (PII) covalent modification nor its precise role under nitrogen limitation is known. In this study, we used LC-Tandem MS to analyse the modification state of mycobacterial GlnK (PII), and demonstrate that during nitrogen limitation GlnK from both non-pathogenic Mycobacterium smegmatis and pathogenic Mycobacterium tuberculosis is adenylylated at the Tyrosine-51 residue; we also show that GlnD is the adenylyl transferase enzyme responsible. Further analysis shows that in contrast to E. coli, GlnK (PII) adenylylation in M. tuberculosis does not regulate GS adenylylation, nor does it mediate the transcriptomic response to nitrogen limitation. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-135]

2013-05-10 | E-BUGS-135 | biostudies-arrayexpress

Nitrogen regulatory protein C couples nitrogen stress response and stringent response in nitrogen starved Escherichia coli.

Project description:Nitrogen regulatory protein C couples nitrogen stress response and stringent response in nitrogen starved Escherichia coli.

| PRJEB5230 | ENA

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.

Project description:Identification of genetic polymorphisms associated with inter-individual variation in immune response to Mycobacterium tuberculosis infection. We performed a genome-wide mapping study of loci that are associated with functional variation in immune response to MTB. Specifically, we characterized transcript and protein expression levels and mapped expression quantitative trait loci (eQTLs) in primary dendritic cells from 65 individuals, before and after infection with MTB

2011-12-06 | E-GEOD-34151 | biostudies-arrayexpress

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