Name: ChIP-seq of M. smegmatis wild type and glnR deletion strains to investigate growth in nitrogen limiting conditions
Keywords: ChIP-seq

Dataset Information

ChIP-seq of M. smegmatis wild type and glnR deletion strains to investigate growth in nitrogen limiting conditions

ABSTRACT: M. smegmatis wild type and glnR deletion strains grown in nitrogen limiting conditions (1 mM ammonium sulphate nitrogen source). Samples taken 1 hour after nitrogen depletion from the media for each strain.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mycolicibacterium smegmatis

SUBMITTER: Geraint Barton

PROVIDER: E-MTAB-1456 | ArrayExpress | 2013-06-12

SECONDARY ACCESSION(S): ERP002151

REPOSITORIES: ArrayExpress, ENA

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Dataset's files

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			Action	DRS
	E-MTAB-1456.idf.txt	Idf
	E-MTAB-1456.sdrf.txt	Txt

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Publications

Genome wide analysis of the complete GlnR nitrogen-response regulon in Mycobacterium smegmatis.

Jenkins Victoria A VA Barton Geraint R GR Robertson Brian D BD Williams Kerstin J KJ

BMC genomics 20130504

<h4>Background</h4>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 lim ...[more]

PMID: 23642041

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Project description:Cell growth rate is regulated in response to resource availability including the abundance, and molecular form, of essential nutrients. In the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast), the molecular form of environmental nitrogen impacts both cell growth rate and mRNA expression. Disentangling causal relationships between nitrogen availability, cell growth rate and differential gene expression poses a considerable challenge. Using experimental control of cell growth rate using chemostats, we studied the effect of variation in environmental nitrogen on differential gene expression. We find that the primary determinant of nitrogen-regulated gene expression is nitrogen abundance whereas variation in nitrogen source affects the expression of only a small number of transcripts with highly specialized functions. To study the dynamics of nitrogen-responsive gene expression we perturbed steady-state nitrogen-limited chemostat cultures by addition of either proline or glutamine. Addition of either proline or glutamine to cells growing in nitrogen-limited chemostats results in repression of the nitrogen catabolite repression (NCR) regulon consistent with nitrogen abundance, and not nitrogen source, being the primary determinant of nitrogen-regulated gene expression. We find that a transition from nitrogen-limited to nitrogen-replete conditions is accompanied by rapid induction of transcripts required for protein translation. We identified a reciprocal relationship between specific regulons required for protein translation (RP and RiBi) and the NCR regulon. Using mathematical modeling we find evidence that cells adopt a metabolically inefficient growth mode during this transition. By means of high resolution time series analysis we find evidence that rapid, and potentially accelerated, mRNA degradation plays an important role in remodeling gene expression programs in response to change in environmental nitrogen. We propose that the evolutionarily conserved TORC1 signaling pathway orchestrates the balance between protein translation and assimilation of nitrogen sources at the transcriptional level to optimize rates of cell proliferation. A total of of 102 samples were analyzed in different nitrogen-limited conditions using chemostats in both steady-state and dynamic conditions. A common reference obtained from an ammonium-limited chemostat growing at a dilution rate of 0.12/hr was used for all two color hybridization experiments.