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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from wild type Sinorhizobium meliloti and mutants in the NSR grown under conditions of high and low nitrogen availability

ABSTRACT: Acquisition and utilization of nitrogen is governed by the Nitrogen Stress Response regulatory cascade. GlnD is the primary nitrogen sensor in this system, and modifies the PII proteins to effect changes in the expression of target genes. We used microarrays to evaluate changes in gene expression due to nitrogen availability, mutation of the glnD gene, and deletion of both PII proteins. Sinorhizobium meliloti cultures were grown at 30C to mid-log phase (0.5–0.6 OD600) for RNA extraction and hybridization on Affymetrix microarrays. Wild-type 1021, a strain containing a mutation in glnD, and a strain with both PII proteins deleted were grown in media containing either 0.05% ammonium chloride or 0.02% sodium glutamate as the nitrogen source.

ORGANISM(S): Sinorhizobium meliloti

SUBMITTER: Jennifer Rice

PROVIDER: E-GEOD-43570 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from wild type Sinorhizobium meliloti and mutants in the NSR grown under conditions of high and low nitrogen availability

Project description:Acquisition and utilization of nitrogen is governed by the Nitrogen Stress Response regulatory cascade. GlnD is the primary nitrogen sensor in this system, and modifies the PII proteins to effect changes in the expression of target genes. We used microarrays to evaluate changes in gene expression due to nitrogen availability, mutation of the glnD gene, and deletion of both PII proteins.

2013-01-18 | GSE43570 | GEO

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

The signal transduction protein PII controls ammonium, nitrate and urea uptake in cyanobacteria

Project description:PII signal transduction proteins are widely spread among all domains of life where they regulate a multitude of carbon and nitrogen metabolism related processes. Non-diazotrophic cyanobacteria can utilize a high variety of organic and inorganic nitrogen sources. In recent years, several physiological studies indicated an involvement of the cyanobacterial PII protein in regulation of ammonium, nitrate/nitrite and cyanate uptake. However, direct interaction of PII has not been demonstrated so far. In this study, we used biochemical, molecular genetic and physiological approaches to demonstrate that PII regulates all relevant nitrogen uptake systems in Synechocystis sp. strain PCC 6803: PII controls ammonium uptake by interacting with the Amt1 ammonium permease, probably similar to the known regulation of E. coli ammonium permease AmtB by the PII homologue GlnK. We could further clarify that PII mediates the ammonium- and dark-induced inhibition of nitrate uptake by interacting with the NrtC and NrtD subunits of the nitrate/nitrite transporter NrtABCD. We further identified the ABC-type urea transporter UrtABCDE as novel PII target. PII interacts with the UrtE subunit without involving the standard interaction surface of PII interactions. The deregulation of urea uptake in a PII deletion mutant causes ammonium excretion when urea is provided as nitrogen source. Furthermore, the urea hydrolyzing urease enzyme complex appears to be coupled to urea uptake. Overall, this study underlines the great importance of the PII signal transduction protein in the regulation of nitrogen utilization in cyanobacteria.

2019-07-10 | PXD013411 | Pride

Transcription profiling of Arabidopsis wild type and PII deficient plants grown on different nitrogen sources

Project description:In E.Coli, PII protein is known to be a sensor of medium nitrogen status and to regulate some nitrogen metabolism steps (e.g.glutamin synthase and ammonium transporter regulations). Arabidopsis PII protein is the only homolog gene found in the arabidopsis genome and its role is still unclear. The goal of this sudy is to obtain transcriptional information from PII mutants grown on different nitrogen sources. Wild type and PII mutant were grown hydroponically in a growth chamber under 1mM nitrate for 5 weeks then they were submitted to N-deficiency for 5 days followed by a resupply of 1 mM or 5mM NH4. The rosette leaves of three plants were harvested and pooled for each genotype and treatment.

2007-01-13 | E-MEXP-446 | biostudies-arrayexpress

The PII protein-protein interaction network in Azospirillum brasilense reveals a novel role of PII in the control of c-di-GMP homeostasis

Project description:The PII family comprises a group of widely distributed signal transduction proteins ubiquitous present in prokaryotes and in the chloroplast of plants. The PII proteins sense the levels of key metabolites ATP, ADP and 2-oxoglutarate which affect the PII structure and the ability of PII to interact with a range of target proteins. Here we performed multiple PII ligand fishing assays to identify proteins that are likely to be part of the PII protein interaction network in plant-growth promoting nitrogen-fixing bacterium Azospirillum brasilense. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, co-enzyme synthesis, RNA catabolism and transcription. Direct binary PII-target complex was confirmed for xx protein complex using pull-down assays with recombinant proteins. Untargeted metabolome showed that PII is required to proper maintenance of Coenzyme A, panthotenate, PRPP and SAICAR levels. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII minus strain showed reduced c-di-GMP levels and swimming behavior. These data support that PII acts as a major metabolic hub controlling key metabolic enzymes and c-di-GMP homeostasis accordingly to the prevailing nutritional status.

2020-10-23 | PXD018530 | Pride

s54 -dependent response to nitrogen limitation and virulence in Burkholderia cenocepacia H111

Project description:Members of the genus Burkholderia are versatile bacteria capable of colonizing highly diverse environmental niches. In this study, we investigated the global response of the opportunistic pathogen Burkholderia cenocepacia H111 to nitrogen limitation at the transcript and protein expression level. In addition to a classical response to nitrogen starvation, including the activation of glutamine synthetase, PII proteins and the two component regulatory system ntrBC, B. cenocepacia H111 also up-regulated polyhydroxybutyrate (PHB) accumulation and exopolysaccharide (EPS) production in response to nitrogen shortage. A search for consensus sequences in promoter regions of nitrogen responsive genes identified a s54 consensus sequence. The mapping of the s54 regulon as well as the characterization of a s54 mutant suggests an important role of s54 not only in control of nitrogen metabolism, but also in virulence of this organism.

2015-04-29 | GSE66328 | GEO

The Novel PII-Interacting Regulator PirC (Sll0944) Identifies 3-Phosphoglycerate Mutase (PGAM) as Central Control Point of Carbon Storage Metabolism in Cyanobacteria

Project description:Nitrogen limitation imposes a major transition in the life-style of non-diazotrophic cyanobacteria, which is regulated via a complex interplay of regulatory factors, involving, the nitrogen-specific transcription factor NtcA and the pervasive signal processor PII. Immediately upon nitrogen-limitation, newly fixed carbon is re-directed towards glycogen synthesis. How operation of the metabolic switch for distributing fixed carbon to either glycogen or cellular building blocks was poorly understood. Here we identify from Synechocystis sp. PCC 6803 a novel PII interactor, PirC, (Sll0944) that controls 3-phosphoglycerate mutase (PGAM), the enzyme that deviates newly fixed CO2 towards lower glycolysis. PirC acts as competitive inhibitor of PGAM and this interaction is tuned by PII/2-oxoglutarate. High oxoglutarate release PirC from PII-complex to inhibit PGAM. Accordingly, PirC deficient mutant, as compared to the wild-type, shows strongly reduced glycogen levels upon nitrogen deprivation whereas polyhydroxybutyrate granules are over-accumulated. Metabolome analysis revealed an imbalance in 3-phosphoglycerate to pyruvate levels in the PirC mutant, conforming that PirC controls the carbon flux in cyanobacteria via mutually exclusive interaction with either PII or PGAM.

2020-12-17 | PXD021415 | Pride

The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3 (ChvI-SyrA)

Project description:We characterized transcriptomes of strains containing a K214T mutation in chvI, with and without overexpression of syrA. Our work shows that overexpression of syrA suppresses many of the transcription changes observed in the chvI K214T mutant. Gene expression profiling of a Sinorhizobium meliloti chvI K214 mutant overexpressing syrA was performed using custom Affymetrix GeneChips

2015-03-31 | E-GEOD-61521 | biostudies-arrayexpress

Expression data from wildtype Sinorhizobium meliloti Rm1021 and an hfq mutant

Project description:The RNA-binding protein Hfq is a global regulator, which controls diverse cellular processes in bacteria. To begin understanding the role of Hfq in the Sinorhizobium meliloti-Medicago truncatula nitrogen-fixing symbiosis, we defined free-living and symbiotic phenotypes of an hfq mutant. Over 500 transcripts were differentially accumulated in the hfq mutant of S. meliloti Rm1021 when grown in a shaking culture. Gene expression profiling of Sinorhizobium meliloti Rm1021 or its isogenic hfq deletion mutant, grown to late exponential phase in rich medium, was performed using custom Affymetrix GeneChips.

2010-06-01 | E-GEOD-19346 | biostudies-arrayexpress

Mycobacterium smegmatis Growth Using Nitrate as a Nitrogen Source LC-MSMS

Project description:PII proteins are signal transduction proteins that belong to a widely distributed family involved in modulating various bacterial metabolisms. These homotrimeric proteins carry a flexible loop, known as the T-loop, whose conformation changes upon recognition of key metabolites such as ADP, ATP, and 2-oxoglutarate. PII proteins interact with various partners to primarily regulate nitrogen pathways, and in some organisms, they can also control carbon metabolism by interacting with the biotin carboxyl carrier protein (BCCP), a critical component of the acetyl-CoA carboxylase (ACC) enzyme complex, inhibiting its activity and consequently reducing fatty acid biosynthesis. In mycobacteria, only one PII protein has been identified; however, its physiological role remains unknown. In this study, we constructed a M. smegmatis deletion mutant, ∆MsPII, which exhibited growth deficiency when nitrate and nitrite were the sole nitrogen sources, leading to nitrite accumulation in the culture supernatant.

2024-03-15 | PXD049128 | Pride

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