Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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.

ORGANISM(S): Medicago truncatula Sinorhizobium meliloti

PROVIDER: GSE43570 | GEO | 2013/01/18

SECONDARY ACCESSION(S): PRJNA186738

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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. 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.

2013-01-18 | E-GEOD-43570 | biostudies-arrayexpress

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

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 small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

Project description:The Alphaproteobacterium Sinorhizobium meliloti lives in soil and is capable of fixing molecular nitrogen in symbiosis with legume plants. In this work, the small proteome of S. meliloti strain 2011 was studied to uncover translation of both annotated and novel small open reading frame (sORF)-encoded proteins (SEPs).

2023-03-13 | PXD034931 | Pride

Genome Variation in the Symbiotic Nitrogen-Fixing Bacterium Sinorhizobium meliloti

Project description:Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti. Using the sequenced strain Rm1021 as a reference, the genome size and gene content variations were analyzed among ten diverse natural strains, through pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01Mbp, with the greatest variation arising from the pSymA replicon, followed by that of pSymB. No observable size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of ORFs on pSymA were variably absent/present, followed by 12.7% on pSymB, and 3.7% on the chromosome. However, the percentages of ORFs that were variably duplicated were more evenly distributed among the three replicons, 11.0%, 16.5% and 15.3% respectively for ORFs on pSymA, pSymB and the chromosome. Among the 10 strains, the percentages of absent ORFs ranged from 1.51% to 6.35% and those of duplicated ORFs ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in their numbers of absent ORFs as well as the numbers of duplicated ORFs, consistent with coordinated gene gains/losses in this important bacterium in nature. microarray:Sm6kOligo

2009-05-01 | GSE15889 | GEO

Interaction between Nitrogen and Phosphate Stress Responses in Sinorhizobium meliloti.

Project description: Not available

| S-EPMC5127829 | biostudies-literature

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

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.

Project description: Not available

| S-EPMC3164228 | biostudies-literature

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

Transcriptional response to nitrogen availability in yeast

Project description:We used cDNA microarray technology to compare the genome-wide expression profiles of a wild type strain (BY4700) (E02, E04, E06) or the isogenic strain deleted of GLN3 and GAT1 genes (E01, E03, E05) grown in YNB medium with glutamine as nitrogen source (M.Gln) against the wild type strain grown in M.Gln after addition of rapamacyn (20 min) (E01, E02), or M.proline (M.Pro) (E03, E04) or after a two hours shift from M.Gln to M.Pro (E05, E06), all growth conditions known to modify the expression of genes involved in nitrogen utilization. These microarrays allowed to identify the set of genes that were up or down-regulated in response to the quality of the nitrogen source. To evaluate whether the majority of genes responding to the nitrogen source were dependent on Gln3 and Gat1, we compared the expression profiles of the wild type strain and of the isogenic strain deleted of GLN3 and GAT1 genes (03167b: ura3, gln3∆, gat1∆), when both strains were grown on M.Gln + rapamycin (E07), or M.Pro (E08) or after a shift from M.Gln to M.Pro (E09). We also used an independent means of identifying Gln3-Gat1 regulated genes by comparing the expression profiles in wild type and ure2∆ (4709∆URE2) strains on M.Gln medium (E10). Keywords: nitrogen availability, knock-out response

2006-07-06 | GSE2891 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data