Stringent response in S. meliloti
Ontology highlight
ABSTRACT:
ORGANISM(S): Sinorhizobium meliloti
SUBMITTER: Elizaveta Krol
PROVIDER: E-MTAB-703 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This study is an analysis of changes in gene expression during stringent response in Vibrio cholerae. V. cholerae cells in mid-log were treated with serine hydroxamate and gene expression was compared to untreated cells. Keywords: Stress response, stringent response
2006-12-28 | GSE6616 | GEO
Project description:The stringent response was defined in Lactococcus lactis through transcript profiling after the addition of a chemical inductor, the norvaline. Gene expression was measured in the exponential growth phase (reference sample) and at 1.6 h after norvaline addition. Four hundred and sixty one differentially expressed genes were identified and constituted the stringent response regulon. Keywords: stress response, time course
2009-04-28 | GSE10254 | GEO
Project description:The stringent response was defined in Lactococcus lactis through transcript profiling after the addition of a chemical inductor, the norvaline. Gene expression was measured in the exponential growth phase (reference sample) and at 1.6 h after norvaline addition. Four hundred and sixty one differentially expressed genes were identified and constituted the stringent response regulon. Keywords: stress response, time course Stringent response was imposed through norvaline addition during the growth of Lactococcus lactis IL1403 under controlled conditions (30 °C, pH 6.6, nitrogen atmosphere). Cell samples were harvested in exponential phase and 1.6 h after norvaline addition. Total RNA was extracted from these samples and radiolabelled cDNA were prepared and hybridized on nylon arrays. 2053 amplicons specific of Lactococcus lactis IL1403 genes were spotted twice on the array. The 2 time-points were analyzed simultaneously and 3 independent repetitions were performed.
2010-06-25 | E-GEOD-10254 | biostudies-arrayexpress
Project description:Transcriptome analysis of Streptococcus agalactiae (group B Streptococcus) grown under control conditions or coincubated with serine hydroxamate to induce the bacterial stringent response
2017-11-14 | GSE98398 | GEO
Project description:The stringent response is an adaptive physiological response triggered by different conditions of nutritional or environmental stress and aimed at increasing survival under harsh conditions. This response is mediated the signalling nucleotides guanosine tetraphosphate (ppGpp) and pentaphospate (pppGpp), collectively known as (p)ppGpp. In this study we aim to identify genome-wide targets of regulation by the stringent-response associated alarmone (p)ppGpp in Pseudomonas putida by performing RNA-seq experiments using the wild-type KT2440tel strain and a KT2440tel-derivative bearing deletions of the (p)ppGpp synthetase-encoding genes relA and spoT (ppGpp0 mutant).
2024-11-18 | GSE281821 | GEO
Project description:Transcriptional regulation by the stringent response-associated alarmone (p)ppGpp in Pseudomonas putida
| PRJNA1185757 | ENA
Project description:The stringent response represses translation and is activated when amino acid levels drop, for example during the stationary phase. Bacillus subtilis, a well-known industrial enzyme production organism, secretes most enzymes during the stationary phase. We were curious whether the stringent response affects ribosome pausing, and whether its absence improves protein production yields in the stationary phase. To investigate this, genome-wide ribosome profiling was used using a stringent response mutant that overexpressed the α-amylase AmyM. Although, blocking the stringent response did increases overall protein synthesis, the secretion of AmyM was actually reduced. The ribosome profiling data revealed that this was not caused by a reduction in translation. In fact, absence of the stringent response did not seem to markedly influence ribosome pausing. However, late in stationary phase an increased ribosome pausing at tryptophane codons emerges, suggesting a depletion of tryptophane. A strong suppression of tryptophane biosynthesis and acquisition genes, under control of the trp RNA-binding attenuation protein TRAP, likely accounts for this, although TRAP does not belong to the stringent response regulon of B. subtilis. Finally, the ribosome profiles revealed several genes with unusually low translation activities, illustrating the importance of translation initiation as a regulatory element of expression.
2025-05-01 | GSE293166 | GEO
Project description:The stringent response represses translation and is activated when amino acid levels drop, for example during the stationary phase. Bacillus subtilis, a well-known industrial enzyme production organism, secretes most enzymes during the stationary phase. We were curious whether the stringent response affects ribosome pausing, and whether its absence improves protein production yields in the stationary phase. To investigate this, genome-wide ribosome profiling was used using a stringent response mutant that overexpressed the α-amylase AmyM. Although, blocking the stringent response did increases overall protein synthesis, the secretion of AmyM was actually reduced. The ribosome profiling data revealed that this was not caused by a reduction in translation. In fact, absence of the stringent response did not seem to markedly influence ribosome pausing. However, late in stationary phase an increased ribosome pausing at tryptophane codons emerges, suggesting a depletion of tryptophane. A strong suppression of tryptophane biosynthesis and acquisition genes, under control of the trp RNA-binding attenuation protein TRAP, likely accounts for this, although TRAP does not belong to the stringent response regulon of B. subtilis. Finally, the ribosome profiles revealed several genes with unusually low translation activities, illustrating the importance of translation initiation as a regulatory element of expression.
2025-05-01 | GSE293165 | GEO
Project description:Sinorhizobium meliloti lives as a soil saprophyte, and engages in a nitrogen fixing symbiosis with plant roots. To succeed in such diverse environments, the bacteria must continually adjust gene expression. Transcriptional plasticity in eubacteria is often mediated by alternative sigma factors interacting with core RNA polymerase. The S. meliloti genome encodes 14 of these alternative sigmas, including 11 extracytoplasmic function (ECF) sigmas. We used custom Affymetrix Symbiosis Chips to characterize the global transcriptional response of S. meliloti overexpressing the ECF sigma factor, RpoE2. Our work identifies over 200 genes whose expression is dependent on RpoE2.
2013-07-22 | GSE40391 | GEO
Project description:Sinorhizobium meliloti is a soil-dwelling symbiotic alphaproteobacterium. Cyclic di-GMP is an important second messenger controlling multiple functions in this microorganism. To understand transcriptional regulation by elevated c-di-GMP in S. meliloti, the transcriptome analysis was performed on the wild type strain S. meliloti Rm2011 carrying either an empty vector pWBT or diguanylate cyclase gene pleD overexpression plasmid pWBT-pleD.
2017-06-01 | E-MTAB-5410 | biostudies-arrayexpress