Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA232363 | ENA |
REPOSITORIES: ENA
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Project description:Serum and glucocorticoid-induced kinase 1 (SGK1) activates the epithselial sodium channel (eNaC) in tubules. We examined renal SGK1 abundance in salt-adaptation and in salt-sensitive hypertension. Sprague-Dawley and Dahl salt-sensitive rats were placed on either 8% or 0.3% NaCl diets for 10 days. Plasma aldosterone levels were approximately 2.5-fold greater on 0.3% versus 8% NaCl diets in both rat strains. Both serum and glucocorticoid-induced kinase 1 transcript and protein abundance were less (P<0.01) in Sprague-Dawley rats and greater (P<0.01) in Dahl salt-sensitive rats on 8% versus 0.3% NaCl diets. The cDNA sequences of serum and glucocorticoid-induced kinase 1 in both strains of rat were the same. The present results provide evidence that the abundance of serum and glucocorticoid-induced kinase 1 in rat kidney may play a role in salt adaptation and the pathogenesis of hypertension and suggests that aldosterone is not the primary inducer of SGK1 in the Sprague-Dawley rat.
2007-10-11 | E-GEOD-599 | biostudies-arrayexpress
Project description:Higher 13C-lactate labeling was seen in the more aggressive tumors, including all triple negative breast cancers. There was a significant correlation between lactate labeling and expression of the monocarboxylate transporter (MCT1), which mediates tumor cell pyruvate uptake, and a weaker correlation with expression of LDHA, which catalyzes label exchange between the injected pyruvate and the endogenous lactate pool.
| EGAS00001004118 | EGA
Project description:Serum and glucocorticoid-induced kinase 1 (SGK1) activates the epithelial sodium channel (eNaC) in tubules. We examined renal SGK1 abundance in salt-adaptation and in salt-sensitive hypertension. Sprague-Dawley and Dahl salt-sensitive rats were placed on either 8% or 0.3% NaCl diets for 10 days. Plasma aldosterone levels were approximately 2.5-fold greater on 0.3% versus 8% NaCl diets in both rat strains. Both serum and glucocorticoid-induced kinase 1 transcript and protein abundance were less (P<0.01) in Sprague-Dawley rats and greater (P<0.01) in Dahl salt-sensitive rats on 8% versus 0.3% NaCl diets. The cDNA sequences of serum and glucocorticoid-induced kinase 1 in both strains of rat were the same. The present results provide evidence that the abundance of serum and glucocorticoid-induced kinase 1 in rat kidney may play a role in salt adaptation and the pathogenesis of hypertension and suggests that aldosterone is not the primary inducer of SGK1 in the Sprague-Dawley rat. Keywords = Rattus norvegicus, Sprague Dawley, Dahl SS/Jr, kidney, NaCl diet Keywords: other
2004-02-14 | GSE599 | GEO
Project description:The context-dependent correlation between mRNA and protein abundance has long been debated. RNA sequencing (RNA-seq), a high-throughput, commonly used method for analyzing transcriptional dynamics and identifying biomarkers, leaves questions about whether we can translate RNA-seq-identified gene signatures directly to protein changes. In this study, we utilized a set of 17 widely assessed immune and wound healing mediators in the context of canine Volumetric Muscle Loss (VML) to investigate the correlation of mRNA and protein abundance. Our data reveal an overall agreement between mRNA and protein levels on these 17 mediators when examining samples from the same experimental condition, such as the same wound biopsy. However, we observed a lack of correlation between mRNA and protein levels for individual genes under different conditions, underscoring the challenges in converting transcript level changes directly into corresponding protein level changes. As an initial attempt to address this discrepancy, we developed a machine-learning model to predict protein abundances from RNA-seq data, achieving high accuracy (Spearman's Rho: 0.78-0.99, imputed versus measured protein abundance; pooling all biopsies; 5-fold cross-validation). Our approach also effectively corrected multiple extreme outliers measured by antibody-based protein assays. Additionally, this model has the potential to detect post-translational modification events, as shown by accurately estimating activated transforming growth factor (TGF)-β1 levels. While preliminary, this study introduces a promising strategy for translating RNA-seq data into protein abundance and the associated biological relevance.
2024-02-26 | GSE242973 | GEO
Project description:Salt stress is one major abiotic stress limiting maize grain yield throughout the world.To better understand maize salt tolerance molecular mechanism, comparative proteomic analysis was conducted on seedling roots of salt-tolerant genotype Jing724 and salt-sensitive genotype D9H under NaCl. Jing724 exhibited significantly higher germination rate and growth parameters (weight/length) than did D9H under salt treatment.We identified 565 differentially regulated proteins (DRP) usingiTRAQ and 89 were specific to Jing724 while 424 were specific to D9H. In salt stressed Jing724, pentose phosphate pathway, glutathione metabolism and nitrogen metabolism were enriched. By pathway enrichment and protein-protein interaction analyses, key DRPs such as glucose-6-phosphate 1-dehydrogenase, NADPH producing dehydrogenase, glutamate synthase and glutamine synthasewere identified.Additionally, salt responsive proteins of Jing724 were indicated to facilitate energy management, maintenance of redox homeostasis, reducing ammonia toxicity, osmotic homeostasis regulation, stress defense, stress adaptation, biotic cross-tolerance and gene transcription regulation. Quantification of multiple metabolic or enzymatic changes including SOD activity, MDA content, relative electrolyte leakage and Proline content were consistent with their predicted changes based on functions of DRPs. DRP analysis was correlated with the mRNA transcripts abundance variation of eight representative DRPs. These results contribute to elucidating molecular networks of salt tolerance.
2017-12-05 | PXD007711 | Pride
Project description:After transcription, a messenger RNA (mRNA) is further post-transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N6-methyladenosine, m6A). Both RNA secondary structure and m6A have been demonstrated to regulate mRNA stability and translation as well as have been independently linked to plant response to excess salt concentrations in the soil. However, the effect of m6A on regulating RNA secondary structure and the combinatorial interplay between these two RNA features during salt stress response has yet to be studied. Here, we globally identify RNA-protein interactions and RNA secondary structure during systemic salt stress. This analysis reveals that RNA secondary structure is highly dynamic during salt stress, which is independent of changes in RNA-protein interactions. Conversely, we find that m6A is anti-correlated with RNA secondary structure in a condition-specific manner, with salt-specific m6A resulting in a decrease in mRNA secondary structure during salt stress. Remarkably, we show that the combination of salt-specific m6A deposition and the associated loss of RNA secondary structure results in increases in mRNA stability and translation of transcripts encoding proteins involved in responses to abiotic stresses. In total, our comprehensive analyses reveal an important epitranscriptome, secondary structure-mediated post-transcriptional regulatory mechanism involved in plant long-term salt stress response and adaptation.
2020-04-01 | GSE147812 | GEO
Project description:Protein synthesis is the most energy consuming process in a proliferating cell, and understanding what controls protein abundances and how this impacts changes in metabolic fluxes is a key question in biology. We quantified mRNA and protein levels in Saccharomyces cerevisiae under ten environmental conditions. Linear correlation across all proteins predicted only 45% of the final protein abundances based on corresponding mRNAs, however, very good condition-dependent correlation was identified for individual proteins pointing to constant translation efficiency across the ten conditions. Hence, protein turnover was measured and combined with quantitative abundances to calculate translation efficiencies which were found to vary more than 400-fold. Non-linear regression analysis detected that mRNA abundance and translation elongation are the dominant factors controlling protein synthesis rate. Protein turnover was detected to play a minor role in determining protein levels, however, contributing markedly to overall cellular energy metabolism. Mitochondrial fluxes were detected to be the only major exception for flux control being at the posttranscriptional level. The here collected quantitative data provide a valuable resource for future studies.
2017-03-07 | PXD005041 | Pride
Project description:The extent to which carbon flux is directed towards fermentation vs. respiration differs between cell types and environmental conditions. Understanding the basic cellular processes governing carbon flux is challenged by the complexity of the metabolic and regulatory networks. To reveal the genetic basis for natural diversity in channeling carbon flux, we applied Quantitative Trait Loci analysis by phenotyping and genotyping hundreds of individual F2 segregants of budding yeast that differ in their capacity to ferment the pentose sugar xylulose. Causal alleles were mapped to the RXT3 and PHO23 genes, two components of the large Rpd3 histone deacetylation complex. We show that these allelic variants modulate the expression of SNF1/AMPK-dependent respiratory genes. Our results suggest that over close evolutionary distances, diversification of carbon flow is driven by changes in global regulators, rather than adaptation of specific metabolic nodes. Such regulators may improve the ability to direct metabolic fluxes for biotechnological applications. mRNA profiles of S. cerevisiae strain BY4741 with either the RXT3 or PHO23 genes either deleted, replaced by S. cerevisiae T73 allele or replaced by S. cerevisiae PHO23 allele
2015-12-04 | E-GEOD-75673 | biostudies-arrayexpress
Project description:The salt acclimation process of the euryhaline model cyanobacterium Synechocystis sp. PCC 6803 was analyzed by combining transcriptomic, proteomic and metabolomic methods. The comparison of salt-induced proteome and transcriptome changes revealed that most stably up-regulated proteins also showed elevated mRNA levels. The Pearson correlation coefficient for salt-induced abundance changes of 1749 transcript/protein pairs was r = 0.58. In addition to the rapid and stable upregulation of compatible solute biochemistry, a dynamic reorganization of the transcriptome occurred during the first hours after salt shock, which probably involves the action of small regulatory RNAs. Based on these data, an extended salt stimulon can be defined comprising many proteins directly or indirectly related to compatible solute metabolism, ion and water movements as well as a defined set of small regulatory RNAs. Our comprehensive data set provides the basis for future attempts to engineer cyanobacterial salt tolerance and to search for processes regulating this important environmental acclimation process.
2022-02-17 | PXD026118 | Pride
Project description:In eukaryotes, mRNA abundance is often a poor proxy for protein abundance. Despite this, the majority of methods used to dissect function in mammalian biology involve measurements of mRNA, with the assumption that changes observed at the mRNA level are reflected at the protein level. The inability to predict protein abundance from mRNA abundance is a major limitation when dissecting the relationship between genotype and phenotype in mammals. To understand the effect of cell-type, splice-variant selection and translation rate on the relationship between mRNA and protein abundance, we performed RNA-sequencing and mass-spectrometry proteomics of primary human naïve CD4+ T helper (NTH) cells at six time points during differentiation into T-helper type 1 (TH1) cells. For the RNA- sequencing, NTH cells were isolated from Human blood donors, subjected to T-helper 1 stimulation (anti-CD3/CD28, IL2 and IL12) for 0.5, 1, 2, 6 and 24 hours. At each time point cells were harvested, snap frozen and stored at -80 degrees Celsius. RNA was isolated from each sample and sequenced on an illumina 2500 instrument. By combining the information from the RNA- sequencing and the proteomics we constructed a simple mRNA-protein model, in which protein expression was defined as a linear combination of the splice variants of a gene, with a time-delay accounting for the dynamical effect induced by post-transcriptional processes and protein synthesis. This simple dynamical model resulted in a gene-protein correlation of rhoTH1 = 0.86, significantly higher than previously reported gene-protein prediction models in mammals.
2021-09-09 | E-MTAB-7775 | biostudies-arrayexpress