Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA340886 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Sequence specific recognition of RNA hairpins by the SAM domain of Vts1
| PRJNA93907 | ENA
Project description:Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region readthrough allows translation into the mRNA 3’-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-acting elements other than stop codon identity, including two nucleotides 5’ of the stop codon, six nucleotides 3’ of the stop codon in the ribosomal mRNA channel, and stem-loop structures in the mRNA 3’-UTR. It is unknown whether these elements are important at a genome-wide level and whether other mRNA features proximal to the stop codon significantly affect termination and readthrough efficiencies in vivo. Accordingly, we carried out ribosome profiling analyses of yeast cells expressing wild-type or temperature-sensitive eRF1 and developed bioinformatics strategies to calculate readthrough efficiency, and to identify mRNA and peptide features which influence that efficiency. We found that the stop codon (nt +1 to +3), the nucleotide after it (nt +4), the codon in the P site (nt -3 to -1), and 3’-UTR length are the most influential features in the control of readthrough efficiency, while nts +5 to +9 and mRNA secondary structure in the 3’-UTR had milder effects. Additionally, we found low readthrough genes to have shorter 3’-UTRs compared to high readthrough genes in cells with thermally inactivated eRF1, while this trend was reversed in wild-type cells. Together, our results demonstrated the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features important for translation termination and readthrough.
2020-12-08 | GSE162780 | GEO
Project description:Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition
| PRJNA255917 | ENA
Project description:<p><em>Saccharomyces cerevisiae</em> is a widely used cell factory; therefore, it is important to understand how it organizes key functional parts when cultured under different conditions. Here, we perform a multiomics analysis of <em>S. cerevisiae</em> by culturing the strain with a wide range of specific growth rates using glucose as the sole limiting nutrient. Under these different conditions, we measure the absolute transcriptome, the absolute proteome, the phosphoproteome, and the metabolome. Most functional protein groups show a linear dependence on the specific growth rate. Proteins engaged in translation show a perfect linear increase with the specific growth rate, while glycolysis and chaperone proteins show a linear decrease under respiratory conditions. Glycolytic enzymes and chaperones, however, show decreased phosphorylation with increasing specific growth rates; at the same time, an overall increased flux through these pathways is observed. Further analysis show that even though mRNA levels do not correlate with protein levels for all individual genes, the transcriptome level of functional groups correlates very well with its corresponding proteome. Finally, using enzyme-constrained genome-scale modeling, we find that enzyme usage plays an important role in controlling flux in amino acid biosynthesis.</p>
2022-08-31 | MTBLS697 | MetaboLights
Project description:The use of alternative polyadenylation sites is common and affects the post-transcriptional fate of mRNA, including its stability, localization, and translation. Here we present a method for genome-wide and strand-specific mapping of poly(A) sites and quantification of RNA levels at unprecedented efficiency by using an on-cluster dark T-fill procedure on the Illumina sequencing platform. Our method outperforms former protocols in quality and throughput, and reveals new insights into polyadenylation in Saccharomyces cerevisiae.
2013-01-10 | GSE40110 | GEO
Project description:Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition
| PRJNA245894 | ENA
Project description:In this study, we utilize high-content microscopy screening and quantitative proteomics to establish a function of nuclear Hsp104 during aging. We find that the cytosolic-nuclear partitioning of Hsp104 is critical to maintain nuclear proteostasis in quiescent cells. Whereas high global translation rates in rapidly growing cells constrain Hsp104 to the cytosol, a decrease in protein biosynthesis re-directs the disaggregase to the nucleus dependent on a specific C-terminal motif. Nuclear Hsp104 interacts with latent eIF2 translation initiation subcomplexes and suppresses protein aggregation. This protects the dormant translation machinery from age-induced damage, enabling the rapid resumption of protein synthesis upon re-entry into the cell cycle. In this project two separate IP-MS experiments are included, KGSBVK (IP-MS, 9 samples) and GMCAVK (UV-inducible crosslinking IP-MS, 12 samples).
2024-01-12 | PXD043093 | Pride
Project description:Translation of poly(A) tails leads to precise mRNA cleavage and widespread ribosome rescue
| PRJNA339793 | ENA
Project description:Roles for Transcript Leaders in Translation and mRNA Decay Revealed by Transcript Leader Sequencing
| PRJNA169917 | ENA