Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA317481 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3337450.fastq.gz | Fastqsanger.gz | |||
| SRR3337460.fastq.gz | Fastqsanger.gz | |||
| SRR3337451.fastq.gz | Fastqsanger.gz | |||
| SRR3337461.fastq.gz | Fastqsanger.gz | |||
| SRR3337452.fastq.gz | Fastqsanger.gz |
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Project description:Early eukaryotic ribosome biogenesis involves large multi-protein complexes, which co-transcriptionally associate with pre-ribosomal RNA to form the small subunit processome. The precise mechanisms by which two of the largest multi-protein complexes – UtpA and UtpB – interact with nascent pre-ribosomal RNA have so far been poorly understood. We have combined biochemical and structural biology approaches with ensembles of RNA-protein cross-linking to elucidate the essential function of both complexes. Here we show that UtpA contains a large composite RNA binding site and captures the 5´ end of pre-ribosomal RNA. UtpB forms an extended structure that binds early pre-ribosomal intermediates in close proximity to key architectural sites such as an RNA duplex formed by the 5´ ETS and U3 snoRNA as well as the 3´ boundary of 18S rRNA. Both complexes therefore act as vital RNA chaperones to initiate eukaryotic ribosome assembly.
2016-09-21 | GSE79950 | GEO
Project description:Eukaryotic ribosome biogenesis begins with the co-transcriptional assembly of the 90S pre-ribosome. The ‘U three protein’ (UTP) complexes and snoRNA particles arrange around the nascent pre-ribosomal RNA chaperoning its folding and further maturation. The earliest event in this hierarchical process is the binding of the UTP-A complex to the 5’-end of the pre-ribosomal RNA (5’-ETS). This oligomeric complex predominantly consists of β-propeller and α-solenoidal proteins. Here we present the structure of the Utp4 subunit from the thermophilic fungus Chaetomium thermophilum at 2.15 Å resolution and analyze its function by UV RNA-crosslinking (CRAC) and in context of a recent cryo-EM structure of the 90S pre-ribosome. Utp4 consists of two orthogonal and highly basic β-propellers that perfectly fit the EM-data. The Utp4 structure highlights an unusual Velcro-closure of its C-terminal β-propeller as relevant for protein integrity and Utp8 recognition in the context of the pre-ribosome. We provide a first model of the 5’-ETS RNA from an internally hidden 5’-end up to the region that hybridizes to the 3’-hinge sequence of U3 snoRNA and validate a specific Utp4/5’-ETS interaction by CRAC analysis. Altogether Utp4 is central to the UTP-A complex and organizes the 5’-ETS for further maturation.
2017-06-06 | GSE98331 | GEO
Project description:SIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-rRNA and promotes rRNA synthesis. Here we show that SIRT7 is also associated with snoRNAs that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA-dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of prerRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA. CLIP-seq was performed in Flag-SIRT7-293T cells.
2016-01-07 | E-GEOD-76578 | biostudies-arrayexpress
Project description:Cotranslational protein folding depends on general chaperones that engage highly diverse nascent chains at the ribosomes. Here we find that the universal cotranslational machinery adapts to accommodate the challenging biogenesis of abundantly expressed eukaryotic translation elongation factor 1A (eEF1A). During eEF1A synthesis, chaperone Chp1 is recruited to the ribosome with the help of the nascent polypeptide-associated complex (NAC), where it safeguards eEF1A biogenesis. Aberrant eEF1A production triggers instant proteolysis, widespread protein aggregation, activation of Hsf1 stress transcription and compromises cellular fitness. The expression of pathogenic eEF1A2 variants linked to epileptic-dyskinetic encephalopathy is protected by Chp1. Thus, eEF1A is a difficult to fold protein that necessitates dedicated folding factor Chp1 at the ribosomal tunnel exit to protect the eukaryotic cell from proteostasis collapse.
2024-01-16 | GSE221651 | GEO
Project description:Prediction of ribosomal elongation rate from ribosome profiling data
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Project description:SIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-rRNA and promotes rRNA synthesis. Here we show that SIRT7 is also associated with snoRNAs that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA-dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of prerRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA.
2016-01-07 | GSE76578 | GEO
Project description:The ribosome associated complex (RAC) is a ribosome bound protein chaperone complex reported to surveil the translation of proteins with positively charged regions. It has been posited that RAC might be able to directly regulate translation by coupling co-translational folding with the peptide-elongation cycle. To identify the targets of RAC in cells and test the hypothesis that the complex modulates translation, we performed ribosome profiling on wild- type yeast cells and cells lacking a key component of the RAC that binds near the ribosome active site (zuo1Δ). Ribosome profiling is a sequencing-based technique that allows us to take a nucleotide resolution snapshot of where every ribosome sits on every mRNA in a cell at a given point in time. This powerful approach can provide information about the contributions of individual proteins to the translational landscape of a cell. We identified >300 targets for the RAC, and unexpectedly observed that the ribosome frameshifts on ~10% of these targets in zuo1Δ cells. The maintenance of ribosome reading frame is essential for cell health because frameshifts can result in the production of non-functional truncated and extended protein products. These studies have the potential to uncover RAC as a critical determinant of translational fidelity in eukaryotic cells.
2023-06-01 | GSE151370 | GEO
Project description:Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains
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Project description:Saccharomyces cerevisiae is one of the most well-studied model organisms used in the scientific community. Its ease of manipulation, accessible growth conditions, short life cycle, and conserved eukaryotic metabolic pathways make it a useful model organism. Consequently, yeast has been used to investigate a myriad of phenomena, from microbial to human studies. Most of the research performed using this model organism utilizes yeast cell populations when they are growing exponentially, a growth phase aptly termed exponential or log phase. However, log phase encompasses several yeast generations and ranges several hours of yeast growth, meaning that there is a potential for variability during this “homogenous” growth phase. Cells in log phase require robust ribosome biogenesis to support their rapid growth and cell division. Interestingly, during log phase, ribosomal RNA (rRNA) synthesis (which is the first and rate limiting step in ribosome biosynthesis) has been shown to decrease prior to growth rate decline in stationary phase. In this study, we utilized several genomic and biochemical methods to elucidate the relationship between subphases of log phase and rRNA synthesis. Our results indicate that as yeast cells progress through subphases of log growth both of Pol I transcription and rRNA processing are repressed. Overall, this study establishes a growth phase dependent control of rRNA synthesis that unexpectedly begins prior to the switch to stationary phase (i.e. pre-diauxic shift) as a putative mechanism of anticipating nutrient starvation.
2024-06-20 | GSE268167 | GEO
Project description:Saccharomyces cerevisiae is one of the most well-studied model organisms used in the scientific community. Its ease of manipulation, accessible growth conditions, short life cycle, and conserved eukaryotic metabolic pathways make it a useful model organism. Consequently, yeast has been used to investigate a myriad of phenomena, from microbial to human studies. Most of the research performed using this model organism utilizes yeast cell populations when they are growing exponentially, a growth phase aptly termed exponential or log phase. However, log phase encompasses several yeast generations and ranges several hours of yeast growth, meaning that there is a potential for variability during this “homogenous” growth phase. Cells in log phase require robust ribosome biogenesis to support their rapid growth and cell division. Interestingly, during log phase, ribosomal RNA (rRNA) synthesis (which is the first and rate limiting step in ribosome biosynthesis) has been shown to decrease prior to growth rate decline in stationary phase. In this study, we utilized several genomic and biochemical methods to elucidate the relationship between subphases of log phase and rRNA synthesis. Our results indicate that as yeast cells progress through subphases of log growth both of Pol I transcription and rRNA processing are repressed. Overall, this study establishes a growth phase dependent control of rRNA synthesis that unexpectedly begins prior to the switch to stationary phase (i.e. pre-diauxic shift) as a putative mechanism of anticipating nutrient starvation.
2024-06-20 | GSE268168 | GEO