GEO DataSets

(Submitter supplied) The yeast Hsp70 chaperone Ssb interacts with ribosomes and nascent chains to co-translationally assist protein folding. Here, we present a proteome-wide analysis of Hsp70 function during translation, based on in vivo selective ribosome profiling, that reveals mechanistic principles coordinating translation with chaperone-assisted protein folding. Ssb binds most cytosolic, nuclear, and mitochondrial proteins and a subset of ER proteins, supporting its general chaperone function. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

40 Samples

Download data: TXT

(Submitter supplied) Folding of newly synthesized proteins to the native state is a major challenge within the crowded cellular environment, since non-productive interactions can lead to misfolding, aggregation and degradation1. Cells cope with this challenge by coupling synthesis with polypeptide folding and by employing molecular chaperones to safeguard folding already cotranslationally2. However, little is known about the final step of folding, the assembly of polypeptides into complexes, although most of the cellular proteome forms oligomeric assemblies3. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL18330

68 Samples

Download data: TXT

(Submitter supplied) Folding newly synthesized proteins relies on the ribosome intricately coordinating mRNA translation with a network of ribosome-associated machinery. The principles that drive the coordination of this diverse machinery remain poorly understood. Here, we use selective ribosome profiling to determine how the essential chaperonin TRiC/CCT and the Hsp70 Ssb are recruited to ribosome-nascent chain complexes to mediate cotranslational protein folding. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

22 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

4 related Platforms

46 Samples

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(Submitter supplied) Translational profiles of wild type yeast strains were identified by microarray analysis by isolating polysomes using sucrose gradients to recover polysome-associated RNA and comparing polysome-associated RNA vs total RNA

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platform:

GPL16964

3 Samples

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(Submitter supplied) Transcriptional profiles on different yeast strain mutants (DEgd2/1, DEgd2/Btt1)were identified by microarray analysis comparing total mutant RNA vs wild type RNA.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16967

6 Samples

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(Submitter supplied) In order to identify what RNA messengers are being translated at the ER membrane, membrane-associated polysomes were separated from free polysomes by subcellular fractionation of WT and delta-egd1/delta-egd2 yeast strains and associated RNA was isolated and then identified by microarray analysis.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platforms:

GPL16964 GPL16965

9 Samples

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(Submitter supplied) Nascent polypeptides emerging from the ribosome during biogenesis can interact with many chaperones and protein homeostasis factors. The high sensitivity of RNA identification can be used to identify substrates of specific cotranslationally acting chaperones. Protein A-tagged (TAP-tag) chaperones associated with translating ribosomes were immunopurified by binding to magnetic IgG beads, washed, and chaperone complexes were eluted with TEV protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

4 related Platforms

28 Samples

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(Submitter supplied) Cotranslational targeting into the endoplasmic reticulum (ER) by the Signal Recognition Particle (SRP) is a key event determining polypeptide fate in eukaryotic cells. Here, we globally define the principles and mechanisms of SRP binding and ER targeting in vivo. Cotranslational targeting through SRP is the dominant route into the ER for all secretory proteins, regardless of targeting signal characteristics. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL21656 GPL17342

30 Samples

Download data: XLSX

(Submitter supplied) Proteostasis is a fundamental network of cellular pathways that ensures the optimal concentration and composition of correctly folded proteins within cells in normal and stress conditions. Among key components of this network are the molecular chaperones, which mediate protein folding but also act as modulators of protein synthesis. We have reported on a functional link between translation and de novo folding of proteins in the yeast Saccharomyces cerevisiae by uncovering a specific synthetic-lethal interaction between apparent unrelated mutant variants, the uL3[W255C] variant of the ribosomal protein uL3 and the null mutants of Zuo1 and Ssz1. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL19756

18 Samples

Download data: BEDGRAPH

(Submitter supplied) Proteostasis is a fundamental network of cellular pathways that ensures the optimal concentration and composition of correctly folded proteins within cells in normal and stress conditions. Among key components of this network are the molecular chaperones, which mediate protein folding but also act as modulators of protein synthesis. We have reported on a functional link between translation and de novo folding of proteins in the yeast Saccharomyces cerevisiae by uncovering a specific synthetic-lethal interaction between apparent unrelated mutant variants, the uL3[W255C] variant of the ribosomal protein uL3 and the null mutants of Zuo1 and Ssz1. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Constituents of multi-protein complexes are required at well-defined levels relative to each other. However, it remains unknown whether eukaryotic cells typically produce precise amounts of subunits, or instead rely on degradation to mitigate imprecise production. Here we quantified the production rates of multi-protein complexes in single- and multi-cellular eukaryotes using ribosome profiling. By resolving read-mapping ambiguities present in a large fraction of ribosome footprints which often distorts quantitation accuracy in eukaryotes, we found that obligate components of multi-protein complexes are produced in proportion to their stoichiometry, indicating that their abundances are already precisely tuned at the synthesis level. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL13821 GPL19756

13 Samples

Download data: WIG

(Submitter supplied) Genome-wide detection of monosome and disome distributions in yeast cells

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL25927 GPL17342

13 Samples

Download data: TXT

(Submitter supplied) The endoplasmic reticulum (ER) supports biosynthesis of proteins with diverse transmembrane domain (TMD) lengths and hydrophobicity. Features in transmembrane domains such as charged residues in ion channels are often functionally important, but could pose a challenge during cotranslational membrane insertion and folding. Our systematic proteomic approaches in both yeast and human cells revealed that the ER membrane protein complex (EMC) binds to and promotes the biogenesis of a range of multipass transmembrane proteins, with a particular enrichment for transporters. more...

Organism:

Saccharomyces cerevisiae; Homo sapiens

Type:

Other

4 related Platforms

13 Samples

Download data: TXT

(Submitter supplied) PIKKs are a family of kinases that control fundamental processes, including cell growth, DNA damage repair, and gene expression. Although their regulation and activities are well characterized, little is known about how PIKKs fold and assemble into active complexes. Previous work identified an Hsp90 cochaperone, the TTT complex, which specifically stabilizes PIKKs. Here we describe a mechanism by which TTT promotes their de novo maturation in fission yeast. more...

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22682

9 Samples

Download data: TXT, XLSX

(Submitter supplied) Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo–electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

4 Samples

Download data: CSV

(Submitter supplied) Control of messenger RNA (mRNA) decay rate is intimately connected to translation elongation, but the spatial coordination of these events is poorly understood. The Ccr4-Not complex initiates mRNA decay through deadenylation and activation of decapping. We used a combination of cryo–electron microscopy, ribosome profiling, and mRNA stability assays to examine the recruitment of Ccr4-Not to the ribosome via specific interaction of the Not5 subunit with the ribosomal E-site in Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

4 Samples

Download data: CSV

(Submitter supplied) A number of enzymes, targeting factors and chaperones engage ribosomes to support fundamental steps of nascent protein maturation, including enzymatic processing, membrane targeting and co-translational folding. The selective ribosome profiling (SeRP) method is a new tool for studying the co-translational activity of maturation factors that provides proteome-wide information on a factor’s nascent interactome, the onset and duration of binding and the mechanisms controlling factor engagement. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

8 Samples

Download data: TXT

(Submitter supplied) Saccharomyces cerevisiae has been engineered to utilize cellobiose, which are prevalent in plant cell wall, by introducing a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa. We previously found that codon-optimization of GH1-1 improved fermentation rates under aerobic and anaerobic conditions. However, we found that the codon-optimized version of the CDT-1 transporter (here denoted OPT for the mRNA) resulted in reduced cellobiose uptake and slower growth in cellobiose by S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL9377

12 Samples

Download data: WIG, XLSX

(Submitter supplied) As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting and folding factors. Here we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone Trigger Factor (TF) reveal that, while TF can interact with many polypeptides, β-barrel outer membrane proteins are the most prominent substrates. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10328

8 Samples

Download data: TAGALIGN, TXT