GEO DataSets

(Submitter supplied) Ribosomes are often seen as monolithic machines produced from uniformly regulated genes. However, in yeast most ribosomal proteins come from duplicated genes. Here, we demonstrate that gene duplication may serve as an adaption mechanism modulating the global proteome through the differential expression of ribosomal proteins paralogs after exposure to stress. Our data indicate that the yeast paralog pair of the ribosomal protein L7/uL30 produces two differentially acetylated proteins. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

18 Samples

Download data: TSV

(Submitter supplied) Ribosomes are ubiquitous ribonucleoprotein complexes required for protein synthesis. We show that in budding yeast exposure to drugs alters ribosome composition leading to modification of translation pattern and increased resistance to drug. Exposure to staurosporine repressed translation of cell wall protein genes. Expression of the major paralog of uL30/RPL7 increased cell sensitivity to staurosporine while expression of the minor paralog induced resistance. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

36 Samples

Download data: CSV

(Submitter supplied) Duplicated genes escape gene loss by conferring a dosage benefit or evolving diverged functions. The yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins. Prior studies have suggested that these duplicated proteins are functionally redundant and affect cellular processes in proportion to their expression. In contrast, through studies of ASH1 mRNA in yeast, we demonstrate paralog-specific requirements for the translation of localized mRNAs. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL5741

4 Samples

Download data: GPR

(Submitter supplied) Duplicated genes escape gene loss by conferring a dosage benefit or evolving diverged functions. The yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins. Prior studies have suggested that these duplicated proteins are functionally redundant and affect cellular processes in proportion to their expression. In contrast, through studies of ASH1 mRNA in yeast, we demonstrate paralog-specific requirements for the translation of localized mRNAs. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS3061

Platform:

GPL90

24 Samples

Download data: CEL

Analysis of several Saccharomyces cerevisiae mutants each deficient in one of various ribosomal proteins. S. cerevisiae contains many duplicated genes encoding ribosomal proteins. Results provide insight into the unique role of each member of a pair of ribosomal protein paralogs.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 12 genotype/variation sets

Platform:

GPL90

Series:

GSE8761

24 Samples

Download data: CEL

(Submitter supplied) Ribosome binding proteins function broadly in protein synthesis, gene regulation and cellular homeostasis but the complete complement of functional ribosome-bound proteins remains unknown. Using quantitative mass spectrometry we identified Late-annotated short open reading frame 2 (Lso2) as a ribosome-associated protein that is broadly conserved in eukaryotes. Genome-wide crosslinking and immunoprecipitation of Lso2 and its human ortholog CCDC124 recovered 25S rRNA in a region near the A site that overlaps the GTPase activating center. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17342 GPL13821 GPL19756

25 Samples

Download data: BED, BEDGRAPH, FASTA, GFF, TXT, WIG

(Submitter supplied) The “Kozak sequence”, immediately upstream of the start codon, regulates the translational efficiency of an mRNA. Nevertheless, how this sequence is recognized remains unexplored. Here, we describe a novel approach to separate two ribosome populations from the same cells and use this method, and RNA-seq, to identify the mRNAs bound to ribosomes with and without Rps26, a protein linked to the pathogenesis of Diamond Blackfan Anemia (DBA). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

7 Samples

Download data: TXT, XLSX

(Submitter supplied) Translation is a core cellular process carried out by a highly conserved macromolecular machine, the ribosome. There has been remarkable evolutionary adaptation of this machine through the addition of eukaryote-specific ribosomal proteins whose individual effects on ribosome function are largely unknown. Here we show that eukaryote-specific Asc1/RACK1 is required for efficient translation of mRNAs with short open reading frames that show greater than average translational efficiency in diverse eukaryotes. more...

Organism:

Saccharomyces cerevisiae Sigma1278b

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL21667 GPL21666

62 Samples

Download data: CSV, TXT

(Submitter supplied) The formation of paralogs through gene duplication is a core evolutionary process. For paralogs that encode components of protein complexes such as the ribosome, a central question is whether they encode functionally distinct proteins, or whether they exist to maintain appropriate total expression of equivalent proteins. Here, we systematically tested evolutionary models of paralog function using the ribosomal protein paralogs Rps27 (eS27) and Rps27l (eS27L) as a case study. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21103

15 Samples

Download data: TXT

(Submitter supplied) eIF2α phosphorylation-mediated translational regulation is crucial for global translation repression by various stresses, including the unfolded protein response (UPR). However, translational control during UPR has not been demonstrated in yeast. This study investigated ribosome ubiquitination-mediated translational controls during UPR. Tunicamycin-induced ER stress enhanced the levels of ubiquitination of the ribosomal proteins uS10, uS3 and eS7. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Expression profiling by high throughput sequencing

Platform:

GPL21656

25 Samples

Download data: TXT

(Submitter supplied) We report on how the presence or absence of a 18 nt long ribosome-bound RNA affects the translation in S. cerevisiae. We observe that translation of all mRNAs is downregulated when the RNA is present.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23014

16 Samples

Download data: TXT

(Submitter supplied) The cohesin protein complex is well known for playing a role in chromosome segregation. However, it has additional less understood roles in transcription, DNA repair, and chromosome condensation. Mutants in two yeast orthologues (Eco1 and Scc2) of human cohesinopathy disease alleles were examined by transcriptional profiling in response to perturbation of the transcriptional program by amino acid starvation.

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

36 Samples

Download data: CEL

(Submitter supplied) In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platforms:

GPL17342 GPL19756

52 Samples

Download data

(Submitter supplied) In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL19756 GPL17342

50 Samples

Download data: CSV, TXT

(Submitter supplied) In Saccharomyces cerevisiae, deletion of genes encoding proteins of the large ribosomal subunit (RPLs) increases the replicative lifespan in a Gcn4-dependent manner. However, how Gcn4, a key transcriptional activator of amino acid biosynthesis genes, increases lifespan, is unknown. Here we show that Gcn4 acts as a repressor of protein synthesis. By analyzing the mRNA and protein abundance, the ribosome occupancy and protein synthesis rate in various yeast strains, we demonstrate that Gcn4 is sufficient to reduce protein synthesis and to increase yeast lifespan. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

2 Samples

Download data: CSV