Transcriptional profiling of Loc1 knockout
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE8765 | GEO | 2007/11/02
SECONDARY ACCESSION(S): PRJNA102047
REPOSITORIES: GEO
Similar Datasets
Project description: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. Intriguingly, these paralog-specific effects are limited to a distinct subset of duplicated ribosomal proteins. Moreover, transcriptional and phenotypic profiling of cells lacking specific ribosomal proteins reveals differences between the functional roles of ribosomal protein paralogs that extend beyond effects on mRNA localization. Finally, we show that ribosomal protein paralogs exhibit differential requirements for assembly and localization. Together, our data indicate complex specialization of ribosomal proteins for specific cellular processes, and support the existence of a ribosomal code. Keywords: genetic modification
2007-11-06 | GSE8761 | GEO
Project description: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. Intriguingly, these paralog-specific effects are limited to a distinct subset of duplicated ribosomal proteins. Moreover, transcriptional and phenotypic profiling of cells lacking specific ribosomal proteins reveals differences between the functional roles of ribosomal protein paralogs that extend beyond effects on mRNA localization. Finally, we show that ribosomal protein paralogs exhibit differential requirements for assembly and localization. Together, our data indicate complex specialization of ribosomal proteins for specific cellular processes, and support the existence of a ribosomal code. Experiment Overall Design: We used Affymetrix arrays to analyze the transcriptional profiles of cells lacking certain duplicated ribosomal protein genes in order to determine if paralogous ribosomal proteins have differing cellular effects and roles. Experiment Overall Design: Two biological replicates were performed for each strain. Each ribosomal protein deletion was then compared to the isogenic wild-type strain.
2008-06-16 | E-GEOD-8761 | biostudies-arrayexpress
Project description:The yeast genome contains a substantial amount of duplicated ribosomal protein genes. Functional characterization of deletion strains of individual paralogs show that the phenotypes upon deletion are not the same for a given paralog pair, suggesting that ribosomal protein paralog genes have distinct functions and thus are not redundant. Here we aimed to explore the differential function of RPL22A and RPL22B in protein synthesis. For this aim, we compared the ribosome-bound mRNAs found in different polysomal fractions: monosome, polysomal low (2-3ribosomes/mRNA), and polysomal high (>3ribosomes/mRNA), relative to total mRNA, for 3 different yeast strains: ∆RPL22A, ∆RPL22B and wild-type. Our results show that the use of one or the other specific ribosomal paralog affects the protein synthesis rates of specific transcripts, suggesting that each ribosomal protein paralog is optimized for decoding a subset of transcripts. We also find that the ratio of these paralogs changes upon oxidative stress, and propose that ribosome heterogeneity might be employed as a strategy to tune protein translation upon oxidative stress.
2021-08-01 | GSE118296 | GEO
Project description: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. Under normal conditions most ribosomes incorporate the hypo-acetylated major form favoring the translation of genes with short open reading frames. Exposure to drugs, on the other hand, increases the production of ribosomes carrying the hyper-acetylated minor paralog that increases translation of long reading frames. Many of these long genes encode cell wall proteins that increase drug resistance in a programed change in translation equilibrium. Together the data reveal a mechanism of translation control through the differential fates of near-identical ribosomal protein isoforms.
2022-08-09 | GSE202803 | GEO
Project description: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 a stress-adaptation mechanism modulating the global proteome through the differential expression of ribosomal protein paralogs. Our data indicate that the yeast paralog pair of the ribosomal protein L7/uL30 produces two differentially acetylated proteins. Under normal conditions most ribosomes incorporate the hypo-acetylated major form favoring the translation of genes with short open reading frames. Exposure to drugs, on the other hand, increases the production of ribosomes carrying the hyper-acetylated minor paralog that increases translation of long open reading frames. Many of these paralogs dependent genes encode cell wall proteins that could promote tolerance to drugs as their translation increases after exposure to drugs. Together the data reveal a mechanism of translation control through the differential use of near-identical ribosomal protein isoforms.
2022-08-09 | PXD033843 | Pride
Project description:We cultured the cells of S. pmbe in EMM2, and harvested them in the OD600 of 0.5 and 10 respectively. We used microarrays to detail the the global program of gene expression of SP-Q01 and SP-Q01 carrying vevtor pESP3X to overexpress either ribosomal protein L32 paralog in the OD600 of 0.5 and 10 respectively. We constructed the ribosomal protein L32 paralog overexpression strains to mimic the expression pattern of RPL32 paralogs in wild-type cells of S.pombe. We cultured the cells to different growth phase, and used microarray to identify the genes were regulated distinctively by RPL32 paralogs.
2013-03-01 | E-GEOD-43827 | biostudies-arrayexpress
Project description:CRISPR knockout screens have accelerated the discovery of important cancer genetic dependencies. However, traditional CRISPR-Cas9 screens are limited in their ability to assay the function of redundant or duplicated genes. Paralogs in multi-gene families constitute two-thirds of the protein-coding genome, so this blind spot is the rule, not the exception. To overcome the limitations of single gene CRISPR knockout screens, we developed paired guide RNAs for Paralog gENetic interaction mapping (pgPEN), a pooled CRISPR/Cas9 approach which targets over a thousand duplicated human paralogs in single knockout and double knockout configurations. We applied pgPEN to two cell lineages and discovered that over 10% of human paralogs exhibit synthetic lethality in at least one cellular context. We recovered known synthetic lethal paralogs such as MAP2K1/MAP2K2, important drug targets such as CDK4/CDK6, and numerous other synthetic lethal pairs such as CCNL1/CCNL2. In addition, we identified ten tumor suppressive paralog pairs whose compound loss promotes cell growth. These findings identify a large number of previously unidentified essential gene families and nominate new druggable targets for oncology drug discovery.
2021-08-31 | GSE178179 | GEO
Project description: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. Evolutionary analysis suggests that Rps27 and Rps27l likely arose during whole-genome duplication(s) in a common vertebrate ancestor. We show that Rps27 and Rps27l have inversely correlated mRNA abundance across mouse cell types, with the highest Rps27 in lymphocytes and the highest Rps27l in mammary alveolar cells and hepatocytes. By endogenously tagging the Rps27 and Rps27l proteins, we demonstrate that Rps27- and Rps27l-ribosomes associate preferentially with different transcripts. Furthermore, murine Rps27 and Rps27l loss-of-function alleles are homozygous lethal at different developmental stages. However, strikingly, expressing Rps27 protein from the endogenous Rps27l locus or vice versa completely rescues loss-of-function lethality and yields mice with no detectable deficits. Together, these findings suggest that Rps27 and Rps27l are evolutionarily retained because their subfunctionalized expression patterns render both genes necessary to achieve the requisite total expression of two equivalent proteins across cell types. Our work represents the most in-depth characterization of a mammalian ribosomal protein paralog to date and highlights the importance of considering both protein function and expression when investigating paralogs.
2023-06-21 | GSE201845 | GEO
Project description: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. Remarkably, we found that differences in paralogs function was due to difference in the translation pattern. The minor paralog promoted the translation of cell wall genes with long open reading frames (ORFs), which are normally under-translated in the presence of the major paralog, leading to drug resistance. Reducing the ORF length repressed the minor paralog and staurosporine effects on translation. Together the data reveal a natural mechanism for the optimization of translation through changes in the identity of ribosomal protein genes.
2020-03-09 | GSE133457 | GEO
Project description:This study measured the rates at which duplicated genes in the Daphnia pulex genome diverge in function, based on significant differences in their gene expression when paralogs of various ages were tested across 8 to 12 contrasting conditions. The conditions were designated A to L. The number and diversity of experiments were designed to uncover condition specific expression. The age of duplicated genes was measured as the level of silent-site nucleotide substitution (Ks) between paralogs. Two methods were used to evaluate the degree to which expression pattern of paralogs differ. (1) The first method investigated variation in the differential expression patterns among duplicates of individual gene families by calculating the M values (log2 treatment – log2 reference) from eight experiments, then calculating Pearson correlations. (2) The second method is a global investigation which defined a distinguishable expression pattern by a significance criterion (p < 0.05) using ANOVA for the simple statistical model of aov( Yab ~ Xab ), for matrices Yab differential expression M values and Xab gene factors, with replicates. We used pr(M) < 0.05 as criterion that expression differs between paralog genes, for zero to twelve treatments. The hypothesis that is tested is one of how many paralog pairs in each Ks category reach the criterion of a distinguishable expression pattern, which is tested for significance with Fisher's exact test for count data. This method is reliable for as few as two probes for one gene and one probe for the other, although a greater number of replicate probes produced more significant results. We compared the gene expression patterns for condition 1 versus condition 2 using four to six biological replicates, including balanced dye-swaps. All probes including random probes were quantile-normalized across chips, subarrays, samples and replicates.
2011-02-01 | E-GEOD-25850 | biostudies-arrayexpress