Ontology highlight
ABSTRACT:
PROVIDER: PRJNA474899 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We have previously shown that the yeast homolog of the RNA-binding vigilin proteins – Scp160p – is involved in enhancing translation efficiency in the context of codon usage. In the current study, we investigated the influence of Scp160p on the biology of polyQ reporters which differ in the codon usage of their polyQ regions. We observe that Scp160p facilitates aggregation of the polyQ reporters independent of codon usage. To explore if Scp160p might also facilitate the aggregation of endogenous polyQ-containing proteins in the yeast proteome, we combined filter trap binding and dimethyl labeling mass spectrometry to assess the aggregation state of the proteome in scp160Δ cells. Filter trap binding allows the isolation of protein aggregates which are SDS-resistant (a feature of polyQ aggregates) from wild-type and scp160Δ cells. Dimethyl labeling with nanoLC-MS/MS provided a quantitative comparison of the amount of aggregated proteins isolated by filter trap binding.
2018-07-03 | PXD008175 | Pride
Project description:Synonymous codon usage regulates translation initiation
| PRJNA837608 | ENA
Project description:Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans, but was not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution. Relative amounts of mRNA for each ORF were measured by DNA microarray using genomic DNA as a reference, and the copy number of mRNA was calculated using an estimate of the total mRNA number in the cell as 100,000 copies.
2010-06-20 | E-GEOD-13554 | biostudies-arrayexpress
Project description:Codon usage influences the local rate of translation elongation to regulate co-translational protein folding
| PRJNA290152 | ENA
Project description:Codon usage optimization in pluripotent embryonic stem cells [RNA-seq]
| PRJNA439265 | ENA
Project description:Stop codon recoding events give rise to longer proteins, which may alter the proteins function and thereby generate short-lasting phenotypic variability from a single gene.
In order to systematically assess the frequency and origin of recoding events, we designed a library of reporters. We introduced premature stop codons into mScarlet that enabled high-throughput quantification of protein synthesis termination errors in E.coli using fluorescent microscopy. We found that under stress conditions, stop codon recoding may occur as high as 80 percent of the time, depending on the genetic context, suggesting that evolution frequently samples stop codon recoding events. Targeted mass spectrometry and RNA-seq analyses showed that not only translational but also transcriptional errors contribute to stop codon recoding. The RNA polymerase is more likely to misincorporate a nucleotide at premature stop codons. Proteome-wide mass -spectrometry revealed that temperature regulates the expression of cryptic peptides generated by stop codon recoding in E.coli.
Overall, our findings suggest that the environment influences the accuracy of protein production which increases protein heterogeneity when the organisms need to adapt to new conditions.
2023-01-14 | MSV000091065 | MassIVE
Project description:Genotyping of RpoD mutants via amplicon sequencing from the following manuscript: \\"Systematic dissection of σ70 sequence diversity and function in bacteria\\" by Park and Wang (2020). Includes raw sequencing reads from samples from MAGE-seq single codon saturation mutagenesis and high-throughput fitness competition experiment as well as the RpoD ortholog mutants generated through recombineering and CRISPR selection.
2022-06-06 | E-MTAB-9103 | biostudies-arrayexpress
Project description:Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosaccharomyces pombe, and compared codon usage bias with expression levels of the gene. In this organism, synonymous codon usage bias was correlated with expression levels of the gene; the bias was most obvious in two-codon amino acids. A similar pattern of the codon usage bias was also observed in Saccharomyces cerevisiae, Arabidopsis thaliana, and Caenorhabditis elegans, but was not obvious in Oryza sativa, Drosophila melanogaster, Takifugu rubripes and Homo sapiens. As codons of the highly expressed genes have greater influence on translational efficiency than codons of genes expressed at lower levels, it is likely that codon usage in the S. pombe genome has been optimized by translational selection through evolution.
2009-04-01 | GSE13554 | GEO
Project description:Codon usage optimization in pluripotent embryonic stem cells
| PRJNA509373 | ENA