Systematic detection of amino acid substitutions in proteome reveals a mechanistic basis of ribosome errors and selection for translation fidelity
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ABSTRACT:
PROVIDER: PRJNA528937 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8782510.fastq.gz | Fastqsanger.gz | |||
| SRR8782502.fastq.gz | Fastqsanger.gz | |||
| SRR8782503.fastq.gz | Fastqsanger.gz | |||
| SRR8782504.fastq.gz | Fastqsanger.gz | |||
| SRR8782505.fastq.gz | Fastqsanger.gz |
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Project description:The translation machinery and the genes it decodes co-evolved to achieve production throughput and accuracy. Nonetheless translation errors are frequent and they affect physiology and protein evolution. Mapping translation errors in proteomes and understanding their causes was hindered by lack of a proteome-wide experimental methodology. We present the first methodology for systematic detection and quantification of errors in entire proteomes. Following proteome mass-spectrometry, we identify in E. coli and yeast peptides whose mass indicates specific amino-acid substitutions. Most substitutions result from codon-anticodon mispairing. Errors occur at sites that evolve rapidly, and that minimally affect energetic stability, indicating selection for high translation fidelity. Ribosome density data show that errors occur at sites where ribosome’s velocity is higher, demonstrating a trade-off between speed and accuracy. Treating bacteria with an aminoglycoside antibiotic or deprivation for specific amino-acids resulted particular patterns of errors. These results reveal a mechanistic and evolutionary basis for translation fidelity.
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Project description:The protein translation machinery and the genes it decodes co-evolved to achieve production throughput and accuracy. Nonetheless translation errors are frequent and they affect physiology, fitness and protein evolution. Mapping translation errors in proteomes and understanding their causes was hindered by lack of a proteome-wide experimental methodology. Here, we present the first methodology for systematic detection and quantification of errors in entire proteomes. Following proteome mass-spectrometry, we identify in E. coli and S. cerevisiae peptides whose mass indicates specific amino acid substitutions. Most substitutions occur due to codon-anticodon mispairing within the ribosome. we performed a deep RNA sequencing of the bacterial tRNA pool at the same time points in which we measured the proteome during E. coli culture growth. We compared ratio of abundances between congate and near-cognate tRNAs and found the changes corespond with changes in translation errors.
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