ArticlePLoS genetics2018
The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 64 papers.
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Who cites it
64 citing papers in PubMed, 116 citations in OpenAlex.
- The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.PLoS genetics · 2026Article
- Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.RNA (New York, N.Y.) · 2026Article
- Predicting the translation efficiency of messenger RNA in mammalian cells.Nature biotechnology · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.bioRxiv : the preprint server for biology · 2025Article
- Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli.Nucleic acids research · 2025Article
- Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines.Scientific data · 2025Article
- Measuring and manipulating localized translation of erm-1 in the C. elegans embryo.Development (Cambridge, England) · 2025Article
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- The assembly factor Reh1 is released from the ribosome during its initial round of translation.Nature communications · 2025Article
- Effect of Translation-Enhancing Nascent SKIK Peptide on the Arrest Peptides Containing Consecutive Proline.ACS synthetic biology · 2024Article
- Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel.Computational and structural biotechnology journal · 2024Article
- A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.Science advances · 2024Article
- Understanding the regulation of protein synthesis under stress conditions.Biophysical journal · 2024Article
- Article
- Translation Rates and Protein Folding.Journal of molecular biology · 2024Review
- Riboformer: a deep learning framework for predicting context-dependent translation dynamics.Nature communications · 2024Article
- Optimal control of ribosome population for gene expression under periodic nutrient intake.Journal of the Royal Society, Interface · 2024Article
- Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM.Nature communications · 2024Article
4 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Previous studies have shown that translation elongation is regulated by multiple factors, but the observed heterogeneity remains only partially explained. To dissect quantitatively the different determinants of elongation speed, we use probabilistic modeling to estimate initiation and local elongation rates from ribosome profiling data. This model-based approach allows us to quantify the extent of interference between ribosomes on the same transcript. We show that neither interference nor the distribution of slow codons is sufficient to explain the observed heterogeneity. Instead, we find that electrostatic interactions between the ribosomal exit tunnel and specific parts of the nascent polypeptide govern the elongation rate variation as the polypeptide makes its initial pass through the tunnel. Once the N-terminus has escaped the tunnel, the hydropathy of the nascent polypeptide within the ribosome plays a major role in modulating the speed. We show that our results are consistent with the biophysical properties of the tunnel.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.