ArticlePLoS computational biology2017
Novel mRNA-specific effects of ribosome drop-off on translation rate and polysome profile.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 42 citations in OpenAlex.
- The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.PLoS genetics · 2026Article
- Stoichiometry-induced differential selection on codon optimization among ribosomal protein genes in bacterial species.Molecular biology and evolution · 2026Article
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- A data-driven estimation of the ribosome drop-off rate inNAR genomics and bioinformatics · 2024Article
- Optimization of ribosome utilization inPNAS nexus · 2023Article
- Large-scale mRNA translation and the intricate effects of competition for the finite pool of ribosomes.Journal of the Royal Society, Interface · 2022Article
- Article
- Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice.BMC genomics · 2021Article
- Modelling the effect of ribosome mobility on the rate of protein synthesis.The European physical journal. E, Soft matter · 2021Article
- Inferring efficiency of translation initiation and elongation from ribosome profiling.Nucleic acids research · 2020Article
- The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels.Nucleic acids research · 2020Article
- Computational design and interpretation of single-RNA translation experiments.PLoS computational biology · 2019Article
- Inverted translational control of eukaryotic gene expression by ribosome collisions.PLoS biology · 2019Article
- A dual role of the ribosome-bound chaperones RAC/Ssb in maintaining the fidelity of translation termination.Nucleic acids research · 2019Article
- Optimizing the dynamics of protein expression.Scientific reports · 2019Article
- A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data.PLoS computational biology · 2019Article
- Gene length as a regulator for ribosome recruitment and protein synthesis: theoretical insights.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
The well established phenomenon of ribosome drop-off plays crucial roles in translational accuracy and nutrient starvation responses during protein translation. When cells are under stress conditions, such as amino acid starvation or aminoacyl-tRNA depletion due to a high level of recombinant protein expression, ribosome drop-off can substantially affect the efficiency of protein expression. Here we introduce a mathematical model that describes the effects of ribosome drop-off on the ribosome density along the mRNA and on the concomitant protein synthesis rate. Our results show that ribosome premature termination may lead to non-intuitive ribosome density profiles, such as a ribosome density which increases from the 5' to the 3' end. Importantly, the model predicts that the effects of ribosome drop-off on the translation rate are mRNA-specific, and we quantify their resilience to drop-off, showing that the mRNAs which present ribosome queues are much less affected by ribosome drop-off than those which do not. Moreover, among those mRNAs that do not present ribosome queues, resilience to drop-off correlates positively with the elongation rate, so that sequences using fast codons are expected to be less affected by ribosome drop-off. This result is consistent with a genome-wide analysis of S. cerevisiae, which reveals that under favourable growth conditions mRNAs coding for proteins involved in the translation machinery, known to be highly codon biased and using preferentially fast codons, are highly resilient to ribosome drop-off. Moreover, in physiological conditions, the translation rate of mRNAs coding for regulatory, stress-related proteins, is less resilient to ribosome drop-off. This model therefore allows analysis of variations in the translational efficiency of individual mRNAs by accounting for the full range of known ribosome behaviours, as well as explaining mRNA-specific variations in ribosome density emerging from ribosome profiling studies.
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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.