ArticleCell2013
Rate-limiting steps in yeast protein translation.
Article in Cell, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 295 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
295 citing papers in PubMed, 1 synthesis or guideline pooled it, 525 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Dynamic redistribution of eIF4F controls cap-dependent translation initiation.bioRxiv : the preprint server for biology · 2026Article
- A ribosomal kinetic checkpoint governs selective mRNA recruitment.bioRxiv : the preprint server for biology · 2026Article
- Nascent protein retention at polysomes reduces kinetic barriers to self-assembly.bioRxiv : the preprint server for biology · 2026Article
- Predicting the translation efficiency of messenger RNA in mammalian cells.Nature biotechnology · 2026Article
- Single-mRNA imaging and modeling reveal coupled translation initiation and elongation rates.eLife · 2026Article
- Article
- UTR-DynaPro: a CNN-transformer multimodal language model for decoding 5'UTR regulatory mechanisms.Scientific reports · 2026Article
- Ribosome-associated quality control of aberrant protein production during amino acid limitation.bioRxiv : the preprint server for biology · 2026Article
- Availability of Charged tRNAs Drives Maximal Protein Synthesis at Intermediate Levels of Codon Usage Bias.Bulletin of mathematical biology · 2026Article
- Decreased cytoplasmic crowding via inhibition of ribosome biogenesis can trigger Candida albicans filamentous growth.Nature microbiology · 2026Article
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Synergistic Methods to Investigate Eukaryotic Translation and Its Quality Control.Journal of molecular biology · 2025Review
- Near-cognate tRNAs dominate codon decoding times in simulated ribosomes.Nucleic acids research · 2025Article
- Ageing-related decline of translation as a consequence of transcription dysregulation.Journal of the Royal Society, Interface · 2025Article
- Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines.Scientific data · 2025Article
- Abundance-biased codon diversification prevents recombination in AAV production and ensures robust in vivo expression of functional FRET sensors.Communications biology · 2025Article
- Macroevolutionary changes in natural selection on codon usage reflect evolution of the tRNA pool across a budding yeast subphylum.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Why AGG is associated with high transgene output: passenger effects and their implications for transgene design.NAR genomics and bioinformatics · 2025Article
235 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Deep sequencing now provides detailed snapshots of ribosome occupancy on mRNAs. We leverage these data to parameterize a computational model of translation, keeping track of every ribosome, tRNA, and mRNA molecule in a yeast cell. We determine the parameter regimes in which fast initiation or high codon bias in a transgene increases protein yield and infer the initiation rates of endogenous Saccharomyces cerevisiae genes, which vary by several orders of magnitude and correlate with 5' mRNA folding energies. Our model recapitulates the previously reported 5'-to-3' ramp of decreasing ribosome densities, although our analysis shows that this ramp is caused by rapid initiation of short genes rather than slow codons at the start of transcripts. We conclude that protein production in healthy yeast cells is typically limited by the availability of free ribosomes, whereas protein production under periods of stress can sometimes be rescued by reducing initiation or elongation rates.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.