ArticlePLoS genetics2014
The effects of codon context on in vivo translation speed.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers, 1 of them a synthesis that pooled it.
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Who cites it
91 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Pleiotropic roles of elongation factor P inMicrobiology spectrum · 2026Article
- Constant trouble with prolines-navigating a global translation dilemma.Nucleic acids research · 2026Review
- Nucleotide Substitution Biases in Related Cancer Driver Genes.International journal of molecular sciences · 2025Article
- Translation elongation: measurements and applications.RNA biology · 2025Review
- 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
- Suboptimal codon pairs trigger ribosome collisions and cellular quality control responses in tRNA modification mutants.Nucleic acids research · 2025Article
- GC3 codons enhance protein production in diverse GC- and AT-rich plant species.bioRxiv : the preprint server for biology · 2025Article
- Two microbiome metabolites compete for tRNA modification to impact mammalian cell proliferation and translation quality control.Nature cell biology · 2025Article
- Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects?Journal of molecular biology · 2025Review
- A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism.Nature communications · 2025Article
- D-stem mutation in an essential tRNA increases translation speed at the cost of fidelity.PLoS genetics · 2025Article
- Secret code: Encoding promoters by synonymous codons.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- On the response of elongating ribosomes to forces opposing translocation.Biophysical journal · 2024Article
- Queuosine salvage inMicrobiology (Reading, England) · 2024Article
- Queuosine Salvage inbioRxiv : the preprint server for biology · 2024Article
- EngineeringEngineering microbiology · 2024Review
- Synthetic biology approach revealed enhancement in haeme oxygenase-1 gene expression by codon pair optimization while reduction by codon deoptimization.Annals of medicine and surgery (2012) · 2024Article
- Rapid Antibacterial Activity Assessment of Chimeric Lysins.International journal of molecular sciences · 2024Article
- Engineering strategies for enhanced heterologous protein production by Saccharomyces cerevisiae.Microbial cell factories · 2024Review
31 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
We developed a bacterial genetic system based on translation of the his operon leader peptide gene to determine the relative speed at which the ribosome reads single or multiple codons in vivo. Low frequency effects of so-called "silent" codon changes and codon neighbor (context) effects could be measured using this assay. An advantage of this system is that translation speed is unaffected by the primary sequence of the His leader peptide. We show that the apparent speed at which ribosomes translate synonymous codons can vary substantially even for synonymous codons read by the same tRNA species. Assaying translation through codon pairs for the 5'- and 3'- side positioning of the 64 codons relative to a specific codon revealed that the codon-pair orientation significantly affected in vivo translation speed. Codon pairs with rare arginine codons and successive proline codons were among the slowest codon pairs translated in vivo. This system allowed us to determine the effects of different factors on in vivo translation speed including Shine-Dalgarno sequence, rate of dipeptide bond formation, codon context, and charged tRNA levels.
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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.