ArticleGenome biology2011
Composite effects of gene determinants on the translation speed and density of ribosomes.
Article in Genome biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 papers.
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Who cites it
122 citing papers in PubMed, 207 citations in OpenAlex.
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- Ramp Sequence May Explain Synonymous Variant Association with Alzheimer's Disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA).Biomedicines · 2025Article
- Synthetic rational design of live-attenuated Zika viruses based on a computational model.Nucleic acids research · 2025Article
- Ramp sequence may explain synonymous variant association with Alzheimer's disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (bioRxiv : the preprint server for biology · 2025Article
- Computational Analysis of MDR1 Variants Predicts Effect on Cancer Cells via their Effect on mRNA Folding.PLoS computational biology · 2024Article
- Synonymous and non-synonymous codon substitutions can alleviate dependence on GroEL for folding.Protein science : a publication of the Protein Society · 2024Article
- Riboformer: a deep learning framework for predicting context-dependent translation dynamics.Nature communications · 2024Article
- Differential Synonymous Codon Selection in the B56 Gene Family of PP2A Regulatory Subunits.International journal of molecular sciences · 2023Article
- Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation.PLoS computational biology · 2023Article
- Large-scale analysis of mRNA sequences localized near the start and amber codons and their impact on the diversity of mRNA display libraries.Nucleic acids research · 2023Article
- Article
- Native functions of short tandem repeats.eLife · 2023Article
- Nascent peptide-induced translation discontinuation in eukaryotes impacts biased amino acid usage in proteomes.Nature communications · 2022Article
- Translation in the cell under fierce competition for shared resources: a mathematical model.Journal of the Royal Society, Interface · 2022Article
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach.BMC genomics · 2022Article
- Large-scale mRNA translation and the intricate effects of competition for the finite pool of ribosomes.Journal of the Royal Society, Interface · 2022Article
- Modeling the ribosomal small subunit dynamic in Saccharomyces cerevisiae based on TCP-seq data.Nucleic acids research · 2022Article
62 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranslation is a central process of life, and its regulation is crucial for cell growth. In this article, focusing on two model organisms, Escherichia coli and Saccharomyces cerevisiae, we study how three major local features of a gene's coding sequence (its adaptation to the tRNA pool, its amino acid charge, and its mRNA folding energy) affect its translation elongation.
resultsWe find that each of these three different features has a non-negligible distinct correlation with the speed of translation elongation. In addition, each of these features might contribute independently to slowing down ribosomal speed at the beginning of genes, which was suggested in previous studies to improve ribosomal allocation and the cost of translation, and to decrease ribosomal jamming. Remarkably, a model of ribosomal translation based on these three basic features highly correlated with the genomic profile of ribosomal density. The robustness to transcription errors in terms of the values of these features is higher at the beginnings of genes, suggesting that this region is important for translation.
conclusionsThe reported results support the conjecture that translation elongation speed is affected by the three coding sequence determinants mentioned above, and not only by adaptation to the tRNA pool; thus, evolution shapes all these determinants along the coding sequences and across genes to improve the organism's translation efficiency.
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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.