ArticleNucleic acids research2009
Universal function-specificity of codon usage.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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.
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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.
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Who cites it
28 citing papers in PubMed, 62 citations in OpenAlex.
- Article
- Dynamic Landscapes of tRNA Transcriptomes and Translatomes in Diverse Mouse Tissues.Genomics, proteomics & bioinformatics · 2023Article
- A Dynamic rRNA Ribomethylome Drives Stemness in Acute Myeloid Leukemia.Cancer discovery · 2023Article
- Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.NPJ biofilms and microbiomes · 2023Article
- Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes.Zoological research · 2022Article
- Codon optimality in cancer.Oncogene · 2021Review
- Translational efficiency across healthy and tumor tissues is proliferation-related.Molecular systems biology · 2020Article
- Translational control plays an important role in the adaptive heat-shock response of Streptomyces coelicolor.Nucleic acids research · 2018Article
- Codon optimality, bias and usage in translation and mRNA decay.Nature reviews. Molecular cell biology · 2018Review
- Integrated analysis of individual codon contribution to protein biosynthesis reveals a new approach to improving the basis of rational gene design.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.BMC genomics · 2016Article
- The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.Journal of molecular evolution · 2016Review
- New insights into the interplay between codon bias determinants in plants.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate.Nucleic acids research · 2015Article
- Bicluster pattern of codon context usages between flavivirus and vector mosquito Aedes aegypti: relevance to infection and transcriptional response of mosquito genes.Molecular genetics and genomics : MGG · 2014Article
- Article
- Translational selection in human: more pronounced in housekeeping genes.Biology direct · 2014Article
- Dependency of codon usage on protein sequence patterns: a statistical study.Theoretical biology & medical modelling · 2014Article
- A comparative analysis of synonymous codon usage bias pattern in human albumin superfamily.TheScientificWorldJournal · 2014Article
- ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants.Plant & cell physiology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Synonymous codon usage has long been known as a factor that affects average expression level of proteins in fast-growing microorganisms, but neither its role in dynamic changes of expression in response to environmental changes nor selective factors shaping it in the genomes of higher eukaryotes have been fully understood. Here, we propose that codon usage is ubiquitously selected to synchronize the translation efficiency with the dynamic alteration of protein expression in response to environmental and physiological changes. Our analysis reveals that codon usage is universally correlated with gene function, suggesting its potential contribution to synchronized regulation of genes with similar functions. We directly show that coexpressed genes have similar synonymous codon usages within the genomes of human, yeast, Caenorhabditis elegans and Escherichia coli. We also demonstrate that perturbing the codon usage directly affects the level or even direction of changes in protein expression in response to environmental stimuli. Perturbing tRNA composition also has tangible phenotypic effects on the cell. By showing that codon usage is universally function-specific, our results expand, to almost all organisms, the notion that cells may need to dynamically alter their intracellular tRNA composition in order to adapt to their new environment or physiological role.
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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.