The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function
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- 作者：Fran Supek
- 关键词：Codon usage bias ; Translation efficiency ; Gene function ; Microbial ecology
- 刊名：Journal of Molecular Evolution
- 出版年：2016
- 出版时间：January 2016
- 年：2016
- 卷：82
- 期：1
- 页码：65-73
- 全文大小：472 KB
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1. Division of electronics, Rudjer Boskovic Institute, 10000, Zagreb, Croatia
2. EMBL-CRG Systems Biology Unit, Centre for Genomic Regulation (CRG), 08003, Barcelona, Spain
3. Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain - 刊物类别：Biomedical and Life Sciences
- 刊物主题：Life Sciences
Cell Biology
Microbiology
Plant Sciences - 出版者：Springer New York
- ISSN：1432-1432
文摘
Some mutations in gene coding regions exchange one synonymous codon for another, and thus do not alter the amino acid sequence of the encoded protein. Even though they are often called ‘silent,’ these mutations may exhibit a plethora of effects on the living cell. Therefore, they are often selected during evolution, causing synonymous codon usage biases in genomes. Comparative analyses of bacterial, archaeal, fungal, and human cancer genomes have found many links between a gene’s biological role and the accrual of synonymous mutations during evolution. In particular, highly expressed genes in certain functional categories are enriched with optimal codons, which are decoded by the abundant tRNAs, thus enhancing the speed and accuracy of the translating ribosome. The set of genes exhibiting codon adaptation differs between genomes, and these differences show robust associations to organismal phenotypes. In addition to selection for translation efficiency, other distinct codon bias patterns have been found in: amino acid starvation genes, cyclically expressed genes, tissue-specific genes in animals and plants, oxidative stress response genes, cellular differentiation genes, and oncogenes. In addition, genomes of organisms harboring tRNA modifications exhibit particular codon preferences. The evolutionary trace of codon bias patterns across orthologous genes may be examined to learn about a gene’s relevance to various phenotypes, or, more generally, its function in the cell. Keywords Codon usage bias Translation efficiency Gene function Microbial ecology