![]() Galtier, N., Piganeau, G., Mouchiroud, D. Codon usage between genomes is constrained by genome-wide mutational processes. Clarifying the translational pausing landscape in bacteria by ribosome profiling. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. The DEAD-box helicase Dhh1 is a necessary link between non-optimal codon content and RNA decay. The DEAD-box protein Dhh1p couples mRNA decay and translation by monitoring codon optimality. Analysis of the association between codon optimality and mRNA stability in Schizosaccharomyces pombe. Codons corresponding to abundant tRNA species are enriched in more stable mRNAs, whereas rare codons are enriched in unstable mRNAs. Codon usage within a transcript determines mRNA stability. Codon optimality is a major determinant of mRNA stability. Codon bias as a means to fine-tune gene expression. Speeding with control: codon usage, tRNAs, and ribosomes. Synonymous but not the same: the causes and consequences of codon bias. Determinants of translation efficiency and accuracy. Hearing silence: non-neutral evolution at synonymous sites in mammals. Codon usage bias from tRNA's point of view: redundancy, specialization, and efficient decoding for translation optimization. laevis and zebrafish and contributes to the MZT by targeting maternally loaded transcripts for degradation. Codon usage varies between maternal and zygotic mRNAs in X. Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. Decoding properties of tRNA leave a detectable signal in codon usage bias. Co-variation of trna abundance and codon usage in Escherichia coli at different growth rates. An evolutionary perspective on synonymous codon usage in unicellular organisms. Modelling the efficiency of codon–tRNA interactions based on codon usage bias. Codon usage bias and tRNA abundance in Drosophila. elegans genome are co-adapted for optimal translation of highly expressed genes. tRNA gene number and codon usage in the C. Solving the riddle of codon usage preferences: a test for translational selection. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. We then discuss how codon effects are leveraged by the cell to tailor the proteome to maintain homeostasis, execute specific gene expression programmes of growth or differentiation and optimize the efficiency of protein production. In this Review, we first discuss the evidence for codon-dependent effects on translation, beginning with the basic mechanisms through which translation perturbation can affect translation efficiency, protein folding and transcript stability. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery. The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. The interdependence between variable codon usage and the composition, charge status and post-transcriptional modifications of the tRNA pool enables global control of translation, which can be used to shape protein production to favour specific cellular programmes and to maintain homeostasis in conditions of stress or changes in nutritional status. The use of non-optimal codons can influence protein production by reducing ribosome translocation rates and causing ribosome collisions that can feed back to the translation initiation site.Ĭonserved, specific patterns of optimal and non-optimal codon use help to guide efficient co-translational folding and to minimize errors in translation.Ĭodon usage affects mRNA stability, and codon-influenced elongation stalling is sensed by the DEAD-box helicase Dhh1, which mediates codon-dependent variation in mRNA stability. Optimal codons are associated with more efficient translation and correspond to cognate tRNA species that are more abundant and that are readily accommodated by the ribosome during translation. Synonymous codons are used non-randomly in the transcriptome to shape multiple aspects of translation. ![]()
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