Codon optimality, bias and usage in translation and mRNA decay

Synonymous codons are used non-randomly in the transcriptome to shape multiple aspects of translation.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.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.Conserved, specific patterns of optimal and non-optimal codon use help to guide efficient co-translational folding and to minimize errors in translation.Codon 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.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.