Roles for Synonymous Codon Usage in Protein Biogenesis

Owing to the degeneracy of the genetic code, a protein sequence can be encoded by many different synonymous mRNA coding sequences. Synonymous codon usage was once thought to be functionally neutral, but evidence now indicates it is shaped by evolutionary selection and affects other aspects of protei...

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Bibliographic Details
Published in:Annual review of biophysics 2015-06, Vol.44 (1), p.143-166
Main Authors: Chaney, Julie L, Clark, Patricia L
Format: Article
Language:English
Subjects:
Animals
Biological Evolution
Codon
cotranslational folding
Humans
Mutation
protein aggregation
Protein Biosynthesis
protein degradation
ribosome
RNA, Messenger - chemistry
translation
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Summary:Owing to the degeneracy of the genetic code, a protein sequence can be encoded by many different synonymous mRNA coding sequences. Synonymous codon usage was once thought to be functionally neutral, but evidence now indicates it is shaped by evolutionary selection and affects other aspects of protein biogenesis beyond specifying the amino acid sequence of the protein. Synonymous rare codons, once thought to have only negative impacts on the speed and accuracy of translation, are now known to play an important role in diverse functions, including regulation of cotranslational folding, covalent modifications, secretion, and expression level. Mutations altering synonymous codon usage are linked to human diseases. However, much remains unknown about the molecular mechanisms connecting synonymous codon usage to efficient protein biogenesis and proper cell physiology. Here we review recent literature on the functional effects of codon usage, including bioinformatics approaches aimed at identifying general roles for synonymous codon usage.
ISSN:1936-122X
1936-1238
DOI:10.1146/annurev-biophys-060414-034333