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.

中文翻译：

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同义密码子使用在蛋白质生物发生中的作用。

由于遗传密码的简并性，蛋白质序列可以由许多不同的同义的mRNA编码序列编码。曾经认为同义密码子在功能上是中性的，但现在有证据表明，它是由进化选择决定的，并影响蛋白质生物合成的其他方面，而不是指定蛋白质的氨基酸序列。曾经被认为仅对翻译的速度和准确性产生负面影响的同义稀有密码子，现在已知在多种功能中起着重要作用，包括调节共翻译折叠，共价修饰，分泌和表达水平。改变同义密码子使用的突变与人类疾病有关。然而，关于将同义密码子使用与有效的蛋白质生物发生和适当的细胞生理学联系起来的分子机制，仍然尚不清楚。在这里，我们回顾有关密码子使用的功能影响的最新文献，包括旨在鉴定同义词的密码子使用的一般作用的生物信息学方法。