eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons

作者：Qian Yang, Chien‐Hung Yu, Fangzhou Zhao, Yunkun Dang, Cheng Wu, Pancheng Xie, Matthew S. Sachs, Yi Liu · 发表于：Nucleic Acids Research · 年份：2019 · DOI：10.1093/nar/gkz710 · 被引用次数：71 · 研究领域：RNA and protein synthesis mechanisms、RNA modifications and cancer、RNA Research and Splicing

Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and plays an important role in regulating gene expression levels. A major role of codon usage is thought to regulate protein expression levels by affecting mRNA translation efficiency, but the underlying mechanism is unclear. By analyzing ribosome profiling results, here we showed that codon usage regulates translation elongation rate and that rare codons are decoded more slowly than common codons in all codon families in Neurospora. Rare codons resulted in ribosome stalling in manners both dependent and independent of protein sequence context and caused premature translation termination. This mechanism was shown to be conserved in Drosophila cells. In both Neurospora and Drosophila cells, codon usage plays an important role in regulating mRNA translation efficiency. We found that the rare codon-dependent premature termination is mediated by the translation termination factor eRF1, which recognizes ribosomes stalled on rare sense codons. Silencing of eRF1 expression resulted in codon usage-dependent changes in protein expression. Together, these results establish a mechanism for how codon usage regulates mRNA translation efficiency.