The Roles of Codon Usage in Translation and Transcription

Abstract

Codon usage biases are found in all eukaryotic and prokaryotic genomes that can regulate gene expression. Although codon usage has been previously shown to regulate translation elongation speed in fungal systems, its effect in animal systems is not clear. In our first study, using a Drosophila cell-free translation system to directly compare the velocity of translation elongation, we demonstrated that optimal codons speed up translation elongation while non-optimal codons slow it down. In addition, codon usage regulates ribosome movement and stalling on mRNA during translation. Finally, we showed that codon usage affects protein structure and function both in vitro and in Drosophila cells, potentially by regulating co-translational protein folding process. This study indicates that the effects of codon usage on translation elongation speed is a conserved mechanism from fungi to animals and there is a codon usage "code" fine tuning translation elongation speed to achieve optimal co-translational folding. In addition to the role of codon usage in translation, it has also been shown to play a role in regulating gene transcription of reporter genes and there is a global correlation between codon usage and mRNA levels. To further characterize the role of codon usage in gene transcription, we performed nuclear RNA-seq in Neurospora and found that there is a genome-wide strong correlation between gene codon usage bias and nuclear RNA levels, suggesting that codon usage has a global role in impacting transcription in a translation-independent manner. To uncover the underlying mechanism, we performed a genetic screening by performing RNA-seq in over 250 Neurospora single gene knockout strains and identified 18 mutants with significantly reduced correlation between codon usage and mRNA levels. In addition, the deletion of these 18 genes resulted in mRNA level changes in a codon usage-dependent manner. Interestingly, most of these identified genes, such as set-2, are predicted to play a role in regulating transcription or chromatin structures. Together, these results further established the role of synonymous codon sequences in regulating gene transcription and identified potential factors contributing to gene transcription level in a codon dependent manner.