Browsing by Subject "Codon"
Now showing 1 - 2 of 2
- Results Per Page
- Sort Options
Item The Role of Codon Usage in Regulating Protein Expression, Structure and Function(2014-06-10) Zhou, Mian; Tu, Benjamin; Liu, Yi; Takahashi, Joseph; Zinn, Andrew R.Codon usage bias has been observed in the genomes of almost all organisms and is thought to result from selection for efficient translation of highly expressed genes. Many genes, however, exhibit little codon usage bias. It's not clear whether the lack of codon bias for a gene is due to lack of selection for mRNA translation or it has some biological significance. The rhythmic expression and the proper function of the Neurospora FREQUENCY (FRQ) protein are essential for circadian clock function. However, unlike most genes inNeurospora, frq exhibits non-optimal codon usage across its entire open reading frame (ORF). Optimization of frq codon usage results in the abolition of both overt and molecular circadian rhythms. Codon optimization not only increases FRQ expression level but surprisingly, also results in conformational changes in FRQ protein, impaired FRQ phosphorylation, and impaired functions in the circadian feedback loops. These results indicate that non-optimal codon usage of frq is essential for maintaining circadian rhythmicity in Neurospora. Interestingly, there is a correlation between codon usage score and FRQ protein structure: the regions that are predicted to be disordered preferentially uses more non-optimal codons. This negative correlation is also found in the proteasome of Neurospora, as well in yeast, Drosophila, C. elegans and E. coli. By making a series of Neurospora strains with frq optimized in different regions, we find that codon optimizations in the predicted disordered regions of FRQ have more prominent effects on FRQ activity and structure. Furthermore, codon optimization of disordered regions in several other Neurospora genes results in altered protein degradation rates, suggesting structural changes by codon optimization. Together, these results suggest that codon usage adapts to protein structures and there is a "code" within genetic codons that allow optimal co-translational protein folding.Item The Roles of Codon Usage in Translation and Transcription(2020-05-01T05:00:00.000Z) Zhao, Fangzhou; Tu, Benjamin; Thomas, Philip J.; Zhang, Xuewu; Liu, YiCodon 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.