The Role of Codon Usage in Regulating Protein Expression, Structure and Function

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.