Non-optimal codon usage is critical for protein structure and function of the master general amino acid control regulator CPC-1

Abstract

Under amino acid starvation condition, eukaryotic organisms activate a general amino acid control response. In Neurospora crassa, Cross Pathway Control-1 (CPC-1), the ortholog of the Saccharomyces cerevisiae bZIP transcription factor GCN4, functions as the master regulator of the general amino acid control response. Codon usage biases are a universal feature of eukaryotic genomes and are critical for regulation of gene expression. Although codon usage has also been implicated in the regulation of protein structure and function, genetic evidence supporting this conclusion is very limited. Here we show that Neurospora cpc-1 has a non-optimal NNU-rich codon usage profile that contrasts with the strong NNC codon preference in the genome. Although substitution of the cpc-1 NNU codons with synonymous NNC codons elevated CPC-1 expression in Neurospora, it altered CPC-1 degradation rate and abolished its amino acid starvation-induced protein stabilization. The codon-manipulated CPC-1 protein also exhibited different sensitivity to limited protease digestion. Furthermore, CPC-1 functions in rescuing the cell growth of the cpc-1 deletion mutant and activating the expression of its target genes were impaired by the synonymous codon changes. Together, these results reveal the critical role of codon usage in regulating of CPC-1 expression and function, and establish a genetic example of the importance of codon usage in protein structure.

The chloroplast genome of two medicinal species (Veronica anagallis-aquatica and Veronica unulata) and its comparative analysis with related Veronica species

“…It is widely known that codon usage bias occurs in different organisms. Codon preferences are in uenced by natural selection, base mutations, and genetic drift, are the result of long-term evolution of species in response to environmental selection, and affect the expression of mRNA and protein levels in the genome [46][47][48][49][50] . The most abundant amino acid in both species is leucine (Leu), with an average of 2,279, which is also common in other angiosperm species 51,52 .…”