Arginine CGA codons as a source of nonsense mutations: a possible role in multivariant gene expression, control of mRNA quality, and aging

Abstract

Methylation of cytosine residues in DNA of higher eukaryotes, including humans, creates “hot spots” of C→T transitions in the genome. The predominantly methylated sequence in mammalian DNAs is CG (CpG). Among CG-containing codons, CGA codons for arginine are unique due to their ability to create stop codons TGA (UGA in mRNA) upon epigenetic-mediated mutation. As such nonsense mutations can have a strong adverse effect on the cell and organism, we have performed a study, on the example of human genes, aimed to characterise the anticipated effects of epigenetic-mediated nonsense mutations CGA→TGA in somatic cells. It is commonly accepted that premature termination codons (PTCs) lead to the biosynthesis of truncated and usually inactive proteins. In addition, transcripts with PTC can be destroyed by a nonsense-mediated mRNA decay (NMD) machinery. We have considered the cell potentialities (gene families, diploidy, and alternative splicing) to overcome the worst consequences of nonsense mutation. As a special case, in the biosynthesis of a particular group of proteins called selenoproteins, the mutation CGA→UGA would not lead to the premature translation termination and NMD but rather to the insertion of selenocysteine or cysteine instead of former arginine. The finding of SECIS (Sel insertion sequence)-like structures in a variety of mRNAs allowed us to postulate the existence of facultative selenoproteins, whose biosynthesis might be coupled with the redefinition of premature UGA stop codons arising upon mutations, as in the case of “classic” selenoproteins. Nevertheless, a detailed structural analysis of 165 transcripts has shown that roughly 80–90% of functional human mRNAs are potential substrates for NMD upon the PTC emergence. A hypothesis was put forward highlighting a role of arginine CGA codons together with glutamine CAA and CAG codons in the control of mRNA quality and life span. According to this hypothesis, the conversion of the ribonucleic codons CGA, CAA, or CAG into stop codons UGA, UAA or UAG owing to spontaneous or enzymatic cytosine deamination might serve as a trigger for the transcript destruction by NMD (C→U control). Thus, the consequences of epigenetic-mediated nonsense mutations are diverse and may largely depend on the structure of the transcript (CGA codon position, the presence and position of introns and SECIS elements, and splicing potential) of the cognate gene. However, this diversity and the presumable role of CGA codons in performing the everyday function by controlling whether genes are expressed correctly do not exclude their long-term role as limiters of the cell and organism life span. Thus, the presumable role of CGA codons in genome functioning and stability opens new perspectives to influence aging and concomitant deceases by codon editing.