Synonymous sites are generally considered to be functionally neutral. However, there are recent contradictory findings suggesting that synonymous alleles might have functional roles in various molecular aspects. For instance, a recent study demonstrated that synonymous single nucleotide polymorphisms have a similar effect size as nonsynonymous single nucleotide polymorphisms in human disease association studies. Researchers have recognized synonymous codon usage bias (SCUB) in the genomes of almost all species and have investigated whether SCUB is due to random nucleotide compositional bias or to natural selection of any functional exposure generated by synonymous mutations. One of the most prominent observations on the non-neutrality of synonymous codons is the correlation between SCUB and levels of gene expression, such that highly expressed genes tend to have a higher preference toward so-called optimal codons than lowly expressed genes. In relation, it is known that amounts of cognate tRNAs that bind to optimal codons are significantly higher than the amounts of cognate tRNAs that bind to non-optimal codons in genomes. In the present paper, we review various functions that synonymous codons might have other than regulating expression levels.
According to the molecular evolutionary theory, mutations occurring in coding regions involved in amino acid changes, called nonsynonymous mutations, are basically harmful and deleterious to organisms and are subject to strong purifying selection [
One clue suggesting the non-neutrality of synonymous codons could be drawn from the study on synonymous codon usage bias (SCUB) [
Two different explanations have been provided so far about what causes the SCUB phenomenon. One is based on uneven nucleotide compositions throughout genomes [
An evolutionary explanation of SCUB, based on natural selection, was investigated under a hypothesis, called Hill-Robertson (HR) interference. The HR hypothesis posits that the efficiency of natural selection of one site will weaken when the site is linked to adjacent sites and does not segregate independently, wherein recombination can play a role in relieving the interference. There is some agreement among researchers that SCUB is positively correlated with recombination rates, although there are opposite observations on the effect of HR [
In the present work, we thus decided to summarize other facets of the functions that synonymous codons might have, other than the functions that are related to translational efficiency and accuracy in the regulation of gene expression (
SCUB is considered to be a general phenomenon that can be observed in the genomes of almost all species [
However, some researchers have tried to provide an opposing explanation regarding why some genes avoid optimal codons within genes. They think that genes tend to harbor codons that are rarely used in translation, because rare codons are beneficial in checking the step right before ribosomes start translation or the protein folding step before secreting nascent protein product in the endoplasmic reticulum [
Intron-exon boundary regions, also known as limited by the GU-AG rule, are important in carrying out splicing events [
It is quite unexpected that synonymous codons are somehow linked to the regulation of transcription. Transcription is a process of copying genic sequences into mRNAs, which requires various specific and delicate controls, usually conducted by the combinatorial actions of cis-acting DNA elements and transacting regulatory factors, called transcription factors (TFs). Promoters are well-established controlling cis-acting elements and are generally located upstream of transcription start sites, which are thought to be separate regions from the coding regions of genes.
Recently, Stergachis
The secondary structure of mRNA is important for controlling translational speed and timing, on which synonymous codon mutations might have crucial effects. For instance, removing rare synonymous codons from an expression construct decreases the enzyme activity of chloramphenicol acetyltransferase [
The same observation has also been made in
Researchers have long been searching for important disease-associated variants, mainly by investigating functional perturbations caused by nonsynonymous mutations. On the other hand, synonymous mutations have not been considered to be variants that are responsible for showing disease phenotypes. Often, synonymous mutations are filtered out and are not even considered, because candidate variants need to be functionally validated for the possibility of causing diseases or phenotypes. In that sense, it is an interesting revelation that there are various functional activities conducted by synonymous codons in molecular processes. Synonymous mutations do not change the amino acid sequence in proteins but can interrupt the formation of correct mRNA secondary structures, reduce translational accuracy and speed, and even alter the start of transcription. We think that advancing our understanding of the functions of synonymous codons will contribute to the identification of all disease-associated genes and mutations.
This research was supported by a 2016 research grant from Kangwon National University (No. 120131854) to S.S.C.
Conceptualization: SSC
Formal analysis: EHI
Funding acquisition: SSC
Writing – original draft: SSC
Writing – review & editing: EHI, SSC
Schematic representation of functional aspects in which synonymous codons might be involved.