A central assumption about so-called synonymous mutations, which are changes in the coding sequence of proteins that do not lead to changes in its amino acid sequence, is being questioned by a study published in the June 8, 2022, issue of Nature.

Working in haploid yeast, scientists have found that synonymous mutations were roughly as likely as nonsynonymous ones to lead to decreased fitness.

In genetic studies, synonymous mutations are "typically ignored when people study disease," Jianzhi "George" Zhang told BioWorld Science. "Because the understanding is that they probably won't have any effect, or very little effect."

Zhang is the Marshall W. Nirenberg Collegiate Professor in the University of Michigan's Department of Ecology and Evolutionary Biology, and the paper's senior author.

If the work turns out to apply to diploid yeast and from there, animals and humans – and there is no particular reason to suspect it wouldn't that understanding will need to be rethought. 

"Revising our expectations about synonymous mutations should expand our view of the genetic underpinnings of human health," Nathaniel Sharp, assistant professor of genetics at the University of Wisconsin, wrote in an editorial that was published alongside the paper. "Synonymous mutations can cause proteins in humans to be inappropriately folded or expressed, just as in yeast and we know this can influence treatment outcomes and disease risk." 

The genetic code consists of 64 possible triple combinations of four nucleic acids, but there are only 20 amino acids that are used in proteins. As a result, most amino acids are coded for by more than one and up to six different nucleic acid triplets. For example, TCT, TCC, TCA, TCG, AGT, AGC all code for serine.

While the use of different synonymous codons has no effect on protein sequence, there have been reports that synonymous codons can affect protein production and ultimately, protein levels. For example, there is a synonymous mutation in the chloride transmembrane cystic fibrosis transmembrane conductance regulator (CFTR) that slows down CFTR production and folding because it interacts with a relatively rare transfer RNA.

Synonymous mutations can also affect messenger RNA concentration, Zhang explained. "During translation, you have a ribosome that moves along the mRNA," he said. "Sometimes when you use a codon that is not preferred by the cell, the ribosome will slow down or even get stuck."

As the cell's protein factories, ribosomes are absolutely essential to cellular functioning. When cells detect that their ribosomes are idling, this may trigger the destruction of the messenger RNA that is slowing things down.

Fitness facts for yeast

In their experiments, Zhang and his colleagues used CRISPR/Cas9 genome editing to introduce a synonymous, nonsynonymous or nonsense mutation in one of 21 genes, creating more than 8,000 mutant yeast strains.

It turned out the 75.9% of synonymous mutations, and 75.8% nonsynonymous mutations, significantly reduced the speed of cell division and thus, fitness. In 5 of the 21 genes the team looked at, nonsynonymous mutations did have a stronger effect on fitness than synonymous ones. Even in those genes, however, the synonymous mutations also reduced fitness. 

Zhang said that the magnitude of the effect was unexpected. While there have been reports in the literature about particular synonymous mutations, "the surprise was that the distributions look the same" for synonymous and nonsynonymous mutations.

Nonsynonymous mutations, after they arise, are less likely to persist under most circumstances, which would suggest they are on the average more harmful than synonymous mutations. Zhang said that two factors could account for this difference. The relatively bountiful conditions of the laboratory are less sensitive to changes in fitness than outside of it. Another possibility is that nonsynonymous mutations are more sensitive to difference in environmental conditions. A mutation can be helpful in some environmental contexts and harmful in others.