Scientists discover that most synonymous mutations are strongly harmful

Marshall Nirenberg, a University of Michigan alumni, and a group of other scientists discovered the genetic code of life in the early 1960s, identifying the mechanisms by which information in DNA molecules is translated into proteins, the live cell’s functioning components.

They discovered codons, three-letter units in DNA sequences that dictate each of the 20 amino acids that make up proteins, for which Nirenberg received a Nobel Prize with two other researchers.

Point mutations are single-letter misspellings in the genetic code that occur occasionally. Nonsynonymous mutations affect protein sequences, whereas silent or synonymous mutations do not.

In protein-coding DNA sequences, approximately one-quarter and one-third of point mutations are synonymous. Those mutations have been thought to be neutral or virtually neutral since the genetic code was broken.

However, University of Michigan scientists reveal that most synonymous mutations are severely damaging in a study published online on June 8^th, 2022, in the journal Nature that entailed genetic manipulation of yeast cells in the lab.

According to the study authors, the high nonneutrality of most synonymous mutations would have major ramifications for the study of human pathological conditions, population and conservation biology, and evolutionary biology if proved to be true for other genes and animals.

Since the genetic code was solved in the 1960s, synonymous mutations have been generally thought to be benign. We now show that this belief is false. Because many biological conclusions rely on the presumption that synonymous mutations are neutral, its invalidation has broad implications.”

Jianzhi Zhang, Study Senior Author and Marshall W. Nirenberg Collegiate Professor, Ecology and Evolutionary Biology, University of Michigan

Jianzhi “George” Zhang added, “For example, synonymous mutations are generally ignored in the study of disease-causing mutations, but they might be an underappreciated and common mechanism.”

Anecdotal evidence has revealed that certain synonymous mutations are nonneutral in the last decade. Zhang and his colleagues sought to see if these kinds of situations are the exception or the rule.

They opted to investigate this issue in budding yeast (Saccharomyces cerevisiae) because the organism’s short generation period (about 80 minutes) and tiny size allowed researchers to swiftly, precisely, and conveniently evaluate the impact of a large number of synonymous changes.

They created almost 8,000 mutant yeast strains using CRISPR/Cas9 genome editing, each with a synonymous, nonsynonymous, or nonsense mutation in one of 21 genes chosen by the researchers.

They next measured how rapidly each mutant strain reproduced in comparison to the nonmutant strain to determine its “fitness.” Simply speaking, Darwinian fitness represents the number of offspring a person has. The reproduction rates of the yeast strains were used to determine if the mutations were advantageous, detrimental, or neutral in this situation.

The researchers were surprised to see that 75.9% of synonymous mutations were considerably harmful, whereas only 1.3% were significantly helpful.

The previous anecdotes of nonneutral synonymous mutations turned out to be the tip of the iceberg.”

Xukang Shen, Study Lead Author and Research Assistant, Ecology and Evolutionary Biology, University of Michigan

“We also studied the mechanisms through which synonymous mutations affect fitness and found that at least one reason is that both synonymous and nonsynonymous mutations alter the gene-expression level, and the extent of this expression effect predicts the fitness effect,” further stated Shen, a graduate student research assistant in Zhang’s lab.

According to Zhang, the researchers were aware that some synonymous mutations would likely turn out to be nonneutral based on anecdotal evidence.

But we were shocked by the large number of such mutations. Our results imply that synonymous mutations are nearly as important as nonsynonymous mutations in causing disease and call for strengthened effort in predicting and identifying pathogenic synonymous mutations.”

Jianzhi Zhang, Study Senior Author and Marshall W. Nirenberg Collegiate Professor, Ecology and Evolutionary Biology, University of Michigan

While there is no reason why their findings should be limited to yeast, the team stated that verification in other species is needed to validate the generality of their findings.