‘Silent’ Mutations Could Have Unexpectedly Far-Reaching Effects that May Impact Health

Genetic mutations affect nearly all human diseases. Some genetic disorders such as cystic fibrosis are caused by mutations in a single gene that a person inherits from their parents. Other diseases can be caused by changes in multiple genes or from a combination of gene mutations and environmental factors. We still have a lot to learn about the complex ways that variations in our genes affect health and disease.

Researchers investigating genetic disorders have primarily studied mutations that cause our cells to alter the makeup of proteins, like the most common mutations that cause cystic fibrosis. Less research has been done on alterations called synonymous mutations, which have been called “silent” because they don’t alter the makeup of proteins, leading scientists to long assume that these kinds of mutations don’t produce any noticeable differences in our biology or health. However, recent research has shown that synonymous mutations can lead to significant changes in a cell’s ability to survive and grow. A new NIH-supported study reported in Proceedings of the National Academy of Sciences sheds additional light on the impact of synonymous mutations and their effect on the way proteins are made.

The researchers behind this study, at the University of Notre Dame in Notre Dame, IN, wanted to understand how synonymous mutations may affect how much protein is made and whether proteins are folded correctly in cells. Misfolded proteins are known to play roles in numerous diseases, including cystic fibrosis, Alzheimer’s disease, and some cancers. The study team, led by Patricia L. Clark , who received an NIH Director’s Pioneer Award in 2021 for this work, has shown that synonymous mutations in a particular gene in Escherichia coli (E. coli) bacteria can alter how the encoded protein folds as it is being made, by altering the rate at which cells produce each copy of the protein. The new research goes a step further and shows that silent mutations in one gene can affect the amount of protein produced from a separate, neighboring gene.

Clark and colleagues, including first author Anabel Rodriquez, created nine synonymous versions of the E. coli chloramphenicol acetyltransferase (cat) gene. This gene encodes a protein enzyme that influences the bacterium’s sensitivity to a particular antibiotic. The researchers found that four of the nine synonymous cat gene sequences significantly affected the number of protein enzymes the E. coli produced from this gene. Unlike in prior work from Clark’s lab, the reason for those differences didn’t stem from changes in protein folding. The differences began one step earlier, in the synthesis of RNA copies, or transcripts, from the cat gene’s DNA. An RNA transcript carries the instructions cells use to produce proteins.

How did it happen? The researchers found that some of the synonymous mutations created new sites on the cat gene where the enzyme that synthesizes RNA could bind. As a result, E. coli cells started making RNA transcripts from part of the cat gene and the entire neighboring gene. These new RNA transcripts led those bacterial cells to make more of the protein encoded by the neighboring gene. In short, these findings unexpectedly showed that synonymous mutations in one gene can alter the production of the protein from other genes.

This discovery in E. coli may have important implications for understanding the bacteria’s biology and evolution. Clark’s team continues to study this system to learn more. Their findings may also prove to have broader implications for biology, including for some genetic disorders. It’s an area that warrants more study and attention, to better understand the roles that synonymous mutations may be playing in genes and their effects on human health.

Reference:

Rodriguez A, et al. Synonymous codon substitutions modulate transcription and translation of a divergent upstream gene by modulating antisense RNA production. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.2405510121 (2024).

NIH Support: National Institute of General Medical Sciences