Image: Yeast cells whose cell wall has been stained blue. An example protein is highlighted in green. The amount of this or other proteins present varies from cell to cell. The genetic basis of such variation has now been demonstrated in the new study. © Charité | Jakob Vowinckel
Science Study: Researchers Map Connections Between Gene Variants and the Proteome
Berlin, October 10, 2025
The genomes of all organisms contain mutations whose biological effects are often unknown. Researchers at Charité – Universitätsmedizin Berlin, in collaboration with Stanford University (USA), have now found a way to predict the effects of numerous mutations in a yeast fungus. The key was the detailed analysis of the proteome – the entirety of a cell’s proteins. The research team sees the new method as a valuable tool for better understanding molecular biological relationships – for example, against the backdrop of increasing resistance in microorganisms to medicinal substances. The study was published in the journal Science*.
Microorganisms are masters of adaptation. Even tiny variations within their genes can help them adapt to changing, sometimes hostile, conditions in their environment. This includes, for example, developing resistance to medicinal substances. “To better assess the risk of a pathogen becoming resistant, or to develop novel, improved drugs, we need to better understand the connections between different gene variants and the resulting biological changes,” says Prof. Markus Ralser, Director of the Charité’s Institute of Biochemistry and one of the two study leaders. “Because genome sequencing has advanced rapidly, we can now identify genetic differences very well. However, we don’t know how these affect a microbe’s growth or resistance, for example, or under which conditions they are significant.”
A Look into the Molecular Black Box
To understand the effects of different gene variants, it helps to take a look at the proteome. The proteome works like a kind of gear system that controls, executes, and keeps cellular processes running. The various proteins interact like cogs and influence each other. “A specific variant in a gene can, for example, cause a protein to no longer be produced at all, or to be produced in a different form or quantity. And that can actually change a lot in the cellular machinery,” says Dr. Johannes Hartl from the Berlin Institute of Health at Charité (BIH) and one of the study’s lead authors. “The proteome and its variability caused by natural genetic variation remain, in its entirety, a molecular black box. With our study, we were able to show that it is possible and necessary to shed more light on this.”
For their studies, the researchers used two naturally occurring strains of yeast cells. Yeasts are single-celled microorganisms that belong to the fungi family. One of the yeast strains came from a Californian vineyard, the other was isolated from an immunosuppressed patient in Italy. The researchers crossed these two strains over many generations. “This resulted in almost a thousand new yeast strains in which the genetic makeup of the parents was well mixed,” explains Johannes Hartl. The crossing experiments and the subsequent genetic analysis of the yeast strains were carried out in the Stanford laboratory. The Charité team led by Markus Ralser analyzed the proteome of the different strains using high-throughput methods, using mass spectrometry, which can be used to unambiguously identify various proteins and precisely quantify their respective amounts present in the cell.
Proteome reveals molecular background
Together, the researchers worked through the vast treasure trove of data. The goal: to find clear connections between the individual gene variants and the resulting changes in the proteome. “To do this, we correlated the genome and proteome data and created a kind of map that reflects the effect of thousands of genetic variants on the amount of thousands of proteins in the cell,” explains Johannes Hartl. “And to test whether the connections we found actually originate from the one specific gene variant and not from other processes within the cell, we used the CRISPR/Cas gene scissors to insert the gene variant into the original parent strain of the yeast cells, which previously did not possess this gene variant. We then looked to see whether the corresponding changes in the proteome could also be found there.”
For some gene variants and the associated changes in the proteome, the researchers went a step further and investigated their specific effects. For example, the survival of the yeast cells under the influence of an antimycotic, i.e., an antifungal agent. “The antifungal agent binds and inhibits an enzyme necessary for the biosynthesis of an essential component of the yeast membrane. This prevents the cell from growing further – provided the agent blocks enough existing enzymes,” says Johannes Hartl. “However, in our genome-proteome map, we were able to see that the amount of this enzyme was increased in certain gene variants. The experiment showed that yeast cells with this gene variant became more resistant to the antifungal agent.”
Small genetic changes can have significant effects
The study also shows that many genetic changes – even those that appear “insignificant” at first glance – can have far-reaching molecular consequences. The researchers found that genetic variants affecting hundreds of cellular proteins had no discernible effects under standard conditions, but had significant effects on cell growth under altered conditions, such as drug treatment or changes in the nutritional supply.
“Genome-proteome mapping is an excellent tool for uncovering molecular biological relationships and understanding the effects of mutations and genetic differences,” emphasizes Markus Ralser. “This allows us to track down many protein functions and interactions much more easily, thus better predicting the development of potential drug resistance and adaptation to new environments – such as humans as host organisms.” In subsequent studies, the researchers therefore plan to expand this approach to include pathogenic fungi that cause particularly severe infections in humans.
*Jakobson CM, Hartl J et al. A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness. Science 2025 Oct 09. doi: 10.1126/science.adu3198