An international team led by Charité – Universitätsmedizin Berlin has constructed the largest cellular proteomic map to date, using yeasts as model organisms

Despite decades of research, the function of many genes remains unknown, limiting our understanding of certain diseases, some of them rare, and hindering the development of new therapies. In the case of yeast and bacterial cells, there is a lack of the fundamental knowledge required to develop the new antimicrobials that are urgently needed in the face of rising drug tolerance and resistance. The current study is one of the most extensive proteomic studies in the world. The team of researchers studied yeast cells to gain a more accurate and detailed picture of the role of genes that were previously not yet associated with specific functions. The goal is to obtain critical information to interpret the ramifications of genetic mutations and help to close diagnostic gaps. The researchers’ objective was to investigate in detail how certain proteins are expressed and regulated, which should ultimately also help lay the groundwork for developing new drugs.

Dr. Markus Ralser, senior author of the study and Director of the Institute of Biochemistry and Einstein Professor of Biochemistry at Charité, explains: “We made use of a collection of yeast strains generated by an international consortium, in which all nonessential genes were missing from at least one strain. We then used mass spectrometry, a technology that can quantify thousands of proteins in parallel, to characterize each of the strains, resulting in the largest proteomic study to date.” The study revealed general principles governing the expression of proteins, including identifying for thousands of proteins how their function or biophysical properties relate to expression.

The research also generated a lot of data on previously understudied proteins. This resulted in the development of new methods for assigning gene function. Mass spectrometry, and especially specific proteomic techniques developed by Ralser and his team in recent years, helped to determine the amounts of specific proteins present in the individual yeast strains in the absence of all nonessential genes. “The research has the potential to fundamentally improve our understanding of cell biology, providing new insights into gene function in life forms whose cells have a nucleus, which are known as eukaryotes,” says Dr. Georg Kustatscher, who contributed to the study by analyzing the large dataset with his research group at the University of Edinburgh. “The proteomes recorded in the study contain key information about potential new drug targets, providing hope for future treatment options.”

The extensive study was made possible by a collaboration between research teams at Charité, the Francis Crick Institute, and the University of Edinburgh. Labs at Cambridge and the University of Toronto also contributed by pioneering essential proteomic technologies and functional genomics methods used in the study. Dr. Christoph Messner, who was initially responsible for the study at the Francis Crick Institute in London and is now a group leader at the University of Zurich, points out: “To our surprise, the study further revealed that the response of a protein to these mutations depends more on its biophysical properties than its function. This opens up a new way of looking at analysis of large biological datasets, which these days are often already collected using advanced sequencing or mass spectrometry techniques, but can still be difficult to interpret.” The researchers thus conclude that their study will have far-reaching implications for the biosciences.

This research has provided critical information on gene function and protein expression, paving the way for future breakthroughs in the field of microbiology. The team is now working on conducting a similar study in human cells, with the goal of generating more information on previously unknown genes. The researchers also aim to link the yeast proteome maps with other molecular data to help develop better antifungal therapies.

*Messner CB et al. The proteomic landscape of genome-wide genetic perturbations. Cell 2023. doi: 10.1016/j.cell.2023.03.026

Mass spectrometry
Mass spectrometry is a technique for analyzing the mass of molecules and atoms. The substance to be analyzed is first converted to a gas phase and then ionized. The ions formed are sharply accelerated using an electric field and then sorted by mass-to-charge ratio in the mass spectrometer’s analytical unit. The mass spectrum of a substance provides information on its molecular composition. Mass spectrometry is therefore useful for identifying, characterizing, and quantifying a large number of biomolecules, such as proteins, metabolites, sugars, and fats, which behave differently depending on the disease and the individual organism.

About the study
The study was funded in part through an academia-industry partnership involving Sciex, a mass spectrometry manufacturer, and the Biotechnology and Biological Sciences Research Council (BBSRC) in London. Further support was provided in the form of an Investigator Award from the Wellcome Trust and a Synergy Grant from the European Research Council.