A basic business principle is that no worker is irreplaceable; that also holds true for most proteins, the cellular factory workers of our bodies. If we fire a protein – that is, permanently delete it from our genome using genetic engineering – the cell will likely initiate a compensatory mechanism to replace it with other proteins. This mechanism is vital for life to exist, but it makes things extremely difficult for researchers trying to understand the role of each protein. What, then, would happen if we were to force a protein to go on a sudden strike? The cell would have no time to locate replacements and that could reveal the exact role of the striking protein. In a new study, published in the Journal of Cell Biology, Weizmann Institute of Science researchers installed thousands of “strike machines” in yeast colonies, uncovering the vital and as-yet hidden roles played by many proteins.
We share around two thirds of our genetic makeup with baker’s yeast. That’s one of the reasons that it is among the most researched organisms in nature. The genetic material of yeast contains around 6,000 genes encoding proteins. Despite decades of research, however, we are still in the dark about what 1,200 of these proteins do. In their new study, researchers from the laboratory of Prof. Maya Schuldiner in Weizmann’s Molecular Genetics Department sought to discover the answer to this question. They accomplished this using a system that allowed them to quickly remove a protein from the cell – in other words, to force it to go on strike at the push of a button. The system is made up of three parts: a label that marks the protein researchers want to study; a destructive protein to degrade the labeled protein and force it to go on strike; and a mediator molecule without which the strike could not take place.
The research team, led by doctoral student Rosario Valenti and Dr. Yotam David from Schuldiner’s lab, did not install their system in just one gene. Instead, using genetic engineering, they created an entire genetic library: a collection of 5,170 strains of yeast, each with a different protein marked to go on strike. “With the help of Weizmann’s IT Infrastructure Branch, we built a digital library that is open to any scientist who wants to ‘borrow’ these genetic strains for their own research,” Schuldiner says. “They can not only access the strains themselves but also learn about the impact of forcing them to ‘strike.’”
""We share hundreds of proteins with yeast, and revealing their roles could be key to understanding rare genetic diseases"
Understanding the mysterious role of genes and proteins in yeast is not of interest only to scientists studying single-celled organisms; these findings could also shed light on many equivalent genes in human cells. “We know the underlying defects of many rare genetic diseases, but when we don’t know the role of the defective gene, there’s no cure,” Schuldiner explains. “We share hundreds of these mysterious proteins with yeast, and revealing their roles could be key to understanding some of these diseases.” Schuldiner is especially interested in genes that are essential for mitochondria, the powerhouses that produce chemical energy for the entire cell. Scientists already know that there is a connection between the shape and distribution of the mitochondria in the cell and the role they play. For example, when they are connected to each other, they tend to convert energy much more efficiently.
The cell is constantly busy remodeling the mitochondrial structure to its needs, and malfunctions in this process are the cause of many diseases. Surprisingly, the mechanism that regulates the arrangement of mitochondria in the cell is only partially known, and even less is known about the regulating factors. Using their new library, the Weizmann researchers discovered 220 genes whose “striking” damaged the mitochondrial structure in the cell, and they identified the genes that were important for maintaining a healthy rate of energy conversion.
The researchers also used the library to study which proteins are vital to the cell’s lifecycle, and they identified new proteins that regulate cell division. All in all, the team uncovered the roles of hundreds of genes that were previously not known to be vital for the cell’s survival. These genes were shown to be vital in specific growth environments, but researchers also discovered several genes that are essential to the cell in any environment but had not been recognized as such until now.
The new library is already a hit in the scientific community. “Labs from the around the world have started to borrow individual strains in order to expand their research into proteins whose role is still a mystery,” Schuldiner says. “They are also invited to borrow entire sections from the library and use them to investigate which elements are important to a specific cellular process, as we demonstrated in our study. I hope that in the coming years the library will also help lift the veil of mystery from some of the processes that occur in human cells – sick and healthy alike.”
Over the years, 8 Nobel Prizes have been awarded for yeast-related discoveries; the first was in 1907, for the discovery of enzymes, and the most recent, in 2016, for research into autophagy, a process in which cells recycle their own components.
Also participating in the study were Dunya Edilbi, Dr. Benjamin Dubreuil, Yeynit Asraf and Dr. Ehud Sass from Weizmann’s Molecular Genetics Department; Angela Boshnakovska and Prof. Peter Rehling from the University Medical Center Goettingen in Goettingen, Germany; and Dr. Tomer-Meir Salame from Weizmann’s Life Sciences Core Facilities Department.
Prof. Maya Schuldiner is the incumbent of the Dr. Gil Omenn and Martha Darling Professorial Chair in Molecular Genetics. Her research is supported by the Blythe Brenden-Mann Foundation.
