A major class of genome instability is chromosome instability (CIN), a phenotype that contributes to the development of 90% of human cancers. While the majority of solid tumours exhibit CIN, its genetic basis is relatively poorly understood. The general research goals of our lab are to define and characterize yeast genes, and cognate human orthologs that play a role in CIN. Recent studies were directed at identifying yeast mutants that display a CIN phenotype in a comprehensive fashion. The functional distribution of the identified genes suggests the existence of multiple unexpected genome integrity pathways. Few of our projects are focused on understanding the CIN mechanisms in these pathways.
In one line of research we demonstrated that failure of the proteasome to localize to the nucleus, and to degrade specific DNA repair proteins from chromatin results in impaired DNA repair, and CIN. This study suggested that the function of additional DNA repair proteins is mediated by the proteasome. Accordingly, in order to identify such targets, we designed a systematic genetic robotic screening approach in yeast. The results from one of our follow up studies reveled for the first time that the assembly of complexes that regulate the cell cycle, and the activity of their catalytic subunits are regulated by the ubiquitin proteasome system (UPS). Currently we want to figure out why cells have a degradation mechanism for these proteins, and the role of this process in keeping the genome stable.
Our second line of research focuses on the identification and functional characterization of new Iron-Sulfur (Fe-S) proteins required for maintaining genome stability. Fe-S clusters are small inorganic cofactors found in hundreds of proteins and are required in virtually all organisms from bacteria to humans. The ultimate goal of this study is to understand why so many DNA maintenance enzymes (such as DNA polymerases and helicases) require Fe-S clusters as cofactors for their function, a broad problem that currently is not well understood.
Our third line of research has developed from a high content microscopy screening aiming to identify proteins that play a role in proteasome nuclear localization. Intrigued by the results of this screen, we started to investigate the role that the proteasome plays in protein quality control. We identified for the first time that the change in cytosolic pH in response to glucose levels serves as a messenger that mediates the formation of proteasome stress granules (PSGs) that form in starving cells (JCB, 2013). We currently try to gain mechanistic insight into the formation of PSGs, and other proteasome granules that form in cases of dysfunctional proteasome, with the ultimate goal to understand their role, and whether they represent similar or different aggregates.
The combination of genetic molecular and high-throughput technology approaches has greatly enhanced the discoveries in our studies. In light of this, we have recently developed a novel systematic genetic approach (termed ‘‘reverse PCA’’) that can be used to systematically identify genes whose products are required for the physical interaction between two given proteins (PLOS Genetics, 2013). This technique was successfully validated in many of our follow-up studies. Furthermore, we believe that it will facilitate the study of protein structure-function relationships, and elucidate the mechanisms that regulate protein-protein interactions.
Overall, our studies combine few research programs with four major projects. The combination of mechanistic follow-up of our discoveries, alongside the creation of novel and creative high-throughput techniques, our research is designed to understand the mechanisms of action of these functions, and how their activities and controls are impaired in disease patients.