There are three main projects in my laboratory. One is on the Hsp90-R2TP complex, the second one is on the Clp system, the third one is on mapping the chaperone interaction network. The three projects deal with the common theme of cellular stress response. We are also interested in developing compounds that target protein homeostasis and that can be used as anticancers or antibacterials.
Through a large-scale proteomics approach, we discovered that 10% of the yeast proteome physically or genetically interacts with Hsp90. Furthermore, we identified new conserved cofactors of the chaperone. Two of these cofactors, which we termed Tah1 and Pih1, were found to link Hsp90 to rRNA processing pathways. This is the first demonstration of a link between chaperones and rRNA processing. Furthermore, Tah1 and Pih1 were found to form a tight complex with the essential helicases Rvb1 and Rvb2. We found that Rvb1 and Rvb2 form a heterohexameric complex with ATPase and helicase activities. We termed the complex of Rvb1-Rvb2-Tah1-Pih1 as R2TP. We solved the structure of Tah1 by NMR and determined the electron microscopy structures of Rvb1/2. We also found that R2TP cycles between the nucleus and the cytoplasm depending on nutrient availability. Our efforts on this project are aimed at elucidating at the molecular level the ultimate effect of Hsp90 and R2TP on ribosome biogenesis and the assembly of other critical complexes. This project sheds further insights into the role of Hsp90, Rvb1, and Rvb2 in cancer.
Our work on the Clp system provided important insights into the function of this chaperone-protease system, especially as regards to its structure and dynamics. Our initial work concentrated on ClpXP from E. coli. ClpX is a hexameric ATP-dependent unfoldase chaperone, while ClpP is a serine protease that forms a cylindrical tetradecamer with narrow axial pores for substrate entry. In the ClpXP complex, ClpX binds target substrates, unfolds them and threads them into ClpP for degradation. We discovered that the mechanism of release of degradation products from the cylindrical protease ClpP is through the formation of transient equatorial side pores that allow for peptide egress. We also discovered compounds that dysregulate ClpP and that have antibacterial activity. Hence, our research in this field sheds novel insights into bacterial infectivity.
We subsequently provided a comprehensive analysis of the Clp chaperones and protease in the human malaria parasite Plasmodium falciparum. The parasite was found to contain four Clp ATPases, which we term PfClpB1, PfClpB2, PfClpC, and PfClpM. In addition, one PfClpP, the proteolytic subunit, and one PfClpR, which is an inactive version of the protease, were also identified. Both PfClpP and PfClpR form mostly homoheptameric rings. The X-ray structure of PfClpP showed the protein as a compacted tetradecamer. We also solved the X-ray structure of PfClpR. Our data suggest the presence of a ClpCRP complex in P. falciparum.
We are also interested in understanding the function of the ClpXP system in different other organisms including humans.
Mapping chaperone interaction networks
Molecular chaperones are essential components of a quality control machinery present in the cell. They can either aid in the folding and maintenance of newly translated proteins or they can lead to the degradation of misfolded and destabilized proteins. They are also known to be involved in many cellular functions, however, a detailed and comprehensive overview of the interactions between chaperones and their cofactors and substrates is still absent. The heat shock proteins Hsp90, Hsp70/Hsp40, and Hsp60/Hsp10 are typical chaperone systems that are highly conserved across organisms. In this project, we are carrying out systematic mapping of the chaperone interaction networks using a wide range of proteomic and genomic methods. The ultimate goal of the project is to determine the mechanisms that govern protein homeostasis inside the cell.