Research Vision

From single proteins to proteomic drifts: Our team explores fundamental biological questions involving protein networks at a multitude of levels. Thousands of different proteins crammed together into each dense cell (the proteome) fulfill almost all essential functions in metabolism, cell regulation and development. To do so they must interact in precise unison, convey messages, and tweak each other’s properties. Starting with individual proteins in isolation or in single cells, through the proteome level, and culminating with the impact of individual proteins on whole organisms during development, we study dynamic protein network responses to the changing environment, as well as to shifting needs during metabolic changes or aging processes. Specifically, we hope to focus on networks determining protein fate, turnover and homeostasis (proteostasis). Functional, regulatory and structural proteins that make up living organisms form a convoluted network of interactions in a dynamic state that continually adapts balancing internal needs and external stress. A classical approach has been to study proteins in isolation either biochemically in a test tube (in vitro) or tracking fate of a specific target in a cellular context (in vivo). A complementary approach emphasizes the importance of multiple proteins simultaneously, in a highly interconnected network (often referred to as “systems biology”). Key to both approaches is the ability to quantify protein-protein interactions in their relevant biological context; be it in a single cell or in a living organism.

The dynamic changes of ubiquitin signaling under varied stress conditions reflect changes to protein-protein interactions, and protein fate. Perturbing the cellular environment by exposure to external stress or by ablating specific components of the network is used to determine the robustness of the system and illuminate processes such as adaptation or aging. We take advantage of yeast as a biochemically dissectible system to characterize changes in protein networks that determine the proteomes of defined organelles such as mitochondria. Key findings are further studied by genetic manipulation in live cells (for instance changes of mitochondrial localization of proteins in response to network perturbation or oxidative stress). One of our strengths is isolation of proteins at will, and characterization of their interactions in isolation. Validations include quantification of kinetic or thermodynamic parameters, affinity constants, and rates of binding or release steps by a variety of biophysical techniques (e.g. by surface plasmon resonance, fluoresce anisotropy, differential -phoresis or affinity isolation). Interactions of mitofusin and proteasomes will serve as particular targets of interest.

Proteasome function, the ubiquitin landscape, and Mitochondria-UPS reciprocity.Our lab is interested in Proteasome structure and function, Mechanistic aspects of protein degradation by the ubiquitin-proteasome system and Charting the cellular ubiquitin-linkage profile using Mass spectrometry and proteomics. Towards this goal we are also analyzing the importance of proteolysis in homeostasis and regulation of the proteome and the specific recognition of ubiquitin and ubiquitin-like proteins. A separate yet related project looks at the biology of mitochondria membrane fusion and fission. More specifically, how does ubiquitination and proteasome-dependent-degradation participate in mitochondria function and dynamics. An additional interest of the lab is to dissect the role of the COP9 signalosome in mediating protein degradation in budding yeast.

Our main focus has been dissection of the 19S regulatory particle of the proteasome into elementary functional units. Mapping subunit composition of the Lid and Base subcomplexes. Identification of a central unit within the Base that links substrate recruitment with proteolytic activation and the mechanistic role of the solenoid fold of the PC repeat (HEAT-like) regions of Rpn1 and Rpn2 that make up the central unit of the Base. How do the ATPases and the central Rpn1-Rpn2 unit in the Base control channel gating and substrate traffic into the 20S chamber. We are interested in dissecting the roles of the proteasome ATPases in the different steps of proteasome function.

Over the last few years we have characterized a ubiquitin-binding subunit, Rpn10, both in and out of the proteasome. Two different functions of Rpn10 are assigned to two distinct structural domains. Its vWA domain stabilizes proteasome structural integrity. Outside of the proteasome, Rpn10, can associate with ubiquitin-like domain containing shuttles via its UIM motif and filter their access to the proteasome. In the case of Dsk2, intricate “ubiquitin gymnastics” guarantees that proteasome access of uncharged Dsk2 is limited, whereas Dsk2 loaded with cargo of polyubiquitin chains longer than 4 units can be recognized by proteasome receptors . Through this selection process, Rpn10-Dsk2 can alter the cellular ubiquitin-landscape. Under normal conditions, absolute quantification of conjugated ubiquitin by mass spectrometry demonstrates that a large portion of high molecular weight conjugated ubiquitin in whole cell extract is in the form of short chains or single ubiquitin modifications. Of polyubiquitin, Lysine48- and lysine63- linked chains are the most abundant linkage types naturally found in intact cells.