Characterization of membrane proteomes from prokaryotic and eukaryotic cells using peptidiscs

Membrane proteins fulfill numerous essential roles in both prokaryotic and eukaryotic cells. They function as membrane transporters, receptors, enzymes, and signal transducers and are the major category of therapeutic targets. However, the characterization of membrane proteomes has lagged compared to soluble proteomes, mainly due to their intrinsic hydrophobicity and low abundance. Although detergents can be used to extract and solubilize membrane proteins, they have adverse effects on membrane protein stability and functionality. Moreover, most of the detergents are not compatible with proteomic analysis. In this thesis, I use a membrane mimetic “peptidisc” to survey membrane proteomes in a detergent-free but the water-soluble environment. By employing a “peptidisc-and-proteomics” approach, we characterize the plasma membrane proteome from eukaryotic cells. This method identifies many naturally low abundant plasma membrane proteins and captures and differentiates the characteristic cell surface proteins from pancreatic cancer cell line Panc-1 and pancreatic stellate cell hPSC. Membrane protein-protein interaction is another critical aspect of understanding cellular membrane protein activities. Using an essential membrane insertase YidC as a case study, I employed multiple proteomic-based methods to identify the interactors of YidC. Encouragingly, we identify a novel interactor YibN and the YidC-YibN complex can be preserved in peptidisc. The overexpression of YibN leads to inner membrane proliferation and overexpression of several YidC “client proteins”. This finding may further shed light on understanding membrane protein biogenesis. Our study indicates that the “peptidisc-and-proteome” method can be easily expandable to survey the membrane proteome and interactome across different systems, such as bacteria, cancer cell lines, and further multilayered tissues.