Trapping intramembrane protease substrates in living cells: focus on RHBDL4 role in ERAD

ended

Intramembrane proteolysis is increasingly understood to control many cellular processes but we still know little about the role of most intramembrane proteases. The major roadblock is the lack of a robust method of protease substrate discovery. In this action, I focus on RHBDL4, a poorly understood but highly conserved member of the rhomboid intramembrane serine protease family, which participates in ER associated degradation (ERAD), apoptosis and exocytosis, and which has been frequently implicated in cancer growth and metastasis. My three objectives are to establish a systematic approach to trapping and identifying rhomboid substrates; to use this to discover the substrates of human RHBDL4; and to explore the mechanism of how RHBDL4 participates in ER quality control. Matthew Freeman's group discovered rhomboids and is a leader in the field. I will also collaborate with Jason Chin in Cambridge, who has pioneered the use of genetically encoded unnatural amino acids (UAAs) to engineer proteins. I will adapt a technique recently published by the Chin lab for use in living cells. Using a cross-linking UAA analogue of the catalytic serine in RHBDL4, I will achieve unprecedented specificity and efficiency of substrate capture. I will thus covalently capture RHBDL4 substrates, which will then be identified by mass spectrometry. Hits will be functionally validated and, using a range of experimental conditions, I will distinguish substrates involved in ERAD from substrates cleaved in other RHBDL4-dependent processes. By establishing the first systematic assay for rhomboid substrates and investigating the role of RHBDL4 in ER quality control, I will pioneer a general approach to intramembrane protease substrate discovery; gain broader understanding of how RHBDL4 contributes to cellular quality control; and finally reveal pathophysiological roles of this human protein, thereby guiding possible future therapeutic targeting.