Mechanistic dissection of eukaryotic protein biogenesis and degradation pathways

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Abstract My lab currently has two main areas of interest: 1) a new chaperone system (eFOLD) that enables biogenesis of eukaryotic translation elongation factor 1 alpha (eEF1A); 2) endoplasmic reticulum (ER) and peroxisome degradation by selective autophagy. Errors in eEF1A biogenesis result in rapid degradation by the ubiquitin-proteasome system (UPS) thus making protein degradation a natural link between the two areas. Both eFOLD and selective autophagy are controlled by distinct stress responses (e.g. heat shock vs. amino acid starvation) but jointly serve as effectors of protein homeostasis (proteostasis). Both areas raise similar questions regarding substrate selectivity: How does a specific eFOLD chaperone co-translationally recognize an aggregation-prone region of eEF1A nascent chains? How is terminally misfolded eEF1A recognized for degradation by the UPS? What signals on damaged or unwanted organelles are detected by specific autophagy receptors to orchestrate encapsulation of organelle targets into autophagosomes? To answer these questions, we are dissecting biogenesis and degradation mechanisms that select substrates of grossly different sizes, respond to distinct physiological cues, and have widely different temporal dynamics. Using yeast and human cell culture in parallel, we are exploring conserved aspects of eFOLD and selective autophagy mechanisms shared by each species, as well as species-specific adaptations. Broadly speaking, our projects spawn from identification of missing factors by genetic screening or biochemical purification but all seek a deep mechanistic understanding of mutant phenotypes through biochemical reconstitution with purified components and protein structure-function analysis. Along this path, we iteratively test our hypotheses by genomics, quantitative cell microscopy, and theoretical modeling approaches.