Biochemistry & Biophysics | Genetics, Epigenetics & Gene Regulation | Structural & Computational Biology
Protein quality control in the endoplasmic reticulum
A healthy proteome is critical for cellular function. Therefore, cells constantly monitor their protein-folding status and respond to physiological and environmental conditions that perturb the delicate balance between protein synthesis, folding and degradation. Protein-folding defects turn on stress response pathways that take corrective actions to restore homeostasis. In our lab, by combining innovative cell biology approaches with biophysical, biochemical and state-of-the-...more
A healthy proteome is critical for cellular function. Therefore, cells constantly monitor their protein-folding status and respond to physiological and environmental conditions that perturb the delicate balance between protein synthesis, folding and degradation. Protein-folding defects turn on stress response pathways that take corrective actions to restore homeostasis. In our lab, by combining innovative cell biology approaches with biophysical, biochemical and state-of-the-art structural biology techniques, we seek to provide mechanistic details into how cells sense and respond to fluctuations in their protein-folding demands.
Tuning protein synthesis for maintaining homeostasis in the endoplasmic reticulum
Cells mount a wide range of stress response pathways to respond to various stimuli, acting at both the cellular or organelle‐specific level. In the endoplasmic reticulum (ER), where secretory and membrane proteins are folded and assembled, protein folding is constantly monitored by a set of signaling pathways called the unfolded protein response (UPR). When the protein-folding capacity of the ER is exceeded, or if dysfunctional proteins that cannot be properly folded accumulate, the UPR is activated, allowing the cell to adjust the folding capacity of the organelle to restore homeostasis. Once activated, the UPR reduces client protein load in the ER by temporarily reducing global protein synthesis. Moreover, it increases the ER folding capacity through the upregulation of chaperones and foldases (Fig. 1). Recent work highlighted an unprecedented level of complexity of the UPR to shape the ER targeted proteome in higher eukaryotes. Even though transcriptional reprogramming is paramount for restoring ER homeostasis, translational and posttranscriptional regulation provides rapid and reversible means for tuning the protein influx into the ER. Yet, the mechanisms regulating the fate of ER-targeted mRNAs during conditions of high protein-folding demand remain largely unknown. My lab aims to reveal processes that regulate the translation and stability of ER targeted mRNAs to adjust protein-folding load of the organelle. To this end, we combine next generation sequencing approaches with cell biology, biochemistry and structural biology methods to uncover the posttranscriptional processes that tune ER protein-folding load to maintain homeostasis.
Sensing protein-folding perturbations in the endoplasmic reticulum
The UPR senses and responds to the accumulation of unfolded proteins in the ER, where unfolded proteins with unique signatures act as activating ligands of the UPR sensors (Fig. 2). The ER resident chaperones also bind to the sensors and regulate the response. Therefore, the interplay among chaperones, unfolded proteins and the UPR sensors together determines the magnitude and duration of the UPR. Yet, currently how ER clients with different folding demands and structural properties are recognized by the UPR sensors and how binding of chaperones to the UPR sensors and unfolded clients influences this interaction remain largely unexplored. In my lab, we employ cutting-edge NMR spectroscopy approaches; biochemistry and cell biology methods to reveal how interplay between unfolded proteins and chaperones tunes the UPR (Karagöz et al., 2017, Karagöz et al., 2014).
Karagöz, GE; Acosta-Alvear, D; Walter, P. (2018). The unfolded protein response: Detecting and responding to fluctuations in the protein folding capacity of the endoplasmic reticulum. Cold Spring Harb Perspect Biol.
Karagöz, G Elif; Acosta-Alvear, Diego; Nguyen, Hieu T; Lee, Crystal P; Chu, Feixia; Walter, Peter (2017). An unfolded protein-induced conformational switch activates mammalian IRE1. eLife;6. PMID: 28971800
Karagöz, G Elif; Duarte, Afonso M S; Akoury, Elias; Ippel, Hans; Biernat, Jacek; Morán Luengo, Tania; Radli, Martina; Didenko, Tatiana; Nordhues, Bryce A; Veprintsev, Dmitry B; Dickey, Chad A; Mandelkow, Eckhard; Zweckstetter, Markus; Boelens, Rolf; Madl, Tobias; Rüdiger, Stefan G D (2014). Hsp90-Tau complex reveals molecular basis for specificity in chaperone action. CELL;156(5):963-74. PMID: 24581495