Biogenesis and Degradation of the Endoplasmic Reticulum
Eukaryotic cells show striking differences in the abundance and architecture of their organelles. Moreover, cells rapidly adjust the size and shape of their organelles to changing physiological demands. This remarkable capacity for adaptation enables cells to maintain homeostasis during differentiation, stress and disease. The underlying molecular mechanisms are fundamental for proper cell function and uncovering them is a fascinating challenge.
ER membrane biogenesis
We want to elucidate how cells ensure homeostasis of the endoplasmic reticulum (ER). We are asking questions such as: How do cells shape their ER? How do they know how much ER they need? How do they adjust ER size and function to physiological demand? How do they recognize damaged ER components and eliminate them? To answer these questions, we investigate three related processes: (1) ER membrane biogenesis, which enables organelle expansion and remodeling, (2) ER-phagy, which mediates autophagic organelle degradation, and (3) SHRED, which regulates proteasomal degradation of misfolded cytosolic and ER membrane proteins. We explore these processes in budding yeast but also in mammalian cells.
The ER is a morphologically complex organelle with vital functions in protein folding and lipid synthesis. When the ER is unable to fold its load of newly synthesized polypeptides, misfolded proteins accumulate and cause ER stress. Misfolded proteins activate the unfolded protein response (UPR), which increases the protein folding capacity of the ER and induces ER-associated degradation. In this way, the UPR promotes the removal of misfolded proteins. Related mechanisms cooperate with the UPR to clear troublesome proteins, including proteasome biogenesis (Schmidt et al, 2019). Furthermore, the UPR triggers massive expansion of the ER membrane by activating lipid synthesis (Figure 1; Schuck et al, 2009). We have identified genes required for ER expansion and determined how they regulate lipid metabolism and ER membrane biogenesis (Papagiannidis, Bircham et al, 2021). Secretory cells, such as antibody-secreting plasma cells, need to expand the ER membrane during differentiation. Therefore, finding out how cells adjust ER size will help us understand how cells respond to stress and also how they differentiate.
Figure 1. ER membrane expansion. Yeast expressing Sec63-GFP to highlight the cytoplasmic ER (cER) and the nuclear envelope (NE). Yeast exposed to ER stress have a vastly expanded cytoplasmic ER.
Autophagy (cellular self-eating) is another response to ER stress. Upon stress, cells turn on selective autophagy of the ER, which can occur by macroautophagy and microautophagy (Schuck, 2020
). Our focus is micro-ER-phagy, which in yeast involves a spectacular restructuring of ER that gives rise multilamellar whorls. These whorls are then sent to the lysosome for degradation (Figure 2; Schuck et al., 2014
). We have shown that micro-ER-phagy does not require the well-known core autophagy machinery but depends on ESCRT proteins (Schäfer et al., 2020
). Nonetheless, our understanding of micro-ER-phagy is still, well, a litte crude
. Through micro-ER-phagy, cells may sacrifice parts of their ER to destroy protein aggregates and damaged organelle membrane. Moreover, when stress has been resolved, micro-ER-phagy may downsize the ER and reverse organelle expansion. In this way, the UPR and ER-phagy may work together to refold or degrade damaged proteins and to expand or shrink the ER as needed. Hence, ER-phagy helps maintain ER homeostasis and may be relevant for diseases impinging on ER function, such as cancer and diabetes. We are keen to learn more about the molecular events during autophagy of ER whorls and to define the physiological roles of micro-ER-phagy in both yeast and mammals.
Figure 2. Correlative light and electron microscopy of micro-ER-phagy. Micro-ER-phagy can be triggered by expression of the 'ER-phagy inducer', an artificial GFP-tagged transmembrane protein. Fluorescence images show a ring-shaped structure positive for a general ER marker and the ER-phagy inducer. The corresponding electron micrograph reveals that this structure is a large multilamellar ER whorl inside the yeast lysosome.
Protein folding is error-prone, especially during stress. Cells possess elaborate quality control machinery, including numerous chaperones and ubiquitin ligases, to promote proper folding and degrade folding failures. Stress responses like the UPR tune quality control to current demand. We have uncovered a novel stress response pathway termed SHRED, for stress-induced homeostatically regulated protein degradation (Figure 3; Szoradi et al., 2018
). SHRED is activated when stress stimulates transcription of the Roq1 gene. The Roq1 protein is cleaved by the protease Ynm3. Truncated Roq1∆21 binds to the ubiquitin ligase Ubr1 as a pseudosubstrate, reprograms Ubr1's substrate specificity and directs it towards misfolded cytosolic and ER membrane proteins. The resulting more stringent quality control enhances stress resistance. Deteriorating protein quality control during aging is a key factor for the onset of neurodegenerative diseases such as Alzheimer’s. Moreover, cancer cells suffer from chronic folding stress and depend on heightened quality control for survival. A deeper understanding of how quality control is regulated may therefore inspire new therapeutic approaches.
Figure 3. SHRED. Under non-stress conditions, the ubiquitin ligase Ubr1 degrades proteins with positively charged N-terminal residues as part of the N-degron pathway (left). Under stress conditions, Roq1 is produced, is cleaved by Ynm3 and binds to Ubr1 as a pseudosubstrate. This reprograms Ubr1 and stimulates the degradation of misfolded proteins (right).
Papagiannidis D*, Bircham PW*, Lüchterborg C, Pajonk O, Ruffini G, Brügger B, Schuck S (2021) Ice2 promotes ER membrane biogenesis in yeast by inhibiting the conserved lipin phosphatase complex. EMBO Journal. (abstract
Schuck S (2020) Microautophagy - distinct molecular mechanisms handle cargoes of many sizes. Journal of Cell Science. (abstract
Schäfer JA, Schessner JP, Bircham PW, Tsuji T, Funaya C, Pajonk O, Schaeff K, Ruffini G, Papagiannidis D, Knop M, Fujimoto T, Schuck S (2020) ESCRT machinery mediates selective microautophagy of endoplasmic reticulum in yeast. EMBO Journal. (abstract
Schmidt RM, Schessner JP, Borner GH, Schuck S (2019) The proteasome biogenesis regulator Rpn4 cooperates with the unfolded protein response to promote ER stress resistance. eLife. (abstract
Szoradi T, Schaeff K, Garcia-Rivera EM, Itzhak DN, Schmidt RM, Bircham PW, Leiss K, Diaz-Miyar J, Chen VK, Muzzey D, Borner GH, Schuck S (2018) SHRED is a regulatory cascade that reprograms Ubr1 substrate specificity for enhanced protein quality control during stress. Molecular Cell. (abstract
Schuck S, Gallagher CM, Walter P (2014) ER-phagy mediates selective degradation of endoplasmic reticulum independently of the core autophagy machinery. Journal of Cell Science. (abstract
Schuck S, Prinz WA, Thorn KS, Voss C, Walter P (2009) Membrane expansion alleviates endoplasmic reticulum stress independently of the unfolded protein response. Journal of Cell Biology. (abstract
since 2021 Professor for Biochemistry and Molecular Cell Biology
Heidelberg University Biochemistry Center
2013-2021 Independent group leader
Center for Molecular Biology at Heidelberg University
2006-2013 Postdoctoral fellow with Peter Walter
University of California, San Francisco
2001-2006 PhD student and postdoctoral fellow with Kai Simons
Max Planck Institute of Molecular Cell Biology, Dresden
1995-2000 Biochemistry student
Universities of Hannover and Tübingen
From left to right, back row: Ayelèn, Inge, Sibylle, Dimitris; middle row: Niklas, Sebastian, Lis,
Giulia, Natalie; front row: Anke, Anna, Oli.
The lab in its natural environment.
From left to right: Oli, Niklas, Dimitris, Sebastian, Giulia, Sibylle, Lis and Uxia.
Lab meeting in times of Corona.
Jasmin has defended her PhD and even the dark side pays its respects.
September 2019, in deep thought at the lab retreat.
From left to right: Jasmin, Giulia, Dimitris, Sebastian,
Niklas (apparently having an idea), Sibylle and Oli.
July 2019, the lab participates in the 10 K run of the National Center for Tumor Diseases.
From left to
right: Oli, Niklas, Dimitris, Sebastian and Sibylle (we blame the red faces on the camera).
From left to right: Oli, Sebastian, Giulia, Dimitris, Rolf, Jasmin and Carlos.
May 2018, the lab goes climbing.
From left to right: Dimitris (giving instructions that Rolf can't see), Rolf,
Tamas and Peter.
From left to right: Tamas, Katharina, Jasmin, Sebastian, Rolf, Peter, Julia and Dimitris.
June 2017, at the lab retreat.
Dimitris, Peter and Jasmin draw up their (fantasy) papers.
Is our ceiling going to withstand the construction work on the floor above us? Jasmin, Peter,
Tamas and Dimitris are not too sure.
June 2016, at the lab retreat.
From left to right: Peter, Rolf, Tamas, Jasmin, Sebastian, Katharina, Julia and
From left to right: Sebastian, Katharina, Peter, Rolf, Jasmin, Dorottya and Tamas.