SEBASTIAN SCHUCK

Organelle Homeostasis

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Organelle Homeostasis

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.

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.

ER membrane biogenesis

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.

ER-phagy

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.

SHRED

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).

Selected publications

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)

Ice2 promotes ER membrane biogenesis in yeast by inhibiting the conserved lipin phosphatase complex. The EMBO Journal 40: e107958. https://doi.org/10.15252/embj.2021107958 Papagiannidis, D., Bircham, P.W., Lüchtenborg, C., Pajonk, O., Ruffini, G., Brügger, B. & Schuck, S. (2021)

ESCRT machinery mediates selective microautophagy of endoplasmic reticulum in yeast. EMBO Journal. (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)

ESCRTing endoplasmic reticulum to microautophagic degradation. Autophagy. Commentary (abstract)
Schäfer JA, Schuck S (2020)

Microautophagy - distinct molecular mechanisms handle cargoes of many sizes. Journal of Cell Science. Review (abstract)
Schuck S (2020)

The proteasome biogenesis regulator Rpn4 cooperates with the unfolded protein response to promote ER stress resistance. eLife. (abstract)
Schmidt RM, Schessner JP, Borner GH, Schuck S (2019)

SHRED is a regulatory cascade that reprograms Ubr1 substrate specificity for enhanced protein quality control during stress. Molecular Cell. (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)

Biogenese und Autophagie des Endoplasmatischen Retikulums. BIOspektrum. Review, in German (abstract)
Schäfer JA, Schuck S (2017)

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy. Review (abstract)
Klionsky DJ, Abdelmohsen K, ..., Schuck S, ... Zughaier SM (2016)

On keeping the right ER size. Nature Cell Biology. Commentary (abstract)
Schuck S (2016)

ER-phagy mediates selective degradation of endoplasmic reticulum independently of the core autophagy machinery. Journal of Cell Science. (abstract)
Schuck S, Gallagher CM, Walter P (2014)

Quantitative analysis and modeling of katanin function in flagellar length control. Molecular Biology of the Cell. (abstract)
Kannegaard E, Rego EH, Schuck S, Feldman JL, Marshall WF (2014)

Seg1 controls eisosome assembly and shape. Journal of Cell Biology. (abstract)
Moreira KE*, Schuck S*, Schrul B, Fröhlich F, Moseley JB, Walther TC, Walter P (2012)

BAX inhibitor-1 regulates autophagy by controlling the IRE1α branch of the unfolded protein response. EMBO Journal. (abstract)
Castillo K, Rojas-Rivera D, Lisbona F, Caballero B, Nassif M, Court FA, Schuck S, Ibar C, Walter P, Sierralta, J, Glavic A, Hetz C (2011)

Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity. Journal of Cell Biology. (abstract)
Rubio C, Pincus D, Korennykh A, Schuck S, El-Samad H, Walter P (2011)

Role of EBAG9 protein in coat protein complex I-dependent glycoprotein maturation and secretion processes in tumor cells. FASEB Journal. (abstract)
Wolf J, Reimer T, Schuck S, Rüder C, Gerlach K, Müller EC, Otto A, Dörken B, Rehm A (2010)

Generation of cubic membranes by controlled homotypic interaction of membrane proteins in the endoplasmic reticulum. Journal of Biological Chemistry. (abstract)
Lingwood D, Schuck S, Ferguson C, Gerl MJ, Simons K (2009)

Membrane expansion alleviates endoplasmic reticulum stress independently of the unfolded protein response. Journal of Cell Biology. (abstract)
Schuck S, Prinz WA, Thorn KS, Voss C, Walter P (2009)

Morphological homeostasis by autophagy. Autophagy. Commentary (abstract)
Lingwood D, Schuck S, Ferguson C, Gerl MJ, Simons K (2009)

Depletion of apical transport proteins perturbs epithelial cyst formation and ciliogenesis. Journal of Cell Science. (abstract)
Torkko JM, Manninen A, Schuck S, Simons K (2008)

ER-phagy: selective autophagy of the endoplasmic reticulum. Autophagy. Commentary (abstract)
Bernales S*, Schuck S*, Walter P (2007)

Rab10 is involved in basolateral transport in polarized MDCK cells. Traffic. (abstract)
Schuck S*, Gerl MJ*, Ang AL, Manninen A, Keller P, Mellman I, Simons K (2007)

Controversy fuels trafficking of GPI-anchored proteins. Journal of Cell Biology. Commentary (abstract)
Schuck S, Simons K (2006)

Detergent-resistant membranes and the use of cholesterol depletion. In Cell Biology: A Laboratory Handbook, Volume 2. J. E. Celis, editor. Elsevier Science, USA. Book chapter (full text) Schuck, S., Honsho, M., & Simons, K. (2006)

Generation of single and double knockdowns in polarized epithelial cells by retrovirus-mediated RNA interference. Proceedings of the National Academy of Sciences USA. (abstract)
Schuck S*, Manninen A*, Honsho M, Füllekrug J, Simons K (2004)

Polarized sorting in epithelial cells: raft clustering and the biogenesis of the apical membrane. Journal of Cell Science. Review (abstract)
Schuck S, Simons K (2004)

Resistance of cell membranes to different detergents. Proceedings of the National Academy of Sciences USA. (abstract)
Schuck S*, Honsho M*, Ekroos K, Shevchenko A, Simons K (2003)

The kinase MSK1 is required for induction of c-fos by lysophosphatidic acid in mouse embryonic stem cells. BMC Molecular Biology (abstract)
Schuck S, Soloaga A, Schratt G, Arthur JS, Nordheim A (2003)

Serum response factor is required for immediate-early gene activation yet is dispensable for proliferation of embryonic stem cells. Molecular and Cellular Biology. (abstract)
Schratt G, Weinhold B, Lundberg A, Schuck S, Berger J, Schwarz H, Weinberg R, Ruther U, Nordheim A (2001)

Sebastian Schuck 2013-		Sebastian still fantasizes about doing experiments himself, but the harsh reality is that he is stuck at the desk. sebastian.schuck@bzh.uni-heidelberg.de 06221-544749
Saccharo Cerevis 2013-		Saccharo has been our resident oracle since the lab started in July 2013. What s/he says is mostly incomprehensible but sometimes reveals amazing insights.
Oliver Pajonk 2018-		Oli started his master thesis with us in September 2018 and stayed for his PhD to investigate ESCRTs. He enjoys music, running and convincing lab members to join running events together with him. oliver.pajonk@bzh.uni-heidelberg.de 06221-544688
Giulia Ruffini 2018-		Giulia started her master thesis with us in November 2018 and stayed for her PhD to work on ER biogenesis. Besides science, Giulia has two great passions: music and food. giulia.ruffini@bzh.uni-heidelberg.de 06221-544688
Sibylle Kanngießer 2019-		Sibylle began her PhD in April 2019 to investigate SHRED. In her spare time, she relaxes doing yoga or joins other lab members for running or bouldering. sibylle.kanngiesser@bzh.uni-heidelberg.de, 06221-544688
Niklas Peters 2019-		Niklas started his PhD in April 2019 and wants to reconstitute SHRED in vitro. When not purifying proteins, he - you guessed it - goes running or bouldering. niklas.peters@bzh.uni-heidelberg.de 06221-544688
Lis Albert 2020-		Lis started her Master thesis with us in January 2020 and stayed for her PhD to find out how ESCRT proteins talk with the ER. In her spare time, she enjoys many activities, including ... bouldering. lis.albert@bzh.uni-heidelberg.de 06221-544688
Ayelén Valko 2020-		Ayelén joined us as a postdoc in October 2020 and is working on micro-ER-phagy. She is also a serious artist and composes science-inspired paintings. ayelen.valko@bzh.uni-heidelberg.de 06221-544688
Anna Platzek 2021-		Anna started her PhD in April 2021 to find out what ER whorls are made of. She already knows exactly what coffee and cake should be made of. anna.platzek@bzh.uni-heidelberg.de 06221-545420
Inge Reckmann 2021-		Inge never joined the lab - the lab joined her when we moved into the lab space that she had been looking after as a technician for many years. inge.reckmann@bzh.uni-heidelberg.de 06221-545420
Anke Heymann 2021-		Anke is our administrative assistant. She fights her way through the bureaucratic jungle, always building bridges between science and administration – and also between duty, coffee and cake. anke.heymann@bzh.uni-heidelberg.de 06221-544160
Rolf Schmidt 2022-		Rolf left us after completing his PhD in 2019 but then thought better of it and returned as postdoc. His guitar collection has been growing all the while. rolf-markus.schmidt@bzh.uni-heidelberg.de, 06221-545420
Rafael Salazar Claros 2022-		Rafael started his Master thesis with us in June 2022, joining the SHREDders.

Katharina Schaeff 2013-2017		Katharina was our technician from September 2013 to October 2017. Besides maintaining the lab in good shape, Katharina worked on both SHRED and ER-phagy.
Tamas Szoradi 2013-2018		Tamas did his PhD from October 2013 to March 2018, unravelling SHRED in all its glory. Tamas then moved to New York to do a postdoc with Liam Holt.
Jasmin Schäfer 2014-2020		Jasmin did her PhD from August 2014 to Januar 2020. The force was strong with this one and Jasmin heroically cracked (some of) the secrets of micro-ER-phagy. She then moved to Frankfurt to do a postdoc with Christian Münch.
Dorottya Polos 2014-2015		Dorottya was an ERASMUS student from October 2014 to June 2015. Afterwards, she returned to London to complete her Bachelor’s degree and do her PhD with Margaret Dallman.
Rolf Schmidt 2014-2019		Rolf did his PhD from December 2014 to April 2019, investigating how cells adapt protein degradation capacity to stress. He then stayed in Heidelberg to do a postdoc with Carlos Bas Orth.
Peter Bircham 2015-2018		Peter was a postdoc with us from February 2015 to September 2018 to study ER size control. Outside the lab, Peter still put yeast to good use brewing beer. This naturally led to his second postdoc with Kevin Verstrepen in Leuven, where Peter engineers better yeast for making beer.
Verena Bittl 2015		Verena did her Master thesis from April to November 2015, exploring potential ER-phagy substrates. She moved to Frankfurt to pursue her PhD with Anja Bremm.
Julia Schessner 2017-2018		Julia did her Master thesis from September 2017 to April 2018, visualizing and quantifying micro-ER-phagy by time lapse microscopy. For her PhD, Julia joined Georg Borner’s group at the MPI for Biochemistry in Munich.
Carlos Martìn de Hijas 2021		Carlos did his Master thesis with us and looked at transcriptional responses to ER stress, mostly by staring at the computer screen.
Dimitris Papagiannidis 2016-2022		Dimitris did his Master thesis and his PhD with us from October 2016 to May 2022. By climbing from tubules to sheets and doing extensive bouldering on the yeast ER, he figured out what Ice2 actually does. He then ventured up another local hill to do a postdoc with Nassos Typas and Mikhail Savitski at EMBL.

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

May 2022. Dimitris graduates! In keeping with local traditions, a silly hat is made (the proud hatters are
Niklas, Rolf, Lis and Anna) ...

... and then the graduate is made to look like a muppet (Dimitris
surrounded by fellow Schuck lab graduates, Jasmin, Rolf and Tamas).

March 2022. From left to right, back row: Ayelèn, Inge, Sibylle, Dimitris; middle row: Niklas, Sebastian, Lis,
Giulia, Natalie; front row: Anke, Anna, Oli.

August 2020. The lab in its natural environment.
From left to right: Oli, Niklas, Dimitris, Sebastian, Giulia, Sibylle, Lis and Uxia.

March 2020. Lab meeting in times of Corona.

February 2020. 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).

October 2018. 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.

September 2017. 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.

May 2017. 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
Tanja.

February 2015. From left to right: Sebastian, Katharina, Peter, Rolf, Jasmin, Dorottya and Tamas.