Groupleader: Sebastian Schuck

Eukaryotic cells show striking differences in the abundance and architecture of their organelles. Moreover, cells rapidly adjust the size, shape and composition 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 their endoplasmic reticulum (ER). We are asking questions such as: How do cells know how much ER they need? How do they balance biogenesis and degradation to reach optimal ER size? How do they shape ER architecture according to their functional needs? How do they recognize damaged or redundant ER components and selectively eliminate them? To answer these questions, we investigate three related processes: (1) ER membrane biogenesis, which enables organelle expansion and remodelling, (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 biogenesis

The ER has a complex morphology and many vital functions, for example 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 (ERAD). In this way, the UPR promotes the removal of misfolded proteins. Related mechanisms cooperate with the UPR to clear troublesome proteins, such as enhanced proteasome biogenesis (Schmidt et al., 2019). Furthermore, the UPR triggers massive ER membrane expansion by activating lipid synthesis (Figure 1; Schuck et al., 2009). We recently identified genes required for ER expansion and determined how they work together to regulate lipid metabolism and ER membrane biogenesis (Papagiannidis, Bircham et al., 2021). Professional secretory cells, such as antibody-secreting plasma cells and pancreatic beta cells, need to expand the ER membrane during differentiation. Finding out how cells adjust ER size will therefore not only help us to understand how cells respond to stress but also how they differentiate.



Figure 1. ER expansion. Yeast expressing Sec63-GFP to highlight the peripheral ER (pER) and the nuclear envelope (NE). Yeast exposed to ER stress have a vastly expanded peripheral ER.

ER-phagy
Another response to ER stress is autophagy (cellular self-eating), which mediates degradation of cytoplasmic components in lysosomes. ER stress turns on selective autophagy of ER, which can occur by macroautophagy and microautophagy. Our focus is micro-ER-phagy, which entails a spectacular restructuring of ER into multilamellar whorls and their microautophagic uptake into the yeast lysosomes, called the vacuole (Figure 2; Schuck et al., 2014). We have recently identified the first components of the molecular machinery for micro-ER-phagy and have begun to unravel how it works (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. Thus, the UPR and ER-phagy 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.