Groupleader: Sebastian Schuck

Organelle Homeostasis
 

Biogenesis and Degradation of the Endoplasmic Reticulum

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, both in yeast (Figure 1; Schuck et al, 2009) and in human cells (Figure 2). 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 in yeast. Cells expressing Sec63-GFP to highlight the cytoplasmic ER (cER) and the nuclear envelope (NE). Cells exposed to ER stress have a vastly expanded cytoplasmic ER.



Figure 2. ER membrane expansion in human cells. Tissue culture cells expressing RFP-KDEL to highlight the ER. Cells exposed to ER stress convert their tubular ER network into sheet-like 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 ER restructuring that gives rise to multilamellar whorls. These whorls are then sent to the lysosome for degradation (Figure 3; 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). Through micro-ER-phagy, cells may sacrifice parts of their ER to destroy protein aggregates. Moreover, when stress has been resolved, micro-ER-phagy can downsize the ER and reverse organelle expansion. In this way, 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 related to 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 3. Correlative light and electron microscopy of micro-ER-phagy. Micro-ER-phagy can be triggered by expression of an artificial GFP-tagged transmembrane protein called 'ER-phagy inducer'. 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.

Figure 4. 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).