Sommer Lab

Ongoing Research

Our group is particularly interested in the characterization of a central ERAD component termed the HRD ubiquitin ligase (Figure 1). We use yeast as a model organism and combine genetic, biochemical and cell biological techniques to get insights into the composition and the topology of this highly conserved protein complex as well as in the function of individual subunits. In the end we want to comprehend, how the HRD ligase specifically discriminates misfolded ER proteins from folded ones, how it moves these polypeptides via a unique transport process through the ER membrane into the cytoplasm, and how the ubiquitylation signals are generated that facilitate the extraction of ERAD substrates from the ER and guide them to the proteasome. We are also working on the analysis of other ERAD ligase complexes like the Doa10 ligase and the Asi complex (Figure 2).

Current projects involve site-specific in vivo crosslinking and microscopic techniques to capture the dynamics of substrate recruitment and processing by the ERAD ligases. We also aim to reconstitute individual ERAD complexes using purified components and analyze them by single particle Cryo-electron microscopy and an approach that combines chemical crosslinking with mass-spectrometry to obtain structural information. 

Fig. 2: ER-associated protein degradation in yeast and mammalian cells.
Molecular chaperones and proteins of the glycosylhydrolase-47 family (Mns1 and Htm1) detect misfolded polypeptides and direct them to membrane bound ligases (Doa10, RMA1, HRD). After dislocation to the cytosolic face of the ER membrane, substrates are ubiquitylated by an ubiquitin ligase. All ligase complexes comprise a central, catalytic active RING finger protein (E3), ubiquitin-conjugating enzymes (E2), and additional factors. The AAA ATPase Cdc48 releases ubiquitylated molecules from the ER membrane. The adapter proteins Rad23 and Dsk2 escort the ubiquitylated substrates to the 26S proteasome for degradation. Concurrently Png1 deglycosylates glycoproteins through its association with Rad23. Proteins containing a glycan-interaction motif or ubiquitin-binding domains are depicted in red and blue, respectively. Proteins are labeled with their yeast names in blue and green letters indicate the mammalian counterpart.

© Hirsch, C., Gauss, R., Horn, S.C., Neuber, O., and Sommer, T. (2009) The ubiquitylation machinery of the endoplasmic reticulum. Nature 26, 453-460

Former Research

We were among the first to show that defects in ERAD elicit a cellular stress program termed the unfolded protein response that upon prolonged activation triggers apoptosis in higher eukaryotes ¹.

Furthermore we showed that an entity encompassing the proteins Yos9 and Hrd3, which both expose large domains into the ER lumen, is involved in the recruitment of malfolded secretory proteins ^2–4. Yos9 identifies a defined glycan structure on misfolded protein species that is generated in the ER by a complex encompassing the mannosidase Htm1 and the protein-oxido-reductase Pdi1 ^5,6. A module containing the cytoplasmic domains of Hrd1, which harbors a RING-finger domain commonly found in many ubiquitin ligases, Cue1 and the ubiquitin conjugating enzyme Ubc7 accomplishes the ubiquitylation reaction, which not only labels ERAD substrates for the efficient degradation by the proteasome, but is also required for the preceding extraction from the ER ^7–10. Ubx2, which is associated with Hrd1, recruits a protein complex containing the AAA-ATPase Cdc48 and its co-factors Npl4 and Ufd1 to the HRD-ligase, which in turn assists in the removal of ubiquitylated substrates from the ER ^9,11. The Usa1 subunit facilitates the assembly of the HRD-ligase and coordinates its oligomerisation ¹². Finally, genetic and biochemical data indicate that the membrane-embedded parts of at least Der1 and Hrd1 participate in an unusual transport process that shuttles misfolded proteins from the ER into the cytoplasm ¹³.

1. Friedlander, R., Jarosch, E., Urban, J., Volkwein, C. & Sommer, T. A regulatory link between ER-associated protein degradation and the unfolded-protein response. Nat. Cell Biol. 2, 379–384 (2000).
2. Gauss, R., Sommer, T. & Jarosch, E. The Hrd1p ligase complex forms a linchpin between ER-lumenal substrate selection and Cdc48p recruitment. EMBO J. 25, 1827–1835 (2006).
3. Gauss, R., Jarosch, E., Sommer, T. & Hirsch, C. A complex of Yos9p and the HRD ligase integrates endoplasmic reticulum quality control into the degradation machinery. Nat. Cell Biol. 8, 849–854 (2006).
4. Mehnert, M. et al. The interplay of Hrd3 and the molecular chaperone system ensures efficient degradation of malfolded secretory proteins. Mol. Biol. Cell 26, 185–194 (2015).
5. Pfeiffer, A. et al. A complex of Htm1 and the oxidoreductase Pdi1 accelerates degradation of misfolded glycoproteins. J. Biol. Chem. 291, 12195–12207 (2016).
6. Clerc, S. et al. Htm1 protein generates the N-glycan signal for glycoprotein degradation in the endoplasmic reticulum. J. Cell Biol. 184, 159–172 (2009).
7. Biederer, T., Volkwein, C. & Sommer, T. Role of Cue1p in ubiquitination and degradation at the ER surface. Science 278, 1806–1809 (1997).
8. von Delbrück, M. et al. The CUE Domain of Cue1 Aligns Growing Ubiquitin Chains with Ubc7 for Rapid Elongation. Mol. Cell 62, 918–928 (2016).
9. Jarosch, E. et al. Protein dislocation from the ER requires polyubiquitination and the AAA-ATPase Cdc48. Nat. Cell Biol. 4, 134–139 (2002).
10. Bagola, K. et al. Ubiquitin Binding by a CUE Domain Regulates Ubiquitin Chain Formation by ERAD E3 Ligases. Mol. Cell 50, 528–539 (2013).
11. Neuber, O., Jarosch, E., Volkwein, C., Walter, J. & Sommer, T. Ubx2 links the Cdc48 complex to ER-associated protein degradation. Nat. Cell Biol. 7, 993–998 (2005).
12. Horn, S. C. et al. Usa1 Functions as a Scaffold of the HRD-Ubiquitin Ligase. Mol. Cell 36, 782–793 (2009).
13. Mehnert, M., Sommer, T. & Jarosch, E. Der1 promotes movement of misfolded proteins through the endoplasmic reticulum membrane. Nat. Cell Biol. 16, 77–86 (2014)