The role of linear ubiquitination in protein aggregation

• Applicant: Professorin Dr. Konstanze Winklhofer
• Subject Area: Cell Biology
• Term: from 2018 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 400967619

• Final Report Year: 2024

Final Report Abstract

To maintain neuronal viability and homeostasis, neurons depend on efficient stress response and quality control pathways. Imbalances in these systems are associated with aging and neurodegenerative diseases. Most if not all of these pathways are regulated by ubiquitylation, such as proteasomal degradation, autophagy, and organellar stress response programs. Our preliminary results showed that the linear ubiquitin chain assembly complex (LUBAC) is recruited to misfolded protein species associated with neurodegenerative diseases, such as mutant huntingtin with an elongated poly-glutamine tract (Htt-polyQ). As a consequence, misfolded huntingtin is modified with linear polyubiquitin chains, leading to a marked decrease in its neuronal toxicity. Based on these observations, we proposed that cytoplasmic protein aggregates are sensed as a special kind of "cellular pathogen", similar to intracellular bacteria, resulting in the recruitment and activation of LUBAC as part of a quality control pathway to remove these “pathogens”. Our work based on this proposal revealed that HOIP, the catalytic component of LUBAC, is recruited to misfolded huntingtin in a p97/VCP-dependent manner, resulting in the assembly of linear ubiquitin chains. As a consequence, the interactive surface of misfolded huntingtin is shielded from unwanted interactions, for example with low complexity sequence domain-containing transcription factors, and proteasomal degradation of huntingtin is facilitated. Though linear polyubiquitin was detected at all cytosolic protein aggregates analyzed, the effect of linear ubiquitin chains on the fate of the aggregates was dependent on the protein species. In the case of α-synuclein, LUBAC promoted both proteasomal and autophagosomal degradation. We identified NEMO as a key player downstream of LUBAC in protein quality control. NEMO, a protein that specifically binds to linear ubiquitin chains, recruits the autophagy receptor protein p62 into condensates at the protein interface and thereby facilitates the removal of aggregates by the autophagic machinery. In support of a physiological relevance of our finding, we identified a patient with a mutation in the NEMO-encoding IKBKG gene resulting in defective binding of NEMO to linear ubiquitin chains. This patient developed a widespread mixed brain proteinopathy, including α-synuclein, tau and TDP-43 pathology.

Publications

• The function of parkin: Revisited. Movement Disorders, 28(14), 1936-1936.
  Yamakado, Hodaka & Takahashi, Ryosuke
  
• A protein quality control pathway regulated by linear ubiquitination. The EMBO Journal, 38(9).
  van Well, Eva M.; Bader, Verian; Patra, Maria; Sánchez‐Vicente, Ana; Meschede, Jens; Furthmann, Nikolas; Schnack, Cathrin; Blusch, Alina; Longworth, Joseph; Petrasch‐Parwez, Elisabeth; Mori, Kohji; Arzberger, Thomas; Trümbach, Dietrich; Angersbach, Lena; Showkat, Cathrin; Sehr, Dominik A.; Berlemann, Lena A.; Goldmann, Petra; Clement, Albrecht M. ... & Winklhofer, Konstanze F.
  
• Lining up for quality control: linear ubiquitin and proteotoxicity. The EMBO Journal, 38(9).
  Wiseman, R. Luke
  
• Linear Ubiquitin Chains: Cellular Functions and Strategies for Detection and Quantification. Frontiers in Chemistry, 7.
  Dittmar, Gunnar & Winklhofer, Konstanze F.
  
• The parkin-coregulated gene product PACRG promotes TNF signaling by stabilizing LUBAC. Science Signaling, 13(617).
  Meschede, Jens; Šadić, Maria; Furthmann, Nikolas; Miedema, Tim; Sehr, Dominik A.; Müller-Rischart, A. Kathrin; Bader, Verian; Berlemann, Lena A.; Pilsl, Anna; Schlierf, Anita; Barkovits, Katalin; Kachholz, Barbara; Rittinger, Katrin; Ikeda, Fumiyo; Marcus, Katrin; Schaefer, Liliana; Tatzelt, Jörg & Winklhofer, Konstanze F.
  
• Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol. The EMBO Journal, 40(16).
  Schlagowski, Anna M.; Knöringer, Katharina; Morlot, Sandrine; Sánchez, Vicente Ana; Flohr, Tamara; Krämer, Lena; Boos, Felix; Khalid, Nabeel; Ahmed, Sheraz; Schramm, Jana; Murschall, Lena M.; Haberkant, Per; Stein, Frank; Riemer, Jan; Westermann, Benedikt; Braun, Ralf J.; Winklhofer, Konstanze F.; Charvin, Gilles & Herrmann, Johannes M.
  
• Protein quality control by the proteasome and autophagy: A regulatory role of ubiquitin and liquid-liquid phase separation. Matrix Biology, 100-101, 9-22.
  Lei, Linlin; Wu, Zhixiao & Winklhofer, Konstanze F.
  
• Remodeling of the Fibrillation Pathway of α‐Synuclein by Interaction with Antimicrobial Peptide LL‐III. Chemistry – A European Journal, 27(46), 11845-11851.
  Oliva, Rosario; Mukherjee, Sanjib K.; Ostermeier, Lena; Pazurek, Lilli A.; Kriegler, Simon; Bader, Verian; Prumbaum, Daniel; Raunser, Stefan; Winklhofer, Konstanze F.; Tatzelt, Jörg & Winter, Roland
  
• The key role of solvent in condensation: Mapping water in liquid-liquid phase-separated FUS. Biophysical Journal, 120(7), 1266-1275.
  Ahlers, Jonas; Adams, Ellen M.; Bader, Verian; Pezzotti, Simone; Winklhofer, Konstanze F.; Tatzelt, Jörg & Havenith, Martina
  
• The Role of Ubiquitin in Regulating Stress Granule Dynamics. Frontiers in Physiology, 13.
  Krause, Laura J.; Herrera, Maria G. & Winklhofer, Konstanze F.
  
• Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Science Alliance, 6(4), e202201607.
  Goel, Simran; Oliva, Rosario; Jeganathan, Sadasivam; Bader, Verian; Krause, Laura J.; Kriegler, Simon; Stender, Isabelle D.; Christine, Chadwick W.; Nakamura, Ken; Hoffmann, Jan-Erik; Winter, Roland; Tatzelt, Jörg & Winklhofer, Konstanze F.
  
• NEMO reshapes the α-Synuclein aggregate interface and acts as an autophagy adapter by co-condensation with p62. Nature Communications, 14(1).
  Furthmann, Nikolas; Bader, Verian; Angersbach, Lena; Blusch, Alina; Goel, Simran; Sánchez-Vicente, Ana; Krause, Laura J.; Chaban, Sarah A.; Grover, Prerna; Trinkaus, Victoria A.; van Well, Eva M.; Jaugstetter, Maximilian; Tschulik, Kristina; Damgaard, Rune Busk; Saft, Carsten; Ellrichmann, Gisa; Gold, Ralf; Koch, Arend; Englert, Benjamin ... & Winklhofer, Konstanze F.