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Hodáková Z, Grishkovskaya I, Brunner HL, Bolhuis DL, Belačić K, Schleiffer A, Kotisch H, Brown NG, Haselbach D. Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. EMBO J 2023; 42:e113348. [PMID: 37409633 PMCID: PMC10425842 DOI: 10.15252/embj.2022113348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.
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Affiliation(s)
- Zuzana Hodáková
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Hanna L Brunner
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Harald Kotisch
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
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Hammerschmidt P, Ostkotte D, Nolte H, Gerl MJ, Jais A, Brunner HL, Sprenger HG, Awazawa M, Nicholls HT, Turpin-Nolan SM, Langer T, Krüger M, Brügger B, Brüning JC. CerS6-Derived Sphingolipids Interact with Mff and Promote Mitochondrial Fragmentation in Obesity. Cell 2020; 177:1536-1552.e23. [PMID: 31150623 DOI: 10.1016/j.cell.2019.05.008] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/26/2019] [Accepted: 05/03/2019] [Indexed: 01/29/2023]
Abstract
Ectopic lipid deposition and altered mitochondrial dynamics contribute to the development of obesity and insulin resistance. However, the mechanistic link between these processes remained unclear. Here we demonstrate that the C16:0 sphingolipid synthesizing ceramide synthases, CerS5 and CerS6, affect distinct sphingolipid pools and that abrogation of CerS6 but not of CerS5 protects from obesity and insulin resistance. We identify proteins that specifically interact with C16:0 sphingolipids derived from CerS5 or CerS6. Here, only CerS6-derived C16:0 sphingolipids bind the mitochondrial fission factor (Mff). CerS6 and Mff deficiency protect from fatty acid-induced mitochondrial fragmentation in vitro, and the two proteins genetically interact in vivo in obesity-induced mitochondrial fragmentation and development of insulin resistance. Our experiments reveal an unprecedented specificity of sphingolipid signaling depending on specific synthesizing enzymes, provide a mechanistic link between hepatic lipid deposition and mitochondrial fragmentation in obesity, and define the CerS6-derived sphingolipid/Mff interaction as a therapeutic target for metabolic diseases.
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Affiliation(s)
- Philipp Hammerschmidt
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne
| | - Daniela Ostkotte
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Hendrik Nolte
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne; Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9B, 50931 Cologne, Germany
| | - Mathias J Gerl
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany; Current address: Lipotype GmbH, Tatzberg 47, 01307 Dresden, Germany
| | - Alexander Jais
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne
| | - Hanna L Brunner
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Hans-Georg Sprenger
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne; Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9B, 50931 Cologne, Germany
| | - Motoharu Awazawa
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne
| | - Hayley T Nicholls
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne
| | - Sarah M Turpin-Nolan
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne
| | - Thomas Langer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne; Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Strasse 9B, 50931 Cologne, Germany
| | - Marcus Krüger
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne
| | - Britta Brügger
- Heidelberg University Biochemistry Center, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jens C Brüning
- Department of Neuronal Control of Metabolism, Max Planck Institute for Metabolism Research, Gleueler Strasse 50, 50931 Cologne, Germany; Center for Endocrinology, Diabetes and Preventive Medicine (CEDP), University Hospital Cologne, Kerpener Strasse 26, 50924 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) and Center for Molecular Medicine Cologne (CMMC), University of Cologne; National Center for Diabetes Research (DZD), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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Gerl MJ, Bittl V, Kirchner S, Sachsenheimer T, Brunner HL, Lüchtenborg C, Özbalci C, Wiedemann H, Wegehingel S, Nickel W, Haberkant P, Schultz C, Krüger M, Brügger B. Sphingosine-1-Phosphate Lyase Deficient Cells as a Tool to Study Protein Lipid Interactions. PLoS One 2016; 11:e0153009. [PMID: 27100999 PMCID: PMC4839656 DOI: 10.1371/journal.pone.0153009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 03/21/2016] [Indexed: 12/11/2022] Open
Abstract
Cell membranes contain hundreds to thousands of individual lipid species that are of structural importance but also specifically interact with proteins. Due to their highly controlled synthesis and role in signaling events sphingolipids are an intensely studied class of lipids. In order to investigate their metabolism and to study proteins interacting with sphingolipids, metabolic labeling based on photoactivatable sphingoid bases is the most straightforward approach. In order to monitor protein-lipid-crosslink products, sphingosine derivatives containing a reporter moiety, such as a radiolabel or a clickable group, are used. In normal cells, degradation of sphingoid bases via action of the checkpoint enzyme sphingosine-1-phosphate lyase occurs at position C2-C3 of the sphingoid base and channels the resulting hexadecenal into the glycerolipid biosynthesis pathway. In case the functionalized sphingosine looses the reporter moiety during its degradation, specificity towards sphingolipid labeling is maintained. In case degradation of a sphingosine derivative does not remove either the photoactivatable or reporter group from the resulting hexadecenal, specificity towards sphingolipid labeling can be achieved by blocking sphingosine-1-phosphate lyase activity and thus preventing sphingosine derivatives to be channeled into the sphingolipid-to-glycerolipid metabolic pathway. Here we report an approach using clustered, regularly interspaced, short palindromic repeats (CRISPR)-associated nuclease Cas9 to create a sphingosine-1-phosphate lyase (SGPL1) HeLa knockout cell line to disrupt the sphingolipid-to-glycerolipid metabolic pathway. We found that the lipid and protein compositions as well as sphingolipid metabolism of SGPL1 knock-out HeLa cells only show little adaptations, which validates these cells as model systems to study transient protein-sphingolipid interactions.
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Affiliation(s)
- Mathias J. Gerl
- Heidelberg University Biochemistry Center, Heidelberg, Germany
- * E-mail: (MJG); (BB)
| | - Verena Bittl
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | | | | | | | | | - Cagakan Özbalci
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | | | | | - Walter Nickel
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Per Haberkant
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | - Britta Brügger
- Heidelberg University Biochemistry Center, Heidelberg, Germany
- * E-mail: (MJG); (BB)
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