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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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Leesch F, Lorenzo-Orts L, Pribitzer C, Grishkovskaya I, Roehsner J, Chugunova A, Matzinger M, Roitinger E, Belačić K, Kandolf S, Lin TY, Mechtler K, Meinhart A, Haselbach D, Pauli A. A molecular network of conserved factors keeps ribosomes dormant in the egg. Nature 2023; 613:712-720. [PMID: 36653451 PMCID: PMC7614339 DOI: 10.1038/s41586-022-05623-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 12/02/2022] [Indexed: 01/20/2023]
Abstract
Ribosomes are produced in large quantities during oogenesis and are stored in the egg. However, the egg and early embryo are translationally repressed1-4. Here, using mass spectrometry and cryo-electron microscopy analyses of ribosomes isolated from zebrafish (Danio rerio) and Xenopus laevis eggs and embryos, we provide molecular evidence that ribosomes transition from a dormant state to an active state during the first hours of embryogenesis. Dormant ribosomes are associated with four conserved factors that form two modules, consisting of Habp4-eEF2 and death associated protein 1b (Dap1b) or Dap in complex with eIF5a. Both modules occupy functionally important sites and act together to stabilize ribosomes and repress translation. Dap1b (also known as Dapl1 in mammals) is a newly discovered translational inhibitor that stably inserts into the polypeptide exit tunnel. Addition of recombinant zebrafish Dap1b protein is sufficient to block translation and reconstitute the dormant egg ribosome state in a mammalian translation extract in vitro. Thus, a developmentally programmed, conserved ribosome state has a key role in ribosome storage and translational repression in the egg.
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Affiliation(s)
- Friederike Leesch
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Laura Lorenzo-Orts
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - Carina Pribitzer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Josef Roehsner
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Anastasia Chugunova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Manuel Matzinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Elisabeth Roitinger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Susanne Kandolf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Tzi-Yang Lin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Anton Meinhart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
| | - Andrea Pauli
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
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Kandolf S, Grishkovskaya I, Belačić K, Bolhuis DL, Amann S, Foster B, Imre R, Mechtler K, Schleiffer A, Tagare HD, Zhong ED, Meinhart A, Brown NG, Haselbach D. Cryo-EM structure of the plant 26S proteasome. Plant Commun 2022; 3:100310. [PMID: 35576154 PMCID: PMC9251434 DOI: 10.1016/j.xplc.2022.100310] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/01/2022] [Accepted: 03/04/2022] [Indexed: 05/17/2023]
Abstract
Targeted proteolysis is a hallmark of life. It is especially important in long-lived cells that can be found in higher eukaryotes, like plants. This task is mainly fulfilled by the ubiquitin-proteasome system. Thus, proteolysis by the 26S proteasome is vital to development, immunity, and cell division. Although the yeast and animal proteasomes are well characterized, there is only limited information on the plant proteasome. We determined the first plant 26S proteasome structure from Spinacia oleracea by single-particle electron cryogenic microscopy at an overall resolution of 3.3 Å. We found an almost identical overall architecture of the spinach proteasome compared with the known structures from mammals and yeast. Nevertheless, we noticed a structural difference in the proteolytic active β1 subunit. Furthermore, we uncovered an unseen compression state by characterizing the proteasome's conformational landscape. We suspect that this new conformation of the 20S core protease, in correlation with a partial opening of the unoccupied gate, may contribute to peptide release after proteolysis. Our data provide a structural basis for the plant proteasome, which is crucial for further studies.
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Affiliation(s)
- Susanne Kandolf
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Derek L Bolhuis
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Sascha Amann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University at Vienna and Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Brent Foster
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06510, USA
| | - Richard Imre
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Hemant D Tagare
- Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT 06510, USA
| | - Ellen D Zhong
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anton Meinhart
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-BioCenter 1, 1030 Vienna, Austria; Institute of Physical Chemistry, University of Freiburg, Albertstraße 21, Freiburg 79104, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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