1
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Abaeva IS, Bulakhov AG, Hellen CUT, Pestova TV. The ribosome-associated quality control factor TCF25 imposes K48 specificity on Listerin-mediated ubiquitination of nascent chains by binding and specifically orienting the acceptor ubiquitin. Genes Dev 2025; 39:617-633. [PMID: 40169231 PMCID: PMC12047659 DOI: 10.1101/gad.352389.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 02/18/2025] [Indexed: 04/03/2025]
Abstract
Polypeptides arising from interrupted translation undergo proteasomal degradation by the ribosome-associated quality control (RQC) pathway. The ASC-1 complex splits stalled ribosomes into 40S subunits and nascent chain-tRNA-associated 60S subunits (60S RNCs). 60S RNCs associate with NEMF that promotes recruitment of the RING-type E3 ubiquitin (Ub) ligase Listerin (Ltn1 in yeast), which ubiquitinates nascent chains. RING-type E3s mediate the transfer of Ub directly from the E2∼Ub conjugate, implying that the specificity of Ub linkage is determined by the given E2. Listerin is most efficient when it is paired with promiscuous Ube2D E2s. We previously found that TCF25 (Rqc1 in yeast) can impose K48 specificity on Listerin paired with Ube2D E2s. To determine the mechanism of TCF25's action, we combined functional biochemical studies and AlphaFold3 modeling and now report that TCF25 specifically interacts with the RING domain of Listerin and the acceptor ubiquitin (UbA) and imposes K48 specificity by orienting UbA such that its K48 is directly positioned to attack the thioester bond of the Ube2D1∼Ub conjugate. We also found that TCF25 itself undergoes K48-specific ubiquitination by Listerin, suggesting a mechanism for the reported upregulation of Rqc1 in the absence of Ltn1 and the observed degradation of TCF25 by the proteasome in vivo.
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Affiliation(s)
- Irina S Abaeva
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Alexander G Bulakhov
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Christopher U T Hellen
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
| | - Tatyana V Pestova
- Department of Cell Biology, State University of New York Downstate Health Sciences University, Brooklyn, New York 11203, USA
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2
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Ai H, Tong Z, Deng Z, Shi Q, Tao S, Sun G, Liang J, Sun M, Wu X, Zheng Q, Liang L, Yin H, Li JB, Gao S, Tian C, Liu L, Pan M. Mechanism of nucleosomal H2A K13/15 monoubiquitination and adjacent dual monoubiquitination by RNF168. Nat Chem Biol 2025; 21:668-680. [PMID: 39394267 DOI: 10.1038/s41589-024-01750-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 09/14/2024] [Indexed: 10/13/2024]
Abstract
The DNA damage repair regulatory protein RNF168, a monomeric RING-type E3 ligase, has a crucial role in regulating cell fate and DNA repair by specific and efficient ubiquitination of the adjacent K13 and K15 (K13/15) sites at the H2A N-terminal tail. However, understanding how RNF168 coordinates with its cognate E2 enzyme UbcH5c to site-specifically ubiquitinate H2A K13/15 has long been hampered by the lack of high-resolution structures of RNF168 and UbcH5c~Ub (ubiquitin) in complex with nucleosomes. Here we developed chemical strategies and determined the cryo-electron microscopy structures of the RNF168-UbcH5c~Ub-nucleosome complex captured in transient H2A K13/15 monoubiquitination and adjacent dual monoubiquitination reactions, providing a 'helix-anchoring' mode for monomeric E3 ligase RNF168 on nucleosome in contrast to the 'compass-binding' mode of dimeric E3 ligases. Our work not only provides structural snapshots of H2A K13/15 site-specific monoubiquitination and adjacent dual monoubiquitination but also offers a near-atomic-resolution structural framework for understanding pathogenic amino acid substitutions and physiological modifications of RNF168.
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Affiliation(s)
- Huasong Ai
- Institute of Translational Medicine, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zebin Tong
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zhiheng Deng
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qiang Shi
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Shixian Tao
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Gaoge Sun
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jiawei Liang
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Maoshen Sun
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Xiangwei Wu
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qingyun Zheng
- Institute of Translational Medicine, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lujun Liang
- Center for Bioanalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei, China
| | - Hang Yin
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Shuai Gao
- Department of Urology, Zhongnan Hospital of Wuhan University, TaiKang Center for Life and Medical Sciences, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Changlin Tian
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Lei Liu
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China.
| | - Man Pan
- Institute of Translational Medicine, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China.
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3
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Kumar M, Banerjee S, Cohen-Kfir E, Mitelberg MB, Tiwari S, Isupov MN, Dessau M, Wiener R. UFC1 reveals the multifactorial and plastic nature of oxyanion holes in E2 conjugating enzymes. Nat Commun 2025; 16:3912. [PMID: 40280917 PMCID: PMC12032130 DOI: 10.1038/s41467-025-58826-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Accepted: 04/03/2025] [Indexed: 04/29/2025] Open
Abstract
The conjugation of ubiquitin (Ub) or ubiquitin-like proteins (UBL) to target proteins is a crucial post-translational modification that typically involves nucleophilic attack by a lysine on a charged E2 enzyme (E2~Ub/UBL), forming an oxyanion intermediate. Stabilizing this intermediate through an oxyanion hole is vital for progression of the reaction. Still, the mechanism of oxyanion stabilization in E2 enzymes remains unclear, although an asparagine residue in the conserved HPN motif of E2 enzymes was suggested to stabilize the oxyanion intermediate. Here, we study the E2 enzyme UFC1, which presents a TAK rather than an HPN motif. Crystal structures of UFC1 mutants, including one that mimics the oxyanion intermediate, combined with in vitro activity assays, suggest that UFC1 utilizes two distinct types of oxyanion holes, one that stabilizes the oxyanion intermediate during trans-ufmylation mediated by the E3 ligase, and another that stabilizes cis-driven auto-ufmylation. Our findings indicate that oxyanion stabilization is influenced by multiple factors, including C-alpha hydrogen bonding, and is adaptable, enabling different modes of action.
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Affiliation(s)
- Manoj Kumar
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Sayanika Banerjee
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Einav Cohen-Kfir
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Marissa Basia Mitelberg
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel
| | - Suryakant Tiwari
- Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, 1311502, Israel
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter, UK
| | - Moshe Dessau
- Azrieli Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, 1311502, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 91120, Israel.
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4
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Coste F, Mishra A, Chapuis C, Mance L, Pukało Z, Bigot N, Goffinont S, Gaudon V, Garnier N, Talhaoui I, Castaing B, Huet S, Suskiewicz MJ. RING dimerisation drives higher-order organisation of SINA/SIAH E3 ubiquitin ligases. FEBS J 2025. [PMID: 39910688 DOI: 10.1111/febs.70000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 12/13/2024] [Accepted: 01/22/2025] [Indexed: 02/07/2025]
Abstract
RING-type E3 ubiquitin ligases promote ubiquitylation by stabilising an active complex between a ubiquitin-loaded E2-conjugating enzyme and a protein substrate. To fulfil this function, the E3 ubiquitin-protein ligase SIAH1 and other SINA/SIAH subfamily RING-type E3 ligases employ an N-terminal catalytic RING domain and a C-terminal substrate-binding domain (SBD), separated by two zinc fingers. Here, we present the first crystal structure of the RING domain of human SIAH1, together with an adjacent zinc finger, revealing a potential RING dimer, which was validated in solution using static light scattering. RING dimerisation contributes to the E3 ligase activity of SIAH1 both in vitro and in cells. Moreover, as the RING domain is the second element, after the SBD, to independently favour homodimerisation within SINA/SIAH E3 ligases, we propose that alternating RING:RING and SBD:SBD interactions organise multiple copies of a SINA/SIAH protein into a higher-order homomultimer. In line with this hypothesis, fluorescently tagged full-length human SIAH1, human SIAH2 and fruit fly SINA show cytoplasmic clusters in human cells, whereas their distribution becomes more diffuse when RING dimerisation is disabled. The wild-type (WT) form of SIAH1, but not its RING dimerisation mutant, colocalises with aggregated synphilin-1A under proteasomal inhibition, suggesting that SIAH1 multimerisation might contribute to its reported preference for aggregated or multimeric substrates.
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Affiliation(s)
- Franck Coste
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
| | - Aanchal Mishra
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
- École Doctorale "Santé, Science Biologique & Chimie du Vivant" (ED549), Université d'Orléans, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique) - UAR 3480, US_S 018, F35000, Rennes, France
| | - Lucija Mance
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
- École Doctorale "Santé, Science Biologique & Chimie du Vivant" (ED549), Université d'Orléans, France
| | - Zofia Pukało
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
| | - Nicolas Bigot
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique) - UAR 3480, US_S 018, F35000, Rennes, France
| | - Stéphane Goffinont
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
| | - Norbert Garnier
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
- Pôle Physique, Université d'Orléans, France
| | - Ibtissam Talhaoui
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
- École Doctorale "Santé, Science Biologique & Chimie du Vivant" (ED549), Université d'Orléans, France
| | - Sebastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSIT (Biologie, Santé, Innovation Technologique) - UAR 3480, US_S 018, F35000, Rennes, France
| | - Marcin J Suskiewicz
- Centre de Biophysique Moléculaire (CBM), UPR 4301, CNRS, Orléans, France
- École Doctorale "Santé, Science Biologique & Chimie du Vivant" (ED549), Université d'Orléans, France
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5
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Zhang L, Deng Z, Du Y, Xu Z, Zhang T, Tong Z, Ai H, Liang LJ, Liu L. RAD18-catalysed formation of ubiquitination intermediate mimic of proliferating cell nuclear antigen PCNA. Bioorg Med Chem 2025; 117:118016. [PMID: 39580855 DOI: 10.1016/j.bmc.2024.118016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2024] [Revised: 11/18/2024] [Accepted: 11/18/2024] [Indexed: 11/26/2024]
Abstract
The 2-((2-chloroethyl)amino)ethane-1-thiol (CAET)-based chemical trapping strategy is a practical tool for mechanistic studies of E3-catalysed ubiquitination. However, the construction of ubiquitination intermediate mimics (E2-Ub-substrate conjugates) via CAET has been limited to peptides, while its application to folded protein substrates remains unexplored. Here, we report that disulfide bond formation between E2-Ub (RAD6A-Ub) and the folded protein substrate PCNA (proliferating cell nuclear antigen) occurs upon the addition of the PCNA-associated E3 ligase RAD18. Leveraging this finding, we employed intein splicing technology to generate a stable, covalently linked RAD18-RAD6A-Ub-PCNA complex, enabling chemical crosslinking mass spectrometry (CX-MS) analysis to study the structure of this complex. This work showcases use of a substrate-associated E3 ligase to promote disulfide bond formation between an E2-Ub conjugate and a folded substrate for CAET-based trapping, thereby expanding the scope of this technique.
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Affiliation(s)
- Liying Zhang
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhiheng Deng
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yunxiang Du
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziyu Xu
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Tianyi Zhang
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zebin Tong
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Huasong Ai
- Institute of Translational Medicine, School of Pharmacy, School of Chemistry and Chemical Engineering, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lu-Jun Liang
- Center for BioAnalytical Chemistry, Hefei National Laboratory of Physical Science at Microscale, University of Science and Technology of China, Hefei 230026, China.
| | - Lei Liu
- New Cornerstone Science Laboratory, Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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6
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Oldham KEA, Mabbitt PD. Ubiquitin E3 ligases in the plant Arg/N-degron pathway. Biochem J 2024; 481:1949-1965. [PMID: 39670824 DOI: 10.1042/bcj20240132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 11/24/2024] [Accepted: 11/26/2024] [Indexed: 12/14/2024]
Abstract
Regulation of protein longevity via the ubiquitin (Ub) - proteasome pathway is fundamental to eukaryotic biology. Ubiquitin E3 ligases (E3s) interact with substrate proteins and provide specificity to the pathway. A small subset of E3s bind to specific exposed N-termini (N-degrons) and promote the ubiquitination of the bound protein. Collectively these E3s, and other N-degron binding proteins, are known as N-recognins. There is considerable functional divergence between fungi, animal, and plant N-recognins. In plants, at least three proteins (PRT1, PRT6, and BIG) participate in the Arg/N-degron pathway. PRT1 has demonstrated E3 ligase activity, whereas PRT6 and BIG are candidate E3s. The Arg/N-degron pathway plays a central role in plant development, germination, and submersion tolerance. The pathway has been manipulated both to improve crop performance and for conditional protein degradation. A more detailed structural and biochemical understanding of the Arg/N-recognins and their substrates is required to fully realise the biotechnological potential of the pathway. This perspective focuses on the structural and molecular details of substrate recognition and ubiquitination in the plant Arg/N-degron pathway. While PRT1 appears to be plant specific, the PRT6 and BIG proteins are similar to UBR1 and UBR4, respectively. Analysis of the cryo-EM structures of Saccharomyces UBR1 suggests that the mode of ubiquitin conjugating enzyme (E2) and substrate recruitment is conserved in PRT6, but regulation of the two N-recognins may be significantly different. The structurally characterised domains from human UBR4 are also likely to be conserved in BIG, however, there are sizeable gaps in our understanding of both proteins.
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Affiliation(s)
- Keely E A Oldham
- Scion, Titokorangi Drive, Private Bag 3020, Rotorua 3046, New Zealand
| | - Peter D Mabbitt
- Scion, Titokorangi Drive, Private Bag 3020, Rotorua 3046, New Zealand
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7
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Swarnkar A, Leidner F, Rout AK, Ainatzi S, Schmidt CC, Becker S, Urlaub H, Griesinger C, Grubmüller H, Stein A. Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes. EMBO J 2024; 43:6705-6739. [PMID: 39533056 PMCID: PMC11649903 DOI: 10.1038/s44318-024-00301-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024] Open
Abstract
Ubiquitin-conjugating enzymes (E2) play a crucial role in the attachment of ubiquitin to proteins. Together with ubiquitin ligases (E3), they catalyze the transfer of ubiquitin (Ub) onto lysines with high chemoselectivity. A subfamily of E2s, including yeast Ubc6 and human Ube2J2, also mediates noncanonical modification of serines, but the structural determinants for this chemical versatility remain unknown. Using a combination of X-ray crystallography, molecular dynamics (MD) simulations, and reconstitution approaches, we have uncovered a two-layered mechanism that underlies this unique reactivity. A rearrangement of the Ubc6/Ube2J2 active site enhances the reactivity of the E2-Ub thioester, facilitating attack by weaker nucleophiles. Moreover, a conserved histidine in Ubc6/Ube2J2 activates a substrate serine by general base catalysis. Binding of RING-type E3 ligases further increases the serine selectivity inherent to Ubc6/Ube2J2, via an allosteric mechanism that requires specific positioning of the ubiquitin tail at the E2 active site. Our results elucidate how subtle structural modifications to the highly conserved E2 fold yield distinct enzymatic activity.
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Affiliation(s)
- Anuruti Swarnkar
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Florian Leidner
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Ashok K Rout
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- Institut für Chemie und Metabolomics, Universität zu Lübeck, 23562, Lübeck, Germany
| | - Sofia Ainatzi
- Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Claudia C Schmidt
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- ETH Zürich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Alexander Stein
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
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8
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Abaeva IS, Bulakhov AG, Hellen CUT, Pestova TV. The ribosome-associated quality control factor TCF25 imposes K48 specificity on Listerin-mediated ubiquitination of nascent chains by binding and specifically orienting the acceptor ubiquitin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.17.618946. [PMID: 39464025 PMCID: PMC11507960 DOI: 10.1101/2024.10.17.618946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Polypeptides arising from interrupted translation undergo proteasomal degradation by the ribosome-associated quality control (RQC) pathway. The ASC-1 complex splits stalled ribosomes into 40S subunits and nascent chain-tRNA-associated 60S subunits (60S RNCs). 60S RNCs associate with NEMF that promotes recruitment of the RING-type E3 ubiquitin (Ub) ligase Listerin (Ltn1 in yeast), which ubiquitinates nascent chains. RING-type E3s mediate the transfer of Ub directly from the E2~Ub conjugate, implying that the specificity of Ub linkage is determined by the given E2. Listerin is most efficient when it is paired with promiscuous Ube2D E2s. We previously found that TCF25 (Rqc1 in yeast) can impose K48-specificity on Listerin paired with Ube2D E2s. To determine the mechanism of TCF25's action, we combined functional biochemical studies and AlphaFold3 modeling and now report that TCF25 specifically interacts with the RING domain of Listerin and the acceptor ubiquitin (UbA) and imposes K48-specificity by orienting UbA such that its K48 is directly positioned to attack the thioester bond of the Ube2D1~Ub conjugate. We also found that TCF25 itself undergoes K48-specific ubiquitination by Listerin suggesting a mechanism for the reported upregulation of Rqc1 in the absence of Ltn1 and the observed degradation of TCF25 by the proteasome in vivo.
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Affiliation(s)
- Irina S. Abaeva
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Alexander G. Bulakhov
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Tatyana V. Pestova
- Department of Cell Biology, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
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9
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Gill JK, Shaw GS. Using Förster Resonance Energy Transfer (FRET) to Understand the Ubiquitination Landscape. Chembiochem 2024; 25:e202400193. [PMID: 38632088 DOI: 10.1002/cbic.202400193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Förster resonance energy transfer (FRET) is a fluorescence technique that allows quantitative measurement of protein interactions, kinetics and dynamics. This review covers the use of FRET to study the structures and mechanisms of ubiquitination and related proteins. We survey FRET assays that have been developed where donor and acceptor fluorophores are placed on E1, E2 or E3 enzymes and ubiquitin (Ub) to monitor steady-state and real-time transfer of Ub through the ubiquitination cascade. Specialized FRET probes placed on Ub and Ub-like proteins have been developed to monitor Ub removal by deubiquitinating enzymes (DUBs) that result in a loss of a FRET signal upon cleavage of the FRET probes. FRET has also been used to understand conformational changes in large complexes such as multimeric E3 ligases and the proteasome, frequently using sophisticated single molecule methods. Overall, FRET is a powerful tool to help unravel the intricacies of the complex ubiquitination system.
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Affiliation(s)
- Jashanjot Kaur Gill
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
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10
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Taylor JD, Barrett N, Martinez Cuesta S, Cassidy K, Pachl F, Dodgson J, Patel R, Eriksson TM, Riley A, Burrell M, Bauer C, Rees DG, Cimbro R, Zhang AX, Minter RR, Hunt J, Legg S. Targeted protein degradation using chimeric human E2 ubiquitin-conjugating enzymes. Commun Biol 2024; 7:1179. [PMID: 39300128 DOI: 10.1038/s42003-024-06803-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
Proteins can be targeted for degradation by engineering biomolecules that direct them to the eukaryotic ubiquitination machinery. For instance, the fusion of an E3 ubiquitin ligase to a suitable target binding domain creates a 'biological Proteolysis-Targeting Chimera' (bioPROTAC). Here we employ an analogous approach where the target protein is recruited directly to a human E2 ubiquitin-conjugating enzyme via an attached target binding domain. Through rational design and screening we develop E2 bioPROTACs that induce the degradation of the human intracellular proteins SHP2 and KRAS. Using global proteomics, we characterise the target-specific and wider effects of E2 vs. VHL-based fusions. Taking SHP2 as a model target, we also employ a route to bioPROTAC discovery based on protein display libraries, yielding a degrader with comparatively weak affinity capable of suppressing SHP2-mediated signalling.
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Affiliation(s)
- Jonathan D Taylor
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK.
| | - Nathalie Barrett
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Sergio Martinez Cuesta
- Data Sciences and Quantitative Biology, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Katelyn Cassidy
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - Fiona Pachl
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - James Dodgson
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Radhika Patel
- Centre for Genomics Research, Dynamic Omics, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Tuula M Eriksson
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Aidan Riley
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Matthew Burrell
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Christin Bauer
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - D Gareth Rees
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Raffaello Cimbro
- Centre for Genomics Research, Dynamic Omics, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Cambridge, CB2 0AA, UK
| | - Andrew X Zhang
- Protein Sciences, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Waltham, MA, 02451, USA
| | - Ralph R Minter
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
| | - James Hunt
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK.
| | - Sandrine Legg
- Biologics Engineering, R&D Oncology, AstraZeneca, Cambridge, CB2 0AA, UK
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11
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Suskiewicz MJ. The logic of protein post-translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments. Bioessays 2024; 46:e2300178. [PMID: 38247183 DOI: 10.1002/bies.202300178] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Protein post-translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half-life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino-acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications.
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Affiliation(s)
- Marcin J Suskiewicz
- Centre de Biophysique Moléculaire, CNRS - Orléans, UPR 4301, affiliated with Université d'Orléans, Orléans, France
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12
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Miyamoto K, Tadokoro T, Matsumoto A. Unique E2-binding specificity of artificial RING fingers in cancer cells. Sci Rep 2024; 14:2545. [PMID: 38291082 PMCID: PMC10828389 DOI: 10.1038/s41598-024-52793-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024] Open
Abstract
Ubiquitin (Ub)-conjugating enzymes (E2s) are involved in various pathways for Ub transfer and deubiquitinating activities. These enzymes are associated with cancers such as breast cancer which is the second deadliest type of malignancy among women. Here, we revealed the unique E2-binding property and the auto-ubiquitination of artificial RING fingers (ARFs). Circular dichroism spectra showed the characteristic structures of ARFs. The proline, lysine, leucine, threonine and cysteine (PKLTC) sequence of ARF was important for E2-recognition and its mutations induced obvious changes in the E2-binding specificity and the auto-ubiquitination activity of ARF. The ARF mutants were applicable to detection of most of E2 activities. Furthermore, adding the ARF mutant C35A to cancer cells promoted its auto-ubiquitination, leading to the preferential detection of E2 UbcH5b activity. The present work opens up a new avenue for investigating intracellular E2 activities for the fatal diseases.
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Affiliation(s)
- Kazuhide Miyamoto
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, 1-1-1 Daigaku-dori, Sanyo-Onoda, Yamaguchi, 756-0884, Japan.
| | - Takashi Tadokoro
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, 1-1-1 Daigaku-dori, Sanyo-Onoda, Yamaguchi, 756-0884, Japan
| | - Atsushi Matsumoto
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, 1-1-1 Daigaku-dori, Sanyo-Onoda, Yamaguchi, 756-0884, Japan
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13
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Park SH, Han J, Jeong BC, Song JH, Jang SH, Jeong H, Kim BH, Ko YG, Park ZY, Lee KE, Hyun J, Song HK. Structure and activation of the RING E3 ubiquitin ligase TRIM72 on the membrane. Nat Struct Mol Biol 2023; 30:1695-1706. [PMID: 37770719 PMCID: PMC10643145 DOI: 10.1038/s41594-023-01111-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/16/2023] [Indexed: 09/30/2023]
Abstract
Defects in plasma membrane repair can lead to muscle and heart diseases in humans. Tripartite motif-containing protein (TRIM)72 (mitsugumin 53; MG53) has been determined to rapidly nucleate vesicles at the site of membrane damage, but the underlying molecular mechanisms remain poorly understood. Here we present the structure of Mus musculus TRIM72, a complete model of a TRIM E3 ubiquitin ligase. We demonstrated that the interaction between TRIM72 and phosphatidylserine-enriched membranes is necessary for its oligomeric assembly and ubiquitination activity. Using cryogenic electron tomography and subtomogram averaging, we elucidated a higher-order model of TRIM72 assembly on the phospholipid bilayer. Combining structural and biochemical techniques, we developed a working molecular model of TRIM72, providing insights into the regulation of RING-type E3 ligases through the cooperation of multiple domains in higher-order assemblies. Our findings establish a fundamental basis for the study of TRIM E3 ligases and have therapeutic implications for diseases associated with membrane repair.
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Affiliation(s)
- Si Hoon Park
- Department of Life Sciences, Korea University, Seoul, South Korea
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Juhyun Han
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Byung-Cheon Jeong
- Department of Life Sciences, Korea University, Seoul, South Korea
- CSL Seqirus, Waltham, MA, USA
| | - Ju Han Song
- Department of Life Sciences, Korea University, Seoul, South Korea
- Department of Pharmacology and Dental Therapeutics, School of Dentistry, Chonnam National University, Gwangju, South Korea
| | - Se Hwan Jang
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Hyeongseop Jeong
- Center for Electron Microscopy Research, Korea Basic Science Institute, Cheongju-si, South Korea
| | - Bong Heon Kim
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Young-Gyu Ko
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Zee-Yong Park
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, South Korea
| | - Kyung Eun Lee
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul, South Korea
| | - Jaekyung Hyun
- School of Pharmacy, Sungkyunkwan University, Suwon, South Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul, South Korea.
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14
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Miyamoto K, Matsumoto A. Artificial RING finger reveals unique auto-ubiquitination with E2 specificity. Protein Sci 2023; 32:e4766. [PMID: 37622280 PMCID: PMC10510468 DOI: 10.1002/pro.4766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/08/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Ubiquitin (Ub)-conjugating enzymes (E2s) transfer activated Ub from Ub-activating enzymes (E1s) to substrates and are associated with various cancers and neurological disorders. In this study, the unique properties of E2-binding and auto-ubiquitination of artificial RING fingers (ARFs) were demonstrated in ubiquitination assays. Circular dichroism spectra indicated the characteristic structures of ARFs. Point mutations of 31 PKLTC35 in ARF by tryptophan (Trp) resulted in dramatic changes in E2 specificity and the type of Ub chain elongation of mono- and polyubiquitination. The Trp residue was a cue that changed the ubiquitination activity of ARF via E2-binding. Furthermore, the ARF mutants interacted with all 11 E2s and then promoted auto-ubiquitination. Thus, the use of the ARF mutants allowed specific detection of E2 activities during ubiquitination. The present study opens up a new avenue for researching E2 activities related to the fatal diseases.
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Affiliation(s)
- Kazuhide Miyamoto
- Faculty of Pharmaceutical SciencesSanyo‐Onoda City UniversityYamaguchiJapan
| | - Atsushi Matsumoto
- Faculty of Pharmaceutical SciencesSanyo‐Onoda City UniversityYamaguchiJapan
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15
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Colson L, Kwon Y, Nam S, Bhandari A, Maya NM, Lu Y, Cho Y. Trends in Single-Molecule Total Internal Reflection Fluorescence Imaging and Their Biological Applications with Lab-on-a-Chip Technology. SENSORS (BASEL, SWITZERLAND) 2023; 23:7691. [PMID: 37765748 PMCID: PMC10537725 DOI: 10.3390/s23187691] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/01/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023]
Abstract
Single-molecule imaging technologies, especially those based on fluorescence, have been developed to probe both the equilibrium and dynamic properties of biomolecules at the single-molecular and quantitative levels. In this review, we provide an overview of the state-of-the-art advancements in single-molecule fluorescence imaging techniques. We systematically explore the advanced implementations of in vitro single-molecule imaging techniques using total internal reflection fluorescence (TIRF) microscopy, which is widely accessible. This includes discussions on sample preparation, passivation techniques, data collection and analysis, and biological applications. Furthermore, we delve into the compatibility of microfluidic technology for single-molecule fluorescence imaging, highlighting its potential benefits and challenges. Finally, we summarize the current challenges and prospects of fluorescence-based single-molecule imaging techniques, paving the way for further advancements in this rapidly evolving field.
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Affiliation(s)
- Louis Colson
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; (L.C.); (A.B.); (N.M.M.); (Y.L.)
| | - Youngeun Kwon
- Department of Chemical Engineering, Myongji University, Yongin 17058, Republic of Korea; (Y.K.); (S.N.)
| | - Soobin Nam
- Department of Chemical Engineering, Myongji University, Yongin 17058, Republic of Korea; (Y.K.); (S.N.)
| | - Avinashi Bhandari
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; (L.C.); (A.B.); (N.M.M.); (Y.L.)
| | - Nolberto Martinez Maya
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; (L.C.); (A.B.); (N.M.M.); (Y.L.)
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; (L.C.); (A.B.); (N.M.M.); (Y.L.)
| | - Yongmin Cho
- Department of Chemical Engineering, Myongji University, Yongin 17058, Republic of Korea; (Y.K.); (S.N.)
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16
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Goffinont S, Coste F, Prieu-Serandon P, Mance L, Gaudon V, Garnier N, Castaing B, Suskiewicz MJ. Structural insights into the regulation of the human E2∼SUMO conjugate through analysis of its stable mimetic. J Biol Chem 2023; 299:104870. [PMID: 37247759 PMCID: PMC10404613 DOI: 10.1016/j.jbc.2023.104870] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023] Open
Abstract
Protein SUMOylation is a ubiquitylation-like post-translational modification (PTM) that is synthesized through an enzymatic cascade involving an E1 (SAE1:SAE2), an E2 (UBC9), and various E3 enzymes. In the final step of this process, the small ubiquitin-like modifier (SUMO) is transferred from the UBC9∼SUMO thioester onto a lysine residue of a protein substrate. This reaction can be accelerated by an E3 ligase. As the UBC9∼SUMO thioester is chemically unstable, a stable mimetic is desirable for structural studies of UBC9∼SUMO alone and in complex with a substrate and/or an E3 ligase. Recently, a strategy for generating a mimetic of the yeast E2∼SUMO thioester by mutating alanine 129 of Ubc9 to a lysine has been reported. Here, we reproduce and further investigate this approach using the human SUMOylation system and characterize the resulting mimetic of human UBC9∼SUMO1. We show that substituting lysine for alanine 129, but not for other active-site UBC9 residues, results in a UBC9 variant that is efficiently auto-SUMOylated. The auto-modification is dependent on cysteine 93 of UBC9, suggesting that it proceeds via this residue, through the same pathway as that for SUMOylation of substrates. The process is also partially dependent on aspartate 127 of UBC9 and accelerated by high pH, highlighting the importance of the substrate lysine protonation state for efficient SUMOylation. Finally, we present the crystal structure of the UBC9-SUMO1 molecule, which reveals the mimetic in an open conformation and its polymerization via the noncovalent SUMO-binding site on UBC9. Similar interactions could regulate UBC9∼SUMO in some cellular contexts.
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Affiliation(s)
| | - Franck Coste
- Centre de Biophysique Moléculaire (CBM), CNRS UPR, Orléans, France
| | | | - Lucija Mance
- Centre de Biophysique Moléculaire (CBM), CNRS UPR, Orléans, France
| | - Virginie Gaudon
- Centre de Biophysique Moléculaire (CBM), CNRS UPR, Orléans, France
| | - Norbert Garnier
- Centre de Biophysique Moléculaire (CBM), CNRS UPR, Orléans, France
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17
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Amhaz S, Boëda B, Chouchène M, Colasse S, Dingli F, Loew D, Henri J, Prunier C, Levy L. The UAS thioredoxin-like domain of UBXN7 regulates E3 ubiquitin ligase activity of RNF111/Arkadia. BMC Biol 2023; 21:73. [PMID: 37024974 PMCID: PMC10080908 DOI: 10.1186/s12915-023-01576-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/24/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND E3 ubiquitin ligases play critical roles in regulating cellular signaling pathways by inducing ubiquitylation of key components. RNF111/Arkadia is a RING E3 ubiquitin ligase that activates TGF-β signaling by inducing ubiquitylation and proteasomal degradation of the transcriptional repressor SKIL/SnoN. In this study, we have sought to identify novel regulators of the E3 ubiquitin ligase activity of RNF111 by searching for proteins that specifically interacts with its RING domain. RESULTS We found that UBXN7, a member of the UBA-UBX family, directly interacts with the RING domain of RNF111 or its related E3 RNF165/ARK2C that shares high sequence homology with RNF111. We showed that UBXN7 docks on RNF111 or RNF165 RING domain through its UAS thioredoxin-like domain. Overexpression of UBXN7 or its UAS domain increases endogenous RNF111, while an UBXN7 mutant devoid of UAS domain has no effect. Conversely, depletion of UBXN7 decreases RNF111 protein level. As a consequence, we found that UBXN7 can modulate degradation of the RNF111 substrate SKIL in response to TGF-β signaling. We further unveiled this mechanism of regulation by showing that docking of the UAS domain of UBXN7 inhibits RNF111 ubiquitylation by preventing interaction of the RING domain with the E2 conjugating enzymes. By analyzing the interactome of the UAS domain of UBXN7, we identified that it also interacts with the RING domain of the E3 TOPORS and similarly regulates its E3 ubiquitin ligase activity by impairing E2 binding. CONCLUSIONS Taken together, our results demonstrate that UBXN7 acts as a direct regulator for the E3 ubiquitin ligases RNF111, RNF165, and TOPORS and reveal that a thioredoxin-like domain can dock on specific RING domains to regulate their E3 ubiquitin ligase activity.
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Affiliation(s)
- Sadek Amhaz
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France
| | - Batiste Boëda
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Université Paris Cité, F-75015, Paris, France
| | - Mouna Chouchène
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France
| | - Sabrina Colasse
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France
| | - Florent Dingli
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- CurieCoreTech Mass Spectrometry Proteomics, Institut Curie, PSL Research University, Paris, France
| | - Julien Henri
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 75005, Paris, France
| | - Céline Prunier
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France.
| | - Laurence Levy
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, 75012, Paris, France.
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18
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Nyenhuis DA, Rajasekaran R, Watanabe S, Strub MP, Khan M, Powell M, Carter CA, Tjandra N. HECT domain interaction with ubiquitin binding sites on Tsg101-UEV controls HIV-1 egress, maturation, and infectivity. J Biol Chem 2023; 299:102901. [PMID: 36642186 PMCID: PMC9944984 DOI: 10.1016/j.jbc.2023.102901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The HECT domain of HECT E3 ligases consists of flexibly linked N- and C-terminal lobes, with a ubiquitin (Ub) donor site on the C-lobe that is directly involved in substrate modification. HECT ligases also possess a secondary Ub binding site in the N-lobe, which is thought to play a role in processivity, specificity, or regulation. Here, we report the use of paramagnetic solution NMR to characterize a complex formed between the isolated HECT domain of neural precursor cell-expressed developmentally downregulated 4-1 and the ubiquitin E2 variant (UEV) domain of tumor susceptibility gene 101 (Tsg101). Both proteins are involved in endosomal trafficking, a process driven by Ub signaling, and are hijacked by viral pathogens for particle assembly; however, a direct interaction between them has not been described, and the mechanism by which the HECT E3 ligase contributes to pathogen formation has not been elucidated. We provide evidence for their association, consisting of multiple sites on the neural precursor cell-expressed developmentally downregulated 4-1 HECT domain and elements of the Tsg101 UEV domain involved in noncovalent ubiquitin binding. Furthermore, we show using an established reporter assay that HECT residues perturbed by UEV proximity define determinants of viral maturation and infectivity. These results suggest the UEV interaction is a determinant of HECT activity in Ub signaling. As the endosomal trafficking pathway is hijacked by several human pathogens for egress, the HECT-UEV interaction could represent a potential novel target for therapeutic intervention.
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Affiliation(s)
- David A. Nyenhuis
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rohith Rajasekaran
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Susan Watanabe
- Department of Microbiology & Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Mahfuz Khan
- Department of Microbiology & Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Michael Powell
- Department of Microbiology & Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Carol A. Carter
- Department of Microbiology & Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York, USA,For correspondence: Nico Tjandra; Carol A. Carter
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA.
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19
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Johnson JAK, Sumner I. On the Possibility That Bond Strain Is the Mechanism of RING E3 Activation in the E2-Catalyzed Ubiquitination Reaction. J Chem Inf Model 2022; 62:6475-6481. [PMID: 35671046 DOI: 10.1021/acs.jcim.2c00423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ubiquitination is a type of post-translational modification wherein the small protein ubiquitin (Ub) is covalently bound to a lysine on a target protein. Ubiquitination can signal for several regulatory pathways including protein degradation. Ubiquitination occurs by a series of reactions catalyzed by three types of enzymes: ubiquitin activating enzymes, E1; ubiquitin conjugating enzymes, E2; and ubiquitin ligases, E3. E2 enzymes directly catalyze the transfer of Ub to the target protein─the RING E3 improves the efficiency. Prior to its transfer, Ub is covalently linked to the E2 via a thioester bond and the Ub∼E2 conjugate forms a quaternary complex with the RING E3. It is hypothesized that the RING E3 improves the catalytic efficiency of ubiquitination by placing the E2∼Ub conjugate in a "closed" position, which tensions and weakens the thioester bond. We interrogate this hypothesis by analyzing the strain on the thioester during molecular dynamics simulations of both open and closed E2∼Ub/E3 complexes. Our data indicate that the thioester is strained when the E2∼Ub conjugate is in the closed position. We also show that the amount of strain is consistent with the experimental rate enhancement caused by the RING E3. Finally, our simulations show that the closed configuration increases the populations of key hydrogen bonds in the E2∼Ub active site. This is consistent with another hypothesis stating that the RING E3 enhances reaction rates by preorganizing the substrates.
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Affiliation(s)
- Jay-Anne K Johnson
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
| | - Isaiah Sumner
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
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20
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Zhu K, Suskiewicz MJ, Hloušek-Kasun A, Meudal H, Mikoč A, Aucagne V, Ahel D, Ahel I. DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on protein substrates. SCIENCE ADVANCES 2022; 8:eadd4253. [PMID: 36197986 PMCID: PMC7615817 DOI: 10.1126/sciadv.add4253] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ubiquitylation had been considered limited to protein lysine residues, but other substrates have recently emerged. Here, we show that DELTEX E3 ligases specifically target the 3' hydroxyl of the adenosine diphosphate (ADP)-ribosyl moiety that can be linked to a protein, thus generating a hybrid ADP-ribosyl-ubiquitin modification. Unlike other known hydroxyl-specific E3s, which proceed via a covalent E3~ubiqutin intermediate, DELTEX enzymes are RING E3s that stimulate a direct ubiquitin transfer from E2~ubiquitin onto a substrate. However, DELTEXes follow a previously unidentified paradigm for RING E3s, whereby the ligase not only forms a scaffold but also provides catalytic residues to activate the acceptor. Comparative analysis of known hydroxyl-ubiquitylating active sites points to the recurring use of a catalytic histidine residue, which, in DELTEX E3s, is potentiated by a glutamate in a catalytic triad-like manner. In addition, we determined the hydrolase specificity profile of this modification, identifying human and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enzymes that could reverse it in cells.
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Affiliation(s)
- Kang Zhu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Marcin J. Suskiewicz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | | | - Hervé Meudal
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vincent Aucagne
- Centre de Biophysique Moléculaire, CNRS UPR 4301, Orléans, France
| | - Dragana Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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21
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Birkou M, Delegkou GN, Marousis KD, Fragkaki N, Toro T, Episkopou V, Spyroulias GA. Unveiling the Essential Role of Arkadia's Non-RING Elements in the Ubiquitination Process. Int J Mol Sci 2022; 23:10585. [PMID: 36142504 PMCID: PMC9501438 DOI: 10.3390/ijms231810585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Arkadia is a positive regulator of the TGFβ-SMAD2/3 pathway, acting through its C-terminal RING-H2 domain and targeting for degradation of its negative regulators. Here we explore the role of regions outside the RING domain (non-RING elements) of Arkadia on the E2-E3 interaction. The contribution of the non-RING elements was addressed using Arkadia RING 68 aa and Arkadia 119 aa polypeptides. The highly conserved NRGA (asparagine-arginine-glycine-alanine) and TIER (threonine-isoleucine-glutamine-arginine) motifs within the 119 aa Arkadia polypeptide, have been shown to be required for pSMAD2/3 substrate recognition and ubiquitination in vivo. However, the role of the NRGA and TIER motifs in the enzymatic activity of Arkadia has not been addressed. Here, nuclear magnetic resonance interaction studies with the E2 enzyme, UBCH5B, C85S UBCH5B-Ub oxyester hydrolysis, and auto-ubiquitination assays were used to address the role of the non-RING elements in E2-E3 interaction and in the enzymatic activity of the RING. The results support that the non-RING elements including the NRGA and TIER motifs are required for E2-E3 recognition and interaction and for efficient auto-ubiquitination. Furthermore, while Arkadia isoform-2 and its close homologue Arkadia 2C are known to interact with free ubiquitin, the results here showed that Arkadia isoform-1 does not interact with free ubiquitin.
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Affiliation(s)
- Maria Birkou
- Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | | | | | - Nefeli Fragkaki
- Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Tamara Toro
- Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Vasso Episkopou
- Department of Brain Sciences, Imperial College, London W12 0NN, UK
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22
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Paluda A, Middleton AJ, Rossig C, Mace PD, Day CL. Ubiquitin and a charged loop regulate the ubiquitin E3 ligase activity of Ark2C. Nat Commun 2022; 13:1181. [PMID: 35246518 PMCID: PMC8897509 DOI: 10.1038/s41467-022-28782-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/03/2022] [Indexed: 12/26/2022] Open
Abstract
A large family of E3 ligases that contain both substrate recruitment and RING domains confer specificity within the ubiquitylation cascade. Regulation of RING E3s depends on modulating their ability to stabilise the RING bound E2~ubiquitin conjugate in the activated (or closed) conformation. Here we report the structure of the Ark2C RING bound to both a regulatory ubiquitin molecule and an activated E2~ubiquitin conjugate. The structure shows that the RING domain and non-covalently bound ubiquitin molecule together make contacts that stabilise the activated conformation of the conjugate, revealing why ubiquitin is a key regulator of Ark2C activity. We also identify a charged loop N-terminal to the RING domain that enhances activity by interacting with both the regulatory ubiquitin and ubiquitin conjugated to the E2. In addition, the structure suggests how Lys48-linked ubiquitin chains might be assembled by Ark2C and UbcH5b. Together this study identifies features common to RING E3s, as well elements that are unique to Ark2C and related E3s, which enhance assembly of ubiquitin chains. Attachment of ubiquitin to proteins is tightly regulated and controls many signalling pathways. Here, the authors show that addition of ubiquitin by the RING E3 ligases Arkadia and Ark2C is enhanced by ubiquitin and a charged loop that precedes the RING domain.
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Affiliation(s)
- Andrej Paluda
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand.,TMDU Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Adam J Middleton
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Claudia Rossig
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Peter D Mace
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand
| | - Catherine L Day
- Biochemistry Department, School of Biomedical Sciences, University of Otago, Dunedin, 9054, New Zealand.
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23
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Tripathi-Giesgen I, Behrends C, Alpi AF. The ubiquitin ligation machinery in the defense against bacterial pathogens. EMBO Rep 2021; 22:e52864. [PMID: 34515402 PMCID: PMC8567218 DOI: 10.15252/embr.202152864] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/21/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin system is an important part of the host cellular defense program during bacterial infection. This is in particular evident for a number of bacteria including Salmonella Typhimurium and Mycobacterium tuberculosis which—inventively as part of their invasion strategy or accidentally upon rupture of seized host endomembranes—become exposed to the host cytosol. Ubiquitylation is involved in the detection and clearance of these bacteria as well as in the activation of innate immune and inflammatory signaling. Remarkably, all these defense responses seem to emanate from a dense layer of ubiquitin which coats the invading pathogens. In this review, we focus on the diverse group of host cell E3 ubiquitin ligases that help to tailor this ubiquitin coat. In particular, we address how the divergent ubiquitin conjugation mechanisms of these ligases contribute to the complexity of the anti‐bacterial coating and the recruitment of different ubiquitin‐binding effectors. We also discuss the activation and coordination of the different E3 ligases and which strategies bacteria evolved to evade the activities of the host ubiquitin system.
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Affiliation(s)
- Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy), Medical Faculty, Ludwig-Maximilians-University München, München, Germany
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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24
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Wolf LM, Lambert AM, Haenlin J, Boutros M. EVI/WLS function is regulated by ubiquitination and linked to ER-associated degradation by ERLIN2. J Cell Sci 2021; 134:271857. [PMID: 34406391 PMCID: PMC8435288 DOI: 10.1242/jcs.257790] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 07/12/2021] [Indexed: 12/16/2022] Open
Abstract
WNT signalling is important for development in all metazoans and is associated with various human diseases. The ubiquitin–proteasome system (UPS) and regulatory endoplasmic reticulum-associated degradation (ERAD) have been implicated in the production of WNT proteins. Here, we investigated how the WNT secretory factor EVI (also known as WLS) is ubiquitylated, recognised by ERAD components and subsequently removed from the secretory pathway. We performed a focused immunoblot-based RNAi screen for factors that influence EVI/WLS protein stability. We identified the VCP-binding proteins FAF2 and UBXN4 as novel interaction partners of EVI/WLS and showed that ERLIN2 links EVI/WLS to the ubiquitylation machinery. Interestingly, we also found that EVI/WLS is ubiquitylated and degraded in cells irrespective of their level of WNT production. This K11, K48 and K63-linked ubiquitylation is mediated by the E2 ubiquitin-conjugating enzymes UBE2J2, UBE2K and UBE2N, but is independent of the E3 ubiquitin ligases HRD1 (also known as SYVN1) and GP78 (also known as AMFR). Taken together, our study identifies factors that link the UPS to the WNT secretory pathway and provides mechanistic details of the fate of an endogenous substrate of regulatory ERAD in mammalian cells. This article has an associated First Person interview with the first author of the paper. Summary: The WNT secretory factor EVI/WLS is ubiquitylated and linked to ER-associated degradation by multiple proteins, providing insight into the link between WNT signalling and the ubiquitin–proteasome system.
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Affiliation(s)
- Lucie M Wolf
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
| | - Annika M Lambert
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
| | - Julie Haenlin
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division of Signalling and Functional Genomics and Heidelberg University, BioQuant & Department for Cell and Molecular Biology, Medical Faculty Mannheim, D-69120 Heidelberg, Germany
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25
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D'Amico F, Mukhopadhyay R, Ovaa H, Mulder MPC. Targeting TRIM Proteins: A Quest towards Drugging an Emerging Protein Class. Chembiochem 2021; 22:2011-2031. [PMID: 33482040 PMCID: PMC8251876 DOI: 10.1002/cbic.202000787] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/22/2021] [Indexed: 02/06/2023]
Abstract
The ubiquitylation machinery regulates several fundamental biological processes from protein homeostasis to a wide variety of cellular signaling pathways. As a consequence, its dysregulation is linked to diseases including cancer, neurodegeneration, and autoimmunity. With this review, we aim to highlight the therapeutic potential of targeting E3 ligases, with a special focus on an emerging class of RING ligases, named tri-partite motif (TRIM) proteins, whose role as targets for drug development is currently gaining pharmaceutical attention. TRIM proteins exert their catalytic activity as scaffolds involved in many protein-protein interactions, whose multidomains and adapter-like nature make their druggability very challenging. Herein, we give an overview of the current understanding of this class of single polypeptide RING E3 ligases and discuss potential targeting options.
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Affiliation(s)
- Francesca D'Amico
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Rishov Mukhopadhyay
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
| | - Monique P. C. Mulder
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical Center (LUMC)Einthovenweg 202333ZCLeidenThe Netherlands
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26
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Li J, Xu C, Zhang J, Jin C, Shi X, Zhang C, Jia S, Xu J, Gui X, Xing L, Lu L, Xu L. Identification of miRNA-Target Gene Pairs in the Parietal and Frontal Lobes of the Brain in Patients with Alzheimer's Disease Using Bioinformatic Analyses. Neurochem Res 2021; 46:964-979. [PMID: 33586092 DOI: 10.1007/s11064-020-03215-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/05/2020] [Accepted: 12/23/2020] [Indexed: 12/17/2022]
Abstract
Alzheimer's disease (AD) is a growing health concern worldwide. MicroRNAs (miRNAs) have been extensively studied in many diseases, including AD. To identify differentially expressed miRNAs (DEmiRNAs) and genes specific to AD, we used bioinformatic analyses to investigate candidate miRNA-mRNA pairs involved in the pathogenesis of AD. We focused on differentially expressed genes (DEGs) that are targets of DEmiRNAs. The GEO2R tool and the HISAT2-DESeq2 software were used to identify DEmiRNAs and DEGs. Bioinformatic tools available online, such as TAM and the Database for Annotation, Visualization and Integrated Discovery (DAVID), were used to perform functional annotation and enrichment analysis. Targets of miRNAs were predicted using the miRTarBase. The Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape, which are available online, were utilized to construct protein-protein interaction (PPI) networks and identify hub genes. Furthermore, transcription factors (TFs) encoded by the DEGs were predicted using the TransmiR database and TF-miRNA-mRNA networks were constructed. Finally, the expression profile of a hub gene in peripheral blood mononuclear cells was compared between healthy individuals and AD patients. We identified 26 correlated miRNA-mRNA pairs. In the parietal lobe, miRNA-mRNA pairs involved in protein folding were enriched, and in the frontal lobe, miRNA-mRNA pairs involved in synaptic transmission, abnormal protein degradation, and apoptosis were enriched. In addition, HSP90AB1 in peripheral blood mononuclear cells was found to be significantly downregulated in AD patients, and this was consistent with its expression profile in the parietal lobe of AD patients. Our results provide brain region-specific changes in miRNA-mRNA associations in AD patients, further our understanding of potential underlying molecular mechanisms of AD, and reveal promising diagnostic and therapeutic targets for AD.
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Affiliation(s)
- Jiao Li
- Teaching Laboratory Center of Medicine and Life Science, Tongji University School of Medicine, Shanghai, 200092, China
| | - Chunli Xu
- Department of Neurology, The Seventh People's Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 200137, China
| | - Junfang Zhang
- Teaching Laboratory Center of Medicine and Life Science, Tongji University School of Medicine, Shanghai, 200092, China
| | - Caixia Jin
- Department of Biochemistry and Molecular Biology, School of Medicine, Tongji University, Shanghai, China
| | - Xiujuan Shi
- Department of Biochemistry and Molecular Biology, School of Medicine, Tongji University, Shanghai, China
| | - Chen Zhang
- Department of Laboratory Research Center, Tongji University School of Medicine, Shanghai, China
| | - Song Jia
- Teaching Laboratory Center of Medicine and Life Science, Tongji University School of Medicine, Shanghai, 200092, China
| | - Jie Xu
- Teaching Laboratory Center of Medicine and Life Science, Tongji University School of Medicine, Shanghai, 200092, China
| | - Xin Gui
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Libo Xing
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Lixia Lu
- Department of Biochemistry and Molecular Biology, School of Medicine, Tongji University, Shanghai, China
| | - Lei Xu
- Department of Biochemistry and Molecular Biology, School of Medicine, Tongji University, Shanghai, China.
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27
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Wang ZH, Ke F, Zhang QY, Gui JF. Structural and Functional Diversity among Five RING Finger Proteins from Carassius Auratus Herpesvirus (CaHV). Viruses 2021; 13:v13020254. [PMID: 33562288 PMCID: PMC7914681 DOI: 10.3390/v13020254] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 12/17/2022] Open
Abstract
Carassius auratus herpesvirus (CaHV) has been identified as a high-virulence pathogenic virus that infects aquatic animals, but the key factor for virus–host interaction is still unclear. Five Really interesting new genes (RING) finger proteins (39L, 52L, 131R, 136L, and 143R) of CaHV were screened to determine structural diversity. RING finger proteins were also predicted in other known fish herpesviruses, with an arrangement and number similar to CaHV. We performed multifaceted analyses of the proteins, including protein sizes, skeleton structures, subcellular localizations, and ubiquitination activities, to determine their precise roles in virus–host interactions. The five proteins were overexpressed and detected different levels of ubiquitination activities, and 143R showed the highest activity. Then, the prokaryotic expressed and purified full-length proteins (131R and 136L), RING domain isolates (131R12–43 and 136L45–87), and RING domain-deleted mutants (131RΔ12–43 and 136LΔ45–87) were prepared to detect their activities through ubiquitination assays. The results indicate that both full-length proteins and their isolates have activities that catalyze ubiquitination, and the full-length proteins possess higher activity than the isolates, but RING domain-deleted mutants lose their activities. Furthermore, the activities of the five proteins were verified as E3 ubiquitin ligase activity, showing that the RING domains determine the ubiquitination activity. These proteins present different subcellular localization. RING domain-deleted mutants showed similar subcellular localization with their full-length proteins, and all the isolates diffused in whole cells. The current results indicate that the sequence outside the RING domain determines subcellular localization and the level of ubiquitination activity, suggesting that the RING finger proteins of fish herpesviruses might have diverse functions in virus–host interaction.
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Affiliation(s)
- Zi-Hao Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.-H.W.); (F.K.)
- College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Ke
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.-H.W.); (F.K.)
- College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi-Ya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.-H.W.); (F.K.)
- College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Q.-Y.Z.); (J.-F.G.); Tel.: +86-027-68780792 (Q.-Y.Z.); +86-027-68780707 (J.-F.G.)
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (Z.-H.W.); (F.K.)
- College of Modern Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Q.-Y.Z.); (J.-F.G.); Tel.: +86-027-68780792 (Q.-Y.Z.); +86-027-68780707 (J.-F.G.)
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28
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Khago D, Fucci IJ, Byrd RA. The Role of Conformational Dynamics in the Recognition and Regulation of Ubiquitination. Molecules 2020; 25:E5933. [PMID: 33333809 PMCID: PMC7765195 DOI: 10.3390/molecules25245933] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 11/23/2022] Open
Abstract
The ubiquitination pathway is central to many cell signaling and regulatory events. One of the intriguing aspects of the pathway is the combinatorial sophistication of substrate recognition and ubiquitin chain building determinations. The abundant structural and biological data portray several characteristic protein folds among E2 and E3 proteins, and the understanding of the combinatorial complexity that enables interaction with much of the human proteome is a major goal to developing targeted and selective manipulation of the pathway. With the commonality of some folds, there are likely other aspects that can provide differentiation and recognition. These aspects involve allosteric effects and conformational dynamics that can direct recognition and chain building processes. In this review, we will describe the current state of the knowledge for conformational dynamics across a wide timescale, address the limitations of present approaches, and illustrate the potential to make new advances in connecting dynamics with ubiquitination regulation.
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Affiliation(s)
| | | | - Robert Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, P.O. Box B, Building 538, Frederick, MD 21702-1201, USA; (D.K.); (I.J.F.)
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29
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Liwocha J, Krist DT, van der Heden van Noort GJ, Hansen FM, Truong VH, Karayel O, Purser N, Houston D, Burton N, Bostock MJ, Sattler M, Mann M, Harrison JS, Kleiger G, Ovaa H, Schulman BA. Linkage-specific ubiquitin chain formation depends on a lysine hydrocarbon ruler. Nat Chem Biol 2020; 17:272-279. [PMID: 33288957 PMCID: PMC7904580 DOI: 10.1038/s41589-020-00696-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 09/10/2020] [Accepted: 10/14/2020] [Indexed: 02/08/2023]
Abstract
Virtually all aspects of cell biology are regulated by a ubiquitin code
where distinct ubiquitin chain architectures guide the binding events and
itineraries of modified substrates. Various combinations of E2 and E3 enzymes
accomplish chain formation by forging isopeptide bonds between the C-terminus of
their transiently-linked donor ubiquitin and a specific nucleophilic amino acid
on the acceptor ubiquitin, yet it is unknown whether the fundamental feature of
most acceptors - the lysine side-chain - affects catalysis. Here, use of
synthetic ubiquitins with non-natural acceptor site replacements reveals that
the aliphatic side-chain specifying reactive amine geometry is a determinant of
the ubiquitin code, through unanticipated and complex reliance of many distinct
ubiquitin carrying enzymes on a canonical acceptor lysine.
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Affiliation(s)
- Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David T Krist
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.,Carle Illinois College of Medicine, Champaign, IL, USA
| | - Gerbrand J van der Heden van Noort
- Oncode Institute and Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Vinh H Truong
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Ozge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Daniel Houston
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Nicole Burton
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Mark J Bostock
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technical University of Munich, Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, CA, USA
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA.
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Centre, Leiden, the Netherlands.
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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30
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Lips C, Ritterhoff T, Weber A, Janowska MK, Mustroph M, Sommer T, Klevit RE. Who with whom: functional coordination of E2 enzymes by RING E3 ligases during poly-ubiquitylation. EMBO J 2020; 39:e104863. [PMID: 33015833 PMCID: PMC7667886 DOI: 10.15252/embj.2020104863] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/31/2020] [Accepted: 09/10/2020] [Indexed: 11/09/2022] Open
Abstract
Protein modification with poly-ubiquitin chains is a crucial process involved in a myriad of cellular pathways. Chain synthesis requires two steps: substrate modification with ubiquitin (priming) followed by repetitive ubiquitin-to-ubiquitin attachment (elongation). RING-type E3 ligases catalyze both reactions in collaboration with specific priming and elongating E2 enzymes. We provide kinetic insight into poly-ubiquitylation during protein quality control by showing that priming is the rate-determining step in protein degradation as directed by the yeast ERAD RING E3 ligases, Hrd1 and Doa10. Doa10 cooperates with the dedicated priming E2, Ubc6, while both E3s use Ubc7 for elongation. Here, we provide direct evidence that Hrd1 uses Ubc7 also for priming. We found that Ubc6 has an unusually high basal activity that does not require strong stimulation from an E3. Doa10 exploits this property to pair with Ubc6 over Ubc7 during priming. Our work not only illuminates the mechanisms of specific E2/E3 interplay in ERAD, but also offers a basis to understand how RING E3s may have properties that are tailored to pair with their preferred E2s.
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Affiliation(s)
- Christian Lips
- Max Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Tobias Ritterhoff
- Department of BiochemistrySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Annika Weber
- Max Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Present address:
MRC Laboratory of Molecular BiologyCambridgeUK
| | - Maria K Janowska
- Department of BiochemistrySchool of MedicineUniversity of WashingtonSeattleWAUSA
| | - Mandy Mustroph
- Max Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
| | - Thomas Sommer
- Max Delbrück‐Center for Molecular Medicine in the Helmholtz AssociationBerlin‐BuchGermany
- Lady Davies Guest ProfessorTechnion‐Israel Institute of TechnologyHaifaIsrael
| | - Rachel E Klevit
- Department of BiochemistrySchool of MedicineUniversity of WashingtonSeattleWAUSA
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31
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Baek K, Scott DC, Schulman BA. NEDD8 and ubiquitin ligation by cullin-RING E3 ligases. Curr Opin Struct Biol 2020; 67:101-109. [PMID: 33160249 DOI: 10.1016/j.sbi.2020.10.007] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/04/2020] [Accepted: 10/05/2020] [Indexed: 01/31/2023]
Abstract
RING E3s comprise the largest family of ubiquitin (UB) and ubiquitin-like protein (UBL) ligases. RING E3s typically promote UB or UBL transfer from the active site of an associated E2 enzyme to a distally-recruited substrate. Many RING E3s - including the cullin-RING ligase family - are multifunctional, interacting with various E2s (or other E3s) to target distinct proteins, transfer different UBLs, or to initially modify substrates with UB or subsequently elongate UB chains. Here we consider recent structures of cullin-RING ligases, and their partner E2 enzymes, representing ligation reactions. The studies collectively reveal multimodal mechanisms - interactions between ancillary E2 or E3 domains, post-translational modifications, or auxiliary binding partners - directing cullin-RING E3-E2 enzyme active sites to modify their specific targets.
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Affiliation(s)
- Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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