1
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Kahraman K, Robson SA, Göcenler O, Yenici CM, Tozkoparan Ceylan CD, Klein JM, Dötsch V, Elgin ES, Haas AL, Ziarek JJ, Dağ Ç. Characterizing the Monomer-Dimer Equilibrium of UbcH8/Ube2L6: A Combined SAXS and NMR Study. ACS OMEGA 2024; 9:39564-39572. [PMID: 39346869 PMCID: PMC11425648 DOI: 10.1021/acsomega.4c03610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/01/2024] [Accepted: 06/18/2024] [Indexed: 10/01/2024]
Abstract
Interferon-stimulated gene-15 (ISG15) is an interferon-induced protein with two ubiquitin-like (Ubl) domains linked by a short peptide chain and is a conjugated protein of the ISGylation system. Similar to ubiquitin and other Ubls, ISG15 is ligated to its target proteins through a series of E1, E2, and E3 enzymes known as Uba7, Ube2L6/UbcH8, and HERC5, respectively. Ube2L6/UbcH8 plays a central role in ISGylation, underscoring it as an important drug target for boosting innate antiviral immunity. Depending on the type of conjugated protein and the ultimate target protein, E2 enzymes have been shown to function as monomers, dimers, or both. UbcH8 has been crystallized in both monomeric and dimeric forms, but its functional state remains unclear. Here, we used a combined approach of small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy to characterize UbcH8's oligomeric state in solution. SAXS revealed a dimeric UbcH8 structure that could be dissociated when fused N-terminally to glutathione S-transferase. NMR spectroscopy validated the presence of a concentration-dependent monomer-dimer equilibrium and suggested a back-side dimerization interface. Chemical shift perturbation and peak intensity analysis further suggest dimer-induced conformational dynamics at the E1 and E3 interfaces, providing hypotheses for the protein's functional mechanisms. Our study highlights the power of combining NMR and SAXS techniques to provide structural information about proteins in solution.
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Affiliation(s)
- Kerem Kahraman
- Nanofabrication
and Nanocharacterization Center for Scientific and Technological Advanced
Research (nSTAR), Koç
University, İstanbul 34450, Turkey
| | - Scott A. Robson
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 East Superior Avenue, Chicago, Illinois 460611, United States
| | - Oktay Göcenler
- Nanofabrication
and Nanocharacterization Center for Scientific and Technological Advanced
Research (nSTAR), Koç
University, İstanbul 34450, Turkey
| | - Cansu M. Yenici
- Nanofabrication
and Nanocharacterization Center for Scientific and Technological Advanced
Research (nSTAR), Koç
University, İstanbul 34450, Turkey
| | - Cansu D. Tozkoparan Ceylan
- Nanofabrication
and Nanocharacterization Center for Scientific and Technological Advanced
Research (nSTAR), Koç
University, İstanbul 34450, Turkey
| | - Jennifer M. Klein
- Department
of Biochemistry and Molecular Biology, LSUHSC-School
of Medicine, 1901 Perdido Street, New Orleans, Louisiana 70112, United States
| | - Volker Dötsch
- Centre
for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Frankfurt 60439, Germany
| | - Emine Sonay Elgin
- College
of Sciences, Department of Chemistry, Muğla
Sıtkı Koçman University, Muğla 48000, Turkey
| | - Arthur L. Haas
- Department
of Biochemistry and Molecular Biology, LSUHSC-School
of Medicine, 1901 Perdido Street, New Orleans, Louisiana 70112, United States
| | - Joshua J. Ziarek
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 East Superior Avenue, Chicago, Illinois 460611, United States
| | - Çağdaş Dağ
- Nanofabrication
and Nanocharacterization Center for Scientific and Technological Advanced
Research (nSTAR), Koç
University, İstanbul 34450, Turkey
- Koç
University Isbank Center for Infectious Diseases (KUISCID), Koç
University, Istanbul 34450, Turkey
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2
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Kahraman K, Robson SA, Göcenler O, Yenici CM, Tozkoparan CD, Klein JM, Dötsch V, Elgin ES, Haas AL, Ziarek JJ, Dağ Ç. Characterizing the monomer-dimer equilibrium of UbcH8/Ube2L6: A combined SAXS and NMR study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.13.536743. [PMID: 37090523 PMCID: PMC10120734 DOI: 10.1101/2023.04.13.536743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Interferon-stimulated gene-15 (ISG15) is an interferon-induced protein with two ubiquitin-like (Ubl) domains linked by a short peptide chain, and the conjugated protein of the ISGylation system. Similar to ubiquitin and other Ubls, ISG15 is ligated to its target proteins through a series of E1, E2, and E3 enzymes known as Uba7, Ube2L6/UbcH8, and HERC5, respectively. Ube2L6/UbcH8 plays a literal central role in ISGylation, underscoring it as an important drug target for boosting innate antiviral immunity. Depending on the type of conjugated protein and the ultimate target protein, E2 enzymes have been shown to function as monomers, dimers, or both. UbcH8 has been crystalized in both monomeric and dimeric forms, but the functional state is unclear. Here, we used a combined approach of small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy to characterize UbcH8's oligomeric state in solution. SAXS revealed a dimeric UbcH8 structure that could be dissociated when fused N-terminally to glutathione S-transferase. NMR spectroscopy validated the presence of a concentration-dependent monomer-dimer equilibrium and suggested a backside dimerization interface. Chemical shift perturbation and peak intensity analysis further suggest dimer-induced conformational dynamics at E1 and E3 interfaces - providing hypotheses for the protein's functional mechanisms. Our study highlights the power of combining NMR and SAXS techniques in providing structural information about proteins in solution.
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Affiliation(s)
- Kerem Kahraman
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
| | - Scott A. Robson
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 East Superior Avenue, Chicago, IL, 460611, USA
| | - Oktay Göcenler
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
| | - Cansu M. Yenici
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
| | - Cansu D. Tozkoparan
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
| | - Jennifer M. Klein
- Department of Biochemistry and Molecular Biology, LSUHSC-School of Medicine, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Volker Dötsch
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Germany
| | - Emine Sonay Elgin
- Muğla Sıtkı Koçman University, College of Sciences, Department of Chemistry, Mugla, 48000, Turkey
| | - Arthur L. Haas
- Department of Biochemistry and Molecular Biology, LSUHSC-School of Medicine, 1901 Perdido Street, New Orleans, LA, 70112, USA
| | - Joshua J. Ziarek
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 320 East Superior Avenue, Chicago, IL, 460611, USA
| | - Çağdaş Dağ
- Nanofabrication and Nanocharacterization Center for Scientific and Technological Advanced Research (nSTAR), Koc University, İstanbul, Turkey
- Koc University Isbank Center for Infectious Diseases (KUISCID), Koc University, Istanbul, Turkey
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3
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Kiss L, Rhinesmith T, Luptak J, Dickson CF, Weidenhausen J, Smyly S, Yang JC, Maslen SL, Sinning I, Neuhaus D, Clift D, James LC. Trim-Away ubiquitinates and degrades lysine-less and N-terminally acetylated substrates. Nat Commun 2023; 14:2160. [PMID: 37061529 PMCID: PMC10105713 DOI: 10.1038/s41467-023-37504-x] [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: 06/29/2022] [Accepted: 03/20/2023] [Indexed: 04/17/2023] Open
Abstract
TRIM proteins are the largest family of E3 ligases in mammals. They include the intracellular antibody receptor TRIM21, which is responsible for mediating targeted protein degradation during Trim-Away. Despite their importance, the ubiquitination mechanism of TRIM ligases has remained elusive. Here we show that while Trim-Away activation results in ubiquitination of both ligase and substrate, ligase ubiquitination is not required for substrate degradation. N-terminal TRIM21 RING ubiquitination by the E2 Ube2W can be inhibited by N-terminal acetylation, but this doesn't prevent substrate ubiquitination nor degradation. Instead, uncoupling ligase and substrate degradation prevents ligase recycling and extends functional persistence in cells. Further, Trim-Away degrades substrates irrespective of whether they contain lysines or are N-terminally acetylated, which may explain the ability of TRIM21 to counteract fast-evolving pathogens and degrade diverse substrates.
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Affiliation(s)
- Leo Kiss
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Tyler Rhinesmith
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jakub Luptak
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Claire F Dickson
- EMBL Australia Node in Single Molecule Science and ARC Centre of Excellence in Advanced Molecular Imaging School of Medical Sciences, UNSW Sydney, NSW, 2052, Australia
| | - Jonas Weidenhausen
- Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany
- EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Shannon Smyly
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Irmgard Sinning
- Biochemiezentrum der Universität Heidelberg (BZH), INF328, D-69120, Heidelberg, Germany
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Leo C James
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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4
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Wang S, Pu J, Li X, Yan Z, Li C, Zheng Y, Luo Z, Cui L. UBE2W Improves the Experimental Colitis by Inhibiting the NF-κB Signaling Pathway. Dig Dis Sci 2022; 67:5529-5539. [PMID: 35314916 DOI: 10.1007/s10620-022-07453-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 02/16/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND The NF-κB signaling cascade regulates immune response and is often dysregulated in tumor development. UBE2W is a novel type I ubiquitin-conjugating enzyme (E2) whose biological function is still unclear. AIMS This study was designed to investigate whether UBE2W regulates NF-κB signaling pathway and is involved in the progression of experimental colitis. METHODS At the cellular level, the effect of UBE2W on NF-κB transcriptional activity was measured using a dual-luciferase reporter assay. The influence of UBE2W on NF-κB pathway activation and the entry of p65 into the nucleus were determined by Western blot and immunofluorescence analyses, respectively. Moreover, the colitis model was established by administering 2.5% dextran sulfate sodium (DSS)/water to UBE2W overexpression, UBE2W-knockdown and control mice. Body weight, stool consistency, colon length and clinical severity were examined. Expression of pro-inflammatory cytokines and phosphorylation of p65 and IκB in the colon tissue were measured by qRT-PCR and Western blot, respectively. RESULTS UBE2W inhibited TNFα-induced NF-κB transcription activity, attenuated IκB and p65 phosphorylation, downregulated TNFα and IL-8 expression and blocked the entry of p65 into the nucleus. In the DSS-induced colitis model, UBE2W-knockdown mice had increased weight loss, more serious diarrhea and mucosal injures compared with the control mice. Moreover, phosphorylation of IκB and p65 and the expression of pro-inflammatory mediators such as TNFα, IL-6 were significantly increased in UBE2W knockdown mice. However, these changes were completely reversed in UBE2W overexpression mice. CONCLUSIONS The overexpression of UBE2W ameliorates the severity of DSS-induced colitis, which may be mediated by inhibiting the expression of pro-inflammatory mediators and activation of the NF-κB signaling pathway. These findings provide evidence that UBE2W might have potential therapeutic implications in IBD.
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Affiliation(s)
- Shaoxin Wang
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Jiang Pu
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Xiaowei Li
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Zhihui Yan
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Chao Li
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Yan Zheng
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Zhe Luo
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China
| | - Lihong Cui
- Department of Gastroenterology, The First Medical Center of Chinese PLA General Hospital, 28 Fuxing Road, Beijing, 100853, China.
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5
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Das A, Thapa P, Santiago U, Shanmugam N, Banasiak K, Dąbrowska K, Nolte H, Szulc NA, Gathungu RM, Cysewski D, Krüger M, Dadlez M, Nowotny M, Camacho CJ, Hoppe T, Pokrzywa W. A heterotypic assembly mechanism regulates CHIP E3 ligase activity. EMBO J 2022; 41:e109566. [PMID: 35762422 PMCID: PMC9340540 DOI: 10.15252/embj.2021109566] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
CHIP (C-terminus of Hsc70-interacting protein) and its worm ortholog CHN-1 are E3 ubiquitin ligases that link the chaperone system with the ubiquitin-proteasome system (UPS). CHN-1 can cooperate with UFD-2, another E3 ligase, to accelerate ubiquitin chain formation; however, the basis for the high processivity of this E3s set has remained obscure. Here, we studied the molecular mechanism and function of the CHN-1-UFD-2 complex in Caenorhabditis elegans. Our data show that UFD-2 binding promotes the cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes by stabilizing the CHN-1 U-box dimer. However, HSP70/HSP-1 chaperone outcompetes UFD-2 for CHN-1 binding, thereby promoting a shift to the autoinhibited CHN-1 state by acting on a conserved residue in its U-box domain. The interaction with UFD-2 enables CHN-1 to efficiently ubiquitylate and regulate S-adenosylhomocysteinase (AHCY-1), a key enzyme in the S-adenosylmethionine (SAM) regeneration cycle, which is essential for SAM-dependent methylation. Our results define the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation.
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Affiliation(s)
- Aniruddha Das
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Pankaj Thapa
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Ulises Santiago
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPAUSA
| | - Nilesh Shanmugam
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Katarzyna Banasiak
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | | | - Hendrik Nolte
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Present address:
Max‐Planck‐Institute for Biology of AgeingCologneGermany
| | - Natalia A Szulc
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | | | | | - Marcus Krüger
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Center for Molecular Medicine (CMMC), Faculty of MedicineUniversity Hospital of CologneCologneGermany
| | - Michał Dadlez
- Institute of Biochemistry and BiophysicsPASWarsawPoland
| | - Marcin Nowotny
- Laboratory of Protein StructureInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
| | - Carlos J Camacho
- Department of Computational and Systems BiologyUniversity of PittsburghPittsburghPAUSA
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD)University of CologneCologneGermany
- Center for Molecular Medicine (CMMC), Faculty of MedicineUniversity Hospital of CologneCologneGermany
| | - Wojciech Pokrzywa
- Laboratory of Protein MetabolismInternational Institute of Molecular and Cell Biology in WarsawWarsawPoland
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6
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Kiss L, James LC. The molecular mechanisms that drive intracellular neutralization by the antibody-receptor and RING E3 ligase TRIM21. Semin Cell Dev Biol 2021; 126:99-107. [PMID: 34823983 DOI: 10.1016/j.semcdb.2021.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022]
Abstract
The cytosolic antibody receptor and RING E3 ligase TRIM21 targets intracellular, antibody-coated immune complexes for degradation and activates the immune system. Here we review how TRIM21 degrades diverse targets and how this activity can be exploited in molecular biology and for the development of new therapeutics. In addition, we compare what is known about TRIM21's mechanism to other TRIM proteins and RING E3 ligases.
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Affiliation(s)
- Leo Kiss
- MRC Laboratory of Molecular Biology, UK.
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7
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Burge RJ, Damianou A, Wilkinson AJ, Rodenko B, Mottram JC. Leishmania differentiation requires ubiquitin conjugation mediated by a UBC2-UEV1 E2 complex. PLoS Pathog 2020; 16:e1008784. [PMID: 33108402 PMCID: PMC7647121 DOI: 10.1371/journal.ppat.1008784] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 11/06/2020] [Accepted: 09/10/2020] [Indexed: 12/27/2022] Open
Abstract
Post-translational modifications such as ubiquitination are important for orchestrating the cellular transformations that occur as the Leishmania parasite differentiates between its main morphological forms, the promastigote and amastigote. 2 E1 ubiquitin-activating (E1), 13 E2 ubiquitin-conjugating (E2), 79 E3 ubiquitin ligase (E3) and 20 deubiquitinating cysteine peptidase (DUB) genes can be identified in the Leishmania mexicana genome but, currently, little is known about the role of E1, E2 and E3 enzymes in this parasite. Bar-seq analysis of 23 E1, E2 and HECT/RBR E3 null mutants generated in promastigotes using CRISPR-Cas9 revealed numerous loss-of-fitness phenotypes in promastigote to amastigote differentiation and mammalian infection. The E2s UBC1/CDC34, UBC2 and UEV1 and the HECT E3 ligase HECT2 are required for the successful transformation from promastigote to amastigote and UBA1b, UBC9, UBC14, HECT7 and HECT11 are required for normal proliferation during mouse infection. Of all ubiquitination enzyme null mutants examined in the screen, Δubc2 and Δuev1 exhibited the most extreme loss-of-fitness during differentiation. Null mutants could not be generated for the E1 UBA1a or the E2s UBC3, UBC7, UBC12 and UBC13, suggesting these genes are essential in promastigotes. X-ray crystal structure analysis of UBC2 and UEV1, orthologues of human UBE2N and UBE2V1/UBE2V2 respectively, reveal a heterodimer with a highly conserved structure and interface. Furthermore, recombinant L. mexicana UBA1a can load ubiquitin onto UBC2, allowing UBC2-UEV1 to form K63-linked di-ubiquitin chains in vitro. Notably, UBC2 can cooperate in vitro with human E3s RNF8 and BIRC2 to form non-K63-linked polyubiquitin chains, showing that UBC2 can facilitate ubiquitination independent of UEV1, but association of UBC2 with UEV1 inhibits this ability. Our study demonstrates the dual essentiality of UBC2 and UEV1 in the differentiation and intracellular survival of L. mexicana and shows that the interaction between these two proteins is crucial for regulation of their ubiquitination activity and function. The post-translational modification of proteins is key for allowing Leishmania parasites to transition between the different life cycle stages that exist in its insect vector and mammalian host. In particular, components of the ubiquitin system are important for the transformation of Leishmania from its insect (promastigote) to mammalian (amastigote) stage and normal infection in mice. However, little is known about the role of the enzymes that generate ubiquitin modifications in Leishmania. Here we characterise 28 enzymes of the ubiquitination pathway and show that many are required for life cycle progression or mouse infection by this parasite. Two proteins, UBC2 and UEV1, were selected for further study based on their importance in the promastigote to amastigote transition. We demonstrate that UBC2 and UEV1 form a heterodimer capable of carrying out ubiquitination and that the structural basis for this activity is conserved between Leishmania, Saccharomyces cerevisiae and humans. We also show that the interaction of UBC2 with UEV1 alters the nature of the ubiquitination activity performed by UBC2. Overall, we demonstrate the important role that ubiquitination enzymes play in the life cycle and infection process of Leishmania and explore the biochemistry underlying UBC2 and UEV1 function.
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Affiliation(s)
- Rebecca J. Burge
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
| | - Andreas Damianou
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Anthony J. Wilkinson
- York Biomedical Research Institute and York Structural Biology Laboratory, Department of Chemistry, University of York, United Kingdom
| | - Boris Rodenko
- UbiQ Bio BV, Amsterdam Science Park, the Netherlands
| | - Jeremy C. Mottram
- York Biomedical Research Institute and Department of Biology, University of York, United Kingdom
- * E-mail:
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8
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Liess AKL, Kucerova A, Schweimer K, Schlesinger D, Dybkov O, Urlaub H, Mansfeld J, Lorenz S. Dimerization regulates the human APC/C-associated ubiquitin-conjugating enzyme UBE2S. Sci Signal 2020; 13:eaba8208. [PMID: 33082289 PMCID: PMC7613103 DOI: 10.1126/scisignal.aba8208] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
At the heart of protein ubiquitination cascades, ubiquitin-conjugating enzymes (E2s) form reactive ubiquitin-thioester intermediates to enable efficient transfer of ubiquitin to cellular substrates. The precise regulation of E2s is thus crucial for cellular homeostasis, and their deregulation is frequently associated with tumorigenesis. In addition to driving substrate ubiquitination together with ubiquitin ligases (E3s), many E2s can also autoubiquitinate, thereby promoting their own proteasomal turnover. To investigate the mechanisms that balance these disparate activities, we dissected the regulatory dynamics of UBE2S, a human APC/C-associated E2 that ensures the faithful ubiquitination of cell cycle regulators during mitosis. We uncovered a dimeric state of UBE2S that confers autoinhibition by blocking a catalytically critical ubiquitin binding site. Dimerization is stimulated by the lysine-rich carboxyl-terminal extension of UBE2S that is also required for the recruitment of this E2 to the APC/C and is autoubiquitinated as substrate abundance becomes limiting. Consistent with this mechanism, we found that dimerization-deficient UBE2S turned over more rapidly in cells and did not promote mitotic slippage during prolonged drug-induced mitotic arrest. We propose that dimerization attenuates the autoubiquitination-induced turnover of UBE2S when the APC/C is not fully active. More broadly, our data illustrate how the use of mutually exclusive macromolecular interfaces enables modulation of both the activities and the abundance of E2s in cells to facilitate precise ubiquitin signaling.
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Affiliation(s)
- Anna K L Liess
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany
| | - Alena Kucerova
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | | | - Dörte Schlesinger
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Olexandr Dybkov
- Department for Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077 Göttingen, Germany
- Bioanalytics Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.
- Institute of Cancer Research, London SW7 3RP, UK
| | - Sonja Lorenz
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, 97080 Würzburg, Germany.
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9
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Ubiquitination is required for the initial removal of paternal organelles in C. elegans. Dev Biol 2019; 453:168-179. [PMID: 31153831 DOI: 10.1016/j.ydbio.2019.05.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/27/2019] [Accepted: 05/29/2019] [Indexed: 12/21/2022]
Abstract
Elimination of paternal mitochondria after fertilization occurs in many species using the process of selective autophagy. The mechanism for targeting paternal mitochondria, but not maternal mitochondria, for elimination in the early embryo is not well understood. The results in this paper suggest that there are at least two different mechanisms for targeting paternal mitochondria for elimination: the first involving ubiquitination and a second involving a mitochondrial associated autophagy receptor, fndc-1. Elimination of paternal mitochondria can be visualized in embryos of the nematode, C. elegans. Paternal mitochondria enter the zygote at fertilization. Initially, they are closely associated with another sperm organelle, the membraneous organelle (MO). The MOs become ubiquitinated within minutes after fertilization. Simultaneous RNAi knockdown of two ubiquitin conjugating enzymes, ubc-18 and ubc-16, reduces MO ubiquitination. Loss of function of ubc-18 alone leads to loss of K48-linked polyubiquitin chains and halts the recruitment of proteasome to MOs. Interestingly, knockdown of ubc-18 or ubc-16 or the combination does not reduce the localization of K63-linked ubiquitin chains to MOs suggesting that some ubiquitin structure other than K63 chains is responsible for recruiting the autophagy machinery to MOs. Double knockdown (ubc-18/ubc-16) inhibits the recruitment of the autophagy protein, LGG-1 (homolog of LC3/GABARAP), to paternal organelles and causes the persistence of paternal mitochondria into the two cell stage. If paternal mitochondria are not eliminated via this early process, they are eventually removed from the embryo in a process that depends on the mitophagy adaptor protein, fndc-1. Thus, there are two redundant, but temporally distinct mechanisms that target paternal mitochondria for elimination in C. elegans. In addition to the involvement of ubiquitination in the elimination of paternal mitochondria, two subunits of the proteasome, rpn-10 and rad-23, are required for elimination of paternal mitochondria. These subunits are known to function as ubiquitin receptors and knockdown of either inhibits the recruitment of proteasome to ubiquitinated MOs. Their knockdown does not affect the localization of LGG-1 to paternal structures indicating that the proteasome is not required for autophagy membrane recruitment but might be involved in autophagosome maturation or its fusion with the lysosome.
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Wang B, Merillat SA, Vincent M, Huber AK, Basrur V, Mangelberger D, Zeng L, Elenitoba-Johnson K, Miller RA, Irani DN, Dlugosz AA, Schnell S, Scaglione KM, Paulson HL. Loss of the Ubiquitin-conjugating Enzyme UBE2W Results in Susceptibility to Early Postnatal Lethality and Defects in Skin, Immune, and Male Reproductive Systems. J Biol Chem 2015; 291:3030-42. [PMID: 26601958 DOI: 10.1074/jbc.m115.676601] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
UBE2W ubiquitinates N termini of proteins rather than internal lysine residues, showing a preference for substrates with intrinsically disordered N termini. The in vivo functions of this intriguing E2, however, remain unknown. We generated Ube2w germ line KO mice that proved to be susceptible to early postnatal lethality without obvious developmental abnormalities. Although the basis of early death is uncertain, several organ systems manifest changes in Ube2w KO mice. Newborn Ube2w KO mice often show altered epidermal maturation with reduced expression of differentiation markers. Mirroring higher UBE2W expression levels in testis and thymus, Ube2w KO mice showed a disproportionate decrease in weight of these two organs (~50%), suggesting a functional role for UBE2W in the immune and male reproductive systems. Indeed, Ube2w KO mice displayed sustained neutrophilia accompanied by increased G-CSF signaling and testicular vacuolation associated with decreased fertility. Proteomic analysis of a vulnerable organ, presymptomatic testis, showed a preferential accumulation of disordered proteins in the absence of UBE2W, consistent with the view that UBE2W preferentially targets disordered polypeptides. These mice further allowed us to establish that UBE2W is ubiquitously expressed as a single isoform localized to the cytoplasm and that the absence of UBE2W does not alter cell viability in response to various stressors. Our results establish that UBE2W is an important, albeit not essential, protein for early postnatal survival and normal functioning of multiple organ systems.
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Affiliation(s)
- Bo Wang
- From the Departments of Neurology, Neuroscience Graduate Program, and
| | | | - Michael Vincent
- Molecular and Integrative Physiology and Computational Medicine and Bioinformatics
| | | | | | | | - Li Zeng
- From the Departments of Neurology
| | | | - Richard A Miller
- Pathology and Geriatrics Center, University of Michigan, Ann Arbor, Michigan 48109 and
| | | | | | - Santiago Schnell
- Molecular and Integrative Physiology and Computational Medicine and Bioinformatics
| | - Kenneth Matthew Scaglione
- Department of Biochemistry and Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin 53226
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Biochemical and structural characterization of a novel ubiquitin-conjugating enzyme E2 from Agrocybe aegeria reveals Ube2w family-specific properties. Sci Rep 2015; 5:16056. [PMID: 26525192 PMCID: PMC4630614 DOI: 10.1038/srep16056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 10/01/2015] [Indexed: 11/08/2022] Open
Abstract
Ubiquitination is a post-translational modification that is involved in myriad cellar regulation and disease pathways. The ubiquitin-conjugating enzyme (E2) is an important player in the ubiquitin transfer pathway. Although many E2 structures are available, not all E2 families have known structures, and three-dimensional structures from fungal organisms other than yeast are lacking. We report here the crystal structure of UbcA1, which is a novel ubiquitin-conjugating enzyme identified from the edible and medicinal mushroom Agrocybe aegerita and displays potential antitumor properties. The protein belongs to the Ube2w family and shows similar biochemical characteristics to human Ube2w, including monomer-dimer equilibrium in solution, α-NH2 ubiquitin-transfer activity and a mechanism to recognize backbone atoms of intrinsically disordered N-termini in substrates. Its structure displays a unique C-terminal conformation with an orientation of helix α3 that is completely different from the reported E2 structures but similar to a recently reported NMR ensemble of Ube2w. A mutagenesis study on this novel enzyme revealed that an intact C-terminus is significant for protein dimerization and enzymatic activity. As the first crystallized full-length protein of this family, UbcA1 may supersede the truncated X-ray structure of Ube2w (PDB entry 2A7L) as the representative structure of the Ube2w family.
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The HIP2~ubiquitin conjugate forms a non-compact monomeric thioester during di-ubiquitin synthesis. PLoS One 2015; 10:e0120318. [PMID: 25799589 PMCID: PMC4370575 DOI: 10.1371/journal.pone.0120318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 02/05/2015] [Indexed: 11/30/2022] Open
Abstract
Polyubiquitination is a post-translational event used to control the degradation of damaged or unwanted proteins by modifying the target protein with a chain of ubiquitin molecules. One potential mechanism for the assembly of polyubiquitin chains involves the dimerization of an E2 conjugating enzyme allowing conjugated ubiquitin molecules to be put into close proximity to assist reactivity. HIP2 (UBE2K) and Ubc1 (yeast homolog of UBE2K) are unique E2 conjugating enzymes that each contain a C-terminal UBA domain attached to their catalytic domains, and they have basal E3-independent polyubiquitination activity. Although the isolated enzymes are monomeric, polyubiquitin formation activity assays show that both can act as ubiquitin donors or ubiquitin acceptors when in the activated thioester conjugate suggesting dimerization of the E2-ubiquitin conjugates. Stable disulfide complexes, analytical ultracentrifugation and small angle x-ray scattering were used to show that the HIP2-Ub and Ubc1-Ub thioester complexes remain predominantly monomeric in solution. Models of the HIP2-Ub complex derived from SAXS data show the complex is not compact but instead forms an open or backbent conformation similar to UbcH5b~Ub or Ubc13~Ub where the UBA domain and covalently attached ubiquitin reside on opposite ends of the catalytic domain. Activity assays showed that full length HIP2 exhibited a five-fold increase in the formation rate of di-ubiquitin compared to a HIP2 lacking the UBA domain. This difference was not observed for Ubc1 and may be attributed to the closer proximity of the UBA domain in HIP2 to the catalytic core than for Ubc1.
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Vittal V, Shi L, Wenzel DM, Scaglione KM, Duncan ED, Basrur V, Elenitoba-Johnson KSJ, Baker D, Paulson HL, Brzovic PS, Klevit RE. Intrinsic disorder drives N-terminal ubiquitination by Ube2w. Nat Chem Biol 2015; 11:83-9. [PMID: 25436519 PMCID: PMC4270946 DOI: 10.1038/nchembio.1700] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 10/09/2014] [Indexed: 12/17/2022]
Abstract
Ubiquitination of the αN-terminus of protein substrates has been reported sporadically since the early 1980s. However, the identity of an enzyme responsible for this unique ubiquitin (Ub) modification has only recently been elucidated. We show the Ub-conjugating enzyme (E2) Ube2w uses a unique mechanism to facilitate the specific ubiquitination of the α-amino group of its substrates that involves recognition of backbone atoms of intrinsically disordered N termini. We present the NMR-based solution ensemble of full-length Ube2w that reveals a structural architecture unlike that of any other E2 in which its C terminus is partly disordered and flexible to accommodate variable substrate N termini. Flexibility of the substrate is critical for recognition by Ube2w, and either point mutations in or the removal of the flexible C terminus of Ube2w inhibits substrate binding and modification. Mechanistic insights reported here provide guiding principles for future efforts to define the N-terminal ubiquitome in cells.
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Affiliation(s)
- Vinayak Vittal
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Lei Shi
- 1] Department of Biochemistry, University of Washington, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Dawn M Wenzel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - K Matthew Scaglione
- 1] Department of Neurology, University of Michigan Medical School, Ann Arbor, Michigan, USA. [2] Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA. [3] Neuroscience Research Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Emily D Duncan
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Venkatesha Basrur
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - David Baker
- 1] Department of Biochemistry, University of Washington, Seattle, Washington, USA. [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Henry L Paulson
- Department of Neurology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter S Brzovic
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Rachel E Klevit
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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