1
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Lange SM, McFarland MR, Lamoliatte F, Carroll T, Krshnan L, Pérez-Ràfols A, Kwasna D, Shen L, Wallace I, Cole I, Armstrong LA, Knebel A, Johnson C, De Cesare V, Kulathu Y. VCP/p97-associated proteins are binders and debranching enzymes of K48-K63-branched ubiquitin chains. Nat Struct Mol Biol 2024:10.1038/s41594-024-01354-y. [PMID: 38977901 DOI: 10.1038/s41594-024-01354-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 06/13/2024] [Indexed: 07/10/2024]
Abstract
Branched ubiquitin (Ub) chains constitute a sizable fraction of Ub polymers in human cells. Despite their abundance, our understanding of branched Ub function in cell signaling has been stunted by the absence of accessible methods and tools. Here we identify cellular branched-chain-specific binding proteins and devise approaches to probe K48-K63-branched Ub function. We establish a method to monitor cleavage of linkages within complex Ub chains and unveil ATXN3 and MINDY as debranching enzymes. We engineer a K48-K63 branch-specific nanobody and reveal the molecular basis of its specificity in crystal structures of nanobody-branched Ub chain complexes. Using this nanobody, we detect increased K48-K63-Ub branching following valosin-containing protein (VCP)/p97 inhibition and after DNA damage. Together with our discovery that multiple VCP/p97-associated proteins bind to or debranch K48-K63-linked Ub, these results suggest a function for K48-K63-branched chains in VCP/p97-related processes.
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Affiliation(s)
- Sven M Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Matthew R McFarland
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Thomas Carroll
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Logesvaran Krshnan
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Anna Pérez-Ràfols
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Dominika Kwasna
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow, Poland
| | - Linnan Shen
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Iona Wallace
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Isobel Cole
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Lee A Armstrong
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Clare Johnson
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK.
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2
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Mori Y, Akizuki Y, Honda R, Takao M, Tsuchimoto A, Hashimoto S, Iio H, Kato M, Kaiho-Soma A, Saeki Y, Hamazaki J, Murata S, Ushijima T, Hattori N, Ohtake F. Intrinsic signaling pathways modulate targeted protein degradation. Nat Commun 2024; 15:5379. [PMID: 38956052 PMCID: PMC11220168 DOI: 10.1038/s41467-024-49519-z] [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: 11/16/2023] [Accepted: 06/10/2024] [Indexed: 07/04/2024] Open
Abstract
Targeted protein degradation is a groundbreaking modality in drug discovery; however, the regulatory mechanisms are still not fully understood. Here, we identify cellular signaling pathways that modulate the targeted degradation of the anticancer target BRD4 and related neosubstrates BRD2/3 and CDK9 induced by CRL2VHL- or CRL4CRBN -based PROTACs. The chemicals identified as degradation enhancers include inhibitors of cellular signaling pathways such as poly-ADP ribosylation (PARG inhibitor PDD00017273), unfolded protein response (PERK inhibitor GSK2606414), and protein stabilization (HSP90 inhibitor luminespib). Mechanistically, PARG inhibition promotes TRIP12-mediated K29/K48-linked branched ubiquitylation of BRD4 by facilitating chromatin dissociation of BRD4 and formation of the BRD4-PROTAC-CRL2VHL ternary complex; by contrast, HSP90 inhibition promotes BRD4 degradation after the ubiquitylation step. Consequently, these signal inhibitors sensitize cells to the PROTAC-induced apoptosis. These results suggest that various cell-intrinsic signaling pathways spontaneously counteract chemically induced target degradation at multiple steps, which could be liberated by specific inhibitors.
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Affiliation(s)
- Yuki Mori
- Laboratory of Protein Degradation, Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
- Graduate School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Yoshino Akizuki
- Laboratory of Protein Degradation, Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
- Graduate School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Rikuto Honda
- Laboratory of Protein Degradation, Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
- Graduate School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Miyu Takao
- Graduate School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Ayaka Tsuchimoto
- Laboratory of Protein Degradation, Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
- Graduate School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Sota Hashimoto
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Hiroaki Iio
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masakazu Kato
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Faculty of Pharmaceutical Sciences, Teikyo Heisei University, Nakano-ku, Tokyo, 1648530, Japan
| | - Ai Kaiho-Soma
- Laboratory of Protein Degradation, Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Yasushi Saeki
- Division of Protein Metabolism, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Sciences, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Jun Hamazaki
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Toshikazu Ushijima
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Naoko Hattori
- Department of Epigenomics, Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Fumiaki Ohtake
- Laboratory of Protein Degradation, Institute for Advanced Life Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
- Graduate School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
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3
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Wu X, Lin T, Zhou X, Zhang W, Liu S, Qiu H, Birch PRJ, Tian Z. Potato E3 ubiquitin ligase StRFP1 positively regulates late blight resistance by degrading sugar transporters StSWEET10c and StSWEET11. THE NEW PHYTOLOGIST 2024; 243:688-704. [PMID: 38769723 DOI: 10.1111/nph.19848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Potato (Solanum tuberosum) is the fourth largest food crop in the world. Late blight, caused by oomycete Phytophthora infestans, is the most devastating disease threatening potato production. Previous research has shown that StRFP1, a potato Arabidopsis Tóxicos en Levadura (ATL) family protein, positively regulates late blight resistance via its E3 ligase activity. However, the underlying mechanism is unknown. Here, we reveal that StRFP1 is associated with the plasma membrane (PM) and undergoes constitutive endocytic trafficking. Its PM localization is essential for inhibiting P. infestans colonization. Through in vivo and in vitro assays, we investigated that StRFP1 interacts with two sugar transporters StSWEET10c and StSWEET11 at the PM. Overexpression (OE) of StSWEET10c or StSWEET11 enhances P. infestans colonization. Both StSWEET10c and StSWEET11 exhibit sucrose transport ability in yeast, and OE of StSWEET10c leads to an increased sucrose content in the apoplastic fluid of potato leaves. StRFP1 ubiquitinates StSWEET10c and StSWEET11 to promote their degradation. We illustrate a novel mechanism by which a potato ATL protein enhances disease resistance by degrading susceptibility (S) factors, such as Sugars Will Eventually be Exported Transporters (SWEETs). This offers a potential strategy for improving disease resistance by utilizing host positive immune regulators to neutralize S factors.
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Affiliation(s)
- Xintong Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan, 430070, China
- Hubei Hongshan Laboratory (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, 430070, China
| | - Tianyu Lin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, 430070, China
| | - Xiaoshuang Zhou
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, 430070, China
| | - Wenjun Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, 430070, China
| | - Shengxuan Liu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, 430070, China
| | - Huishan Qiu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, 430070, China
| | - Paul R J Birch
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK
- Cell and Molecular Science, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Zhendong Tian
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University (HZAU), Wuhan, 430070, China
- Hubei Hongshan Laboratory (HZAU), Wuhan, 430070, China
- Key Laboratory of Potato Biology and Biotechnology (HZAU), Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
- Potato Engineering and Technology Research Center of Hubei Province (HZAU), Wuhan, 430070, China
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4
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Shi L, Lu J, Xia X, Liu X, Li H, Li X, Zhu J, Li X, Sun H, Yang X. Clinically used drug arsenic trioxide targets XIAP and overcomes apoptosis resistance in an organoid-based preclinical cancer model. Chem Sci 2024; 15:8311-8322. [PMID: 38846391 PMCID: PMC11151819 DOI: 10.1039/d4sc01294a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/29/2024] [Indexed: 06/09/2024] Open
Abstract
Drug resistance in tumor cells remains a persistent clinical challenge in the pursuit of effective anticancer therapy. XIAP, a member of the inhibitor of apoptosis protein (IAP) family, suppresses apoptosis via its Baculovirus IAP Repeat (BIR) domains and is responsible for drug resistance in various human cancers. Therefore, XIAP has attracted significant attention as a potential therapeutic target. However, no XIAP inhibitor is available for clinical use to date. In this study, we surprisingly observed that arsenic trioxide (ATO) induced a rapid depletion of XIAP in different cancer cells. Mechanistic studies revealed that arsenic attacked the cysteine residues of BIR domains and directly bound to XIAP, resulting in the release of zinc ions from this protein. Arsenic-XIAP binding suppressed the normal anti-apoptosis functions of BIR domains, and led to the ubiquitination-dependent degradation of XIAP. Importantly, we further demonstrate that arsenic sensitized a variety of apoptosis-resistant cancer cells, including patient-derived colon cancer organoids, to the chemotherapy drug using cisplatin as a showcase. These findings suggest that targeting XIAP with ATO offers an attractive strategy for combating apoptosis-resistant cancers in clinical practice.
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Affiliation(s)
- Liwa Shi
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
| | - Jing Lu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
| | - Xin Xia
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
| | - Xue Liu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
| | - Hongyan Li
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Hong Kong SAR China
| | - Xinghua Li
- Department of Infectious Diseases, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
| | - Jun Zhu
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
| | - Xiaofeng Li
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
| | - Hongzhe Sun
- Department of Chemistry, CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong Hong Kong SAR China
| | - Xinming Yang
- Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai China
- Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University Zhuhai 519000 China
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5
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Akizuki Y, Kaypee S, Ohtake F, Ikeda F. The emerging roles of non-canonical ubiquitination in proteostasis and beyond. J Cell Biol 2024; 223:e202311171. [PMID: 38517379 PMCID: PMC10959754 DOI: 10.1083/jcb.202311171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Ubiquitin regulates various cellular functions by posttranslationally modifying substrates with diverse ubiquitin codes. Recent discoveries of new ubiquitin chain topologies, types of bonds, and non-protein substrates have substantially expanded the complexity of the ubiquitin code. Here, we describe the ubiquitin system covering the basic principles and recent discoveries related to mechanisms, technologies, and biological importance.
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Affiliation(s)
- Yoshino Akizuki
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Stephanie Kaypee
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Fumiyo Ikeda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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6
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Fang Z, Li X, Yoshino Y, Suzuki M, Qi H, Murooka H, Katakai R, Shirota M, Mai Pham TA, Matsuzawa A, Otsuka K, Ishioka C, Mori T, Chiba N. Aurora A polyubiquitinates the BRCA1-interacting protein OLA1 to promote centrosome maturation. Cell Rep 2023; 42:112850. [PMID: 37481721 DOI: 10.1016/j.celrep.2023.112850] [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: 01/20/2023] [Revised: 06/03/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023] Open
Abstract
The BRCA1-interacting protein Obg-like ATPase 1 (OLA1) functions in centriole duplication. In this study, we show the role of the mitotic kinase Aurora A in the reduction of centrosomal OLA1. Aurora A binds to and polyubiquitinates OLA1, targeting it for proteasomal degradation. NIMA-related kinase 2 (NEK2) phosphorylates the T124 residue of OLA1, increases binding of OLA1 to Aurora A and OLA1 polyubiquitination by Aurora A, and reduces centrosomal OLA1 in G2 phase. The kinase activity of Aurora A suppresses OLA1 polyubiquitination. The decrease in centrosomal OLA1 caused by Aurora A-mediated polyubiquitination promotes the recruitment of pericentriolar material proteins in G2 phase. The E3 ligase activity of Aurora A is critical for centrosome amplification induced by its overexpression. The results suggest a dual function of Aurora A as an E3 ubiquitin ligase and a kinase in the regulation of centrosomal OLA1, which is essential for proper centrosome maturation in G2 phase.
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Affiliation(s)
- Zhenzhou Fang
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Department of Cancer Biology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Xingming Li
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Yuki Yoshino
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Department of Cancer Biology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Moe Suzuki
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Huicheng Qi
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Department of Cancer Biology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Hinari Murooka
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Riko Katakai
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Science, Tohoku University Graduate School of Medicine, 2-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Thi Anh Mai Pham
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Ayako Matsuzawa
- Department of Molecular Immunology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Kei Otsuka
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Takahiro Mori
- Department of Clinical Oncology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Departemt of Medical Oncology and Hematology, Okinawa Chubu Hospital, 281 Miyazato, Uruma, Okinawa 904-2293, Japan; Genome Medical Science Project, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku, Tokyo 162-8655, Japan
| | - Natsuko Chiba
- Department of Cancer Biology, Institute of Development, Aging and Cancer (IDAC), Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Department of Cancer Biology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan.
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7
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Mikami T, Majima S, Song H, Bode JW. Biocompatible Lysine Protecting Groups for the Chemoenzymatic Synthesis of K48/K63 Heterotypic and Branched Ubiquitin Chains. ACS CENTRAL SCIENCE 2023; 9:1633-1641. [PMID: 37637747 PMCID: PMC10450881 DOI: 10.1021/acscentsci.3c00389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 08/29/2023]
Abstract
The elucidation of emerging biological functions of heterotypic and branched ubiquitin (Ub) chains requires new strategies for their preparation with defined lengths and connectivity. While in vitro enzymatic assembly using expressed E1-activating and E2-conjugating enzymes can deliver homotypic chains, the synthesis of branched chains typically requires extensive mutations of lysines or other sequence modifications. The combination of K48- and K63-biased E2-conjugating enzymes and two new carbamate protecting groups-pyridoxal 5'-phosphate (PLP)-cleavable aminobutanamide carbamate (Abac group) and periodate-cleavable aminobutanol carbamate (Aboc group)-provides a strategy for the synthesis of heterotypic and branched Ub trimers, tetramers, and pentamers. The Abac- and Aboc-protected lysines are readily prepared and incorporated into synthetic ubiquitin monomers. As these masking groups contain a basic amine, they preserve the overall charge and properties of the Ub structure, facilitating folding and enzymatic conjugations. These protecting groups can be chemoselectively removed from folded Ub chains and monomers by buffered solutions of PLP or NaIO4. Through the incorporation of a cleavable C-terminal His-tag on the Ub acceptor, the entire process of chain building, iterative Abac deprotections, and global Aboc cleavage can be conducted on a resin support, obviating the need for handling and purification of the intermediate oligomers. Simple modulation of the Ub monomers affords various K48/K63 branched chains, including tetramers and pentamers not previously accessible by synthetic or biochemical methods.
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Affiliation(s)
- Toshiki Mikami
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Sohei Majima
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Haewon Song
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
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8
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Gregor JB, Xu D, French ME. Assembly and disassembly of branched ubiquitin chains. Front Mol Biosci 2023; 10:1197272. [PMID: 37325469 PMCID: PMC10267395 DOI: 10.3389/fmolb.2023.1197272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Abstract
Protein ubiquitylation is an essential post-translational modification that regulates nearly all aspects of eukaryotic cell biology. A diverse collection of ubiquitylation signals, including an extensive repertoire of polymeric ubiquitin chains, leads to a range of different functional outcomes for the target protein. Recent studies have shown that ubiquitin chains can be branched and that branched chains have a direct impact on the stability or the activity of the target proteins they are attached to. In this mini review, we discuss the mechanisms that control the assembly and disassembly of branched chains by the enzymes of the ubiquitylation and deubiquitylation machinery. Existing knowledge regarding the activities of chain branching ubiquitin ligases and the deubiquitylases responsible for cleaving branched chains is summarized. We also highlight new findings concerning the formation of branched chains in response to small molecules that induce the degradation of otherwise stable proteins and examine the selective debranching of heterotypic chains by the proteasome-bound deubiquitylase UCH37.
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Affiliation(s)
- Justin B. Gregor
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Dantong Xu
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
| | - Michael E. French
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, United States
- Department of Chemistry and Biochemistry, University of Tampa, Tampa, FL, United States
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Furuhata T, Devadasan Racheal PA, Murayama I, Toyoda U, Okamoto A. One-Pot, Photocontrolled Enzymatic Assembly of the Structure-Defined Heterotypic Polyubiquitin Chain. J Am Chem Soc 2023; 145:11690-11700. [PMID: 37200097 DOI: 10.1021/jacs.3c01912] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Heterotypic polyubiquitins are an emerging class of polyubiquitins that have attracted interest because of their potential diversity of structures and physiological functions. There is an increasing demand for structure-defined synthesis of heterotypic chains to investigate the topological factors underlying the intracellular signals that are characteristically mediated by the heterotypic chain. However, the applicability of chemical and enzymatic polyubiquitin synthesis developed to date has been limited by laborious rounds of ligation and purification or by a lack of modularity of the chain structure with respect to the length and the branch position. Here, we established a one-pot, photocontrolled synthesis of structurally defined heterotypic polyubiquitin chains. We designed ubiquitin derivatives with a photolabile protecting group at a lysine residue used for polymerization. Repetitive cycles of linkage-specific enzymatic elongation and photoinduced deprotection of the protected ubiquitin units enabled stepwise addition of ubiquitins with appropriate functionalities to control the length and branching positions. The positional control of branching was achieved without isolation of intermediates, allowing one-pot synthesis of K63 triubiqutin chains and a K63/K48 heterotypic tetraubiquitin chain with defined branching positions. The present study provides a chemical platform for the efficient construction of long polyubiquitin chains with defined branch structures that will facilitate the understanding of the essential relationships between functions and structures of the heterotypic chain that have hitherto been overlooked.
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Affiliation(s)
- Takafumi Furuhata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Phebee Angeline Devadasan Racheal
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Iori Murayama
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Usano Toyoda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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From seeds to trees: how E2 enzymes grow ubiquitin chains. Biochem Soc Trans 2023; 51:353-362. [PMID: 36645006 PMCID: PMC9987950 DOI: 10.1042/bst20220880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/17/2023]
Abstract
Modification of proteins by ubiquitin is a highly regulated process that plays a critical role in eukaryotes, from the construction of signalling platforms to the control of cell division. Aberrations in ubiquitin transfer are associated with many diseases, including cancer and neurodegenerative disorders. The ubiquitin machinery generates a rich code on substrate proteins, spanning from single ubiquitin modifications to polyubiquitin chains with diverse linkage types. Central to this process are the E2 enzymes, which often determine the exact nature of the ubiquitin code. The focus of this mini-review is on the molecular details of how E2 enzymes can initiate and grow ubiquitin chains. In particular, recent developments and biochemical breakthroughs that help explain how the degradative E2 enzymes, Ube2s, Ube2k, and Ube2r, generate complex ubiquitin chains with exquisite specificity will be discussed.
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