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Güngör E, Savary J, Adema K, Dijkhuizen LW, Keilwagen J, Himmelbach A, Mascher M, Koppers N, Bräutigam A, Van Hove C, Riant O, Nierzwicki-Bauer S, Schluepmann H. The crane fly glycosylated triketide δ-lactone cornicinine elicits akinete differentiation of the cyanobiont in aquatic Azolla fern symbioses. PLANT, CELL & ENVIRONMENT 2024; 47:2675-2692. [PMID: 38600764 DOI: 10.1111/pce.14907] [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: 12/14/2023] [Revised: 03/02/2024] [Accepted: 03/22/2024] [Indexed: 04/12/2024]
Abstract
The restriction of plant-symbiont dinitrogen fixation by an insect semiochemical had not been previously described. Here we report on a glycosylated triketide δ-lactone from Nephrotoma cornicina crane flies, cornicinine, that causes chlorosis in the floating-fern symbioses from the genus Azolla. Only the glycosylated trans-A form of chemically synthesized cornicinine was active: 500 nM cornicinine in the growth medium turned all cyanobacterial filaments from Nostoc azollae inside the host leaf-cavities into akinetes typically secreting CTB-bacteriocins. Cornicinine further inhibited akinete germination in Azolla sporelings, precluding re-establishment of the symbiosis during sexual reproduction. It did not impact development of the plant Arabidopsis thaliana or several free-living cyanobacteria from the genera Anabaena or Nostoc but affected the fern host without cyanobiont. Fern-host mRNA sequencing from isolated leaf cavities confirmed high NH4-assimilation and proanthocyanidin biosynthesis in this trichome-rich tissue. After cornicinine treatment, it revealed activation of Cullin-RING ubiquitin-ligase-pathways, known to mediate metabolite signaling and plant elicitation consistent with the chlorosis phenotype, and increased JA-oxidase, sulfate transport and exosome formation. The work begins to uncover molecular mechanisms of cyanobiont differentiation in a seed-free plant symbiosis important for wetland ecology or circular crop-production today, that once caused massive CO2 draw-down during the Eocene geological past.
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Affiliation(s)
- Erbil Güngör
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Jérôme Savary
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Kelvin Adema
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | | | | | - Axel Himmelbach
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Martin Mascher
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Nils Koppers
- Computational Biology, Center for Biotechnology and Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Andrea Bräutigam
- Computational Biology, Center for Biotechnology and Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Charles Van Hove
- Emeritus Professor from the Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Olivier Riant
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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2
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Wang Y, Deng X, Xie J, Lu T, Qian R, Guo Z, Zeng X, Liao J, Ding Z, Zhou M, Niu X. The COP9 signalosome stabilized MALT1 promotes Non-Small Cell Lung Cancer progression through activation of NF-κB pathway. Cell Biol Toxicol 2024; 40:45. [PMID: 38864940 DOI: 10.1007/s10565-024-09888-z] [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: 09/30/2023] [Accepted: 06/03/2024] [Indexed: 06/13/2024]
Abstract
MALT1 has been implicated as an upstream regulator of NF-κB signaling in immune cells and tumors. This study determined the regulatory mechanisms and biological functions of MALT1 in non-small cell lung cancer (NSCLC). In cell culture and orthotopic xenograft models, MALT1 suppression via gene expression interference or protein activity inhibition significantly impaired malignant phenotypes and enhanced radiation sensitivity of NSCLC cells. CSN5, the core subunit of COP9 signalosome, was firstly verified to stabilize MALT1 via disturbing the interaction with E3 ligase FBXO3. Loss of FBXO3 in NSCLC cells reduced MALT1 ubiquitination and promoted its accumulation, which was reversed by CSN5 interference. An association between CSN5/FBXO3/MALT1 regulatory axis and poor prognosis in NSCLC patients was identified. Our findings revealed the detail mechanism of continuous MALT1 activation in NF-κB signaling, highlighting its significance as predictor and potential therapeutic target in NSCLC.
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Affiliation(s)
- Yinghui Wang
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong Province, China
| | - Xuyi Deng
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jing Xie
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Tianhao Lu
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Rui Qian
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Zhi Guo
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Xin Zeng
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Jing Liao
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Zhenhua Ding
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Meijuan Zhou
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China.
| | - Xinli Niu
- Department of Radiation Medicine, Guangdong Provincial Key Laboratory of Tropical Disease Research, NMPA Key Laboratory for Safety Evaluation of Cosmetics, School of Public Health, Southern Medical University, Guangzhou, Guangdong Province, China.
- Jiangmen Central Hospital, Affiliated Jiangmen Hospital of Sun Yat-Sen University, Jiangmen, Guangdong Province, China.
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3
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Sinha NK, McKenney C, Yeow ZY, Li JJ, Nam KH, Yaron-Barir TM, Johnson JL, Huntsman EM, Cantley LC, Ordureau A, Regot S, Green R. The ribotoxic stress response drives UV-mediated cell death. Cell 2024:S0092-8674(24)00527-0. [PMID: 38843833 DOI: 10.1016/j.cell.2024.05.018] [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: 08/03/2023] [Revised: 03/03/2024] [Accepted: 05/09/2024] [Indexed: 06/13/2024]
Abstract
While ultraviolet (UV) radiation damages DNA, eliciting the DNA damage response (DDR), it also damages RNA, triggering transcriptome-wide ribosomal collisions and eliciting a ribotoxic stress response (RSR). However, the relative contributions, timing, and regulation of these pathways in determining cell fate is unclear. Here we use time-resolved phosphoproteomic, chemical-genetic, single-cell imaging, and biochemical approaches to create a chronological atlas of signaling events activated in cells responding to UV damage. We discover that UV-induced apoptosis is mediated by the RSR kinase ZAK and not through the DDR. We identify two negative-feedback modules that regulate ZAK-mediated apoptosis: (1) GCN2 activation limits ribosomal collisions and attenuates ZAK-mediated RSR and (2) ZAK activity leads to phosphodegron autophosphorylation and its subsequent degradation. These events tune ZAK's activity to collision levels to establish regimes of homeostasis, tolerance, and death, revealing its key role as the cellular sentinel for nucleic acid damage.
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Affiliation(s)
- Niladri K Sinha
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Connor McKenney
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhong Y Yeow
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey J Li
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tomer M Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Sergi Regot
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Rachel Green
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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4
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Gottemukkala KV, Chrustowicz J, Sherpa D, Sepic S, Vu DT, Karayel Ö, Papadopoulou EC, Gross A, Schorpp K, von Gronau S, Hadian K, Murray PJ, Mann M, Schulman BA, Alpi AF. Non-canonical substrate recognition by the human WDR26-CTLH E3 ligase regulates prodrug metabolism. Mol Cell 2024; 84:1948-1963.e11. [PMID: 38759627 DOI: 10.1016/j.molcel.2024.04.014] [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: 09/13/2023] [Revised: 02/05/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024]
Abstract
The yeast glucose-induced degradation-deficient (GID) E3 ubiquitin ligase forms a suite of complexes with interchangeable receptors that selectively recruit N-terminal degron motifs of metabolic enzyme substrates. The orthologous higher eukaryotic C-terminal to LisH (CTLH) E3 complex has been proposed to also recognize substrates through an alternative subunit, WDR26, which promotes the formation of supramolecular CTLH E3 assemblies. Here, we discover that human WDR26 binds the metabolic enzyme nicotinamide/nicotinic-acid-mononucleotide-adenylyltransferase 1 (NMNAT1) and mediates its CTLH E3-dependent ubiquitylation independently of canonical GID/CTLH E3-family substrate receptors. The CTLH subunit YPEL5 inhibits NMNAT1 ubiquitylation and cellular turnover by WDR26-CTLH E3, thereby affecting NMNAT1-mediated metabolic activation and cytotoxicity of the prodrug tiazofurin. Cryoelectron microscopy (cryo-EM) structures of NMNAT1- and YPEL5-bound WDR26-CTLH E3 complexes reveal an internal basic degron motif of NMNAT1 essential for targeting by WDR26-CTLH E3 and degron mimicry by YPEL5's N terminus antagonizing substrate binding. Thus, our data provide a mechanistic understanding of how YPEL5-WDR26-CTLH E3 acts as a modulator of NMNAT1-dependent metabolism.
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Affiliation(s)
- Karthik V Gottemukkala
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; TUM School of Natural Sciences, Technical University, Munich 85748, Germany
| | - Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Sara Sepic
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; TUM School of Natural Sciences, Technical University, Munich 85748, Germany
| | - Duc Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry,Martinsried 82152, Germany
| | - Özge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry,Martinsried 82152, Germany
| | - Eleftheria C Papadopoulou
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; TUM School of Natural Sciences, Technical University, Munich 85748, Germany
| | - Annette Gross
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Immunoregulation, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Kenji Schorpp
- Research Unit-Signaling and Translation, Cell Signaling and Chemical Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Kamyar Hadian
- Research Unit-Signaling and Translation, Cell Signaling and Chemical Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
| | - Peter J Murray
- Immunoregulation, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry,Martinsried 82152, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; TUM School of Natural Sciences, Technical University, Munich 85748, Germany
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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5
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Xian W, Fu J, Zhang Q, Li C, Zhao YB, Tang Z, Yuan Y, Wang Y, Zhou Y, Brzoic PS, Zheng N, Ouyang S, Luo ZQ, Liu X. The Shigella kinase effector OspG modulates host ubiquitin signaling to escape septin-cage entrapment. Nat Commun 2024; 15:3890. [PMID: 38719850 PMCID: PMC11078946 DOI: 10.1038/s41467-024-48205-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
Shigella flexneri is a Gram-negative bacterium causing severe bloody dysentery. Its pathogenesis is largely dictated by a plasmid-encoded type III secretion system (T3SS) and its associated effectors. Among these, the effector OspG has been shown to bind to the ubiquitin conjugation machinery (E2~Ub) to activate its kinase activity. However, the cellular targets of OspG remain elusive despite years of extensive efforts. Here we show by unbiased phosphoproteomics that a major target of OspG is CAND1, a regulatory protein controlling the assembly of cullin-RING ubiquitin ligases (CRLs). CAND1 phosphorylation weakens its interaction with cullins, which is expected to impact a large panel of CRL E3s. Indeed, global ubiquitome profiling reveals marked changes in the ubiquitination landscape when OspG is introduced. Notably, OspG promotes ubiquitination of a class of cytoskeletal proteins called septins, thereby inhibiting formation of cage-like structures encircling cytosolic bacteria. Overall, we demonstrate that pathogens have evolved an elaborate strategy to modulate host ubiquitin signaling to evade septin-cage entrapment.
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Affiliation(s)
- Wei Xian
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Jiaqi Fu
- Department of Respiratory Medicine, Center for Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, The First Hospital of Jilin University, 130021, Changchun, China
| | - Qinxin Zhang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Chuang Li
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Yan-Bo Zhao
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhiheng Tang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Yi Yuan
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Ying Wang
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Yan Zhou
- Institute of Microbiology, College of Life Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Peter S Brzoic
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Songying Ouyang
- Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, the Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Zhao-Qing Luo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, NHC Key Laboratory of Medical Immunology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China.
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6
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Wang W, Liang L, Dai Z, Zuo P, Yu S, Lu Y, Ding D, Chen H, Shan H, Jin Y, Mao Y, Yin Y. A conserved N-terminal motif of CUL3 contributes to assembly and E3 ligase activity of CRL3 KLHL22. Nat Commun 2024; 15:3789. [PMID: 38710693 PMCID: PMC11074293 DOI: 10.1038/s41467-024-48045-2] [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: 10/12/2023] [Accepted: 04/19/2024] [Indexed: 05/08/2024] Open
Abstract
The CUL3-RING E3 ubiquitin ligases (CRL3s) play an essential role in response to extracellular nutrition and stress stimuli. The ubiquitin ligase function of CRL3s is activated through dimerization. However, how and why such a dimeric assembly is required for its ligase activity remains elusive. Here, we report the cryo-EM structure of the dimeric CRL3KLHL22 complex and reveal a conserved N-terminal motif in CUL3 that contributes to the dimerization assembly and the E3 ligase activity of CRL3KLHL22. We show that deletion of the CUL3 N-terminal motif impairs dimeric assembly and the E3 ligase activity of both CRL3KLHL22 and several other CRL3s. In addition, we found that the dynamics of dimeric assembly of CRL3KLHL22 generates a variable ubiquitination zone, potentially facilitating substrate recognition and ubiquitination. These findings demonstrate that a CUL3 N-terminal motif participates in the assembly process and provide insights into the assembly and activation of CRL3s.
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Affiliation(s)
- Weize Wang
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Ling Liang
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China.
| | - Zonglin Dai
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Shang Yu
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Yishuo Lu
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Dian Ding
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Hongyi Chen
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Hui Shan
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Yan Jin
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China
| | - Youdong Mao
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
- State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Center for Quantitative Biology, National Biomedical Imaging Center, School of Physics, Peking University, 100871, Beijing, China
| | - Yuxin Yin
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
- Institute of Systems Biomedicine, Department of Pathology, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, 100191, Beijing, China.
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7
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Chen Y, Xue H, Jin J. Applications of protein ubiquitylation and deubiquitylation in drug discovery. J Biol Chem 2024; 300:107264. [PMID: 38582446 PMCID: PMC11087986 DOI: 10.1016/j.jbc.2024.107264] [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: 07/09/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024] Open
Abstract
The ubiquitin (Ub)-proteasome system (UPS) is the major machinery mediating specific protein turnover in eukaryotic cells. By ubiquitylating unwanted, damaged, or harmful proteins and driving their degradation, UPS is involved in many important cellular processes. Several new UPS-based technologies, including molecular glue degraders and PROTACs (proteolysis-targeting chimeras) to promote protein degradation, and DUBTACs (deubiquitinase-targeting chimeras) to increase protein stability, have been developed. By specifically inducing the interactions between different Ub ligases and targeted proteins that are not otherwise related, molecular glue degraders and PROTACs degrade targeted proteins via the UPS; in contrast, by inducing the proximity of targeted proteins to deubiquitinases, DUBTACs are created to clear degradable poly-Ub chains to stabilize targeted proteins. In this review, we summarize the recent research progress in molecular glue degraders, PROTACs, and DUBTACs and their applications. We discuss immunomodulatory drugs, sulfonamides, cyclin-dependent kinase-targeting molecular glue degraders, and new development of PROTACs. We also introduce the principle of DUBTAC and its applications. Finally, we propose a few future directions of these three technologies related to targeted protein homeostasis.
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Affiliation(s)
- Yilin Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Haoan Xue
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Jianping Jin
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China; Cancer Center, Zhejiang University, Hangzhou, China.
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8
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Chen X, Raiff A, Li S, Guo Q, Zhang J, Zhou H, Timms RT, Yao X, Elledge SJ, Koren I, Zhang K, Xu C. Mechanism of Ψ-Pro/C-degron recognition by the CRL2 FEM1B ubiquitin ligase. Nat Commun 2024; 15:3558. [PMID: 38670995 PMCID: PMC11053023 DOI: 10.1038/s41467-024-47890-5] [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: 10/13/2023] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The E3 ligase-degron interaction determines the specificity of the ubiquitin‒proteasome system. We recently discovered that FEM1B, a substrate receptor of Cullin 2-RING ligase (CRL2), recognizes C-degrons containing a C-terminal proline. By solving several cryo-EM structures of CRL2FEM1B bound to different C-degrons, we elucidate the dimeric assembly of the complex. Furthermore, we reveal distinct dimerization states of unmodified and neddylated CRL2FEM1B to uncover the NEDD8-mediated activation mechanism of CRL2FEM1B. Our research also indicates that, FEM1B utilizes a bipartite mechanism to recognize both the C-terminal proline and an upstream aromatic residue within the substrate. These structural findings, complemented by in vitro ubiquitination and in vivo cell-based assays, demonstrate that CRL2FEM1B-mediated polyubiquitination and subsequent protein turnover depend on both FEM1B-degron interactions and the dimerization state of the E3 ligase complex. Overall, this study deepens our molecular understanding of how Cullin-RING E3 ligase substrate selection mediates protein turnover.
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Affiliation(s)
- Xinyan Chen
- MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
| | - Anat Raiff
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Shanshan Li
- MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
| | - Qiong Guo
- MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
| | - Jiahai Zhang
- MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
| | - Hualin Zhou
- MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
| | - Richard T Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Xuebiao Yao
- MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China.
| | - Chao Xu
- MOE Key Laboratory for Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, PR China.
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9
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Offensperger F, Tin G, Duran-Frigola M, Hahn E, Dobner S, Ende CWA, Strohbach JW, Rukavina A, Brennsteiner V, Ogilvie K, Marella N, Kladnik K, Ciuffa R, Majmudar JD, Field SD, Bensimon A, Ferrari L, Ferrada E, Ng A, Zhang Z, Degliesposti G, Boeszoermenyi A, Martens S, Stanton R, Müller AC, Hannich JT, Hepworth D, Superti-Furga G, Kubicek S, Schenone M, Winter GE. Large-scale chemoproteomics expedites ligand discovery and predicts ligand behavior in cells. Science 2024; 384:eadk5864. [PMID: 38662832 DOI: 10.1126/science.adk5864] [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: 08/31/2023] [Accepted: 03/22/2024] [Indexed: 05/04/2024]
Abstract
Chemical modulation of proteins enables a mechanistic understanding of biology and represents the foundation of most therapeutics. However, despite decades of research, 80% of the human proteome lacks functional ligands. Chemical proteomics has advanced fragment-based ligand discovery toward cellular systems, but throughput limitations have stymied the scalable identification of fragment-protein interactions. We report proteome-wide maps of protein-binding propensity for 407 structurally diverse small-molecule fragments. We verified that identified interactions can be advanced to active chemical probes of E3 ubiquitin ligases, transporters, and kinases. Integrating machine learning binary classifiers further enabled interpretable predictions of fragment behavior in cells. The resulting resource of fragment-protein interactions and predictive models will help to elucidate principles of molecular recognition and expedite ligand discovery efforts for hitherto undrugged proteins.
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Affiliation(s)
- Fabian Offensperger
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Miquel Duran-Frigola
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Ersilia Open Source Initiative, Cambridge CB1 3DE, UK
| | - Elisa Hahn
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Andrea Rukavina
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Vincenth Brennsteiner
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Kevin Ogilvie
- Medicine Design, Pfizer Worldwide Research and Development, Groton, CT 06340, USA
| | - Nara Marella
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Katharina Kladnik
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Rodolfo Ciuffa
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | | | - Ariel Bensimon
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Luca Ferrari
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Evandro Ferrada
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Amanda Ng
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Zhechun Zhang
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - Gianluca Degliesposti
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna Biocenter 5, 1030 Vienna, Austria
- University of Vienna, Max Perutz Labs, Vienna Biocenter 5, 1030 Vienna, Austria
| | - Robert Stanton
- Molecular Informatics, Machine Learning and Computational Sciences, Early Clinical Development, Pfizer, Cambridge, MA 02139, USA
| | - André C Müller
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Georg E Winter
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
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10
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Nguyen DM, Rath DH, Devost D, Pétrin D, Rizk R, Ji AX, Narayanan N, Yong D, Zhai A, Kuntz DA, Mian MUQ, Pomroy NC, Keszei AFA, Benlekbir S, Mazhab-Jafari MT, Rubinstein JL, Hébert TE, Privé GG. Structure and dynamics of a pentameric KCTD5/CUL3/Gβγ E3 ubiquitin ligase complex. Proc Natl Acad Sci U S A 2024; 121:e2315018121. [PMID: 38625940 PMCID: PMC11047111 DOI: 10.1073/pnas.2315018121] [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: 09/21/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
Heterotrimeric G proteins can be regulated by posttranslational modifications, including ubiquitylation. KCTD5, a pentameric substrate receptor protein consisting of an N-terminal BTB domain and a C-terminal domain, engages CUL3 to form the central scaffold of a cullin-RING E3 ligase complex (CRL3KCTD5) that ubiquitylates Gβγ and reduces Gβγ protein levels in cells. The cryo-EM structure of a 5:5:5 KCTD5/CUL3NTD/Gβ1γ2 assembly reveals a highly dynamic complex with rotations of over 60° between the KCTD5BTB/CUL3NTD and KCTD5CTD/Gβγ moieties of the structure. CRL3KCTD5 engages the E3 ligase ARIH1 to ubiquitylate Gβγ in an E3-E3 superassembly, and extension of the structure to include full-length CUL3 with RBX1 and an ARIH1~ubiquitin conjugate reveals that some conformational states position the ARIH1~ubiquitin thioester bond to within 10 Å of lysine-23 of Gβ and likely represent priming complexes. Most previously described CRL/substrate structures have consisted of monovalent complexes and have involved flexible peptide substrates. The structure of the KCTD5/CUL3NTD/Gβγ complex shows that the oligomerization of a substrate receptor can generate a polyvalent E3 ligase complex and that the internal dynamics of the substrate receptor can position a structured target for ubiquitylation in a CRL3 complex.
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Affiliation(s)
- Duc Minh Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Deanna H. Rath
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
| | - Dominic Devost
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QCH3G 1Y6, Canada
| | - Darlaine Pétrin
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QCH3G 1Y6, Canada
| | - Robert Rizk
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QCH3G 1Y6, Canada
| | - Alan X. Ji
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
| | - Naveen Narayanan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
| | - Darren Yong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
| | - Andrew Zhai
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
| | - Douglas A. Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
| | - Maha U. Q. Mian
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
| | - Neil C. Pomroy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
| | | | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
| | - Mohammad T. Mazhab-Jafari
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ONM5G 2M9, Canada
| | - John L. Rubinstein
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ONM5G 0A4, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ONM5G 2M9, Canada
| | - Terence E. Hébert
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QCH3G 1Y6, Canada
| | - Gilbert G. Privé
- Princess Margaret Cancer Centre, University Health Network, Toronto, ONM5G 1L7, Canada
- Department of Biochemistry, University of Toronto, Toronto, ONM5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ONM5G 2M9, Canada
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11
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 PMCID: PMC11088880 DOI: 10.1042/bcj20230284] [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: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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12
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Li J, Purser N, Liwocha J, Scott DC, Byers HA, Steigenberger B, Hill S, Tripathi-Giesgen I, Hinkle T, Hansen FM, Prabu JR, Radhakrishnan SK, Kirkpatrick DS, Reichermeier KM, Schulman BA, Kleiger G. Cullin-RING ligases employ geometrically optimized catalytic partners for substrate targeting. Mol Cell 2024; 84:1304-1320.e16. [PMID: 38382526 PMCID: PMC10997478 DOI: 10.1016/j.molcel.2024.01.022] [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: 09/13/2023] [Revised: 12/07/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Cullin-RING ligases (CRLs) ubiquitylate specific substrates selected from other cellular proteins. Substrate discrimination and ubiquitin transferase activity were thought to be strictly separated. Substrates are recognized by substrate receptors, such as Fbox or BCbox proteins. Meanwhile, CRLs employ assorted ubiquitin-carrying enzymes (UCEs, which are a collection of E2 and ARIH-family E3s) specialized for either initial substrate ubiquitylation (priming) or forging poly-ubiquitin chains. We discovered specific human CRL-UCE pairings governing substrate priming. The results reveal pairing of CUL2-based CRLs and UBE2R-family UCEs in cells, essential for efficient PROTAC-induced neo-substrate degradation. Despite UBE2R2's intrinsic programming to catalyze poly-ubiquitylation, CUL2 employs this UCE for geometrically precise PROTAC-dependent ubiquitylation of a neo-substrate and for rapid priming of substrates recruited to diverse receptors. Cryo-EM structures illuminate how CUL2-based CRLs engage UBE2R2 to activate substrate ubiquitylation. Thus, pairing with a specific UCE overcomes E2 catalytic limitations to drive substrate ubiquitylation and targeted protein degradation.
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Affiliation(s)
- Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Joanna Liwocha
- 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
| | - Holly A Byers
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Spencer Hill
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Trent Hinkle
- Genentech, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Fynn M Hansen
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | | | | | | | - 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.
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.
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13
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Sun X, LaVoie M, Lefebvre PA, Gallaher SD, Glaesener AG, Strenkert D, Mehta R, Merchant SS, Silflow CD. Mutation of negative regulatory gene CEHC1 encoding an FBXO3 protein results in normoxic expression of HYDA genes in Chlamydomonas reinhardtii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586359. [PMID: 38586028 PMCID: PMC10996464 DOI: 10.1101/2024.03.22.586359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Oxygen is known to prevent hydrogen production in Chlamydomonas, both by inhibiting the hydrogenase enzyme and by preventing the accumulation of HYDA-encoding transcripts. We developed a screen for mutants showing constitutive accumulation of HYDA1 transcripts in the presence of oxygen. A reporter gene required for ciliary motility, placed under the control of the HYDA1 promoter, conferred motility only in hypoxic conditions. By selecting for mutants able to swim even in the presence of oxygen we obtained strains that express the reporter gene constitutively. One mutant identified a gene encoding an F-box only protein 3 (FBXO3), known to participate in ubiquitylation and proteasomal degradation pathways in other eukaryotes. Transcriptome profiles revealed that the mutation, termed cehc1-1 , leads to constitutive expression of HYDA1 and other genes regulated by hypoxia, and of many genes known to be targets of CRR1, a transcription factor in the nutritional copper signaling pathway. CRR1 was required for the constitutive expression of the HYDA1 reporter gene in cehc1-1 mutants. The CRR1 protein, which is normally degraded in Cu-supplemented cells, was stabilized in cehc1-1 cells, supporting the conclusion that CEHC1 acts to facilitate the degradation of CRR1. Our results reveal a novel negative regulator in the CRR1 pathway and possibly other pathways leading to complex metabolic changes associated with response to hypoxia.
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14
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Rong Z, Zheng K, Chen J, Jin X. The cross talk of ubiquitination and chemotherapy tolerance in colorectal cancer. J Cancer Res Clin Oncol 2024; 150:154. [PMID: 38521878 PMCID: PMC10960765 DOI: 10.1007/s00432-024-05659-9] [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: 09/21/2023] [Accepted: 02/20/2024] [Indexed: 03/25/2024]
Abstract
Ubiquitination, a highly adaptable post-translational modification, plays a pivotal role in maintaining cellular protein homeostasis, encompassing cancer chemoresistance-associated proteins. Recent findings have indicated a potential correlation between perturbations in the ubiquitination process and the emergence of drug resistance in CRC cancer. Consequently, numerous studies have spurred the advancement of compounds specifically designed to target ubiquitinates, offering promising prospects for cancer therapy. In this review, we highlight the role of ubiquitination enzymes associated with chemoresistance to chemotherapy via the Wnt/β-catenin signaling pathway, epithelial-mesenchymal transition (EMT), and cell cycle perturbation. In addition, we summarize the application and role of small compounds that target ubiquitination enzymes for CRC treatment, along with the significance of targeting ubiquitination enzymes as potential cancer therapies.
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Affiliation(s)
- Ze Rong
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
| | - Kaifeng Zheng
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Jun Chen
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
| | - Xiaofeng Jin
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
- Department of Biochemistry and Molecular Biology, Health Science Center, Ningbo, 315211, China.
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15
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Huang HT, Lumpkin RJ, Tsai RW, Su S, Zhao X, Xiong Y, Chen J, Mageed N, Donovan KA, Fischer ES, Sellers WR. Ubiquitin-specific proximity labeling for the identification of E3 ligase substrates. Nat Chem Biol 2024:10.1038/s41589-024-01590-9. [PMID: 38514884 DOI: 10.1038/s41589-024-01590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Protein ubiquitylation controls diverse processes within eukaryotic cells, including protein degradation, and is often dysregulated in disease. Moreover, small-molecule degraders that redirect ubiquitylation activities toward disease targets are an emerging and promising therapeutic class. Over 600 E3 ubiquitin ligases are expressed in humans, but their substrates remain largely elusive, necessitating the development of new methods for their discovery. Here we report the development of E3-substrate tagging by ubiquitin biotinylation (E-STUB), a ubiquitin-specific proximity labeling method that biotinylates ubiquitylated substrates in proximity to an E3 ligase of interest. E-STUB accurately identifies the direct ubiquitylated targets of protein degraders, including collateral targets and ubiquitylation events that do not lead to substrate degradation. It also detects known substrates of E3 ligase CRBN and VHL with high specificity. With the ability to elucidate proximal ubiquitylation events, E-STUB may facilitate the development of proximity-inducing therapeutics and act as a generalizable method for E3-substrate mapping.
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Affiliation(s)
- Hai-Tsang Huang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan W Tsai
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Shuyao Su
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xu Zhao
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yuan Xiong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - James Chen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Nada Mageed
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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16
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Zubkova E, Kalinin A, Bolotskaya A, Beloglazova I, Menshikov M. Autophagy-Dependent Secretion: Crosstalk between Autophagy and Exosome Biogenesis. Curr Issues Mol Biol 2024; 46:2209-2235. [PMID: 38534758 DOI: 10.3390/cimb46030142] [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: 11/30/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 03/28/2024] Open
Abstract
The cellular secretome is pivotal in mediating intercellular communication and coordinating responses to stressors. Exosomes, initially recognized for their role in waste disposal, have now emerged as key intercellular messengers with significant therapeutic and diagnostic potential. Similarly, autophagy has transcended its traditional role as a waste removal mechanism, emerging as a regulator of intracellular communication pathways and a contributor to a unique autophagy-dependent secretome. Secretory authophagy, initiated by various stress stimuli, prompts the selective release of proteins implicated in inflammation, including leaderless proteins that bypass the conventional endoplasmic reticulum-Golgi secretory pathway. This reflects the significant impact of stress-induced autophagy on cellular secretion profiles, including the modulation of exosome release. The convergence of exosome biogenesis and autophagy is exemplified by the formation of amphisomes, vesicles that integrate autophagic and endosomal pathways, indicating their synergistic interplay. Regulatory proteins common to both pathways, particularly mTORC1, emerge as potential therapeutic targets to alter cellular secretion profiles involved in various diseases. This review explores the dynamic interplay between autophagy and exosome formation, highlighting the potential to influence the secretome composition. While the modulation of exosome secretion and cytokine preconditioning is well-established in regenerative medicine, the strategic manipulation of autophagy is still underexplored, presenting a promising but uncharted therapeutic landscape.
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Affiliation(s)
- Ekaterina Zubkova
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
| | - Alexander Kalinin
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Anastasya Bolotskaya
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
- Institute of Clinical Medicine, Sechenov University, 119435 Moscow, Russia
| | - Irina Beloglazova
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
| | - Mikhail Menshikov
- National Medical Research Centre of Cardiology Named after Academician E.I. Chazov, 121552 Moscow, Russia
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17
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Shim T, Kim JY, Kim W, Lee YI, Cho B, Moon C. Cullin-RING E3 ubiquitin ligase 4 regulates neurite morphogenesis during neurodevelopment. iScience 2024; 27:108933. [PMID: 38318354 PMCID: PMC10839267 DOI: 10.1016/j.isci.2024.108933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Neuritogenesis is crucial for establishing proper neuronal connections during brain development; its failure causes neurodevelopmental defects. Cullin-RING E3 ubiquitin ligase complexes participate in various neurodevelopmental processes by regulating protein stability. We demonstrated the regulatory function of Cullin-RING E3 ubiquitin ligase 4 (CRL4) in neurite morphogenesis during early neurodevelopment. Cul4a and Cul4b, the core scaffold proteins of CRL4, exhibit high expression and activation within the cytosol of developing neurons, regulated by neuronal stimulation through N-methyl D-aspartate (NMDA) receptor signaling. CRL4 also interacts with cytoskeleton-regulating proteins involved in neurite morphogenesis. Notably, genetic depletion and inhibition of cytosolic CRL4 enhance neurite extension and branching in developing neurons. Conversely, Cul4a overexpression suppresses basal and NMDA-enhanced neuritogenesis. Furthermore, CRL4 and its substrate adaptor regulate the polyubiquitination and proteasomal degradation of doublecortin protein. Collectively, our findings suggest that CRL4 ensures proper neurite morphogenesis in developing neurons by regulating cytoskeleton-regulating proteins.
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Affiliation(s)
- Tammy Shim
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
| | - Jae Yeon Kim
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - WonCheol Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
| | - Yun-Il Lee
- Division of Biotechnology, DGIST, Daegu 42988, Republic of Korea
| | - Bongki Cho
- Division of Biotechnology, DGIST, Daegu 42988, Republic of Korea
| | - Cheil Moon
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
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18
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Zhang L, Hao P, Chen X, Lv S, Gao W, Li C, Li Z, Zhang W. CRL4B E3 ligase recruited by PRPF19 inhibits SARS-CoV-2 infection by targeting ORF6 for ubiquitin-dependent degradation. mBio 2024; 15:e0307123. [PMID: 38265236 PMCID: PMC10865787 DOI: 10.1128/mbio.03071-23] [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: 11/15/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
The accessory protein ORF6 of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a key interferon (IFN) antagonist that strongly suppresses the production of primary IFN as well as the expression of IFN-stimulated genes. However, how host cells respond to ORF6 remains largely unknown. Our research of ORF6-binding proteins by pulldown revealed that E3 ligase components such as Cullin 4B (CUL4B), DDB1, and RBX1 are potential ORF6-interacting proteins. Further study found that the substrate recognition receptor PRPF19 interacts with CUL4B, DDB1, and RBX1 to form a CRL4B-based E3 ligase, which catalyzes ORF6 ubiquitination and subsequent degradation. Overexpression of PRPF19 promotes ORF6 degradation, releasing ORF6-mediated IFN inhibition, which inhibits SARS-CoV-2 replication. Moreover, we found that activation of CUL4B by the neddylation inducer etoposide alleviates lung lesions in a SARS-CoV-2 mouse infection model. Therefore, targeting ORF6 for degradation may be an effective therapeutic strategy against SARS-CoV-2 infection.IMPORTANCEThe cellular biological function of the ubiquitin-proteasome pathway as an important modulator for the regulation of many fundamental cellular processes has been greatly appreciated. The critical role of the ubiquitin-proteasome pathway in viral pathogenesis has become increasingly apparent. It is a powerful tool that host cells use to defend against viral infection. Some cellular proteins can function as restriction factors to limit viral infection by ubiquitin-dependent degradation. In this research, we identificated of CUL4B-DDB1-PRPF19 E3 Ubiquitin Ligase Complex can mediate proteasomal degradation of ORF6, leading to inhibition of viral replication. Moreover, the CUL4B activator etoposide alleviates disease development in a mouse infection model, suggesting that this agent or its derivatives may be used to treat infections caused by SARS-CoV-2. We believe that these results will be extremely useful for the scientific and clinic communities in their search for cues and preventive measures to combat the COVID-19 pandemic.
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Affiliation(s)
- Linran Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Pengfei Hao
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Xiang Chen
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Shuai Lv
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenying Gao
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Chang Li
- Research Unit of Key Technologies for Prevention and Control of Virus Zoonoses, Chinese Academy of Medical Sciences, Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, Jilin, China
| | - Zhaolong Li
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Wenyan Zhang
- Institute of Virology and AIDS Research, The First Hospital of Jilin University, Changchun, Jilin, China
- Department of Infectious Diseases, Infectious Diseases and Pathogen Biology Center, Key Laboratory of Organ Regeneration and Transplantation of The Ministry of Education, The First Hospital of Jilin University, Changchun, China
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19
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Hickey CM, Digianantonio KM, Zimmermann K, Harbin A, Quinn C, Patel A, Gareiss P, Chapman A, Tiberi B, Dobrodziej J, Corradi J, Cacace AM, Langley DR, Békés M. Co-opting the E3 ligase KLHDC2 for targeted protein degradation by small molecules. Nat Struct Mol Biol 2024; 31:311-322. [PMID: 38177675 DOI: 10.1038/s41594-023-01146-w] [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: 04/14/2023] [Accepted: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Targeted protein degradation (TPD) by PROTAC (proteolysis-targeting chimera) and molecular glue small molecules is an emerging therapeutic strategy. To expand the roster of E3 ligases that can be utilized for TPD, we describe the discovery and biochemical characterization of small-molecule ligands targeting the E3 ligase KLHDC2. Furthermore, we functionalize these KLHDC2-targeting ligands into KLHDC2-based BET-family and AR PROTAC degraders and demonstrate KLHDC2-dependent target-protein degradation. Additionally, we offer insight into the assembly of the KLHDC2 E3 ligase complex. Using biochemical binding studies, X-ray crystallography and cryo-EM, we show that the KLHDC2 E3 ligase assembles into a dynamic tetramer held together via its own C terminus, and that this assembly can be modulated by substrate and ligand engagement.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bernadette Tiberi
- Arvinas, Inc, New Haven, CT, USA
- Genetics, Genomics and Cancer Biology Graduate Program, Thomas Jefferson University, Philadelphia, PA, USA
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20
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Liwocha J, Li J, Purser N, Rattanasopa C, Maiwald S, Krist DT, Scott DC, Steigenberger B, Prabu JR, Schulman BA, Kleiger G. Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases. Nat Struct Mol Biol 2024; 31:378-389. [PMID: 38326650 PMCID: PMC10873206 DOI: 10.1038/s41594-023-01206-1] [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: 08/07/2023] [Accepted: 12/21/2023] [Indexed: 02/09/2024]
Abstract
E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked poly-ubiquitin chains to control an enormous swath of eukaryotic biology. Yet the molecular mechanisms underlying this exceptional linkage specificity and millisecond kinetics of poly-ubiquitylation remain unclear. Here we obtain cryogenic-electron microscopy (cryo-EM) structures that provide pertinent insight into how such poly-ubiquitin chains are forged. The CRL RING domain not only activates the E2-bound ubiquitin but also shapes the conformation of a distinctive UBE2R2 loop, positioning both the ubiquitin to be transferred and the substrate-linked acceptor ubiquitin within the active site. The structures also reveal how the ubiquitin-like protein NEDD8 uniquely activates CRLs during chain formation. NEDD8 releases the RING domain from the CRL, but unlike previous CRL-E2 structures, does not contact UBE2R2. These findings suggest how poly-ubiquitylation may be accomplished by many E2s and E3s.
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Affiliation(s)
- Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Chutima Rattanasopa
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Samuel Maiwald
- 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
| | - Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Gary Kleiger
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA.
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21
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Wang K, Diaz S, Li L, Lohman JR, Liu X. CAND1 inhibits Cullin-2-RING ubiquitin ligases for enhanced substrate specificity. Nat Struct Mol Biol 2024; 31:323-335. [PMID: 38177676 PMCID: PMC10923007 DOI: 10.1038/s41594-023-01167-5] [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: 03/13/2023] [Accepted: 10/29/2023] [Indexed: 01/06/2024]
Abstract
Through targeting essential cellular regulators for ubiquitination and serving as a major platform for discovering proteolysis-targeting chimera (PROTAC) drugs, Cullin-2 (CUL2)-RING ubiquitin ligases (CRL2s) comprise an important family of CRLs. The founding members of CRLs, the CUL1-based CRL1s, are known to be activated by CAND1, which exchanges the variable substrate receptors associated with the common CUL1 core and promotes the dynamic assembly of CRL1s. Here we find that CAND1 inhibits CRL2-mediated protein degradation in human cells. This effect arises due to altered binding kinetics, involving CAND1 and CRL2VHL, as we illustrate that CAND1 dramatically increases the dissociation rate of CRL2s but barely accelerates the assembly of stable CRL2s. Using PROTACs that differently recruit neo-substrates to CRL2VHL, we demonstrate that the inhibitory effect of CAND1 helps distinguish target proteins with different affinities for CRL2s, presenting a mechanism for selective protein degradation with proper pacing in the changing cellular environment.
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Affiliation(s)
- Kankan Wang
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Stephanie Diaz
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Neurosurgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Lihong Li
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA
| | - Jeremy R Lohman
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Xing Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
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22
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Zambrano-Carrasco J, Zou J, Wang W, Sun X, Li J, Su H. Emerging Roles of Cullin-RING Ubiquitin Ligases in Cardiac Development. Cells 2024; 13:235. [PMID: 38334627 PMCID: PMC10854628 DOI: 10.3390/cells13030235] [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: 12/23/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Heart development is a spatiotemporally regulated process that extends from the embryonic phase to postnatal stages. Disruption of this highly orchestrated process can lead to congenital heart disease or predispose the heart to cardiomyopathy or heart failure. Consequently, gaining an in-depth understanding of the molecular mechanisms governing cardiac development holds considerable promise for the development of innovative therapies for various cardiac ailments. While significant progress in uncovering novel transcriptional and epigenetic regulators of heart development has been made, the exploration of post-translational mechanisms that influence this process has lagged. Culling-RING E3 ubiquitin ligases (CRLs), the largest family of ubiquitin ligases, control the ubiquitination and degradation of ~20% of intracellular proteins. Emerging evidence has uncovered the critical roles of CRLs in the regulation of a wide range of cellular, physiological, and pathological processes. In this review, we summarize current findings on the versatile regulation of cardiac morphogenesis and maturation by CRLs and present future perspectives to advance our comprehensive understanding of how CRLs govern cardiac developmental processes.
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Affiliation(s)
- Josue Zambrano-Carrasco
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
| | - Jianqiu Zou
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
| | - Wenjuan Wang
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
| | - Xinghui Sun
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Jie Li
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; (J.Z.-C.); (J.Z.)
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
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23
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Dong J, Li Y, Cheng S, Li X, Wei N. COP9 signalosome-mediated deneddylation of CULLIN1 is necessary for SCF EBF1 assembly in Arabidopsis thaliana. Cell Rep 2024; 43:113638. [PMID: 38184853 DOI: 10.1016/j.celrep.2023.113638] [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: 06/08/2023] [Revised: 11/06/2023] [Accepted: 12/15/2023] [Indexed: 01/09/2024] Open
Abstract
Functions of the SKP1-CUL1-F box (SCF) ubiquitin E3 ligases are essential in plants. The F box proteins (FBPs) are substrate receptors that recruit substrates and assemble an active SCF complex, but the regulatory mechanism underlying the FBPs binding to CUL1 to activate the SCF cycle is not fully understood. We show that Arabidopsis csn1-10 is defective in SCFEBF1-mediated PIF3 degradation during de-etiolation, due to impaired association of EBF1 with CUL1 in csn1-10. EBF1 preferentially associates with un-neddylated CUL1 that is deficient in csn1-10 and the EBF1-CUL1 binding is rescued by the neddylation inhibitor MLN4924. Furthermore, we identify a subset of FBPs with impaired binding to CUL1 in csn1-10, indicating their assembly to form SCF complexes may depend on COP9 signalosome (CSN)-mediated deneddylation of CUL1. This study reports that a key role of CSN-mediated CULLIN deneddylation is to gate the binding of the FBP-substrate module to CUL1, thus initiating the SCF cycle of substrate ubiquitination.
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Affiliation(s)
- Jie Dong
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Li
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shuyang Cheng
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xuehui Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang 261325, China
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing 400715, China.
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24
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Chrustowicz J, Sherpa D, Li J, Langlois CR, Papadopoulou EC, Vu DT, Hehl LA, Karayel Ö, Beier V, von Gronau S, Müller J, Prabu JR, Mann M, Kleiger G, Alpi AF, Schulman BA. Multisite phosphorylation dictates selective E2-E3 pairing as revealed by Ubc8/UBE2H-GID/CTLH assemblies. Mol Cell 2024; 84:293-308.e14. [PMID: 38113892 PMCID: PMC10843684 DOI: 10.1016/j.molcel.2023.11.027] [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: 07/11/2023] [Revised: 10/29/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
Ubiquitylation is catalyzed by coordinated actions of E3 and E2 enzymes. Molecular principles governing many important E3-E2 partnerships remain unknown, including those for RING-family GID/CTLH E3 ubiquitin ligases and their dedicated E2, Ubc8/UBE2H (yeast/human nomenclature). GID/CTLH-Ubc8/UBE2H-mediated ubiquitylation regulates biological processes ranging from yeast metabolic signaling to human development. Here, cryoelectron microscopy (cryo-EM), biochemistry, and cell biology reveal this exquisitely specific E3-E2 pairing through an unconventional catalytic assembly and auxiliary interactions 70-100 Å away, mediated by E2 multisite phosphorylation. Rather than dynamic polyelectrostatic interactions reported for other ubiquitylation complexes, multiple Ubc8/UBE2H phosphorylation sites within acidic CK2-targeted sequences specifically anchor the E2 C termini to E3 basic patches. Positions of phospho-dependent interactions relative to the catalytic domains correlate across evolution. Overall, our data show that phosphorylation-dependent multivalency establishes a specific E3-E2 partnership, is antagonistic with dephosphorylation, rigidifies the catalytic centers within a flexing GID E3-substrate assembly, and facilitates substrate collision with ubiquitylation active sites.
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Affiliation(s)
- Jakub Chrustowicz
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Dawafuti Sherpa
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV 89154, USA
| | - Christine R Langlois
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Eleftheria C Papadopoulou
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Technical University of Munich, School of Natural Sciences, Munich 85748, Germany
| | - D Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Laura A Hehl
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Technical University of Munich, School of Natural Sciences, Munich 85748, Germany
| | - Özge Karayel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Viola Beier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Judith Müller
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV 89154, USA
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; Technical University of Munich, School of Natural Sciences, Munich 85748, Germany.
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25
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Tener SJ, Lin Z, Park SJ, Oraedu K, Ulgherait M, Van Beek E, Martínez-Muñiz A, Pantalia M, Gatto JA, Volpi J, Stavropoulos N, Ja WW, Canman JC, Shirasu-Hiza M. Neuronal knockdown of Cullin3 as a Drosophila model of autism spectrum disorder. Sci Rep 2024; 14:1541. [PMID: 38233464 PMCID: PMC10794434 DOI: 10.1038/s41598-024-51657-9] [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: 06/01/2023] [Accepted: 01/06/2024] [Indexed: 01/19/2024] Open
Abstract
Mutations in Cullin-3 (Cul3), a conserved gene encoding a ubiquitin ligase, are strongly associated with autism spectrum disorder (ASD). Here, we characterize ASD-related pathologies caused by neuron-specific Cul3 knockdown in Drosophila. We confirmed that neuronal Cul3 knockdown causes short sleep, paralleling sleep disturbances in ASD. Because sleep defects and ASD are linked to metabolic dysregulation, we tested the starvation response of neuronal Cul3 knockdown flies; they starved faster and had lower triacylglyceride levels than controls, suggesting defects in metabolic homeostasis. ASD is also characterized by increased biomarkers of oxidative stress; we found that neuronal Cul3 knockdown increased sensitivity to hyperoxia, an exogenous oxidative stress. Additional hallmarks of ASD are deficits in social interactions and learning. Using a courtship suppression assay that measures social interactions and memory of prior courtship, we found that neuronal Cul3 knockdown reduced courtship and learning compared to controls. Finally, we found that neuronal Cul3 depletion alters the anatomy of the mushroom body, a brain region required for memory and sleep. Taken together, the ASD-related phenotypes of neuronal Cul3 knockdown flies establish these flies as a genetic model to study molecular and cellular mechanisms underlying ASD pathology, including metabolic and oxidative stress dysregulation and neurodevelopment.
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Affiliation(s)
- Samantha J Tener
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Zhi Lin
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Scarlet J Park
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Kairaluchi Oraedu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Matthew Ulgherait
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Emily Van Beek
- Waksman Institute, Rutgers University, Piscataway, NJ, 08854, USA
| | - Andrés Martínez-Muñiz
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Meghan Pantalia
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jared A Gatto
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Julia Volpi
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - William W Ja
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technology, Jupiter, FL, 33458, USA
| | - Julie C Canman
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Mimi Shirasu-Hiza
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA.
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26
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Botsch JJ, Junker R, Sorgenfrei M, Ogger PP, Stier L, von Gronau S, Murray PJ, Seeger MA, Schulman BA, Bräuning B. Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE. Nat Commun 2024; 15:410. [PMID: 38195637 PMCID: PMC10776854 DOI: 10.1038/s41467-023-44670-5] [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: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign. The majority of Doa10/MARCH6 adopts a unique circular structure within the membrane. This channel is established by a lipid-binding scaffold, and gated by a flexible helical bundle. The ubiquitylation active site is positioned over the channel by connections between the cytosolic E3 ligase RING domain and the membrane-spanning scaffold and gate. Here, by assaying 95 MARCH6 variants for effects on stability of the well-characterized substrate SQLE, which regulates cholesterol levels, we reveal crucial roles of the gated channel and RING domain consistent with AlphaFold-models of substrate-engaged and ubiquitylation complexes. SQLE degradation further depends on connections between the channel and RING domain, and lipid binding sites, revealing how interconnected Doa10/MARCH6 elements could orchestrate metabolic signals, substrate binding, and E3 ligase activity.
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Affiliation(s)
- J Josephine Botsch
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Roswitha Junker
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Patricia P Ogger
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Luca Stier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Peter J Murray
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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27
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Wang Y, Manzi M, Feswick A, Renshaw L, Oliver PM, Tibbetts SA, Moser EK. B cell expression of E3 ubiquitin ligase Cul4b promotes chronic gammaherpesvirus infection in vivo. J Virol 2023; 97:e0100823. [PMID: 37962378 PMCID: PMC10734415 DOI: 10.1128/jvi.01008-23] [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: 07/14/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023] Open
Abstract
IMPORTANCE The human gammaherpesviruses Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus are etiologic agents of numerous B cell lymphomas. A hallmark of gammaherpesvirus infection is their ability to establish lifelong latency in B cells. However, the specific mechanisms that mediate chronic infection in B cells in vivo remain elusive. Cellular E3 ubiquitin ligases regulate numerous biological processes by catalyzing ubiquitylation and modifying protein location, function, or half-life. Many viruses hijack host ubiquitin ligases to evade antiviral host defense and promote viral fitness. Here, we used the murine gammaherpesvirus 68 in vivo system to demonstrate that the E3 ligase Cul4b is essential for this virus to establish latency in germinal center B cells. These findings highlight an essential role for this E3 ligase in promoting chronic gammaherpesvirus infection in vivo and suggest that targeted inhibition of E3 ligases may provide a novel and effective intervention strategy against gammaherpesvirus-associated diseases.
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Affiliation(s)
- Yiping Wang
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, UF Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Mikayla Manzi
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, UF Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - April Feswick
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, UF Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Lindsay Renshaw
- Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Paula M. Oliver
- Cell Pathology Division, The Children’s Hospital of Philadelphia, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Scott A. Tibbetts
- Department of Molecular Genetics and Microbiology, UF Health Cancer Center, UF Genetics Institute, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Emily K. Moser
- Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, USA
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Colding-Christensen CS, Kakulidis ES, Arroyo-Gomez J, Hendriks IA, Arkinson C, Fábián Z, Gambus A, Mailand N, Duxin JP, Nielsen ML. Profiling ubiquitin signalling with UBIMAX reveals DNA damage- and SCF β-Trcp1-dependent ubiquitylation of the actin-organizing protein Dbn1. Nat Commun 2023; 14:8293. [PMID: 38097601 PMCID: PMC10721886 DOI: 10.1038/s41467-023-43873-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Ubiquitin widely modifies proteins, thereby regulating most cellular functions. The complexity of ubiquitin signalling necessitates unbiased methods enabling global detection of dynamic protein ubiquitylation. Here, we describe UBIMAX (UBiquitin target Identification by Mass spectrometry in Xenopus egg extracts), which enriches ubiquitin-conjugated proteins and quantifies regulation of protein ubiquitylation under precise and adaptable conditions. We benchmark UBIMAX by investigating DNA double-strand break-responsive ubiquitylation events, identifying previously known targets and revealing the actin-organizing protein Dbn1 as a major target of DNA damage-induced ubiquitylation. We find that Dbn1 is targeted for proteasomal degradation by the SCFβ-Trcp1 ubiquitin ligase, in a conserved mechanism driven by ATM-mediated phosphorylation of a previously uncharacterized β-Trcp1 degron containing an SQ motif. We further show that this degron is sufficient to induce DNA damage-dependent protein degradation of a model substrate. Collectively, we demonstrate UBIMAX's ability to identify targets of stimulus-regulated ubiquitylation and reveal an SCFβ-Trcp1-mediated ubiquitylation mechanism controlled directly by the apical DNA damage response kinases.
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Affiliation(s)
- Camilla S Colding-Christensen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ellen S Kakulidis
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Javier Arroyo-Gomez
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Ivo A Hendriks
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Connor Arkinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
- California Institute for Quantitative Biosciences and Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Zita Fábián
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Niels Mailand
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
| | - Michael L Nielsen
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark.
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29
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Ren Z, Tang H, Zhang W, Guo M, Cui J, Wang H, Xie B, Yu J, Chen Y, Zhang M, Han C, Chu T, Liang Q, Zhao S, Huang Y, He X, Liu K, Liu C, Chen C. The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling During Neurodevelopment. Neurosci Bull 2023:10.1007/s12264-023-01161-3. [PMID: 38060137 DOI: 10.1007/s12264-023-01161-3] [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: 07/06/2023] [Accepted: 09/13/2023] [Indexed: 12/08/2023] Open
Abstract
Intellectual disability (ID) is a condition characterized by cognitive impairment and difficulties in adaptive functioning. In our research, we identified two de novo mutations (c.955C>T and c.732C>A) at the KDM2A locus in individuals with varying degrees of ID. In addition, by using the Gene4Denovo database, we discovered five additional cases of de novo mutations in KDM2A. The mutations we identified significantly decreased the expression of the KDM2A protein. To investigate the role of KDM2A in neural development, we used both 2D neural stem cell models and 3D cerebral organoids. Our findings demonstrated that the reduced expression of KDM2A impairs the proliferation of neural progenitor cells (NPCs), increases apoptosis, induces premature neuronal differentiation, and affects synapse maturation. Through ChIP-Seq analysis, we found that KDM2A exhibited binding to the transcription start site regions of genes involved in neurogenesis. In addition, the knockdown of KDM2A hindered H3K36me2 binding to the downstream regulatory elements of genes. By integrating ChIP-Seq and RNA-Seq data, we made a significant discovery of the core genes' remarkable enrichment in the MAPK signaling pathway. Importantly, this enrichment was specifically linked to the p38 MAPK pathway. Furthermore, disease enrichment analysis linked the differentially-expressed genes identified from RNA-Seq of NPCs and cerebral organoids to neurodevelopmental disorders such as ID, autism spectrum disorder, and schizophrenia. Overall, our findings suggest that KDM2A plays a crucial role in regulating the H3K36me2 modification of downstream genes, thereby modulating the MAPK signaling pathway and potentially impacting early brain development.
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Affiliation(s)
- Zongyao Ren
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Haiyan Tang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Wendiao Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Minghui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jingjie Cui
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Children's Hospital, Changsha, 410007, China
| | - Bin Xie
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Jing Yu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yonghao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Ming Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Cong Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Tianyao Chu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Qiuman Liang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Shunan Zhao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Yingjie Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China
| | - Xuelian He
- Precision Medical Center, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, 430014, China.
| | - Kefu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
| | - Chunyu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY, 13210, USA.
| | - Chao Chen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, and Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center on Mental Disorders, The Second Xiangya Hospital, Central South University, Changsha, 410028, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410011, China.
- Furong Laboratory, Changsha, 410000, China.
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30
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Henneberg LT, Singh J, Duda DM, Baek K, Yanishevski D, Murray PJ, Mann M, Sidhu SS, Schulman BA. Activity-based profiling of cullin-RING E3 networks by conformation-specific probes. Nat Chem Biol 2023; 19:1513-1523. [PMID: 37653169 PMCID: PMC10667097 DOI: 10.1038/s41589-023-01392-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 06/29/2023] [Indexed: 09/02/2023]
Abstract
The cullin-RING ubiquitin ligase (CRL) network comprises over 300 unique complexes that switch from inactive to activated conformations upon site-specific cullin modification by the ubiquitin-like protein NEDD8. Assessing cellular repertoires of activated CRL complexes is critical for understanding eukaryotic regulation. However, probes surveying networks controlled by site-specific ubiquitin-like protein modifications are lacking. We developed a synthetic antibody recognizing the active conformation of NEDD8-linked cullins. Implementing the probe to profile cellular networks of activated CUL1-, CUL2-, CUL3- and CUL4-containing E3s revealed the complexes responding to stimuli. Profiling several cell types showed their baseline neddylated CRL repertoires vary, and prime efficiency of targeted protein degradation. Our probe also unveiled differential rewiring of CRL networks across distinct primary cell activation pathways. Thus, conformation-specific probes can permit nonenzymatic activity-based profiling across a system of numerous multiprotein complexes, which in the case of neddylated CRLs reveals widespread regulation and could facilitate the development of degrader drugs.
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Affiliation(s)
- Lukas T Henneberg
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jaspal Singh
- School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada
| | - David M Duda
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
- Siduma Therapeutics, New Haven, CT, USA
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David Yanishevski
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter J Murray
- Immunoregulation, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sachdev S Sidhu
- School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada.
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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31
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Park HM, Le L, Nguyen TT, Nam KH, Ordureau A, Lee JE, Nguyen TV. The CRL3 gigaxonin ubiquitin ligase-USP15 pathway governs the destruction of neurofilament proteins. Proc Natl Acad Sci U S A 2023; 120:e2306395120. [PMID: 37903270 PMCID: PMC10636361 DOI: 10.1073/pnas.2306395120] [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: 04/19/2023] [Accepted: 09/20/2023] [Indexed: 11/01/2023] Open
Abstract
Giant axonal neuropathy (GAN) is caused by mutations in the GAN gene encoding for gigaxonin (GIG), which functions as an adaptor of the CUL3-RBX1-GIG (CRL3GIG) E3 ubiquitin ligase complex. The pathological hallmark of GAN is characterized by the accumulation of densely packed neurofilaments (NFs) in the axons. However, there are fundamental knowledge gaps in our understanding of the molecular mechanisms by which the ubiquitin-proteasome system controls the homeostasis of NF proteins. Recently, the deubiquitylating enzyme USP15 was reported to play a crucial role in regulating ubiquitylation and proteasomal degradation of CRL4CRBN substrate proteins. Here, we report that the CRL3GIG-USP15 pathway governs the destruction of NF proteins NEFL and INA. We identified a specific degron called NEFLL12 degron for CRL3GIG. Notably, mutations in the C-terminal Kelch domain of GIG, represented by L309R, R545C, and C570Y, disrupted the binding of GIG to NEFL and INA, leading to the accumulation of these NF proteins. This accounts for the loss-of-function mutations in GAN patients. In addition to regulating NFs, CRL3GIG also controls actin filaments by directly targeting actin-filament-binding regulatory proteins TPM1, TPM2, TAGLN, and CNN2 for proteasomal degradation. Thus, our findings broadly impact the field by providing fundamental mechanistic insights into regulating extremely long-lived NF proteins NEFL and INA by the CRL3GIG-USP15 pathway and offering previously unexplored therapeutic opportunities to treat GAN patients and other neurodegenerative diseases by explicitly targeting downstream substrates of CRL3GIG.
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Affiliation(s)
- Hyoung-Min Park
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon34113, Korea
| | - Ly Le
- Division of Quantum Simulation and Optimization, SandboxAQ, New York, NY10591
| | - Thao T. Nguyen
- Gehrke Proteomics Center, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO65211
| | - Ki Hong Nam
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY10065
| | - J. Eugene Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon34113, Korea
| | - Thang Van Nguyen
- Center for Precision Medicine, Department of Medicine, University of Missouri, Columbia, MO65212
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32
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Schwefel D. Cullin(g) glutamate dehydrogenase: Insights into multivalent CRL3 KLHL22 substrate recognition. Structure 2023; 31:1294-1296. [PMID: 37922866 DOI: 10.1016/j.str.2023.10.004] [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: 10/04/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 11/07/2023]
Abstract
Substrate specificity is central to the regulation of cellular ubiquitylation. In this issue of Structure, Teng et al. employ biochemistry and cryo-EM single-particle reconstruction to clarify the intricate interaction of the dimeric CRL3KLHL22 E3 ligase assembly with a hexameric substrate and its possible implications for metabolic adaptation and oncogenesis.
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Affiliation(s)
- David Schwefel
- Technische Universität Berlin, Chair of Bioanalytics, 10623 Berlin, Germany.
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33
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Tang L, Wei D, Xu X, Mo D, Cheng D, Yan F. FOXO1-regulated lncRNA CYP1B1-AS1 suppresses breast cancer cell proliferation by inhibiting neddylation. Breast Cancer Res Treat 2023; 202:397-408. [PMID: 37640964 PMCID: PMC10505597 DOI: 10.1007/s10549-023-07090-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
PURPOSE Overactivated neddylation is considered to be a common event in cancer. Long non-coding RNAs (lncRNAs) can regulate cancer development by mediating post-translational modifications. However, the role of lncRNA in neddylation modification remains unclear. METHODS LncRNA cytochrome P450 family 1 subfamily B member 1 antisense RNA 1 (CYP1B1-AS1) expression in breast cancer tissues was evaluated by RT-PCR and TCGA BRCA data. Gain and loss of function experiments were performed to explore the role of CYP1B1-AS1 in breast cancer cell proliferation and apoptosis in vitro and in vivo. Luciferase assay, CHIP-qPCR assay, transcriptome sequencing, RNA-pulldown assay, mass spectrometry, RIP-PCR and Western blot were used to investigate the regulatory factors of CYP1B1-AS1 expression and the molecular mechanism of CYP1B1-AS1 involved in neddylation modification. RESULTS We found that CYP1B1-AS1 was down-regulated in breast cancer tissues and correlated with prognosis. In vivo and in vitro functional experiments confirmed that CYP1B1-AS1 inhibited cell proliferation and induced apoptosis. Mechanistically, CYP1B1-AS1 was regulated by the transcription factor, forkhead box O1 (FOXO1), and could be upregulated by inhibiting the PI3K/FOXO1 pathway. Moreover, CYP1B1-AS1 bound directly to NEDD8 activating enzyme E1 subunit 1 (NAE1) to regulate protein neddylation. CONCLUSION This study reports for the first time that CYP1B1-AS1 inhibits protein neddylation to affect breast cancer cell proliferation, which provides a new strategy for the treatment of breast cancer by lncRNA targeting neddylation modification.
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Affiliation(s)
- Li Tang
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, People's Republic of China.
| | - Da Wei
- Department of Surgery, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Xinyu Xu
- Department of Pathology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Dongping Mo
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, People's Republic of China
| | - Daofu Cheng
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, People's Republic of China
| | - Feng Yan
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, People's Republic of China.
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34
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Schiffmacher DL, Lee SH, Kliza KW, Theil AF, Akita M, Helfricht A, Bezstarosti K, Gonzalo-Hansen C, van Attikum H, Verlaan-de Vries M, Vertegaal AC, Hoeijmakers JH, Marteijn JA, Lans H, Demmers JA, Vermeulen M, Sixma T, Ogi T, Vermeulen W, Pines A. DDA1, a novel factor in transcription-coupled repair, modulates CRL4 CSA dynamics at DNA damage-stalled RNA polymerase II. RESEARCH SQUARE 2023:rs.3.rs-3385435. [PMID: 37886519 PMCID: PMC10602077 DOI: 10.21203/rs.3.rs-3385435/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Transcription-blocking DNA lesions are specifically targeted by transcription-coupled nucleotide excision repair (TC-NER), which removes a broad spectrum of DNA lesions to preserve transcriptional output and thereby cellular homeostasis to counteract aging. TC-NER is initiated by the stalling of RNA polymerase II at DNA lesions, which triggers the assembly of the TC-NER-specific proteins CSA, CSB and UVSSA. CSA, a WD40-repeat containing protein, is the substrate receptor subunit of a cullin-RING ubiquitin ligase complex composed of DDB1, CUL4A/B and RBX1 (CRL4CSA). Although ubiquitination of several TC-NER proteins by CRL4CSA has been reported, it is still unknown how this complex is regulated. To unravel the dynamic molecular interactions and the regulation of this complex, we applied a single-step protein-complex isolation coupled to mass spectrometry analysis and identified DDA1 as a CSA interacting protein. Cryo-EM analysis showed that DDA1 is an integral component of the CRL4CSA complex. Functional analysis revealed that DDA1 coordinates ubiquitination dynamics during TC-NER and is required for efficient turnover and progression of this process.
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Affiliation(s)
- Diana Llerena Schiffmacher
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- These authors contributed equally
| | - Shun-Hsiao Lee
- Division of Biochemistry and Oncode institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
- These authors contributed equally
| | - Katarzyna W. Kliza
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
- Current address: Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Arjan F. Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Masaki Akita
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- Current address: Department of Biology and National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A7, Brno, Czech Republic
| | - Angela Helfricht
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Camila Gonzalo-Hansen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Matty Verlaan-de Vries
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Alfred C.O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Jan H.J. Hoeijmakers
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- University Hospital of Cologne, CECAD Forschungszentrum, Institute for Genome Stability in Aging and Disease, Joseph Stelzmann Strasse 26, 50931 Köln, Germany
- Princess Maxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, the Netherlands
- Oncode Institute, The Netherlands
| | - Jurgen A. Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Jeroen A.A. Demmers
- Proteomics Center, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences (RIMLS), Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
- Division of Molecular Genetics and Oncode institute, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, the Netherlands
- Oncode Institute, The Netherlands
| | - Titia Sixma
- Division of Biochemistry and Oncode institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine (RIeM), Nagoya University, Nagoya, Japan; Department of Human Genetics and Molecular Biology, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 CN, Rotterdam, The Netherlands
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35
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Miao Q, Kadam VD, Mukherjee A, Tan Z, Teng M. Unlocking DCAFs To Catalyze Degrader Development: An Arena for Innovative Approaches. J Med Chem 2023; 66:13369-13383. [PMID: 37738232 DOI: 10.1021/acs.jmedchem.3c01209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Chemically induced proximity-based targeted protein degradation (TPD) has become a prominent paradigm in drug discovery. With the clinical benefit demonstrated by certain small-molecule protein degraders that target the cullin-RING E3 ubiquitin ligases (CRLs), the field has proactively strategized to tackle anticipated drug resistance by harnessing additional E3 ubiquitin ligases to enrich the arsenal of this therapeutic approach. Here, we endeavor to explore the collaborative efforts involved in unlocking a broad range of CRL4DCAF for degrader drug development. Throughout the discussion, we also highlight how both conventional and innovative approaches in drug discovery can be taken to realize this objective. Moving ahead, we expect a greater allocation of resources in TPD to pursue these high-hanging fruits.
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Affiliation(s)
- Qi Miao
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Vilas D Kadam
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ayan Mukherjee
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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36
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Zhi F, Li B, Zhang C, Xia F, Wang R, Xie W, Cai S, Zhang D, Kong R, Hu Y, Yang Y, Peng Y, Cui J. NLRP6 potentiates PI3K/AKT signalling by promoting autophagic degradation of p85α to drive tumorigenesis. Nat Commun 2023; 14:6069. [PMID: 37770465 PMCID: PMC10539329 DOI: 10.1038/s41467-023-41739-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: 10/03/2022] [Accepted: 09/01/2023] [Indexed: 09/30/2023] Open
Abstract
The PI3K/AKT pathway plays an essential role in tumour development. NOD-like receptors (NLRs) regulate innate immunity and are implicated in cancer, but whether they are involved in PI3K/AKT pathway regulation is poorly understood. Here, we report that NLRP6 potentiates the PI3K/AKT pathway by binding and destabilizing p85α, the regulatory subunit of PI3K. Mechanistically, NLRP6 recruits the E3 ligase RBX1 to p85α and ubiquitinates lysine 256 on p85α, which is recognized by the autophagy cargo receptor OPTN, causing selective autophagic degradation of p85α and subsequent activation of the PI3K/AKT pathway by reducing PTEN stability. We further show that loss of NLRP6 suppresses cell proliferation, colony formation, cell migration, and tumour growth in glioblastoma cells in vitro and in vivo. Disruption of the NLRP6/p85α interaction using the Pep9 peptide inhibits the PI3K/AKT pathway and generates potent antitumour effects. Collectively, our results suggest that NLRP6 promotes p85α degradation via selective autophagy to drive tumorigenesis, and the interaction between NLRP6 and p85α can be a promising therapeutic target for tumour treatment.
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Affiliation(s)
- Feng Zhi
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Bowen Li
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Chuanxia Zhang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Medical Research Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Fan Xia
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Rong Wang
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Weihong Xie
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Sihui Cai
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Dawei Zhang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, China
| | - Yiqiao Hu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School and School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Yilin Yang
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Ya Peng
- Department of Neurosurgery, Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China.
| | - Jun Cui
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.
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Boland AW, Gas-Pascual E, van der Wel H, Kim HW, West CM. Synergy between a cytoplasmic vWFA/VIT protein and a WD40-repeat F-box protein controls development in Dictyostelium. Front Cell Dev Biol 2023; 11:1259844. [PMID: 37779900 PMCID: PMC10539598 DOI: 10.3389/fcell.2023.1259844] [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: 07/16/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023] Open
Abstract
Like most eukaryotes, the pre-metazoan social amoeba Dictyostelium depends on the SCF (Skp1/cullin-1/F-box protein) family of E3 ubiquitin ligases to regulate its proteome. In Dictyostelium, starvation induces a transition from unicellular feeding to a multicellular slug that responds to external signals to culminate into a fruiting body containing terminally differentiated stalk and spore cells. These transitions are subject to regulation by F-box proteins and O2-dependent posttranslational modifications of Skp1. Here we examine in greater depth the essential role of FbxwD and Vwa1, an intracellular vault protein inter-alpha-trypsin (VIT) and von Willebrand factor-A (vWFA) domain containing protein that was found in the FbxwD interactome by co-immunoprecipitation. Reciprocal co-IPs using gene-tagged strains confirmed the interaction and similar changes in protein levels during multicellular development suggested co-functioning. FbxwD overexpression and proteasome inhibitors did not affect Vwa1 levels suggesting a non-substrate relationship. Forced FbxwD overexpression in slug tip cells where it is normally enriched interfered with terminal cell differentiation by a mechanism that depended on its F-box and RING domains, and on Vwa1 expression itself. Whereas vwa1-disruption alone did not affect development, overexpression of either of its three conserved domains arrested development but the effect depended on Vwa1 expression. Based on structure predictions, we propose that the Vwa1 domains exert their negative effect by artificially activating Vwa1 from an autoinhibited state, which in turn imbalances its synergistic function with FbxwD. Autoinhibition or homodimerization might be relevant to the poorly understood tumor suppressor role of the evolutionarily related VWA5A/BCSC-1 in humans.
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Affiliation(s)
- Andrew W. Boland
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Elisabet Gas-Pascual
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
| | - Hanke van der Wel
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Hyun W. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Christopher M. West
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, United States
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38
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Baxi A, Werner A. You can "tail" them apart: paralog-specific functions of CRL4B ubiquitin ligases during mitosis and brain development. EMBO J 2023; 42:e114931. [PMID: 37528760 PMCID: PMC10476272 DOI: 10.15252/embj.2023114931] [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: 07/06/2023] [Accepted: 07/21/2023] [Indexed: 08/03/2023] Open
Abstract
The CUL4 paralogs CUL4A and CUL4B assemble into structurally similar multisubunit ubiquitin E3 ligases (CRL4A/B) that regulate diverse aspects of cell biology. New work in this issue of The EMBO Journal shows that the longer N-terminal tail of CUL4B tells these molecular twins apart, by promoting the formation of paralog-specific CRL4B complexes that control cytoskeletal processes during mitosis and brain development.
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Affiliation(s)
- Aparna Baxi
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial ResearchNational Institutes of HealthBethesdaMDUSA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial ResearchNational Institutes of HealthBethesdaMDUSA
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39
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Hodáková Z, Grishkovskaya I, Brunner HL, Bolhuis DL, Belačić K, Schleiffer A, Kotisch H, Brown NG, Haselbach D. Cryo-EM structure of the chain-elongating E3 ubiquitin ligase UBR5. EMBO J 2023; 42:e113348. [PMID: 37409633 PMCID: PMC10425842 DOI: 10.15252/embj.2022113348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/30/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023] Open
Abstract
UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT domain-containing ubiquitin ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of human UBR5, revealing an α-solenoid scaffold with numerous protein-protein interacting motifs, assembled into an antiparallel dimer that adopts further oligomeric states. Using cryo-EM processing tools, we observe the dynamic nature of the UBR5 catalytic domain, which we postulate is important for its enzymatic activity. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates and several distinct domains for protein-protein interactions may explain how UBR5 is linked to several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3 ligases.
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Affiliation(s)
- Zuzana Hodáková
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Irina Grishkovskaya
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Hanna L Brunner
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
- Vienna BioCenter PhD ProgramDoctoral School of the University of Vienna and Medical University of ViennaViennaAustria
| | - Derek L Bolhuis
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - Katarina Belačić
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Harald Kotisch
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillNCUSA
| | - David Haselbach
- Research Institute of Molecular Pathology (IMP), ViennaBioCenter (VBC)ViennaAustria
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Mark KG, Kolla S, Aguirre JD, Garshott DM, Schmitt S, Haakonsen DL, Xu C, Kater L, Kempf G, Martínez-González B, Akopian D, See SK, Thomä NH, Rapé M. Orphan quality control shapes network dynamics and gene expression. Cell 2023; 186:3460-3475.e23. [PMID: 37478862 DOI: 10.1016/j.cell.2023.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/13/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-Myc oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over unpaired transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers opportunities to modulate gene expression in disease.
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Affiliation(s)
- Kevin G Mark
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - SriDurgaDevi Kolla
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Danielle M Garshott
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Stefan Schmitt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Diane L Haakonsen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA
| | - Christina Xu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - David Akopian
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Stephanie K See
- Center for Emerging and Neglected Diseases, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Michael Rapé
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California at Berkeley, Berkeley, CA 94720, USA.
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41
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Adamson RJ, Payne NC, Bartual SG, Mazitschek R, Bullock AN. Structural and biochemical characterization establishes a detailed understanding of KEAP1-CUL3 complex assembly. Free Radic Biol Med 2023; 204:215-225. [PMID: 37156295 PMCID: PMC10564622 DOI: 10.1016/j.freeradbiomed.2023.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/22/2023] [Accepted: 04/28/2023] [Indexed: 05/10/2023]
Abstract
KEAP1 promotes the ubiquitin-dependent degradation of NRF2 by assembling into a CUL3-dependent ubiquitin ligase complex. Oxidative and electrophilic stress inhibit KEAP1 allowing NRF2 to accumulate for the transactivation of stress response genes. To date there are no structures of the KEAP1-CUL3 interaction nor binding data to show the contributions of different domains to their binding affinity. We determined a crystal structure of the BTB and 3-box domains of human KEAP1 in complex with the CUL3 N-terminal domain that showed a heterotetrameric assembly with 2:2 stoichiometry. To support the structural data, we developed a versatile TR-FRET-based assay system to profile the binding of BTB-domain-containing proteins to CUL3 and determine the contribution of distinct protein features, revealing the importance of the CUL3 N-terminal extension for high affinity binding. We further provide direct evidence that the investigational drug CDDO does not disrupt the KEAP1-CUL3 interaction, even at high concentrations, but reduces the affinity of KEAP1-CUL3 binding. The TR-FRET-based assay system offers a generalizable platform for profiling this protein class and may form a suitable screening platform for ligands that disrupt these interactions by targeting the BTB or 3-box domains to block E3 ligase function.
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Affiliation(s)
- Roslin J Adamson
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - N Connor Payne
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Sergio G Bartual
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, 02114, USA; Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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Aguilan JT, Pedrosa E, Dolstra H, Baykara RN, Barnes J, Zhang J, Sidoli S, Lachman HM. Proteomics and phosphoproteomics profiling in glutamatergic neurons and microglia in an iPSC model of Jansen de Vries Syndrome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.08.548192. [PMID: 37461463 PMCID: PMC10350077 DOI: 10.1101/2023.07.08.548192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Background Jansen de Vries Syndrome (JdVS) is a rare neurodevelopmental disorder (NDD) caused by gain-of-function (GOF) truncating mutations in PPM1D exons 5 or 6. PPM1D is a serine/threonine phosphatase that plays an important role in the DNA damage response (DDR) by negatively regulating TP53 (P53). JdVS-associated mutations lead to the formation of a truncated PPM1D protein that retains catalytic activity and has a GOF effect because of reduced degradation. Somatic PPM1D exons 5 and 6 truncating mutations are well-established factors in a number of cancers, due to excessive dephosphorylation and reduced function of P53 and other substrates involved in DDR. Children with JdVS have a variety of neurodevelopmental, psychiatric, and physical problems. In addition, a small fraction has acute neuropsychiatric decompensation apparently triggered by infection or severe non-infectious environmental stress factors. Methods To understand the molecular basis of JdVS, we developed an induced pluripotent stem cell (iPSC) model system. iPSCs heterozygous for the truncating variant (PPM1D+/tr), were made from a patient, and control lines engineered using CRISPR-Cas9 gene editing. Proteomics and phosphoprotemics analyses were carried out on iPSC-derived glutamatergic neurons and microglia from three control and three PPM1D+/tr iPSC lines. We also analyzed the effect of the TLR4 agonist, lipopolysaccharide, to understand how activation of the innate immune system in microglia could account for acute behavioral decompensation. Results One of the major findings was the downregulation of POGZ in unstimulated microglia. Since loss-of-function variants in the POGZ gene are well-known causes of autism spectrum disorder, the decrease in PPM1D+/tr microglia suggests this plays a role in the neurodevelopmental aspects of JdVS. In addition, neurons, baseline, and LPS-stimulated microglia show marked alterations in the expression of several E3 ubiquitin ligases, most notably UBR4, and regulators of innate immunity, chromatin structure, ErbB signaling, and splicing. In addition, pathway analysis points to overlap with neurodegenerative disorders. Limitations Owing to the cost and labor-intensive nature of iPSC research, the sample size was small. Conclusions Our findings provide insight into the molecular basis of JdVS and can be extrapolated to understand neuropsychiatric decompensation that occurs in subgroups of patients with ASD and other NDDs.
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Affiliation(s)
- Jennifer T. Aguilan
- Department of Pathology, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
| | - Hedwig Dolstra
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
| | - Refia Nur Baykara
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
| | - Jesse Barnes
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
| | - Jinghang Zhang
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
| | - Herbert M. Lachman
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave. Bronx, NY, 10461
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Hjerpe R, Kurz T. Cryo-EM reveals important regulatory mechanism of the workhorses of targeted protein degradation. Mol Cell 2023; 83:2159-2160. [PMID: 37419088 DOI: 10.1016/j.molcel.2023.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/09/2023]
Abstract
Most methods for targeted protein degradation (TPD) deliver targets to E3 ubiquitin ligases, leading to proteasomal degradation. In this issue of Molecular Cell, Shaaban et al.1 illuminate cullin-RING ubiquitin ligase (CRL) modulation by CAND1, which can be utilized for TPD.
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Affiliation(s)
- Roland Hjerpe
- Sygnature Discovery, BioCity, Pennyfoot Street, Nottingham NG1 1GR, UK
| | - Thimo Kurz
- School of Molecular Biosciences, University of Glasgow, Glasgow G12 8QQ, UK; Evotec SE, Innovation Dr, Milton, Abingdon OX14 4RT, UK.
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44
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Rowland RJ, Heath R, Maskell D, Thompson RF, Ranson NA, Blaza JN, Endicott JA, Noble MEM, Salamina M. Cryo-EM structure of SKP1-SKP2-CKS1 in complex with CDK2-cyclin A-p27KIP1. Sci Rep 2023; 13:10718. [PMID: 37400515 PMCID: PMC10318019 DOI: 10.1038/s41598-023-37609-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/24/2023] [Indexed: 07/05/2023] Open
Abstract
p27KIP1 (cyclin-dependent kinase inhibitor 1B, p27) is a member of the CIP/KIP family of CDK (cyclin dependent kinase) regulators that inhibit cell cycle CDKs. p27 phosphorylation by CDK1/2, signals its recruitment to the SCFSKP2 (S-phase kinase associated protein 1 (SKP1)-cullin-SKP2) E3 ubiquitin ligase complex for proteasomal degradation. The nature of p27 binding to SKP2 and CKS1 was revealed by the SKP1-SKP2-CKS1-p27 phosphopeptide crystal structure. Subsequently, a model for the hexameric CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex was proposed by overlaying an independently determined CDK2-cyclin A-p27 structure. Here we describe the experimentally determined structure of the isolated CDK2-cyclin A-CKS1-p27-SKP1-SKP2 complex at 3.4 Å global resolution using cryogenic electron microscopy. This structure supports previous analysis in which p27 was found to be structurally dynamic, transitioning from disordered to nascent secondary structure on target binding. We employed 3D variability analysis to further explore the conformational space of the hexameric complex and uncovered a previously unidentified hinge motion centred on CKS1. This flexibility gives rise to open and closed conformations of the hexameric complex that we propose may contribute to p27 regulation by facilitating recognition with SCFSKP2. This 3D variability analysis further informed particle subtraction and local refinement approaches to enhance the local resolution of the complex.
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Affiliation(s)
- Rhianna J Rowland
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Richard Heath
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Daniel Maskell
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Rebecca F Thompson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
- Life Sciences Electron Microscopy, Thermo Fisher Scientific, Leeds, UK
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - James N Blaza
- Department of Chemistry, York Structural Biology Laboratory and York Biomedical Research Institute, University of York, Heslington, YO10 5DD, York, UK
| | - Jane A Endicott
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.
| | - Martin E M Noble
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK
| | - Marco Salamina
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.
- Evotec (UK) Ltd., Milton, Abingdon, OX14 4RZ, UK.
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45
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Nguyen‐Dien GT, Kozul K, Cui Y, Townsend B, Kulkarni PG, Ooi SS, Marzio A, Carrodus N, Zuryn S, Pagano M, Parton RG, Lazarou M, Millard SS, Taylor RW, Collins BM, Jones MJK, Pagan JK. FBXL4 suppresses mitophagy by restricting the accumulation of NIX and BNIP3 mitophagy receptors. EMBO J 2023; 42:e112767. [PMID: 37161784 PMCID: PMC10308361 DOI: 10.15252/embj.2022112767] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023] Open
Abstract
To maintain both mitochondrial quality and quantity, cells selectively remove damaged or excessive mitochondria through mitophagy, which is a specialised form of autophagy. Mitophagy is induced in response to diverse conditions, including hypoxia, cellular differentiation and mitochondrial damage. However, the mechanisms that govern the removal of specific dysfunctional mitochondria under steady-state conditions to fine-tune mitochondrial content are not well understood. Here, we report that SCFFBXL4 , an SKP1/CUL1/F-box protein ubiquitin ligase complex, localises to the mitochondrial outer membrane in unstressed cells and mediates the constitutive ubiquitylation and degradation of the mitophagy receptors NIX and BNIP3 to suppress basal levels of mitophagy. We demonstrate that the pathogenic variants of FBXL4 that cause encephalopathic mtDNA depletion syndrome (MTDPS13) do not efficiently interact with the core SCF ubiquitin ligase machinery or mediate the degradation of NIX and BNIP3. Thus, we reveal a molecular mechanism whereby FBXL4 actively suppresses mitophagy by preventing NIX and BNIP3 accumulation. We propose that the dysregulation of NIX and BNIP3 turnover causes excessive basal mitophagy in FBXL4-associated mtDNA depletion syndrome.
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Affiliation(s)
- Giang Thanh Nguyen‐Dien
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
- Department of Biotechnology, School of BiotechnologyViet Nam National University‐International UniversityHo Chi Minh CityVietnam
| | - Keri‐Lyn Kozul
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Yi Cui
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Brendan Townsend
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | | | - Soo Siang Ooi
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Antonio Marzio
- Department of Biochemistry and Molecular PharmacologyNew York University Grossman School of MedicineNew YorkNYUSA
- Perlmutter Cancer CenterNew York University Grossman School of MedicineNew YorkNYUSA
- Department of Pathology and Lab Medicine, Meyer Cancer CenterWeill Cornell MedicineNew YorkNYUSA
| | - Nissa Carrodus
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Steven Zuryn
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneQLDAustralia
| | - Michele Pagano
- Department of Biochemistry and Molecular PharmacologyNew York University Grossman School of MedicineNew YorkNYUSA
- Perlmutter Cancer CenterNew York University Grossman School of MedicineNew YorkNYUSA
| | - Robert G Parton
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLDAustralia
- Centre for Microscopy and MicroanalysisUniversity of QueenslandBrisbaneQLDAustralia
| | - Michael Lazarou
- Walter and Eliza Hall Institute of Medical ResearchParkvilleVICAustralia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash UniversityMelbourneVICAustralia
- Department of Medical BiologyUniversity of MelbourneMelbourneVICAustralia
| | - S Sean Millard
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Service for Rare Mitochondrial DisordersNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Brett M Collins
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLDAustralia
| | - Mathew JK Jones
- The University of Queensland Diamantina Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
- School of Chemistry & Molecular BiosciencesUniversity of QueenslandBrisbaneQLDAustralia
| | - Julia K Pagan
- Faculty of Medicine, School of Biomedical SciencesUniversity of QueenslandBrisbaneQLDAustralia
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQLDAustralia
- The University of Queensland Diamantina Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
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46
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Wilhelm LP, Ganley IG. Eating your mitochondria-when too much of a good thing turns bad. EMBO J 2023; 42:e114542. [PMID: 37272260 PMCID: PMC10308347 DOI: 10.15252/embj.2023114542] [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: 05/17/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023] Open
Abstract
How mitophagy is turned on to remove damaged or excess mitochondria from cells has been well-studied, but less is known about how the pathway is turned off to avoid "over-eating" of mitochondria under basal conditions. Three new studies now reveal the disease-associated FBXL4 protein as an important negative regulator of constitutive mitophagy, controlling the stability of mitophagy receptors BNIP3 and NIX.
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Affiliation(s)
- Léa P Wilhelm
- MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK
| | - Ian G Ganley
- MRC Protein Phosphorylation and Ubiquitylation UnitUniversity of DundeeDundeeUK
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47
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Su Y, Luo Y, Zhang P, Lin H, Pu W, Zhang H, Wang H, Hao Y, Xiao Y, Zhang X, Wei X, Nie S, Zhang K, Fu Q, Chen H, Huang N, Ren Y, Wu M, Chow BKC, Chen X, Jin W, Wang F, Zhao L, Rao F. Glucose-induced CRL4 COP1-p53 axis amplifies glycometabolism to drive tumorigenesis. Mol Cell 2023:S1097-2765(23)00432-X. [PMID: 37390815 DOI: 10.1016/j.molcel.2023.06.010] [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: 08/11/2022] [Revised: 04/19/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
The diabetes-cancer association remains underexplained. Here, we describe a glucose-signaling axis that reinforces glucose uptake and glycolysis to consolidate the Warburg effect and overcome tumor suppression. Specifically, glucose-dependent CK2 O-GlcNAcylation impedes its phosphorylation of CSN2, a modification required for the deneddylase CSN to sequester Cullin RING ligase 4 (CRL4). Glucose, therefore, elicits CSN-CRL4 dissociation to assemble the CRL4COP1 E3 ligase, which targets p53 to derepress glycolytic enzymes. A genetic or pharmacologic disruption of the O-GlcNAc-CK2-CSN2-CRL4COP1 axis abrogates glucose-induced p53 degradation and cancer cell proliferation. Diet-induced overnutrition upregulates the CRL4COP1-p53 axis to promote PyMT-induced mammary tumorigenesis in wild type but not in mammary-gland-specific p53 knockout mice. These effects of overnutrition are reversed by P28, an investigational peptide inhibitor of COP1-p53 interaction. Thus, glycometabolism self-amplifies via a glucose-induced post-translational modification cascade culminating in CRL4COP1-mediated p53 degradation. Such mutation-independent p53 checkpoint bypass may represent the carcinogenic origin and targetable vulnerability of hyperglycemia-driven cancer.
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Affiliation(s)
- Yang Su
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yifan Luo
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China; School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Peitao Zhang
- Department of Thyroid and Neck Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hong Lin
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Weijie Pu
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Hongyun Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Huifang Wang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yi Hao
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yihang Xiao
- School of Science, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, and Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Xiaozhe Zhang
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Xiayun Wei
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Siyue Nie
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong, 518083, China
| | - Qiuyu Fu
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Hao Chen
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Niu Huang
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Yan Ren
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Mingxuan Wu
- School of Science, Westlake University, Westlake Laboratory of Life Sciences and Biomedicine, and Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | | | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenfei Jin
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Fengchao Wang
- National Institute of Biological Sciences, Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
| | - Li Zhao
- Department of Thyroid and Neck Oncology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Feng Rao
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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48
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Shaaban M, Clapperton JA, Ding S, Kunzelmann S, Mäeots ME, Maslen SL, Skehel JM, Enchev RI. Structural and mechanistic insights into the CAND1-mediated SCF substrate receptor exchange. Mol Cell 2023:S1097-2765(23)00418-5. [PMID: 37339624 DOI: 10.1016/j.molcel.2023.05.034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/22/2023]
Abstract
Modular SCF (SKP1-CUL1-Fbox) ubiquitin E3 ligases orchestrate multiple cellular pathways in eukaryotes. Their variable SKP1-Fbox substrate receptor (SR) modules enable regulated substrate recruitment and subsequent proteasomal degradation. CAND proteins are essential for the efficient and timely exchange of SRs. To gain structural understanding of the underlying molecular mechanism, we reconstituted a human CAND1-driven exchange reaction of substrate-bound SCF alongside its co-E3 ligase DCNL1 and visualized it by cryo-EM. We describe high-resolution structural intermediates, including a ternary CAND1-SCF complex, as well as conformational and compositional intermediates representing SR- or CAND1-dissociation. We describe in molecular detail how CAND1-induced conformational changes in CUL1/RBX1 provide an optimized DCNL1-binding site and reveal an unexpected dual role for DCNL1 in CAND1-SCF dynamics. Moreover, a partially dissociated CAND1-SCF conformation accommodates cullin neddylation, leading to CAND1 displacement. Our structural findings, together with functional biochemical assays, help formulate a detailed model for CAND-SCF regulation.
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Affiliation(s)
- Mohammed Shaaban
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Julie A Clapperton
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Shan Ding
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Simone Kunzelmann
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Märt-Erik Mäeots
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Sarah L Maslen
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - J Mark Skehel
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Radoslav I Enchev
- The Visual Biochemistry Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
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49
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De Cesare V. MALDI-TOF Mass Spectrometry for interrogating ubiquitin enzymes. Front Mol Biosci 2023; 10:1184934. [PMID: 37234921 PMCID: PMC10206504 DOI: 10.3389/fmolb.2023.1184934] [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: 03/12/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
The attachment of ubiquitin to a substrate (ubiquitination or ubiquitylation) impacts its lifetime and regulates its function within the cell. Several classes of enzymes oversee the attachment of ubiquitin to the substrate: an E1 activating enzyme that makes ubiquitin chemically susceptible prior to the following stages of conjugation and ligation, respectively mediated by E2 conjugating enzymes (E2s) and E3 ligases (E3s). Around 40 E2s and more than 600 E3s are encoded in the human genome, and their combinatorial and cooperative behaviour dictate the tight specificity necessary for the regulation of thousands of substrates. The removal of ubiquitin is orchestrated by a network of about 100 deubiquitylating enzymes (DUBs). Many cellular processes are tightly controlled by ubiquitylation, which is essential in maintaining cellular homeostasis. Because of the fundamental role(s) of ubiquitylation, there is an interest in better understanding the function and specificity of the ubiquitin machinery. Since 2014, an expanding array of Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) Mass Spectrometry (MS) assays have been developed to systematically characterise the activity of a variety of ubiquitin enzymes in vitro. Here we recapitulate how MALDI-TOF MS aided the in vitro characterization of ubiquitin enzymes and the discovery of new and unexpected of E2s and DUBs functions. Given the versatility of the MALDI-TOF MS approach, we foreseen the use of this technology to further expand our understanding of ubiquitin and ubiquitin-like enzymes.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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50
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Monda JK, Ge X, Hunkeler M, Donovan KA, Ma MW, Jin CY, Leonard M, Fischer ES, Bennett EJ. HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways. Cell Rep 2023; 42:112496. [PMID: 37167062 DOI: 10.1016/j.celrep.2023.112496] [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: 11/21/2022] [Revised: 03/21/2023] [Accepted: 04/25/2023] [Indexed: 05/13/2023] Open
Abstract
HUWE1 is a large, enigmatic HECT-domain ubiquitin ligase implicated in the regulation of diverse pathways, including DNA repair, apoptosis, and differentiation. How HUWE1 engages its structurally diverse substrates and how HUWE1 activity is regulated are unknown. Using unbiased quantitative proteomics, we find that HUWE1 targets substrates in a largely cell-type-specific manner. However, we identify C16orf72/HAPSTR1 as a robust HUWE1 substrate in multiple cell lines. Previously established physical and genetic interactions between HUWE1 and HAPSTR1 suggest that HAPSTR1 positively regulates HUWE1 function. Here, we show that HAPSTR1 is required for HUWE1 nuclear localization and nuclear substrate targeting. Nuclear HUWE1 is required for both cell proliferation and modulation of stress signaling pathways, including p53 and nuclear factor κB (NF-κB)-mediated signaling. Combined, our results define a role for HAPSTR1 in gating critical nuclear HUWE1 functions.
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Affiliation(s)
- Julie K Monda
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xuezhen Ge
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle W Ma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marilyn Leonard
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric J Bennett
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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