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Zhou QX, Tian SY, Liu XN, Xiang SP, Lin XJ, Tan F, Mou YN. Research progress of ubiquitin and ubiquitin-like signaling in Toxoplasma gondii. Acta Trop 2024; 257:107283. [PMID: 38955322 DOI: 10.1016/j.actatropica.2024.107283] [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: 04/01/2024] [Revised: 06/03/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
Toxoplasmosis, a zoonotic parasitic disease caused by Toxoplasma gondii (T. gondii), is prevalent worldwide. The fact should be emphasized that a considerable proportion of individuals infected with T. gondii may remain asymptomatic; nevertheless, the condition can have severe implications for pregnant women or immunocompromised individuals. The current treatment of toxoplasmosis primarily relies on medication; however, traditional anti-toxoplasmosis drugs exhibit significant limitations in terms of efficacy, side effects, and drug resistance. The life cycles of T. gondii are characterized by distinct stages and its body morphology goes through dynamic alterations during the growth cycle that are intricately governed by a wide array of post-translational modifications (PTMs). Ubiquitin (Ub) signaling and ubiquitin-like (Ubl) signaling are two crucial post-translational modification pathways within cells, regulating protein function, localization, stability, or interactions by attaching Ub or ubiquitin-like proteins (Ubls) to target proteins. While these signaling mechanisms share some functional similarities, they have distinct regulatory mechanisms and effects. T. gondii possesses both Ub and Ubls and plays a significant role in regulating the parasite's life cycle and maintaining its morphology through PTMs of substrate proteins. Investigating the role and mechanism of protein ubiquitination in T. gondii will provide valuable insights for preventing and treating toxoplasmosis. This review explores the distinctive characteristics of Ub and Ubl signaling in T. gondii, with the aim of inspiring research ideas for the identification of safer and more effective drug targets against toxoplasmosis.
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Affiliation(s)
- Qi-Xin Zhou
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, PR China
| | - Si-Yu Tian
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, PR China
| | - Xiao-Na Liu
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, PR China
| | - Shi-Peng Xiang
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, PR China
| | - Xue-Jing Lin
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, PR China
| | - Feng Tan
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, PR China
| | - Ya-Ni Mou
- Department of Parasitology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, Zhejiang, PR China.
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2
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Lu K, Zhang M, Qin H, Shen S, Song H, Jiang H, Zhang C, Xiao G, Tong L, Jiang Q, Chen D. Disruption of cyclin D1 degradation leads to the development of mantle cell lymphoma. Acta Pharm Sin B 2024; 14:2977-2991. [PMID: 39027231 PMCID: PMC11252481 DOI: 10.1016/j.apsb.2024.03.013] [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: 11/23/2023] [Revised: 01/12/2024] [Accepted: 02/28/2024] [Indexed: 07/20/2024] Open
Abstract
Cyclin D1 has been recognized as an oncogene due to its abnormal upregulation in different types of cancers. Here, we demonstrated that cyclin D1 is SUMOylated, and we identified Itch as a specific E3 ligase recognizing SUMOylated cyclin D1 and mediating SUMO-induced ubiquitination and proteasome degradation of cyclin D1. We generated cyclin D1 mutant mice with mutations in the SUMOylation site, phosphorylation site, or both sites of cyclin D1, and found that double mutant mice developed a Mantle cell lymphoma (MCL)-like phenotype. We showed that arsenic trioxide (ATO) enhances cyclin D1 SUMOylation-mediated degradation through inhibition of cyclin D1 deSUMOylation enzymes, leading to MCL cell apoptosis. Treatment of severe combined immunodeficiency (SCID) mice grafted with MCL cells with ATO resulted in a significant reduction in tumor growth. In this study, we provide novel insights into the mechanisms of MCL tumor development and cyclin D1 regulation and discover a new strategy for MCL treatment.
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Affiliation(s)
- Ke Lu
- Research Center for Computer-aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518055, China
| | - Ming Zhang
- Oncology Department, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongyu Qin
- Research Center for Computer-aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518055, China
- Division of Spine Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Siyu Shen
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China
| | - Haiqing Song
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Hua Jiang
- Division of Spine Surgery, the First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Chunxiang Zhang
- Department of Cardiology, Basic Medicine Innovation Center for Cardiometabolic Diseases of Ministry of Education, Institute of Cardiovascular Research, the Affiliated Hospital, Southwest Medical University, Luzhou 646000, China
| | - Guozhi Xiao
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liping Tong
- Research Center for Computer-aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qing Jiang
- Division of Sports Medicine and Adult Reconstructive Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210008, China
| | - Di Chen
- Research Center for Computer-aided Drug Discovery, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology, Shenzhen 518055, China
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3
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Rodrigues JS, Chenlo M, Bravo SB, Perez-Romero S, Suarez-Fariña M, Sobrino T, Sanz-Pamplona R, González-Prieto R, Blanco Freire MN, Nogueiras R, López M, Fugazzola L, Cameselle-Teijeiro JM, Alvarez CV. dsRNAi-mediated silencing of PIAS2beta specifically kills anaplastic carcinomas by mitotic catastrophe. Nat Commun 2024; 15:3736. [PMID: 38744818 PMCID: PMC11094195 DOI: 10.1038/s41467-024-47751-1] [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: 08/02/2022] [Accepted: 04/11/2024] [Indexed: 05/16/2024] Open
Abstract
The E3 SUMO ligase PIAS2 is expressed at high levels in differentiated papillary thyroid carcinomas but at low levels in anaplastic thyroid carcinomas (ATC), an undifferentiated cancer with high mortality. We show here that depletion of the PIAS2 beta isoform with a transcribed double-stranded RNA-directed RNA interference (PIAS2b-dsRNAi) specifically inhibits growth of ATC cell lines and patient primary cultures in vitro and of orthotopic patient-derived xenografts (oPDX) in vivo. Critically, PIAS2b-dsRNAi does not affect growth of normal or non-anaplastic thyroid tumor cultures (differentiated carcinoma, benign lesions) or cell lines. PIAS2b-dsRNAi also has an anti-cancer effect on other anaplastic human cancers (pancreas, lung, and gastric). Mechanistically, PIAS2b is required for proper mitotic spindle and centrosome assembly, and it is a dosage-sensitive protein in ATC. PIAS2b depletion promotes mitotic catastrophe at prophase. High-throughput proteomics reveals the proteasome (PSMC5) and spindle cytoskeleton (TUBB3) to be direct targets of PIAS2b SUMOylation at mitotic initiation. These results identify PIAS2b-dsRNAi as a promising therapy for ATC and other aggressive anaplastic carcinomas.
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Affiliation(s)
- Joana S Rodrigues
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Miguel Chenlo
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Susana B Bravo
- Department of Proteomics, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Servicio Galego de Saúde (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Sihara Perez-Romero
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Maria Suarez-Fariña
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Tomas Sobrino
- Department of NeuroAging Group - Clinical Neurosciences Research Laboratory (LINC), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Servicio Galego de Saúde (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Rebeca Sanz-Pamplona
- University Hospital Lozano Blesa, Institute for Health Research Aragon (IISA), ARAID Foundation, Aragon Government and CIBERESP, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Román González-Prieto
- Cell Dynamics and Signaling Department, Andalusian Center for Molecular Biology and Regenerative Medicine, Universidad de Sevilla - CSIC - Universidad Pablo de Olavide-Junta de Andalucía, 41092, Sevilla, Spain
- Department of Cell Biology, Faculty of Biology, University of Sevilla, 41012, Sevilla, Spain
| | - Manuel Narciso Blanco Freire
- Department of Surgery, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Servicio Galego de Saúde (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Ruben Nogueiras
- Molecular Metabolism, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Miguel López
- NeurObesity, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain
| | - Laura Fugazzola
- Department of Endocrine and Metabolic Diseases and Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano, Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS); Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - José Manuel Cameselle-Teijeiro
- Department of Pathology, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), Servicio Galego de Saúde (SERGAS), Instituto de Investigación Sanitaria de Santiago (IDIS), University of Santiago de Compostela (USC), Santiago de Compostela, Spain.
| | - Clara V Alvarez
- Neoplasia & Endocrine Differentiation, Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), University of Santiago de Compostela (USC), Instituto de Investigación Sanitaria (IDIS), Santiago de Compostela, Spain.
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Wu W, Huang C. SUMOylation and DeSUMOylation: Prospective therapeutic targets in cancer. Life Sci 2023; 332:122085. [PMID: 37722589 DOI: 10.1016/j.lfs.2023.122085] [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: 08/05/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
The SUMO family is a type of ubiquitin-like protein modification molecule. Its protein modification mechanism is similar to that of ubiquitination: both involve modifier-activating enzyme E1, conjugating enzyme E2 and substrate-specific ligase E3. However, polyubiquitination can lead to the degradation of substrate proteins, while poly-SUMOylation only leads to the degradation of substrate proteins through the proteasome pathway after being recognized by ubiquitin as a signal factor. There are currently five reported subtypes in the SUMO family, namely SUMO1-5. As a reversible dynamic modification, intracellular sentrin/SUMO-specific proteases (SENPs) mainly regulate the reverse reaction pathway of SUMOylation. The SUMOylation modification system affects the localization, activation and turnover of proteins in cells and participates in regulating most nuclear and extranuclear molecular reactions. Abnormal expression of proteins related to the SUMOylation pathway is commonly observed in tumors, indicating that this pathway is closely related to tumor occurrence, metastasis and invasion. This review mainly discusses the composition of members in the protein family related to SUMOylation pathways, mutual connections between SUMOylation and other post-translational modifications on proteins as well as therapeutic drugs developed based on these pathways.
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Affiliation(s)
- Wenyan Wu
- Kunming University of Science and Technology, Medical School, Kunming 650500, China
| | - Chao Huang
- Kunming University of Science and Technology, Medical School, Kunming 650500, China.
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Mandel N, Büttner M, Poschet G, Kuner R, Agarwal N. SUMOylation Modulates Reactive Oxygen Species (ROS) Levels and Acts as a Protective Mechanism in the Type 2 Model of Diabetic Peripheral Neuropathy. Cells 2023; 12:2511. [PMID: 37947589 PMCID: PMC10648122 DOI: 10.3390/cells12212511] [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: 08/08/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
Diabetic peripheral neuropathy (DPN) is the prevalent type of peripheral neuropathy; it primarily impacts extremity nerves. Its multifaceted nature makes the molecular mechanisms of diabetic neuropathy intricate and incompletely elucidated. Several types of post-translational modifications (PTMs) have been implicated in the development and progression of DPN, including phosphorylation, glycation, acetylation and SUMOylation. SUMOylation involves the covalent attachment of small ubiquitin-like modifier (SUMO) proteins to target proteins, and it plays a role in various cellular processes, including protein localization, stability, and function. While the specific relationship between high blood glucose and SUMOylation is not extensively studied, recent evidence implies its involvement in the development of DPN in type 1 diabetes. In this study, we investigated the impact of SUMOylation on the onset and progression of DPN in a type 2 diabetes model using genetically modified mutant mice lacking SUMOylation, specifically in peripheral sensory neurons (SNS-Ubc9-/-). Behavioural measurement for evoked pain, morphological analyses of nerve fibre loss in the epidermis, measurement of reactive oxygen species (ROS) levels, and antioxidant molecules were analysed over several months in SUMOylation-deficient and control mice. Our longitudinal analysis at 30 weeks post-high-fat diet revealed that SNS-Ubc9-/- mice exhibited earlier and more pronounced thermal and mechanical sensation loss and accelerated intraepidermal nerve fibre loss compared to control mice. Mechanistically, these changes are associated with increased levels of ROS both in sensory neuronal soma and in peripheral axonal nerve endings in SNS-Ubc9-/- mice. In addition, we observed compromised detoxifying potential, impaired respiratory chain complexes, and reduced levels of protective lipids in sensory neurons upon deletion of SUMOylation in diabetic mice. Importantly, we also identified mitochondrial malate dehydrogenase (MDH2) as a SUMOylation target, the activity of which is negatively regulated by SUMOylation. Our results indicate that SUMOylation is an essential neuroprotective mechanism in sensory neurons in type 2 diabetes, the deletion of which causes oxidative stress and an impaired respiratory chain, resulting in energy depletion and subsequent damage to sensory neurons.
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Affiliation(s)
- Nicolas Mandel
- Institute of Pharmacology, Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany (R.K.)
| | - Michael Büttner
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Gernot Poschet
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany
| | - Rohini Kuner
- Institute of Pharmacology, Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany (R.K.)
| | - Nitin Agarwal
- Institute of Pharmacology, Medical Faculty Heidelberg, Heidelberg University, Im Neuenheimer Feld 366, 69120 Heidelberg, Germany (R.K.)
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Hertz EPT, Vega IAD, Kruse T, Wang Y, Hendriks IA, Bizard AH, Eugui-Anta A, Hay RT, Nielsen ML, Nilsson J, Hickson ID, Mailand N. The SUMO-NIP45 pathway processes toxic DNA catenanes to prevent mitotic failure. Nat Struct Mol Biol 2023; 30:1303-1313. [PMID: 37474739 PMCID: PMC10497417 DOI: 10.1038/s41594-023-01045-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
SUMOylation regulates numerous cellular processes, but what represents the essential functions of this protein modification remains unclear. To address this, we performed genome-scale CRISPR-Cas9-based screens, revealing that the BLM-TOP3A-RMI1-RMI2 (BTRR)-PICH pathway, which resolves ultrafine anaphase DNA bridges (UFBs) arising from catenated DNA structures, and the poorly characterized protein NIP45/NFATC2IP become indispensable for cell proliferation when SUMOylation is inhibited. We demonstrate that NIP45 and SUMOylation orchestrate an interphase pathway for converting DNA catenanes into double-strand breaks (DSBs) that activate the G2 DNA-damage checkpoint, thereby preventing cytokinesis failure and binucleation when BTRR-PICH-dependent UFB resolution is defective. NIP45 mediates this new TOP2-independent DNA catenane resolution process via its SUMO-like domains, promoting SUMOylation of specific factors including the SLX4 multi-nuclease complex, which contributes to catenane conversion into DSBs. Our findings establish that SUMOylation exerts its essential role in cell proliferation by enabling resolution of toxic DNA catenanes via nonepistatic NIP45- and BTRR-PICH-dependent pathways to prevent mitotic failure.
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Affiliation(s)
- Emil P T Hertz
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Ignacio Alonso-de Vega
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Kruse
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Yiqing Wang
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna H Bizard
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ania Eugui-Anta
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark.
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Cheng X, Yang W, Lin W, Mei F. Paradoxes of Cellular SUMOylation Regulation: A Role of Biomolecular Condensates? Pharmacol Rev 2023; 75:979-1006. [PMID: 37137717 PMCID: PMC10441629 DOI: 10.1124/pharmrev.122.000784] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
Protein SUMOylation is a major post-translational modification essential for maintaining cellular homeostasis. SUMOylation has long been associated with stress responses as a diverse array of cellular stress signals are known to trigger rapid alternations in global protein SUMOylation. In addition, while there are large families of ubiquitination enzymes, all small ubiquitin-like modifiers (SUMOs) are conjugated by a set of enzymatic machinery comprising one heterodimeric SUMO-activating enzyme, a single SUMO-conjugating enzyme, and a small number of SUMO protein ligases and SUMO-specific proteases. How a few SUMOylation enzymes specifically modify thousands of functional targets in response to diverse cellular stresses remains an enigma. Here we review recent progress toward understanding the mechanisms of SUMO regulation, particularly the potential roles of liquid-liquid phase separation/biomolecular condensates in regulating cellular SUMOylation during cellular stresses. In addition, we discuss the role of protein SUMOylation in pathogenesis and the development of novel therapeutics targeting SUMOylation. SIGNIFICANCE STATEMENT: Protein SUMOylation is one of the most prevalent post-translational modifications and plays a vital role in maintaining cellular homeostasis in response to stresses. Protein SUMOylation has been implicated in human pathogenesis, such as cancer, cardiovascular diseases, neurodegeneration, and infection. After more than a quarter century of extensive research, intriguing enigmas remain regarding the mechanism of cellular SUMOylation regulation and the therapeutic potential of targeting SUMOylation.
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Affiliation(s)
- Xiaodong Cheng
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Wenli Yang
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Wei Lin
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Fang Mei
- Department of Integrative Biology & Pharmacology and Texas Therapeutics Institute, Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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Mao K, Luo J, Ye J, Li L, Lin F, Zhou M, Wang D, Yu L, Zhu Z, Zuo D, Ye J. 2-D-gal Targets Terminal Fucosylation to Inhibit T-cell Response in a Mouse Skin Transplant Model. Transplantation 2023; 107:1291-1301. [PMID: 36367925 DOI: 10.1097/tp.0000000000004408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Organ allograft rejection is mainly driven by T-cell response. Studies have shown that fucosylation plays essential roles in the immune cell development and function. Terminal fucosylation inhibitor, 2-deoxy-D-galactose (2-D-gal), has been reported to suppress immunoresponse of macrophages, but its effects on T-cell-mediated immune response and transplant rejection have not been fully explored. METHODS The terminal fucosylation level in T cells was detected through ulex europaeus agglutinin-I staining. The consequences of 2-D-gal on murine T-cell proliferation, activation, cytokine secretion, and cell cycle were investigated in vitro. T-cell receptor signaling cascades were examined. Last, mouse skin transplant model was utilized to evaluate the regulatory effects of 2-D-gal on T-cell response in vivo. RESULTS The expression of fucosyltransferase1 was upregulated in CD3/CD28-activated T cells along with an elevation of α(1,2)-fucosylation level as seen by ulex europaeus agglutinin-I staining. Furthermore, 2-D-gal suppressed T-cell activation and proliferation, decrease cytokines production, arrest cell cycle, and prevent the activation of T-cell receptor signaling cascades. In vivo experiments showed that 2-D-gal limited T-cell proliferation to prolong skin allograft in mice. This was accompanied by lower level of inflammatory cytokines, and were comparable to those treated with Cyclosporin A. CONCLUSIONS Terminal fucosylation appears to play a role in T-cell activation and proliferation, and its inhibitor, 2-D-gal, can suppress T-cell activation and proliferation both in vitro and in vivo. In a therapeutic context, inhibiting terminal fucosylation may be a potential strategy to prevent allogeneic transplant rejection.
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Affiliation(s)
- Kaifeng Mao
- Department of Kidney Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Jialiang Luo
- Department of Dermatology, the Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Junli Ye
- Department of Physiology and Pathophysiology, School of Basic Medicine, Medical College, Qingdao University, Qingdao, China
| | - Lei Li
- Department of Dermatology, the Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Fenwang Lin
- Department of Kidney Transplantation, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Minjie Zhou
- Department of Kidney Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Di Wang
- Department of Dermatology, Dermatology Hospital of Southern Medical University, Southern Medical University, Guangzhou, Guangdong, China
| | - Lu Yu
- Department of Dermatology, the Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Zhengyumeng Zhu
- Department of Dermatology, the Fifth Affiliated Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Daming Zuo
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China
| | - Junsheng Ye
- Department of Kidney Transplantation, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Department of Kidney Transplantation, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
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Moallem M, Akhter A, Burke GL, Babu J, Bergey BG, McNeil JB, Baig MS, Rosonina E. Sumoylation is Largely Dispensable for Normal Growth but Facilitates Heat Tolerance in Yeast. Mol Cell Biol 2023; 43:64-84. [PMID: 36720466 PMCID: PMC9936996 DOI: 10.1080/10985549.2023.2166320] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Numerous proteins are sumoylated in normally growing yeast and SUMO conjugation levels rise upon exposure to several stress conditions. We observe high levels of sumoylation also during early exponential growth and when nutrient-rich medium is used. However, we find that reduced sumoylation (∼75% less than normal) is remarkably well-tolerated, with no apparent growth defects under nonstress conditions or under osmotic, oxidative, or ethanol stresses. In contrast, strains with reduced activity of Ubc9, the sole SUMO conjugase, are temperature-sensitive, implicating sumoylation in the heat stress response, specifically. Aligned with this, a mild heat shock triggers increased sumoylation which requires functional levels of Ubc9, but likely also depends on decreased desumoylation, since heat shock reduces protein levels of Ulp1, the major SUMO protease. Furthermore, we find that a ubc9 mutant strain with only ∼5% of normal sumoylation levels shows a modest growth defect, has abnormal genomic distribution of RNA polymerase II (RNAPII), and displays a greatly expanded redistribution of RNAPII after heat shock. Together, our data implies that SUMO conjugations are largely dispensable under normal conditions, but a threshold level of Ubc9 activity is needed to maintain transcriptional control and to modulate the redistribution of RNAPII and promote survival when temperatures rise.
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Affiliation(s)
- Marjan Moallem
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Akhi Akhter
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Giovanni L Burke
- Department of Biology, York University, Toronto, Ontario, Canada
| | - John Babu
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - J Bryan McNeil
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Mohammad S Baig
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Emanuel Rosonina
- Department of Biology, York University, Toronto, Ontario, Canada
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10
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Jiang H, Sun M, Zhao Y, Liu G, Zhong L, Xue H, Chen X, Zheng Y, Wang M. The early function of cortisol in liver during Aeromonas hydrophila infection: Dynamics of the transcriptome and accessible chromatin landscapes. Front Immunol 2022; 13:989075. [PMID: 36532002 PMCID: PMC9751032 DOI: 10.3389/fimmu.2022.989075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
In China, channel catfish (Ictalurus punctatus) is an important aquaculture species; however, haemorrhagic disease (Aeromonas hydrophila induced disease) in these fish has caused tremendous economic loss due to high morbidity and mass mortality in the breeding industry. The role of cortisol in bacterial diseases, particularly in the acute phase, remains unclear. In this study, liver transcriptome (RNA-seq) and chromatin accessibility (ATAC-seq) analyses were employed to investigate the early functional role of cortisol in Aeromonas hydrophila-stimulated responses. Our experiments confirmed that A. hydrophila infection can initially significantly increase serum cortisol levels at 1 h after infection. At this time point, the increased serum cortisol levels can significantly regulate A. hydrophila-regulated genes by affecting both transcriptome and chromatin accessibility. Cross-analysis of RNA-seq and ATAC-seq revealed that a certain gene group (92 target_DEGs) was regulated at an early time point by cortisol. KEGG enrichment analysis revealed that the top three pathways according to target_DEGs were cancer, glutathione metabolism, and the Notch signalling pathway. The protein-protein interaction analysis of target_DEGs revealed that they may be primarily involved in cell proliferation, CD8+ T cell function, glutathione synthesis, and activation of the NF-κB signalling pathway. This suggests that after the emergence of immune stress, the early regulation of cortisol is positive against the immune response. It is possible that in this situation, the animal is attempting to avoid dangerous situations and risks and then cope with the imbalance produced by the stressor to ultimately restore homeostasis. Our results will contribute to future research on fish and provide valuable insight regarding the mechanism of immune regulation by cortisol and the study of bacterial haemorrhagic disease in channel catfish.
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11
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Kumar S, Schoonderwoerd MJA, Kroonen JS, de Graaf IJ, Sluijter M, Ruano D, González-Prieto R, Verlaan-de Vries M, Rip J, Arens R, de Miranda NFCC, Hawinkels LJAC, van Hall T, Vertegaal ACO. Targeting pancreatic cancer by TAK-981: a SUMOylation inhibitor that activates the immune system and blocks cancer cell cycle progression in a preclinical model. Gut 2022; 71:2266-2283. [PMID: 35074907 PMCID: PMC9554032 DOI: 10.1136/gutjnl-2021-324834] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 12/29/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Pancreatic ductal adenocarcinoma (PDAC) has the characteristics of high-density desmoplastic stroma, a distinctive immunosuppressive microenvironment and is profoundly resistant to all forms of chemotherapy and immunotherapy, leading to a 5-year survival rate of 9%. Our study aims to add novel small molecule therapeutics for the treatment of PDAC. DESIGN We have studied whether TAK-981, a novel highly selective and potent small molecule inhibitor of the small ubiquitin like modifier (SUMO) activating enzyme E1 could be used to treat a preclinical syngeneic PDAC mouse model and we have studied the mode of action of TAK-981. RESULTS We found that SUMOylation, a reversible post-translational modification required for cell cycle progression, is increased in PDAC patient samples compared with normal pancreatic tissue. TAK-981 decreased SUMOylation in PDAC cells at the nanomolar range, thereby causing a G2/M cell cycle arrest, mitotic failure and chromosomal segregation defects. TAK-981 efficiently limited tumour burden in the KPC3 syngeneic mouse model without evidence of systemic toxicity. In vivo treatment with TAK-981 enhanced the proportions of activated CD8 T cells and natural killer (NK) cells but transiently decreased B cell numbers in tumour, peripheral blood, spleen and lymph nodes. Single cell RNA sequencing revealed activation of the interferon response on TAK-981 treatment in lymphocytes including T, B and NK cells. TAK-981 treatment of CD8 T cells ex vivo induced activation of STAT1 and interferon target genes. CONCLUSION Our findings indicate that pharmacological inhibition of the SUMO pathway represents a potential strategy to target PDAC via a dual mechanism: inhibiting cancer cell cycle progression and activating anti-tumour immunity by inducing interferon signalling.
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Affiliation(s)
- Sumit Kumar
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Jessie S Kroonen
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ilona J de Graaf
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Sluijter
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Román González-Prieto
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Jasper Rip
- Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ramon Arens
- Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Thorbald van Hall
- Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Center, Leiden, The Netherlands
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12
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Vertegaal ACO. Signalling mechanisms and cellular functions of SUMO. Nat Rev Mol Cell Biol 2022; 23:715-731. [PMID: 35750927 DOI: 10.1038/s41580-022-00500-y] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2022] [Indexed: 12/22/2022]
Abstract
Sumoylation is an essential post-translational modification that is catalysed by a small number of modifying enzymes but regulates thousands of target proteins in a dynamic manner. Small ubiquitin-like modifiers (SUMOs) can be attached to target proteins as one or more monomers or in the form of polymers of different types. Non-covalent readers recognize SUMO-modified proteins via SUMO interaction motifs. SUMO simultaneously modifies groups of functionally related proteins to regulate predominantly nuclear processes, including gene expression, the DNA damage response, RNA processing, cell cycle progression and proteostasis. Recent progress has increased our understanding of the cellular and pathophysiological roles of SUMO modifications, extending their functions to the regulation of immunity, pluripotency and nuclear body assembly in response to oxidative stress, which partly occurs through the recently characterized mechanism of liquid-liquid phase separation. Such progress in understanding the roles and regulation of sumoylation opens new avenues for the targeting of SUMO to treat disease, and indeed the first drug blocking sumoylation is currently under investigation in clinical trials as a possible anticancer agent.
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Affiliation(s)
- Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands.
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13
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Mete B, Pekbilir E, Bilge BN, Georgiadou P, Çelik E, Sutlu T, Tabak F, Sahin U. Human immunodeficiency virus type 1 impairs sumoylation. Life Sci Alliance 2022; 5:5/6/e202101103. [PMID: 35181598 PMCID: PMC8860096 DOI: 10.26508/lsa.202101103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 12/18/2022] Open
Abstract
The HIV type 1 dampens host cell sumoylation in vitro and reduces the expression of UBA2 protein, a subunit of the SUMO E1–activating enzyme. In vivo, infection in patients is associated with diminished global leukocyte sumoylation activity. During infection, the human immunodeficiency virus type 1 (HIV-1) manipulates host cell mechanisms to its advantage, thereby controlling its replication or latency, and evading immune responses. Sumoylation is an essential post-translational modification that controls vital cellular activities including proliferation, stemness, or anti-viral immunity. SUMO peptides oppose pathogen replication and mediate interferon-dependent anti-viral activities. In turn, several viruses and bacteria attack sumoylation to disarm host immune responses. Here, we show that HIV-1 impairs cellular sumoylation and targets the host SUMO E1–activating enzyme. HIV-1 expression in cultured HEK293 cells or in CD4+ Jurkat T lymphocytes diminishes sumoylation by both SUMO paralogs, SUMO1 and SUMO2/3. HIV-1 causes a sharp and specific decline in UBA2 protein levels, a subunit of the heterodimeric SUMO E1 enzyme, which likely serves to reduce the efficiency of global protein sumoylation. Furthermore, HIV-1–infected individuals display a significant reduction in total leukocyte sumoylation that is uncoupled from HIV-induced cytopenia. Because sumoylation is vital for immune function, T-cell expansion and activity, loss of sumoylation during HIV disease may contribute to immune system deterioration in patients.
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Affiliation(s)
- Bilgül Mete
- Department of Infectious Diseases and Clinical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Istanbul, Turkey
| | - Emre Pekbilir
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Bilge Nur Bilge
- Department of Medical Biology, Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Istanbul, Turkey
| | - Panagiota Georgiadou
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Elif Çelik
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Tolga Sutlu
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
| | - Fehmi Tabak
- Department of Infectious Diseases and Clinical Microbiology, Istanbul University-Cerrahpasa, Cerrahpasa School of Medicine, Istanbul, Turkey
| | - Umut Sahin
- Department of Molecular Biology and Genetics, Bogazici University, Center for Life Sciences and Technologies, Istanbul, Turkey
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14
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Ghimire S, Tang X, Liu W, Fu X, Zhang H, Zhang N, Si H. SUMO conjugating enzyme: a vital player of SUMO pathway in plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2421-2431. [PMID: 34744375 PMCID: PMC8526628 DOI: 10.1007/s12298-021-01075-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plants face numerous challenges such as biotic and abiotic stresses during their whole lifecycle. As they are sessile in nature, they ought to develop multiple ways to act during stressed conditions to maintain cellular homeostasis. Among various defense mechanisms, the small ubiquitin-like modifiers (SUMO) pathway is considered as the most important because several nuclear proteins regulated by this pathway are involved in several cellular functions such as response to stress, transcription, translation, metabolism of RNA, energy metabolism, repairing damaged DNA, ensuring genome stability and nuclear trafficking. In general, the SUMO pathway has its own particular set of enzymes E1, E2, and E3. The SUMO conjugating enzyme [SCE (E2)] is a very crucial member of the pathway which can transfer SUMO to its target protein even without the involvement of E3. More than just a middle player, it has shown its involvement in effective triggered immunity in crops like tomato and various abiotic stresses like drought and salinity in maize, rice, and Arabidopsis. This review tries to explore the importance of the SUMOylation process, focusing on the E2 enzyme and its regulatory role in the abiotic stress response, plant immunity, and DNA damage repair.
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Affiliation(s)
- Shantwana Ghimire
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Xun Tang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Weigang Liu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Xue Fu
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Huanhuan Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Ning Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
| | - Huaijun Si
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 People’s Republic of China
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15
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Baig MS, Dou Y, Bergey BG, Bahar R, Burgener JM, Moallem M, McNeil JB, Akhter A, Burke GL, Sri Theivakadadcham VS, Richard P, D’Amours D, Rosonina E. Dynamic sumoylation of promoter-bound general transcription factors facilitates transcription by RNA polymerase II. PLoS Genet 2021; 17:e1009828. [PMID: 34587155 PMCID: PMC8505008 DOI: 10.1371/journal.pgen.1009828] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/11/2021] [Accepted: 09/15/2021] [Indexed: 11/18/2022] Open
Abstract
Transcription-related proteins are frequently identified as targets of sumoylation, including multiple subunits of the RNA polymerase II (RNAPII) general transcription factors (GTFs). However, it is not known how sumoylation affects GTFs or whether they are sumoylated when they assemble at promoters to facilitate RNAPII recruitment and transcription initiation. To explore how sumoylation can regulate transcription genome-wide, we performed SUMO ChIP-seq in yeast and found, in agreement with others, that most chromatin-associated sumoylated proteins are detected at genes encoding tRNAs and ribosomal proteins (RPGs). However, we also detected 147 robust SUMO peaks at promoters of non-ribosomal protein-coding genes (non-RPGs), indicating that sumoylation also regulates this gene class. Importantly, SUMO peaks at non-RPGs align specifically with binding sites of GTFs, but not other promoter-associated proteins, indicating that it is GTFs specifically that are sumoylated there. Predominantly, non-RPGs with SUMO peaks are among the most highly transcribed, have high levels of TFIIF, and show reduced RNAPII levels when cellular sumoylation is impaired, linking sumoylation with elevated transcription. However, detection of promoter-associated SUMO by ChIP might be limited to sites with high levels of substrate GTFs, and promoter-associated sumoylation at non-RPGs may actually be far more widespread than we detected. Among GTFs, we found that TFIIF is a major target of sumoylation, specifically at lysines 60/61 of its Tfg1 subunit, and elevating Tfg1 sumoylation resulted in decreased interaction of TFIIF with RNAPII. Interestingly, both reducing promoter-associated sumoylation, in a sumoylation-deficient Tfg1-K60/61R mutant strain, and elevating promoter-associated SUMO levels, by constitutively tethering SUMO to Tfg1, resulted in reduced RNAPII occupancy at non-RPGs. This implies that dynamic GTF sumoylation at non-RPG promoters, not simply the presence or absence of SUMO, is important for maintaining elevated transcription. Together, our findings reveal a novel mechanism of regulating the basal transcription machinery through sumoylation of promoter-bound GTFs. Six general transcription factors (GTFs) assemble at promoters of protein-coding genes to enable recruitment of RNA polymerase II (RNAPII) and facilitate transcription initiation, but little is known about how they are regulated once promoter-bound. Here, we demonstrate that, in budding yeast, some components of GTFs are post-translationally modified by the SUMO peptide specifically when they are assembled at promoters. We determined that the large subunit of TFIIF, Tgf1, is the major target of sumoylation among GTFs and that increasing Tfg1 sumoylation reduces the interaction of TFIIF with RNAPII. Consistent with this, we found that increasing levels of SUMO at promoters of some protein-coding genes, by permanently attaching SUMO to Tfg1, resulted in reduced RNAPII levels associated with those genes. On the other hand, reducing promoter-associated sumoylation, by mutating SUMO-modified residues on Tfg1, also reduced RNAPII occupancy levels. Explaining these apparently contradictory findings, we propose that dynamic sumoylation of promoter-bound GTFs, not merely the presence or absence of SUMO, is important for facilitating rearrangements of promoter-bound GTF components that enhance transcription. Together, our data reveal a novel level of regulating the basal transcription machinery through SUMO modification at promoters of protein-coding genes.
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Affiliation(s)
- Mohammad S. Baig
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Yimo Dou
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Russell Bahar
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Marjan Moallem
- Department of Biology, York University, Toronto, Ontario, Canada
| | - James B. McNeil
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Akhi Akhter
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | | | - Patricia Richard
- Stellate Therapeutics, New York, New York, United States of America
| | - Damien D’Amours
- Ottawa Institute of Systems Biology, Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Emanuel Rosonina
- Department of Biology, York University, Toronto, Ontario, Canada
- * E-mail:
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16
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Coordinating DNA Replication and Mitosis through Ubiquitin/SUMO and CDK1. Int J Mol Sci 2021; 22:ijms22168796. [PMID: 34445496 PMCID: PMC8395760 DOI: 10.3390/ijms22168796] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022] Open
Abstract
Post-translational modification of the DNA replication machinery by ubiquitin and SUMO plays key roles in the faithful duplication of the genetic information. Among other functions, ubiquitination and SUMOylation serve as signals for the extraction of factors from chromatin by the AAA ATPase VCP. In addition to the regulation of DNA replication initiation and elongation, we now know that ubiquitination mediates the disassembly of the replisome after DNA replication termination, a process that is essential to preserve genomic stability. Here, we review the recent evidence showing how active DNA replication restricts replisome ubiquitination to prevent the premature disassembly of the DNA replication machinery. Ubiquitination also mediates the removal of the replisome to allow DNA repair. Further, we discuss the interplay between ubiquitin-mediated replisome disassembly and the activation of CDK1 that is required to set up the transition from the S phase to mitosis. We propose the existence of a ubiquitin–CDK1 relay, where the disassembly of terminated replisomes increases CDK1 activity that, in turn, favors the ubiquitination and disassembly of more replisomes. This model has important implications for the mechanism of action of cancer therapies that induce the untimely activation of CDK1, thereby triggering premature replisome disassembly and DNA damage.
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17
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Subramonian D, Chen TA, Paolini N, Zhang XDD. Poly-SUMO-2/3 chain modification of Nuf2 facilitates CENP-E kinetochore localization and chromosome congression during mitosis. Cell Cycle 2021; 20:855-873. [PMID: 33910471 DOI: 10.1080/15384101.2021.1907509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
SUMO modification is required for the kinetochore localization of the kinesin-like motor protein CENP-E, which subsequently mediates the alignment of chromosomes to the spindle equator during mitosis. However, the underlying mechanisms by which sumoylation regulates CENP-E kinetochore localization are still unclear. In this study, we first elucidate that the kinetochore protein Nuf2 is not only required for CENP-E kinetochore localization but also preferentially modified by poly-SUMO-2/3 chains. In addition, poly-SUMO-2/3 modification of Nuf2 is significantly upregulated during mitosis, which is temporally correlated to the kinetochore localization of CENP-E during mitosis. We further show that the mitotic defects in CENP-E kinetochore localization and chromosome congression caused by global inhibition of sumoylation can be rescued by expressing a fusion protein between Nuf2 and the SUMO-conjugating enzyme Ubc9 for stimulating Nuf2 SUMO-2/3 modification. Moreover, the expression of another fusion protein between Nuf2 and three SUMO-2 moieties (SUMO-2 trimer), which mimics the trimeric SUMO-2/3 chain modification of Nuf2, can also rescue the mitotic defects due to global inhibition of sumoylation. Conversely, expressing the other forms of Nuf2-SUMO fusion proteins, which imitate Nuf2 modifications by SUMO-2/3 monomer, SUMO-2/3 dimer, and SUMO-1 trimer, respectively, cannot rescue the same mitotic defects. Lastly, compared to Nuf2, the fusion protein simulating the trimeric SUMO-2 chain-modified Nuf2 exhibits a significantly higher binding affinity to CENP-E wild type containing a functional SUMO-interacting motif (SIM) but not the CENP-E SIM mutant. Hence, our results support a model that poly-SUMO-2/3 chain modification of Nuf2 facilitates CENP-E kinetochore localization and chromosome congression during mitosis.Abbreviations: CENP-E, centromere-associated protein E; SUMO, small ubiquitin-related modifier; SIM, SUMO-interacting motif.
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Affiliation(s)
- Divya Subramonian
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Te-An Chen
- Department of Biology, SUNY Buffalo State, Buffalo, NY, USA
| | | | - Xiang-Dong David Zhang
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA.,Department of Biology, SUNY Buffalo State, Buffalo, NY, USA
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18
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DNA-damage tolerance through PCNA ubiquitination and sumoylation. Biochem J 2021; 477:2655-2677. [PMID: 32726436 DOI: 10.1042/bcj20190579] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022]
Abstract
DNA-damage tolerance (DDT) is employed by eukaryotic cells to bypass replication-blocking lesions induced by DNA-damaging agents. In budding yeast Saccharomyces cerevisiae, DDT is mediated by RAD6 epistatic group genes and the central event for DDT is sequential ubiquitination of proliferating cell nuclear antigen (PCNA), a DNA clamp required for replication and DNA repair. DDT consists of two parallel pathways: error-prone DDT is mediated by PCNA monoubiquitination, which recruits translesion synthesis DNA polymerases to bypass lesions with decreased fidelity; and error-free DDT is mediated by K63-linked polyubiquitination of PCNA at the same residue of monoubiquitination, which facilitates homologous recombination-mediated template switch. Interestingly, the same PCNA residue is also subjected to sumoylation, which leads to inhibition of unwanted recombination at replication forks. All three types of PCNA posttranslational modifications require dedicated conjugating and ligation enzymes, and these enzymes are highly conserved in eukaryotes, from yeast to human.
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19
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Lee HS, Jeong GS. Salinosporamide A, a Marine-Derived Proteasome Inhibitor, Inhibits T Cell Activation through Regulating Proliferation and the Cell Cycle. Molecules 2020; 25:molecules25215031. [PMID: 33138297 PMCID: PMC7663257 DOI: 10.3390/molecules25215031] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 12/31/2022] Open
Abstract
The appropriate regulation of T cell activity under inflammatory conditions is crucial for maintaining immune homeostasis. Salinosporamide A discovered as a self-resistance product from the marine bacterium Salinospora tropica, has been used as a potent proteasome inhibitor (PI). Although PIs have been developed as novel therapeutics for autoimmune diseases, due to their immunosuppressive effect, whether salinosporamide A inhibits T cell activation remains unknown. The current study finds that salinosporamide A is not cytotoxic, but controls T cell proliferation. Results from our cell cycle arrest analysis revealed that salinosporamide A leads to cell cycle arrest and regulates the expression of cyclin-dependent kinases. Under activated conditions, salinosporamide A abrogated T cell activation by T cell receptor-mediated stimulation, in which the production of cytokines was inhibited by pretreatment with salinosporamide A. Furthermore, we demonstrated that the regulation of T cell activation by salinosporamide A is mediated by suppressing the MAPK pathway. Therefore, our results suggest that salinosporamide A effectively suppresses T cell activation through regulating T cell proliferation and the cell cycle and provides great insight into the development of novel therapeutics for autoimmune diseases or graft-versus-host disease.
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Affiliation(s)
| | - Gil-Saeng Jeong
- Correspondence: ; Tel.: +82-53-580-6649; Fax: +82-53-580-6645
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20
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Shetty PMV, Rangrez AY, Frey N. SUMO proteins in the cardiovascular system: friend or foe? J Biomed Sci 2020; 27:98. [PMID: 33099299 PMCID: PMC7585181 DOI: 10.1186/s12929-020-00689-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/16/2020] [Indexed: 02/07/2023] Open
Abstract
Post-translational modifications (PTMs) are crucial for the adaptation of various signalling pathways to ensure cellular homeostasis and proper adaptation to stress. PTM is a covalent addition of a small chemical functional group such as a phosphate group (phosphorylation), methyl group (methylation), or acetyl group (acetylation); lipids like hydrophobic isoprene polymers (isoprenylation); sugars such as a glycosyl group (glycosylation); or even small peptides such as ubiquitin (ubiquitination), SUMO (SUMOylation), NEDD8 (neddylation), etc. SUMO modification changes the function and/or fate of the protein especially under stress conditions, and the consequences of this conjugation can be appreciated from development to diverse disease processes. The impact of SUMOylation in disease has not been monotonous, rather SUMO is found playing a role on both sides of the coin either facilitating or impeding disease progression. Several recent studies have implicated SUMO proteins as key regulators in various cardiovascular disorders. The focus of this review is thus to summarize the current knowledge on the role of the SUMO family in the pathophysiology of cardiovascular diseases.
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Affiliation(s)
- Prithviraj Manohar Vijaya Shetty
- Department of Internal Medicine III (Cardiology, Angiology, Intensive Care), University Medical Center Kiel, Rosalind-Franklin Str. 12, 24105, Kiel, Germany
- Manipal Institute of Regenerative Medicine, MAHE-Bengaluru, Bangalore, India
| | - Ashraf Yusuf Rangrez
- Department of Internal Medicine III (Cardiology, Angiology, Intensive Care), University Medical Center Kiel, Rosalind-Franklin Str. 12, 24105, Kiel, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany.
| | - Norbert Frey
- Department of Internal Medicine III (Cardiology, Angiology, Intensive Care), University Medical Center Kiel, Rosalind-Franklin Str. 12, 24105, Kiel, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, Kiel, Germany.
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21
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López I, Chalatsi E, Ellenbroek SIJ, Andrieux A, Roux PF, Cerapio JP, Jouvion G, van Rheenen J, Seeler JS, Dejean A. An unanticipated tumor-suppressive role of the SUMO pathway in the intestine unveiled by Ubc9 haploinsufficiency. Oncogene 2020; 39:6692-6703. [PMID: 32948837 PMCID: PMC7581512 DOI: 10.1038/s41388-020-01457-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 08/20/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022]
Abstract
Sumoylation is an essential posttranslational modification in eukaryotes that has emerged as an important pathway in oncogenic processes. Most human cancers display hyperactivated sumoylation and many cancer cells are remarkably sensitive to its inhibition, thus supporting application of chemical sumoylation inhibitors in cancer treatment. Here we show, first, that transformed embryonic fibroblasts derived from mice haploinsufficient for Ubc9, the essential and unique gene encoding the SUMO E2 conjugating enzyme, exhibit enhanced proliferation and transformed phenotypes in vitro and as xenografts ex vivo. To then evaluate the possible impact of loss of one Ubc9 allele in vivo, we used a mouse model of intestinal tumorigenesis. We crossed Ubc9+/- mice with mice harboring a conditional ablation of Apc either all along the crypt-villus axis or only in Lgr5+ crypt-based columnar (CBC) cells, the cell compartment that includes the intestinal stem cells proposed as cells-of-origin of intestinal cancer. While Ubc9+/- mice display no overt phenotypes and no globally visible hyposumoylation in cells of the small intestine, we found, strikingly, that, upon loss of Apc in both models, Ubc9+/- mice develop more (>2-fold) intestinal adenomas and show significantly shortened survival. This is accompanied by reduced global sumoylation levels in the polyps, indicating that Ubc9 levels become critical upon oncogenic stress. Moreover, we found that, in normal conditions, Ubc9+/- mice show a moderate but robust (15%) increase in the number of Lgr5+ CBC cells when compared to their wild-type littermates, and further, that these cells display higher degree of stemness and cancer-related and inflammatory gene expression signatures that, altogether, may contribute to enhanced intestinal tumorigenesis. The phenotypes of Ubc9 haploinsufficiency discovered here indicate an unanticipated tumor-suppressive role of sumoylation, one that may have important implications for optimal use of sumoylation inhibitors in the clinic.
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Affiliation(s)
- Ignacio López
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015, Paris, France
| | - Eleftheria Chalatsi
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015, Paris, France
- Collège Doctoral, Sorbonne Université, 75005, Paris, France
- Bio-Rad Laboratories, Marnes-la-Coquette, France
| | - Saskia I J Ellenbroek
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Alexandra Andrieux
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015, Paris, France
| | - Pierre-François Roux
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015, Paris, France
| | - Juan P Cerapio
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015, Paris, France
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Toulouse, France
| | - Grégory Jouvion
- Experimental Neuropathology Unit, Institut Pasteur, 75015, Paris, France
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jacob-S Seeler
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015, Paris, France.
| | - Anne Dejean
- Nuclear Organization and Oncogenesis Unit, INSERM U993, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, 75015, Paris, France.
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22
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Lin YL, Chung CL, Huang PJ, Chen CH, Fang SC. Revised annotation and extended characterizations of components of the Chlamydomonas reinhardtii SUMOylation system. PLANT DIRECT 2020; 4:e00266. [PMID: 33015534 PMCID: PMC7522501 DOI: 10.1002/pld3.266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 05/16/2023]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation, or SUMOylation, is a reversible post-translational modification that is important for regulation of many cellular processes including cell division cycle in the eukaryotic kingdom. However, only a portion of the components of the Chlamydomonas SUMOylation system are known and their functions and regulation investigated. The present studies are aimed at extending discovery and characterization of new components and improving the annotation and nomenclature of all known proteins and genes involved in the system. Even though only one copy of the heterodimerized SUMO-activating enzyme, SAE1 and SAE2, was identified, the number of SUMO-conjugating enzymes (SCEs) and SUMO proteases/isopeptidase was expanded in Chlamydomonas. Using the reconstituted SUMOylation system, we showed that SCE1, SCE2, and SCE3 have SUMO-conjugating activity. In addition to SUMOylation, components required for other post-translational modifications such as NEDDylation, URMylation, and UFMylation, were confirmed to be present in Chlamydomonas. Our data also showed that besides isopeptidase activity, the SUMO protease domain of SUPPRESSOR OF MAT3 7/SENTRIN-SPECIFIC PROTEASE 1 (SMT7/SENP1) has endopeptidase activity that is capable of processing SUMO precursors. Moreover, the key cell cycle regulators of Chlamydomonas E2F1, DP1, CDKG1, CYCD2, and CYCD3 were SUMOylated in vitro, suggesting SUMOylation may be part of regulatory pathway modulating cell cycle regulators.
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Affiliation(s)
- Yen-Ling Lin
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
- Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan
| | - Chin-Lin Chung
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Pin-Jui Huang
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
- Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan
- Institute of Tropical Plant Sciences and Microbiology National Cheng Kung University Tainan Taiwan
- National Cheng Kung University-Academia Sinica Graduate Program in Translational Agricultural Sciences Tainan Taiwan
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23
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Cuijpers SAG, Willemstein E, Ruppert JG, van Elsland DM, Earnshaw WC, Vertegaal ACO. Chromokinesin KIF4A teams up with stathmin 1 to regulate abscission in a SUMO-dependent manner. J Cell Sci 2020; 133:jcs248591. [PMID: 32591481 PMCID: PMC7390632 DOI: 10.1242/jcs.248591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 05/27/2020] [Indexed: 12/19/2022] Open
Abstract
Cell division ends when two daughter cells physically separate via abscission, the cleavage of the intercellular bridge. It is not clear how the anti-parallel microtubule bundles bridging daughter cells are severed. Here, we present a novel abscission mechanism. We identified chromokinesin KIF4A, which is adjacent to the midbody during cytokinesis, as being required for efficient abscission. KIF4A is regulated by post-translational modifications. We evaluated modification of KIF4A by the ubiquitin-like protein SUMO. We mapped lysine 460 in KIF4A as the SUMO acceptor site and employed CRISPR-Cas9-mediated genome editing to block SUMO conjugation of endogenous KIF4A. Failure to SUMOylate this site in KIF4A delayed cytokinesis. SUMOylation of KIF4A enhanced the affinity for the microtubule destabilizer stathmin 1 (STMN1). We here present a new level of abscission regulation through the dynamic interactions between KIF4A and STMN1 as controlled by SUMO modification of KIF4A.
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Affiliation(s)
- Sabine A G Cuijpers
- Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Edwin Willemstein
- Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Jan G Ruppert
- Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3JR Edinburgh, Scotland, UK
| | - Daphne M van Elsland
- Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, University of Edinburgh, EH9 3JR Edinburgh, Scotland, UK
| | - Alfred C O Vertegaal
- Cell and Chemical Biology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
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24
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Zhao Y, Wang D, Zhang Z, Lu Y, Yang X, Ouyang Q, Tang C, Li F. Critical slowing down and attractive manifold: A mechanism for dynamic robustness in the yeast cell-cycle process. Phys Rev E 2020; 101:042405. [PMID: 32422801 DOI: 10.1103/physreve.101.042405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 01/13/2020] [Indexed: 11/07/2022]
Abstract
Biological processes that execute complex multiple functions, such as the cell cycle, must ensure the order of sequential events and maintain dynamic robustness against various fluctuations. Here, we examine the mechanisms and fundamental structure that achieve these properties in the cell cycle of the budding yeast Saccharomyces cerevisiae. We show that this process behaves like an excitable system containing three well-decoupled saddle-node bifurcations to execute DNA replication and mitosis events. The yeast cell-cycle regulatory network can be divided into three modules-the G1/S phase, early M phase, and late M phase-wherein both positive feedback loops in each module and interactions among modules play important roles. Specifically, when the cell-cycle process operates near the critical points of the saddle-node bifurcations, a critical slowing down effect takes place. Such interregnum then allows for an attractive manifold and sufficient duration for cell-cycle events, within which to assess the completion of DNA replication and mitosis, e.g., spindle assembly. Moreover, such arrangement ensures that any fluctuation in an early module or event will not transmit to a later module or event. Thus, our results suggest a possible dynamical mechanism of the cell-cycle process to ensure event order and dynamic robustness and give insight into the evolution of eukaryotic cell-cycle processes.
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Affiliation(s)
- Yao Zhao
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Dedi Wang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Zhiwen Zhang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Xiaojing Yang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Qi Ouyang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Chao Tang
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Fangting Li
- School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Peking University, Beijing 100871, China
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25
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Celen AB, Sahin U. Sumoylation on its 25th anniversary: mechanisms, pathology, and emerging concepts. FEBS J 2020; 287:3110-3140. [DOI: 10.1111/febs.15319] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/04/2020] [Accepted: 03/30/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Arda B. Celen
- Department of Molecular Biology and Genetics Center for Life Sciences and Technologies Bogazici University Istanbul Turkey
| | - Umut Sahin
- Department of Molecular Biology and Genetics Center for Life Sciences and Technologies Bogazici University Istanbul Turkey
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26
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Sahu MS, Patra S, Kumar K, Kaur R. SUMOylation in Human Pathogenic Fungi: Role in Physiology and Virulence. J Fungi (Basel) 2020; 6:E32. [PMID: 32143470 PMCID: PMC7096222 DOI: 10.3390/jof6010032] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 02/07/2023] Open
Abstract
The small ubiquitin-related modifier (SUMO) protein is an important component of the post-translational protein modification systems in eukaryotic cells. It is known to modify hundreds of proteins involved in diverse cellular processes, ranging from nuclear pore dynamics to signal transduction pathways. Owing to its reversible nature, the SUMO-conjugation of proteins (SUMOylation) holds a prominent place among mechanisms that regulate the functions of a wide array of cellular proteins. The dysfunctional SUMOylation system has been associated with many human diseases, including neurodegenerative and autoimmune disorders. Furthermore, the non-pathogenic yeast Saccharomyces cerevisiae has served as an excellent model to advance our understanding of enzymes involved in SUMOylation and proteins modified by SUMOylation. Taking advantage of the tools and knowledge obtained from the S. cerevisiae SUMOylation system, research on fungal SUMOylation is beginning to gather pace, and new insights into the role of SUMOylation in the pathobiology of medically important fungi are emerging. Here, we summarize the known information on components of the SUMOylation machinery, and consequences of overexpression or deletion of these components in the human pathogenic fungi, with major focus on two prevalent Candida bloodstream pathogens, C. albicans and C. glabrata. Additionally, we have identified SUMOylation components, through in silico analysis, in four medically relevant fungi, and compared their sequence similarity with S. cerevisiae counterparts. SUMOylation modulates the virulence of C. albicans and C. glabrata, while it is required for conidia production in Aspergillus nidulans and A. flavus. In addition to highlighting these recent developments, we discuss how SUMOylation fine tunes the expression of virulence factors, and influences survival of fungal cells under diverse stresses in vitro and in the mammalian host.
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Affiliation(s)
- Mahima Sagar Sahu
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India; (M.S.S.); (S.P.); (K.K.)
- Graduate studies, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Sandip Patra
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India; (M.S.S.); (S.P.); (K.K.)
- Graduate studies, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Kundan Kumar
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India; (M.S.S.); (S.P.); (K.K.)
- Graduate studies, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Rupinder Kaur
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India; (M.S.S.); (S.P.); (K.K.)
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27
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Hegde S, Soory A, Kaduskar B, Ratnaparkhi GS. SUMO conjugation regulates immune signalling. Fly (Austin) 2020; 14:62-79. [PMID: 32777975 PMCID: PMC7714519 DOI: 10.1080/19336934.2020.1808402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
Post-translational modifications (PTMs) are critical drivers and attenuators for proteins that regulate immune signalling cascades in host defence. In this review, we explore functional roles for one such PTM, the small ubiquitin-like modifier (SUMO). Very few of the SUMO conjugation targets identified by proteomic studies have been validated in terms of their roles in host defence. Here, we compare and contrast potential SUMO substrate proteins in immune signalling for flies and mammals, with an emphasis on NFκB pathways. We discuss, using the few mechanistic studies that exist for validated targets, the effect of SUMO conjugation on signalling and also explore current molecular models that explain regulation by SUMO. We also discuss in detail roles of evolutionary conservation of mechanisms, SUMO interaction motifs, crosstalk of SUMO with other PTMs, emerging concepts such as group SUMOylation and finally, the potentially transforming roles for genome-editing technologies in studying the effect of PTMs.
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Affiliation(s)
- Sushmitha Hegde
- Biology, Indian Institute of Science Education & Research (IISER), Pune, India
| | - Amarendranath Soory
- Biology, Indian Institute of Science Education & Research (IISER), Pune, India
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28
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Gong X, Nie Q, Xiao Y, Xiang JW, Wang L, Liu F, Fu JL, Liu Y, Yang L, Gan Y, Chen H, Luo Z, Qi R, Chen Z, Tang X, Li DWC. Localization Patterns of Sumoylation Enzymes E1, E2 and E3 in Ocular Cell Lines Predict Their Functional Importance. Curr Mol Med 2019; 18:516-522. [PMID: 30636611 DOI: 10.2174/1566524019666190112144436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/18/2018] [Accepted: 01/07/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE It is well established now that protein sumoylation acts as an important regulatory mechanism mediating control of ocular development through regulation of multiple transcription factors. Yet the functional mechanisms of each factor modulated remain to be further explored using the available in vitro systems. In this regard, various ocular cell lines including HLE, FHL124, αTN4-1, N/N1003A and ARPE-19 have been demonstrated to be useful for biochemical and molecular analyses of normal physiology and pathogenesis. We have recently examined that these cell lines express a full set of sumoylation enzymes E1, E2 and E3. Following this study, here we have examined the localization of these enzymes and determined their differential localization patterns in these major ocular cell lines. METHODS The 5 major ocular cell lines were cultured in Dulbecco's modified Eagle's medium (DMEM) containing fetal bovine serum (FBS) or rabbit serum (RBS) and 1% Penicillin- Streptomycin. The localization of the 3 major sumoylation enzymes in the 5 major ocular cell lines were determined with immunohistochemistry. The images were captured with a Zeiss LSM 880 confocal microscope. RESULTS we have obtained the following results: 1) The sumoylation enzymes SAE1, UBC9 and PIAS1 are distributed in both nucleus and cytoplasm, with a much higher level concentrated in the nucleus and the neighboring cellular organelle zone in all cell lines; 2) The sumoylation enzyme UBA2 was highly concentrated in both cytoplasm membrane, cytoskeleton and nucleus of all cell lines; 3) The ligase E3, RanBP2 was exclusively localized in the nucleus with homogeneous distribution. CONCLUSIONS Our results for the first time established the differential localization patterns of the three types of sumoylation enzymes in 5 major ocular cell lines. Our establishment of the differential localization patterns of the three types of sumoylation enzymes in these cell lines help to predict their functional importance of sumoylation in the vision system. Together, our results demonstrate that these cell lines can be used for assay systems to explore the functional mechanisms of sumoylation mediating ocular development and pathogenesis.
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Affiliation(s)
- Xiaodong Gong
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Qian Nie
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Yuan Xiao
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China.,Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Jia-Wen Xiang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China.,Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Ling Wang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Fangyuan Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Jia-Ling Fu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Yunfei Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Lan Yang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China.,Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Yuwen Gan
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China.,Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Huimin Chen
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China.,Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
| | - Zhongwen Luo
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Ruili Qi
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Zhigang Chen
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Xiangcheng Tang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - David Wan-Cheng Li
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China.,Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China
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29
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Ubc9 deficiency selectively impairs the functionality of common lymphoid progenitors (CLPs) during bone marrow hematopoiesis. Mol Immunol 2019; 114:314-322. [PMID: 31442915 DOI: 10.1016/j.molimm.2019.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 10/26/2022]
Abstract
Hematopoietic development occurs in the bone marrow, and this process begins with hematopoietic stem cells (HSCs). Ubc9 is a unique E2-conjugating enzyme required for SUMOylation, an evolutionarily conserved post-translational modification system. We herein show that a conditional Ubc9 deletion in the hematopoietic system caused decreased thymus weight and reduced lymphocyte to myeloid cell ratio. Importantly, Ubc9 deletion in the hematopoietic system only selectively impaired the development of common lymphoid progenitors (CLPs) in the bone marrow and perturbed their potential to differentiate into lymphocytes, thereby decreasing the number of T/B cells in the periphery. Ubc9 was found to be required for CLP viability, and therefore, Ubc9 deficiency rendered CLPs to undergo apoptosis and attenuated their proliferation. Thus, Ubc9 plays a critical role in the regulation of CLP function during hematopoietic development in the bone marrow.
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30
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Ryu H, Su D, Wilson‐Eisele NR, Zhao D, López‐Giráldez F, Hochstrasser M. The Ulp2 SUMO protease promotes transcription elongation through regulation of histone sumoylation. EMBO J 2019; 38:e102003. [PMID: 31313851 PMCID: PMC6694223 DOI: 10.15252/embj.2019102003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/22/2019] [Accepted: 06/26/2019] [Indexed: 01/07/2023] Open
Abstract
Many eukaryotic proteins are regulated by modification with the ubiquitin-like protein small ubiquitin-like modifier (SUMO). This linkage is reversed by SUMO proteases, of which there are two in Saccharomyces cerevisiae, Ulp1 and Ulp2. SUMO-protein conjugation regulates transcription, but the roles of SUMO proteases in transcription remain unclear. We report that Ulp2 is recruited to transcriptionally active genes to control local polysumoylation. Mutant ulp2 cells show impaired association of RNA polymerase II (RNAPII) with, and diminished expression of, constitutively active genes and the inducible CUP1 gene. Ulp2 loss sensitizes cells to 6-azauracil, a hallmark of transcriptional elongation defects. We also describe a novel chromatin regulatory mechanism whereby histone-H2B ubiquitylation stimulates histone sumoylation, which in turn appears to inhibit nucleosome association of the Ctk1 kinase. Ctk1 phosphorylates serine-2 (S2) in the RNAPII C-terminal domain (CTD) and promotes transcript elongation. Removal of both ubiquitin and SUMO from histones is needed to overcome the impediment to S2 phosphorylation. These results suggest sequential ubiquitin-histone and SUMO-histone modifications recruit Ulp2, which removes polySUMO chains and promotes RNAPII transcription elongation.
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Affiliation(s)
- Hong‐Yeoul Ryu
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
| | - Dan Su
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
- Present address:
Protein Science Corp.MeridenCTUSA
| | - Nicole R Wilson‐Eisele
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
- Present address:
Max Planck Institute of BiochemistryMartinsriedGermany
| | - Dejian Zhao
- Yale Center for Genome AnalysisYale UniversityNew HavenCTUSA
| | | | - Mark Hochstrasser
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenCTUSA
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Villajuana-Bonequi M, Matei A, Ernst C, Hallab A, Usadel B, Doehlemann G. Cell type specific transcriptional reprogramming of maize leaves during Ustilago maydis induced tumor formation. Sci Rep 2019; 9:10227. [PMID: 31308451 PMCID: PMC6629649 DOI: 10.1038/s41598-019-46734-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 07/04/2019] [Indexed: 02/05/2023] Open
Abstract
Ustilago maydis is a biotrophic pathogen and well-established genetic model to understand the molecular basis of biotrophic interactions. U. maydis suppresses plant defense and induces tumors on all aerial parts of its host plant maize. In a previous study we found that U. maydis induced leaf tumor formation builds on two major processes: the induction of hypertrophy in the mesophyll and the induction of cell division (hyperplasia) in the bundle sheath. In this study we analyzed the cell-type specific transcriptome of maize leaves 4 days post infection. This analysis allowed identification of key features underlying the hypertrophic and hyperplasic cell identities derived from mesophyll and bundle sheath cells, respectively. We examined the differentially expressed (DE) genes with particular focus on maize cell cycle genes and found that three A-type cyclins, one B-, D- and T-type are upregulated in the hyperplasic tumorous cells, in which the U. maydis effector protein See1 promotes cell division. Additionally, most of the proteins involved in the formation of the pre-replication complex (pre-RC, that assure that each daughter cell receives identic DNA copies), the transcription factors E2F and DPa as well as several D-type cyclins are deregulated in the hypertrophic cells.
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Affiliation(s)
- Mitzi Villajuana-Bonequi
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), BioCenter, University of Cologne, Zülpicher Str. 47a, Cologne, 50674, Germany
| | - Alexandra Matei
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), BioCenter, University of Cologne, Zülpicher Str. 47a, Cologne, 50674, Germany
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Medical Faculty, University Hospital Cologne, University of Cologne, Cologne, 50931, Germany
| | - Asis Hallab
- BioSC, IBG-2, Institute of Botany, RWTH Aachen, Worringer Weg 3, Aachen, 52074, Germany
| | - Björn Usadel
- BioSC, IBG-2, Institute of Botany, RWTH Aachen, Worringer Weg 3, Aachen, 52074, Germany
| | - Gunther Doehlemann
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), BioCenter, University of Cologne, Zülpicher Str. 47a, Cologne, 50674, Germany.
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32
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Li X, Cheng G, Qin F, Liu J, Li H, Jin Y. Function of the lesswright (lwr) gene in the growth, development, and reproduction of Schistosoma japonicum. Vet Parasitol 2019; 272:31-39. [PMID: 31395202 DOI: 10.1016/j.vetpar.2019.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/12/2019] [Accepted: 06/13/2019] [Indexed: 01/21/2023]
Abstract
The lesswright (lwr) gene and its products are essential molecules in mitosis, DNA repair, and embryo formation in many eukaryotes. In this study, immunohistochemical analysis revealed that the Lwr protein was located in the internal tissues and the surface layer of the adult Schistosoma japonicum (Sj) worms. The mRNA expression levels of SjLwr at different points were evaluated by quantitative real-time RT-PCR. The expression of SjLwr peaked at 14 days and then decreased thereafter. SjLwr expression was relatively more stable in male worms than in female worms. The functions of SjLwr were explored by siRNA-based gene silencing with a simple soaking method. The results showed that knockdown of the SjLwr gene impaired the growth and development of S. japonicum in mice, as well as survival, morphology, reproductive capacity, and egg vitality. These observations imply that SjLwr presents a novel target for the development of immuno- and/or small molecule-based therapeutics for the control and treatment of schistosome infections.
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Affiliation(s)
- Xiaochun Li
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Guifeng Cheng
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Shanxi, China
| | - Fanglin Qin
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China; College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jinming Liu
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hao Li
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yamei Jin
- Key Laboratory of Animal Parasitology, Ministry of Agriculture of China, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China.
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Vera Rodriguez A, Frey S, Görlich D. Engineered SUMO/protease system identifies Pdr6 as a bidirectional nuclear transport receptor. J Cell Biol 2019; 218:2006-2020. [PMID: 31023724 PMCID: PMC6548132 DOI: 10.1083/jcb.201812091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 01/07/2023] Open
Abstract
Cleavage of affinity tags by specific proteases can be exploited for highly selective affinity chromatography. The SUMO/SENP1 system is the most efficient for such application but fails in eukaryotic expression because it cross-reacts with endogenous proteases. Using a novel selection system, we have evolved the SUMOEu/SENP1Eu pair to orthogonality with the yeast and animal enzymes. SUMOEu fusions therefore remain stable in eukaryotic cells. Likewise, overexpressing a SENP1Eu protease is nontoxic in yeast. We have used the SUMOEu system in an affinity-capture-proteolytic-release approach to identify interactors of the yeast importin Pdr6/Kap122. This revealed not only further nuclear import substrates such as Ubc9, but also Pil1, Lsp1, eIF5A, and eEF2 as RanGTP-dependent binders and thus as export cargoes. We confirmed that Pdr6 functions as an exportin in vivo and depletes eIF5A and eEF2 from cell nuclei. Thus, Pdr6 is a bidirectional nuclear transport receptor (i.e., a biportin) that shuttles distinct sets of cargoes in opposite directions.
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Affiliation(s)
- Arturo Vera Rodriguez
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Steffen Frey
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Aksu M, Trakhanov S, Vera Rodriguez A, Görlich D. Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122. J Cell Biol 2019; 218:1839-1852. [PMID: 31023722 PMCID: PMC6548137 DOI: 10.1083/jcb.201812093] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 12/26/2022] Open
Abstract
Importins ferry proteins into nuclei while exportins carry cargoes to the cytoplasm. In the accompanying paper in this issue (Vera Rodriguez et al. 2019. J. Cell Biol. https://doi.org/10.1083/jcb.201812091), we discovered that Pdr6 is a biportin that imports, e.g., the SUMO E2 ligase Ubc9 while depleting the translation factor eIF5A from the nuclear compartment. In this paper, we report the structures of key transport intermediates, namely, of the Ubc9•Pdr6 import complex, of the RanGTP•Pdr6 heterodimer, and of the trimeric RanGTP•Pdr6•eIF5A export complex. These revealed nonlinear transport signals, chaperone-like interactions, and how the RanGTPase system drives Pdr6 to transport Ubc9 and eIF5A in opposite directions. The structures also provide unexpected insights into the evolution of transport selectivity. Specifically, they show that recognition of Ubc9 by Pdr6 differs fundamentally from that of the human Ubc9-importer Importin 13. Likewise, Pdr6 recognizes eIF5A in a nonhomologous manner compared with the mammalian eIF5A-exporter Exportin 4. This suggests that the import of Ubc9 and active nuclear exclusion of eIF5A evolved in different eukaryotic lineages more than once and independently from each other.
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Affiliation(s)
- Metin Aksu
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Sergei Trakhanov
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Arturo Vera Rodriguez
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Dirk Görlich
- Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Distribution of Proteins at the Inner Nuclear Membrane Is Regulated by the Asi1 E3 Ligase in Saccharomyces cerevisiae. Genetics 2019; 211:1269-1282. [PMID: 30709848 PMCID: PMC6456303 DOI: 10.1534/genetics.119.301911] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 01/30/2019] [Indexed: 12/11/2022] Open
Abstract
Inner nuclear membrane (INM) protein composition regulates nuclear function, affecting processes such as gene expression, chromosome organization, nuclear shape, and stability. Mechanisms that drive changes in the INM proteome are poorly understood, in part because it is difficult to definitively assay INM composition rigorously and systematically. Using a split-GFP complementation system to detect INM access, we examined the distribution of all C-terminally tagged Saccharomyces cerevisiae membrane proteins in wild-type cells and in mutants affecting protein quality control pathways, such as INM-associated degradation (INMAD), ER-associated degradation, and vacuolar proteolysis. Deletion of the E3 ligase Asi1 had the most specific effect on the INM compared to mutants in vacuolar or ER-associated degradation pathways, consistent with a role for Asi1 in the INMAD pathway. Our data suggest that Asi1 not only removes mistargeted proteins at the INM, but also controls the levels and distribution of native INM components, such as the membrane nucleoporin Pom33. Interestingly, loss of Asi1 does not affect Pom33 protein levels but instead alters Pom33 distribution in the nuclear envelope through Pom33 ubiquitination, which drives INM redistribution. Taken together, our data demonstrate that the Asi1 E3 ligase has a novel function in INM protein regulation in addition to protein turnover.
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36
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Cdc48/VCP Promotes Chromosome Morphogenesis by Releasing Condensin from Self-Entrapment in Chromatin. Mol Cell 2019; 69:664-676.e5. [PMID: 29452641 DOI: 10.1016/j.molcel.2018.01.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 11/04/2017] [Accepted: 01/22/2018] [Indexed: 01/26/2023]
Abstract
The morphological transformation of amorphous chromatin into distinct chromosomes is a hallmark of mitosis. To achieve this, chromatin must be compacted and remodeled by a ring-shaped enzyme complex known as condensin. However, the mechanistic basis underpinning condensin's role in chromosome remodeling has remained elusive. Here we show that condensin has a strong tendency to trap itself in its own reaction product during chromatin compaction and yet is capable of interacting with chromatin in a highly dynamic manner in vivo. To resolve this apparent paradox, we identified specific chromatin remodelers and AAA-class ATPases that act in a coordinated manner to release condensin from chromatin entrapment. The Cdc48 segregase is the central linchpin of this regulatory mechanism and promotes ubiquitin-dependent cycling of condensin on mitotic chromatin as well as effective chromosome condensation. Collectively, our results show that condensin inhibition by its own reaction product is relieved by forceful enzyme extraction from chromatin.
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Watanabe L, Gomes F, Vianez J, Nunes M, Cardoso J, Lima C, Schneider H, Sampaio I. De novo transcriptome based on next-generation sequencing reveals candidate genes with sex-specific expression in Arapaima gigas (Schinz, 1822), an ancient Amazonian freshwater fish. PLoS One 2018; 13:e0206379. [PMID: 30372461 PMCID: PMC6205615 DOI: 10.1371/journal.pone.0206379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/11/2018] [Indexed: 12/24/2022] Open
Abstract
Background The Arapaima (Arapaima gigas) is one of the world's largest freshwater bony fish, and is found in the rivers of the Amazon basin. This species is a potential aquaculture resource, although reproductive management in captivity is limited in particular due to the lack of external sexual dimorphism. In this study, using the 454 Roche platform (pyrosequencing) techniques, we evaluated a major portion of the transcriptome of this important Amazonian species. Results Four libraries obtained from the liver and skin tissue of juvenile specimens (representing males and females separately) were sequenced, yielding 5,453,919 high-quality reads. The de novo transcriptome assembly resulted in 175,792 contigs, with 51,057 significant blast hits. A total of 38,586 transcripts were mapped by Gene Ontology using Blast2GO. We identified 20,219 genes in the total transcriptome (9,551 in the liver and 16,818 in the skin). The gene expression analyses indicated 105 genes in the liver and 204 in the skin with differentiated expression profiles, with 95 being over-expressed in the females and 214 in the males. The log2 Fold Change and heatmap based on Reads Per Kilobase per Million mapped reads (RPKM) revealed that the gene expression in the skin is highly differentiated between male and female arapaima, while the levels of expression in the liver are similar between the sexes. Conclusion Transcriptome analysis based on pyrosequencing proved to be a reliable tool for the identification of genes with differentiated expression profiles between male and female arapaima. These results provide useful insights into the molecular pathways of sexual dimorphism in this important Amazonian species, and for comparative analyses with other teleosts.
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Affiliation(s)
- Luciana Watanabe
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brazil
- * E-mail:
| | - Fátima Gomes
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brazil
| | - João Vianez
- Centro de Inovações Tecnológicas (CIT), Instituto Evandro Chagas (IEC), Ananindeua, Pará, Brazil
| | - Márcio Nunes
- Centro de Inovações Tecnológicas (CIT), Instituto Evandro Chagas (IEC), Ananindeua, Pará, Brazil
| | - Jedson Cardoso
- Centro de Inovações Tecnológicas (CIT), Instituto Evandro Chagas (IEC), Ananindeua, Pará, Brazil
| | - Clayton Lima
- Centro de Inovações Tecnológicas (CIT), Instituto Evandro Chagas (IEC), Ananindeua, Pará, Brazil
| | - Horacio Schneider
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brazil
| | - Iracilda Sampaio
- Laboratório de Genética e Biologia Molecular, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Campus de Bragança, Pará, Brazil
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38
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Fang S, Qiu J, Wu Z, Bai T, Guo W. Down-regulation of UBC9 increases the sensitivity of hepatocellular carcinoma to doxorubicin. Oncotarget 2018; 8:49783-49795. [PMID: 28572537 PMCID: PMC5564807 DOI: 10.18632/oncotarget.17939] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/05/2017] [Indexed: 12/21/2022] Open
Abstract
UBC9 is an E2-conjugating enzyme that is required for SUMOylation and has been implicated in regulating several critical cellular pathways. UBC9 is overexpressed in certain tumors, such as lung adenocarcinoma, ovarian carcinoma and melanoma, which implies that it has special clinical significance. However, the role of UBC9 in Hepatocellular carcinoma (HCC) drug responsiveness is not clear. In this study, we investigated the clinicopathological significance of UBC9 in HCC and investigated the mechanism of UBC9-mediated chemosensitivity to doxorubicin (DOX) in hepatocellular carcinoma cells. We found that relative to adjacent normal tissues, UBC9 was markedly overexpressed in HCC, which closely correlated with tumor size, tumor microsatellite formation, and tumor encapsulation. Our results also showed that down-regulation of UBC9 by shRNA reduced the expression of Bcl-2 and Bcl-xl and increased the expression of cleaved-Caspase3, which is a proapoptotic protein. These changes were associated with reduced apoptosis in response to DOX. Furthermore, we observed a mechanism involving modulation of the P38 and ERK1/2 signaling pathways. Together, our results indicate that down-regulation of UBC9 sensitizes cells to anticancer drugs, is possibly associated with the regulation of ERK1/2 and P38 activation and interacts with the intrinsic apoptosis pathway. Thus, knockdown of UBC9 may have a tumor suppressor effect and UBC9 could be a potential target for the treatment of HCC cancer.
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Affiliation(s)
- Sufen Fang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Junyao Qiu
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Zheng Wu
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Tao Bai
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China
| | - Wuhua Guo
- Department of Interventional Radiology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
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39
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Feitosa WB, Morris PL. SUMOylation regulates germinal vesicle breakdown and the Akt/PKB pathway during mouse oocyte maturation. Am J Physiol Cell Physiol 2018; 315:C115-C121. [PMID: 29669220 DOI: 10.1152/ajpcell.00038.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
SUMOylation, a process of posttranslational modification of proteins by the small ubiquitin-related modifier (SUMO) family of proteins, is known to be involved in yeast and mammalian somatic cell-cycle regulation. However, the identities of the SUMO-modified oocyte targets are largely unknown and the functional role(s) for SUMOylation during mammalian oocyte maturation remains unclear. On the basis of studies in non-germline cells, protein kinase B/Akt is a potential SUMOylation target in the mouse oocyte, where it plays an essential role in cell-cycle resumption and progression during maturation. This study investigated the temporal patterns and prospective role(s) for interactions between SUMOylation and Akt serine-phosphorylation during oocyte meiotic resumption. Pharmacological inhibition of SUMOylation significantly decreased follicular fluid meiosis-activating sterol-induced cell-cycle resumption in oocytes matured in vitro and negatively affected the phosphorylation and nuclear translocation of Akt. Similarly, nuclear localization of cyclin D1, a downstream target of Akt activation, was significantly decreased following SUMOylation inhibition. Together these data show that SUMO and the posttranslational process of SUMOylation are involved in cell-cycle resumption during murine oocyte maturation and exert a regulatory influence on the Akt pathway during germinal vesicle breakdown.
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Affiliation(s)
| | - Patricia L Morris
- Center for Biomedical Research, Population Council , New York, New York.,The Rockefeller University , New York, New York
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40
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Thiruvalluvan M, Barghouth PG, Tsur A, Broday L, Oviedo NJ. SUMOylation controls stem cell proliferation and regional cell death through Hedgehog signaling in planarians. Cell Mol Life Sci 2018; 75:1285-1301. [PMID: 29098326 PMCID: PMC7083543 DOI: 10.1007/s00018-017-2697-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 10/21/2017] [Accepted: 10/24/2017] [Indexed: 12/15/2022]
Abstract
Mechanisms underlying anteroposterior body axis differences during adult tissue maintenance and regeneration are poorly understood. Here, we identify that post-translational modifications through the SUMO (Small Ubiquitin-like Modifier) machinery are evolutionarily conserved in the Lophotrocozoan Schmidtea mediterranea. Disruption of SUMOylation in adult animals by RNA-interference of the only SUMO E2 conjugating enzyme Ubc9 leads to a systemic increase in DNA damage and a remarkable regional defect characterized by increased cell death and loss of the posterior half of the body. We identified that Ubc9 is mainly expressed in planarian stem cells (neoblasts) but it is also transcribed in differentiated cells including neurons. Regeneration in Ubc9(RNAi) animals is impaired and associated with low neoblast proliferation. We present evidence indicating that Ubc9-induced regional cell death is preceded by alterations in transcription and spatial expression of repressors and activators of the Hedgehog signaling pathway. Our results demonstrate that SUMOylation acts as a regional-specific cue to regulate cell fate during tissue renewal and regeneration.
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Affiliation(s)
- Manish Thiruvalluvan
- Department of Molecular and Cell Biology, University of California, 5200 North Lake Road, Merced, CA, 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Paul G Barghouth
- Department of Molecular and Cell Biology, University of California, 5200 North Lake Road, Merced, CA, 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Assaf Tsur
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Limor Broday
- Department of Cell and Developmental Biology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Néstor J Oviedo
- Department of Molecular and Cell Biology, University of California, 5200 North Lake Road, Merced, CA, 95343, USA.
- Quantitative and Systems Biology Graduate Program, University of California, Merced, USA.
- Health Sciences Research Institute, University of California, Merced, USA.
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Kunz K, Piller T, Müller S. SUMO-specific proteases and isopeptidases of the SENP family at a glance. J Cell Sci 2018; 131:131/6/jcs211904. [DOI: 10.1242/jcs.211904] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
ABSTRACT
The ubiquitin-related SUMO system controls many cellular signaling networks. In mammalian cells, three SUMO forms (SUMO1, SUMO2 and SUMO3) act as covalent modifiers of up to thousands of cellular proteins. SUMO conjugation affects cell function mainly by regulating the plasticity of protein networks. Importantly, the modification is reversible and highly dynamic. Cysteine proteases of the sentrin-specific protease (SENP) family reverse SUMO conjugation in mammalian cells. In this Cell Science at a Glance article and the accompanying poster, we will summarize how the six members of the mammalian SENP family orchestrate multifaceted deconjugation events to coordinate cell processes, such as gene expression, the DNA damage response and inflammation.
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Affiliation(s)
- Kathrin Kunz
- Institute of Biochemistry II, Goethe University, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Tanja Piller
- Institute of Biochemistry II, Goethe University, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Goethe University, Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
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42
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SUMO targets the APC/C to regulate transition from metaphase to anaphase. Nat Commun 2018; 9:1119. [PMID: 29549242 PMCID: PMC5856775 DOI: 10.1038/s41467-018-03486-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/15/2018] [Indexed: 01/25/2023] Open
Abstract
Signal transduction by small ubiquitin-like modifier (SUMO) regulates a myriad of nuclear processes. Here we report on the role of SUMO in mitosis in human cell lines. Knocking down the SUMO conjugation machinery results in a delay in mitosis and defects in mitotic chromosome separation. Searching for relevant SUMOylated proteins in mitosis, we identify the anaphase-promoting complex/cyclosome (APC/C), a master regulator of metaphase to anaphase transition. The APC4 subunit is the major SUMO target in the complex, containing SUMO acceptor lysines at positions 772 and 798. SUMOylation is crucial for accurate progression of cells through mitosis and increases APC/C ubiquitylation activity toward a subset of its targets, including the newly identified target KIF18B. Combined, our findings demonstrate the importance of SUMO signal transduction for genome integrity during mitotic progression and reveal how SUMO and ubiquitin cooperate to drive mitosis.
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Abstract
The Anaphase Promoting Complex/Cyclosome (APC/C) is a ubiquitin E3 ligase that functions as the gatekeeper to mitotic exit. APC/C activity is controlled by an interplay of multiple pathways during mitosis, including the spindle assembly checkpoint (SAC), that are not yet fully understood. Here, we show that sumoylation of the APC4 subunit of the APC/C peaks during mitosis and is critical for timely APC/C activation and anaphase onset. We have also identified a functionally important SUMO interacting motif in the cullin-homology domain of APC2 located near the APC4 sumoylation sites and APC/C catalytic core. Our findings provide evidence of an important regulatory role for SUMO modification and binding in affecting APC/C activation and mitotic exit.
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Affiliation(s)
- Christine C Lee
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, United States
| | - Bing Li
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Hongtao Yu
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael J Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Baltimore, United States
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44
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Matunis MJ, Rodriguez MS. Concepts and Methodologies to Study Protein SUMOylation: An Overview. Methods Mol Biol 2018; 1475:3-22. [PMID: 27631794 DOI: 10.1007/978-1-4939-6358-4_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein modification by the small ubiquitin-related modifier (SUMO) was simultaneously discovered by several groups at the middle of the 1990s. Although distinct names were proposed including Sentrin, GMP1, PIC1, or SMT3, SUMO became the most popular. Early studies on the functions of SUMOylation focused on activities in the nucleus, including transcription activation, chromatin structure, and DNA repair. However, it is now recognized that SUMOylation affects a large diversity of cellular processes both in the nucleus and the cytoplasm and functions of SUMOylation appear to have undefined limits. SUMO-conjugating enzymes and specific proteases actively regulate the modification status of target proteins. The recent discoveries of ubiquitin-SUMO hybrid chains, multiple SUMO-interacting motifs, and macromolecular complexes regulated by SUMOylation underscore the high complexity of this dynamic reversible system. New conceptual frameworks suggested by these findings have motivated the development of new methodologies to study pre- and post-SUMOylation events in vitro and in vivo, using distinct model organisms. Here we summarize some of the new developments and methodologies in the field, particularly those that will be further elaborated on in the chapters integrating this book.
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Affiliation(s)
- Michael J Matunis
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe St., Room W8118, Baltimore, MD, 21205, USA.
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Zhang S, Bisterfeld C, Bramski J, Vanparijs N, De Geest BG, Pietruszka J, Böker A, Reinicke S. Biocatalytically Active Thin Films via Self-Assembly of 2-Deoxy-d-ribose-5-phosphate Aldolase-Poly(N-isopropylacrylamide) Conjugates. Bioconjug Chem 2017; 29:104-116. [PMID: 29182313 DOI: 10.1021/acs.bioconjchem.7b00645] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
2-Deoxy-d-ribose-5-phosphate aldolase (DERA) is a biocatalyst that is capable of converting acetaldehyde and a second aldehyde as acceptor into enantiomerically pure mono- and diyhydroxyaldehydes, which are important structural motifs in a number of pharmaceutically active compounds. However, substrate as well as product inhibition requires a more-sophisticated process design for the synthesis of these motifs. One way to do so is to the couple aldehyde conversion with transport processes, which, in turn, would require an immobilization of the enzyme within a thin film that can be deposited on a membrane support. Consequently, we developed a fabrication process for such films that is based on the formation of DERA-poly(N-isopropylacrylamide) conjugates that are subsequently allowed to self-assemble at an air-water interface to yield the respective film. In this contribution, we discuss the conjugation conditions, investigate the interfacial properties of the conjugates, and, finally, demonstrate a successful film formation under the preservation of enzymatic activity.
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Affiliation(s)
- Shuhao Zhang
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute for Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476 Potsdam-Golm, Germany.,Polymer Materials and Polymer Technologies, University of Potsdam , 14476, Potsdam-Golm, Germany
| | - Carolin Bisterfeld
- Institute of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, 52426 Jülich, Germany
| | - Julia Bramski
- Institute of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, 52426 Jülich, Germany
| | - Nane Vanparijs
- Department of Pharmaceutics, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Bruno G De Geest
- Department of Pharmaceutics, Ghent University , Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich Heine University of Düsseldorf at Forschungszentrum Jülich , Stetternicher Forst, 52426 Jülich, Germany.,IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany
| | - Alexander Böker
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute for Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476 Potsdam-Golm, Germany.,Polymer Materials and Polymer Technologies, University of Potsdam , 14476, Potsdam-Golm, Germany
| | - Stefan Reinicke
- Department of Functional Protein Systems and Biotechnology, Fraunhofer Institute for Applied Polymer Research (IAP) , Geiselbergstraße 69, 14476 Potsdam-Golm, Germany
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Wen D, Wu J, Wang L, Fu Z. SUMOylation Promotes Nuclear Import and Stabilization of Polo-like Kinase 1 to Support Its Mitotic Function. Cell Rep 2017; 21:2147-2159. [PMID: 29166606 PMCID: PMC5728694 DOI: 10.1016/j.celrep.2017.10.085] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/22/2017] [Accepted: 10/23/2017] [Indexed: 02/08/2023] Open
Abstract
As a pivotal mitotic regulator, polo-like kinase 1 (PLK1) is under highly coordinated and multi-layered regulation. However, the pathways that control PLK1's activity and function have just begun to be elucidated. PLK1 has recently been shown to be functionally modulated by post-translational modifications (PTMs), including phosphorylation and ubiquitination. Herein, we report that SUMOylation plays an essential role in regulating PLK1's mitotic function. We found that Ubc9 was recruited to PLK1 upon initial phosphorylation and activation by CDK1/cyclin B. By in vivo and in vitro SUMOylation assays, PLK1 was identified as a physiologically relevant small ubiquitin-related modifier (SUMO)-targeted protein, preferentially modified by SUMO-1. We further showed that K492 on PLK1 is essential for SUMOylation. SUMOylation causes PLK1's nuclear import and significantly increases its protein stability, both of which are critical for normal mitotic progression and genomic integrity. Our findings suggest that SUMOylation is an important regulatory mechanism governing PLK1's mitotic function.
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Affiliation(s)
- Donghua Wen
- Department of Human and Molecular Genetics, Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
| | - Jianguo Wu
- Department of Human and Molecular Genetics, Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
| | - Lei Wang
- Department of Human and Molecular Genetics, Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA
| | - Zheng Fu
- Department of Human and Molecular Genetics, Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, VA 23298, USA.
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Pichler A, Fatouros C, Lee H, Eisenhardt N. SUMO conjugation - a mechanistic view. Biomol Concepts 2017; 8:13-36. [PMID: 28284030 DOI: 10.1515/bmc-2016-0030] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/06/2017] [Indexed: 02/08/2023] Open
Abstract
The regulation of protein fate by modification with the small ubiquitin-related modifier (SUMO) plays an essential and crucial role in most cellular pathways. Sumoylation is highly dynamic due to the opposing activities of SUMO conjugation and SUMO deconjugation. SUMO conjugation is performed by the hierarchical action of E1, E2 and E3 enzymes, while its deconjugation involves SUMO-specific proteases. In this review, we summarize and compare the mechanistic principles of how SUMO gets conjugated to its substrate. We focus on the interplay of the E1, E2 and E3 enzymes and discuss how specificity could be achieved given the limited number of conjugating enzymes and the thousands of substrates.
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Affiliation(s)
- Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Chronis Fatouros
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Heekyoung Lee
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
| | - Nathalie Eisenhardt
- Max Planck Institute of Immunobiology and Epigenetics, Department of Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany
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Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ. A high throughput mutagenic analysis of yeast sumo structure and function. PLoS Genet 2017; 13:e1006612. [PMID: 28166236 PMCID: PMC5319795 DOI: 10.1371/journal.pgen.1006612] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/21/2017] [Accepted: 01/31/2017] [Indexed: 11/18/2022] Open
Abstract
Sumoylation regulates a wide range of essential cellular functions through diverse mechanisms that remain to be fully understood. Using S. cerevisiae, a model organism with a single essential SUMO gene (SMT3), we developed a library of >250 mutant strains with single or multiple amino acid substitutions of surface or core residues in the Smt3 protein. By screening this library using plate-based assays, we have generated a comprehensive structure-function based map of Smt3, revealing essential amino acid residues and residues critical for function under a variety of genotoxic and proteotoxic stress conditions. Functionally important residues mapped to surfaces affecting Smt3 precursor processing and deconjugation from protein substrates, covalent conjugation to protein substrates, and non-covalent interactions with E3 ligases and downstream effector proteins containing SUMO-interacting motifs. Lysine residues potentially involved in formation of polymeric chains were also investigated, revealing critical roles for polymeric chains, but redundancy in specific chain linkages. Collectively, our findings provide important insights into the molecular basis of signaling through sumoylation. Moreover, the library of Smt3 mutants represents a valuable resource for further exploring the functions of sumoylation in cellular stress response and other SUMO-dependent pathways.
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Affiliation(s)
- Heather A. Newman
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Pamela B. Meluh
- High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
| | - Jian Lu
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Jeremy Vidal
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Caryn Carson
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Elizabeth Lagesse
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jef D. Boeke
- High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University, School of Medicine, Baltimore, MD, United States of America
| | - Michael J. Matunis
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, United States of America
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Kaplan GS, Torcun CC, Grune T, Ozer NK, Karademir B. Proteasome inhibitors in cancer therapy: Treatment regimen and peripheral neuropathy as a side effect. Free Radic Biol Med 2017; 103:1-13. [PMID: 27940347 DOI: 10.1016/j.freeradbiomed.2016.12.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/22/2016] [Accepted: 12/04/2016] [Indexed: 01/10/2023]
Abstract
Proteasomal system plays an important role in protein turnover, which is essential for homeostasis of cells. Besides degradation of oxidized proteins, it is involved in the regulation of many different signaling pathways. These pathways include mainly cell differentiation, proliferation, apoptosis, transcriptional activation and angiogenesis. Thus, proteasomal system is a crucial target for treatment of several diseases including neurodegenerative diseases, cystic fibrosis, atherosclerosis, autoimmune diseases, diabetes and cancer. Over the last fifteen years, proteasome inhibitors have been tested to highlight their mechanisms of action and used in the clinic to treat different types of cancer. Proteasome inhibitors are mainly used in combinational therapy along with classical chemo-radiotherapy. Several studies have proved their significant effects but serious side effects such as peripheral neuropathy, limits their use in required effective doses. Recent studies focus on peripheral neuropathy as the primary side effect of proteasome inhibitors. Therefore, it is important to delineate the underlying mechanisms of peripheral neuropathy and develop new inhibitors according to obtained data. This review will detail the role of proteasome inhibition in cancer therapy and development of peripheral neuropathy as a side effect. Additionally, new approaches to prevent treatment-limiting side effects will be discussed in order to help researchers in developing effective strategies to overcome side effects of proteasome inhibitors.
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Affiliation(s)
- Gulce Sari Kaplan
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34854 Maltepe, Istanbul, Turkey
| | - Ceyda Corek Torcun
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34854 Maltepe, Istanbul, Turkey
| | - Tilman Grune
- Department for Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Nuthetal, Germany
| | - Nesrin Kartal Ozer
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34854 Maltepe, Istanbul, Turkey
| | - Betul Karademir
- Department of Biochemistry, School of Medicine/Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, 34854 Maltepe, Istanbul, Turkey.
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50
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Liu JB, Cai X, Xiong H, Zhang HF. Effects of feeding frequency on meat quality traits and Longissimus muscle proteome in finishing pigs. J Anim Physiol Anim Nutr (Berl) 2017; 101:1175-1184. [PMID: 28063249 DOI: 10.1111/jpn.12636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 10/09/2016] [Indexed: 12/12/2022]
Abstract
Sixty-four barrows with an initial body weight of 59.8 ± 2.1 kg were allocated to one of the two feeding frequency regimes (had free access to diet and fed two meals per day). Pigs had free access (FA) to feed were fed on an ad libitum basis during the 8-week experimental period. Pigs fed twice daily (M2) were allowed to consume their meals in 2 h. Pigs fed twice daily had lower average daily feed intake (p < 0.01) and average daily gain (p < 0.1), but a greater G:F (p < 0.05) than FA pigs. Lower perirenal fat deposition, hot carcass weight, intramuscular fat content (p < 0.05) and dressing percentage (p < 0.1) were found in M2 pigs compared with FA pigs. Activities of citrate synthase, β-hydroxylacyl-CoA dehydrogenase and lactate dehydrogenase were greater in the Longissimus muscle (LM) of M2 pigs compared with FA pigs (p < 0.05). Proteomic analysis revealed that expression abundances of proteins involved in glucose metabolism, energy production and lipid utilization were upregulated, but expression levels of proteins participating in protein and amino acid metabolism, stress response and redox homeostasis were downregulated in the LM of M2 pigs than those in FA pigs (p < 0.05). In conclusion, the less meal frequency impairs growth rate, has marginal effects on carcass and meat quality traits and affects expression abundances of proteins in the LM of finishing pigs.
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Affiliation(s)
- J B Liu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China.,State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Cai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - H Xiong
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - H F Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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