1
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Liu D, Che X, Wu G. Deciphering the role of neddylation in tumor microenvironment modulation: common outcome of multiple signaling pathways. Biomark Res 2024; 12:5. [PMID: 38191508 PMCID: PMC10773064 DOI: 10.1186/s40364-023-00545-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 11/10/2023] [Indexed: 01/10/2024] Open
Abstract
Neddylation is a post-translational modification process, similar to ubiquitination, that controls several biological processes. Notably, it is often aberrantly activated in neoplasms and plays a critical role in the intricate dynamics of the tumor microenvironment (TME). This regulatory influence of neddylation permeates extensively and profoundly within the TME, affecting the behavior of tumor cells, immune cells, angiogenesis, and the extracellular matrix. Usually, neddylation promotes tumor progression towards increased malignancy. In this review, we highlight the latest understanding of the intricate molecular mechanisms that target neddylation to modulate the TME by affecting various signaling pathways. There is emerging evidence that the targeted disruption of the neddylation modification process, specifically the inhibition of cullin-RING ligases (CRLs) functionality, presents a promising avenue for targeted therapy. MLN4924, a small-molecule inhibitor of the neddylation pathway, precisely targets the neural precursor cell-expressed developmentally downregulated protein 8 activating enzyme (NAE). In recent years, significant advancements have been made in the field of neddylation modification therapy, particularly the integration of MLN4924 with chemotherapy or targeted therapy. This combined approach has demonstrated notable success in the treatment of a variety of hematological and solid tumors. Here, we investigated the inhibitory effects of MLN4924 on neddylation and summarized the current therapeutic outcomes of MLN4924 against various tumors. In conclusion, this review provides a comprehensive, up-to-date, and thorough overview of neddylation modifications, and offers insight into the critical importance of this cellular process in tumorigenesis.
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Affiliation(s)
- Dequan Liu
- Department of Urology, the First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Xiangyu Che
- Department of Urology, the First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China.
| | - Guangzhen Wu
- Department of Urology, the First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China.
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2
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Zou J, Wang W, Lu Y, Ayala J, Dong K, Zhou H, Wang J, Chen W, Weintraub NL, Zhou J, Li J, Su H. Neddylation is required for perinatal cardiac development through stimulation of metabolic maturation. Cell Rep 2023; 42:112018. [PMID: 36662623 PMCID: PMC10029150 DOI: 10.1016/j.celrep.2023.112018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/23/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Cardiac maturation is crucial for postnatal cardiac development and is increasingly known to be regulated by a series of transcription factors. However, post-translational mechanisms regulating this process remain unclear. Here we report the indispensable role of neddylation in cardiac maturation. Mosaic deletion of NAE1, an essential enzyme for neddylation, in neonatal hearts results in the rapid development of cardiomyopathy and heart failure. NAE1 deficiency disrupts transverse tubule formation, inhibits physiological hypertrophy, and represses fetal-to-adult isoform switching, thus culminating in cardiomyocyte immaturation. Mechanistically, we find that neddylation is needed for the perinatal metabolic transition from glycolytic to oxidative metabolism in cardiomyocytes. Further, we show that HIF1α is a putative neddylation target and that inhibition of neddylation accumulates HIF1α and impairs fatty acid utilization and bioenergetics in cardiomyocytes. Together, our data show neddylation is required for cardiomyocyte maturation through promoting oxidative metabolism in the developing heart.
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Affiliation(s)
- Jianqiu Zou
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Wenjuan Wang
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Key Laboratory of Protein Modification and Degradation, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, Guangdong 511436, China
| | - Yi Lu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Juan Ayala
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Kunzhe Dong
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Hongyi Zhou
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jinxi Wang
- Department of Medicine, University of Iowa, 200 Hawkins Drive, CBRB 2270B, Iowa City, IA 52242, USA
| | - Weiqin Chen
- Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Neal L Weintraub
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jiliang Zhou
- Department of Medicine, University of Iowa, 200 Hawkins Drive, CBRB 2270B, Iowa City, IA 52242, USA
| | - Jie Li
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Division of Cardiology, Department of Medicine, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA; Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA.
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3
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Meszka I, Polanowska J, Xirodimas DP. Mixed in chains: NEDD8 polymers in the Protein Quality Control system. Semin Cell Dev Biol 2022; 132:27-37. [PMID: 35078718 DOI: 10.1016/j.semcdb.2022.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/11/2022] [Accepted: 01/14/2022] [Indexed: 12/14/2022]
Abstract
Post-translational modification of proteins with the Ubiquitin-like molecule NEDD8 is a critical regulatory mechanism for several biological processes and a potential target for therapeutic intervention. The role of NEDD8 has been mainly characterised through its modification as single moiety on the cullin family of proteins and control of Cullin-Ring-Ligases, but also on non-cullin substrates. In addition to monoNEDDylation, recent studies have now revealed that NEDD8 can also generate diverse polymers. This is either through modification of the 9 available lysines in NEDD8 and the formation of polyNEDD8 chains, or NEDDylation of Ubiquitin and SUMO-2 for the generation of hybrid NEDD8 chains. Here, we review recent findings that characterise the formation of NEDD8 polymers under distinct modes of protein NEDDylation (canonical/atypical) and their potential role as regulatory signals of the proteotoxic stress response and the Protein Quality Control system.
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Affiliation(s)
- Igor Meszka
- CRBM, Univ. Montpellier, CNRS, Montpellier, France
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4
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Steger M, Karayel Ö, Demichev V. Ubiquitinomics: history, methods and applications in basic research and drug discovery. Proteomics 2022; 22:e2200074. [PMID: 35353442 DOI: 10.1002/pmic.202200074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/08/2022]
Abstract
The ubiquitin-proteasome system (UPS) was discovered about 40 years ago and is known to regulate a multitude of cellular processes including protein homeostasis. ubiquitylated proteins are recognized by downstream effectors, resulting in alterations of protein abundance, activity, or localization. Not surprisingly, the ubiquitylation machinery is dysregulated in numerous diseases, including cancers and neurodegeneration. Mass spectrometry (MS)-based proteomics has emerged as a transformative technology for characterizing protein ubiquitylation in an unbiased fashion. Here, we provide an overview of the different MS-based approaches for studying protein ubiquitylation. We review various methods for enriching and quantifying ubiquitin modifications at the peptide or protein level, outline MS acquisition and data processing approaches and discuss key challenges. Finally, we examine how MS-based ubiquitinomics can aid both basic biology and drug discovery research. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Martin Steger
- Evotec München GmbH, Martinsried, 82152, Germany.,Present address: Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Özge Karayel
- Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.,Current address: Department of Physiological Chemistry, Genentech, South San Francisco, CA, 94080, USA
| | - Vadim Demichev
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
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5
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Yu H, Luo H, Chang L, Wang S, Geng X, Kang L, Zhong Y, Cao Y, Wang R, Yang X, Zhu Y, Shi M, Hu Y, Liu Z, Yin X, Ran Y, Yang H, Fan W, Zhao B. The NEDD8-activating enzyme inhibitor MLN4924 reduces ischemic brain injury in mice. Proc Natl Acad Sci U S A 2022; 119:e2111896119. [PMID: 35101976 PMCID: PMC8833173 DOI: 10.1073/pnas.2111896119] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 02/03/2023] Open
Abstract
Ischemic stroke is a leading cause of death and disability with limited therapies. Neuronal precursor cell-expressed developmentally downregulated protein 8 (NEDD8) is a ubiquitin-like protein that is involved in protein neddylation. The first-in-class anticancer agent called MLN4924 plays a crucial role in suppressing tumorigenesis and attenuating inflammatory responses due to specifically inhibiting NEDD8-activating enzyme. Here, we investigated the potential protective role of MLN4924 after experimental stroke. We showed that the neddylation pathway is overactivated in the brain following cerebral ischemia. Inhibition of neddylation by MLN4924 protects the brain against ischemic injury by attenuating neutrophil extravasation and maintaining blood–brain barrier integrity. Our findings provide insights into the promising treatment with neddylation inhibition for ischemic brain injury. Blood–brain barrier (BBB) breakdown and inflammation occurring at the BBB have a key, mainly a deleterious role in the pathophysiology of ischemic stroke. Neddylation is a ubiquitylation-like pathway that is critical in various cellular functions by conjugating neuronal precursor cell-expressed developmentally down-regulated protein 8 (NEDD8) to target proteins. However, the roles of neddylation pathway in ischemic stroke remain elusive. Here, we report that NEDD8 conjugation increased during acute phase after ischemic stroke and was present in intravascular and intraparenchymal neutrophils. Inhibition of neddylation by MLN4924, also known as pevonedistat, inactivated cullin-RING E3 ligase (CRL), and reduced brain infarction and improved functional outcomes. MLN4924 treatment induced the accumulation of the CRL substrate neurofibromatosis 1 (NF1). By using virus-mediated NF1 silencing, we show that NF1 knockdown abolished MLN4924-dependent inhibition of neutrophil trafficking. These effects were mediated through activation of endothelial P-selectin and intercellular adhesion molecule-1 (ICAM-1), and blocking antibodies against P-selectin or anti–ICAM-1 antibodies reversed NF1 silencing-induced increase in neutrophil infiltration in MLN4924-treated mice. Furthermore, we found that NF1 silencing blocked MLN4924-afforded BBB protection and neuroprotection through activation of protein kinase C δ (PKCδ), myristoylated alanine-rich C-kinase substrate (MARCKS), and myosin light chain (MLC) in cerebral microvessels after ischemic stroke, and treatment of mice with the PKCδ inhibitor rottlerin reduced this increased BBB permeability. Our study demonstrated that increased neddylation promoted neutrophil trafficking and thus exacerbated injury of the BBB and stroke outcomes. We suggest that the neddylation inhibition may be beneficial in ischemic stroke.
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6
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Kim S, Kwon M, Hwang Y, Yoon J, Park S, Kang HC. Stress-induced NEDDylation promotes cytosolic protein aggregation through HDAC6 in a p62-dependent manner. iScience 2021; 24:102146. [PMID: 33665565 PMCID: PMC7903351 DOI: 10.1016/j.isci.2021.102146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/07/2021] [Accepted: 02/01/2021] [Indexed: 02/08/2023] Open
Abstract
Stress-coupled NEDDylation potentially regulates the aggregation of nuclear proteins, which could protect the nuclear ubiquitin-proteasome system from proteotoxic stress. However, it remains unclear how NEDDylation controls protein-aggregation responses to diverse stress conditions. Here, we identified HDAC6 as a direct NEDD8-binding partner that regulates the formation of aggresome-like bodies (ALBs) containing NEDDylated cytosolic protein aggregates during ubiquitin stress. HDAC6 colocalizes with stress-induced ALBs, and HDAC6 inhibition suppresses ALBs formation, but not stress-induced NEDDylation, suggesting that HDAC6 carries NEDDylated-proteins to generate ALBs. Then, we monitored the ALBs-associated proteostasis network and found that p62 directly controls ALBs formation as an acceptor of NEDDylated cytosolic aggregates. Interestingly, we also observed that ALBs are highly condensed in chloroquine-treated cells with impaired autophagic flux, indicating that ALBs rely on autophagy. Collectively, our data suggest that NEDD8, HDAC6, and p62 are involved in the management of proteotoxic stress by forming cytosolic ALBs coupled to the aggresome-autophagy flux. NEDD8 directly binds to HDAC6 and regulates the formation of aggresome-like body (ALB) HDAC6 carries NEDDylated cytosolic protein aggregates into ALBs under ubiquitin stress p62 directly controls ALBs formation as an acceptor of NEDDylated cytosolic aggregates The NEDD8-HDAC6-p62 axis controls proteostasis by forming ALB-coupled autophagy
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Affiliation(s)
- Soyeon Kim
- Department of Physiology, Ajou University School of Medicine, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Graduate School of Ajou University, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea
| | - Mira Kwon
- Department of Physiology, Ajou University School of Medicine, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Graduate School of Ajou University, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea
| | - Yiseul Hwang
- Department of Physiology, Ajou University School of Medicine, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Graduate School of Ajou University, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea
| | - Junghyun Yoon
- Department of Physiology, Ajou University School of Medicine, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Graduate School of Ajou University, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea
| | - Sangwook Park
- Department of Physiology, Ajou University School of Medicine, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Graduate School of Ajou University, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea
| | - Ho Chul Kang
- Department of Physiology, Ajou University School of Medicine, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Graduate School of Ajou University, World cup-ro, Yeongtong-gu, Suwon, Gyeonggi 16499, Republic of Korea
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7
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Pick E. The necessity of NEDD8/Rub1 for vitality and its association with mitochondria-derived oxidative stress. Redox Biol 2020; 37:101765. [PMID: 33099217 PMCID: PMC7582104 DOI: 10.1016/j.redox.2020.101765] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Access of molecular oxygen to the respiratory electron transport chain at the mitochondria costs in the generation of reactive oxygen-derived species (ROS). ROS induces progressive damage to macromolecules in all living cells, hence, rapid defense mechanisms to maintain cellular redox homeostasis are vital. NEDD8/Rub1 is a highly conserved ubiquitin-like modifier that has recently been identified as a key regulator of cellular redox homeostasis. In this review, I will present NEDD8/Rub1, its modification cascade of enzymes, substrates and hydrolases. After introduction, I will show that the NEDD8/Rub1 pathway is linked with mitochondria physiology, namely, oxidative stress. In the rest of the review, I will approach the Ascomycota phylum of the kingdom fungi instrumentally, to present existing links between NEDD8/Rub1 vitality and the aerobic lifestyle of model species belonging to three subphyla: Saccharomycotina (S. cerevisiae and C. albicans), Pezizomycotina (A. nidulans and N. crassa), and Taphrinomycotina (S. pombe). NEDD8/Rub1 is a key regulator of cellular redox homeostasis. Ascomycota species that produce mitochondria-derived ROS during glycolysis require NEDD8/Rub1for viability. NEDD8/Rub1 essentiality correlates with the existence of NEDP1 in the organism genome.
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Affiliation(s)
- Elah Pick
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Tivon, 3600600, Israel.
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8
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Karpiyevich M, Artavanis-Tsakonas K. Ubiquitin-Like Modifiers: Emerging Regulators of Protozoan Parasites. Biomolecules 2020; 10:E1403. [PMID: 33022940 PMCID: PMC7600729 DOI: 10.3390/biom10101403] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 09/28/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
Post-translational protein regulation allows for fine-tuning of cellular functions and involves a wide range of modifications, including ubiquitin and ubiquitin-like modifiers (Ubls). The dynamic balance of Ubl conjugation and removal shapes the fates of target substrates, in turn modulating various cellular processes. The mechanistic aspects of Ubl pathways and their biological roles have been largely established in yeast, plants, and mammalian cells. However, these modifiers may be utilised differently in highly specialised and divergent organisms, such as parasitic protozoa. In this review, we explore how these parasites employ Ubls, in particular SUMO, NEDD8, ATG8, ATG12, URM1, and UFM1, to regulate their unconventional cellular physiology. We discuss emerging data that provide evidence of Ubl-mediated regulation of unique parasite-specific processes, as well as the distinctive features of Ubl pathways in parasitic protozoa. We also highlight the potential to leverage these essential regulators and their cognate enzymatic machinery for development of therapeutics to protect against the diseases caused by protozoan parasites.
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9
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Pérez Berrocal DA, Witting KF, Ovaa H, Mulder MPC. Hybrid Chains: A Collaboration of Ubiquitin and Ubiquitin-Like Modifiers Introducing Cross-Functionality to the Ubiquitin Code. Front Chem 2020; 7:931. [PMID: 32039151 PMCID: PMC6987259 DOI: 10.3389/fchem.2019.00931] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/20/2019] [Indexed: 01/31/2023] Open
Abstract
The Ubiquitin CODE constitutes a unique post-translational modification language relying on the covalent attachment of Ubiquitin (Ub) to substrates, with Ub serving as the minimum entity to generate a message that is translated into different cellular pathways. The creation of this message is brought about by the dedicated action of writers, erasers, and readers of the Ubiquitin CODE. This CODE is greatly expanded through the generation of polyUb chains of different architectures on substrates thus regulating their fate. Through additional post-translational modification by Ub-like proteins (UbL), hybrid Ub/UbL chains, which either alter the originally encrypted message or encode a completely new one, are formed. Hybrid Ub/UbL chains are generated under both stress or physiological conditions and seem to confer improved specificity and affinity toward their cognate receptors. In such a manner, their formation must play a specific, yet still undefined role in cellular signaling and thus understanding the UbCODE message is crucial. Here, we discuss the evidence for the existence of hybrid Ub/UbL chains in addition to the current understanding of its biology. The modification of Ub by another UbL complicates the deciphering of the spatial and temporal order of events warranting the development of a hybrid chain toolbox. We discuss this unmet need and expand upon the creation of tailored tools adapted from our previously established toolkit for the Ubiquitin Proteasome System to specifically target these hybrid Ub/UbL chains.
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Affiliation(s)
- David A Pérez Berrocal
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Katharina F Witting
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Chemical Immunology, Leiden University Medical Center, Oncode Institute, Leiden, Netherlands
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10
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Keuss MJ, Hjerpe R, Hsia O, Gourlay R, Burchmore R, Trost M, Kurz T. Unanchored tri-NEDD8 inhibits PARP-1 to protect from oxidative stress-induced cell death. EMBO J 2019; 38:embj.2018100024. [PMID: 30804002 PMCID: PMC6418418 DOI: 10.15252/embj.2018100024] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 01/10/2019] [Accepted: 01/28/2019] [Indexed: 12/18/2022] Open
Abstract
NEDD8 is a ubiquitin‐like protein that activates cullin‐RING E3 ubiquitin ligases (CRLs). Here, we identify a novel role for NEDD8 in regulating the activity of poly(ADP‐ribose) polymerase 1 (PARP‐1) in response to oxidative stress. We show that treatment of cells with H2O2 results in the accumulation of NEDD8 chains, likely by directly inhibiting the deneddylase NEDP1. One chain type, an unanchored NEDD8 trimer, specifically bound to the second zinc finger domain of PARP‐1 and attenuated its activation. In cells in which Nedp1 is deleted, large amounts of tri‐NEDD8 constitutively form, resulting in inhibition of PARP‐1 and protection from PARP‐1‐dependent cell death. Surprisingly, these NEDD8 trimers are additionally acetylated, as shown by mass spectrometry analysis, and their binding to PARP‐1 is reduced by the overexpression of histone de‐acetylases, which rescues PARP‐1 activation. Our data suggest that trimeric, acetylated NEDD8 attenuates PARP‐1 activation after oxidative stress, likely to delay the initiation of PARP‐1‐dependent cell death.
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Affiliation(s)
- Matthew J Keuss
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Roland Hjerpe
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Oliver Hsia
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
| | - Robert Gourlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, UK
| | - Richard Burchmore
- Glasgow Polyomics, College of Veterinary, Medical and Life Sciences, University of Glasgow, Glasgow, UK
| | - Matthias Trost
- The MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Centre, College of Life Sciences, University of Dundee, Dundee, UK.,Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Thimo Kurz
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, UK
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11
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Schwechheimer C. NEDD8-its role in the regulation of Cullin-RING ligases. Curr Opin Plant Biol 2018; 45:112-119. [PMID: 29909289 DOI: 10.1016/j.pbi.2018.05.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 05/26/2018] [Accepted: 05/31/2018] [Indexed: 05/10/2023]
Abstract
The ubiquitin-related protein NEDD8 is conjugated and deconjugated to and from proteins in processes related to ubiquitin conjugation and deconjugation. Neddylation is a well-studied posttranslational modification of Cullin-RING E3 ligases (CRLs). Biochemical and structural studies aiming at understanding the role of NEDD8 in CRL function have now resulted in a convincing model of how neddylation and deneddylation antagonistically regulate CRL stability, conformation, activity as well as degradation substrate receptor exchange. Studies of the Arabidopsis thaliana deneddylation-deficient den1 mutant led to the identification of many low abundant, non-Cullin NEDD8 conjugates. Examination of neddylated AUXIN RESISTANT1 (AXR1), a prominent neddylated protein in den1, suggests, however, that AXR1 neddylation may be an auto-catalytic side-reaction of Cullin-targeted neddylation and that DEN1 may serve to antagonize non-productive, auto-neddylation from substrates to provide free NEDD8 for CRL regulation.
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Affiliation(s)
- Claus Schwechheimer
- Plant Systems Biology, Emil-Ramann-Strasse 8, Technical University of Munich, 85354 Freising, Germany.
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12
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Delgado TC, Barbier-Torres L, Zubiete-Franco I, Lopitz-Otsoa F, Varela-Rey M, Fernández-Ramos D, Martínez-Chantar ML. Neddylation, a novel paradigm in liver cancer. Transl Gastroenterol Hepatol 2018; 3:37. [PMID: 30050997 DOI: 10.21037/tgh.2018.06.05] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/19/2018] [Indexed: 12/16/2022] Open
Abstract
Liver cancer is the sixth most prevailing cancer worldwide. Hepatocellular carcinoma (HCC), the most common form of primary liver cancer, has a rather heterogeneous pathogenesis making it highly refractive to current therapeutic approaches. Hence, HCC patients have a poor and gloomy prognosis making liver cancer the second leading cause of global cancer-related deaths. On this basis, a more global mechanism, such as post-translational modifications (PTMs) of proteins, may provide a valuable therapeutic approach for HCC clinical management by simultaneously regulating multiple disrupted signaling pathways. In the last years, the ubiquitin-like molecule NEDD8 (Neural precursor cell-expressed developmentally downregulated-8) conjugation pathway, neddylation, was shown to be aberrant in HCC patients with a significant positive correlation found among global levels of neddylation and poorer prognosis. Even though the best-established role for NEDD8 is the activation of ubiquitin E3 ligase family of cullin-RING ligases, the putative role for other NEDD8 substrates has been explored in recent years leading to the identification of novel neddylation targets in HCC. Importantly, treatment with the small pharmacological inhibitor Pevonedistat (MLN4924) (Millennium Pharmaceuticals, Takeda Pharmaceutical), currently in clinical trials for the treatment of some types of leukemias and other advanced solid tumors, was shown to suppress the outgrowth of hepatoma cells and liver cancer in pre-clinical mouse models. Overall, considering that the neddylation inhibitor Pevonedistat was well-tolerated and displayed a significant antitumor effect in pre-clinical models, combinatory pharmacological treatment based on Pevonedistat are highly recommended to enter clinical trials targeting advanced HCC.
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Affiliation(s)
- Teresa Cardoso Delgado
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - Lúcia Barbier-Torres
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain.,Division of Gastroenterology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Imanol Zubiete-Franco
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain.,Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Fernando Lopitz-Otsoa
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - Marta Varela-Rey
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - David Fernández-Ramos
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
| | - María-Luz Martínez-Chantar
- CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Derio, Bizkaia, Spain
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13
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Thomas Y, Scott DC, Kristariyanto YA, Rinehart J, Clark K, Cohen P, Kurz T. The NEDD8 E3 ligase DCNL5 is phosphorylated by IKK alpha during Toll-like receptor activation. PLoS One 2018; 13:e0199197. [PMID: 29958295 PMCID: PMC6025869 DOI: 10.1371/journal.pone.0199197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/01/2018] [Indexed: 11/19/2022] Open
Abstract
The activity of Cullin-RING ubiquitin E3 ligases (CRL) is regulated by NEDD8 modification. DCN-like proteins promote Cullin neddylation as scaffold-like E3s. One DCNL, DCNL5, is highly expressed in immune tissue. Here, we provide evidence that DCNL5 may be involved in innate immunity, as it is a direct substrate of the kinase IKKα during immune signalling. We find that upon activation of Toll-like receptors, DCNL5 gets rapidly and transiently phosphorylated on a specific N-terminal serine residue (S41). This phosphorylation event is specifically mediated by IKKα and not IKKβ. Our data for the first time provides evidence that DCNL proteins are post-translationally modified in an inducible manner. Our findings also provide the first example of a DCNL member as a kinase substrate in a signalling pathway, indicating that the activity of at least some DCNLs may be regulated.
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Affiliation(s)
- Yann Thomas
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Daniel C. Scott
- Department of Structural Biology, Howard Hughes Medical Institute, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yosua Adi Kristariyanto
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Jesse Rinehart
- Department of Cellular & Molecular Physiology, Yale University, New Haven, Connecticut, United States of America
- Systems Biology Institute, Yale University, West Haven, Connecticut, United States of America
| | - Kristopher Clark
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Philip Cohen
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Thimo Kurz
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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14
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Moreno-Gonzalo O, Fernandez-Delgado I, Sanchez-Madrid F. Post-translational add-ons mark the path in exosomal protein sorting. Cell Mol Life Sci 2018; 75:1-19. [PMID: 29080091 DOI: 10.1007/s00018-017-2690-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/11/2017] [Accepted: 10/23/2017] [Indexed: 02/07/2023]
Abstract
Extracellular vesicles (EVs) are released by cells to the extracellular environment to mediate inter-cellular communication. Proteins, lipids, nucleic acids and metabolites shuttled in these vesicles modulate specific functions in recipient cells. The enrichment of selected sets of proteins in EVs compared with global cellular levels suggests the existence of specific sorting mechanisms to specify EV loading. Diverse post-translational modifications (PTMs) of proteins participate in the loading of specific elements into EVs. In this review, we offer a perspective on PTMs found in EVs and discuss the specific role of some PTMs, specifically Ubiquitin and Ubiquitin-like modifiers, in exosomal sorting of protein components. The understanding of these mechanisms will provide new strategies for biomedical applications. Examples include the presence of defined PTM marks on EVs as novel biomarkers for the diagnosis and prognosis of certain diseases, or the specific import of immunogenic components into EVs for vaccine generation.
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15
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Schwertman P, Bekker-Jensen S, Mailand N. Regulation of DNA double-strand break repair by ubiquitin and ubiquitin-like modifiers. Nat Rev Mol Cell Biol 2017; 17:379-94. [PMID: 27211488 DOI: 10.1038/nrm.2016.58] [Citation(s) in RCA: 254] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. The swift recognition and faithful repair of such damage is crucial for the maintenance of genomic stability, as well as for cell and organismal fitness. Signalling by ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs) orchestrates and regulates cellular responses to DSBs at multiple levels, often involving extensive crosstalk between these modifications. Recent findings have revealed compelling insights into the complex mechanisms by which ubiquitin and UBLs regulate protein interactions with DSB sites to promote accurate lesion repair and protection of genome integrity in mammalian cells. These advances offer new therapeutic opportunities for diseases linked to genetic instability.
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Affiliation(s)
- Petra Schwertman
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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16
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Bonacci T, Audebert S, Camoin L, Baudelet E, Iovanna JL, Soubeyran P. Regulation of NUB1 Activity through Non-Proteolytic Mdm2-Mediated Ubiquitination. PLoS One 2017; 12:e0169988. [PMID: 28099510 DOI: 10.1371/journal.pone.0169988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/27/2016] [Indexed: 11/19/2022] Open
Abstract
NUB1 (Nedd8 ultimate buster 1) is an adaptor protein which negatively regulates the ubiquitin-like protein Nedd8 as well as neddylated proteins levels through proteasomal degradation. However, molecular mechanisms underlying this function are not completely understood. Here, we report that the oncogenic E3 ubiquitin ligase Mdm2 is a new NUB1 interacting protein which induces its ubiquitination. Interestingly, we found that Mdm2-mediated ubiquitination of NUB1 is not a proteolytic signal. Instead of promoting the conjugation of polyubiquitin chains and the subsequent proteasomal degradation of NUB1, Mdm2 rather induces its di-ubiquitination on lysine 159. Importantly, mutation of lysine 159 into arginine inhibits NUB1 activity by impairing its negative regulation of Nedd8 and of neddylated proteins. We conclude that Mdm2 acts as a positive regulator of NUB1 function, by modulating NUB1 ubiquitination on lysine 159.
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17
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Pirone L, Xolalpa W, Sigurðsson JO, Ramirez J, Pérez C, González M, de Sabando AR, Elortza F, Rodriguez MS, Mayor U, Olsen JV, Barrio R, Sutherland JD. A comprehensive platform for the analysis of ubiquitin-like protein modifications using in vivo biotinylation. Sci Rep 2017; 7:40756. [PMID: 28098257 PMCID: PMC5241687 DOI: 10.1038/srep40756] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/09/2016] [Indexed: 12/19/2022] Open
Abstract
Post-translational modification by ubiquitin and ubiquitin-like proteins (UbLs) is fundamental for maintaining protein homeostasis. Efficient isolation of UbL conjugates is hampered by multiple factors, including cost and specificity of reagents, removal of UbLs by proteases, distinguishing UbL conjugates from interactors, and low quantities of modified substrates. Here we describe bioUbLs, a comprehensive set of tools for studying modifications in Drosophila and mammals, based on multicistronic expression and in vivo biotinylation using the E. coli biotin protein ligase BirA. While the bioUbLs allow rapid validation of UbL conjugation for exogenous or endogenous proteins, the single vector approach can facilitate biotinylation of most proteins of interest. Purification under denaturing conditions inactivates deconjugating enzymes and stringent washes remove UbL interactors and non-specific background. We demonstrate the utility of the method in Drosophila cells and transgenic flies, identifying an extensive set of putative SUMOylated proteins in both cases. For mammalian cells, we show conjugation and localization for many different UbLs, with the identification of novel potential substrates for UFM1. Ease of use and the flexibility to modify existing vectors will make the bioUbL system a powerful complement to existing strategies for studying this important mode of protein regulation.
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Affiliation(s)
- Lucia Pirone
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - Wendy Xolalpa
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - Jón Otti Sigurðsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Juanma Ramirez
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Coralia Pérez
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - Monika González
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | | | - Félix Elortza
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - Manuel S Rodriguez
- ITAV, IPBS, Université de Toulouse, CNRS, UPS, 1 Place Pierre Potier Oncopole entrée B, BP 50624, 31106 Toulouse Cedex 1, France
| | - Ugo Mayor
- Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain.,Ikerbasque, Basque Foundation for Science, Alameda Urquijo, 36-5 Plaza Bizkaia, 48011 Bilbao, Spain
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Rosa Barrio
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
| | - James D Sutherland
- CIC bioGUNE, Bizkaia Technology Park, Building 801-A, 48160 DERIO, Bizkaia, Spain
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18
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Mergner J, Kuster B, Schwechheimer C. DENEDDYLASE1 Protein Counters Automodification of Neddylating Enzymes to Maintain NEDD8 Protein Homeostasis in Arabidopsis. J Biol Chem 2017; 292:3854-3865. [PMID: 28096463 DOI: 10.1074/jbc.m116.767103] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/10/2017] [Indexed: 11/06/2022] Open
Abstract
In eukaryotes, the conjugation of the ubiquitin-like protein NEDD8 onto protein targets is an important post-translational modification. The best understood neddylation targets are the cullins, scaffold subunits of E3 ubiquitin ligases, where neddylation as well as deneddylation, facilitated by the protease activity of the CSN (COP9 signalosome), are required to control ubiquitin ligase assembly, function, and ultimately substrate degradation. Little is known about the role of other deneddylating enzymes besides CSN and the role of neddylation and deneddylation of their substrates. We previously characterized Arabidopsis thaliana mutants with defects in the conserved NEDD8-specific protease DEN1 (DENEDDYLASE1). These mutants display only subtle growth phenotypes despite the strong accumulation of a broad range of neddylated proteins. Specifically, we identified AXR1 (AUXIN-RESISTANT1), a subunit of the heterodimeric NAE (E1 NEDD8-ACTIVATING ENZYME), as highly neddylated in den1 mutants. Here, we examined the mechanism and consequences of AXR1 neddylation in more detail. We find that AXR1 as well as other neddylation enzymes are autoneddylated at multiple lysines. NAE autoneddylation can be linked to reduced NCE (E2 NEDD8-CONJUGATING ENZYME) NEDD8 thioester levels, either by critically reducing the pool of free NEDD8 or by reducing NAE activity. In planta, increasing NEDD8 gene dosage is sufficient to suppress den1 mutant phenotypes. We therefore suggest that DEN1 serves to recover diverted NEDD8 moieties from autoneddylated NAE subunits, and possibly also other neddylated proteins, to maintain NEDD8 pathway activity toward other NEDD8-dependent processes such as cullin E3 ligase regulation.
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Affiliation(s)
- Julia Mergner
- From the Chair of Plant Systems Biology, Technische Universität München, Emil-Ramann-Strasse 8 and.,the Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Bernhard Kuster
- the Chair of Proteomics and Bioanalytics, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising, Germany
| | - Claus Schwechheimer
- From the Chair of Plant Systems Biology, Technische Universität München, Emil-Ramann-Strasse 8 and
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19
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Jayabalan AK, Sanchez A, Park RY, Yoon SP, Kang GY, Baek JH, Anderson P, Kee Y, Ohn T. NEDDylation promotes stress granule assembly. Nat Commun 2016; 7:12125. [PMID: 27381497 PMCID: PMC4935812 DOI: 10.1038/ncomms12125] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 06/02/2016] [Indexed: 12/21/2022] Open
Abstract
Stress granules (SGs) harbour translationally stalled messenger ribonucleoproteins and play important roles in regulating gene expression and cell fate. Here we show that neddylation promotes SG assembly in response to arsenite-induced oxidative stress. Inhibition or depletion of key components of the neddylation machinery concomitantly inhibits stress-induced polysome disassembly and SG assembly. Affinity purification and subsequent mass-spectrometric analysis of Nedd8-conjugated proteins from translationally stalled ribosomal fractions identified ribosomal proteins, translation factors and RNA-binding proteins (RBPs), including SRSF3, a previously known SG regulator. We show that SRSF3 is selectively neddylated at Lys85 in response to arsenite. A non-neddylatable SRSF3 (K85R) mutant do not prevent arsenite-induced polysome disassembly, but fails to support the SG assembly, suggesting that the neddylation pathway plays an important role in SG assembly.
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Affiliation(s)
- Aravinth Kumar Jayabalan
- Department of Cellular &Molecular Medicine, College of Medicine, Chosun University, Gwangju 61452, Republic of Korea
| | - Anthony Sanchez
- Department of Cell Biology, Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida, Tampa, Florida 33620, USA
| | - Ra Young Park
- Department of Cellular &Molecular Medicine, College of Medicine, Chosun University, Gwangju 61452, Republic of Korea
| | - Sang Pil Yoon
- Department of Anatomy, School of Medicine, Jeju National University, Jeju-Do 690-756, Republic of Korea
| | - Gum-Yong Kang
- Diatech Korea Co, Ltd, Saemal-ro 5-gil, Songpa-gu, Seoul 05807, Republic of Korea
| | - Je-Hyun Baek
- Diatech Korea Co, Ltd, Saemal-ro 5-gil, Songpa-gu, Seoul 05807, Republic of Korea
| | - Paul Anderson
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Smith652, One Jimmy Fund Way, Boston, Massachusetts 02115, USA
| | - Younghoon Kee
- Department of Cell Biology, Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida, Tampa, Florida 33620, USA
| | - Takbum Ohn
- Department of Cellular &Molecular Medicine, College of Medicine, Chosun University, Gwangju 61452, Republic of Korea
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20
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Keuss MJ, Thomas Y, Mcarthur R, Wood NT, Knebel A, Kurz T. Characterization of the mammalian family of DCN-type NEDD8 E3 ligases. J Cell Sci 2016; 129:1441-54. [PMID: 26906416 PMCID: PMC4886823 DOI: 10.1242/jcs.181784] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/14/2016] [Indexed: 01/25/2023] Open
Abstract
Cullin-RING ligases (CRL) are ubiquitin E3 enzymes that bind substrates through variable substrate receptor proteins and are activated by attachment of the ubiquitin-like protein NEDD8 to the cullin subunit. DCNs are NEDD8 E3 ligases that promote neddylation. Mammalian cells express five DCN-like (DCNL) proteins but little is known about their specific functions or interaction partners. We found that DCNLs form stable stoichiometric complexes with CAND1 and cullins that can only be neddylated in the presence of a substrate adaptor. These CAND-cullin-DCNL complexes might represent 'reserve' CRLs that can be rapidly activated when needed. We further found that all DCNLs interact with most cullin subtypes, but that they are probably responsible for the neddylation of different subpopulations of any given cullin. This is consistent with the fact that the subcellular localization of DCNLs in tissue culture cells differs and that they show unique tissue-specific expression patterns in mice. Thus, the specificity between DCNL-type NEDD8 E3 enzymes and their cullin substrates is only apparent in well-defined physiological contexts and related to their subcellular distribution and restricted expression.
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Affiliation(s)
- Matthew J Keuss
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Yann Thomas
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Robin Mcarthur
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Nicola T Wood
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Axel Knebel
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thimo Kurz
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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21
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Li J, Ma W, Li H, Hou N, Wang X, Kim IM, Li F, Su H. NEDD8 Ultimate Buster 1 Long (NUB1L) Protein Suppresses Atypical Neddylation and Promotes the Proteasomal Degradation of Misfolded Proteins. J Biol Chem 2015; 290:23850-62. [PMID: 26260793 DOI: 10.1074/jbc.m115.664375] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 11/06/2022] Open
Abstract
Neddylation is a posttranslational modification that controls diverse biological processes by covalently conjugating the ubiquitin-like protein NEDD8 to specific targets. Neddylation is commonly mediated by NEDD8-specific enzymes (typical neddylation) and, sometimes, by ubiquitin enzymes (atypical neddylation). Although typical neddylation is known to regulate protein function in many ways, the regulatory mechanisms and biological consequence of atypical neddylation remain largely unexplored. Here we report that NEDD8 conjugates were accumulated in the diseased hearts from mouse models and human patients. Proteotoxic stresses induced typical and atypical neddylation in cardiomyocytes. Loss of NUB1L exaggerated atypical neddylation, whereas NUB1L overexpression repressed atypical neddylation through promoting the degradation of NEDD8. Activation of atypical neddylation accumulated a surrogate misfolded protein, GFPu. In contrast, suppression of atypical neddylation by NUB1L overexpression enhanced GFPu degradation. Moreover, NUB1L depletion accumulated a cardiomyopathy-linked misfolded protein, CryAB(R120G), whereas NUB1L overexpression promoted its degradation through suppressing neddylation of ubiquitinated proteins in cardiomyocytes. Consequently, NUB1L protected cells from proteotoxic stress-induced cell injury. In summary, these data indicate that NUB1L suppresses atypical neddylation and promotes the degradation of misfolded proteins by the proteasome. Our findings also suggest that induction of NUB1L could potentially become a novel therapeutic strategy for diseases with increased proteotoxic stress.
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Affiliation(s)
- Jie Li
- From the Vascular Biology Center and
| | - Wenxia Ma
- From the Vascular Biology Center and
| | | | - Ning Hou
- the Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Xuejun Wang
- the Division of Basic Biomedical Sciences, Sanford School of Medicine, University of South Dakota, Vermillion, South Dakota 57069
| | | | - Faqian Li
- the Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York 14642, and
| | - Huabo Su
- From the Vascular Biology Center and Department of Pharmacology and Toxicology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912,
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22
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Fan JB, Arimoto K, Motamedchaboki K, Yan M, Wolf DA, Zhang DE. Identification and characterization of a novel ISG15-ubiquitin mixed chain and its role in regulating protein homeostasis. Sci Rep 2015; 5:12704. [PMID: 26226047 DOI: 10.1038/srep12704] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As a ubiquitin-like modifier, ISG15 is conjugated to many cellular proteins in a process termed protein ISGylation. However, the crosstalk between protein ISGylation and the ubiquitin proteasome system is not fully understood. Here, we report that cellular ubiquitin is a substrate of ISG15 and Lys 29 on ubiquitin is the major ISG15 acceptor site. Using a model substrate, we demonstrate that ISG15 can modify ubiquitin, which is immobilized on its substrate, to form ISG15-ubiquitin mixed chains. Furthermore, our results indicate that ISG15-ubiquitin mixed chains do not serve as degradation signals for a ubiquitin fusion degradation substrate. Accordingly, an ISG15-ubiquitin fusion protein, which mimics an ISG15-ubiquitin mixed chain, negatively regulates cellular turnover of ubiquitylated proteins. In addition, ISG15-ubiquitin mixed chains, which are detectable on endogenously ubiquitylated proteins, dampen cellular turnover of these proteins. Thus, our studies unveil an unanticipated interplay between two protein modification systems and highlight its role in coordinating protein homeostasis.
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23
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Abstract
Proteasome inhibitors have revolutionized the treatment of multiple myeloma, and validated the therapeutic potential of the ubiquitin proteasome system (UPS). It is believed that in part, proteasome inhibitors elicit their therapeutic effect by inhibiting the degradation of misfolded proteins, which is proteotoxic and causes cell death. In spite of these successes, proteasome inhibitors are not effective against solid tumors, thus necessitating the need to explore alternative approaches. Furthermore, proteasome inhibitors lead to the formation of aggresomes that clear misfolded proteins via the autophagy-lysosome degradation pathway. Importantly, aggresome formation depends on the presence of polyubiquitin tags on misfolded proteins. We therefore hypothesized that inhibitors of ubiquitin conjugation should inhibit both degradation of misfolded proteins, and ubiquitin dependent aggresome formation, thus outlining the path forward toward more effective anticancer therapeutics. To explore the therapeutic potential of targeting the UPS to treat solid cancers, we have developed an inhibitor of ubiquitin conjugation (ABP A3) that targets ubiquitin and Nedd8 E1 enzymes, enzymes that are required to maintain the activity of the entire ubiquitin system. We have shown that ABP A3 inhibits conjugation of ubiquitin to intracellular proteins and prevents the formation of cytoprotective aggresomes in A549 lung cancer cells. Furthermore, ABP A3 induces activation of the unfolded protein response and apoptosis. Thus, similar to proteasome inhibitors MG132, bortezomib, and carfilzomib, ABP A3 can serve as a novel probe to explore the therapeutic potential of the UPS in solid and hematological malignancies.
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Affiliation(s)
- Heeseon An
- Department of Chemistry , Center for Molecular Innovation and Drug Discovery , Chemistry of Life Processes Institute , Northwestern University , Silverman Hall, 2145 Sheridan Road , Evanston , Illinois 60208 , USA
| | - Alexander V Statsyuk
- Department of Chemistry , Center for Molecular Innovation and Drug Discovery , Chemistry of Life Processes Institute , Northwestern University , Silverman Hall, 2145 Sheridan Road , Evanston , Illinois 60208 , USA
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24
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Brown JS, Lukashchuk N, Sczaniecka-Clift M, Britton S, le Sage C, Calsou P, Beli P, Galanty Y, Jackson SP. Neddylation promotes ubiquitylation and release of Ku from DNA-damage sites. Cell Rep 2015; 11:704-14. [PMID: 25921528 PMCID: PMC4431666 DOI: 10.1016/j.celrep.2015.03.058] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/12/2014] [Accepted: 03/25/2015] [Indexed: 11/24/2022] Open
Abstract
The activities of many DNA-repair proteins are controlled through reversible covalent modification by ubiquitin and ubiquitin-like molecules. Nonhomologous end-joining (NHEJ) is the predominant DNA double-strand break (DSB) repair pathway in mammalian cells and is initiated by DSB ends being recognized by the Ku70/Ku80 (Ku) heterodimer. By using MLN4924, an anti-cancer drug in clinical trials that specifically inhibits conjugation of the ubiquitin-like protein, NEDD8, to target proteins, we demonstrate that NEDD8 accumulation at DNA-damage sites is a highly dynamic process. In addition, we show that depleting cells of the NEDD8 E2-conjugating enzyme, UBE2M, yields ionizing radiation hypersensitivity and reduced cell survival following NHEJ. Finally, we demonstrate that neddylation promotes Ku ubiquitylation after DNA damage and release of Ku and Ku-associated proteins from damage sites following repair. These studies provide insights into how the NHEJ core complex dissociates from repair sites and highlight its importance for cell survival following DSB induction.
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Affiliation(s)
- Jessica S Brown
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Natalia Lukashchuk
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Sébastien Britton
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse-Université Paul Sabatier, Equipe Labellisée Ligue contre le Cancer, 31077 Toulouse, France
| | - Carlos le Sage
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Patrick Calsou
- Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse-Université Paul Sabatier, Equipe Labellisée Ligue contre le Cancer, 31077 Toulouse, France
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Yaron Galanty
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK.
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK.
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25
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McIntyre J, Woodgate R. Regulation of translesion DNA synthesis: Posttranslational modification of lysine residues in key proteins. DNA Repair (Amst) 2015; 29:166-79. [PMID: 25743599 PMCID: PMC4426011 DOI: 10.1016/j.dnarep.2015.02.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/09/2015] [Accepted: 02/10/2015] [Indexed: 01/30/2023]
Abstract
Posttranslational modification of proteins often controls various aspects of their cellular function. Indeed, over the past decade or so, it has been discovered that posttranslational modification of lysine residues plays a major role in regulating translesion DNA synthesis (TLS) and perhaps the most appreciated lysine modification is that of ubiquitination. Much of the recent interest in ubiquitination stems from the fact that proliferating cell nuclear antigen (PCNA) was previously shown to be specifically ubiquitinated at K164 and that such ubiquitination plays a key role in regulating TLS. In addition, TLS polymerases themselves are now known to be ubiquitinated. In the case of human polymerase η, ubiquitination at four lysine residues in its C-terminus appears to regulate its ability to interact with PCNA and modulate TLS. Within the past few years, advances in global proteomic research have revealed that many proteins involved in TLS are, in fact, subject to a previously underappreciated number of lysine modifications. In this review, we will summarize the known lysine modifications of several key proteins involved in TLS; PCNA and Y-family polymerases η, ι, κ and Rev1 and we will discuss the potential regulatory effects of such modification in controlling TLS in vivo.
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Affiliation(s)
- Justyna McIntyre
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, ul. Pawinskiego 5a, 02-106 Warsaw, Poland.
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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26
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Mergner J, Heinzlmeir S, Kuster B, Schwechheimer C. DENEDDYLASE1 deconjugates NEDD8 from non-cullin protein substrates in Arabidopsis thaliana. Plant Cell 2015; 27:741-53. [PMID: 25783028 PMCID: PMC4558671 DOI: 10.1105/tpc.114.135996] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 02/05/2015] [Accepted: 02/26/2015] [Indexed: 05/25/2023]
Abstract
The evolutionarily conserved 8-kD protein NEDD8 (NEURAL PRECURSOR CELL EXPRESSED, DEVELOPMENTALLY DOWN-REGULATED8) belongs to the family of ubiquitin-like modifiers. Like ubiquitin, NEDD8 is conjugated to and deconjugated from target proteins. Many targets and functions of ubiquitylation have been described; by contrast, few targets of NEDD8 have been identified. In plants as well as in non-plant organisms, the cullin subunits of cullin-RING E3 ligases are NEDD8 conjugates with a demonstrated functional role for the NEDD8 modification. The existence of other non-cullin NEDD8 targets has generally been questioned. NEDD8 is translated as a precursor protein and proteolytic processing exposes a C-terminal glycine required for NEDD8 conjugation. In animals and yeast, DENEDDYLASE1 (DEN1) processes NEDD8. Here, we show that mutants of a DEN1 homolog from Arabidopsis thaliana have no detectable defects in NEDD8 processing but do accumulate a broad range of NEDD8 conjugates; this provides direct evidence for the existence of non-cullin NEDD8 conjugates. We further identify AUXIN RESISTANT1 (AXR1), a subunit of the heterodimeric NEDD8 E1 activating enzyme, as a NEDD8-modified protein in den1 mutants and wild type and provide evidence that AXR1 function may be compromised in the absence of DEN1 activity. Thus, in plants, neddylation may serve as a regulatory mechanism for cullin and non-cullin proteins.
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Affiliation(s)
- Julia Mergner
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Stephanie Heinzlmeir
- Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Technische Universität München, 85354 Freising, Germany
| | - Claus Schwechheimer
- Plant Systems Biology, Technische Universität München, 85354 Freising, Germany
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27
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Abstract
Post-translational modification of proteins with ubiquitin and ubiquitin-like molecules (UBLs) controls a vast if not every biological process in the cell. It is not surprising that deregulation in ubiquitin and UBL signalling has been implicated in the pathogenesis of many diseases and that these pathways are considered as major targets for therapeutic intervention. In this review, we summarise recent advances in our understanding of the role of the UBL neural precursor cell expressed developmentally downregulated-8 (NEDD8) in cancer-related processes and potential strategies for the use of NEDD8 inhibitors as chemotherapeutics.
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Affiliation(s)
- Naima Abidi
- Centre de Recherche de Biochimie MacromoléculaireUMR5235, 1919 Route de Mende, Montpellier 34293, France
| | - Dimitris P Xirodimas
- Centre de Recherche de Biochimie MacromoléculaireUMR5235, 1919 Route de Mende, Montpellier 34293, France
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28
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Abstract
Ubiquitin-dependent proteolysis is a major mechanism that downregulates misfolded proteins or those that have finished a programmed task. In the last two decades, neddylation has emerged as a major regulatory pathway for ubiquitination. Central to the neddylation pathway is the amyloid precursor protein (APP)-binding protein APP-BP1, which together with Uba3, plays an analogous role to the ubiquitin-activating enzyme E1 in nedd8 activation. Activated nedd8 covalently modifies and activates a major class of ubiquitin ligases called Cullin-RING ligases (CRLs). New evidence suggests that neddylation also modifies Type-1 transmembrane receptors such as APP. Here we review the functions of neddylation and summarize evidence suggesting that dysfunction of neddylation is involved in Alzheimer's disease.
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Affiliation(s)
- Yuzhi Chen
- Department of Geriatrics and Department of Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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29
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Abstract
NEDD8, in plants and yeasts also known as RELATED TO UBIQUITIN (RUB), is an evolutionarily conserved 76 amino acid protein highly related to ubiquitin. Like ubiquitin, NEDD8 can be conjugated to and deconjugated from target proteins, but unlike ubiquitin, NEDD8 has not been reported to form chains similar to the different polymeric ubiquitin chains that have a role in a diverse set of cellular processes. NEDD8-modification is best known as a post-translational modification of the cullin subunits of cullin-RING E3 ubiquitin ligases. In this context, structural analyses have revealed that neddylation induces a conformation change of the cullin that brings the ubiquitylation substrates into proximity of the interacting E2 conjugating enzyme. In turn, NEDD8 deconjugation destabilizes the cullin RING ligase complex allowing for the exchange of substrate recognition subunits via the exchange factor CAND1. In plants, components of the neddylation and deneddylation pathway were identified based on mutants with defects in auxin and light responses and the characterization of these mutants has been instrumental for the elucidation of the neddylation pathway. More recently, there has been evidence from animal and plant systems that NEDD8 conjugation may also regulate the behavior or fate of non-cullin substrates in a number of ways. Here, the current knowledge on NEDD8 processing, conjugation and deconjugation is presented, where applicable, in the context of specific signaling pathways from plants.
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Affiliation(s)
| | - Claus Schwechheimer
- *Correspondence: Claus Schwechheimer, Plant Systems Biology, Technische Universität München, Emil-Ramann-Straße 4, 85354 Freising, Germany e-mail:
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30
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Abstract
Ubiquitin and ubiquitin-like (UBL) proteins regulate a vast variety of cellular functions. Some UBL proteins are present in all cell types, while others are expressed only in certain cells or under certain environmental conditions. This highlights the central role of UBL systems in regulation of ubiquitous as well as specific cellular functions. UBL proteins share little amino acid sequence identity to each other, yet they share similar 3D shapes, which is exemplified by the β-grasp fold. Central to UBL protein signaling pathways are UBL protein-activating E1 enzymes that activate the C-terminus of UBL proteins for subsequent conjugation to the protein substrates. Due to their critical roles in biology, E1 enzymes have been recognized as emerging drug targets to treat human diseases. In spite of their biological significance, however, methods to discover UBL proteins and to monitor the intracellular activity of E1 enzymes are lacking. Thus, there is a critical need for methods to evaluate the intracellular mechanisms of action of E1 enzyme inhibitors. Here we describe the development of a mechanism-based small-molecule probe, ABP1, that can be used to discover and to detect active UBL proteins, and to monitor the intracellular activity of E1 enzymes inside intact cells. The developed probe can also be used to profile the selectivity of E1 enzyme-targeting drugs in vitro and inside intact cells.
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Affiliation(s)
- Heeseon An
- Department of Chemistry, Center for Molecular Innovation and Drug Discovery, Chemistry of Life Processes Institute, Northwestern University , Silverman Hall, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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31
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Choy A, Severo MS, Sun R, Girke T, Gillespie JJ, Pedra JHF. Decoding the ubiquitin-mediated pathway of arthropod disease vectors. PLoS One 2013; 8:e78077. [PMID: 24205097 PMCID: PMC3804464 DOI: 10.1371/journal.pone.0078077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/16/2013] [Indexed: 11/19/2022] Open
Abstract
Protein regulation by ubiquitin has been extensively described in model organisms. However, characterization of the ubiquitin machinery in disease vectors remains mostly unknown. This fundamental gap in knowledge presents a concern because new therapeutics are needed to control vector-borne diseases, and targeting the ubiquitin machinery as a means for disease intervention has been already adopted in the clinic. In this study, we employed a bioinformatics approach to uncover the ubiquitin-mediated pathway in the genomes of Anopheles gambiae, Aedes aegypti, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus and Rhodnius prolixus. We observed that (1) disease vectors encode a lower percentage of ubiquitin-related genes when compared to Drosophila melanogaster, Mus musculus and Homo sapiens but not Saccharomyces cerevisiae; (2) overall, there are more proteins categorized as E3 ubiquitin ligases when compared to E2-conjugating or E1-activating enzymes; (3) the ubiquitin machinery within the three mosquito genomes is highly similar; (4) ubiquitin genes are more than doubled in the Chagas disease vector (R. prolixus) when compared to other arthropod vectors; (5) the deer tick I. scapularis and the body louse (P. humanus) genomes carry low numbers of E1-activating enzymes and HECT-type E3 ubiquitin ligases; (6) R. prolixus have low numbers of RING-type E3 ubiquitin ligases; and (7) C. quinquefasciatus present elevated numbers of predicted F-box E3 ubiquitin ligases, JAB and UCH deubiquitinases. Taken together, these findings provide novel opportunities to study the interaction between a pathogen and an arthropod vector.
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Affiliation(s)
- Anthony Choy
- Institute for Integrative Genome Biology, Center for Disease Vector Research and Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Maiara S. Severo
- Institute for Integrative Genome Biology, Center for Disease Vector Research and Department of Entomology, University of California Riverside, Riverside, California, United States of America
| | - Ruobai Sun
- "Institute for Integrative Genome Biology, Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
| | - Thomas Girke
- "Institute for Integrative Genome Biology, Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, California, United States of America
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Joao H. F. Pedra
- Institute for Integrative Genome Biology, Center for Disease Vector Research and Department of Entomology, University of California Riverside, Riverside, California, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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32
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Zhao B, Zhang K, Bhuripanyo K, Choi CHJ, Villhauer EB, Li H, Zheng N, Kiyokawa H, Schindelin H, Yin J. Profiling the cross reactivity of ubiquitin with the Nedd8 activating enzyme by phage display. PLoS One 2013; 8:e70312. [PMID: 23936405 PMCID: PMC3731359 DOI: 10.1371/journal.pone.0070312] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/18/2013] [Indexed: 11/23/2022] Open
Abstract
The C-terminal peptides of ubiquitin (UB) and UB-like proteins (UBLs) play a key role in their recognition by the specific activating enzymes (E1s) to launch their transfer through the respective enzymatic cascades thus modifying cellular proteins. UB and Nedd8, a UBL regulating the activity of cullin-RING UB ligases, only differ by one residue at their C-termini; yet each has its specific E1 for the activation reaction. It has been reported recently that UAE can cross react with Nedd8 to enable its passage through the UB transfer cascade for protein neddylation. To elucidate differences in UB recognition by UAE and NAE, we carried out phage selection of a UB library with randomized C-terminal sequences based on the catalytic formation of UB∼NAE thioester conjugates. Our results confirmed the previous finding that residue 72 of UB plays a “gate-keeping” role in E1 selectivity. We also found that diverse sequences flanking residue 72 at the UB C-terminus can be accommodated by NAE for activation. Furthermore heptameric peptides derived from the C-terminal sequences of UB variants selected for NAE activation can function as mimics of Nedd8 to form thioester conjugates with NAE and the downstream E2 enzyme Ubc12 in the Nedd8 transfer cascade. Once the peptides are charged onto the cascade enzymes, the full-length Nedd8 protein is effectively blocked from passing through the cascade for the critical modification of cullin. We have thus identified a new class of inhibitors of protein neddylation based on the profiles of the UB C-terminal sequences recognized by NAE.
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Affiliation(s)
- Bo Zhao
- Department of Chemistry, University of Chicago, Chicago, Illinois, United States of America
| | - Keya Zhang
- Department of Chemistry, University of Chicago, Chicago, Illinois, United States of America
| | - Karan Bhuripanyo
- Department of Chemistry, University of Chicago, Chicago, Illinois, United States of America
| | - Chan Hee J. Choi
- Department of Chemistry, University of Chicago, Chicago, Illinois, United States of America
| | - Eric B. Villhauer
- Department of Chemistry, University of Chicago, Chicago, Illinois, United States of America
| | - Heng Li
- Department of Pharmacology, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
| | - Ning Zheng
- Department of Pharmacology, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
| | - Hiroaki Kiyokawa
- Department of Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine and Institute for Structural Biology, University of Würzburg, Würzburg, Germany
| | - Jun Yin
- Department of Chemistry, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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33
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Zhao B, Zhang K, Villhauer EB, Bhuripanyo K, Kiyokawa H, Schindelin H, Yin J. Phage display to identify Nedd8-mimicking peptides as inhibitors of the Nedd8 transfer cascade. Chembiochem 2013; 14:1323-30. [PMID: 23824602 DOI: 10.1002/cbic.201300234] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Indexed: 11/07/2022]
Abstract
The Nedd8 activating enzyme (NAE) launches the transfer of the ubiquitin-like protein Nedd8 through an enzymatic cascade to covalently modify a diverse array of proteins, thus regulating their biological functions in the cell. The C-terminal peptide of Nedd8 extends deeply into the active site of NAE and plays an important role in the specific recognition of Nedd8 by NAE. We used phage display to profile C-terminal mutant sequences of Nedd8 that could be recognized by NAE for the activation reaction. We found that NAE can accommodate diverse changes in the Nedd8 C-terminal sequence (⁷¹ LALRGG⁷⁶), including Arg and Ile replacing Leu71, Leu, Ser, and Gln replacing Ala72, and substitutions by bulky aromatic residues at positions 73 and 74. We also observed that short peptides corresponding to the C-terminal sequences of the Nedd8 variants can be activated by NAE to form peptide~NAE thioester conjugates. Once NAE is covalently loaded with these Nedd8-mimicking peptides, it can no longer activate full-length Nedd8 for transfer to the neddylation targets, such as the cullin subunits of cullin-RING E3 ubiquitin ligases (CRLs). We have thus developed a new method to inhibit protein neddylation by Nedd8-mimicking peptides.
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Affiliation(s)
- Bo Zhao
- Department of Chemistry, University of Chicago, 929 E57th Street, Chicago, IL 60637, USA
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34
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Abstract
The ubiquitin system is essential for the maintenance of proper protein homeostasis function across eukaryotic species. Although the general enzymatic architecture for adding and removing ubiquitin from substrates is well defined, methods for the comprehensive investigation of cellular ubiquitylation targets have just started to emerge. Recent advances in ubiquitin-modified peptide enrichment have greatly increased the number of identified endogenous ubiquitylation targets, as well as the number of sites of ubiquitin attachment within these substrates. Herein we evaluate current strategies using mass-spectrometry-based proteomics to characterize ubiquitin and ubiquitin-like modifications. Using existing data, we describe the characteristics of the ubiquitin-modified proteome and discuss strategies for the biological interpretation of existing and future ubiquitin-based proteomic studies.
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Affiliation(s)
- Andrea C Carrano
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093
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35
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Williamson A, Werner A, Rape M. The Colossus of ubiquitylation: decrypting a cellular code. Mol Cell 2013; 49:591-600. [PMID: 23438855 DOI: 10.1016/j.molcel.2013.01.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/19/2013] [Accepted: 01/24/2013] [Indexed: 11/20/2022]
Abstract
Ubiquitylation is an essential posttranslational modification that can regulate the stability, activity, and localization of thousands of proteins. The reversible attachment of ubiquitin as well as interpretation of the ubiquitin signal depends on dynamic protein networks that are challenging to analyze. In this perspective, we discuss tools of the trade that have recently been developed to dissect mechanisms of ubiquitin-dependent signaling, thereby revealing the critical features of an important cellular code.
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Affiliation(s)
- Adam Williamson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
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36
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Abstract
The bacterial effector protein cycle inhibiting factor (CIF) converts glutamine 40 of NEDD8 to glutamate (Q40E), causing cytopathic effects and inhibiting cell proliferation. Although these have been attributed to blocking the functions of cullin-RING ubiquitin ligases, how CIF modulates NEDD8-dependent signaling is unclear. Here we use conditional NEDD8-dependent yeast to explore the effects of CIF on cullin neddylation. Although CIF causes cullin deneddylation and the generation of free NEDD8 Q40E, inhibiting the COP9 signalosome (CSN) allows Q40E to form only on NEDD8 attached to cullins. In the presence of the CSN, NEDD8 Q40E is removed from cullins more rapidly than NEDD8, leading to a decrease in steady-state cullin neddylation. As NEDD8 Q40E is competent for cullin conjugation in the absence of functional CSN and with overexpression of the NEDD8 ligase Dcn1, our data are consistent with NEDD8 deamidation causing enhanced deneddylation of cullins by the CSN. This leads to a dramatic change in the extent of activated cullin-RING ubiquitin ligases.
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Affiliation(s)
- Tasha B Toro
- Signal Transduction Program, NCI-designated Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, California 92037, USA
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37
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Aillet F, Lopitz-Otsoa F, Egaña I, Hjerpe R, Fraser P, Hay RT, Rodriguez MS, Lang V. Heterologous SUMO-2/3-ubiquitin chains optimize IκBα degradation and NF-κB activity. PLoS One 2012; 7:e51672. [PMID: 23284737 PMCID: PMC3527444 DOI: 10.1371/journal.pone.0051672] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Accepted: 11/05/2012] [Indexed: 01/09/2023] Open
Abstract
The NF-κB pathway is regulated by SUMOylation at least at three levels: the inhibitory molecule IκBα, the IKK subunit γ/NEMO and the p52 precursor p100. Here we investigate the role of SUMO-2/3 in the degradation of IκBα and activation of NF-κB mediated by TNFα. We found that under conditions of deficient SUMOylation, an important delay in both TNFα-mediated proteolysis of IκBα and NF-κB dependent transcription occurs. In vitro and ex vivo approaches, including the use of ubiquitin-traps (TUBEs), revealed the formation of chains on IκBα containing SUMO-2/3 and ubiquitin after TNFα stimulation. The integration of SUMO-2/3 appears to promote the formation of ubiquitin chains on IκBα after activation of the TNFα signalling pathway. Furthermore, heterologous chains of SUMO-2/3 and ubiquitin promote a more efficient degradation of IκBα by the 26S proteasome in vitro compared to chains of either SUMO-2/3 or ubiquitin alone. Consistently, Ubc9 silencing reduced the capture of IκBα modified with SUMO-ubiquitin hybrid chains that display a defective proteasome-mediated degradation. Thus, hybrid SUMO-2/3-ubiquitin chains increase the susceptibility of modified IκBα to the action of 26S proteasome, contributing to the optimal control of NF-κB activity after TNFα-stimulation.
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Affiliation(s)
- Fabienne Aillet
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Bizkaia, Spain
- Ubiquitylation & Cancer Molecular Biology Laboratory, Inbiomed, San Sebastián-Donostia, Gipuzkoa, Spain
| | | | - Isabel Egaña
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Bizkaia, Spain
| | - Roland Hjerpe
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Bizkaia, Spain
| | - Paul Fraser
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Medical Biophysics, University of Toronto, Ontario, Canada
| | - Ron T. Hay
- Centre for Interdisciplinary Research, School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | | | - Valérie Lang
- Proteomics Unit, CIC bioGUNE, CIBERehd, Derio, Bizkaia, Spain
- Ubiquitylation & Cancer Molecular Biology Laboratory, Inbiomed, San Sebastián-Donostia, Gipuzkoa, Spain
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