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Song JM, Kang M, Lee S, Kim J, Park S, Park DH, Lee S, Suh YH. Deneddylating enzyme SENP8 regulates neuronal development. J Neurochem 2023; 165:348-361. [PMID: 36847487 DOI: 10.1111/jnc.15797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 01/16/2023] [Accepted: 02/13/2023] [Indexed: 03/01/2023]
Abstract
Neddylation is a cellular process in which the neural precursor cell expressed, developmentally down-regulated 8 (NEDD8) is conjugated to the lysine residue of target proteins via serial enzymatic cascades. Recently, it has been demonstrated that neddylation is required for synaptic clustering of metabotropic glutamate receptor 7 (mGlu7) and postsynaptic density protein 95 (PSD-95), and the inhibition of neddylation impairs neurite outgrowth and excitatory synaptic maturation. Similar to the balanced role of deubiquitylating enzymes (DUBs) in the ubiquitination process, we hypothesized that deneddylating enzymes can regulate neuronal development by counteracting the process of neddylation. We find that the SUMO peptidase family member, NEDD8 specific (SENP8) acts as a key neuronal deneddylase targeting the global neuronal substrates in primary rat cultured neurons. We demonstrate that SENP8 expression levels are developmentally regulated, peaking around the first postnatal week and gradually diminishing in mature brain and neurons. We find that SENP8 negatively regulates neurite outgrowth through multiple pathways, including actin dynamics, Wnt/β-catenin signaling, and autophagic processes. Alterations in neurite outgrowth by SENP8 subsequently result in the impairment of excitatory synapse maturation. Our data indicate that SENP8 plays an essential role in neuronal development and is a promising therapeutic target for neurodevelopmental disorders.
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Affiliation(s)
- Jae-Man Song
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Minji Kang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Seungha Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jungho Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Sunha Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Da-Ha Park
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Sanghyeon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Young Ho Suh
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.,Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea.,Transplantation Research Institute, Seoul National University College of Medicine, Seoul, South Korea
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2
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Kim WD, Mathavarajah S, Huber RJ. The Cellular and Developmental Roles of Cullins, Neddylation, and the COP9 Signalosome in Dictyostelium discoideum. Front Physiol 2022; 13:827435. [PMID: 35586714 PMCID: PMC9108976 DOI: 10.3389/fphys.2022.827435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
Cullins (CULs) are a core component of cullin-RING E3 ubiquitin ligases (CRLs), which regulate the degradation, function, and subcellular trafficking of proteins. CULs are post-translationally regulated through neddylation, a process that conjugates the ubiquitin-like modifier protein neural precursor cell expressed developmentally downregulated protein 8 (NEDD8) to target cullins, as well as non-cullin proteins. Counteracting neddylation is the deneddylase, COP9 signalosome (CSN), which removes NEDD8 from target proteins. Recent comparative genomics studies revealed that CRLs and the CSN are highly conserved in Amoebozoa. A well-studied representative of Amoebozoa, the social amoeba Dictyostelium discoideum, has been used for close to 100 years as a model organism for studying conserved cellular and developmental processes owing to its unique life cycle comprised of unicellular and multicellular phases. The organism is also recognized as an exceptional model system for studying cellular processes impacted by human diseases, including but not limited to, cancer and neurodegeneration. Recent work shows that the neddylation inhibitor, MLN4924 (Pevonedistat), inhibits growth and multicellular development in D. discoideum, which supports previous work that revealed the cullin interactome in D. discoideum and the roles of cullins and the CSN in regulating cellular and developmental processes during the D. discoideum life cycle. Here, we review the roles of cullins, neddylation, and the CSN in D. discoideum to guide future work on using this biomedical model system to further explore the evolutionarily conserved functions of cullins and neddylation.
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Affiliation(s)
- William D. Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | | | - Robert J. Huber
- Department of Biology, Trent University, Peterborough, ON, Canada
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3
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Huber RJ, Kim WD, Mathavarajah S. Inhibiting Neddylation with MLN4924 Suppresses Growth and Delays Multicellular Development in Dictyostelium discoideum. Biomolecules 2021; 11:482. [PMID: 33807046 PMCID: PMC8005062 DOI: 10.3390/biom11030482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/18/2022] Open
Abstract
Neddylation is a post-translational modification that is essential for a variety of cellular processes and is linked to many human diseases including cancer, neurodegeneration, and autoimmune disorders. Neddylation involves the conjugation of the ubiquitin-like modifier neural precursor cell expressed developmentally downregulated protein 8 (NEDD8) to target proteins, and has been studied extensively in various eukaryotes including fungi, plants, and metazoans. Here, we examine the biological processes influenced by neddylation in the social amoeba, Dictyostelium discoideum, using a well-established inhibitor of neddylation, MLN4924 (pevonedistat). NEDD8, and the target of MLN4924 inhibition, NEDD8-activating enzyme E1 (NAE1), are highly conserved in D. discoideum (Nedd8 and Nae1, respectively). Treatment of D. discoideum cells with MLN4924 increased the amount of free Nedd8, suggesting that MLN4924 inhibited neddylation. During growth, MLN4924 suppressed cell proliferation and folic acid-mediated chemotaxis. During multicellular development, MLN4924 inhibited cyclic adenosine monophosphate (cAMP)-mediated chemotaxis, delayed aggregation, and suppressed fruiting body formation. Together, these findings indicate that neddylation plays an important role in regulating cellular and developmental events during the D. discoideum life cycle and that this organism can be used as a model system to better understand the essential roles of neddylation in eukaryotes, and consequently, its involvement in human disease.
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Affiliation(s)
- Robert J. Huber
- Department of Biology, Trent University, Peterborough, ON K9L 0G2, Canada
| | - William D. Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9L 0G2, Canada;
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4
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Lobato-Gil S, Heidelberger JB, Maghames C, Bailly A, Brunello L, Rodriguez MS, Beli P, Xirodimas DP. Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation. Cell Rep 2021; 34:108635. [PMID: 33472076 DOI: 10.1016/j.celrep.2020.108635] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 11/20/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin-like molecule NEDD8 controls several biological processes and is a promising target for therapeutic intervention. NEDDylation occurs through specific NEDD8 enzymes (canonical) or enzymes of the ubiquitin system (atypical). Identification of NEDD8 sites on substrates is critical for delineating the processes controlled by NEDDylation. By combining the use of the NEDD8 R74K mutant with anti-di-glycine (anti-diGly) antibodies, we identified 1,101 unique NEDDylation sites in 620 proteins. Bioinformatics analysis reveals that canonical and atypical NEDDylation have distinct proteomes; the spliceosome/mRNA surveillance/DNA replication and ribosome/proteasome, respectively. The data also reveal the formation of poly-NEDD8, hybrid NEDD8-ubiquitin, and NEDD8-SUMO-2 chains as potential molecular signals. In particular, NEDD8-SUMO-2 chains are induced upon proteotoxic stress (atypical) through NEDDylation of K11 in SUMO-2, and conjugates accumulate in previously described nucleolus-related inclusions. The study uncovers a diverse proteome for NEDDylation and is consistent with the concept of extensive cross-talk between ubiquitin and Ubls under proteotoxic stress conditions.
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Affiliation(s)
| | | | | | - Aymeric Bailly
- CRBM, University of Montpellier, CNRS, Montpellier, France
| | | | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination (LCC), UPR 8241, CNRS, Toulouse, France; IPBS-University of Toulouse III-Paul Sabatier, Toulouse, France
| | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz, Germany.
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5
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Li J, Zou J, Littlejohn R, Liu J, Su H. Neddylation, an Emerging Mechanism Regulating Cardiac Development and Function. Front Physiol 2020; 11:612927. [PMID: 33391028 PMCID: PMC7773599 DOI: 10.3389/fphys.2020.612927] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/20/2020] [Indexed: 12/13/2022] Open
Abstract
Defects in protein quality control have been increasingly recognized as pathogenic factors in the development of heart failure, a persistent devastating disease lacking efficacious therapies. Ubiquitin and ubiquitin-like proteins, a family of post-translational modifying polypeptides, play important roles in controlling protein quality by maintaining the stability and functional diversity of the proteome. NEDD8 (neural precursor cell expressed, developmentally downregulated 8), a small ubiquitin-like protein, was discovered two decades ago but until recently the biological significance of NEDD8 modifications (neddylation) in the heart has not been appreciated. In this review, we summarize the current knowledge of the biology of neddylation, highlighting several mechanisms by which neddylation regulates the function of its downstream targets, and discuss the expanding roles for neddylation in cardiac physiology and disease, with an emphasis on cardiac protein quality control. Finally, we outline challenges linked to the study of neddylation in health and disease.
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Affiliation(s)
- Jie Li
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Jianqiu Zou
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Rodney Littlejohn
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
| | - Jinbao Liu
- Protein Modification and Degradation Lab, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, United States
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6
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Bailly AP, Perrin A, Serrano-Macia M, Maghames C, Leidecker O, Trauchessec H, Martinez-Chantar ML, Gartner A, Xirodimas DP. The Balance between Mono- and NEDD8-Chains Controlled by NEDP1 upon DNA Damage Is a Regulatory Module of the HSP70 ATPase Activity. Cell Rep 2020; 29:212-224.e8. [PMID: 31577950 PMCID: PMC6899524 DOI: 10.1016/j.celrep.2019.08.070] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/27/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ubiquitin and ubiquitin-like chains are finely balanced by conjugating and de-conjugating enzymes. Alterations in this balance trigger the response to stress conditions and are often observed in pathologies. How such changes are detected is not well understood. We identify the HSP70 chaperone as a sensor of changes in the balance between mono- and poly-NEDDylation. Upon DNA damage, the induction of the de-NEDDylating enzyme NEDP1 restricts the formation of NEDD8 chains, mainly through lysines K11/K48. This promotes APAF1 oligomerization and apoptosis induction, a step that requires the HSP70 ATPase activity. HSP70 binds to NEDD8, and, in vitro, the conversion of NEDD8 chains into mono-NEDD8 stimulates HSP70 ATPase activity. This effect is independent of NEDD8 conjugation onto substrates. The study indicates that the NEDD8 cycle is a regulatory module of HSP70 function. These findings may be important in tumorigenesis, as we find decreased NEDP1 levels in hepatocellular carcinoma with concomitant accumulation of NEDD8 conjugates. Restriction of NEDD8 chains by NEDP1 is required for DNA damage-induced apoptosis The HSP70 chaperone is a sensor of the balance between mono- and NEDD8 chains Mono-NEDD8 stimulates HSP70 activity, which allows the formation of the apoptosome NEDP1 levels are downregulated in mouse hepatocellular carcinoma
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Affiliation(s)
- Aymeric P Bailly
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France.
| | - Aurelien Perrin
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Marina Serrano-Macia
- Liver Disease Laboratory, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Chantal Maghames
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Orsolya Leidecker
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - Helene Trauchessec
- CRBM, CNRS, Univ. Montpellier, UMR5237, Montpellier 34090, Cedex 5, France
| | - M L Martinez-Chantar
- Liver Disease Laboratory, CIC bioGUNE, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 48160 Derio, Bizkaia, Spain
| | - Anton Gartner
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
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7
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Lin YL, Chung CL, Huang PJ, Chen CH, Fang SC. Revised annotation and extended characterizations of components of the Chlamydomonas reinhardtii SUMOylation system. PLANT DIRECT 2020; 4:e00266. [PMID: 33015534 PMCID: PMC7522501 DOI: 10.1002/pld3.266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 05/16/2023]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation, or SUMOylation, is a reversible post-translational modification that is important for regulation of many cellular processes including cell division cycle in the eukaryotic kingdom. However, only a portion of the components of the Chlamydomonas SUMOylation system are known and their functions and regulation investigated. The present studies are aimed at extending discovery and characterization of new components and improving the annotation and nomenclature of all known proteins and genes involved in the system. Even though only one copy of the heterodimerized SUMO-activating enzyme, SAE1 and SAE2, was identified, the number of SUMO-conjugating enzymes (SCEs) and SUMO proteases/isopeptidase was expanded in Chlamydomonas. Using the reconstituted SUMOylation system, we showed that SCE1, SCE2, and SCE3 have SUMO-conjugating activity. In addition to SUMOylation, components required for other post-translational modifications such as NEDDylation, URMylation, and UFMylation, were confirmed to be present in Chlamydomonas. Our data also showed that besides isopeptidase activity, the SUMO protease domain of SUPPRESSOR OF MAT3 7/SENTRIN-SPECIFIC PROTEASE 1 (SMT7/SENP1) has endopeptidase activity that is capable of processing SUMO precursors. Moreover, the key cell cycle regulators of Chlamydomonas E2F1, DP1, CDKG1, CYCD2, and CYCD3 were SUMOylated in vitro, suggesting SUMOylation may be part of regulatory pathway modulating cell cycle regulators.
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Affiliation(s)
- Yen-Ling Lin
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
- Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan
| | - Chin-Lin Chung
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Pin-Jui Huang
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
- Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan
- Institute of Tropical Plant Sciences and Microbiology National Cheng Kung University Tainan Taiwan
- National Cheng Kung University-Academia Sinica Graduate Program in Translational Agricultural Sciences Tainan Taiwan
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8
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Guo Z, Wang S, Xie Y, Han Y, Hu S, Guan H, Xie D, Bai C, Liu X, Gu Y, Zhou PK, Ma T. HUWE1-dependent DNA-PKcs neddylation modulates its autophosphorylation in DNA damage response. Cell Death Dis 2020; 11:400. [PMID: 32457294 PMCID: PMC7250858 DOI: 10.1038/s41419-020-2611-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is the core component of DNA-PK complex in the non-homologous end-joining (NHEJ) repair of DNA double-strand breaks, and its activity is strictly controlled by DNA-PKcs phosphorylation. The ubiquitin-like protein, NEDD8 is involved in regulation of DNA damage response, but it remains mysterious whether and how NEDD8-related neddylation affects DNA-PKcs and the NHEJ process. Here, we show that DNA-PKcs is poly-neddylated at its kinase domain. The neddylation E2-conjugating enzyme UBE2M and E3 ligase HUWE1 (HECT, UBA, and WWE domain containing E3 ubiquitin protein ligase 1) are responsible for the DNA-PKcs neddylation. Moreover, inhibition of HUWE1-dependent DNA-PKcs neddylation impairs DNA-PKcs autophosphorylation at Ser2056. Finally, depletion of HUWE1-dependent DNA-PKcs neddylation reduces the efficiency of NHEJ. These studies provide insights how neddylation modulates the activity of NHEJ core complex.
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Affiliation(s)
- Zongpei Guo
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Shaozheng Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Ying Xie
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Yang Han
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China.,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China
| | - Sai Hu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China.,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China
| | - Hua Guan
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Dafei Xie
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Chenjun Bai
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Xiaodan Liu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Yongqing Gu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Ping-Kun Zhou
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China. .,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China.
| | - Teng Ma
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China. .,Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, P. R. China.
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9
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Global site-specific neddylation profiling reveals that NEDDylated cofilin regulates actin dynamics. Nat Struct Mol Biol 2020; 27:210-220. [PMID: 32015554 DOI: 10.1038/s41594-019-0370-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/27/2019] [Indexed: 01/19/2023]
Abstract
Neddylation is the post-translational protein modification most closely related to ubiquitination. Whereas the ubiquitin-like protein NEDD8 is well studied for its role in activating cullin-RING E3 ubiquitin ligases, little is known about other substrates. We developed serial NEDD8-ubiquitin substrate profiling (sNUSP), a method that employs NEDD8 R74K knock-in HEK293 cells, allowing discrimination of endogenous NEDD8- and ubiquitin-modification sites by MS after Lys-C digestion and K-εGG-peptide enrichment. Using sNUSP, we identified 607 neddylation sites dynamically regulated by the neddylation inhibitor MLN4924 and the de-neddylating enzyme NEDP1, implying that many non-cullin proteins are neddylated. Among the candidates, we characterized lysine 112 of the actin regulator cofilin as a novel neddylation event. Global inhibition of neddylation in developing neurons leads to cytoskeletal defects, altered actin dynamics and neurite growth impairments, whereas site-specific neddylation of cofilin at K112 regulates neurite outgrowth, suggesting that cofilin neddylation contributes to the regulation of neuronal actin organization.
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10
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COP9 Signalosome Interaction with UspA/Usp15 Deubiquitinase Controls VeA-Mediated Fungal Multicellular Development. Biomolecules 2019; 9:biom9060238. [PMID: 31216760 PMCID: PMC6627422 DOI: 10.3390/biom9060238] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/02/2019] [Accepted: 06/16/2019] [Indexed: 12/26/2022] Open
Abstract
COP9 signalosome (CSN) and Den1/A deneddylases physically interact and promote multicellular development in fungi. CSN recognizes Skp1/cullin-1/Fbx E3 cullin-RING ligases (CRLs) without substrate and removes their posttranslational Nedd8 modification from the cullin scaffold. This results in CRL complex disassembly and allows Skp1 adaptor/Fbx receptor exchange for altered substrate specificity. We characterized the novel ubiquitin-specific protease UspA of the mold Aspergillusnidulans, which corresponds to CSN-associated human Usp15 and interacts with six CSN subunits. UspA reduces amounts of ubiquitinated proteins during fungal development, and the uspA gene expression is repressed by an intact CSN. UspA is localized in proximity to nuclei and recruits proteins related to nuclear transport and transcriptional processing, suggesting functions in nuclear entry control. UspA accelerates the formation of asexual conidiospores, sexual development, and supports the repression of secondary metabolite clusters as the derivative of benzaldehyde (dba) genes. UspA reduces protein levels of the fungal NF-kappa B-like velvet domain protein VeA, which coordinates differentiation and secondary metabolism. VeA stability depends on the Fbx23 receptor, which is required for light controlled development. Our data suggest that the interplay between CSN deneddylase, UspA deubiquitinase, and SCF-Fbx23 ensures accurate levels of VeA to support fungal development and an appropriate secondary metabolism.
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11
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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] [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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12
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Schwechheimer C. NEDD8-its role in the regulation of Cullin-RING ligases. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:112-119. [PMID: 29909289 DOI: 10.1016/j.pbi.2018.05.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [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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13
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Castro PH, Bachmair A, Bejarano ER, Coupland G, Lois LM, Sadanandom A, van den Burg HA, Vierstra RD, Azevedo H. Revised nomenclature and functional overview of the ULP gene family of plant deSUMOylating proteases. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4505-4509. [PMID: 30124991 PMCID: PMC6117577 DOI: 10.1093/jxb/ery301] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Affiliation(s)
- Pedro Humberto Castro
- CIBIO, InBIO – Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Vairão, Portugal
- Correspondence: ,
| | - Andreas Bachmair
- Dept of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Eduardo R Bejarano
- Area de Genética, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - George Coupland
- Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Ari Sadanandom
- Durham Centre for Crop Improvement Technology, Department of BioSciences, Durham University, Durham, United Kingdom
| | - Harrold A van den Burg
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Richard D Vierstra
- Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
| | - Herlander Azevedo
- CIBIO, InBIO – Research Network in Biodiversity and Evolutionary Biology, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Correspondence: ,
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14
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Coleman KE, Békés M, Chapman JR, Crist SB, Jones MJK, Ueberheide BM, Huang TT. SENP8 limits aberrant neddylation of NEDD8 pathway components to promote cullin-RING ubiquitin ligase function. eLife 2017; 6:e24325. [PMID: 28475037 PMCID: PMC5419743 DOI: 10.7554/elife.24325] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 04/19/2017] [Indexed: 01/02/2023] Open
Abstract
NEDD8 is a ubiquitin-like modifier most well-studied for its role in activating the largest family of ubiquitin E3 ligases, the cullin-RING ligases (CRLs). While many non-cullin neddylation substrates have been proposed over the years, validation of true NEDD8 targets has been challenging, as overexpression of exogenous NEDD8 can trigger NEDD8 conjugation through the ubiquitylation machinery. Here, we developed a deconjugation-resistant form of NEDD8 to stabilize the neddylated form of cullins and other non-cullin substrates. Using this strategy, we identified Ubc12, a NEDD8-specific E2 conjugating enzyme, as a substrate for auto-neddylation. Furthermore, we characterized SENP8/DEN1 as the protease that counteracts Ubc12 auto-neddylation, and observed aberrant neddylation of Ubc12 and other NEDD8 conjugation pathway components in SENP8-deficient cells. Importantly, loss of SENP8 function contributes to accumulation of CRL substrates and defective cell cycle progression. Thus, our study highlights the importance of SENP8 in maintaining proper neddylation levels for CRL-dependent proteostasis.
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Affiliation(s)
- Kate E Coleman
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Miklós Békés
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Jessica R Chapman
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, United States
| | - Sarah B Crist
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - Mathew JK Jones
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, Unites States
| | - Beatrix M Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, United States
| | - Tony T Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
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15
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Kim K, Yoon J, Yim J, Kim HJ. Deneddylase 1 regulates deneddylase activity of the Cop9 signalosome in Drosophila melanogaster. INSECT SCIENCE 2017; 24:27-34. [PMID: 26332639 DOI: 10.1111/1744-7917.12274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/10/2015] [Indexed: 06/05/2023]
Abstract
NEDD8 conjugation of Cullin has an important role in ubiquitin-mediated protein degradation. The COP9 signalosome, of which CSN5 is the major catalytic subunit, is a major Cullin deneddylase. Another deneddylase, Deneddylase 1, has also been shown to process the Nedd8 precursor. In Drosophila, the DEN1 mutants do not have increased levels of Cullin neddylation, but instead show a significant decrease in neddylated Cullin. This characteristic decrease in neddylated Cullins in the DEN1null background can be rescued by UAS-dDEN1WT overexpression but not by overexpression of mature NEDD8, indicating that this phenotype is distinct from the NEDD8-processing function of DEN1. We examined the role of DEN1-CSN interaction in regulating Cullin neddylation. Overexpression of DEN1 in a CSN5hypo background slightly reduced unneddylated Cullin levels. The CSN5, DEN1 double mutation partially rescues the premature lethality associated with the CSN5 single mutation. These results suggest that DEN1 regulates Cullin neddylation by suppressing CSN deneddylase activity.
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Affiliation(s)
- Kiyoung Kim
- Department of Medical Biotechnology, Soonchunhyang University, Asan, 336-745
| | - Jeongsook Yoon
- Division of Intractable Diseases, Center for Biomedical Sciences, National Institute of Health, Cheongwon, 361-951
| | - Jeongbin Yim
- Department of Medical Biotechnology, Soonchunhyang University, Asan, 336-745
| | - Hyung-Jun Kim
- Department of Neural Development and Disease, Korea Brain Research Institute, Daegu, 701-300, Korea
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16
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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] [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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17
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Parreira J, Bouraada J, Fitzpatrick M, Silvestre S, Bernardes da Silva A, Marques da Silva J, Almeida A, Fevereiro P, Altelaar A, Araújo S. Differential proteomics reveals the hallmarks of seed development in common bean ( Phaseolus vulgaris L.). J Proteomics 2016; 143:188-198. [DOI: 10.1016/j.jprot.2016.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/12/2022]
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18
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Schinke J, Kolog Gulko M, Christmann M, Valerius O, Stumpf SK, Stirz M, Braus GH. The DenA/DEN1 Interacting Phosphatase DipA Controls Septa Positioning and Phosphorylation-Dependent Stability of Cytoplasmatic DenA/DEN1 during Fungal Development. PLoS Genet 2016; 12:e1005949. [PMID: 27010942 PMCID: PMC4806917 DOI: 10.1371/journal.pgen.1005949] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/01/2016] [Indexed: 11/18/2022] Open
Abstract
DenA/DEN1 and the COP9 signalosome (CSN) represent two deneddylases which remove the ubiquitin-like Nedd8 from modified target proteins and are required for distinct fungal developmental programmes. The cellular DenA/DEN1 population is divided into a nuclear and a cytoplasmatic subpopulation which is especially enriched at septa. DenA/DEN1 stability control mechanisms are different for the two cellular subpopulations and depend on different physical interacting proteins and the C-terminal DenA/DEN1 phosphorylation pattern. Nuclear DenA/DEN1 is destabilized during fungal development by five of the eight CSN subunits which target nuclear DenA/DEN1 for degradation. DenA/DEN1 becomes stabilized as a phosphoprotein at S243/S245 during vegetative growth, which is necessary to support further asexual development. After the initial phase of development, the newly identified cytoplasmatic DenA/DEN1 interacting phosphatase DipA and an additional developmental specific C-terminal phosphorylation site at serine S253 destabilize DenA/DEN1. Outside of the nucleus, DipA is co-transported with DenA/DEN1 in the cytoplasm between septa and nuclei. Deletion of dipA resulted in increased DenA/DEN1 stability in a strain which is unresponsive to illumination. The mutant strain is dysregulated in cytokinesis and impaired in asexual development. Our results suggest a dual phosphorylation-dependent DenA/DEN1 stability control with stabilizing and destabilizing modifications and physical interaction partner proteins which function as control points in the nucleus and the cytoplasm.
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Affiliation(s)
- Josua Schinke
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Miriam Kolog Gulko
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Martin Christmann
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Sina Kristin Stumpf
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Margarita Stirz
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), and Georg-August-University, Göttingen, Germany
- * E-mail:
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19
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Nagels Durand A, Pauwels L, Goossens A. The Ubiquitin System and Jasmonate Signaling. PLANTS 2016; 5:plants5010006. [PMID: 27135226 PMCID: PMC4844421 DOI: 10.3390/plants5010006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/21/2015] [Accepted: 12/28/2015] [Indexed: 01/04/2023]
Abstract
The ubiquitin (Ub) system is involved in most, if not all, biological processes in eukaryotes. The major specificity determinants of this system are the E3 ligases, which bind and ubiquitinate specific sets of proteins and are thereby responsible for target recruitment to the proteasome or other cellular processing machineries. The Ub system contributes to the regulation of the production, perception and signal transduction of plant hormones. Jasmonic acid (JA) and its derivatives, known as jasmonates (JAs), act as signaling compounds regulating plant development and plant responses to various biotic and abiotic stress conditions. We provide here an overview of the current understanding of the Ub system involved in JA signaling.
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Affiliation(s)
- Astrid Nagels Durand
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
| | - Laurens Pauwels
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
| | - Alain Goossens
- Department of Plant Systems Biology, Vlaams Instituut voor Biotechnologie, B-9052 Ghent, Belgium.
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.
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20
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Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Durand AN, Timmerman E, Heyman J, Pauwels L, De Veylder L, Goossens A, De Smet I, Coppens F, Goormachtig S, Gevaert K. It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana. THE PLANT CELL 2016; 28:6-16. [PMID: 26744219 PMCID: PMC4746685 DOI: 10.1105/tpc.15.00878] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/11/2015] [Accepted: 01/07/2016] [Indexed: 05/19/2023]
Abstract
Ubiquitination, the covalent binding of the small protein modifier ubiquitin to a target protein, is an important and frequently studied posttranslational protein modification. Multiple reports provide useful insights into the plant ubiquitinome, but mostly at the protein level without comprehensive site identification. Here, we implemented ubiquitin combined fractional diagonal chromatography (COFRADIC) for proteome-wide ubiquitination site mapping on Arabidopsis thaliana cell cultures. We identified 3009 sites on 1607 proteins, thereby greatly increasing the number of known ubiquitination sites in this model plant. Finally, The Ubiquitination Site tool (http://bioinformatics.psb.ugent.be/webtools/ubiquitin_viewer/) gives access to the obtained ubiquitination sites, not only to consult the ubiquitination status of a given protein, but also to conduct intricate experiments aiming to study the roles of specific ubiquitination events. Together with the antibodies recognizing the ubiquitin remnant motif, ubiquitin COFRADIC represents a powerful tool to resolve the ubiquitination maps of numerous cellular processes in plants.
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Affiliation(s)
- Alan Walton
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Nicolas Cybulski
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sabrina Iñigo
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Astrid Nagels Durand
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Evy Timmerman
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Jefri Heyman
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
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21
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Chung D, Dellaire G. The Role of the COP9 Signalosome and Neddylation in DNA Damage Signaling and Repair. Biomolecules 2015; 5:2388-416. [PMID: 26437438 PMCID: PMC4693240 DOI: 10.3390/biom5042388] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/28/2023] Open
Abstract
The maintenance of genomic integrity is an important process in organisms as failure to sense and repair damaged DNA can result in a variety of diseases. Eukaryotic cells have developed complex DNA repair response (DDR) mechanisms to accurately sense and repair damaged DNA. Post-translational modifications by ubiquitin and ubiquitin-like proteins, such as SUMO and NEDD8, have roles in coordinating the progression of DDR. Proteins in the neddylation pathway have also been linked to regulating DDR. Of interest is the COP9 signalosome (CSN), a multi-subunit metalloprotease present in eukaryotes that removes NEDD8 from cullins and regulates the activity of cullin-RING ubiquitin ligases (CRLs). This in turn regulates the stability and turnover of a host of CRL-targeted proteins, some of which have established roles in DDR. This review will summarize the current knowledge on the role of the CSN and neddylation in DNA repair.
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Affiliation(s)
- Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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22
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Vittal V, Stewart MD, Brzovic PS, Klevit RE. Regulating the Regulators: Recent Revelations in the Control of E3 Ubiquitin Ligases. J Biol Chem 2015; 290:21244-51. [PMID: 26187467 DOI: 10.1074/jbc.r115.675165] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Since its discovery as a post-translational signal for protein degradation, our understanding of ubiquitin (Ub) has vastly evolved. Today, we recognize that the role of Ub signaling is expansive and encompasses diverse processes including cell division, the DNA damage response, cellular immune signaling, and even organismal development. With such a wide range of functions comes a wide range of regulatory mechanisms that control the activity of the ubiquitylation machinery. Ub attachment to substrates occurs through the sequential action of three classes of enzymes, E1s, E2s, and E3s. In humans, there are 2 E1s, ∼ 35 E2s, and hundreds of E3s that work to attach Ub to thousands of cellular substrates. Regulation of ubiquitylation can occur at each stage of the stepwise Ub transfer process, and substrates can also impact their own modification. Recent studies have revealed elegant mechanisms that have evolved to control the activity of the enzymes involved. In this minireview, we highlight recent discoveries that define some of the various mechanisms by which the activities of E3-Ub ligases are regulated.
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Affiliation(s)
- Vinayak Vittal
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Mikaela D Stewart
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Peter S Brzovic
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
| | - Rachel E Klevit
- From the Department of Biochemistry, University of Washington, Seattle, Washington 98195-7742
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