1
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Liang CT, Roscow O, Zhang W. Generation and Characterization of Engineered Ubiquitin Variants to Modulate the Ubiquitin Signaling Cascade. Cold Spring Harb Protoc 2024; 2024:107784. [PMID: 36997275 DOI: 10.1101/pdb.over107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The ubiquitin signaling cascade plays a crucial role in human cells. Consistent with this, malfunction of ubiquitination and deubiquitination is implicated in the initiation and progression of numerous human diseases, including cancer. Therefore, the development of potent and specific modulators of ubiquitin signal transduction has been at the forefront of drug development. In the past decade, a structure-based combinatorial protein-engineering approach has been used to generate ubiquitin variants (UbVs) as protein-based modulators of multiple components in the ubiquitin-proteasome system. Here, we review the design and generation of phage-displayed UbV libraries, including the processes of binder selection and library improvement. We also provide a comprehensive overview of the general in vitro and cellular methodologies involved in characterizing UbV binders. Finally, we describe two recent applications of UbVs for developing molecules with therapeutic potential.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Olivia Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, Ontario N1G2W1, Canada
- CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre, Toronto, Ontario M5G1M1, Canada
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2
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Wu W, Huang C. SUMOylation and DeSUMOylation: Prospective therapeutic targets in cancer. Life Sci 2023; 332:122085. [PMID: 37722589 DOI: 10.1016/j.lfs.2023.122085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
The SUMO family is a type of ubiquitin-like protein modification molecule. Its protein modification mechanism is similar to that of ubiquitination: both involve modifier-activating enzyme E1, conjugating enzyme E2 and substrate-specific ligase E3. However, polyubiquitination can lead to the degradation of substrate proteins, while poly-SUMOylation only leads to the degradation of substrate proteins through the proteasome pathway after being recognized by ubiquitin as a signal factor. There are currently five reported subtypes in the SUMO family, namely SUMO1-5. As a reversible dynamic modification, intracellular sentrin/SUMO-specific proteases (SENPs) mainly regulate the reverse reaction pathway of SUMOylation. The SUMOylation modification system affects the localization, activation and turnover of proteins in cells and participates in regulating most nuclear and extranuclear molecular reactions. Abnormal expression of proteins related to the SUMOylation pathway is commonly observed in tumors, indicating that this pathway is closely related to tumor occurrence, metastasis and invasion. This review mainly discusses the composition of members in the protein family related to SUMOylation pathways, mutual connections between SUMOylation and other post-translational modifications on proteins as well as therapeutic drugs developed based on these pathways.
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Affiliation(s)
- Wenyan Wu
- Kunming University of Science and Technology, Medical School, Kunming 650500, China
| | - Chao Huang
- Kunming University of Science and Technology, Medical School, Kunming 650500, China.
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3
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Gu Y, Fang Y, Wu X, Xu T, Hu T, Xu Y, Ma P, Wang Q, Shu Y. The emerging roles of SUMOylation in the tumor microenvironment and therapeutic implications. Exp Hematol Oncol 2023; 12:58. [PMID: 37415251 DOI: 10.1186/s40164-023-00420-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/12/2023] [Indexed: 07/08/2023] Open
Abstract
Tumor initiation, progression, and response to therapies depend to a great extent on interactions between malignant cells and the tumor microenvironment (TME), which denotes the cancerous/non-cancerous cells, cytokines, chemokines, and various other factors around tumors. Cancer cells as well as stroma cells can not only obtain adaption to the TME but also sculpt their microenvironment through a series of signaling pathways. The post-translational modification (PTM) of eukaryotic cells by small ubiquitin-related modifier (SUMO) proteins is now recognized as a key flexible pathway. Proteins involved in tumorigenesis guiding several biological processes including chromatin organization, DNA repair, transcription, protein trafficking, and signal conduction rely on SUMOylation. The purpose of this review is to explore the role that SUMOylation plays in the TME formation and reprogramming, emphasize the importance of targeting SUMOylation to intervene in the TME and discuss the potential of SUMOylation inhibitors (SUMOi) in ameliorating tumor prognosis.
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Affiliation(s)
- Yunru Gu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029, Nanjing, People's Republic of China
| | - Yuan Fang
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029, Nanjing, People's Republic of China
| | - Xi Wu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029, Nanjing, People's Republic of China
| | - Tingting Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029, Nanjing, People's Republic of China
| | - Tong Hu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029, Nanjing, People's Republic of China
| | - Yangyue Xu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029, Nanjing, People's Republic of China
| | - Pei Ma
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029, Nanjing, People's Republic of China.
| | - Qiang Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, 230022, Hefei, Anhui Province, People's Republic of China.
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, 210029, Nanjing, People's Republic of China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China.
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4
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Zhang S, Jin B, Liang W, Guo A, Luo X, Pu L, Chen X, Cai X, Wang S. Identification and expression analysis of a new small ubiquitin-like modifier from Taenia pisiformis. Exp Parasitol 2022; 242:108403. [DOI: 10.1016/j.exppara.2022.108403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/20/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022]
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5
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Cai H, Ma X, Lu D, Chen L, Bian X, Zhang N, Tang W, Liu X, Li Z. Mild Hypothermia Promotes Ischemic Tolerance and Survival of Neural Stem Cell Grafts by Enhancing Global SUMOylation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:6503504. [PMID: 35669854 PMCID: PMC9166982 DOI: 10.1155/2022/6503504] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/07/2022] [Accepted: 04/18/2022] [Indexed: 11/17/2022]
Abstract
Cerebral infarct penumbra due to hypoxia and toxin accumulation is not conducive to the transplantation of neural stem cells (NSCs), although mild hypothermia can improve the local microenvironment of the ischemic penumbra and exert neuroprotective effects. However, insufficient understanding of the molecular mechanism by which mild hypothermia protects the brain limits widespread clinical application. This study evaluated the molecular mechanism of mild hypothermia-induced brain protection from the perspective of global protein small ubiquitin-like modifier (SUMO) modification, with the aim of improving NSC transplant survival rates in the penumbra to enhance neurological function. NSCs from neonatal rats were extracted to detect the effects of hypoxia and mild hypothermia on SUMOylation modification levels, cell stemness, and hypoxia-induced injury. Overexpression and knockdown of UBC9 in NSCs were used to evaluate their ability to maintain stemness and withstand hypoxic injury. Finally, a rat middle cerebral artery occlusion (MCAO) model was used to verify the effect of mild hypothermia treatment and UBC9 overexpression on neural function of NSCs following penumbra transplantation in rats. Results showed that hypoxia and mild hypothermia promoted both the SUMOylation modification and maintenance of NSC stemness. Overexpression of UBC9 enhanced the abilities of NSCs to maintain stemness and resist hypoxic injury, while UBC9 knockdown had the opposite effect. Following transplantation into the ischemic penumbra of MCAO model rats, mild hypothermia and Ubc9-overexpressing NSCs significantly reduced cerebral infarct areas and improved neurological function. In conclusion, this study demonstrated that global protein SUMOylation is an important molecular mechanism for NSCs to tolerate hypoxia, and mild hypothermia can further increase the degree of global SUMOylation to enhance the hypoxia tolerance of NSCs, which increases their survival during transplantation in situ and ability to perform nerve repair in the penumbra of cerebral infarction.
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Affiliation(s)
- Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Xiaofang Ma
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Preterm Infants, The Fifth Central Hospital of Tianjin, Tianjin 300450, China
| | - Dading Lu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Liangyu Chen
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Xiyun Bian
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Preterm Infants, The Fifth Central Hospital of Tianjin, Tianjin 300450, China
| | - Nan Zhang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Wei Tang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Xiaozhi Liu
- Central Laboratory, The Fifth Central Hospital of Tianjin, Tianjin 300450, China
- Tianjin Key Laboratory of Epigenetics for Organ Development of Preterm Infants, The Fifth Central Hospital of Tianjin, Tianjin 300450, China
| | - Zhiqing Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
- Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang 110004, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
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6
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Kukkula A, Ojala VK, Mendez LM, Sistonen L, Elenius K, Sundvall M. Therapeutic Potential of Targeting the SUMO Pathway in Cancer. Cancers (Basel) 2021; 13:4402. [PMID: 34503213 PMCID: PMC8431684 DOI: 10.3390/cancers13174402] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023] Open
Abstract
SUMOylation is a dynamic and reversible post-translational modification, characterized more than 20 years ago, that regulates protein function at multiple levels. Key oncoproteins and tumor suppressors are SUMO substrates. In addition to alterations in SUMO pathway activity due to conditions typically present in cancer, such as hypoxia, the SUMO machinery components are deregulated at the genomic level in cancer. The delicate balance between SUMOylation and deSUMOylation is regulated by SENP enzymes possessing SUMO-deconjugation activity. Dysregulation of SUMO machinery components can disrupt the balance of SUMOylation, contributing to the tumorigenesis and drug resistance of various cancers in a context-dependent manner. Many molecular mechanisms relevant to the pathogenesis of specific cancers involve SUMO, highlighting the potential relevance of SUMO machinery components as therapeutic targets. Recent advances in the development of inhibitors targeting SUMOylation and deSUMOylation permit evaluation of the therapeutic potential of targeting the SUMO pathway in cancer. Finally, the first drug inhibiting SUMO pathway, TAK-981, is currently also being evaluated in clinical trials in cancer patients. Intriguingly, the inhibition of SUMOylation may also have the potential to activate the anti-tumor immune response. Here, we comprehensively and systematically review the recent developments in understanding the role of SUMOylation in cancer and specifically focus on elaborating the scientific rationale of targeting the SUMO pathway in different cancers.
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Affiliation(s)
- Antti Kukkula
- Cancer Research Unit, FICAN West Cancer Center Laboratory, Institute of Biomedicine, Turku University Hospital, University of Turku, FI-20520 Turku, Finland; (A.K.); (V.K.O.); (K.E.)
| | - Veera K. Ojala
- Cancer Research Unit, FICAN West Cancer Center Laboratory, Institute of Biomedicine, Turku University Hospital, University of Turku, FI-20520 Turku, Finland; (A.K.); (V.K.O.); (K.E.)
- Turku Doctoral Programme of Molecular Medicine, University of Turku, FI-20520 Turku, Finland
- Medicity Research Laboratories, University of Turku, FI-20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland;
| | - Lourdes M. Mendez
- Beth Israel Deaconess Cancer Center, Beth Israel Deaconess Medical Center, Department of Medicine and Pathology, Cancer Research Institute, Harvard Medical School, Boston, MA 02115, USA;
| | - Lea Sistonen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland;
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, FI-20520 Turku, Finland
| | - Klaus Elenius
- Cancer Research Unit, FICAN West Cancer Center Laboratory, Institute of Biomedicine, Turku University Hospital, University of Turku, FI-20520 Turku, Finland; (A.K.); (V.K.O.); (K.E.)
- Medicity Research Laboratories, University of Turku, FI-20520 Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520 Turku, Finland;
- Department of Oncology, Turku University Hospital, FI-20521 Turku, Finland
| | - Maria Sundvall
- Cancer Research Unit, FICAN West Cancer Center Laboratory, Institute of Biomedicine, Turku University Hospital, University of Turku, FI-20520 Turku, Finland; (A.K.); (V.K.O.); (K.E.)
- Department of Oncology, Turku University Hospital, FI-20521 Turku, Finland
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7
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Targeted truncated TGF-β receptor type II delivery to fibrotic liver by PDGFβ receptor-binding peptide modification for improving the anti-fibrotic activity against hepatic fibrosis in vitro and in vivo. Int J Biol Macromol 2021; 188:941-949. [PMID: 34389395 DOI: 10.1016/j.ijbiomac.2021.08.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 07/05/2021] [Accepted: 08/06/2021] [Indexed: 01/15/2023]
Abstract
Truncated transforming growth factor-β receptor type II (tTβRII) is a promising anti-fibrotic candidate because it attenuates excessive transforming growth factor-β1 (TGF-β1) and then blocks TGF-β1 activity in hepatic fibrosis. However, its use has been greatly limited due to the fact that it is expensive to chemically synthesize and it does not specifically target to the lesion site. In this study, we describe that platelet- derived growth factor β receptor (PDGFβR)-binding peptide BiPPB modified tTβRII (BiPPB-tTβRII) was prepared from the cleavage of SUMO-BiPPB-tTβRII by digestion with SUMO-specific protease. Moreover, compared to the unmodified tTβRII, the target protein BiPPB-tTβRII not only highly specific targeted activated hepatic stellate cells (HSCs) and fibrotic liver tissue, but also significantly inhibited the protein levels of fibrosis-related genes in TGF-β1-induced HSC-T6 cells and CCl4-induced liver fibrosis in mice. Furthermore, BiPPB-tTβRII markedly ameliorated liver morphology, fibrotic responses and the damage of liver function in fibrosis animal. More importantly, BiPPB-tTβRII showed a much lesser extent in binding to quiescent HSCs and non-fibrotic liver tissue. Taken together, our results suggested that the target protein BiPPB-tTβRII, with its high specific fibrotic liver-targeting potential and its improved anti-fibrotic activity in liver fibrosis, may be a potential therapeutic agent for liver fibrosis.
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8
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Wang L, Qian J, Yang Y, Gu C. Novel insights into the impact of the SUMOylation pathway in hematological malignancies (Review). Int J Oncol 2021; 59:73. [PMID: 34368858 PMCID: PMC8360622 DOI: 10.3892/ijo.2021.5253] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/26/2021] [Indexed: 12/17/2022] Open
Abstract
The small ubiquitin-like modifier (SUMO) system serves an important role in the regulation of protein stability and function. SUMOylation sustains the homeostatic equilibrium of protein function in normal tissues and numerous types of tumor. Accumulating evidence has revealed that SUMO enzymes participate in carcinogenesis via a series of complex cellular or extracellular processes. The present review outlines the physiological characteristics of the SUMOylation pathway and provides examples of SUMOylation participation in different cancer types, including in hematological malignancies (leukemia, lymphoma and myeloma). It has been indicated that the SUMO pathway may influence chromosomal instability, cell cycle progression, apoptosis and chemical drug resistance. The present review also discussed the possible relationship between SUMOylation and carcinogenic mechanisms, and evaluated their potential as biomarkers and therapeutic targets in the diagnosis and treatment of hematological malignancies. Developing and investigating inhibitors of SUMO conjugation in the future may offer promising potential as novel therapeutic strategies.
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Affiliation(s)
- Ling Wang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, P.R. China
| | - Jinjun Qian
- School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P.R. China
| | - Ye Yang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, P.R. China
| | - Chunyan Gu
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210022, P.R. China
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9
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Osborne HC, Irving E, Forment JV, Schmidt CK. E2 enzymes in genome stability: pulling the strings behind the scenes. Trends Cell Biol 2021; 31:628-643. [PMID: 33685796 DOI: 10.1016/j.tcb.2021.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
Ubiquitin and ubiquitin-like proteins (UBLs) function as critical post-translational modifiers in the maintenance of genome stability. Ubiquitin/UBL-conjugating enzymes (E2s) are responsible, as part of a wider enzymatic cascade, for transferring single moieties or polychains of ubiquitin/UBLs to one or multiple residues on substrate proteins. Recent advances in structural and mechanistic understanding of how ubiquitin/UBL substrate attachment is orchestrated indicate that E2s can exert control over chain topology, substrate-site specificity, and downstream physiological effects to help maintain genome stability. Drug discovery efforts have typically focussed on modulating other members of the ubiquitin/UBL cascades or the ubiquitin-proteasome system. Here, we review the current standing of E2s in genome stability and revisit their potential as pharmacological targets for developing novel anti-cancer therapies.
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Affiliation(s)
- Hugh C Osborne
- Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK
| | - Elsa Irving
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Josep V Forment
- Bioscience, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, UK
| | - Christine K Schmidt
- Manchester Cancer Research Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine, and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, UK.
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10
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Liang CT, Roscow OMA, Zhang W. Recent developments in engineering protein-protein interactions using phage display. Protein Eng Des Sel 2021; 34:6297171. [PMID: 34117768 DOI: 10.1093/protein/gzab014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/09/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Targeted inhibition of misregulated protein-protein interactions (PPIs) has been a promising area of investigation in drug discovery and development for human diseases. However, many constraints remain, including shallow binding surfaces and dynamic conformation changes upon interaction. A particularly challenging aspect is the undesirable off-target effects caused by inherent structural similarity among the protein families. To tackle this problem, phage display has been used to engineer PPIs for high-specificity binders with improved binding affinity and greatly reduced undesirable interactions with closely related proteins. Although general steps of phage display are standardized, library design is highly variable depending on experimental contexts. Here in this review, we examined recent advances in the structure-based combinatorial library design and the advantages and limitations of different approaches. The strategies described here can be explored for other protein-protein interactions and aid in designing new libraries or improving on previous libraries.
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Affiliation(s)
- Chen T Liang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Olivia M A Roscow
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, 50 Stone Rd E, Guelph, Ontario N1G2W1, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, MaRS Centre West Tower, 661 University Avenue, Toronto, Ontario M5G1M1, Canada
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11
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Kroonen JS, Vertegaal ACO. Targeting SUMO Signaling to Wrestle Cancer. Trends Cancer 2020; 7:496-510. [PMID: 33353838 DOI: 10.1016/j.trecan.2020.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 01/16/2023]
Abstract
The small ubiquitin-like modifier (SUMO) signaling cascade is critical for gene expression, genome integrity, and cell cycle progression. In this review, we discuss the important role SUMO may play in cancer and how to target SUMO signaling. Recently developed small molecule inhibitors enable therapeutic targeting of the SUMOylation pathway. Blocking SUMOylation not only leads to reduced cancer cell proliferation but also to an increased antitumor immune response by stimulating interferon (IFN) signaling, indicating that SUMOylation inhibitors have a dual mode of action that can be employed in the fight against cancer. The search for tumor types that can be treated with SUMOylation inhibitors is ongoing. Employing SUMO conjugation inhibitory drugs in the years to come has potential as a new therapeutic strategy.
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Affiliation(s)
- Jessie S Kroonen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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12
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Jansen NS, Vertegaal ACO. A Chain of Events: Regulating Target Proteins by SUMO Polymers. Trends Biochem Sci 2020; 46:113-123. [PMID: 33008689 DOI: 10.1016/j.tibs.2020.09.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/21/2020] [Accepted: 09/04/2020] [Indexed: 02/07/2023]
Abstract
Small ubiquitin-like modifiers (SUMOs) regulate virtually all nuclear processes. The fate of the target protein is determined by the architecture of the attached SUMO protein, which can be of polymeric nature. Here, we highlight the multifunctional aspects of dynamic signal transduction by SUMO polymers. The SUMO-targeted ubiquitin ligases (STUbLs) RING-finger protein 4 (RNF4) and RNF111 recognize SUMO polymers in a chain-architecture-dependent manner, leading to the formation of hybrid chains, which could enable proteasomal destruction of proteins. Recent publications have highlighted essential roles for SUMO chain disassembly by the mammalian SUMO proteases SENP6 and SENP7 and the yeast SUMO protease Ulp2. SENP6 is particularly important for centromere assembly. These recent findings demonstrate the diversity of SUMO polymer signal transduction for proteolytic and nonproteolytic purposes.
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Affiliation(s)
- Nicolette S Jansen
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
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13
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Maculins T, Garcia-Pardo J, Skenderovic A, Gebel J, Putyrski M, Vorobyov A, Busse P, Varga G, Kuzikov M, Zaliani A, Rahighi S, Schaeffer V, Parnham MJ, Sidhu SS, Ernst A, Dötsch V, Akutsu M, Dikic I. Discovery of Protein-Protein Interaction Inhibitors by Integrating Protein Engineering and Chemical Screening Platforms. Cell Chem Biol 2020; 27:1441-1451.e7. [PMID: 32726587 DOI: 10.1016/j.chembiol.2020.07.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 02/06/2023]
Abstract
Protein-protein interactions (PPIs) govern intracellular life, and identification of PPI inhibitors is challenging. Roadblocks in assay development stemming from weak binding affinities of natural PPIs impede progress in this field. We postulated that enhancing binding affinity of natural PPIs via protein engineering will aid assay development and hit discovery. This proof-of-principle study targets PPI between linear ubiquitin chains and NEMO UBAN domain, which activates NF-κB signaling. Using phage display, we generated ubiquitin variants that bind to the functional UBAN epitope with high affinity, act as competitive inhibitors, and structurally maintain the existing PPI interface. When utilized in assay development, variants enable generation of robust cell-based assays for chemical screening. Top compounds identified using this approach directly bind to UBAN and dampen NF-κB signaling. This study illustrates advantages of integrating protein engineering and chemical screening in hit identification, a development that we anticipate will have wide application in drug discovery.
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Affiliation(s)
- Timurs Maculins
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany.
| | - Javier Garcia-Pardo
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | | | - Jakob Gebel
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Mateusz Putyrski
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Andrew Vorobyov
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Philipp Busse
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Gabor Varga
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, Hamburg, Germany
| | - Simin Rahighi
- Chapman University School of Pharmacy (CUSP), Harry and Diane Rinker Health Science Campus, Chapman University, Irvine, CA 92618, USA
| | | | - Michael J Parnham
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry & Center for Biomolecular Magnetic Resonance, Goethe University, Max-von-Laue-Strasse 9, 60438 Frankfurt am Main, Germany
| | - Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University, Frankfurt am Main, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany.
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14
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Putyrski M, Vakhrusheva O, Bonn F, Guntur S, Vorobyov A, Brandts C, Dikic I, Ernst A. Disrupting the LC3 Interaction Region (LIR) Binding of Selective Autophagy Receptors Sensitizes AML Cell Lines to Cytarabine. Front Cell Dev Biol 2020; 8:208. [PMID: 32296703 PMCID: PMC7137635 DOI: 10.3389/fcell.2020.00208] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/10/2020] [Indexed: 12/26/2022] Open
Abstract
Short linear motifs (SLiMs) located in disordered regions of multidomain proteins are important for the organization of protein-protein interaction networks. By dynamic association with their binding partners, SLiMs enable assembly of multiprotein complexes, pivotal for the regulation of various aspects of cell biology in higher organisms. Despite their importance, there is a paucity of molecular tools to study SLiMs of endogenous proteins in live cells. LC3 interacting regions (LIRs), being quintessential for orchestrating diverse stages of autophagy, are a prominent example of SLiMs and mediate binding to the ubiquitin-like LC3/GABARAP family of proteins. The role of LIRs ranges from the posttranslational processing of their binding partners at early stages of autophagy to the binding of selective autophagy receptors (SARs) to the autophagosome. In order to generate tools to study LIRs in cells, we engineered high affinity binders of LIR motifs of three archetypical SARs: OPTN, p62, and NDP52. In an array of in vitro and cellular assays, the engineered binders were shown to have greatly improved affinity and specificity when compared with the endogenous LC3/GABARAP family of proteins, thus providing a unique possibility for modulating LIR interactions in living systems. We exploited these novel tools to study the impact of LIR inhibition on the fitness and the responsiveness to cytarabine treatment of THP-1 cells - a model for studying acute myeloid leukemia (AML). Our results demonstrate that inhibition of LIR of a single autophagy receptor is insufficient to sensitize the cells to cytarabine, while simultaneous inhibition of three LIR motifs in three distinct SARs reduces the IC50 of the chemotherapeutic.
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Affiliation(s)
- Mateusz Putyrski
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
| | - Olesya Vakhrusheva
- Department of Medicine, Hematology/Oncology, Goethe-University, Frankfurt, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany
| | - Suchithra Guntur
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany
| | - Andrew Vorobyov
- Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
| | - Christian Brandts
- Department of Medicine, Hematology/Oncology, Goethe-University, Frankfurt, Germany.,German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany.,University Cancer Center Frankfurt, Goethe-University, Frankfurt, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt, Germany
| | - Andreas Ernst
- Institute of Biochemistry II, Medical Faculty, Goethe-University, Frankfurt, Germany.,Project Group Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology, Frankfurt, Germany
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15
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Wiechmann S, Maisonneuve P, Grebbin BM, Hoffmeister M, Kaulich M, Clevers H, Rajalingam K, Kurinov I, Farin HF, Sicheri F, Ernst A. Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids. J Biol Chem 2020; 295:4526-4540. [PMID: 32086379 DOI: 10.1074/jbc.ra119.011025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
The small GTPases H, K, and NRAS are molecular switches indispensable for proper regulation of cellular proliferation and growth. Several mutations in the genes encoding members of this protein family are associated with cancer and result in aberrant activation of signaling processes caused by a deregulated recruitment of downstream effector proteins. In this study, we engineered variants of the Ras-binding domain (RBD) of the C-Raf proto-oncogene, Ser/Thr kinase (CRAF). These variants bound with high affinity with the effector-binding site of Ras in an active conformation. Structural characterization disclosed how the newly identified RBD mutations cooperate and thereby enhance affinity with the effector-binding site in Ras compared with WT RBD. The engineered RBD variants closely mimicked the interaction mode of naturally occurring Ras effectors and acted as dominant-negative affinity reagents that block Ras signal transduction. Experiments with cancer cells showed that expression of these RBD variants inhibits Ras signaling, reducing cell growth and inducing apoptosis. Using these optimized RBD variants, we stratified patient-derived colorectal cancer organoids with known Ras mutational status according to their response to Ras inhibition. These results revealed that the presence of Ras mutations was insufficient to predict sensitivity to Ras inhibition, suggesting that not all of these tumors required Ras signaling for proliferation. In summary, by engineering the Ras/Raf interface of the CRAF-RBD, we identified potent and selective inhibitors of Ras in its active conformation that outcompete binding of Ras-signaling effectors.
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Affiliation(s)
- Svenja Wiechmann
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60596 Frankfurt am Main, Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Pierre Maisonneuve
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Britta M Grebbin
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Meike Hoffmeister
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60596 Frankfurt am Main, Germany.,Institute of Biochemistry, Brandenburg Medical School (MHB) Theodor Fontane, 14770 Brandenburg an der Havel, Germany
| | - Manuel Kaulich
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60596 Frankfurt am Main, Germany.,Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany
| | - Hans Clevers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.,Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands.,Center for Molecular Medicine, Department of Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | | | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, Illinois 60439
| | - Henner F Farin
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, 60596 Frankfurt am Main, Germany.,German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Goethe University Frankfurt-Medical Faculty, University Hospital, 60596 Frankfurt am Main, Germany .,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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16
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Wagner K, Kunz K, Piller T, Tascher G, Hölper S, Stehmeier P, Keiten-Schmitz J, Schick M, Keller U, Müller S. The SUMO Isopeptidase SENP6 Functions as a Rheostat of Chromatin Residency in Genome Maintenance and Chromosome Dynamics. Cell Rep 2019; 29:480-494.e5. [PMID: 31597105 DOI: 10.1016/j.celrep.2019.08.106] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/21/2019] [Accepted: 08/29/2019] [Indexed: 11/20/2022] Open
Abstract
Signaling by the ubiquitin-related SUMO pathway relies on coordinated conjugation and deconjugation events. SUMO-specific deconjugating enzymes counterbalance SUMOylation, but comprehensive insight into their substrate specificity and regulation is missing. By characterizing SENP6, we define an N-terminal multi-SIM domain as a critical determinant in targeting SENP6 to SUMO chains. Proteomic profiling reveals a network of SENP6 functions at the crossroads of chromatin organization and DNA damage response (DDR). SENP6 acts as a SUMO eraser at telomeric and centromeric chromatin domains and determines the SUMOylation status and chromatin association of the cohesin complex. Importantly, SENP6 is part of the hPSO4/PRP19 complex that drives ATR-Chk1 activation. SENP6 deficiency impairs chromatin association of the ATR cofactor ATRIP, thereby compromising the activation of Chk1 signaling in response to aphidicolin-induced replicative stress and sensitizing cells to DNA damage. We propose a general role of SENP6 in orchestrating chromatin dynamics and genome stability networks by balancing chromatin residency of protein complexes.
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Affiliation(s)
- Kristina Wagner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Kathrin Kunz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Tanja Piller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Soraya Hölper
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Per Stehmeier
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Jan Keiten-Schmitz
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Markus Schick
- Internal Medicine III, School of Medicine, Technische Universität München, Ismaninger Strasse 22, 81675 Munich, Germany; Department of Hematology, Oncology and Tumor Immunology (Campus Benjamin Franklin), Charité Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Ulrich Keller
- Internal Medicine III, School of Medicine, Technische Universität München, Ismaninger Strasse 22, 81675 Munich, Germany; Department of Hematology, Oncology and Tumor Immunology (Campus Benjamin Franklin), Charité Universitätsmedizin Berlin, Hindenburgdamm 30, 12203 Berlin, Germany; German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stefan Müller
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
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17
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Zhu B, Cui G, Zhang Q, Cheng X, Tang S. Desumoylation of aggrecan and collagen II facilitates degradation via aggrecanases in IL-1β-mediated osteoarthritis. J Pain Res 2019; 12:2145-2153. [PMID: 31372032 PMCID: PMC6634300 DOI: 10.2147/jpr.s194306] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/01/2019] [Indexed: 12/29/2022] Open
Abstract
Background: Aggrecan plays a crucial role in the ability of tissues to withstand compressive loads during the pathological progression of osteoarthritis (OA). Progressive loss of aggrecan from cartilage may result in exposure of the collagen matrix and can lead to its disintegration by metalloproteases. Although aggrecanases are expressed constitutively in human chondrocytes, the degradation of aggrecan is induced by proinflammatory cytokines; however, little is known about the underlying mechanisms. Methods: Human primary chondrocytes from OA patients or healthy donors and human chondrogenic SW1353 cells were cultured and stimulated with IL-1β in vitro, the mRNA expressions and protein levels of MMP-13, ADAMTS-4, ADAMTS-5, SENP1, and SENP2 were determined using real time PCR and Western blot, respectively. The localizations of aggrecan and Col-II, as well as the SUMOylation modification of these proteins were analyzed using immunofluorescence and immunoprecipitation assays, respectively. Results: Our results showed that a proinflammatory cytokine interleukin-1β induced the OA model and desumoylation of aggrecan and collagen type II because the small ubiquitin-like modifier 2/3 (SUMO2/3) was co-localized with aggrecan and collagen type II proteins and interacted physically with them. Mechanistic studies have shown that knockdown of SUMO2/3 expression can significantly enhance the rate of degradation of aggrecan and collagen type II at both the mRNA and protein levels in the OA model. In addition, SUMO-specific protease 2 (SENP2) plays important roles in the desumoylation of aggrecan, while knockdown of SENP2 can protect aggrecan and collagen type II. Clinical assays have shown that OA patients have higher SENP2 levels than healthy controls, and the SENP2 level correlates negatively with both aggrecan and collagen type II levels. Conclusion: SENP2 desumoylates aggrecan and collagen type II proteins in the inflammation induced OA, and SENP2 expression correlates with OA progression.
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Affiliation(s)
- Bing Zhu
- Department of Joint Surgery, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Guanxing Cui
- Department of Joint Surgery, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Qifu Zhang
- Department of Cancer Radiotherapy, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, People's Republic of China
| | - Xiankui Cheng
- Department of Pathology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, People's Republic of China
| | - Shusen Tang
- Department of Joint Surgery, The Affiliated Hospital of Weifang Medical University, Weifang, Shandong, People's Republic of China
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18
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Rosa MT, Abreu IA. Exploring the regulatory levels of SUMOylation to increase crop productivity. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:43-51. [PMID: 31177030 DOI: 10.1016/j.pbi.2019.04.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/17/2019] [Accepted: 04/25/2019] [Indexed: 06/09/2023]
Abstract
SUMOylation is an essential post-translational modification that affects several cellular processes, from gene replication to stress response. Studies using the SUMO (de)conjugation machinery have provided evidence regarding its potential to improve crop performance and productivity under normal and adverse conditions. However, the pleiotropic effect of SUMOylation can be a disadvantage in both situations, especially when considering unpredictable environmental conditions caused by climate changes. Here, we discuss the pleiotropic effects caused by disrupting the SUMOylation machinery, and new strategies that may help to overcome pleiotropy. We propose exploring the several regulatory levels of SUMOylation recently revealed, including transcriptional, post-transcriptional regulation by alternative splicing, and post-translational modifications. These new findings may provide valuable tools to increase crop productivity.
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Affiliation(s)
- Margarida Tg Rosa
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal.
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19
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Mattern M, Sutherland J, Kadimisetty K, Barrio R, Rodriguez MS. Using Ubiquitin Binders to Decipher the Ubiquitin Code. Trends Biochem Sci 2019; 44:599-615. [PMID: 30819414 DOI: 10.1016/j.tibs.2019.01.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/13/2022]
Abstract
Post-translational modifications (PTMs) by ubiquitin (Ub) are versatile, highly dynamic, and involved in nearly all aspects of eukaryote biological function. The reversibility and heterogeneity of Ub chains attached to protein substrates have complicated their isolation, quantification, and characterization. Strategies have emerged to isolate endogenous ubiquitylated targets, including technologies based on the use of Ub-binding peptides, such as tandem-repeated Ub-binding entities (TUBEs). TUBEs allow the identification and characterization of Ub chains, and novel substrates for deubiquitylases (DUBs) and Ub ligases (E3s). Here we review their impact on purification, analysis of pan or chain-selective polyubiquitylated proteins and underline the biological relevance of this information. Together with peptide aptamers and other Ub affinity-based approaches, TUBEs will contribute to unraveling the secrets of the Ub code.
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Affiliation(s)
- Michael Mattern
- Progenra Inc., 277 Great Valley Parkway, Malvern 19355, Pennsylvania, USA; These authors contributed equally
| | - James Sutherland
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain; These authors contributed equally
| | - Karteek Kadimisetty
- LifeSensors Inc., 271 Great Valley Parkway, Malvern 19355, Pennsylvania, USA
| | - Rosa Barrio
- CIC bioGUNE, Technology Park of Bizkaia, Bldg. 801A, 48160 Derio, Spain
| | - Manuel S Rodriguez
- ITAV-IPBS-UPS CNRS USR3505, 1 place Pierre Potier, Oncopole entrée B, 31106 Toulouse, France.
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20
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UBC9 regulates cardiac sodium channel Na v1.5 ubiquitination, degradation and sodium current density. J Mol Cell Cardiol 2019; 129:79-91. [PMID: 30772377 DOI: 10.1016/j.yjmcc.2019.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/29/2022]
Abstract
Voltage-gated sodium channel Nav1.5 is critical for generation and conduction of cardiac action potentials. Mutations and expression level changes of Nav1.5 are associated with cardiac arrhythmias and sudden death. The ubiquitin (Ub) conjugation machinery utilizes three enzyme activities, E1, E2, and E3, to regulate protein degradation. Previous studies from us and others showed that Nedd4-2 acts as an E3 ubiquitin-protein ligase involved in ubiquitination and degradation of Nav1.5, however, more key regulators remain to be identified. In this study, we show that UBC9, a SUMO-conjugating enzyme, regulates ubiquitination and degradation of Nav1.5. Overexpression of UBC9 significantly decreased Nav1.5 expression and reduced sodium current densities, whereas knockdown of UBC9 expression significantly enhanced Nav1.5 expression and increased sodium current densities, in both HEK293 cells and primary neonatal cardiomyocytes. Overexpression of UBC9 increased ubiquitination of Nav1.5, and proteasome inhibitor MG132 blocked the effect of UBC9 overexpression on Nav1.5 degradation. Co-immunoprecipitation showed that UBC9 interacts with Nedd4-2. UBC9 with mutation C93S, which suppresses SUMO-conjugating activity of UBC9, was as active as wild type UBC9 in regulating Nav1.5 levels, suggesting that UBC9 regulates Nav1.5 expression levels in a SUMOylation-independent manner. Our findings thus identify a key structural element of the ubiquitin-conjugation machinery for Nav1.5 and provide important insights into the regulatory mechanism for ubiquitination and turnover of Nav1.5.
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21
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Gärtner A, Wagner K, Hölper S, Kunz K, Rodriguez MS, Müller S. Acetylation of SUMO2 at lysine 11 favors the formation of non-canonical SUMO chains. EMBO Rep 2018; 19:embr.201846117. [PMID: 30201799 DOI: 10.15252/embr.201846117] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 08/16/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
Post-translational modifications by ubiquitin-related SUMO modifiers regulate cellular signaling networks and protein homeostasis. While SUMO1 is mainly conjugated to proteins as a monomer, SUMO2/3 can form polymeric chains. Poly-SUMOylation is best understood in the SUMO-targeted ubiquitin ligase (StUbL) pathway, where chains prime proteins for subsequent ubiquitylation by StUbLs. SUMO chains typically form in response to genotoxic or proteotoxic stress and are preferentially linked via lysine 11 of SUMO2/3. Here, we report that K11 of SUMO2/3 undergoes reversible acetylation with SIRT1 being the K11 deacetylase. In a purified in vitro system, acetylation of SUMO2/3 impairs chain formation and restricts chain length. In a cellular context, however, K11 acetyl-mimicking SUMO2 does not affect the StUbL pathway, indicating that in cells non-canonical chains are more prevalent. MS-based SUMO proteomics indeed identified non-canonical chain types under basal and stress conditions. Importantly, mimicking K11 acetylation alters chain architecture by favoring K5- and K35-linked chains, while inhibiting K7 and K21 linkages. These data provide insight into SUMO chain signaling and point to a role of K11 acetylation as a modulator of SUMO2/3 chains.
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Affiliation(s)
- Anne Gärtner
- Institute of Biochemistry II, Medical School, Goethe University, Frankfurt, Germany
| | - Kristina Wagner
- Institute of Biochemistry II, Medical School, Goethe University, Frankfurt, Germany
| | - Soraya Hölper
- Institute of Biochemistry II, Medical School, Goethe University, Frankfurt, Germany
| | - Kathrin Kunz
- Institute of Biochemistry II, Medical School, Goethe University, Frankfurt, Germany
| | - Manuel S Rodriguez
- Institut des Technologies Avancées en sciences du Vivant-UPS and IPBS-CNRS, Toulouse Cedex 1, France
| | - Stefan Müller
- Institute of Biochemistry II, Medical School, Goethe University, Frankfurt, Germany
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