201
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Zhang Z, Zhou Z, Huang J, Sun X, Haseeb M, Ahmed S, Shah MAA, Yan R, Song X, Xu L, Li X. Molecular characterization of a potential receptor of Eimeria acervulina microneme protein 3 from chicken duodenal epithelial cells. Parasite 2020; 27:18. [PMID: 32195662 PMCID: PMC7083106 DOI: 10.1051/parasite/2020014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/07/2020] [Indexed: 01/20/2023] Open
Abstract
Eimeria acervulina is one of seven Eimeria spp. that can infect chicken duodenal epithelial cells. Eimeria microneme protein 3 (MIC3) plays a vital role in the invasion of host epithelial tissue by the parasite. In this study, we found that chicken (Gallus gallus) ubiquitin conjugating enzyme E2F (UBE2F) could bind to the MIC3 protein of E. acervulina (EaMIC3), as screened using the yeast two-hybrid system, and that it might be the putative receptor protein of EaMIC3. The UBE2F gene was cloned from chicken duodenal epithelial cells. The recombinant protein of UBE2F (rUBE2F) was expressed in E. coli and the reactogenicity of rUBE2F was analyzed by Western blot. Gene sequencing revealed that the opening reading frame (ORF) of UBE2F was 558 base pairs and encoded a protein of 186 amino acids with a molecular weight of 20.46 kDa. The predicted UBE2F protein did not contain signal peptides or a transmembrane region, but had multiple O-glycosylation and phosphorylation sites. A phylogenetic analysis showed that the chicken UBE2F protein is closely related to those of quail and pigeon (Coturnix japonica and Columba livia). A sporozoite invasion-blocking assay showed that antisera against rUBE2F significantly inhibited the invasion of E. acervulina sporozoites in vitro. Animal experiments indicated that the antisera could significantly enhance average body weight gains and reduce mean lesion scores following a challenge with E. acervulina. These results therefore imply that the chicken UBE2F protein might be the target receptor molecule of EaMIC3 that is involved in E. acervulina invasion.
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Affiliation(s)
- Zhenchao Zhang
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
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School of Basic Medical Sciences, Xinxiang Medical University Xinxiang 453003 Henan PR China
| | - Zhouyang Zhou
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
| | - Jianmei Huang
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
| | - Xiaoting Sun
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
| | - Muhammad Haseeb
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
| | - Shakeel Ahmed
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
| | - Muhammad Ali A. Shah
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Department of Pathobiology, Faculty of Veterinary & Animal Sciences, Pir Mehr Ali Shah Arid Agriculture University 46000 Rawalpindi Pakistan
| | - Ruofeng Yan
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
| | - Xiaokai Song
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
| | - Lixin Xu
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
| | - Xiangrui Li
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MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University Nanjing 210095 PR China
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202
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Zuo Y, Chong BK, Jiang K, Finley D, Klenerman D, Ye Y. A General in Vitro Assay for Studying Enzymatic Activities of the Ubiquitin System. Biochemistry 2020; 59:851-861. [PMID: 31951392 DOI: 10.1021/acs.biochem.9b00602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ubiquitin (Ub) system regulates a wide range of cellular signaling pathways. Several hundred E1, E2, and E3 enzymes are together responsible for protein ubiquitination, thereby controlling cellular activities. Due to the numerous enzymes and processes involved, studies of ubiquitination activities have been challenging. We here report a novel Förster resonance energy transfer (FRET)-based assay for studying the in vitro kinetics of ubiquitination. FRET is established upon binding of fluorophore-labeled Ub to eGFP-tagged ZnUBP, a domain that exclusively binds unconjugated Ub. We name this assay the free Ub sensor system (FUSS). Using Uba1, UbcH5, and CHIP as model E1, E2, and E3 enzymes, respectively, we demonstrate that ubiquitination results in decreasing FRET efficiency, from which reaction rates can be determined. Further treatment with USP21, a deubiquitinase, leads to increased FRET efficiency, confirming the reversibility of the assay. We subsequently use this assay to show that increasing the concentration of CHIP or UbcH5 but not Uba1 enhances ubiquitination rates and develop a novel machine learning approach to model ubiquitination. The overall ubiquitination activity is also increased upon incubation with tau, a substrate of CHIP. Our data together demonstrate the versatile applications of a novel ubiquitination assay that does not require labeling of E1, E2, E3, or substrates and is thus likely compatible with any E1-E2-E3 combinations.
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Affiliation(s)
- Yukun Zuo
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K.,UK Dementia Research Institute at University of Cambridge , Cambridge CB2 0XY , U.K
| | - Boon Keat Chong
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K
| | - Kun Jiang
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K
| | - Daniel Finley
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - David Klenerman
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K.,UK Dementia Research Institute at University of Cambridge , Cambridge CB2 0XY , U.K
| | - Yu Ye
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K.,Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.,Department of Brain Sciences, Division of Neuroscience , Imperial College London , London W12 0NN , U.K.,UK Dementia Research Institute at Imperial College London , London W12 0NN , U.K
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203
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Abstract
Protein ubiquitylation is essential for the maintenance of cellular homeostasis. E3 ubiquitin ligases are key components of the enzymatic machinery catalyzing the attachment of ubiquitin to substrate proteins. Consequently, enzymatic dysfunction has been associated with medical conditions including cancer, diabetes, and cardiovascular and neurodegenerative disorders. To safeguard substrate selection and ubiquitylation, the activity of E3 ligases is tightly regulated by post-translational modifications including phosphorylation, sumoylation, and ubiquitylation, as well as binding of alternative adaptor molecules and cofactors. Recent structural studies identified homotypic and heterotypic interactions between E3 ligases, adding another layer of control for rapid adaptation to changing environmental and physiological conditions. Here, we discuss the regulation of E3 ligase activity by combinatorial oligomerization and summarize examples of associated ubiquitylation pathways and mechanisms.
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Affiliation(s)
- Vishnu Balaji
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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204
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Garcia-Barcena C, Osinalde N, Ramirez J, Mayor U. How to Inactivate Human Ubiquitin E3 Ligases by Mutation. Front Cell Dev Biol 2020; 8:39. [PMID: 32117970 PMCID: PMC7010608 DOI: 10.3389/fcell.2020.00039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/16/2020] [Indexed: 12/24/2022] Open
Abstract
E3 ubiquitin ligases are the ultimate enzymes involved in the transfer of ubiquitin to substrate proteins, a process that determines the fate of the modified protein. Numerous diseases are caused by defects in the ubiquitin-proteasome machinery, including when the activity of a given E3 ligase is hampered. Thus, inactivation of E3 ligases and the resulting effects at molecular or cellular level have been the focus of many studies during the last few years. For this purpose, site-specific mutation of key residues involved in either protein interaction, substrate recognition or ubiquitin transfer have been reported to successfully inactivate E3 ligases. Nevertheless, it is not always trivial to predict which mutation(s) will block the catalytic activity of a ligase. Here we review over 250 site-specific inactivating mutations that have been carried out in 120 human E3 ubiquitin ligases. We foresee that the information gathered here will be helpful for the design of future experimental strategies.
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Affiliation(s)
- Cristina Garcia-Barcena
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Ikerbasque - Basque Foundation for Science, Bilbao, Spain
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205
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Cai Z, Moten A, Peng D, Hsu CC, Pan BS, Manne R, Li HY, Lin HK. The Skp2 Pathway: A Critical Target for Cancer Therapy. Semin Cancer Biol 2020; 67:16-33. [PMID: 32014608 DOI: 10.1016/j.semcancer.2020.01.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/22/2020] [Accepted: 01/25/2020] [Indexed: 12/16/2022]
Abstract
Strictly regulated protein degradation by ubiquitin-proteasome system (UPS) is essential for various cellular processes whose dysregulation is linked to serious diseases including cancer. Skp2, a well characterized component of Skp2-SCF E3 ligase complex, is able to conjugate both K48-linked ubiquitin chains and K63-linked ubiquitin chains on its diverse substrates, inducing proteasome mediated proteolysis or modulating the function of tagged substrates respectively. Overexpression of Skp2 is observed in various human cancers associated with poor survival and adverse therapeutic outcomes, which in turn suggests that Skp2 engages in tumorigenic activity. To that end, the oncogenic properties of Skp2 are demonstrated by various genetic mouse models, highlighting the potential of Skp2 as a target for tackling cancer. In this article, we will describe the downstream substrates of Skp2 as well as upstream regulators for Skp2-SCF complex activity. We will further summarize the comprehensive oncogenic functions of Skp2 while describing diverse strategies and therapeutic platforms currently available for developing Skp2 inhibitors.
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Affiliation(s)
- Zhen Cai
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA.
| | - Asad Moten
- National Capital Consortium, Department of Defense, Washington DC, 20307, USA; Institute for Complex Systems, HealthNovations International, Houston, TX, 77089, USA; Center for Cancer Research, National Institutes of Health, Bethesda, MD, 20814, USA; Center on Genomics, Vulnerable Populations, and Health Disparities, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Danni Peng
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA
| | - Che-Chia Hsu
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA
| | - Bo-Syong Pan
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA
| | - Rajeshkumar Manne
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA
| | - Hong-Yu Li
- University of Arkansas for Medical Sciences, College of Pharmacy, Division of Pharmaceutical Science, 200 South Cedar, Little Rock AR 72202, USA
| | - Hui-Kuan Lin
- Department of Cancer Biology, Wake Forest Baptist Medical Center, Wake Forest University, Winston Salem, NC, 27101, USA; Graduate Institute of Basic Medical Science, China Medical University, Taichung 404, Taiwan; Department of Biotechnology, Asia University, Taichung 41354, Taiwan.
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206
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Wang Q, Liu M, Zang Y, Xiao W. The C-terminal extension of Arabidopsis Uev1A/B with putative prenylation site plays critical roles in protein interaction, subcellular distribution and membrane association. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110324. [PMID: 31928655 DOI: 10.1016/j.plantsci.2019.110324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 10/18/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Lysine (K) 63-linked polyubiquitination plays important roles in cellular processes including DNA-damage tolerance (DDT), NF-κB signaling and endocytosis. Compared to yeast and mammals, little is known about K63-linked polyubiquitination in plants. To date, a Uev-Ubc13 complex is the only known Ub-conjugating enzyme to catalyze K63-linked polyubiquitination, in which Uev serves as a regulatory subunit. The Arabidopsis thaliana genome contains four UEV1 genes that can be classified into two subfamilies (UEV1A/B and UEV1C/D), in which Uev1A/B have a C-terminal extension. Database analysis reveals that all higher plant genomes contain both subfamily UEV1s, which were evolved as early as angiosperm plants. Interestingly, all C-terminal tails in the Uev1A/B subfamily contain a putative prenylation motif, CaaX. Combined experimental results using AtUev1B demonstrated that it is most likely farnesylated and that its C-terminal tail, particularly the catalytic Cys residue in the CaaX motif, plays critical roles in protein-protein interaction, nuclear exclusion and membrane association. Using AtUev1B as bait for a yeast-two-hybrid screen, we identified 14 interaction proteins in a prenylation-dependent manner. These results collectively imply that prenylation of AtUev1A/B plays a critical role in its functional differentiation from AtUev1C/D.
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Affiliation(s)
- Qian Wang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China; Shanxi Provincial People's Hospital, Taiyuan, Shanxi, 030012, China
| | - Maoqing Liu
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Yuepeng Zang
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Wei Xiao
- Beijing Key Laboratory of DNA Damage Responses and College of Life Sciences, Capital Normal University, Beijing, 100048, China; Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada.
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207
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Toyofuku T, Okamoto Y, Ishikawa T, Sasawatari S, Kumanogoh A. LRRK2 regulates endoplasmic reticulum-mitochondrial tethering through the PERK-mediated ubiquitination pathway. EMBO J 2020; 39:e100875. [PMID: 31821596 PMCID: PMC6960452 DOI: 10.15252/embj.2018100875] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/24/2019] [Accepted: 11/05/2019] [Indexed: 11/23/2022] Open
Abstract
Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most common cause of familial Parkinson's disease (PD). Impaired mitochondrial function is suspected to play a major role in PD. Nonetheless, the underlying mechanism by which impaired LRRK2 activity contributes to PD pathology remains unclear. Here, we identified the role of LRRK2 in endoplasmic reticulum (ER)-mitochondrial tethering, which is essential for mitochondrial bioenergetics. LRRK2 regulated the activities of E3 ubiquitin ligases MARCH5, MULAN, and Parkin via kinase-dependent protein-protein interactions. Kinase-active LRRK2(G2019S) dissociated from these ligases, leading to their PERK-mediated phosphorylation and activation, thereby increasing ubiquitin-mediated degradation of ER-mitochondrial tethering proteins. By contrast, kinase-dead LRRK2(D1994A)-bound ligases blocked PERK-mediated phosphorylation and activation of E3 ligases, thereby increasing the levels of ER-mitochondrial tethering proteins. Thus, the role of LRRK2 in the ER-mitochondrial interaction represents an important control point for cell fate and pathogenesis in PD.
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Affiliation(s)
- Toshihiko Toyofuku
- Department of Immunology and Molecular MedicineGraduate School of MedicineOsaka UniversitySuitaJapan
| | - Yuki Okamoto
- Department of Immunology and Molecular MedicineGraduate School of MedicineOsaka UniversitySuitaJapan
| | - Takako Ishikawa
- Department of Immunology and Molecular MedicineGraduate School of MedicineOsaka UniversitySuitaJapan
| | - Shigemi Sasawatari
- Department of Immunology and Molecular MedicineGraduate School of MedicineOsaka UniversitySuitaJapan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical ImmunologyGraduate School of MedicineOsaka UniversitySuitaJapan
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208
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Li HL, Wang X, Ji XL, Qiao ZW, You CX, Hao YJ. Genome-Wide Identification of Apple Ubiquitin SINA E3 Ligase and Functional Characterization of MdSINA2. FRONTIERS IN PLANT SCIENCE 2020; 11:1109. [PMID: 32793265 PMCID: PMC7393226 DOI: 10.3389/fpls.2020.01109] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/06/2020] [Indexed: 05/22/2023]
Abstract
SINA (Seven in absentia) proteins are a small family of ubiquitin ligases that play important roles in regulating plant growth and developmental processes as well as in responses to diverse types of biotic and abiotic stress. However, the characteristics of the apple SINA family have not been previously studied. Here, we identified 11 MdSINAs members in the apple genome based on their conserved, N-terminal RING and C-terminal SINA domains. We also reconstructed a phylogeny of these genes; characterized their chromosomal location, structure, and motifs; and identified two major groups of MdSINA genes. Subsequent qRT-PCR analyses were used to characterize the expression of MdSINA genes in various tissues and organs, and levels of expression were highest in leaves. MdSINAs were significantly induced under ABA and carbon- and nitrate-starvation treatment. Except for MdSINA1 and MdSINA7, the other MdSINA proteins could interact with each other. Moreover, MdSINA2 was found to be localized in the nucleus using Agrobacterium-mediated transient expression. Western-blot analysis showed that MdSINA2 accumulated extensively under light, decreased under darkness, and became insensitive to light when the RING domain was disrupted. Finally, ABA-hypersensitive phenotypes were confirmed by transgenic calli and the ectopic expression of MdSINA2 in Arabidopsis. In conclusion, our results suggest that MdSINA genes participate in the responses to different types of stress, and that MdSINA2 might act as a negative regulator in the ABA stress response.
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209
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CRL3s: The BTB-CUL3-RING E3 Ubiquitin Ligases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:211-223. [PMID: 31898230 DOI: 10.1007/978-981-15-1025-0_13] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ubiquitin proteasome pathway is one of the major regulatory tools used by eukaryotic cells. The evolutionarily conserved cullin family proteins can assemble as many as >600 distinct E3 ubiquitin ligase complexes that regulate diverse cellular pathways. In most of Cullin-RING ubiquitin ligase (CRL) complexes, separate linker and adaptor proteins build the substrate recognition module. Differently, a single BTB-containing adaptor molecule utilizing two protein interaction sites can link the CUL3 scaffold to the substrate, forming as many as 188 CUL3-BTB E3 ligase complexes in mammals. Here, we review the most recent studies on CRL3 complexes, with a focus on the model for CUL3 assembly with its BTB-containing substrate receptors. Also, we summarize the current knowledge of CRL3 substrates and their relevant biological functions. Next, we discuss the mutual exclusivity of somatic mutations in KEAP1, NRF2, and CUL3 in human lung cancer. Finally, we highlight new strategies to expand CUL3 substrates and discuss outstanding questions remaining in the field.
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210
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Marente J, Ortega P, Pardo-Medina J, Avalos J, Limón MC. Modulation of Activity of a Carotenoid Pathway Through the Use of the TeT-on Regulatory System: Application in the Fungus Fusarium fujikuroi. Methods Mol Biol 2020; 2083:343-360. [PMID: 31745934 DOI: 10.1007/978-1-4939-9952-1_26] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Carotenoids are widespread pigments in photosynthetic species, but they are also found in nonphotosynthetic microorganisms, such as bacteria and fungi. The amenability of fungi to genetic studies have made some fungal species advantageous models in the study of the genetics and biochemistry of carotenoid biosynthesis, while others have been used for biotechnological carotenoid production. The availability of molecular techniques that allow modulating the expression of target genes is a powerful tool in the manipulation of carotenoid synthesis. An example of an adjustable gene expression is based on the tetracycline-controlled transcriptional activation system, known as Tet-on. We describe here the material and protocols for the construction of a Tet-on regulated gene, its introduction in the filamentous fungus F. fujikuroi, and its use to modulate the expression of a negative regulator of carotenoid biosynthesis.
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Affiliation(s)
- Julia Marente
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Pedro Ortega
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Seville, Spain
| | - Javier Pardo-Medina
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Javier Avalos
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - M Carmen Limón
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
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211
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Ballar Kirmizibayrak P, Erbaykent-Tepedelen B, Gozen O, Erzurumlu Y. Divergent Modulation of Proteostasis in Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:117-151. [PMID: 32274755 DOI: 10.1007/978-3-030-38266-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteostasis regulates key cellular processes such as cell proliferation, differentiation, transcription, and apoptosis. The mechanisms by which proteostasis is regulated are crucial and the deterioration of cellular proteostasis has been significantly associated with tumorigenesis since it specifically targets key oncoproteins and tumor suppressors. Prostate cancer (PCa) is the second most common cause of cancer death in men worldwide. Androgens mediate one of the most central signaling pathways in all stages of PCa via the androgen receptor (AR). In addition to their regulation by hormones, PCa cells are also known to be highly secretory and are particularly prone to ER stress as proper ER function is essential. Alterations in various complex signaling pathways and cellular processes including cell cycle control, transcription, DNA repair, apoptosis, cell adhesion, epithelial-mesenchymal transition (EMT), and angiogenesis are critical factors influencing PCa development through key molecular changes mainly by posttranslational modifications in PCa-related proteins, including AR, NKX3.1, PTEN, p53, cyclin D1, and p27. Several ubiquitin ligases like MDM2, Siah2, RNF6, CHIP, and substrate-binding adaptor SPOP; deubiquitinases such as USP7, USP10, USP26, and USP12 are just some of the modifiers involved in the regulation of these key proteins via ubiquitin-proteasome system (UPS). Some ubiquitin-like modifiers, especially SUMOs, have been also closely associated with PCa. On the other hand, the proteotoxicity resulting from misfolded proteins and failure of ER adaptive capacity induce unfolded protein response (UPR) that is an indispensable signaling mechanism for PCa development. Lastly, ER-associated degradation (ERAD) also plays a crucial role in prostate tumorigenesis. In this section, the relationship between prostate cancer and proteostasis will be discussed in terms of UPS, UPR, SUMOylation, ERAD, and autophagy.
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Affiliation(s)
| | | | - Oguz Gozen
- Faculty of Medicine, Department of Physiology, Ege University, Izmir, Turkey
| | - Yalcin Erzurumlu
- Faculty of Pharmacy, Department of Biochemistry, Suleyman Demirel University, Isparta, Turkey
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212
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Lee SO, Lee CK, Ryu KS, Chi SW. The RING domain of mitochondrial E3 ubiquitin ligase 1 and its complex with Ube2D2: crystallization and X-ray diffraction. Acta Crystallogr F Struct Biol Commun 2020; 76:1-7. [PMID: 31929179 PMCID: PMC6957114 DOI: 10.1107/s2053230x19015395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 11/14/2019] [Indexed: 11/10/2022] Open
Abstract
Mitochondrial E3 ubiquitin ligase 1 (MUL1) is located in the mitochondrial outer membrane and regulates various biological processes, including apoptosis, cell growth, mitophagy and mitochondrial dynamics. The C-terminal region of MUL1 faces the cytoplasm and contains the RING domain (MUL1-RING) where the Ub~E2 thioester binds. Unlike most RING-type E3 enzymes, MUL1-RING alone does not have an additional region that recruits a substrate protein, yet is still able to ubiquitylate the substrate, the p53 protein. Nevertheless, the exact mechanism of the ubiquitylation of p53 by MUL1-RING has not yet been elucidated. In order to understand this novel ubiquitylation mechanism, it is necessary to determine the three-dimensional structures of MUL1-RING and of its complex with the cognate E2 enzyme. Here, Ube2D2 was validated as a functional E2 enzyme for the ubiquitylation of the p53 transactivation domain (p53-TAD) by MUL1-RING, and purification and crystallization processes for MUL1-RING and the MUL1-RING-Ube2D2 complex are reported.
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Affiliation(s)
- Sang-Ok Lee
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Chong-Kil Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Kyoung-Seok Ryu
- Protein Structure Research Group, Korea Basic Science Institute, 162 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungcheongbuk-do 28119, Republic of Korea
- Department of Bio-Analytical Science, KBSI School of Bio-Analytical Science, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, KRIBB, Daejeon 34141, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
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213
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Antoniou N, Lagopati N, Balourdas DI, Nikolaou M, Papalampros A, Vasileiou PVS, Myrianthopoulos V, Kotsinas A, Shiloh Y, Liontos M, Gorgoulis VG. The Role of E3, E4 Ubiquitin Ligase (UBE4B) in Human Pathologies. Cancers (Basel) 2019; 12:cancers12010062. [PMID: 31878315 PMCID: PMC7017255 DOI: 10.3390/cancers12010062] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/21/2019] [Accepted: 11/23/2019] [Indexed: 12/18/2022] Open
Abstract
The genome is exposed daily to many deleterious factors. Ubiquitination is a mechanism that regulates several crucial cellular functions, allowing cells to react upon various stimuli in order to preserve their homeostasis. Ubiquitin ligases act as specific regulators and actively participate among others in the DNA damage response (DDR) network. UBE4B is a newly identified member of E3 ubiquitin ligases that appears to be overexpressed in several human neoplasms. The aim of this review is to provide insights into the role of UBE4B ubiquitin ligase in DDR and its association with p53 expression, shedding light particularly on the molecular mechanisms of carcinogenesis.
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Affiliation(s)
- Nikolaos Antoniou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str., Goudi, GR-11527 Athens, Greece; (N.A.); (N.L.); (P.V.S.V.); (M.L.)
| | - Nefeli Lagopati
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str., Goudi, GR-11527 Athens, Greece; (N.A.); (N.L.); (P.V.S.V.); (M.L.)
| | - Dimitrios Ilias Balourdas
- Department of Pharmacy, National Kapodistrian University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece; (D.I.B.); (V.M.)
| | - Michail Nikolaou
- General Maternal Hospital of Athens “Elena Venizelou”, GR-11521 Athens, Greece;
| | - Alexandros Papalampros
- First Department of Surgery, Laikon Teaching Hospital, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str., Goudi, GR-11527 Athens, Greece;
| | - Panagiotis V. S. Vasileiou
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str., Goudi, GR-11527 Athens, Greece; (N.A.); (N.L.); (P.V.S.V.); (M.L.)
| | - Vassilios Myrianthopoulos
- Department of Pharmacy, National Kapodistrian University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece; (D.I.B.); (V.M.)
| | - Athanassios Kotsinas
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str., Goudi, GR-11527 Athens, Greece; (N.A.); (N.L.); (P.V.S.V.); (M.L.)
- Correspondence: (A.K.); (V.G.G.); Tel.: +30-210-746-2350 (V.G.G.)
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel;
| | - Michalis Liontos
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str., Goudi, GR-11527 Athens, Greece; (N.A.); (N.L.); (P.V.S.V.); (M.L.)
- Oncology Unit, Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra Hospital, GR-11528 Athens, Greece
| | - Vassilis G. Gorgoulis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, National Kapodistrian University of Athens, 75 Mikras Asias Str., Goudi, GR-11527 Athens, Greece; (N.A.); (N.L.); (P.V.S.V.); (M.L.)
- Biomedical Research Foundation of the Academy of Athens, GR-11527 Athens, Greece
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M20 4GJ, UK
- Correspondence: (A.K.); (V.G.G.); Tel.: +30-210-746-2350 (V.G.G.)
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214
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Hill S, Reichermeier K, Scott DC, Samentar L, Coulombe-Huntington J, Izzi L, Tang X, Ibarra R, Bertomeu T, Moradian A, Sweredoski MJ, Caberoy N, Schulman BA, Sicheri F, Tyers M, Kleiger G. Robust cullin-RING ligase function is established by a multiplicity of poly-ubiquitylation pathways. eLife 2019; 8:e51163. [PMID: 31868589 PMCID: PMC6975927 DOI: 10.7554/elife.51163] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 12/22/2019] [Indexed: 12/24/2022] Open
Abstract
The cullin-RING ligases (CRLs) form the major family of E3 ubiquitin ligases. The prototypic CRLs in yeast, called SCF enzymes, employ a single E2 enzyme, Cdc34, to build poly-ubiquitin chains required for degradation. In contrast, six different human E2 and E3 enzyme activities, including Cdc34 orthologs UBE2R1 and UBE2R2, appear to mediate SCF-catalyzed substrate polyubiquitylation in vitro. The combinatorial interplay of these enzymes raises questions about genetic buffering of SCFs in human cells and challenges the dogma that E3s alone determine substrate specificity. To enable the quantitative comparisons of SCF-dependent ubiquitylation reactions with physiological enzyme concentrations, mass spectrometry was employed to estimate E2 and E3 levels in cells. In combination with UBE2R1/2, the E2 UBE2D3 and the E3 ARIH1 both promoted SCF-mediated polyubiquitylation in a substrate-specific fashion. Unexpectedly, UBE2R2 alone had negligible ubiquitylation activity at physiological concentrations and the ablation of UBE2R1/2 had no effect on the stability of SCF substrates in cells. A genome-wide CRISPR screen revealed that an additional E2 enzyme, UBE2G1, buffers against the loss of UBE2R1/2. UBE2G1 had robust in vitro chain extension activity with SCF, and UBE2G1 knockdown in cells lacking UBE2R1/2 resulted in stabilization of the SCF substrates p27 and CYCLIN E as well as the CUL2-RING ligase substrate HIF1α. The results demonstrate the human SCF enzyme system is diversified by association with multiple catalytic enzyme partners.
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Affiliation(s)
- Spencer Hill
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
| | - Kurt Reichermeier
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaUnited States
- Department of Discovery ProteomicsGenentech IncSouth San FranciscoUnited States
- Department of Discovery OncologyGenentech IncSouth San FranciscoUnited States
| | - Daniel C Scott
- Department of Structural BiologySt Jude Children's Research HospitalMemphisUnited States
| | - Lorena Samentar
- School of Life SciencesUniversity of NevadaLas VegasUnited States
- University of the PhilippinesIloiloPhilippines
| | - Jasmin Coulombe-Huntington
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Luisa Izzi
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Xiaojing Tang
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
| | - Rebeca Ibarra
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
| | - Thierry Bertomeu
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Annie Moradian
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman InstituteCalifornia Institute of TechnologyPasadenaUnited States
| | - Michael J Sweredoski
- Proteome Exploration Laboratory, Division of Biology and Biological Engineering, Beckman InstituteCalifornia Institute of TechnologyPasadenaUnited States
| | - Nora Caberoy
- School of Life SciencesUniversity of NevadaLas VegasUnited States
| | - Brenda A Schulman
- Max Planck Institute of Biochemistry, Molecular Machines and SignalingMartinsriedGermany
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research InstituteMount Sinai HospitalTorontoCanada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Department of MedicineUniversity of MontrealMontrealCanada
| | - Gary Kleiger
- Department of Chemistry and BiochemistryUniversity of NevadaLas VegasUnited States
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215
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Mathur S, Fletcher AJ, Branigan E, Hay RT, Virdee S. Photocrosslinking Activity-Based Probes for Ubiquitin RING E3 Ligases. Cell Chem Biol 2019; 27:74-82.e6. [PMID: 31859248 PMCID: PMC6963778 DOI: 10.1016/j.chembiol.2019.11.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/13/2019] [Accepted: 11/20/2019] [Indexed: 12/13/2022]
Abstract
Activity-based protein profiling is an invaluable technique for studying enzyme biology and facilitating the development of therapeutics. Ubiquitin E3 ligases (E3s) are one of the largest enzyme families and regulate a host of (patho)physiological processes. The largest subtype are the RING E3s of which there are >600 members. RING E3s have adaptor-like activity that can be subject to diverse regulatory mechanisms and have become attractive drug targets. Activity-based probes (ABPs) for measuring RING E3 activity do not exist. Here we re-engineer ubiquitin-charged E2 conjugating enzymes to produce photocrosslinking ABPs. We demonstrate activity-dependent profiling of two divergent cancer-associated RING E3s, RNF4 and c-Cbl, in response to their native activation signals. We also demonstrate profiling of endogenous RING E3 ligase activation in response to epidermal growth factor (EGF) stimulation. These photocrosslinking ABPs should advance E3 ligase research and the development of selective modulators against this important class of enzymes. Photoactivated activity-based probes developed for large class of ubiquitin E3 ligases ABPs are compatible with divergent RING E3 activation mechanisms Parallelized E3 profiling and detection of growth factor-induced E3 activation
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Affiliation(s)
- Sunil Mathur
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Adam J Fletcher
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK
| | - Emma Branigan
- Division of Gene Regulation and Expression, University of Dundee, Scotland, UK
| | - Ronald T Hay
- Division of Gene Regulation and Expression, University of Dundee, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Scotland, UK.
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216
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The Enigmatic Function of PARP1: From PARylation Activity to PAR Readers. Cells 2019; 8:cells8121625. [PMID: 31842403 PMCID: PMC6953017 DOI: 10.3390/cells8121625] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 12/16/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) is catalysed by poly(ADP-ribose) polymerases (PARPs, also known as ARTDs) and then rapidly removed by degrading enzymes. Poly(ADP-ribose) (PAR) is produced from PARylation and provides a delicate and spatiotemporal interaction scaffold for numerous target proteins. The PARylation system, consisting of PAR synthesizers and erasers and PAR itself and readers, plays diverse roles in the DNA damage response (DDR), DNA repair, transcription, replication, chromatin remodeling, metabolism, and cell death. Despite great efforts by scientists in biochemistry, cell and molecular biology, genetics, and pharmacology over the last five decades, the biology of PARPs and PARylation remains enigmatic. In this review, we summarize the current understanding of the biological function of PARP1 (ARTD1), the founding member of the PARP family, focusing on the inter-dependent or -independent nature of different functional domains of the PARP1 protein. We also discuss the readers of PAR, whose function may transduce signals and coordinate the cellular processes, which has recently emerged as a new research avenue for PARP biology. We aim to provide some perspective on how future research might disentangle the biology of PARylation by dissecting the structural and functional relationship of PARP1, a major effector of the PARPs family.
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217
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Boyer NP, McCormick LE, Menon S, Urbina FL, Gupton SL. A pair of E3 ubiquitin ligases compete to regulate filopodial dynamics and axon guidance. J Biophys Biochem Cytol 2019; 219:132731. [PMID: 31820781 PMCID: PMC7039193 DOI: 10.1083/jcb.201902088] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 09/25/2019] [Accepted: 10/25/2019] [Indexed: 02/08/2023] Open
Abstract
Appropriate axon guidance is necessary to form accurate neuronal connections. Axon guidance cues that stimulate cytoskeletal reorganization within the growth cone direct axon navigation. Filopodia at the growth cone periphery have long been considered sensors for axon guidance cues, yet how they respond to extracellular cues remains ill defined. Our previous work found that the filopodial actin polymerase VASP and consequently filopodial stability are negatively regulated via nondegradative TRIM9-dependent ubiquitination. Appropriate VASP ubiquitination and deubiquitination are required for axon turning in response to the guidance cue netrin-1. Here we show that the TRIM9-related protein TRIM67 outcompetes TRIM9 for interacting with VASP and antagonizes TRIM9-dependent VASP ubiquitination. The surprising antagonistic roles of two closely related E3 ubiquitin ligases are required for netrin-1-dependent filopodial responses, axon turning and branching, and fiber tract formation. We suggest a novel model in which coordinated regulation of VASP ubiquitination by a pair of interfering ligases is a critical element of VASP dynamics, filopodial stability, and axon guidance.
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Affiliation(s)
- Nicholas P. Boyer
- Neurobiology Curriculum, University of North Carolina, Chapel Hill, Chapel Hill, NC
| | - Laura E. McCormick
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, Chapel Hill, NC
| | - Shalini Menon
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, Chapel Hill, NC
| | - Fabio L. Urbina
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, Chapel Hill, NC
| | - Stephanie L. Gupton
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, Chapel Hill, NC,Neuroscience Center, University of North Carolina, Chapel Hill, Chapel Hill, NC,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, Chapel Hill, NC,Correspondence to Stephanie L. Gupton:
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218
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Zhao C, Rispe C, Nabity PD. Secretory RING finger proteins function as effectors in a grapevine galling insect. BMC Genomics 2019; 20:923. [PMID: 31795978 PMCID: PMC6892190 DOI: 10.1186/s12864-019-6313-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/20/2019] [Indexed: 11/10/2022] Open
Abstract
Background All eukaryotes share a conserved network of processes regulated by the proteasome and fundamental to growth, development, or perception of the environment, leading to complex but often predictable responses to stress. As a specialized component of the ubiquitin-proteasome system (UPS), the RING finger domain mediates protein-protein interactions and displays considerable versatility in regulating many physiological processes in plants. Many pathogenic organisms co-opt the UPS through RING-type E3 ligases, but little is known about how insects modify these integral networks to generate novel plant phenotypes. Results Using a combination of transcriptome sequencing and genome annotation of a grapevine galling species, Daktulosphaira vitifoliae, we identified 138 putatively secretory protein RING-type (SPRINGs) E3 ligases that showed structure and evolutionary signatures of genes under rapid evolution. Moreover, the majority of the SPRINGs were more expressed in the feeding stage than the non-feeding egg stage, in contrast to the non-secretory RING genes. Phylogenetic analyses indicated that the SPRINGs formed clusters, likely resulting from species-specific gene duplication and conforming to features of arthropod host-manipulating (effector) genes. To test the hypothesis that these SPRINGs evolved to manipulate cellular processes within the plant host, we examined SPRING interactions with grapevine proteins using the yeast two-hybrid assay. An insect SPRING interacted with two plant proteins, a cellulose synthase, CSLD5, and a ribosomal protein, RPS4B suggesting secretion reprograms host immune signaling, cell division, and stress response in favor of the insect. Plant UPS gene expression during gall development linked numerous processes to novel organogenesis. Conclusions Taken together, D. vitifoliae SPRINGs represent a novel gene expansion that evolved to interact with Vitis hosts. Thus, a pattern is emerging for gall forming insects to manipulate plant development through UPS targeting.
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Affiliation(s)
- Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | | | - Paul D Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
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219
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Gori Savellini G, Anichini G, Gandolfo C, Prathyumnan S, Cusi MG. Toscana virus non-structural protein NSs acts as E3 ubiquitin ligase promoting RIG-I degradation. PLoS Pathog 2019; 15:e1008186. [PMID: 31815967 PMCID: PMC6901176 DOI: 10.1371/journal.ppat.1008186] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 11/04/2019] [Indexed: 01/04/2023] Open
Abstract
It is known that the non-structural protein (NSs) of Toscana virus (TOSV), an emergent sandfly-borne virus causing meningitis or more severe central nervous system injuries in humans, exerts its function triggering RIG-I for degradation in a proteasome-dependent manner, thus breaking off the IFN-β production. The non-structural protein of different members of Bunyavirales has recently appeared as a fundamental protagonist in immunity evasion through ubiquitination-mediated protein degradation targets. We showed that TOSV NSs has an E3 ubiquitin ligase activity, mapping at the carboxy-terminal domain and also involving the amino-terminal of the protein. Indeed, neither the amino- (NSsΔN) nor the carboxy- (NSsΔC) terminal-deleted mutants of TOSV NSs were able to cause ubiquitin-mediated proteasome degradation of RIG-I. Moreover, the addition of the C-terminus of TOSV NSs to the homologous protein of the Sandfly Fever Naples Virus, belonging to the same genus and unable to inhibit IFN-β activity, conferred new properties to this protein, favoring RIG-I ubiquitination and its degradation. NSs lost its antagonistic activity to IFN when one of the terminal residues was missing. Therefore, we showed that NSs could behave as an atypical RING between RING (RBR) E3 ubiquitin ligases. This is the first report which identified the E3 ubiquitin ligase activity in a viral protein among negative strand RNA viruses.
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Affiliation(s)
| | - Gabriele Anichini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Claudia Gandolfo
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Maria Grazia Cusi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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220
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Research Progress on Plant RING-Finger Proteins. Genes (Basel) 2019; 10:genes10120973. [PMID: 31779262 PMCID: PMC6969932 DOI: 10.3390/genes10120973] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 11/21/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022] Open
Abstract
E3 ubiquitin ligases are the most expanded components of the ubiquitin proteasome system (UPS). They mediate the recognition of substrates and later transfer the ubiquitin (Ub) of the system. Really Interesting New Gene (RING) finger proteins characterized by the RING domain, which contains 40–60 residues, are thought to be E3 ubiquitin ligase. RING-finger proteins play significant roles in plant growth, stress resistance, and signal transduction. In this study, we mainly describe the structural characteristics, classifications, and subcellular localizations of RING-finger proteins, as well the physiological processes of RING-finger proteins in plant growth and development. We also summarize the functions of plant RING-finger proteins in plant stress resistance. Finally, further research on plant RING-finger proteins is suggested, thereby establishing a strong foundation for the future study of plant RING-finger proteins.
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221
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Wang F, Bach I. Rlim/Rnf12, Rex1, and X Chromosome Inactivation. Front Cell Dev Biol 2019; 7:258. [PMID: 31737626 PMCID: PMC6834644 DOI: 10.3389/fcell.2019.00258] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/16/2019] [Indexed: 12/28/2022] Open
Abstract
RLIM/Rnf12 is an E3 ubiquitin ligase that has originally been identified as a transcriptional cofactor associated with LIM domain transcription factors. Indeed, this protein modulates transcriptional activities and multiprotein complexes recruited by several classes of transcription factors thereby enhancing or repressing transcription. Around 10 years ago, RLIM/Rnf12 has been identified as a major regulator for the process of X chromosome inactivation (XCI), the transcriptional silencing of one of the two X chromosomes in female mice and ESCs. However, the precise roles of RLIM during XCI have been controversial. Here, we discuss the cellular and developmental functions of RLIM as an E3 ubiquitin ligase and its roles during XCI in conjunction with its target protein Rex1.
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Affiliation(s)
- Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA, United States
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222
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Zhu H, Li Y, Liu Y, Han B. Bivalent SMAC Mimetics for Treating Cancer by Antagonizing Inhibitor of Apoptosis Proteins. ChemMedChem 2019; 14:1951-1962. [DOI: 10.1002/cmdc.201900410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/10/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Hongping Zhu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of PharmacyChengdu University of Traditional Chinese Medicine 1166 Liutai Avenue Chengdu 611137 China
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Huaguan Road Chengdu 610052 China
| | - Yi Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Huaguan Road Chengdu 610052 China
| | - Yue Liu
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of AntibioticsChengdu University 168 Huaguan Road Chengdu 610052 China
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of PharmacyChengdu University of Traditional Chinese Medicine 1166 Liutai Avenue Chengdu 611137 China
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223
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Wang F, Chen X, Yu X, Lin Q. Degradation of CCNB1 mediated by APC11 through UBA52 ubiquitination promotes cell cycle progression and proliferation of non-small cell lung cancer cells. Am J Transl Res 2019; 11:7166-7185. [PMID: 31814919 PMCID: PMC6895529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE Mechanism by which CCNB1 regulates the cell cycle progression and its prognostic function in non-squamous non-small cell lung cancer (NSCLC) are necessary to be further elucidated. METHODS Data retrieved from gene expression omnibus (GEO) and cancer genome atlas (TCGA) combined with clinical data were used. Survival analysis was conducted in public datasets. Proteomics and co-immunoprecipation assays were designed to unravel proteins with interaction with CCNB1. Short hairpin RNA and small interfering RNA as well as overexpressing genes of interest were used. RESULTS CCNB1 was not implicated in apoptosis, migration and invasion of NSCLC cells. After either knockdown or overexpression of CCNB1, the occurrence of cell cycle arrest in G2/M phase, fewer cloning formation and diminished dimension of xenograft tumors were observed. CCNB1 expression level was clinically associated with several clinicopathological parameters including gender, smoking, T stage and N stage. Survival analysis showed that the higher level of CCNB1, the more dismal outcome in overall survival as well as in disease-free survival. Mechanistically, we confirmed that the role of CCNB1 on cell cycle and cloning formation was dependent on UBA52, which was able to promote degradation of CCNB1; nevertheless, this consequence relied on APC11. Knockdown of APC11 led to cell cycle arrest in G2/M and less cloning formation even in the presence of overexpressed UBA52. Following upregulation of APC11, the protein of CCNB1 degraded with resultant cell cycle progression and more cloning formation. CONCLUSION Degradation of CCNB1 by APC11 via UBA52 ubiquitylation was critical in cell cycle progression and proliferation of NSCLC cell lines.
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Affiliation(s)
- Fajiu Wang
- Department of Thoracic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Xi Chen
- Department of Thoracic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Xiaobo Yu
- Department of Thoracic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
| | - Qiang Lin
- Department of Thoracic Surgery, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University Shanghai, China
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224
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New Aspects of HECT-E3 Ligases in Cell Senescence and Cell Death of Plants. PLANTS 2019; 8:plants8110483. [PMID: 31717304 PMCID: PMC6918304 DOI: 10.3390/plants8110483] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/31/2019] [Accepted: 11/06/2019] [Indexed: 01/17/2023]
Abstract
Plant cells undergo massive orderly changes in structure, biochemistry, and gene expression during cell senescence. These changes cannot be distinguished from the hydrolysis/degradation function controlled by the ubiquitination pathway, autophagy, and various hydrolases in cells. In this mini-review, we summarized current research progress that the human HECT (homologous to the E6AP carboxyl terminus)-type ubiquitin E3 ligases have non-redundant functions in regulating specific signaling pathways, involved in a number of human diseases, especially aging-related diseases, through the influence of DNA repair, protein stability, and removal efficiency of damaged proteins or organelles. We further compared HECT E3 ligases’ structure and functions between plant and mammalian cells, and speculated new aspects acting as degrading signals and regulating signals of HECT E3 ligase in cell senescence and the cell death of plants.
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225
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UCHL3 Regulates Topoisomerase-Induced Chromosomal Break Repair by Controlling TDP1 Proteostasis. Cell Rep 2019; 23:3352-3365. [PMID: 29898404 PMCID: PMC6019701 DOI: 10.1016/j.celrep.2018.05.033] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 04/17/2018] [Accepted: 05/11/2018] [Indexed: 11/21/2022] Open
Abstract
Genomic damage can feature DNA-protein crosslinks whereby their acute accumulation is utilized to treat cancer and progressive accumulation causes neurodegeneration. This is typified by tyrosyl DNA phosphodiesterase 1 (TDP1), which repairs topoisomerase-mediated chromosomal breaks. Although TDP1 levels vary in multiple clinical settings, the mechanism underpinning this variation is unknown. We reveal that TDP1 is controlled by ubiquitylation and identify UCHL3 as the deubiquitylase that controls TDP1 proteostasis. Depletion of UCHL3 increases TDP1 ubiquitylation and turnover rate and sensitizes cells to TOP1 poisons. Overexpression of UCHL3, but not a catalytically inactive mutant, suppresses TDP1 ubiquitylation and turnover rate. TDP1 overexpression in the topoisomerase therapy-resistant rhabdomyosarcoma is driven by UCHL3 overexpression. In contrast, UCHL3 is downregulated in spinocerebellar ataxia with axonal neuropathy (SCAN1), causing elevated levels of TDP1 ubiquitylation and faster turnover rate. These data establish UCHL3 as a regulator of TDP1 proteostasis and, consequently, a fine-tuner of protein-linked DNA break repair. TDP1 proteostasis is controlled by a UCHL3-dependent ubiquitylation mechanism UCHL3 depletion sensitizes mammalian cells to TOP1 inhibitors Increased TDP1 protein in rhabdomyosarcoma is driven by UCHL3 upregulation Decreased TDP1 protein in spinocerebellar ataxia is driven by UCHL3 downregulation
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Shakeel S, Rajendra E, Alcón P, O'Reilly F, Chorev DS, Maslen S, Degliesposti G, Russo CJ, He S, Hill CH, Skehel JM, Scheres SHW, Patel KJ, Rappsilber J, Robinson CV, Passmore LA. Structure of the Fanconi anaemia monoubiquitin ligase complex. Nature 2019; 575:234-237. [PMID: 31666700 PMCID: PMC6858856 DOI: 10.1038/s41586-019-1703-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/18/2019] [Indexed: 11/17/2022]
Abstract
The Fanconi anaemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks, and responds to replication stress1,2. Genetic inactivation of this pathway by mutation of genes encoding FA complementation group (FANC) proteins impairs development, prevents blood production and promotes cancer1,3. The key molecular step in the FA pathway is the monoubiquitination of a pseudosymmetric heterodimer of FANCD2-FANCI4,5 by the FA core complex-a megadalton multiprotein E3 ubiquitin ligase6,7. Monoubiquitinated FANCD2 then recruits additional protein factors to remove the DNA crosslink or to stabilize the stalled replication fork. A molecular structure of the FA core complex would explain how it acts to maintain genome stability. Here we reconstituted an active, recombinant FA core complex, and used cryo-electron microscopy and mass spectrometry to determine its structure. The FA core complex comprises two central dimers of the FANCB and FA-associated protein of 100 kDa (FAAP100) subunits, flanked by two copies of the RING finger subunit, FANCL. These two heterotrimers act as a scaffold to assemble the remaining five subunits, resulting in an extended asymmetric structure. Destabilization of the scaffold would disrupt the entire complex, resulting in a non-functional FA pathway. Thus, the structure provides a mechanistic basis for the low numbers of patients with mutations in FANCB, FANCL and FAAP100. Despite a lack of sequence homology, FANCB and FAAP100 adopt similar structures. The two FANCL subunits are in different conformations at opposite ends of the complex, suggesting that each FANCL has a distinct role. This structural and functional asymmetry of dimeric RING finger domains may be a general feature of E3 ligases. The cryo-electron microscopy structure of the FA core complex provides a foundation for a detailed understanding of its E3 ubiquitin ligase activity and DNA interstrand crosslink repair.
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Affiliation(s)
| | | | - Pablo Alcón
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Francis O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Shaoda He
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Chris H Hill
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
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227
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Zheng SC, Chang XJ, Li WD, Wang H, Guo LM, Wang KJ, Liu HP. A novel RING finger protein CqRNF152-like with self-ubiquitination activity inhibits white spot syndrome virus infection in a crustacean Cherax quadricarinatus. FISH & SHELLFISH IMMUNOLOGY 2019; 94:934-943. [PMID: 31600596 DOI: 10.1016/j.fsi.2019.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/29/2019] [Accepted: 10/06/2019] [Indexed: 06/10/2023]
Abstract
Really Interesting New Gene (RING) finger proteins are highly conserved molecules that participate in a variety of biological processes such as regulation of development, apoptosis and antiviral immunity in vertebrates. However, the functions of RING finger proteins are still poorly understood in crustaceans. Previously, we found that the transcript of a homolog of RING finger protein 152 (CqRNF152-like) was up-regulated in a differentially expressed transcriptome library of the haematopietic tissue (Hpt) cells from red claw crayfish Cherax quadricarinatus upon white spot syndrome virus (WSSV) infection, which is one of the most devastating viral diseases for crustaceans like shrimp and crayfish. The full-length cDNA sequence of CqRNF152-like was then identified with 975 bp, including an ORF of 685 bp that encoded a 195 amino acids protein, a 5'- UTR of 180 bp, and a 3'-UTR with a poly (A) tail of 207 bp. The conserved domain prediction showed that CqRNF152-like contained a conserved RING-finger domain. Gene expression analysis showed that CqRNF152-like was distributed in all tissues examined and the transcript is significantly up-regulated after WSSV challenge both in vivo in Hpt tissue and in vitro in cultured Hpt cells. Furthermore, the transcripts of both an immediate early gene ie1 and a late envelope protein gene vp28 of WSSV were clearly increased in the Hpt tissues, hemocytes and cultured Hpt cells after gene silencing of CqRNF152-like, which were further proved to be significantly decreased after overloading of recombinant CqRNF152-like protein in Hpt cell cultures. Meanwhile, CqRNF152-like was found to bind with WSSV envelope protein VP28 by proteins pull-down assay. Similar to most of RNF proteins, CqRNF152-like protein sequence contained a conserved RING-finger domain and showed self-ubiquitination activity in a RING finger domain dependent manner. Taken together, CqRNF152-like is likely to function as an antiviral molecular against WSSV infection through interaction with the envelope protein VP28 in a crustacean C. quadricarinatus. This is the first report that a RING finger protein with directly antiviral functions via interaction with viral protein and self-ubiquitination activity in crustacean, which sheds new light on the molecular mechanism of WSSV infection and the control of white spot disease.
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Affiliation(s)
- Shu-Cheng Zheng
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Xue-Jiao Chang
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Wei-Dong Li
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hao Wang
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Li-Mei Guo
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Ke-Jian Wang
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Hai-Peng Liu
- State Key Laboratory of Marine Environmental Science, State-Province Joint Engineering Laboratory of Marine Bioproducts and Technology, Xiamen University, Xiamen, 361102, Fujian, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), China.
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228
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de la Rocha-Muñoz A, Núñez E, Arribas-González E, López-Corcuera B, Aragón C, de Juan-Sanz J. E3 ubiquitin ligases LNX1 and LNX2 are major regulators of the presynaptic glycine transporter GlyT2. Sci Rep 2019; 9:14944. [PMID: 31628376 PMCID: PMC6802383 DOI: 10.1038/s41598-019-51301-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 09/27/2019] [Indexed: 12/15/2022] Open
Abstract
The neuronal glycine transporter GlyT2 is an essential regulator of glycinergic neurotransmission that recaptures glycine in presynaptic terminals to facilitate transmitter packaging in synaptic vesicles. Alterations in GlyT2 expression or activity result in lower cytosolic glycine levels, emptying glycinergic synaptic vesicles and impairing neurotransmission. Lack of glycinergic neurotransmission caused by GlyT2 loss-of-function mutations results in Hyperekplexia, a rare neurological disease characterized by generalized stiffness and motor alterations that may cause sudden infant death. Although the importance of GlyT2 in pathology is known, how this transporter is regulated at the molecular level is poorly understood, limiting current therapeutic strategies. Guided by an unbiased screening, we discovered that E3 ubiquitin ligase Ligand of Numb proteins X1/2 (LNX1/2) modulate the ubiquitination status of GlyT2. The N-terminal RING-finger domain of LNX1/2 ubiquitinates a cytoplasmic C-terminal lysine cluster in GlyT2 (K751, K773, K787 and K791), and this process regulates the expression levels and transport activity of GlyT2. The genetic deletion of endogenous LNX2 in spinal cord primary neurons causes an increase in GlyT2 expression and we find that LNX2 is required for PKC-mediated control of GlyT2 transport. This work identifies, to our knowledge, the first E3 ubiquitin-ligases acting on GlyT2, revealing a novel molecular mechanism that controls presynaptic glycine availability. Providing a better understanding of the molecular regulation of GlyT2 may help future investigations into the molecular basis of human disease states caused by dysfunctional glycinergic neurotransmission, such as hyperekplexia and chronic pain.
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Affiliation(s)
- A de la Rocha-Muñoz
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
- IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - E Núñez
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
- IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - E Arribas-González
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, 28002, Madrid, Spain
| | - B López-Corcuera
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain
- IdiPAZ, Hospital Universitario La Paz, Madrid, Spain
| | - C Aragón
- Centro de Biología Molecular "Severo Ochoa", Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, 28049, Madrid, Spain.
- IdiPAZ, Hospital Universitario La Paz, Madrid, Spain.
| | - J de Juan-Sanz
- Sorbonne Université and Institut du Cerveau et de la Moelle Epinière (ICM) - Hôpital Pitié-Salpêtrière, Inserm, CNRS, Paris, France.
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229
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Xing G, Jing H, Zhang L, Cao Y, Li L, Zhao K, Dong Z, Chen W, Wang H, Cao R, Xiong WC, Mei L. A mechanism in agrin signaling revealed by a prevalent Rapsyn mutation in congenital myasthenic syndrome. eLife 2019; 8:e49180. [PMID: 31549961 PMCID: PMC6779466 DOI: 10.7554/elife.49180] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Neuromuscular junction is a synapse between motoneurons and skeletal muscles, where acetylcholine receptors (AChRs) are concentrated to control muscle contraction. Studies of this synapse have contributed to our understanding of synapse assembly and pathological mechanisms of neuromuscular disorders. Nevertheless, underlying mechanisms of NMJ formation was not well understood. To this end, we took a novel approach - studying mutant genes implicated in congenital myasthenic syndrome (CMS). We showed that knock-in mice carrying N88K, a prevalent CMS mutation of Rapsyn (Rapsn), died soon after birth with profound NMJ deficits. Rapsn is an adapter protein that bridges AChRs to the cytoskeleton and possesses E3 ligase activity. In investigating how N88K impairs the NMJ, we uncovered a novel signaling pathway by which Agrin-LRP4-MuSK induces tyrosine phosphorylation of Rapsn, which is required for its self-association and E3 ligase activity. Our results also provide insight into pathological mechanisms of CMS.
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Affiliation(s)
- Guanglin Xing
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Hongyang Jing
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Lei Zhang
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Yu Cao
- Department of Neuroscience and Regenerative MedicineAugusta UniversityAugustaUnited States
| | - Lei Li
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Kai Zhao
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
- Department of Neuroscience and Regenerative MedicineAugusta UniversityAugustaUnited States
| | - Zhaoqi Dong
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Wenbing Chen
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Hongsheng Wang
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Rangjuan Cao
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
| | - Wen-Cheng Xiong
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
- Louis Stokes Cleveland Veterans Affairs Medical CenterClevelandUnited States
| | - Lin Mei
- Department of Neurosciences, School of MedicineCase Western Reserve UniversityClevelandUnited States
- Louis Stokes Cleveland Veterans Affairs Medical CenterClevelandUnited States
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230
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Kwon D, Kim SM, Jacob P, Liu Y, Correia MA. Induction via Functional Protein Stabilization of Hepatic Cytochromes P450 upon gp78/Autocrine Motility Factor Receptor (AMFR) Ubiquitin E3-Ligase Genetic Ablation in Mice: Therapeutic and Toxicological Relevance. Mol Pharmacol 2019; 96:641-654. [PMID: 31492698 DOI: 10.1124/mol.119.117069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/22/2019] [Indexed: 02/06/2023] Open
Abstract
The hepatic endoplasmic reticulum (ER)-anchored monotopic proteins, cytochromes P450 (P450s), are enzymes that metabolize endobiotics (physiologically active steroids and fatty acids), as well as xenobiotics including therapeutic/chemotherapeutic drugs, nutrients, carcinogens, and toxins. Alterations of hepatic P450 content through synthesis, inactivation, or proteolytic turnover influence their metabolic function. P450 proteolytic turnover occurs via ER-associated degradation (ERAD) involving ubiquitin (Ub)-dependent proteasomal degradation (UPD) as a major pathway. UPD critically involves P450 protein ubiquitination by E2/E3 Ub-ligase complexes. We have previously identified the ER-polytopic gp78/AMFR (autocrine motility factor receptor) as a relevant E3 in CYP3A4, CYP3A23, and CYP2E1 UPD. We now document that liver-conditional genetic ablation of gp78/AMFR in male mice disrupts P450 ERAD, resulting in statistically significant stabilization of Cyp2a5 and Cyp2c, in addition to that of Cyp3a and Cyp2e1. More importantly, we establish that such stabilization is of the functionally active P450 proteins, leading to corresponding statistically significant enhancement of their drug-metabolizing capacities. Our findings, with clinically relevant therapeutic drugs (nicotine, coumarin, chlorzoxazone, and acetaminophen) and the prodrug (tamoxifen) as P450 substrates, reveal that P450 ERAD disruption could influence therapeutic drug response and/or toxicity, warranting serious consideration as a potential source of clinically relevant drug-drug interactions (DDIs). Because gp78/AMFR is not only an E3 Ub-ligase, but also a cell-surface prometastatic oncogene that is upregulated in various malignant cancers, our finding that hepatic gp78/AMFR knockout can enhance P450-dependent bioactivation of relevant cancer chemotherapeutic prodrugs is of therapeutic relevance and noteworthy in prospective drug design and development. SIGNIFICANCE STATEMENT: The cell-surface and ER transmembrane protein gp78/AMFR, a receptor for the prometastatic autocrine motility factor (AMF), as well as an E3 ubiquitin-ligase involved in the ER-associated degradation (ERAD) of not only the tumor metastatic suppressor KAI1 but also of hepatic cytochromes P450, is upregulated in various human cancers, enhancing their invasiveness, metastatic potential, and poor prognosis. Liver-specific gp78/AMFR genetic ablation results in functional protein stabilization of several hepatic P450s and consequently enhanced drug and prodrug metabolism, a feature that could be therapeutically exploited in the bioactivation of chemotherapeutic prodrugs through design and development of novel short-term gp78/AMFR chemical inhibitors.
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Affiliation(s)
- Doyoung Kwon
- Departments of Cellular and Molecular Pharmacology (D.K., S.-M.K., Y.L., M.A.C.), Pharmaceutical Chemistry (M.A.C.), and Bioengineering and Therapeutic Sciences (M.A.C.) and The Liver Center (M.A.C.), University of California San Francisco, San Francisco, California; and Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, Center for Tobacco Control Research and Education, University of California, San Francisco, California (P.J.)
| | - Sung-Mi Kim
- Departments of Cellular and Molecular Pharmacology (D.K., S.-M.K., Y.L., M.A.C.), Pharmaceutical Chemistry (M.A.C.), and Bioengineering and Therapeutic Sciences (M.A.C.) and The Liver Center (M.A.C.), University of California San Francisco, San Francisco, California; and Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, Center for Tobacco Control Research and Education, University of California, San Francisco, California (P.J.)
| | - Peyton Jacob
- Departments of Cellular and Molecular Pharmacology (D.K., S.-M.K., Y.L., M.A.C.), Pharmaceutical Chemistry (M.A.C.), and Bioengineering and Therapeutic Sciences (M.A.C.) and The Liver Center (M.A.C.), University of California San Francisco, San Francisco, California; and Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, Center for Tobacco Control Research and Education, University of California, San Francisco, California (P.J.)
| | - Yi Liu
- Departments of Cellular and Molecular Pharmacology (D.K., S.-M.K., Y.L., M.A.C.), Pharmaceutical Chemistry (M.A.C.), and Bioengineering and Therapeutic Sciences (M.A.C.) and The Liver Center (M.A.C.), University of California San Francisco, San Francisco, California; and Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, Center for Tobacco Control Research and Education, University of California, San Francisco, California (P.J.)
| | - Maria Almira Correia
- Departments of Cellular and Molecular Pharmacology (D.K., S.-M.K., Y.L., M.A.C.), Pharmaceutical Chemistry (M.A.C.), and Bioengineering and Therapeutic Sciences (M.A.C.) and The Liver Center (M.A.C.), University of California San Francisco, San Francisco, California; and Clinical Pharmacology Program, Division of Cardiology, Department of Medicine, Center for Tobacco Control Research and Education, University of California, San Francisco, California (P.J.)
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231
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Vivelo CA, Ayyappan V, Leung AKL. Poly(ADP-ribose)-dependent ubiquitination and its clinical implications. Biochem Pharmacol 2019; 167:3-12. [PMID: 31077644 PMCID: PMC6702056 DOI: 10.1016/j.bcp.2019.05.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/04/2019] [Indexed: 12/11/2022]
Abstract
ADP-ribosylation-the addition of one or multiple ADP-ribose units onto proteins-is a therapeutically important post-translational modification implicated in cancer, neurodegeneration, and infectious diseases. The protein modification regulates a broad range of biological processes, including DNA repair, transcription, RNA metabolism, and the structural integrity of nonmembranous structures. The polymeric form of ADP-ribose, poly(ADP-ribose), was recently identified as a signal for triggering protein degradation through the ubiquitin-proteasome system. Using informatics analyses, we found that these ubiquitinated substrates tend to be low abundance proteins, which may serve as rate-limiting factors within signaling networks or metabolic processes. In this review, we summarize the current literature on poly(ADP-ribose)-dependent ubiquitination (PARdU) regarding its biological mechanisms, substrates, and relevance to diseases.
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Affiliation(s)
- Christina A Vivelo
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Vinay Ayyappan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA; Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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232
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Protein engineering of a ubiquitin-variant inhibitor of APC/C identifies a cryptic K48 ubiquitin chain binding site. Proc Natl Acad Sci U S A 2019; 116:17280-17289. [PMID: 31350353 DOI: 10.1073/pnas.1902889116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ubiquitin (Ub)-mediated proteolysis is a fundamental mechanism used by eukaryotic cells to maintain homeostasis and protein quality, and to control timing in biological processes. Two essential aspects of Ub regulation are conjugation through E1-E2-E3 enzymatic cascades and recognition by Ub-binding domains. An emerging theme in the Ub field is that these 2 properties are often amalgamated in conjugation enzymes. In addition to covalent thioester linkage to Ub's C terminus for Ub transfer reactions, conjugation enzymes often bind noncovalently and weakly to Ub at "exosites." However, identification of such sites is typically empirical and particularly challenging in large molecular machines. Here, studying the 1.2-MDa E3 ligase anaphase-promoting complex/cyclosome (APC/C), which controls cell division and many aspects of neurobiology, we discover a method for identifying unexpected Ub-binding sites. Using a panel of Ub variants (UbVs), we identify a protein-based inhibitor that blocks Ub ligation to APC/C substrates in vitro and ex vivo. Biochemistry, NMR, and cryo-electron microscopy (cryo-EM) structurally define the UbV interaction, explain its inhibitory activity through binding the surface on the APC2 subunit that recruits the E2 enzyme UBE2C, and ultimately reveal that this APC2 surface is also a Ub-binding exosite with preference for K48-linked chains. The results provide a tool for probing APC/C activity, have implications for the coordination of K48-linked Ub chain binding by APC/C with the multistep process of substrate polyubiquitylation, and demonstrate the power of UbV technology for identifying cryptic Ub-binding sites within large multiprotein complexes.
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233
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The mammalian CTLH complex is an E3 ubiquitin ligase that targets its subunit muskelin for degradation. Sci Rep 2019; 9:9864. [PMID: 31285494 PMCID: PMC6614414 DOI: 10.1038/s41598-019-46279-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022] Open
Abstract
The multi-subunit C-terminal to LisH (CTLH) complex is the mammalian homologue of the yeast Gid E3 ubiquitin ligase complex. In this study, we investigated the human CTLH complex and characterized its E3 ligase activity. We confirm that the complex immunoprecipitated from human cells comprises RanBPM, ARMC8 α/β, muskelin, WDR26, GID4 and the RING domain proteins RMND5A and MAEA. We find that loss of expression of individual subunits compromises the stability of other complex members and that MAEA and RMND5A protein levels are interdependent. Using in vitro ubiquitination assays, we demonstrate that the CTLH complex has E3 ligase activity which is dependent on RMND5A and MAEA. We report that the complex can pair with UBE2D1, UBE2D2 and UBE2D3 E2 enzymes and that recombinant RMND5A mediates K48 and K63 poly-ubiquitin chains. Finally, we show a proteasome-dependent increase in the protein levels of CTLH complex member muskelin in RMND5A KO cells. Furthermore, muskelin ubiquitination is dependent on RMND5A, suggesting that it may be a target of the complex. Overall, we further the characterization of the CTLH complex as an E3 ubiquitin ligase complex in human cells and reveal a potential autoregulation mechanism.
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234
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Deol KK, Lorenz S, Strieter ER. Enzymatic Logic of Ubiquitin Chain Assembly. Front Physiol 2019; 10:835. [PMID: 31333493 PMCID: PMC6624479 DOI: 10.3389/fphys.2019.00835] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Protein ubiquitination impacts virtually every biochemical pathway in eukaryotic cells. The fate of a ubiquitinated protein is largely dictated by the type of ubiquitin modification with which it is decorated, including a large variety of polymeric chains. As a result, there have been intense efforts over the last two decades to dissect the molecular details underlying the synthesis of ubiquitin chains by ubiquitin-conjugating (E2) enzymes and ubiquitin ligases (E3s). In this review, we highlight these advances. We discuss the evidence in support of the alternative models of transferring one ubiquitin at a time to a growing substrate-linked chain (sequential addition model) versus transferring a pre-assembled ubiquitin chain (en bloc model) to a substrate. Against this backdrop, we outline emerging principles of chain assembly: multisite interactions, distinct mechanisms of chain initiation and elongation, optimal positioning of ubiquitin molecules that are ultimately conjugated to each other, and substrate-assisted catalysis. Understanding the enzymatic logic of ubiquitin chain assembly has important biomedical implications, as the misregulation of many E2s and E3s and associated perturbations in ubiquitin chain formation contribute to human disease. The resurgent interest in bifunctional small molecules targeting pathogenic proteins to specific E3s for polyubiquitination and subsequent degradation provides an additional incentive to define the mechanisms responsible for efficient and specific chain synthesis and harness them for therapeutic benefit.
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Affiliation(s)
- Kirandeep K Deol
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg, Germany
| | - Eric R Strieter
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States.,Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, United States
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235
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Vidal M. Polycomb Assemblies Multitask to Regulate Transcription. EPIGENOMES 2019; 3:12. [PMID: 34968234 PMCID: PMC8594731 DOI: 10.3390/epigenomes3020012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 02/06/2023] Open
Abstract
The Polycomb system is made of an evolutionary ancient group of proteins, present throughout plants and animals. Known initially from developmental studies with the fly Drosophila melanogaster, they were associated with stable sustainment of gene repression and maintenance of cell identity. Acting as multiprotein assemblies with an ability to modify chromatin, through chemical additions to histones and organization of topological domains, they have been involved subsequently in control of developmental transitions and in cell homeostasis. Recent work has unveiled an association of Polycomb components with transcriptionally active loci and the promotion of gene expression, in clear contrast with conventional recognition as repressors. Focusing on mammalian models, I review here advances concerning roles in transcriptional control. Among new findings highlighted is the regulation of their catalytic properties, recruiting to targets, and activities in chromatin organization and compartmentalization. The need for a more integrated approach to the study of the Polycomb system, given its fundamental complexity and its adaptation to cell context, is discussed.
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Affiliation(s)
- Miguel Vidal
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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236
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Liess AKL, Kucerova A, Schweimer K, Yu L, Roumeliotis TI, Diebold M, Dybkov O, Sotriffer C, Urlaub H, Choudhary JS, Mansfeld J, Lorenz S. Autoinhibition Mechanism of the Ubiquitin-Conjugating Enzyme UBE2S by Autoubiquitination. Structure 2019; 27:1195-1210.e7. [PMID: 31230944 DOI: 10.1016/j.str.2019.05.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/01/2019] [Accepted: 05/17/2019] [Indexed: 12/16/2022]
Abstract
Ubiquitin-conjugating enzymes (E2s) govern key aspects of ubiquitin signaling. Emerging evidence suggests that the activities of E2s are modulated by posttranslational modifications; the structural underpinnings, however, are largely unclear. Here, we unravel the structural basis and mechanistic consequences of a conserved autoubiquitination event near the catalytic center of E2s, using the human anaphase-promoting complex/cyclosome-associated UBE2S as a model system. Crystal structures we determined of the catalytic ubiquitin carrier protein domain combined with MD simulations reveal that the active-site region is malleable, which permits an adjacent ubiquitin acceptor site, Lys+5, to be ubiquitinated intramolecularly. We demonstrate by NMR that the Lys+5-linked ubiquitin inhibits UBE2S by obstructing its reloading with ubiquitin. By immunoprecipitation, quantitative mass spectrometry, and siRNA-and-rescue experiments we show that Lys+5 ubiquitination of UBE2S decreases during mitotic exit but does not influence proteasomal turnover of this E2. These findings suggest that UBE2S activity underlies inherent regulation during the cell cycle.
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Affiliation(s)
- Anna K L Liess
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany
| | - Alena Kucerova
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | | | - Lu Yu
- Functional Proteomics Group, The Institute of Cancer Research, London SW3 6JB, UK
| | | | - Mathias Diebold
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Olexandr Dybkov
- Department for Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077 Göttingen, Germany
| | - Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, University of Würzburg, 97074 Würzburg, Germany
| | - Henning Urlaub
- Group for Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, 37077 Göttingen, Germany; Proteomics Service Facility, Georg-August-Universität, Göttingen, 37077 Göttingen, Germany
| | - Jyoti S Choudhary
- Functional Proteomics Group, The Institute of Cancer Research, London SW3 6JB, UK
| | - Jörg Mansfeld
- Cell Cycle, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080 Würzburg, Germany.
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237
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Gerez JA, Prymaczok NC, Rockenstein E, Herrmann US, Schwarz P, Adame A, Enchev RI, Courtheoux T, Boersema PJ, Riek R, Peter M, Aguzzi A, Masliah E, Picotti P. A cullin-RING ubiquitin ligase targets exogenous α-synuclein and inhibits Lewy body-like pathology. Sci Transl Med 2019; 11:eaau6722. [PMID: 31167929 PMCID: PMC10697662 DOI: 10.1126/scitranslmed.aau6722] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/16/2018] [Accepted: 05/08/2019] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD) is a neurological disorder characterized by the progressive accumulation of neuronal α-synuclein (αSyn) inclusions called Lewy bodies. It is believed that Lewy bodies spread throughout the nervous system due to the cell-to-cell propagation of αSyn via cycles of secretion and uptake. Here, we investigated the internalization and intracellular accumulation of exogenous αSyn, two key steps of Lewy body pathogenesis, amplification and spreading. We found that stable αSyn fibrils substantially accumulate in different cell lines upon internalization, whereas αSyn monomers, oligomers, and dissociable fibrils do not. Our data indicate that the uptake-mediated accumulation of αSyn in a human-derived neuroblastoma cell line triggered an adaptive response that involved proteins linked to ubiquitin ligases of the S-phase kinase-associated protein 1 (SKP1), cullin-1 (Cul1), and F-box domain-containing protein (SCF) family. We found that SKP1, Cul1, and the F-box/LRR repeat protein 5 (FBXL5) colocalized and physically interacted with internalized αSyn in cultured cells. Moreover, the SCF containing the F-box protein FBXL5 (SCFFBXL5) catalyzed αSyn ubiquitination in reconstitution experiments in vitro using recombinant proteins and in cultured cells. In the human brain, SKP1 and Cul1 were recruited into Lewy bodies from brainstem and neocortex of patients with PD and related neurological disorders. In both transgenic and nontransgenic mice, intracerebral administration of exogenous αSyn fibrils triggered a Lewy body-like pathology, which was amplified by SKP1 or FBXL5 loss of function. Our data thus indicate that SCFFXBL5 regulates αSyn in vivo and that SCF ligases may constitute targets for the treatment of PD and other α-synucleinopathies.
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Affiliation(s)
- Juan A Gerez
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Natalia C Prymaczok
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Edward Rockenstein
- Department of Neurosciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Uli S Herrmann
- Institute of Neuropathology, University Hospital Zurich, Zurich CH-8091, Switzerland
| | - Petra Schwarz
- Institute of Neuropathology, University Hospital Zurich, Zurich CH-8091, Switzerland
| | - Anthony Adame
- Department of Neurosciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Radoslav I Enchev
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Thibault Courtheoux
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Paul J Boersema
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Matthias Peter
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, Zurich CH-8091, Switzerland
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, San Diego, CA 92093, USA
| | - Paola Picotti
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
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238
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Anandapadamanaban M, Kyriakidis NC, Csizmók V, Wallenhammar A, Espinosa AC, Ahlner A, Round AR, Trewhella J, Moche M, Wahren-Herlenius M, Sunnerhagen M. E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2. J Biol Chem 2019; 294:11404-11419. [PMID: 31160341 DOI: 10.1074/jbc.ra119.008485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/28/2019] [Indexed: 12/23/2022] Open
Abstract
The E3 ubiquitin-protein ligase TRIM21, of the RING-containing tripartite motif (TRIM) protein family, is a major autoantigen in autoimmune diseases and a modulator of innate immune signaling. Together with ubiquitin-conjugating enzyme E2 E1 (UBE2E1), TRIM21 acts both as an E3 ligase and as a substrate in autoubiquitination. We here report a 2.82-Å crystal structure of the human TRIM21 RING domain in complex with the human E2-conjugating UBE2E1 enzyme, in which a ubiquitin-targeted TRIM21 substrate lysine was captured in the UBE2E1 active site. The structure revealed that the direction of lysine entry is similar to that described for human proliferating cell nuclear antigen (PCNA), a small ubiquitin-like modifier (SUMO)-targeted substrate, and thus differs from the canonical SUMO-targeted substrate entry. In agreement, we found that critical UBE2E1 residues involved in the capture of the TRIM21 substrate lysine are conserved in ubiquitin-conjugating E2s, whereas residues critical for SUMOylation are not conserved. We noted that coordination of the acceptor lysine leads to remodeling of amino acid side-chain interactions between the UBE2E1 active site and the E2-E3 direct interface, including the so-called "linchpin" residue conserved in RING E3s and required for ubiquitination. The findings of our work support the notion that substrate lysine activation of an E2-E3-connecting allosteric path may trigger catalytic activity and contribute to the understanding of specific lysine targeting by ubiquitin-conjugating E2s.
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Affiliation(s)
| | - Nikolaos C Kyriakidis
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden.,Escuela de Medicina, Facultad de Ciencias de la Salud, Grupo de Investigación en Biotecnología Aplicada a Biomedicina (BIOMED), Universidad de Las Américas (UDLA), Quito, EC170504 Ecuador
| | - Veronika Csizmók
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Amélie Wallenhammar
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Alexander C Espinosa
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Alexandra Ahlner
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
| | - Adam R Round
- European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France
| | - Jill Trewhella
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden.,School of Life and Environmental Sciences (SoLES), The University of Sydney, New South Wales 2006, Australia
| | - Martin Moche
- Department of Medical Biochemistry and Biophysics, Protein Science Facility, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Unit of Experimental Rheumatology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Maria Sunnerhagen
- Department of Physics, Chemistry and Biology, Division of Chemistry, Linköping University, SE-58183 Linköping, Sweden
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239
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Liu H, Mintern JD, Villadangos JA. MARCH ligases in immunity. Curr Opin Immunol 2019; 58:38-43. [PMID: 31063934 DOI: 10.1016/j.coi.2019.03.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/06/2019] [Indexed: 01/13/2023]
Abstract
Membrane associated RING-CH (MARCH) ubiquitin ligases control the stability, trafficking and function of important immunoreceptors, including MHC molecules and costimulatory molecule CD86. Regulation of the critical antigen presenting molecule MHC II by MARCH1 and the control of MARCH1 expression by inflammatory stimuli is a key step in the function of antigen presenting cells. MHC II ubiquitination by MARCH8 and CD83 plays a critical role in T cell thymic selection. Recent studies reveal new immune functions of MARCH ligases in innate immunity, regulation of FcγR expression and Treg development. In addition, we review the importance of MARCH in immunomodulation at the host-pathogen interface. Both bacterial and viral pathogens manipulate MARCH function, while MARCH ligases act as an important host anti-viral defence mechanism. Here, we review the role of membrane-bound MARCH ligases in immune function and provide an update on new substrates and concepts. Understanding the increasingly complex roles of MARCH E3 ligases will be vital to develop therapeutic strategies for their regulation.
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Affiliation(s)
- Haiyin Liu
- The Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Justine D Mintern
- The Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Jose A Villadangos
- The Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia; The Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Parkville, Victoria 3010, Australia.
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240
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Hacker K, Benke S, Agerer B, Scinicariello S, Budroni V, Versteeg GA. A repetitive acidic region contributes to the extremely rapid degradation of the cell-context essential protein TRIM52. Sci Rep 2019; 9:7901. [PMID: 31133683 PMCID: PMC6536530 DOI: 10.1038/s41598-019-44359-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022] Open
Abstract
Tripartite motif protein 52 (TRIM52) is a non-canonical TRIM family member harbouring the largest RING domain encoded in the human genome. In humans TRIM52 is conserved and has been under positive selection pressure, yet it has been lost in many non-primates. Competitive cell fitness assays demonstrated that TRIM52 ablation reduces cellular fitness in multiple different cell types. To better understand how this cell-essential factor is controlled, we investigated how expression of this non-canonical protein is regulated. Here, we show that TRIM52 mRNA is constitutively expressed from an intergenic region preceding the TRIM52 gene. Yet, TRIM52 protein is rapidly turned-over by the proteasome with a 3.5-minute half-life, one of the shortest in the human proteome. Consistent with this extremely rapid degradation rate, all three TRIM52 domains were identified to contribute to its instability. Intriguingly, a repetitive acidic loop in the RING domain was identified as one of the main destabilizing regions, which was unexpected given the prevailing notion that these sequences are poor proteasome substrates. This work indicates that the effect of such repetitive acidic regions on proteasomal degradation depends on the protein context, and it identifies TRIM52 as an attractive model protein to study what these contextual properties are.
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Affiliation(s)
- Kathrin Hacker
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Stefan Benke
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Benedikt Agerer
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT25.3, 1090, Vienna, Austria
| | - Sara Scinicariello
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Valentina Budroni
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Gijs A Versteeg
- Department of Microbiology, Immunobiology, and Genetics, Max F. Perutz Laboratories (MFPL), University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030, Vienna, Austria.
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241
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Park KR, Yun JS, Park MH, Jung YY, Yeo IJ, Nam KT, Kim HD, Song JK, Choi DY, Park PH, Han SB, Yun HM, Hong JT. Loss of parkin reduces lung tumor development by blocking p21 degradation. PLoS One 2019; 14:e0217037. [PMID: 31112565 PMCID: PMC6528990 DOI: 10.1371/journal.pone.0217037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 05/02/2019] [Indexed: 12/24/2022] Open
Abstract
Several epidemiological studies have demonstrated the reciprocal relationship between the development of cancer and Parkinson’s disease (PD). However, the possible mechanisms underlying this relationship remain unclear. To identify this relationship, we first compared lung tumor growth in parkin knockout (KO) mice and wild-type (WT) mice. Parkin KO mice showed decreased lung tumor growth and increased expression of p21, a cell cycle arrester, as compared with WT mice. We also found that parkin interacts with p21, resulting in its degradation; however, parkin KO, knockdown, as well as mutation (R275W or G430D) reduced the degradation of p21. We investigated whether parkin KO increases the association of p21 with proliferating cell nuclear antigen (PCNA) or CDK2 by reducing p21 degradation, and, thus, arresting the cell cycle. The interaction between p21 and PCNA or CDK2 was also enhanced by parkin knockdown, and this increased interaction induced sub G0/G1 arrest, leading to cell death. Therefore, our data indicate that parkin KO reduces the development of lung tumors via cell cycle arrest by blocking the degradation of p21. These findings suggest that PD could be associated with lower lung cancer incidence.
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Affiliation(s)
- Kyung-Ran Park
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Kyung Hee University, Dongdaemun-Gu, Seoul, Republic of Korea
| | - Jae Suk Yun
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
| | - Mi Hee Park
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
| | - Yu Yeon Jung
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
| | - In Jun Yeo
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
| | - Kyung Tak Nam
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
| | - Hae Deun Kim
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
| | - Ju Kyoung Song
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
| | - Dong-Young Choi
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Pil-Hoon Park
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Sang-Bae Han
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
| | - Hyung-Mun Yun
- Department of Oral and Maxillofacial Pathology, School of Dentistry, Kyung Hee University, Dongdaemun-Gu, Seoul, Republic of Korea
- * E-mail: (JTH); (HMY)
| | - Jin Tae Hong
- College of Pharmacy and Medical Research Center, Chungbuk National University, Osong-eup, Heungduk-gu, Cheongju, Chungbuk, Republic of Korea
- * E-mail: (JTH); (HMY)
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242
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Chen I, Chang J, Wu C, Huang Y, Hsu Y, Tsai C. An E3 ubiquitin ligase from Nicotiana benthamiana targets the replicase of Bamboo mosaic virus and restricts its replication. MOLECULAR PLANT PATHOLOGY 2019; 20:673-684. [PMID: 30924604 PMCID: PMC6637893 DOI: 10.1111/mpp.12784] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
One up-regulated host gene identified previously was found involved in the infection process of Bamboo mosaic virus (BaMV), a single-stranded positive-sense RNA virus. The full length cDNA of this gene was cloned by 5' and 3'-rapid amplification of cDNA ends and found to encode a polypeptide containing a conserved really interesting new gene (RING) domain and a transmembrane domain. The gene might function as an ubiquitin E3 ligase. We designated this protein in Nicotiana benthamiana as ubiquitin E3 ligase containing RING domain 1 (NbUbE3R1). Further characterization by using Tobacco rattle virus-based virus-induced gene silencing (loss-of-function) revealed that increased BaMV accumulation was in both knockdown plants and protoplasts. The gene might have a defensive role in the replication step of BaMV infection. To further inspect the functional role of NbUbE3R1 in BaMV accumulation, NbUbE3R1 was expressed in N. benthamiana plants. The wild-type NbUbE3R1-orange fluorescent protein (NbUbE3R1-OFP), NbUbE3R1/△TM-OFP (removal of the transmembrane domain) and NbUbE3R1/mRING-OFP (mutation at the RING domain, the E2 interaction site) were transiently expressed in plants. NbUbE3R1 and its derivatives all functioned in restricting the accumulation of BaMV. The common feature of these constructs was the intact substrate-interacting domain. Yeast two-hybrid and co-immunoprecipitation experiments used to determine the possible viral-encoded substrate of NbUbE3R1 revealed the replicase of BaMV as the possible substrate. In conclusion, we identified an up-regulated gene, NbUbE3R1 that plays a role in BaMV replication.
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Affiliation(s)
- I‐Hsuan Chen
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Jui‐En Chang
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Chen‐Yu Wu
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Ying‐Ping Huang
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
| | - Yau‐Huei Hsu
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichung402Taiwan
| | - Ching‐Hsiu Tsai
- Graduate Institute of BiotechnologyNational Chung Hsing UniversityTaichung402Taiwan
- Advanced Plant Biotechnology CenterNational Chung Hsing UniversityTaichung402Taiwan
- Research Center for Sustainable Energy and NanotechnologyNational Chung Hsing UniversityTaichung402Taiwan
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243
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Stevens RV, Esposito D, Rittinger K. Characterisation of class VI TRIM RING domains: linking RING activity to C-terminal domain identity. Life Sci Alliance 2019; 2:2/3/e201900295. [PMID: 31028095 PMCID: PMC6487577 DOI: 10.26508/lsa.201900295] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 12/22/2022] Open
Abstract
TRIM E3 ubiquitin ligases regulate multiple cellular processes, and their dysfunction is linked to disease. They are characterised by a conserved N-terminal tripartite motif comprising a RING, B-box domains, and a coiled-coil region, with C-terminal domains often mediating substrate recruitment. TRIM proteins are grouped into 11 classes based on C-terminal domain identity. Class VI TRIMs, TRIM24, TRIM33, and TRIM28, have been described as transcriptional regulators, a function linked to their C-terminal plant homeodomain and bromodomain, and independent of their ubiquitination activity. It is unclear whether E3 ligase activity is regulated in family members where the C-terminal domains function independently. Here, we provide a detailed biochemical characterisation of the RING domains of class VI TRIMs and describe the solution structure of the TRIM28 RING. Our study reveals a lack of activity of the isolated RING domains, which may be linked to the absence of self-association. We propose that class VI TRIMs exist in an inactive state and require additional regulatory events to stimulate E3 ligase activity, ensuring that associated chromatin-remodelling factors are not injudiciously degraded.
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Affiliation(s)
- Rebecca V Stevens
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Diego Esposito
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK
| | - Katrin Rittinger
- Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK
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244
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Liu H, Lu W, He H, Wu J, Zhang C, Gong H, Yang C. Inflammation-dependent overexpression of c-Myc enhances CRL4 DCAF4 E3 ligase activity and promotes ubiquitination of ST7 in colitis-associated cancer. J Pathol 2019; 248:464-475. [PMID: 30945288 DOI: 10.1002/path.5273] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 03/04/2019] [Accepted: 04/01/2019] [Indexed: 02/05/2023]
Abstract
Inflammation is well known as an important driver of the initiation of colitis-associated cancer (CAC). Some cytokines, such as IL-6 and TNF-α can activate expression of the oncogene c-Myc (MYC) and regulate its downstream effects. Cullin-RING E3 Ligases (CRLs) are emerging as master regulators controlling tumorigenesis. Here, we demonstrate that two cullin genes, CUL4A and CUL4B, but not other members, are specifically overexpressed in CAC tumour samples and positively correlate with levels of the proinflammatory cytokines IL-1β and IL-6. In vitro experiments revealed that the transcription factor c-Myc can specifically activate the expression of CUL4A and CUL4B by binding to a conserved site (CACGTG) located in their promoters. Additionally, we found that both CUL4A and CUL4B can form an E3 complex with DNA damage-binding protein 1 (DDB1) and DDB1-CUL4-associated factor 4 (DCAF4). In vitro and in vivo ubiquitination analyses indicate that CRL4DCAF4 E3 ligase specifically directs degradation of ST7 (suppression of tumorigenicity 7). Overexpression of c-Myc in human colon epithelial cells resulted in the accumulation of CUL4A, CUL4B and DCAF4, but degradation of ST7. In contrast, knockdown of c-Myc, CUL4A or CUL4B in the colon adenocarcinoma cell line HT29 caused accumulation of ST7 and inhibition of cell proliferation, colony formation ability and in vivo tumour growth. Collectively, our results provide in vitro and in vivo evidence that c-Myc regulates CRL4DCAF4 E3 ligase activity to mediate ubiquitination of ST7, whose presence is physiologically essential for CAC tumorigenesis. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Hong Liu
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Wenzhu Lu
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Hongbo He
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Jin Wu
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Caiguo Zhang
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hanlin Gong
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Chunmei Yang
- Department of Integrated Traditional and Western Medicine, West China Hospital of Sichuan University, Chengdu, China
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245
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Kosztyu P, Slaninová I, Valčíková B, Verlande A, Müller P, Paleček JJ, Uldrijan S. A Single Conserved Amino Acid Residue as a Critical Context-Specific Determinant of the Differential Ability of Mdm2 and MdmX RING Domains to Dimerize. Front Physiol 2019; 10:390. [PMID: 31024344 PMCID: PMC6465955 DOI: 10.3389/fphys.2019.00390] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/21/2019] [Indexed: 12/02/2022] Open
Abstract
Mdm2 and MdmX are related proteins serving in the form of the Mdm2 homodimer or Mdm2/MdmX heterodimer as an E3 ubiquitin ligase for the tumor suppressor p53. The dimerization is required for the E3 activity and is mediated by the conserved RING domains present in both proteins, but only the RING domain of Mdm2 can form homodimers efficiently. We performed a systematic mutational analysis of human Mdm2, exchanging parts of the RING with the corresponding MdmX sequence, to identify the molecular determinants of this difference. Mdm2 can also promote MdmX degradation, and we identified several mutations blocking it. They were located mainly at the Mdm2/E2 interface and did not disrupt the MdmX-Mdm2 interaction. Surprisingly, some mutations of the Mdm2/E2 interface inhibited MdmX degradation, which is mediated by the Mdm2/MdmX heterodimer, but did not affect p53 degradation, mediated by the Mdm2 homodimer. Only one mutant, replacing a conserved cysteine 449 with asparagine (C449N), disrupted the ability of Mdm2 to dimerize with MdmX. When we introduced the cysteine residue into the corresponding site in MdmX, the RING domain became capable of forming dimers with other MdmX molecules in vivo, suggesting that one conserved amino acid residue in the RINGs of Mdm2 and MdmX could serve as the determinant of the differential ability of these domains to form dimers and their E3 activity. In immunoprecipitations, however, the homodimerization of MdmX could be observed only when the asparagine residue was replaced with cysteine in both RINGs. This result suggested that heterocomplexes consisting of one mutated MdmX RING with cysteine and one wild-type MdmX RING with asparagine might be less stable, despite being readily detectable in the cell-based assay. Moreover, Mdm2 C449N blocked Mdm2-MdmX heterodimerization but did not disrupt the ability of Mdm2 homodimer to promote p53 degradation, suggesting that the effect of the conserved cysteine and asparagine residues on dimerization was context-specific. Collectively, our results indicate that the effects of individual exchanges of conserved residues between Mdm2 and MdmX RING domains might be context-specific, supporting the hypothesis that Mdm2 RING homodimers and Mdm2-MdmX heterodimers may not be entirely structurally equivalent, despite their apparent similarity.
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Affiliation(s)
- Pavlína Kosztyu
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Iva Slaninová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Barbora Valčíková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czechia
| | - Amandine Verlande
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czechia
| | - Petr Müller
- Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czechia
| | - Jan J Paleček
- Central European Institute of Technology, Masaryk University, Brno, Czechia.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Stjepan Uldrijan
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia.,International Clinical Research Center, St. Anne's University Hospital, Brno, Czechia
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246
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Weber J, Polo S, Maspero E. HECT E3 Ligases: A Tale With Multiple Facets. Front Physiol 2019; 10:370. [PMID: 31001145 PMCID: PMC6457168 DOI: 10.3389/fphys.2019.00370] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/18/2019] [Indexed: 12/19/2022] Open
Abstract
Ubiquitination plays a pivotal role in several cellular processes and is critical for protein degradation and signaling. E3 ubiquitin ligases are the matchmakers in the ubiquitination cascade, responsible for substrate recognition. In order to achieve selectivity and specificity on their substrates, HECT E3 enzymes are tightly regulated and exert their function in a spatially and temporally controlled fashion in the cells. These characteristics made HECT E3s intriguing targets in drug discovery in the context of cancer biology.
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Affiliation(s)
- Janine Weber
- Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Simona Polo
- Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy.,Dipartimento di Oncologia ed Emato-Oncologia, Università degli Studi di Milano, Milan, Italy
| | - Elena Maspero
- Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
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247
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Tecalco-Cruz AC, Ramírez-Jarquín JO, Cruz-Ramos E. Estrogen Receptor Alpha and its Ubiquitination in Breast Cancer Cells. Curr Drug Targets 2019; 20:690-704. [DOI: 10.2174/1389450119666181015114041] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 12/23/2022]
Abstract
More than 70% of all breast cancer cases are estrogen receptor alpha-positive (ERα). ERα is a member of the nuclear receptor family, and its activity is implicated in the gene transcription linked to the proliferation of breast cancer cells, as well as in extranuclear signaling pathways related to the development of resistance to endocrine therapy. Protein-protein interactions and posttranslational modifications of ERα underlie critical mechanisms that modulate its activity. In this review, the relationship between ERα and ubiquitin protein (Ub), was investigated in the context of breast cancer cells. Interestingly, Ub can bind covalently or non-covalently to ERα resulting in either a proteolytic or non-proteolytic fate for this receptor. Thereby, Ub-dependent molecular pathways that modulate ERα signaling may play a central role in breast cancer progression, and consequently, present critical targets for treatment of this disease.
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Affiliation(s)
- Angeles C. Tecalco-Cruz
- Instituto de Investigaciones Biomedicas. Universidad Nacional Autonoma de Mexico. Mexico City, 04510, Mexico
| | - Josué O. Ramírez-Jarquín
- Instituto de Fisiologia Celular. Universidad Nacional Autonoma de Mexico. Mexico City, 04510, Mexico
| | - Eduardo Cruz-Ramos
- Instituto de Investigaciones Biomedicas. Universidad Nacional Autonoma de Mexico. Mexico City, 04510, Mexico
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248
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Silva MC, Ferguson FM, Cai Q, Donovan KA, Nandi G, Patnaik D, Zhang T, Huang HT, Lucente DE, Dickerson BC, Mitchison TJ, Fischer ES, Gray NS, Haggarty SJ. Targeted degradation of aberrant tau in frontotemporal dementia patient-derived neuronal cell models. eLife 2019; 8:e45457. [PMID: 30907729 PMCID: PMC6450673 DOI: 10.7554/elife.45457] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 03/23/2019] [Indexed: 12/11/2022] Open
Abstract
Tauopathies are neurodegenerative diseases characterized by aberrant forms of tau protein accumulation leading to neuronal death in focal brain areas. Positron emission tomography (PET) tracers that bind to pathological tau are used in diagnosis, but there are no current therapies to eliminate these tau species. We employed targeted protein degradation technology to convert a tau PET-probe into a functional degrader of pathogenic tau. The hetero-bifunctional molecule QC-01-175 was designed to engage both tau and Cereblon (CRBN), a substrate-receptor for the E3-ubiquitin ligase CRL4CRBN, to trigger tau ubiquitination and proteasomal degradation. QC-01-175 effected clearance of tau in frontotemporal dementia (FTD) patient-derived neuronal cell models, with minimal effect on tau from neurons of healthy controls, indicating specificity for disease-relevant forms. QC-01-175 also rescued stress vulnerability in FTD neurons, phenocopying CRISPR-mediated MAPT-knockout. This work demonstrates that aberrant tau in FTD patient-derived neurons is amenable to targeted degradation, representing an important advance for therapeutics.
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Affiliation(s)
- M Catarina Silva
- Chemical Neurobiology Laboratory, Center for Genomic MedicineMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Department of PsychiatryMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Fleur M Ferguson
- Department of Cancer BiologyDana-Farber Cancer InstituteBostonUnited States
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonUnited States
| | - Quan Cai
- Department of Cancer BiologyDana-Farber Cancer InstituteBostonUnited States
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonUnited States
| | - Katherine A Donovan
- Department of Cancer BiologyDana-Farber Cancer InstituteBostonUnited States
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonUnited States
| | - Ghata Nandi
- Chemical Neurobiology Laboratory, Center for Genomic MedicineMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Department of PsychiatryMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Debasis Patnaik
- Chemical Neurobiology Laboratory, Center for Genomic MedicineMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Department of PsychiatryMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
| | - Tinghu Zhang
- Department of Cancer BiologyDana-Farber Cancer InstituteBostonUnited States
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonUnited States
| | - Hai-Tsang Huang
- Department of Cancer BiologyDana-Farber Cancer InstituteBostonUnited States
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonUnited States
| | - Diane E Lucente
- Molecular Neurogenetics Unit, Center for Genomic MedicineMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- MGH Frontotemporal Disorders Unit, Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolCharlestownUnited States
- Gerontology Research Unit, Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolCharlestownUnited States
- Alzheimer’s Disease Research Center, Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolCharlestownUnited States
| | - Bradford C Dickerson
- MGH Frontotemporal Disorders Unit, Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolCharlestownUnited States
- Gerontology Research Unit, Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolCharlestownUnited States
- Alzheimer’s Disease Research Center, Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolCharlestownUnited States
| | - Timothy J Mitchison
- Department of Systems BiologyHarvard Medical SchoolBostonUnited States
- Laboratory of Systems PharmacologyHarvard Medical SchoolBostonUnited States
| | - Eric S Fischer
- Department of Cancer BiologyDana-Farber Cancer InstituteBostonUnited States
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonUnited States
| | - Nathanael S Gray
- Department of Cancer BiologyDana-Farber Cancer InstituteBostonUnited States
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic MedicineMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Department of NeurologyMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
- Department of PsychiatryMassachusetts General Hospital, Harvard Medical SchoolBostonUnited States
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249
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Transcriptomic atlas of mushroom development reveals conserved genes behind complex multicellularity in fungi. Proc Natl Acad Sci U S A 2019; 116:7409-7418. [PMID: 30902897 DOI: 10.1073/pnas.1817822116] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The evolution of complex multicellularity has been one of the major transitions in the history of life. In contrast to simple multicellular aggregates of cells, it has evolved only in a handful of lineages, including animals, embryophytes, red and brown algae, and fungi. Despite being a key step toward the evolution of complex organisms, the evolutionary origins and the genetic underpinnings of complex multicellularity are incompletely known. The development of fungal fruiting bodies from a hyphal thallus represents a transition from simple to complex multicellularity that is inducible under laboratory conditions. We constructed a reference atlas of mushroom formation based on developmental transcriptome data of six species and comparisons of >200 whole genomes, to elucidate the core genetic program of complex multicellularity and fruiting body development in mushroom-forming fungi (Agaricomycetes). Nearly 300 conserved gene families and >70 functional groups contained developmentally regulated genes from five to six species, covering functions related to fungal cell wall remodeling, targeted protein degradation, signal transduction, adhesion, and small secreted proteins (including effector-like orphan genes). Several of these families, including F-box proteins, expansin-like proteins, protein kinases, and transcription factors, showed expansions in Agaricomycetes, many of which convergently expanded in multicellular plants and/or animals too, reflecting convergent solutions to genetic hurdles imposed by complex multicellularity among independently evolved lineages. This study provides an entry point to studying mushroom development and complex multicellularity in one of the largest clades of complex eukaryotic organisms.
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250
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Braganza A, Quesnelle K, Bickta J, Reyes C, Wang Y, Jessup M, St Croix C, Arlotti J, Singh SV, Shiva S. Myoglobin induces mitochondrial fusion, thereby inhibiting breast cancer cell proliferation. J Biol Chem 2019; 294:7269-7282. [PMID: 30872402 DOI: 10.1074/jbc.ra118.006673] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/21/2019] [Indexed: 01/11/2023] Open
Abstract
Myoglobin is a monomeric heme protein expressed ubiquitously in skeletal and cardiac muscle and is traditionally considered to function as an oxygen reservoir for mitochondria during hypoxia. It is now well established that low concentrations of myoglobin are aberrantly expressed in a significant proportion of breast cancer tumors. Despite being expressed only at low levels in these tumors, myoglobin is associated with attenuated tumor growth and a better prognosis in breast cancer patients, but the mechanism of this myoglobin-mediated protection against further cancer growth remains unclear. Herein, we report a signaling pathway by which myoglobin regulates mitochondrial dynamics and thereby decreases cell proliferation. We demonstrate in vitro that expression of human myoglobin in MDA-MB-231, MDA-MB-468, and MCF7 breast cancer cells induces mitochondrial hyperfusion by up-regulating mitofusins 1 and 2, the predominant catalysts of mitochondrial fusion. This hyperfusion causes cell cycle arrest and subsequent inhibition of cell proliferation. Mechanistically, increased mitofusin expression was due to myoglobin-dependent free-radical production, leading to the oxidation and degradation of the E3 ubiquitin ligase parkin. We recapitulated this pathway in a murine model in which myoglobin-expressing xenografts exhibited decreased tumor volume with increased mitofusin, markers of cell cycle arrest, and decreased parkin expression. Furthermore, in human triple-negative breast tumor tissues, mitofusin and myoglobin levels were positively correlated. Collectively, these results elucidate a new function for myoglobin as a modulator of mitochondrial dynamics and reveal a novel pathway by which myoglobin decreases breast cancer cell proliferation and tumor growth by up-regulating mitofusin levels.
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Affiliation(s)
| | | | - Janelle Bickta
- the Department of Bioengineering, University of Pittsburgh Swanson School of Engineering, Pittsburgh, Pennsylvania 15261
| | - Christopher Reyes
- the Department of Bioengineering, University of Pittsburgh Swanson School of Engineering, Pittsburgh, Pennsylvania 15261
| | - Yinna Wang
- From the Vascular Medicine Institute and
| | | | | | - Julie Arlotti
- Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, and.,University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15232
| | - Shivendra V Singh
- Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, and.,University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania 15232
| | - Sruti Shiva
- From the Vascular Medicine Institute and .,Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, and.,Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
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