1
|
Xu Y, Li W, Chen Y, Xu T, Sun Y. STAM2 negatively regulates the MyD88-mediated NF-κB signaling pathway in miiuy croaker, Miichthys miiuy. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109550. [PMID: 38593891 DOI: 10.1016/j.fsi.2024.109550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/10/2024] [Accepted: 04/06/2024] [Indexed: 04/11/2024]
Abstract
Signal transducing adapter molecule 2 (STAM2), a member of the Signal Transducing Adapter Molecule (STAM) family, is a protein with significant implications in diverse signaling pathways and endocytic membrane trafficking. However, the role of the STAM2, especially in fish, remains largely unknown. In this study, we discovered that STAM2 negatively regulates the NF-κB signaling pathway, and its inhibitory effect is enhanced upon LPS induction. Our study confirmed that STAM2 can enhance the degradation of myeloid differentiation primary-response protein 88 (MyD88), an upstream regulator of NF-κB pathway. Furthermore, the UIM domain of STAM2 is important for the inhibition of MyD88. Mechanistically, STAM2 inhibits the NF-κB signaling pathway by targeting the MyD88 autophagy pathway. In addition, we showed that STAM2 promotes the proliferation of Vibrio harveyi. In summary, our study reveals that STAM2 inhibits NF-κB signaling activation and mediates innate immunity in teleost via the autophagy pathway.
Collapse
Affiliation(s)
- Yan Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Wenxin Li
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Ya Chen
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, China; Marine Biomedical Science and Technology Innovation Platform of Lin-gang Special Area, Shanghai, China.
| | - Yuena Sun
- National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China; Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture and Rural Affairs, Shanghai Ocean University, China.
| |
Collapse
|
2
|
Potapenko A, Davidson JM, Lee A, Laird AS. The deubiquitinase function of ataxin-3 and its role in the pathogenesis of Machado-Joseph disease and other diseases. Biochem J 2024; 481:461-480. [PMID: 38497605 PMCID: PMC11088879 DOI: 10.1042/bcj20240017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/19/2024]
Abstract
Machado-Joseph disease (MJD) is a devastating and incurable neurodegenerative disease characterised by progressive ataxia, difficulty speaking and swallowing. Consequently, affected individuals ultimately become wheelchair dependent, require constant care, and face a shortened life expectancy. The monogenic cause of MJD is expansion of a trinucleotide (CAG) repeat region within the ATXN3 gene, which results in polyglutamine (polyQ) expansion within the resultant ataxin-3 protein. While it is well established that the ataxin-3 protein functions as a deubiquitinating (DUB) enzyme and is therefore critically involved in proteostasis, several unanswered questions remain regarding the impact of polyQ expansion in ataxin-3 on its DUB function. Here we review the current literature surrounding ataxin-3's DUB function, its DUB targets, and what is known regarding the impact of polyQ expansion on ataxin-3's DUB function. We also consider the potential neuroprotective effects of ataxin-3's DUB function, and the intersection of ataxin-3's role as a DUB enzyme and regulator of gene transcription. Ataxin-3 is the principal pathogenic protein in MJD and also appears to be involved in cancer. As aberrant deubiquitination has been linked to both neurodegeneration and cancer, a comprehensive understanding of ataxin-3's DUB function is important for elucidating potential therapeutic targets in these complex conditions. In this review, we aim to consolidate knowledge of ataxin-3 as a DUB and unveil areas for future research to aid therapeutic targeting of ataxin-3's DUB function for the treatment of MJD and other diseases.
Collapse
Affiliation(s)
- Anastasiya Potapenko
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jennilee M. Davidson
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Albert Lee
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Angela S. Laird
- Motor Neuron Disease Research Centre, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| |
Collapse
|
3
|
Barzak FM, Lu A, Geltzeiler AR, Ledgerwood EC, Chung WK, Day CL. A novel RNF125 variant associated with Tenorio syndrome alters ubiquitin chain binding. Clin Genet 2024; 105:254-261. [PMID: 37986019 DOI: 10.1111/cge.14457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023]
Abstract
A key signalling pathway required for clearance of viruses from host cells relies on the receptor protein, retinoic acid-inducible gene I (RIG-I). The activity of RIG-I is tightly controlled, and once bound to viral dsRNA, addition of lysine 63-linked ubiquitin chains activates signalling. Meanwhile, the addition of lysine 48-linked ubiquitin chains to RIG-I is required to terminate signalling when the infection has been resolved. Really interesting new gene (RING) finger protein 125 (RNF125) is the E3 ligase responsible for addition of the ubiquitin chains that terminate signalling, with disruption of its function associated with Tenorio syndrome. Here we describe a novel RNF125 gene variant in an individual with clinical symptoms including intellectual disability, macrocephaly and congenital heart disease, consistent with Tenorio syndrome. The newly identified Tenorio syndrome-associated variant [(NM_017831.4):c.670G>C p.Glu224Gln] is the first to be found in the ubiquitin interaction motif (UIM) of RNF125. While the E3 ligase activity of this RNF125 variant is retained, it has an impaired ability to interact with lysine 63-linked ubiquitin chains. The function of the UIM in RNF125 is uncertain; however, this study suggests that the UIM binds lysine 63-linked ubiquitin chains, and that this interaction is required for the normal function of RNF125.
Collapse
Affiliation(s)
- Fareeda M Barzak
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Anita Lu
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Alexa R Geltzeiler
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School Boston, Boston, Massachusetts, USA
| | - Elizabeth C Ledgerwood
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital Harvard Medical School Boston, Boston, Massachusetts, USA
| | - Catherine L Day
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| |
Collapse
|
4
|
Yang E, Fan X, Ye H, Sun X, Ji Q, Ding Q, Zhong S, Zhao S, Xuan C, Fang M, Ding X, Cao J. Exploring the role of ubiquitin regulatory X domain family proteins in cancers: bioinformatics insights, mechanisms, and implications for therapy. J Transl Med 2024; 22:157. [PMID: 38365777 PMCID: PMC10870615 DOI: 10.1186/s12967-024-04890-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/13/2024] [Indexed: 02/18/2024] Open
Abstract
UBXD family (UBXDF), a group of proteins containing ubiquitin regulatory X (UBX) domains, play a crucial role in the imbalance of proliferation and apoptotic in cancer. In this study, we summarised bioinformatics proof on multi-omics databases and literature on UBXDF's effects on cancer. Bioinformatics analysis revealed that Fas-associated factor 1 (FAF1) has the largest number of gene alterations in the UBXD family and has been linked to survival and cancer progression in many cancers. UBXDF may affect tumour microenvironment (TME) and drugtherapy and should be investigated in the future. We also summarised the experimental evidence of the mechanism of UBXDF in cancer, both in vitro and in vivo, as well as its application in clinical and targeted drugs. We compared bioinformatics and literature to provide a multi-omics insight into UBXDF in cancers, review proof and mechanism of UBXDF effects on cancers, and prospect future research directions in-depth. We hope that this paper will be helpful for direct cancer-related UBXDF studies.
Collapse
Affiliation(s)
- Enyu Yang
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xiaowei Fan
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Haihan Ye
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Xiaoyang Sun
- School of Biological Sciences, The University of Hong Kong, Hong Kong , 999077, Special Administrative Region, China
| | - Qing Ji
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Department of Head and Neck and Rare Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Qianyun Ding
- Department of 'A', The Children's Hospital, National Clinical Research Center for Child Health, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Shulian Zhong
- Zhejiang Sci-Tech University Hospital, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Shuo Zhao
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Cheng Xuan
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Meiyu Fang
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Department of Head and Neck and Rare Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China.
| | - Xianfeng Ding
- School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
| | - Jun Cao
- Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Department of Head and Neck and Rare Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China.
| |
Collapse
|
5
|
Park CR, Min JH, Gong Y, Sang H, Lee KH, Kim CS. Arabidopsis thaliana ubiquitin-associated protein 2 (AtUAP2) functions as an E4 ubiquitin factor and negatively modulates dehydration stress response. PLANT MOLECULAR BIOLOGY 2024; 114:13. [PMID: 38324104 DOI: 10.1007/s11103-024-01419-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/11/2024] [Indexed: 02/08/2024]
Abstract
E4, a ubiquitin (Ub) chain assembly factor and post-translational modification protein, plays a key role in the regulation of multiple cellular functions in plants during biotic or abiotic stress. We have more recently reported that E4 factor AtUAP1 is a negative regulator of the osmotic stress response and enhances the multi-Ub chain assembly of E3 ligase Arabidopsis thaliana RING Zinc Finger 1 (AtRZF1). To further investigate the function of other E4 Ub factors in osmotic stress, we isolated AtUAP2, an AtUAP1 homolog, which interacted with AtRZF1, using pull-down assay and bimolecular fluorescence complementation analysis. AtUAP2, a Ub-associated motif-containing protein, interacts with oligo-Ub5, -Ub6, and -Ub7 chains. The yeast functional complementation experiment revealed that AtUAP2 functions as an E4 Ub factor. In addition, AtUAP2 is localized in the cytoplasm, different from AtUAP1. The activity of AtUAP2 was relatively strongly induced in the leaf tissue of AtUAP2 promoter-β-glucuronidase transgenic plants by abscisic acid, dehydration, and oxidative stress. atuap2 RNAi lines were more insensitive to osmotic stress condition than wild-type during the early growth of seedlings, whereas the AtUAP2-overexpressing line exhibited relatively more sensitive responses. Analyses of molecular and physiological experiments showed that AtUAP2 could negatively mediate the osmotic stress-induced signaling. Genetic studies showed that AtRZF1 mutation could suppress the dehydration-induced sensitive phenotype of the AtUAP2-overexpressing line, suggesting that AtRZF1 acts genetically downstream of AtUAP2 during osmotic stress. Taken together, our findings show that the AtRZF1-AtUAP2 complex may play important roles in the ubiquitination pathway, which controls the osmotic stress response in Arabidopsis.
Collapse
Affiliation(s)
- Cho-Rong Park
- Department of Applied Biology, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Ji-Hee Min
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, 77843-2128, College Station, TX, USA
| | - Ying Gong
- Department of Applied Biology, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Kyeong-Hwan Lee
- Department of Convergence Biosystems Engineering, Chonnam National University, 61186, Gwangju, Republic of Korea
| | - Cheol Soo Kim
- Department of Applied Biology, Chonnam National University, 61186, Gwangju, Republic of Korea.
| |
Collapse
|
6
|
Cowan DB, Wu H, Chen H. Epsin Endocytic Adaptor Proteins in Angiogenic and Lymphangiogenic Signaling. Cold Spring Harb Perspect Med 2024; 14:a041165. [PMID: 37217282 PMCID: PMC10759987 DOI: 10.1101/cshperspect.a041165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Circulating vascular endothelial growth factor (VEGF) ligands and receptors are central regulators of vasculogenesis, angiogenesis, and lymphangiogenesis. In response to VEGF ligand binding, VEGF receptor tyrosine kinases initiate the chain of events that transduce extracellular signals into endothelial cell responses such as survival, proliferation, and migration. These events are controlled by intricate cellular processes that include the regulation of gene expression at multiple levels, interactions of numerous proteins, and intracellular trafficking of receptor-ligand complexes. Endocytic uptake and transport of macromolecular complexes through the endosome-lysosome system helps fine-tune endothelial cell responses to VEGF signals. Clathrin-dependent endocytosis remains the best understood means of macromolecular entry into cells, although the importance of non-clathrin-dependent pathways is increasingly recognized. Many of these endocytic events rely on adaptor proteins that coordinate internalization of activated cell-surface receptors. In the endothelium of both blood and lymphatic vessels, epsins 1 and 2 are functionally redundant adaptors involved in receptor endocytosis and intracellular sorting. These proteins are capable of binding both lipids and proteins and are important for promoting curvature of the plasma membrane as well as binding ubiquitinated cargo. Here, we discuss the role of epsin proteins and other endocytic adaptors in governing VEGF signaling in angiogenesis and lymphangiogenesis and discuss their therapeutic potential as molecular targets.
Collapse
Affiliation(s)
- Douglas B Cowan
- Vascular Biology Program, Boston Children's Hospital, and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hao Wu
- Vascular Biology Program, Boston Children's Hospital, and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hong Chen
- Vascular Biology Program, Boston Children's Hospital, and Department of Surgery, Harvard Medical School, Boston, Massachusetts 02115, USA
| |
Collapse
|
7
|
Luo R, Yang K, Xiao W. Plant deubiquitinases: from structure and activity to biological functions. PLANT CELL REPORTS 2023; 42:469-486. [PMID: 36567335 DOI: 10.1007/s00299-022-02962-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
This article attempts to provide comprehensive review of plant deubiquitinases, paying special attention to recent advances in their biochemical activities and biological functions. Proteins in eukaryotes are subjected to post-translational modifications, in which ubiquitination is regarded as a reversible process. Cellular deubiquitinases (DUBs) are a key component of the ubiquitin (Ub)-proteasome system responsible for cellular protein homeostasis. DUBs recycle Ub by hydrolyzing poly-Ub chains on target proteins, and maintain a balance of the cellular Ub pool. In addition, some DUBs prefer to cleave poly-Ub chains not linked through the conventional K48 residue, which often alter the substrate activity instead of its stability. In plants, all seven known DUB subfamilies have been identified, namely Ub-binding protease/Ub-specific protease (UBP/USP), Ub C-terminal hydrolase (UCH), Machado-Joseph domain-containing protease (MJD), ovarian-tumor domain-containing protease (OTU), zinc finger with UFM1-specific peptidase domain protease (ZUFSP), motif interacting with Ub-containing novel DUB family (MINDY), and JAB1/MPN/MOV34 protease (JAMM). This review focuses on recent advances in the structure, activity, and biological functions of plant DUBs, particularly in the model plant Arabidopsis.
Collapse
Affiliation(s)
- Runbang Luo
- 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
| | - Kun Yang
- 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
| | - 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.
| |
Collapse
|
8
|
Makri V, Feidantsis K, Porlou D, Ntokou A, Georgoulis I, Giantsis IA, Anestis A, Michaelidis B. Red porgy's (Pagrus pagrus) cellular physiology and antioxidant defense in response to seasonality. J Therm Biol 2023; 113:103527. [PMID: 37055131 DOI: 10.1016/j.jtherbio.2023.103527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Physiological stress patterns of marine organisms in their natural habitats are considerably complex in space and time. These patterns can eventually contribute in the shaping of fish' thermal limits under natural conditions. In the view of the knowledge gap regarding red porgy's thermal physiology, in combination with the characterization of the Mediterranean Sea as a climate change ''hotspot'', the aim of the present study was to investigate this species biochemical responses to constantly changing field conditions. To achieve this goal, Heat Shock Response (HSR), MAPKs pathway, autophagy, apoptosis, lipid peroxidation and antioxidant defense were estimated and exhibited a seasonal pattern. In general, all the examined biochemical indicators expressed high levels parallel to the increasing seawater temperature in spring, although several bio-indicators have shown increased levels when fish were cold-acclimatized. Similar to other sparids, the observed patterns of physiological responses in red porgy may support the concept of eurythermy.
Collapse
|
9
|
Zhang J, Vancea AI, Arold ST. Targeting plant UBX proteins: AI-enhanced lessons from distant cousins. TRENDS IN PLANT SCIENCE 2022; 27:1099-1108. [PMID: 35718708 DOI: 10.1016/j.tplants.2022.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/21/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Across all eukaryotic kingdoms, ubiquitin regulatory X (UBX) domain-containing adaptor proteins control the segregase cell division control protein 48 (CDC48), and thereby also control cellular proteostasis and adaptation. The structures and biological roles of UBX proteins in animals and fungi have garnered considerable attention. However, their counterparts in plants remain markedly understudied. Since 2021, the artificial intelligence (AI)-based algorithm AlphaFold has provided predictions of protein structural features that can be highly accurate. Predictions of the proteomes of all major model organisms are now freely accessible to the entire research community through user-friendly web interfaces. We propose that the combination of cross-kingdom comparison with AF analysis produces a wealth of testable hypotheses to inspire and guide experimental research on plant UBX domain-containing (PUX) proteins.
Collapse
Affiliation(s)
- Junrui Zhang
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Alexandra I Vancea
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia; Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France.
| |
Collapse
|
10
|
The resurrection of RIP kinase 1 as an early cell death checkpoint regulator-a potential target for therapy in the necroptosis era. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1401-1411. [PMID: 36171264 PMCID: PMC9534832 DOI: 10.1038/s12276-022-00847-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/07/2022] [Accepted: 07/15/2022] [Indexed: 01/05/2023]
Abstract
Receptor-interacting serine threonine protein kinase 1 (RIPK1) has emerged as a central molecular switch in controlling the balance between cell survival and cell death. The pro-survival role of RIPK1 in maintaining cell survival is achieved via its ability to induce NF-κB-dependent expression of anti-apoptotic genes. However, recent advances have identified the pro-death function of RIPK1: posttranslational modifications of RIPK1 in the tumor necrosis factor receptor 1 (TNFR1)-associated complex-I, in the cytosolic complex-IIb or in necrosomes regulate the cytotoxic potential of RIPK1, forming an early cell death checkpoint. Since the kinase activity of RIPK1 is indispensable in RIPK3- and MLKL-mediated necroptosis induction, while it is dispensable in apoptosis, a better understanding of this early cell death checkpoint via RIPK1 might lead to new insights into the molecular mechanisms controlling both apoptotic and necroptotic modes of cell death and help develop novel therapeutic approaches for cancer. Here, we present an emerging view of the regulatory mechanisms for RIPK1 activity, especially with respect to the early cell death checkpoint. We also discuss the impact of dysregulated RIPK1 activity in pathophysiological settings and highlight its therapeutic potential in treating human diseases. Improved understanding of the molecular mechanisms that allow a protein to control the balance between cell survival or early death could reveal new approaches to treating conditions including chronic inflammatory disease and cancer. Gang Min Hur and colleagues at Chungnam National University in Daejeon, South Korea, with Han-Ming Shen at the University of Macau in China, review emerging evidence about how the protein called receptor-interacting serine/threonine-protein kinase 1 (RIPK1) influences whether cells move towards death or survival at a key ‘checkpoint’ in cell development. Cells can undergo a natural process of programmed cell death called apoptosis, die abnormally in a disease process called necroptosis, or survive. RIPK1 appears able to influence which path is chosen depending on which genes it regulates and which proteins it interacts with. Many details are still unclear, and need further investigation.
Collapse
|
11
|
Agaoua A, Rittener V, Troadec C, Desbiez C, Bendahmane A, Moquet F, Dogimont C. A single substitution in Vacuolar protein sorting 4 is responsible for resistance to Watermelon mosaic virus in melon. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4008-4021. [PMID: 35394500 DOI: 10.1093/jxb/erac135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
In plants, introgression of genetic resistance is a proven strategy for developing new resistant lines. While host proteins involved in genome replication and cell to cell movement are widely studied, other cell mechanisms responsible for virus infection remain under investigated. Endosomal sorting complexes required for transport (ESCRT) play a key role in membrane trafficking in plants and are involved in the replication of several plant RNA viruses. In this work, we describe the role of the ESCRT protein CmVPS4 as a new susceptibility factor to the Potyvirus Watermelon mosaic virus (WMV) in melon. Using a worldwide collection of melons, we identified three different alleles carrying non-synonymous substitutions in CmVps4. Two of these alleles were shown to be associated with WMV resistance. Using a complementation approach, we demonstrated that resistance is due to a single non-synonymous substitution in the allele CmVps4P30R. This work opens up new avenues of research on a new family of host factors required for virus infection and new targets for resistance.
Collapse
Affiliation(s)
- Aimeric Agaoua
- Genetics and Breeding of Fruit and Vegetables (GAFL-INRAE), 84000 Avignon, France
| | - Vincent Rittener
- Genetics and Breeding of Fruit and Vegetables (GAFL-INRAE), 84000 Avignon, France
| | - Christelle Troadec
- Institute of Plant Sciences-Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | | | | | | | - Catherine Dogimont
- Genetics and Breeding of Fruit and Vegetables (GAFL-INRAE), 84000 Avignon, France
| |
Collapse
|
12
|
Won M, Park KA, Kim S, Ju E, Ko Y, Yoo H, Ro H, Lee J, Oh J, Lee EG, Kim SY, Nam SW, Shen HM, Yeo MK, Kim JM, Hur GM. ANKRD13a controls early cell-death checkpoint by interacting with RIP1 independent of NF-κB. Cell Death Differ 2022; 29:1152-1163. [PMID: 34839354 PMCID: PMC9177599 DOI: 10.1038/s41418-021-00906-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022] Open
Abstract
In TNF signaling, ubiquitination of RIP1 functions as an early cell-death checkpoint, which prevents the spatial transition of the signaling complex from complex-I to death-inducing complex-II. Here, we report that ankyrin repeat domain 13a (ANKRD13a) acts as a novel component of complex-II to set a higher signal threshold for the cytotoxic potential of TNF. ANKRD13a deficiency is sufficient to turn the response to TNF from survival to death by promoting the formation of complex-II without affecting NF-κB activation. ANKRD13a binds to ubiquitinated-RIP1 via its UIM, and subsequently limits the association of FADD and caspase-8 with RIP1. Moreover, high ANKRD13a expression is inversely correlated with apoptotic phenotypes in ovarian cancer tissues and is associated with poor prognosis. Our work identifies ANKRD13a as a novel gatekeeper of the early cell-death checkpoint, which may function as part of an escape mechanism from cell death in some cancers.
Collapse
Affiliation(s)
- Minho Won
- Department of Pharmacology and Department of Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju, 28116, Republic of Korea
| | - Kyeong Ah Park
- Department of Pharmacology and Department of Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Sup Kim
- Department of Radiation Oncology, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Eunjin Ju
- Department of Pharmacology and Department of Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Youngbok Ko
- Department of Obstetrics and Gynecology, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Heonjong Yoo
- Department of Obstetrics and Gynecology, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Biosciences and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jaeseob Lee
- Department of Biomedical Science, Korea University Graduate School, Seoul, 02841, Republic of Korea
| | - Junseo Oh
- Department of Biomedical Science, Korea University Graduate School, Seoul, 02841, Republic of Korea
| | - Eun Gyo Lee
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology, Cheongju, 28116, Republic of Korea
| | - Sang Yean Kim
- Department of Pathology, College of Medicine, The Catholic University, Seoul, 06591, Republic of Korea
| | - Suk Woo Nam
- Department of Pathology, College of Medicine, The Catholic University, Seoul, 06591, Republic of Korea
| | - Han-Ming Shen
- Faculty of Health Sciences, University of Macau, Macau, China
| | - Min-Kyung Yeo
- Department of Pathology, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Jin Man Kim
- Department of Pathology, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Gang Min Hur
- Department of Pharmacology and Department of Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea.
| |
Collapse
|
13
|
Veggiani G, Yates BP, Martyn GD, Manczyk N, Singer AU, Kurinov I, Sicheri F, Sidhu SS. Panel of Engineered Ubiquitin Variants Targeting the Family of Human Ubiquitin Interacting Motifs. ACS Chem Biol 2022; 17:941-956. [PMID: 35385646 PMCID: PMC9305627 DOI: 10.1021/acschembio.2c00089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ubiquitin (Ub)-binding domains embedded in intracellular proteins act as readers of the complex Ub code and contribute to regulation of numerous eukaryotic processes. Ub-interacting motifs (UIMs) are short α-helical modular recognition elements whose role in controlling proteostasis and signal transduction has been poorly investigated. Moreover, impaired or aberrant activity of UIM-containing proteins has been implicated in numerous diseases, but targeting modular recognition elements in proteins remains a major challenge. To overcome this limitation, we developed Ub variants (UbVs) that bind to 42 UIMs in the human proteome with high affinity and specificity. Structural analysis of a UbV:UIM complex revealed the molecular determinants of enhanced affinity and specificity. Furthermore, we showed that a UbV targeting a UIM in the cancer-associated Ub-specific protease 28 potently inhibited catalytic activity. Our work demonstrates the versatility of UbVs to target short α-helical Ub receptors with high affinity and specificity. Moreover, the UbVs provide a toolkit to investigate the role of UIMs in regulating and transducing Ub signals and establish a general strategy for the systematic development of probes for Ub-binding domains.
Collapse
Affiliation(s)
- Gianluca Veggiani
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Bradley P. Yates
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Gregory D. Martyn
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Noah Manczyk
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Alex U. Singer
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, NE-CAT, Cornell University, Argonne, Illinois 60439, United States
| | - Frank Sicheri
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| |
Collapse
|
14
|
SUMO-mediated recruitment allows timely function of the Yen1 nuclease in mitotic cells. PLoS Genet 2022; 18:e1009860. [PMID: 35333860 PMCID: PMC8986097 DOI: 10.1371/journal.pgen.1009860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 04/06/2022] [Accepted: 03/02/2022] [Indexed: 11/19/2022] Open
Abstract
The post-translational modification of DNA damage response proteins with SUMO is an important mechanism to orchestrate a timely and orderly recruitment of repair factors to damage sites. After DNA replication stress and double-strand break formation, a number of repair factors are SUMOylated and interact with other SUMOylated factors, including the Yen1 nuclease. Yen1 plays a critical role in ensuring genome stability and unperturbed chromosome segregation by removing covalently linked DNA intermediates between sister chromatids that are formed by homologous recombination. Here we show how this important role of Yen1 depends on interactions mediated by non-covalent binding to SUMOylated partners. Mutations in the motifs that allow SUMO-mediated recruitment of Yen1 impair its ability to resolve DNA intermediates and result in chromosome mis-segregation and increased genome instability.
Collapse
|
15
|
Liu D, Jin X, Yu G, Wang M, Liu L, Zhang W, Wu J, Wang F, Yang J, Luo Q, Cai L, Yang X, Ke X, Qu Y, Xu Z, Jia L, Chen WL. Oleanolic acid blocks the purine salvage pathway for cancer therapy by inactivating SOD1 and stimulating lysosomal proteolysis. MOLECULAR THERAPY-ONCOLYTICS 2021; 23:107-123. [PMID: 34703880 PMCID: PMC8505360 DOI: 10.1016/j.omto.2021.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 08/24/2021] [Indexed: 12/28/2022]
Abstract
Metabolic reprogramming is a core hallmark of cancer and is key for tumorigenesis and tumor progression. Investigation of metabolic perturbation by anti-cancer compounds would allow a thorough understanding of the underlying mechanisms of these agents and identification of new anti-cancer targets. Here, we demonstrated that the administration of oleanolic acid (OA) rapidly altered cancer metabolism, particularly suppressing the purine salvage pathway (PSP). PSP restoration significantly opposed OA-induced DNA replication and cell proliferation arrest, underscoring the importance of this pathway for the anti-cancer activity of OA. Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and 5′-nucleotidase (5′-NT), two metabolic enzymes essential for PSP activity, were promptly degraded by OA via the lysosome pathway. Mechanistically, OA selectively targeted superoxide dismutase 1 (SOD1) and yielded reactive oxygen species (ROS) to activate the AMP-activated protein kinase (AMPK)/mammalian target of rapamycin complex 1 (mTORC1)/macroautophagy pathway, thus eliciting lysosomal degradation of HGPRT and 5′-NT. Furthermore, we found that the PSP was overactivated in human lung and breast cancers, with a negative correlation with patient survival. The results of this study elucidated a new anti-cancer mechanism of OA by restraining the PSP via the SOD1/ROS/AMPK/mTORC1/macroautophagy/lysosomal pathway. We also identified the PSP as a new target for cancer treatment and highlighted OA as a potential therapeutic agent for cancers with high PSP activity.
Collapse
Affiliation(s)
- Dan Liu
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xing Jin
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Guanzhen Yu
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Mingsong Wang
- Department of Thoracic Cardiovascular Surgery, Xinhua Hospital of Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Lei Liu
- Department of Thoracic Surgery, the Affiliated Tumor Hospital of Nantong University, Nantong 226361, China
| | - Wenjuan Zhang
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jia Wu
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Fengying Wang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Jing Yang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Qin Luo
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lili Cai
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xi Yang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Xisong Ke
- Center for Chemical Biology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yi Qu
- Center for Chemical Biology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Zhenye Xu
- Department of Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Lijun Jia
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Wen-Lian Chen
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| |
Collapse
|
16
|
Jiang DJ, Hao XH, Zhang J, Tang H, Wang F. Reducing expression of TaOTUB1s decreases tiller number in wheat. PLANT SIGNALING & BEHAVIOR 2021; 16:2018217. [PMID: 34968411 PMCID: PMC9208779 DOI: 10.1080/15592324.2021.2018217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Tiller number is an important agronomic trait that affects crop yield. The roles of OTUB1 in regulating tiller numbers in rice have been reported. However, the roles of OTUB1 in wheat remain elusive. In this study, TaOTUB1s were identified in wheat. TaOTUB1 proteins were localized in the nucleus and cytoplasm. Compared with wild-type Fielder, TaOTUB1-RNAi transgenic wheat plants had fewer tillers. Similar to OTUB1 in rice, the yeast double hybrid indicated that the TaOTUB1-A protein could interact with TaSPL17 and TaUBC13 proteins. The results of quantitative real-time polymerase chain reaction revealed that the expression levels of TaOTUB1s decreased while those of TaSPL17 significantly improved in TaOTUB1-RNAi lines. These findings suggested that TaOTUB1s influenced tiller number in wheat.
Collapse
Affiliation(s)
- Deng Ji Jiang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Xiao Hua Hao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Jing Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Heng Tang
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Fang Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| |
Collapse
|
17
|
Liu W, Liu Z, Mo Z, Guo S, Liu Y, Xie Q. ATG8-Interacting Motif: Evolution and Function in Selective Autophagy of Targeting Biological Processes. FRONTIERS IN PLANT SCIENCE 2021; 12:783881. [PMID: 34912364 PMCID: PMC8666691 DOI: 10.3389/fpls.2021.783881] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 10/28/2021] [Indexed: 05/26/2023]
Abstract
Autophagy is an evolutionarily conserved vacuolar process functioning in the degradation of cellular components for reuse. In plants, autophagy is generally activated upon stress and its regulation is executed by numbers of AuTophaGy-related genes (ATGs), of which the ATG8 plays a dual role in both biogenesis of autophagosomes and recruitment of ATG8-interacting motif (AIM) anchored selective autophagy receptors (SARs). Such motif is either termed as AIM or ubiquitin-interacting motif (UIM), corresponding to the LC3-interacting region (LIR)/AIM docking site (LDS) or the UIM docking site (UDS) of ATG8, respectively. To date, dozens of AIM or UIM containing SARs have been characterized. However, the knowledge of these motifs is still obscured. In this review, we intend to summarize the current understanding of SAR proteins and discuss the conservation and diversification of the AIMs/UIMs, expectantly providing new insights into the evolution of them in various biological processes in plants.
Collapse
Affiliation(s)
- Wanqing Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zinan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Zulong Mo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Shaoying Guo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Qingjun Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China
| |
Collapse
|
18
|
Tan J, Wen Y, Li M. Emerging biosensing platforms for quantitative detection of exosomes as diagnostic biomarkers. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214111] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
19
|
Gao Q, Zhang N, Wang WQ, Shen SY, Bai C, Song XJ. The ubiquitin-interacting motif-type ubiquitin receptor HDR3 interacts with and stabilizes the histone acetyltransferase GW6a to control the grain size in rice. THE PLANT CELL 2021; 33:3331-3347. [PMID: 34323980 PMCID: PMC8505875 DOI: 10.1093/plcell/koab194] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 07/23/2021] [Indexed: 05/02/2023]
Abstract
For grain crops such as rice (Oryza sativa), grain size substantially affects yield. The histone acetyltransferase GRAIN WEIGHT 6a (GW6a) determines grain size and yield in rice. However, the gene regulatory network underlying GW6a-mediated regulation of grain size has remained elusive. In this study, we show that GW6a interacts with HOMOLOG OF DA1 ON RICE CHROMOSOME 3 (HDR3), a ubiquitin-interacting motif-containing ubiquitin receptor. Transgenic rice plants overexpressing HDR3 produced larger grains, whereas HDR3 knockout lines produce smaller grains compared to the control. Cytological data suggest that HDR3 modulates grain size in a similar manner to GW6a, by altering cell proliferation in spikelet hulls. Mechanistically, HDR3 physically interacts with and stabilizes GW6a in an ubiquitin-dependent manner, delaying protein degradation by the 26S proteasome. The delay in GW6a degradation results in dramatic enhancement of the local acetylation of H3 and H4 histones. Furthermore, RNA sequencing analysis and chromatin immunoprecipitation assays reveal that HDR3 and GW6a bind to the promoters of and modulate a common set of downstream genes. In addition, genetic analysis demonstrates that HDR3 functions in the same genetic pathway as GW6a to regulate the grain size. Therefore, we identified the grain size regulatory module HDR3-GW6a as a potential target for crop yield improvement.
Collapse
Affiliation(s)
- Qiong Gao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ning Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei-Qing Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shao-Yan Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Bai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xian-Jun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing 100093, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Author for correspondence:
| |
Collapse
|
20
|
Min JH, Park CR, Chung JS, Kim CS. Arabidopsis thaliana Ubiquitin-Associated Protein 1 (AtUAP1) Interacts with redundant RING Zinc Finger 1 (AtRZF1) to Negatively Regulate Dehydration Response. PLANT & CELL PHYSIOLOGY 2021; 62:1044-1057. [PMID: 34086919 DOI: 10.1093/pcp/pcab082] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 05/24/2021] [Accepted: 06/03/2021] [Indexed: 05/16/2023]
Abstract
Ubiquitination, one of the most frequently occurring post-translational modifications, is essential for regulating diverse cellular processes in plants during abiotic stress. The E3 ubiquitin (Ub) ligase Arabidopsis thaliana really interesting new gene (RING) zinc finger 1 (AtRZF1) mutation is known to enhance drought tolerance in A. thaliana seedlings. To further investigate the function of AtRZF1 in osmotic stress, we isolated Ub-associated protein 1 (AtUAP1) which interacts with AtRZF1 using a yeast two-hybrid system. AtUAP1, a Ub-associated motif containing protein, increased the amount of Ub-conjugated AtRZF1. Moreover, AtUAP1 RNA interference lines were more tolerant to osmotic stress than wild type, whereas AtUAP1-overexpressing (OX) transgenic lines showed sensitive responses, including cotyledon greening, water loss, proline accumulation and changes in stress-related genes expression, indicating that AtUAP1 could negatively regulate dehydration-mediated signaling. In addition, AtUAP1-green fluorescent protein fusion protein was observed in the nuclei of root cells of transgenic seedlings. Genetic studies showed that the AtRZF1 mutation could rescue the sensitive phenotype of AtUAP1-OX lines in response to osmotic stress, suggesting that AtRZF1 was epistatic to AtUAP1 in dehydration signaling. Taken together, our findings describe a new component in the AtRZF1 ubiquitination pathway which controls the dehydration response in A. thaliana.
Collapse
Affiliation(s)
- Ji-Hee Min
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
- Department of Biochemistry and Biophysics, Texas A&M University, 300 Olsen Blvd, College Station, TX 77843-2128, USA
| | - Cho-Rong Park
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jung-Sung Chung
- Department of Agricultural Plant Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Cheol Soo Kim
- Department of Applied Biology, Chonnam National University, Gwangju 61186, Republic of Korea
| |
Collapse
|
21
|
Lambrughi M, Maiani E, Aykac Fas B, Shaw GS, Kragelund BB, Lindorff-Larsen K, Teilum K, Invernizzi G, Papaleo E. Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs. Front Mol Biosci 2021; 8:676235. [PMID: 34262938 PMCID: PMC8273247 DOI: 10.3389/fmolb.2021.676235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/14/2021] [Indexed: 01/11/2023] Open
Abstract
Ubiquitin is a small protein at the heart of many cellular processes, and several different protein domains are known to recognize and bind ubiquitin. A common motif for interaction with ubiquitin is the Ubiquitin Interacting Motif (UIM), characterized by a conserved sequence signature and often found in multi-domain proteins. Multi-domain proteins with intrinsically disordered regions mediate interactions with multiple partners, orchestrating diverse pathways. Short linear motifs for binding are often embedded in these disordered regions and play crucial roles in modulating protein function. In this work, we investigated the structural propensities of UIMs using molecular dynamics simulations and NMR chemical shifts. Despite the structural portrait depicted by X-crystallography of stable helical structures, we show that UIMs feature both helical and intrinsically disordered conformations. Our results shed light on a new class of disordered UIMs. This group is here exemplified by the C-terminal domain of one isoform of ataxin-3 and a group of ubiquitin-specific proteases. Intriguingly, UIMs not only bind ubiquitin. They can be a recruitment point for other interactors, such as parkin and the heat shock protein Hsc70-4. Disordered UIMs can provide versatility and new functions to the client proteins, opening new directions for research on their interactome.
Collapse
Affiliation(s)
- Matteo Lambrughi
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.,Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milano, Italy
| | - Emiliano Maiani
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Burcu Aykac Fas
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Gary S Shaw
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, ON, Canada
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Gaetano Invernizzi
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark.,Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Lyngby, Denmark
| |
Collapse
|
22
|
Zhang J, Vancea AI, Shahul Hameed UF, Arold ST. Versatile control of the CDC48 segregase by the plant UBX-containing (PUX) proteins. Comput Struct Biotechnol J 2021; 19:3125-3132. [PMID: 34141135 PMCID: PMC8181520 DOI: 10.1016/j.csbj.2021.05.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 11/26/2022] Open
Abstract
In plants, AAA-adenosine triphosphatase (ATPase) Cell Division Control Protein 48 (CDC48) uses the force generated through ATP hydrolysis to pull, extract, and unfold ubiquitylated or sumoylated proteins from the membrane, chromatin, or protein complexes. The resulting changes in protein or RNA content are an important means for plants to control protein homeostasis and thereby adapt to shifting environmental conditions. The activity and targeting of CDC48 are controlled by adaptor proteins, of which the plant ubiquitin regulatory X (UBX) domain-containing (PUX) proteins constitute the largest family. Emerging knowledge on the structure and function of PUX proteins highlights that these proteins are versatile factors for plant homeostasis and adaptation that might inspire biotechnological applications.
Collapse
Affiliation(s)
- Junrui Zhang
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Alexandra I Vancea
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Umar F Shahul Hameed
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.,Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
| |
Collapse
|
23
|
Kandasamy G, Pradhan AK, Palanimurugan R. Ccr4-Not complex subunits Ccr4, Caf1, and Not4 are novel proteolysis factors promoting the degradation of ubiquitin-dependent substrates by the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119010. [PMID: 33727038 DOI: 10.1016/j.bbamcr.2021.119010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 02/16/2021] [Accepted: 03/07/2021] [Indexed: 12/22/2022]
Abstract
Degradation of short-lived and abnormal proteins is essential for normal cellular homeostasis. In eukaryotes, such unstable cellular proteins are selectively degraded by the ubiquitin proteasome system (UPS). Abnormalities in protein degradation by the UPS have been linked to several human diseases. Ccr4, Caf1, and Not4 proteins are known components of the Ccr4-Not multimeric complex. Ccr4 and Caf1 have established roles in transcription, mRNA de-adenylation and RNA degradation etc., while Not4 was shown to have important roles in regulating translation and protein quality control pathways. Here we show that Ccr4, Caf1, and Not4 have a novel function at a post-ubiquitylation step in the UPS pathway by promoting ubiquitin-dependent degradation of short-lived proteins by the 26S proteasome. Using a substrate of the well-studied ubiquitin fusion degradation (UFD) pathway, we found that its UPS-mediated degradation was severely impaired upon deletion of CCR4, CAF1, or NOT4 genes in Saccharomyces cerevisiae. Additionally, we show that Ccr4, Caf1, and Not4 bind to cellular ubiquitin conjugates, and that Ccr4 and Caf1 proteins interact with the proteasome. In contrast to Ccr4, Caf1, and Not4, other subunits of the Ccr4-Not complex are dispensable for UFD substrate degradation. From our findings we conclude that the Ccr4-Not complex subunits Ccr4, Caf1, and Not4 have a novel function outside of the canonical Ccr4-Not complex as a factor targeting ubiquitylated substrates for proteasomal degradation.
Collapse
Affiliation(s)
- Ganapathi Kandasamy
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, Telangana, India.
| | - Ashis Kumar Pradhan
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, Telangana, India
| | - R Palanimurugan
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, Telangana, India
| |
Collapse
|
24
|
Mattioni A, Boldt K, Auciello G, Komada M, Rappoport JZ, Ueffing M, Castagnoli L, Cesareni G, Santonico E. Ring Finger Protein 11 acts on ligand-activated EGFR via the direct interaction with the UIM region of ANKRD13 protein family. FEBS J 2020; 287:3526-3550. [PMID: 31985874 DOI: 10.1111/febs.15226] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 11/13/2019] [Accepted: 01/22/2020] [Indexed: 01/07/2023]
Abstract
RING finger protein 11 (RNF11) is an evolutionary conserved Really Interesting New Gene E3 ligase that is overexpressed in several human tumours. Although several reports have highlighted its involvement in crucial cellular processes, the mechanistic details underlying its function are still poorly understood. Utilizing stable isotope labelling by amino acids in culture (SILAC)-based proteomics analysis, we identified 51 proteins that co-immunoprecipitate with wild-type RNF11 and/or with its catalytically inactive mutant. We focused our attention on the interaction of RNF11 with Ankyrin repeat domain-containing protein 13 (ANKRD13)s family. Members of the ANKRD13 family contain ubiquitin-interacting motifs (UIM) that recognize the Lys-63-linked ubiquitin (Ub) chains appended to Epidermal growth factor receptor (EGFR) soon after ligand binding. We show that ANKRD13A, ANKRD13B and ANKRD13D form a complex with RNF11 in vivo and that the UIMs are required for complex formation. However, at odds with the conventional UIM binding mode, Ub modification of RNF11 is not required for the interaction with ANKRD13 proteins. We also show that the interaction between ANKRD13A and RNF11 is modulated by the EGF stimulus and that a complex formed by ANKRD13A, RNF11 and activated EGFR is transiently assembled in the early phases of receptor endocytosis. Moreover, loss of function of the E3 ligases Itchy E3 ubiquitin-protein ligase (ITCH) or RNF11, respectively, abrogates or increases the ubiquitination of endogenous ANKRD13A, affecting its ability to bind activated EGFR. We propose a model whereby the ANKRD13 proteins act as molecular scaffolds that promote the transient formation of a complex between the activated EGFR and the E3 ligases ITCH and RNF11. By regulating the ubiquitination status of ANKRD13A and consequently its endocytic adaptor function, RNF11 promotes sorting of the activated EGFR for lysosomal degradation.
Collapse
Affiliation(s)
- Anna Mattioni
- Department of Biology, University of Rome Tor Vergata, Italy
| | - Karsten Boldt
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Germany
| | - Giulio Auciello
- Istituto di Ricerche di Biologia Molecolare (IRBM), Pomezia, Italy
| | - Masayuki Komada
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | | | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Germany
| | | | - Gianni Cesareni
- Department of Biology, University of Rome Tor Vergata, Italy
- Fondazione Santa Lucia Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rome, Italy
| | - Elena Santonico
- Department of Biology, University of Rome Tor Vergata, Italy
| |
Collapse
|
25
|
Aichem A, Groettrup M. The ubiquitin-like modifier FAT10 - much more than a proteasome-targeting signal. J Cell Sci 2020; 133:133/14/jcs246041. [PMID: 32719056 DOI: 10.1242/jcs.246041] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10) also called ubiquitin D (UBD) is a member of the ubiquitin-like modifier (ULM) family. The FAT10 gene is localized in the MHC class I locus and FAT10 protein expression is mainly restricted to cells and organs of the immune system. In all other cell types and tissues, FAT10 expression is highly inducible by the pro-inflammatory cytokines interferon (IFN)-γ and tumor necrosis factor (TNF). Besides ubiquitin, FAT10 is the only ULM which directly targets its substrates for degradation by the 26S proteasome. This poses the question as to why two ULMs sharing the proteasome-targeting function have evolved and how they differ from each other. This Review summarizes the current knowledge of the special structure of FAT10 and highlights its differences from ubiquitin. We discuss how these differences might result in differential outcomes concerning proteasomal degradation mechanisms and non-covalent target interactions. Moreover, recent insights about the structural and functional impact of FAT10 interacting with specific non-covalent interaction partners are reviewed.
Collapse
Affiliation(s)
- Annette Aichem
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280 Kreuzlingen, Switzerland.,Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marcus Groettrup
- Biotechnology Institute Thurgau at the University of Konstanz, CH-8280 Kreuzlingen, Switzerland .,Division of Immunology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| |
Collapse
|
26
|
Santonico E. Old and New Concepts in Ubiquitin and NEDD8 Recognition. Biomolecules 2020; 10:biom10040566. [PMID: 32272761 PMCID: PMC7226360 DOI: 10.3390/biom10040566] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/16/2022] Open
Abstract
Post-translational modifications by ubiquitin and ubiquitin-like proteins (Ubls) have known roles in a myriad of cellular processes. Ubiquitin- and Ubl-binding domains transmit the information conferred by these post-translational modifications by recognizing functional surfaces and, when present, different chain structures. Numerous domains binding to ubiquitin have been characterized and their structures solved. Analogously, motifs selectively interacting with SUMO (small ubiquitin-like modifier) have been identified in several proteins and their role in SUMO-dependent processes investigated. On the other hand, proteins that specifically recognize other Ubl modifications are known only in a few cases. The high sequence identity between NEDD8 and ubiquitin has made the identification of specific NEDD8-binding domains further complicated due to the promiscuity in the recognition by several ubiquitin-binding domains. Two evolutionarily related domains, called CUBAN (cullin-binding domain associating with NEDD8) and CoCUN (cousin of CUBAN), have been recently described. The CUBAN binds monomeric NEDD8 and neddylated cullins, but it also interacts with di-ubiquitin chains. Conversely, the CoCUN domain only binds ubiquitin. CUBAN and CoCUN provide an intriguing example of how nature solved the issue of promiscuity versus selectivity in the recognition of these two highly related molecules. The structural information available to date suggests that the ancestor of CUBAN and CoCUN was a three-helix bundle domain that diversified in KHNYN (KH and NYN domain-containing) and N4BP1 (NEDD4-binding protein-1) by acquiring different features. Indeed, these domains diverged towards two recognition modes, that recall respectively the electrostatic interaction utilized by the E3-ligase RBX1/2 in the interaction with NEDD8, and the hydrophobic features described in the recognition of ubiquitin by CUE (coupling ubiquitin conjugation to ER degradation) domains. Intriguingly, CUBAN and CoCUN domains are only found in KHNYN and N4BP1, respectively, both proteins belonging to the PRORP family whose members are characterized by the combination of protein modules involved in RNA metabolism with domains mediating ubiquitin/NEDD8 recognition. This review recapitulates the current knowledge and recent findings of CUBAN and CoCUN domains and the proteins containing them.
Collapse
Affiliation(s)
- Elena Santonico
- Department of Biology, University of Rome Tor Vergata, Via della ricerca scientifica, 00133 Rome, Italy
| |
Collapse
|
27
|
The 'dark matter' of ubiquitin-mediated processes: opportunities and challenges in the identification of ubiquitin-binding domains. Biochem Soc Trans 2020; 47:1949-1962. [PMID: 31829417 DOI: 10.1042/bst20190869] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/05/2019] [Accepted: 11/28/2019] [Indexed: 12/19/2022]
Abstract
Ubiquitin modifications of target proteins act to localise, direct and specify a diverse range of cellular processes, many of which are biomedically relevant. To allow this diversity, ubiquitin modifications exhibit remarkable complexity, determined by a combination of polyubiquitin chain length, linkage type, numbers of ubiquitin chains per target, and decoration of ubiquitin with other small modifiers. However, many questions remain about how different ubiquitin signals are specifically recognised and transduced by the decoding ubiquitin-binding domains (UBDs) within ubiquitin-binding proteins. This review briefly outlines our current knowledge surrounding the diversity of UBDs, identifies key challenges in their discovery and considers recent structural studies with implications for the increasing complexity of UBD function and identification. Given the comparatively low numbers of functionally characterised polyubiquitin-selective UBDs relative to the ever-expanding variety of polyubiquitin modifications, it is possible that many UBDs have been overlooked, in part due to limitations of current approaches used to predict their presence within the proteome. Potential experimental approaches for UBD discovery are considered; web-based informatic analyses, Next-Generation Phage Display, deubiquitinase-resistant diubiquitin, proximity-dependent biotinylation and Ubiquitin-Phototrap, including possible advantages and limitations. The concepts discussed here work towards identifying new UBDs which may represent the 'dark matter' of the ubiquitin system.
Collapse
|
28
|
Liu C, Yang M, Liu L, Zhang Y, Zhu Q, Huang C, Wang H, Zhang Y, Li H, Li C, Huang B, Feng C, Zhou Y. Molecular basis of degenerative spinal disorders from a proteomic perspective (Review). Mol Med Rep 2019; 21:9-19. [PMID: 31746390 PMCID: PMC6896343 DOI: 10.3892/mmr.2019.10812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023] Open
Abstract
Intervertebral disc degeneration (IDD) and ligamentum flavum hypertrophy (LFH) are major causes of degenerative spinal disorders. Comparative and proteomic analysis was used to identify differentially expressed proteins (DEPs) in IDD and LFH discs compared with normal discs. Subsequent gene ontology term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of the DEPs in human IDD discs or LFH samples were performed to identify the biological processes and signaling pathways involved in IDD and LFH. The PI3K-AKT signaling pathway, advanced glycation endproducts-receptor for advanced glycation endproducts signaling pathway, p53 signaling pathway, and transforming growth factor-b signaling pathway were activated in disc degeneration. This review summarizes the recently identified DEPs, including prolargin, fibronectin 1, cartilage intermediate layer protein, cartilage oligomeric matrix protein, and collagen types I, II and IV, and their pathophysiological roles in degenerative spinal disorders, and may provide a deeper understanding of the pathological processes of human generative spinal disorders. The present review aimed to summarize significantly changed proteins in degenerative spinal disorders and provide a deeper understanding to prevent these diseases.
Collapse
Affiliation(s)
- Chang Liu
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Minghui Yang
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Libangxi Liu
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Yang Zhang
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Qi Zhu
- Medical Research Center, Southwestern Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Cong Huang
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Hongwei Wang
- Department of Orthopedics, General Hospital of Shenyang Military Area Command of Chinese PLA, Shenyang, Liaoning 110016, P.R. China
| | - Yaqing Zhang
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Haiyin Li
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Changqing Li
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Bo Huang
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Chencheng Feng
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| | - Yue Zhou
- Department of Orthopedics, Xinqiao Hospital, Army Medical University, Chongqing 400037, P.R. China
| |
Collapse
|
29
|
Wang L, Yang R, Cao Y, Zheng F, Meng X, Zhong Y, Chen G, Zhang W, Liu W. CLP1, a Novel Plant Homeo Domain Protein, Participates in Regulating Cellulase Gene Expression in the Filamentous Fungus Trichoderma reesei. Front Microbiol 2019; 10:1700. [PMID: 31447796 PMCID: PMC6691364 DOI: 10.3389/fmicb.2019.01700] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023] Open
Abstract
The stringent regulatory network of cellulase gene expression in the filamentous fungus Trichoderma reesei involves multiple transcriptional regulators. However, identification and mechanistic investigation of these regulators are still insufficient. Here, we identified a novel transcriptional regulator, CLP1, a plant homeo domain (PHD) Protein that participates in regulating T. reesei cellulase gene expression. Phylogenetic analyses demonstrated that CLP1 homologs are widely distributed in filamentous fungi including Trichoderma, Penicillium, Fusarium, Neurospora, and Aspergillus species. We demonstrated that CLP1 is a nuclear protein and lack of CLP1 significantly impaired the induced expression of cellulase genes. ChIP experiments showed CLP1 binding to the cellulase gene promoters specifically under cellulose conditions and compromised XYR1 occupancy on the same promoters in the absence of CLP1 at the early induction stage. XYR1 overexpression fully rescued the defect in cellulase production but not the defect in conidia formation in the clp1 null mutant. Further analysis showed that the PHD is required for the CLP1 appropriate subcellular localization as well as the induced cellulase gene expression and conidiation. Taken together, these data demonstrated an important role of CLP1 in the regulation of cellulase and xylanase gene expression in T. reesei.
Collapse
Affiliation(s)
- Lei Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Renfei Yang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yanli Cao
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Fanglin Zheng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| |
Collapse
|
30
|
Marshall RS, Vierstra RD. Dynamic Regulation of the 26S Proteasome: From Synthesis to Degradation. Front Mol Biosci 2019; 6:40. [PMID: 31231659 PMCID: PMC6568242 DOI: 10.3389/fmolb.2019.00040] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/09/2019] [Indexed: 01/12/2023] Open
Abstract
All eukaryotes rely on selective proteolysis to control the abundance of key regulatory proteins and maintain a healthy and properly functioning proteome. Most of this turnover is catalyzed by the 26S proteasome, an intricate, multi-subunit proteolytic machine. Proteasomes recognize and degrade proteins first marked with one or more chains of poly-ubiquitin, the addition of which is actuated by hundreds of ligases that individually identify appropriate substrates for ubiquitylation. Subsequent proteasomal digestion is essential and influences a myriad of cellular processes in species as diverse as plants, fungi and humans. Importantly, dysfunction of 26S proteasomes is associated with numerous human pathologies and profoundly impacts crop performance, thus making an understanding of proteasome dynamics critically relevant to almost all facets of human health and nutrition. Given this widespread significance, it is not surprising that sophisticated mechanisms have evolved to tightly regulate 26S proteasome assembly, abundance and activity in response to demand, organismal development and stress. These include controls on transcription and chaperone-mediated assembly, influences on proteasome localization and activity by an assortment of binding proteins and post-translational modifications, and ultimately the removal of excess or damaged particles via autophagy. Intriguingly, the autophagic clearance of damaged 26S proteasomes first involves their modification with ubiquitin, thus connecting ubiquitylation and autophagy as key regulatory events in proteasome quality control. This turnover is also influenced by two distinct biomolecular condensates that coalesce in the cytoplasm, one attracting damaged proteasomes for autophagy, and the other reversibly storing proteasomes during carbon starvation to protect them from autophagic clearance. In this review, we describe the current state of knowledge regarding the dynamic regulation of 26S proteasomes at all stages of their life cycle, illustrating how protein degradation through this proteolytic machine is tightly controlled to ensure optimal growth, development and longevity.
Collapse
Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| |
Collapse
|
31
|
Traub LM. A nanobody-based molecular toolkit provides new mechanistic insight into clathrin-coat initiation. eLife 2019; 8:41768. [PMID: 31038455 PMCID: PMC6524969 DOI: 10.7554/elife.41768] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/24/2019] [Indexed: 12/21/2022] Open
Abstract
Besides AP-2 and clathrin triskelia, clathrin coat inception depends on a group of early-arriving proteins including Fcho1/2 and Eps15/R. Using genome-edited cells, we described the role of the unstructured Fcho linker in stable AP-2 membrane deposition. Here, expanding this strategy in combination with a new set of llama nanobodies against EPS15 shows an FCHO1/2–EPS15/R partnership plays a decisive role in coat initiation. A nanobody containing an Asn-Pro-Phe peptide within the complementarity-determining region 3 loop is a function-blocking pseudoligand for tandem EPS15/R EH domains. Yet, in living cells, EH domains gathered at clathrin-coated structures are poorly accessible, indicating residence by endogenous NPF-bearing partners. Forcibly sequestering cytosolic EPS15 in genome-edited cells with nanobodies tethered to early endosomes or mitochondria changes the subcellular location and availability of EPS15. This combined approach has strong effects on clathrin coat structure and function by dictating the stability of AP-2 assemblies at the plasma membrane.
Collapse
Affiliation(s)
- Linton M Traub
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, United States
| |
Collapse
|
32
|
de Macêdo Mendes C, Teixeira DG, Lima JPMS, Lanza DCF. Characterization of putative proteins encoded by variable ORFs in white spot syndrome virus genome. BMC STRUCTURAL BIOLOGY 2019; 19:8. [PMID: 30999895 PMCID: PMC6474068 DOI: 10.1186/s12900-019-0106-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/28/2019] [Indexed: 01/07/2023]
Abstract
Background White Spot Syndrome Virus (WSSV) is an enveloped double-stranded DNA virus which causes mortality of several species of shrimp, being considered one of the main pathogens that affects global shrimp farming. This virus presents a complex genome of ~ 300 kb and viral isolates that present genomes with great identity. Despite this conservation, some variable regions in the WSSV genome occur in coding regions, and these putative proteins may have some relationship with viral adaptation and virulence mechanisms. Until now, the functions of these proteins were little studied. In this work, sequences and putative proteins encoded by WSSV variable regions were characterized in silico. Results The in silico approach enabled determining the variability of some sequences, as well as the identification of some domains resembling the Formin homology 2, RNA recognition motif, Xeroderma pigmentosum group D repair helicase, Hemagglutinin and Ankyrin motif. The information obtained from the sequences and the analysis of secondary and tertiary structure models allow to infer that some of these proteins possibly have functions related to protein modulation/degradation, intracellular transport, recombination and endosome fusion events. Conclusions The bioinformatics approaches were efficient in generating three-dimensional models and to identify domains, thereby enabling to propose possible functions for the putative polypeptides produced by the ORFs wsv129, wsv178, wsv249, wsv463a, wsv477, wsv479, wsv492, and wsv497. Electronic supplementary material The online version of this article (10.1186/s12900-019-0106-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cayro de Macêdo Mendes
- Applied Molecular Biology Lab - LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Diego Gomes Teixeira
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - João Paulo Matos Santos Lima
- Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel Carlos Ferreira Lanza
- Applied Molecular Biology Lab - LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil. .,Postgraduate Program in Bioinformatics, Federal University of Rio Grande do Norte, Natal, RN, Brazil. .,Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil.
| |
Collapse
|
33
|
Marshall RS, Hua Z, Mali S, McLoughlin F, Vierstra RD. ATG8-Binding UIM Proteins Define a New Class of Autophagy Adaptors and Receptors. Cell 2019; 177:766-781.e24. [PMID: 30955882 DOI: 10.1016/j.cell.2019.02.009] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/14/2019] [Accepted: 02/08/2019] [Indexed: 01/02/2023]
Abstract
During autophagy, vesicle dynamics and cargo recruitment are driven by numerous adaptors and receptors that become tethered to the phagophore through interactions with lipidated ATG8/LC3 decorating the expanding membrane. Most currently described ATG8-binding proteins exploit a well-defined ATG8-interacting motif (AIM, or LC3-interacting region [LIR]) that contacts a hydrophobic patch on ATG8 known as the LIR/AIM docking site (LDS). Here we describe a new class of ATG8 interactors that exploit ubiquitin-interacting motif (UIM)-like sequences for high-affinity binding to an alternative ATG8 interaction site. Assays with candidate UIM-containing proteins together with unbiased screens identified a large collection of UIM-based ATG8 interactors in plants, yeast, and humans. Analysis of a subset also harboring ubiquitin regulatory X (UBX) domains revealed a role for UIM-directed autophagy in clearing non-functional CDC48/p97 complexes, including some impaired in human disease. With this new class of adaptors and receptors, we greatly extend the reach of selective autophagy and identify new factors regulating autophagic vesicle dynamics.
Collapse
Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Sujina Mali
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
| |
Collapse
|
34
|
Schwintzer L, Aguado Roca E, Broemer M. TRIAD3/RNF216 E3 ligase specifically synthesises K63-linked ubiquitin chains and is inactivated by mutations associated with Gordon Holmes syndrome. Cell Death Discov 2019; 5:75. [PMID: 30886743 PMCID: PMC6411869 DOI: 10.1038/s41420-019-0158-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 02/23/2019] [Indexed: 11/13/2022] Open
Abstract
TRIAD3/RNF216 is a ubiquitin ligase of the RING-in-between-RING family. Recent publications identified TRIAD3 mutations in patients with neurological diseases, including Gordon Holmes syndrome and Huntington-like disorder. To understand the functional relevance of these disease-associated mutations, we have tested the ubiquitin ligase activity of mutated TRIAD3 in vitro. Several of these point mutations completely abrogated TRIAD3’s catalytic activity. Using mass spectrometry, we identified new TRIAD3-interacting proteins/substrates from mouse brain lysate, which provide a new link between TRIAD3 and processes involving clathrin-mediated endocytosis. Strikingly, we found that TRIAD3 synthesises specifically lysine-63 (K63)-linked poly-ubiquitin chains in vitro, a chain type that usually plays a role in mediating signalling events rather than triggering proteasomal degradation. Therefore, this finding is of great importance to further understand TRIAD3’s cellular role and loss-of-function in disease.
Collapse
Affiliation(s)
- Lukas Schwintzer
- Ubiquitin Signaling Group, German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
| | - Eva Aguado Roca
- Ubiquitin Signaling Group, German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
| | - Meike Broemer
- Ubiquitin Signaling Group, German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Str. 27, 53127 Bonn, Germany
| |
Collapse
|
35
|
Zuidema A, Wang W, Kreft M, Te Molder L, Hoekman L, Bleijerveld OB, Nahidiazar L, Janssen H, Sonnenberg A. Mechanisms of integrin αVβ5 clustering in flat clathrin lattices. J Cell Sci 2018; 131:jcs221317. [PMID: 30301780 DOI: 10.1242/jcs.221317] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/27/2018] [Indexed: 12/17/2023] Open
Abstract
The family of integrin transmembrane receptors is essential for the normal function of multicellular organisms by facilitating cell-extracellular matrix adhesion. The vitronectin-binding integrin αVβ5 localizes to focal adhesions (FAs) as well as poorly characterized flat clathrin lattices (FCLs). Here, we show that, in human keratinocytes, αVβ5 is predominantly found in FCLs, and formation of the αVβ5-containing FCLs requires the presence of vitronectin as ligand, Ca2+, and the clathrin adaptor proteins ARH (also known as LDLRAP1), Numb and EPS15/EPS15L1. Integrin chimeras, containing the extracellular and transmembrane domains of β5 and the cytoplasmic domains of β1 or β3, almost exclusively localize in FAs. Interestingly, lowering actomyosin-mediated contractility promotes integrin redistribution to FLCs in an integrin tail-dependent manner, while increasing cellular tension favors αVβ5 clustering in FAs. Our findings strongly indicate that clustering of integrin αVβ5 in FCLs is dictated by the β5 subunit cytoplasmic domain, cellular tension and recruitment of specific adaptor proteins to the β5 subunit cytoplasmic domains.
Collapse
Affiliation(s)
- Alba Zuidema
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Wei Wang
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Maaike Kreft
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Lisa Te Molder
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Liesbeth Hoekman
- Mass spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Onno B Bleijerveld
- Mass spectrometry/Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Leila Nahidiazar
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Hans Janssen
- Electron Microscopy Facility, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| | - Arnoud Sonnenberg
- Division of Cell Biology I, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, The Netherlands
| |
Collapse
|
36
|
Yadav U, Arya R, Kundu S, Sundd M. The “Recognition Helix” of the Type II Acyl Carrier Protein (ACP) Utilizes a “Ubiquitin Interacting Motif (UIM)”-like Surface To Bind Its Partners. Biochemistry 2018; 57:3690-3701. [DOI: 10.1021/acs.biochem.8b00220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Usha Yadav
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Richa Arya
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| |
Collapse
|
37
|
Bustamante HA, González AE, Cerda-Troncoso C, Shaughnessy R, Otth C, Soza A, Burgos PV. Interplay Between the Autophagy-Lysosomal Pathway and the Ubiquitin-Proteasome System: A Target for Therapeutic Development in Alzheimer's Disease. Front Cell Neurosci 2018; 12:126. [PMID: 29867359 PMCID: PMC5954036 DOI: 10.3389/fncel.2018.00126] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/20/2018] [Indexed: 12/14/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of age-related dementia leading to severe irreversible cognitive decline and massive neurodegeneration. While therapeutic approaches for managing symptoms are available, AD currently has no cure. AD associates with a progressive decline of the two major catabolic pathways of eukaryotic cells—the autophagy-lysosomal pathway (ALP) and the ubiquitin-proteasome system (UPS)—that contributes to the accumulation of harmful molecules implicated in synaptic plasticity and long-term memory impairment. One protein recently highlighted as the earliest initiator of these disturbances is the amyloid precursor protein (APP) intracellular C-terminal membrane fragment β (CTFβ), a key toxic agent with deleterious effects on neuronal function that has become an important pathogenic factor for AD and a potential biomarker for AD patients. This review focuses on the involvement of regulatory molecules and specific post-translational modifications (PTMs) that operate in the UPS and ALP to control a single proteostasis network to achieve protein balance. We discuss how these aspects can contribute to the development of novel strategies to strengthen the balance of key pathogenic proteins associated with AD.
Collapse
Affiliation(s)
- Hianara A Bustamante
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia, Chile
| | - Alexis E González
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Fundación Ciencia y Vida, Santiago, Chile
| | - Cristobal Cerda-Troncoso
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile
| | - Ronan Shaughnessy
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carola Otth
- Center for Interdisciplinary Studies on the Nervous System (CISNe), Universidad Austral de Chile, Valdivia, Chile.,Institute of Clinical Microbiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Andrea Soza
- Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Patricia V Burgos
- Institute of Physiology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Centro de Biología Celular y Biomedicina (CEBICEM), Facultad de Medicina y Ciencia, Universidad San Sebastián, Santiago, Chile.,Center for Aging and Regeneration (CARE), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
38
|
Critchley WR, Pellet-Many C, Ringham-Terry B, Harrison MA, Zachary IC, Ponnambalam S. Receptor Tyrosine Kinase Ubiquitination and De-Ubiquitination in Signal Transduction and Receptor Trafficking. Cells 2018; 7:E22. [PMID: 29543760 PMCID: PMC5870354 DOI: 10.3390/cells7030022] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 12/13/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are membrane-based sensors that enable rapid communication between cells and their environment. Evidence is now emerging that interdependent regulatory mechanisms, such as membrane trafficking, ubiquitination, proteolysis and gene expression, have substantial effects on RTK signal transduction and cellular responses. Different RTKs exhibit both basal and ligand-stimulated ubiquitination, linked to trafficking through different intracellular compartments including the secretory pathway, plasma membrane, endosomes and lysosomes. The ubiquitin ligase superfamily comprising the E1, E2 and E3 enzymes are increasingly implicated in this post-translational modification by adding mono- and polyubiquitin tags to RTKs. Conversely, removal of these ubiquitin tags by proteases called de-ubiquitinases (DUBs) enables RTK recycling for another round of ligand sensing and signal transduction. The endocytosis of basal and activated RTKs from the plasma membrane is closely linked to controlled proteolysis after trafficking and delivery to late endosomes and lysosomes. Proteolytic RTK fragments can also have the capacity to move to compartments such as the nucleus and regulate gene expression. Such mechanistic diversity now provides new opportunities for modulating RTK-regulated cellular responses in health and disease states.
Collapse
Affiliation(s)
- William R Critchley
- Endothelial Cell Biology Unit, School of Molecular & Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Caroline Pellet-Many
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | - Benjamin Ringham-Terry
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | | | - Ian C Zachary
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | - Sreenivasan Ponnambalam
- Endothelial Cell Biology Unit, School of Molecular & Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
39
|
Aguirre JD, Dunkerley KM, Lam R, Rusal M, Shaw GS. Impact of altered phosphorylation on loss of function of juvenile Parkinsonism-associated genetic variants of the E3 ligase parkin. J Biol Chem 2018. [PMID: 29530980 PMCID: PMC5925814 DOI: 10.1074/jbc.ra117.000605] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Autosomal recessive juvenile Parkinsonism (ARJP) is an inherited neurodegenerative disease in which 50% of affected individuals harbor mutations in the gene encoding the E3 ligase parkin. Parkin regulates the mitochondrial recycling pathway, which is induced by oxidative stress. In its native state, parkin is auto-inhibited by its N-terminal ubiquitin-like (Ubl) domain, which blocks the binding site for an incoming E2∼ubiquitin conjugate, needed for parkin's ubiquitination activity. Parkin is activated via phosphorylation of Ser-65 in its Ubl domain by PTEN-induced putative kinase 1 (PINK1) and a ubiquitin molecule phosphorylated at a position equivalent to Ser-65 in parkin. Here we have examined the underlying molecular mechanism of phosphorylation of parkin's Ubl domain carrying ARJP-associated substitutions and how altered phosphorylation modulates parkin activation and ubiquitination. We found that three substitutions in the Ubl domain (G12R, R33Q, and R42P) significantly decrease PINK1's ability to phosphorylate the Ubl domain. We noted that two basic loss-of-function substitutions (R33Q and R42P) are close to acidic patches in the proposed PINK1–parkin interface, indicating that ionic interactions at this site may be important for efficient parkin phosphorylation. Increased auto-ubiquitination with unique ubiquitin chain patterns was observed for two other Ubl domain substitutions (G12R and T55I), suggesting that these substitutions, along with phosphorylation, increase parkin degradation. Moreover, Ubl domain phosphorylation decreased its affinity for the potential effector protein ataxin-3, which edits ubiquitin chain building by parkin. Overall, our work provides a framework for the mechanisms of parkin's loss-of-function, indicating an interplay between ARJP-associated substitutions and phosphorylation of its Ubl domain.
Collapse
Affiliation(s)
- Jacob D Aguirre
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Karen M Dunkerley
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Rica Lam
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Michele Rusal
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Gary S Shaw
- From the Department of Biochemistry, University of Western Ontario, London, Ontario N6A 5C1, Canada
| |
Collapse
|
40
|
Polyglutamine-Independent Features in Ataxin-3 Aggregation and Pathogenesis of Machado-Joseph Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1049:275-288. [PMID: 29427109 DOI: 10.1007/978-3-319-71779-1_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The expansion of a trinucleotide (CAG) repeat, translated into a polyglutamine expanded sequence in the protein encoded by the MJD gene, was identified over 20 years ago as the causative mutation in a severe neurodegenerative disorder originally diagnosed in individuals of Portuguese ancestry. This incapacitating disease, called Machado-Joseph disease or spinocebellar ataxia type 3, is integrated into a larger group of neurodegenerative disorders-the polyglutamine expansion disorders-caused by extension of a CAG repeat in the coding sequence of otherwise unrelated genes. These diseases are generally linked with the appearance of intracellular inclusions , which despite having a controversial role in disease appearance and development represent a characteristic common fingerprint in all polyglutamine-related disorders. Although polyglutamine expansion is an obvious trigger for neuronal dysfunction, the role of the different domains of these complex proteins in the function and aggregation properties of the carrier proteins is being uncovered in recent studies. In this review the current knowledge about the structural and functional features of full-length ataxin-3 protein will be discussed. The intrinsic conformational dynamics and interplay between the globular and intrinsically disordered regions of ataxin-3 will be highlighted, and a perspective picture of the role of known ataxin-3 post-translational modifications on regulating ataxin-3 aggregation and function will be drawn.
Collapse
|
41
|
Gα s protein binds ubiquitin to regulate epidermal growth factor receptor endosomal sorting. Proc Natl Acad Sci U S A 2017; 114:13477-13482. [PMID: 29192023 DOI: 10.1073/pnas.1708215114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The Gαs subunit is classically involved in the signal transduction of G protein-coupled receptors (GPCRs) at the plasma membrane. Recent evidence has revealed noncanonical roles for Gαs in endosomal sorting of receptors to lysosomes. However, the mechanism of action of Gαs in this sorting step is still poorly characterized. Here, we report that Gαs interacts with ubiquitin to regulate the endosomal sorting of receptors for lysosomal degradation. We reveal that the N-terminal extremity of Gαs contains a ubiquitin-interacting motif (UIM), a sorting element usually found in the endosomal sorting complex required for transport (ESCRT) machinery responsible for sorting ubiquitinated receptors into intraluminal vesicles (ILVs) of multivesicular bodies (MVBs). Mutation of the UIM in Gαs confirmed the importance of ubiquitin interaction for the sorting of epidermal growth factor receptor (EGFR) into ILVs for lysosomal degradation. These findings demonstrate a role for Gαs as an integral component of the ubiquitin-dependent endosomal sorting machinery and highlight the dual role of Gαs in receptor trafficking and signaling for the fine-tuning of the cellular response.
Collapse
|
42
|
Teyssou E, Chartier L, Amador MDM, Lam R, Lautrette G, Nicol M, Machat S, Da Barroca S, Moigneu C, Mairey M, Larmonier T, Saker S, Dussert C, Forlani S, Fontaine B, Seilhean D, Bohl D, Boillée S, Meininger V, Couratier P, Salachas F, Stevanin G, Millecamps S. Novel UBQLN2 mutations linked to amyotrophic lateral sclerosis and atypical hereditary spastic paraplegia phenotype through defective HSP70-mediated proteolysis. Neurobiol Aging 2017; 58:239.e11-239.e20. [PMID: 28716533 DOI: 10.1016/j.neurobiolaging.2017.06.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/14/2017] [Accepted: 06/20/2017] [Indexed: 11/26/2022]
Abstract
Mutations in UBQLN2 have been associated with rare cases of X-linked juvenile and adult forms of amyotrophic lateral sclerosis (ALS) and ALS linked to frontotemporal dementia (FTD). Here, we report 1 known (c.1489C>T, p.Pro497Ser, P497S) and 3 novel (c.1481C>T, p.Pro494Leu, P494L; c.1498C>T, p.Pro500Ser, P500S; and c.1516C>G, p.Pro506Ala, P506A) missense mutations in the PXX domain of UBQLN2 in familial motor neuron diseases including ALS and spastic paraplegia (SP). A novel missense mutation (c.1462G>A, p.Ala488Thr, A488T) adjacent to this hotspot UBQLN2 domain was identified in a sporadic case of ALS. These mutations are conserved in mammals, are absent from ExAC and gnomAD browsers, and are predicted to be deleterious by SIFT in silico analysis. Patient lymphoblasts carrying a UBQLN2 mutation showed absence of ubiquilin-2 accumulation, disrupted binding with HSP70, and impaired autophagic pathway. Our results confirm the role of PXX repeat in ALS pathogenesis, show that UBQLN2-linked disease can manifest like a SP phenotype, evidence a highly reduced disease penetrance in females carrying UBQLN2 mutations, which is important information for genetic counseling, and underline the pivotal role of ubiquilin-2 in proteolysis regulation pathways.
Collapse
Affiliation(s)
- Elisa Teyssou
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Laura Chartier
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Maria-Del-Mar Amador
- Département de Neurologie, Assistance Publique Hôpitaux de Paris (APHP), Centre de ressources et de compétences SLA Ile de France, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Roselina Lam
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Géraldine Lautrette
- Service de Neurologie, Centre de ressources et de compétences SLA, CHU Dupuytren, Limoges, France
| | - Marie Nicol
- Service de Neurologie, Centre de ressources et de compétences SLA, CHU Dupuytren, Limoges, France
| | - Selma Machat
- Service de Neurologie, Centre de ressources et de compétences SLA, CHU Dupuytren, Limoges, France
| | - Sandra Da Barroca
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Carine Moigneu
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Mathilde Mairey
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Ecole Pratique des Hautes Etudes, EPHE, Université de recherche Paris Sciences et Lettres, Paris, France
| | | | - Safaa Saker
- Banque d'ADN et de cellules du Généthon, Evry, France
| | - Christelle Dussert
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Sylvie Forlani
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Bertrand Fontaine
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Département de Neurologie, Assistance Publique Hôpitaux de Paris (APHP), Centre de ressources et de compétences SLA Ile de France, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Danielle Seilhean
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Département de Neuropathologie, APHP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Delphine Bohl
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Séverine Boillée
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
| | - Vincent Meininger
- Département de Neurologie, Assistance Publique Hôpitaux de Paris (APHP), Centre de ressources et de compétences SLA Ile de France, Hôpital de la Pitié-Salpêtrière, Paris, France; Hôpital des Peupliers, Ramsay Générale de Santé, Paris, France
| | - Philippe Couratier
- Service de Neurologie, Centre de ressources et de compétences SLA, CHU Dupuytren, Limoges, France
| | - François Salachas
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Département de Neurologie, Assistance Publique Hôpitaux de Paris (APHP), Centre de ressources et de compétences SLA Ile de France, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Giovanni Stevanin
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France; Ecole Pratique des Hautes Etudes, EPHE, Université de recherche Paris Sciences et Lettres, Paris, France; Centre de Référence de Neurogénétique, Fédération de Génétique, APHP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Stéphanie Millecamps
- Inserm U1127, CNRS UMR7225, Sorbonne Universités, UPMC Univ Paris 6 UMRS1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.
| |
Collapse
|
43
|
Dong Y, Wu H, Dong J, Song K, Rahman HA, Towner R, Chen H. Mimetic peptide of ubiquitin-interacting motif of epsin as a cancer therapeutic-perspective in brain tumor therapy through regulating VEGFR2 signaling. VESSEL PLUS 2017; 1:3-11. [PMID: 29905336 PMCID: PMC5997290 DOI: 10.20517/2574-1209.2016.01] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Epsins, endocytic adaptor proteins required for internalization of ubiquitylated receptors, are generally upregulated in human cancers. It has been characterized that mice deficient of epsins in the endothelium inhibit tumor growth by dysregulating vascular endothelial growth factor receptor-2 (VEGFR2) signaling and non-productive tumor angiogenesis. Binding of the epsin ubiquitin (Ub)-interacting motif (UIM) with ubiquitylated VEGFR2 is a critical mechanism for epsin-dependent VEGFR2 endocytosis and degradation, indicative of epsin UIM as a potential therapeutic target. A Computer Assisted Drug Design approach was utilized to create the UIM mimetic peptides for the functional competition of epsin binding sites in ubiquitylated VEGFR2 in vivo. Specifically targeting VEGFR2 in the tumor vasculature, the chemically synthesized chimeric UIM peptide, UPI, causes non-functional tumor angiogenesis, retards tumor growth, and increases survival rates in several tumor models. The authors showed that UPI binds ubiquitylated VEGFR2 to form a supercomplex in an Ub-dependent fashion. Collectively, the UPI targeting strategy offers a potentially novel treatment for cancer patients who are resistant to current anti-angiogenic therapies. In this review, the authors outline the main points of this research specifically as a potential application for glioma tumor therapy.
Collapse
Affiliation(s)
- Yunzhou Dong
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hao Wu
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jerry Dong
- Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma, OK 73104, USA
| | - Kai Song
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Habibunnabi Ashiqur Rahman
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rheal Towner
- Advanced Magnetic Resonance Center, Oklahoma Medical Research Foundation, Oklahoma, OK 73104, USA
| | - Hong Chen
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
44
|
Manczyk N, Yates BP, Veggiani G, Ernst A, Sicheri F, Sidhu SS. Structural and functional characterization of a ubiquitin variant engineered for tight and specific binding to an alpha-helical ubiquitin interacting motif. Protein Sci 2017; 26:1060-1069. [PMID: 28276594 DOI: 10.1002/pro.3155] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/06/2017] [Indexed: 12/20/2022]
Abstract
Ubiquitin interacting motifs (UIMs) are short α-helices found in a number of eukaryotic proteins. UIMs interact weakly but specifically with ubiquitin conjugated to other proteins, and in so doing, mediate specific cellular signals. Here we used phage display to generate ubiquitin variants (UbVs) targeting the N-terminal UIM of the yeast Vps27 protein. Selections yielded UbV.v27.1, which recognized the cognate UIM with high specificity relative to other yeast UIMs and bound with an affinity more than two orders of magnitude higher than that of ubiquitin. Structural and mutational studies of the UbV.v27.1-UIM complex revealed the molecular details for the enhanced affinity and specificity of UbV.v27.1, and underscored the importance of changes at the binding interface as well as at positions that do not contact the UIM. Our study highlights the power of the phage display approach for selecting UbVs with unprecedented affinity and high selectivity for particular α-helical UIM domains within proteomes, and it establishes a general approach for the development of inhibitors targeting interactions of this type.
Collapse
Affiliation(s)
- Noah Manczyk
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Bradley P Yates
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Gianluca Veggiani
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Andreas Ernst
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, 60590, Germany
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| |
Collapse
|
45
|
Kawaguchi K, Uo K, Tanaka T, Komada M. Tandem UIMs confer Lys48 ubiquitin chain substrate preference to deubiquitinase USP25. Sci Rep 2017; 7:45037. [PMID: 28327663 PMCID: PMC5361193 DOI: 10.1038/srep45037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 02/20/2017] [Indexed: 11/21/2022] Open
Abstract
Ubiquitin-specific protease (USP) 25, belonging to the USP family of deubiquitinases, harbors two tandem ubiquitin-interacting motifs (UIMs), a ~20-amino-acid α-helical stretch that binds to ubiquitin. However, the role of the UIMs in USP25 remains unclear. Here we show that the tandem UIM region binds to Lys48-, but not Lys63-, linked ubiquitin chains, where the two UIMs played a critical and cooperative role. Purified USP25 exhibited higher ubiquitin isopeptidase activity to Lys48-, than to Lys63-, linked ubiquitin chains. Mutations that disrupted the ubiquitin-binding ability of the tandem UIMs resulted in a reduced ubiquitin isopeptidase activity of USP25, suggesting a role for the UIMs in exerting the full catalytic activity of USP25. Moreover, when mutations that convert the binding preference from Lys48- to Lys63-linked ubiquitin chains were introduced into the tandem UIM region, the USP25 mutants acquired elevated and reduced isopeptidase activity toward Lys63- and Lys48-linked ubiquitin chains, respectively. These results suggested that the binding preference of the tandem UIMs toward Lys48-linked ubiquitin chains contributes not only to the full catalytic activity but also to the ubiquitin chain substrate preference of USP25, possibly by selectively holding the Lys48-linked ubiquitin chain substrates in the proximity of the catalytic core.
Collapse
Affiliation(s)
- Kohei Kawaguchi
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Kazune Uo
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Toshiaki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Masayuki Komada
- Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama 226-8501, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| |
Collapse
|
46
|
Ottaviani D, Marin O, Arrigoni G, Franchin C, Vilardell J, Sandre M, Li W, Parfitt DA, Pinna LA, Cheetham ME, Ruzzene M. Protein kinase CK2 modulates HSJ1 function through phosphorylation of the UIM2 domain. Hum Mol Genet 2017; 26:611-623. [PMID: 28031292 PMCID: PMC5409130 DOI: 10.1093/hmg/ddw420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 11/13/2022] Open
Abstract
HSJ1 (DNAJB2), a member of the DNAJ family of molecular chaperones, is a key player in neuronal proteostasis maintenance. It binds ubiquitylated proteins through its Ubiquitin Interacting Motifs (UIMs) and facilitates their delivery to the proteasome for degradation. Mutations in the DNAJB2 gene lead to inherited neuropathies such as Charcot-Marie-Tooth type-2, distal hereditary motor neuropathies, spinal muscular atrophy with parkinsonism and the later stages can resemble amyotrophic lateral sclerosis. HSJ1 overexpression can reduce aggregation of neurodegeneration-associated proteins in vitro and in vivo; however, the regulation of HSJ1 function is little understood. Here we show that CK2, a ubiquitous and constitutively active protein kinase, phosphorylates HSJ1 within its second UIM, at the dominant site Ser250 and the hierarchical site Ser247. A phospho-HSJ1 specific antibody confirmed phosphorylation of endogenous HSJ1a and HSJ1b. A tandem approach of phospho-site mutation and treatment with CK2 specific inhibitors demonstrated that phosphorylation at these sites is accompanied by a reduced ability of HSJ1 to bind ubiquitylated clients and to exert its chaperone activity. Our results disclose a novel interplay between ubiquitin- and phosphorylation-dependent signalling, and represent the first report of a regulatory mechanism for UIM-dependent function. They also suggest that CK2 inhibitors could release the full neuroprotective potential of HSJ1, and deserve future interest as therapeutic strategies for neurodegenerative disease.
Collapse
Affiliation(s)
- Daniele Ottaviani
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| | - Oriano Marin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129 Padova, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129 Padova, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129 Padova, Italy
| | - Jordi Vilardell
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| | - Michele Sandre
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| | - Wenwen Li
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - David A. Parfitt
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Lorenzo A. Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| | | | - Maria Ruzzene
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| |
Collapse
|
47
|
Kristariyanto YA, Abdul Rehman SA, Weidlich S, Knebel A, Kulathu Y. A single MIU motif of MINDY-1 recognizes K48-linked polyubiquitin chains. EMBO Rep 2017; 18:392-402. [PMID: 28082312 DOI: 10.15252/embr.201643205] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 11/09/2022] Open
Abstract
The eight different types of ubiquitin (Ub) chains that can be formed play important roles in diverse cellular processes. Linkage-selective recognition of Ub chains by Ub-binding domain (UBD)-containing proteins is central to coupling different Ub signals to specific cellular responses. The motif interacting with ubiquitin (MIU) is a small UBD that has been characterized for its binding to monoUb. The recently discovered deubiquitinase MINDY-1/FAM63A contains a tandem MIU repeat (tMIU) that is highly selective at binding to K48-linked polyUb. We here identify that this linkage-selective binding is mediated by a single MIU motif (MIU2) in MINDY-1. The crystal structure of MIU2 in complex with K48-linked polyubiquitin chains reveals that MIU2 on its own binds to all three Ub moieties in an open conformation that can only be accommodated by K48-linked triUb. The weak Ub binder MIU1 increases overall affinity of the tMIU for polyUb chains without affecting its linkage selectivity. Our analyses reveal new concepts for linkage selectivity and polyUb recognition by UBDs.
Collapse
Affiliation(s)
- Yosua Adi Kristariyanto
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Syed Arif Abdul Rehman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| |
Collapse
|
48
|
SNX-1 and RME-8 oppose the assembly of HGRS-1/ESCRT-0 degradative microdomains on endosomes. Proc Natl Acad Sci U S A 2017; 114:E307-E316. [PMID: 28053230 DOI: 10.1073/pnas.1612730114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
After endocytosis, transmembrane cargo reaches endosomes, where it encounters complexes dedicated to opposing functions: recycling and degradation. Microdomains containing endosomal sorting complexes required for transport (ESCRT)-0 component Hrs [hepatocyte growth factor-regulated tyrosine kinase substrate (HGRS-1) in Caenorhabditis elegans] mediate cargo degradation, concentrating ubiquitinated cargo and organizing the activities of ESCRT. At the same time, retromer associated sorting nexin one (SNX-1) and its binding partner, J-domain protein RME-8, sort cargo away from degradation, promoting cargo recycling to the Golgi. Thus, we hypothesized that there could be important regulatory interactions between retromer and ESCRT that balance degradative and recycling functions. Taking advantage of the naturally large endosomes of the C. elegans coelomocyte, we visualized complementary ESCRT-0 and RME-8/SNX-1 microdomains in vivo and assayed the ability of retromer and ESCRT microdomains to regulate one another. We found in snx-1(0) and rme-8(ts) mutants increased endosomal coverage and intensity of HGRS-1-labeled microdomains, as well as increased total levels of HGRS-1 bound to membranes. These effects are specific to SNX-1 and RME-8, as loss of other retromer components SNX-3 and vacuolar protein sorting-associated protein 35 (VPS-35) did not affect HGRS-1 microdomains. Additionally, knockdown of hgrs-1 had little to no effect on SNX-1 and RME-8 microdomains, suggesting directionality to the interaction. Separation of the functionally distinct ESCRT-0 and SNX-1/RME-8 microdomains was also compromised in the absence of RME-8 and SNX-1, a phenomenon we observed to be conserved, as depletion of Snx1 and Snx2 in HeLa cells also led to greater overlap of Rme-8 and Hrs on endosomes.
Collapse
|
49
|
Song K, Wu H, Rahman HNA, Dong Y, Wen A, Brophy ML, Wong S, Kwak S, Bielenberg DR, Chen H. Endothelial epsins as regulators and potential therapeutic targets of tumor angiogenesis. Cell Mol Life Sci 2016; 74:393-398. [PMID: 27572288 DOI: 10.1007/s00018-016-2347-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/17/2016] [Accepted: 08/22/2016] [Indexed: 12/16/2022]
Abstract
VEGF-driven tumor angiogenesis has been validated as a central target in several tumor types deserving of continuous and further considerations to improve the efficacy and selectivity of the current therapeutic paradigms. Epsins, a family of endocytic clathrin adaptors, have been implicated in regulating endothelial cell VEGFR2 signaling, where its inactivation leads to nonproductive leaky neo-angiogenesis and, therefore, impedes tumor development and progression. Targeting endothelial epsins is of special significance due to its lack of affecting other angiogenic-signaling pathways or disrupting normal quiescent vessels, suggesting a selective modulation of tumor angiogenesis. This review highlights seminal findings on the critical role of endothelial epsins in tumor angiogenesis and their underlying molecular events, as well as strategies to prohibit the normal function of endogenous endothelial epsins that capitalize on these newly understood mechanisms.
Collapse
Affiliation(s)
- Kai Song
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Hao Wu
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - H N Ashiqur Rahman
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Yunzhou Dong
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Aiyun Wen
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Megan L Brophy
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Scott Wong
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Sukyoung Kwak
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Diane R Bielenberg
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Hong Chen
- Vascular Biology Program, Karp Family Research Laboratory, Department of Surgery, Boston Children's Hospital, Harvard Medical School, 12.214, 300 Longwood Avenue, Boston, MA, 02115, USA.
| |
Collapse
|
50
|
Sarath Babu N, Krishnan S, Brahmendra Swamy CV, Venkata Subbaiah GP, Gurava Reddy AV, Idris MM. Quantitative proteomic analysis of normal and degenerated human intervertebral disc. Spine J 2016; 16:989-1000. [PMID: 27125197 DOI: 10.1016/j.spinee.2016.03.051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 03/04/2016] [Accepted: 03/31/2016] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT Degenerative disc disease (DDD) is the most common disease of aging in humans. DDD is characterized by the gradual damage of the intervertebral discs. The disease is characterized by progressive dehydration of nucleus pulposus and disruption of annulus fibrosus of intervertebral disc. PURPOSE Even though it is highly prevalent, there is no effective therapy to regenerate the degenerated disc, or decrease or halt the disease progression. Therefore, novel monitoring and diagnostic tests are essential to develop an alternative therapeutic strategies which can prevent further progression of disc degeneration. STUDY DESIGN The study was designed to understand the proteome map of annulus fibrosus and nucleus pulposus tissues of intervertebral disc and its differential expression in patients with DDD. METHODS The proteome map of the annulus fibrosus and nucleus pulposus tissues of intervertebral disc was cataloged involving one-dimensional gel electrophoresis-Fourier transform mass spectrometry/ion trap tandem mass spectrometry (FTMS/ITMSMS) analysis. The altered proteome patterns of annulus fibrosus and nucleus pulposus tissues for DDD were identified using Isobaric tag for relative and absolute quantification (iTRAQ)-based quantitative proteomics coupled with FTMS/ITMSMS and network pathway analysis. RESULTS The study identified a total of 759 and 692 proteins from the annulus fibrosus and the nucleus pulposus tissues of the disc based on FTMS/ITMSMS analysis, which includes 118 proteins commonly identified between the two tissues. Vibrant changes were observed between the normal and the degenerating annulus fibrosus and nucleus pulposus tissues. A total of 73 and 54 proteins were identified as differentially regulated in the annulus and the nucleus tissues, respectively, between the normal and the degenerated tissues independently. Network pathway analysis mapped the differentially expressed proteins to cell adhesion, cell migration, and interleukin13 signaling pathways. CONCLUSIONS Altogether, the current study provides a novel vision in the biomechanism of human disc degeneration and a certain number of proteins with the potential biomarker value for the preliminary diagnosis and scenario of DDD.
Collapse
Affiliation(s)
| | | | | | - Goli P Venkata Subbaiah
- Sunshine Hospitals, SMART (Sunshine Medical Academy For Research and Training), Penderghast Rd, Secunderabad, 500003, India
| | | | | |
Collapse
|