1
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Valentino IM, Llivicota-Guaman JG, Dao TP, Mulvey EO, Lehman AM, Galagedera SKK, Mallon EL, Castañeda CA, Kraut DA. Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate. Proc Natl Acad Sci U S A 2024; 121:e2405964121. [PMID: 39121161 DOI: 10.1073/pnas.2405964121] [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: 03/22/2024] [Accepted: 06/26/2024] [Indexed: 08/11/2024] Open
Abstract
Ubiquitination is one of the most common posttranslational modifications in eukaryotic cells. Depending on the architecture of polyubiquitin chains, substrate proteins can meet different cellular fates, but our understanding of how chain linkage controls protein fate remains limited. UBL-UBA shuttle proteins, such as UBQLN2, bind to ubiquitinated proteins and to the proteasome or other protein quality control machinery elements and play a role in substrate fate determination. Under physiological conditions, UBQLN2 forms biomolecular condensates through phase separation, a physicochemical phenomenon in which multivalent interactions drive the formation of a macromolecule-rich dense phase. Ubiquitin and polyubiquitin chains modulate UBQLN2's phase separation in a linkage-dependent manner, suggesting a possible link to substrate fate determination, but polyubiquitinated substrates have not been examined directly. Using sedimentation assays and microscopy we show that polyubiquitinated substrates induce UBQLN2 phase separation and incorporate into the resulting condensates. This substrate effect is strongest with K63-linked substrates, intermediate with mixed-linkage substrates, and weakest with K48-linked substrates. Proteasomes can be recruited to these condensates, but proteasome activity toward K63-linked and mixed linkage substrates is inhibited in condensates. Substrates are also protected from deubiquitinases by UBQLN2-induced phase separation. Our results suggest that phase separation could regulate the fate of ubiquitinated substrates in a chain-linkage-dependent manner, thus serving as an interpreter of the ubiquitin code.
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Affiliation(s)
| | | | - Thuy P Dao
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erin O Mulvey
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Andrew M Lehman
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Sarasi K K Galagedera
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erica L Mallon
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Carlos A Castañeda
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Daniel A Kraut
- Department of Chemistry, Villanova University, Villanova, PA 19085
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2
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Suranjika S, Barla P, Sharma N, Dey N. A review on ubiquitin ligases: Orchestrators of plant resilience in adversity. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112180. [PMID: 38964613 DOI: 10.1016/j.plantsci.2024.112180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/19/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Ubiquitin- proteasome system (UPS) is universally present in plants and animals, mediating many cellular processes needed for growth and development. Plants constantly defend themselves against endogenous and exogenous stimuli such as hormonal signaling, biotic stresses such as viruses, fungi, nematodes, and abiotic stresses like drought, heat, and salinity by developing complex regulatory mechanisms. Ubiquitination is a regulatory mechanism involving selective elimination and stabilization of regulatory proteins through the UPS system where E3 ligases play a central role; they can bind to the targets in a substrate-specific manner, followed by poly-ubiquitylation, and subsequent protein degradation by 26 S proteasome. Increasing evidence suggests different types of E3 ligases play important roles in plant development and stress adaptation. Herein, we summarize recent advances in understanding the regulatory roles of different E3 ligases and primarily focus on protein ubiquitination in plant-environment interactions. It also highlights the diversity and complexity of these metabolic pathways that enable plant to survive under challenging conditions. This reader-friendly review provides a comprehensive overview of E3 ligases and their substrates associated with abiotic and biotic stresses that could be utilized for future crop improvement.
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Affiliation(s)
- Sandhya Suranjika
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India; Department of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), KIIT Road, Patia, Bhubaneswar, Odisha, India
| | - Preeti Barla
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India
| | - Namisha Sharma
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India
| | - Nrisingha Dey
- Institute of Life Sciences (ILS), an autonomous institute under Department of Biotechnology Government of India, NALCO Square, Bhubaneswar, Odisha, India.
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3
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Valentino IM, Llivicota-Guaman JG, Dao TP, Mulvey EO, Lehman AM, Galagedera SKK, Mallon EL, Castañeda CA, Kraut DA. Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585243. [PMID: 38559018 PMCID: PMC10980000 DOI: 10.1101/2024.03.15.585243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Ubiquitination is one of the most common post-translational modifications in eukaryotic cells. Depending on the architecture of polyubiquitin chains, substrate proteins can meet different cellular fates, but our understanding of how chain linkage controls protein fate remains limited. UBL-UBA shuttle proteins, such as UBQLN2, bind to ubiquitinated proteins and to the proteasome or other protein quality control machinery elements and play a role in substrate fate determination. Under physiological conditions, UBQLN2 forms biomolecular condensates through phase separation, a physicochemical phenomenon in which multivalent interactions drive the formation of a macromolecule-rich dense phase. Ubiquitin and polyubiquitin chains modulate UBQLN2's phase separation in a linkage-dependent manner, suggesting a possible link to substrate fate determination, but polyubiquitinated substrates have not been examined directly. Using sedimentation assays and microscopy we show that polyubiquitinated substrates induce UBQLN2 phase separation and incorporate into the resulting condensates. This substrate effect is strongest with K63-linked substrates, intermediate with mixed-linkage substrates, and weakest with K48-linked substrates. Proteasomes can be recruited to these condensates, but proteasome activity towards K63-linked and mixed linkage substrates is inhibited in condensates. Substrates are also protected from deubiquitinases by UBQLN2-induced phase separation. Our results suggest that phase separation could regulate the fate of ubiquitinated substrates in a chain-linkage dependent manner, thus serving as an interpreter of the ubiquitin code.
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Affiliation(s)
| | | | - Thuy P. Dao
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erin O. Mulvey
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Andrew M. Lehman
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Sarasi K. K. Galagedera
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Erica L. Mallon
- Department of Chemistry, Villanova University, Villanova, PA 19085
| | - Carlos A. Castañeda
- Department of Biology, Department of Chemistry, Bioinspired Institute, Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244
| | - Daniel A. Kraut
- Department of Chemistry, Villanova University, Villanova, PA 19085
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4
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Dao TP, Rajendran A, Galagedera SKK, Haws W, Castañeda CA. Short disordered termini and proline-rich domain are major regulators of UBQLN1/2/4 phase separation. Biophys J 2024; 123:1449-1457. [PMID: 38041404 PMCID: PMC11163289 DOI: 10.1016/j.bpj.2023.11.3401] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/03/2023] Open
Abstract
Highly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2, and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates, and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2, and UBQLN4 exhibit distinct phase behaviors in vitro. Strikingly, UBQLN4 phase separates at a much lower saturation concentration than UBQLN1. However, neither UBQLN1 nor UBQLN4 phase separates with a strong temperature dependence, unlike UBQLN2. We determined that the temperature-dependent phase behavior of UBQLN2 stems from its unique proline-rich region, which is absent in the other UBQLNs. We found that the short N-terminal disordered regions of UBQLN1, UBQLN2, and UBQLN4 inhibit UBQLN phase separation via electrostatics interactions. Charge variants of the N-terminal regions exhibit altered phase behaviors. Consistent with the sensitivity of UBQLN phase separation to the composition of the N-terminal regions, epitope tags placed on the N-termini of the UBQLNs tune phase separation. Overall, our in vitro results have important implications for studies of UBQLNs in cells, including the identification of phase separation as a potential mechanism to distinguish the cellular roles of UBQLNs and the need to apply caution when using epitope tags to prevent experimental artifacts.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | - Anitha Rajendran
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | | | - William Haws
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York
| | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York; Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, New York; BioInspired Institute, Syracuse University, Syracuse, New York.
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5
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Uceda AB, Mariño L, Casasnovas R, Adrover M. An overview on glycation: molecular mechanisms, impact on proteins, pathogenesis, and inhibition. Biophys Rev 2024; 16:189-218. [PMID: 38737201 PMCID: PMC11078917 DOI: 10.1007/s12551-024-01188-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/14/2024] Open
Abstract
The formation of a heterogeneous set of advanced glycation end products (AGEs) is the final outcome of a non-enzymatic process that occurs in vivo on long-life biomolecules. This process, known as glycation, starts with the reaction between reducing sugars, or their autoxidation products, with the amino groups of proteins, DNA, or lipids, thus gaining relevance under hyperglycemic conditions. Once AGEs are formed, they might affect the biological function of the biomacromolecule and, therefore, induce the development of pathophysiological events. In fact, the accumulation of AGEs has been pointed as a triggering factor of obesity, diabetes-related diseases, coronary artery disease, neurological disorders, or chronic renal failure, among others. Given the deleterious consequences of glycation, evolution has designed endogenous mechanisms to undo glycation or to prevent it. In addition, many exogenous molecules have also emerged as powerful glycation inhibitors. This review aims to provide an overview on what glycation is. It starts by explaining the similarities and differences between glycation and glycosylation. Then, it describes in detail the molecular mechanism underlying glycation reactions, and the bio-molecular targets with higher propensity to be glycated. Next, it discusses the precise effects of glycation on protein structure, function, and aggregation, and how computational chemistry has provided insights on these aspects. Finally, it reports the most prevalent diseases induced by glycation, and the endogenous mechanisms and the current therapeutic interventions against it.
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Affiliation(s)
- Ana Belén Uceda
- Departament de Química, Universitat de Les Illes Balears, Health Research Institute of the Balearic Islands (IdISBa), Ctra. Valldemossa Km 7.5, 07122 Palma, Spain
| | - Laura Mariño
- Departament de Química, Universitat de Les Illes Balears, Health Research Institute of the Balearic Islands (IdISBa), Ctra. Valldemossa Km 7.5, 07122 Palma, Spain
| | - Rodrigo Casasnovas
- Departament de Química, Universitat de Les Illes Balears, Health Research Institute of the Balearic Islands (IdISBa), Ctra. Valldemossa Km 7.5, 07122 Palma, Spain
| | - Miquel Adrover
- Departament de Química, Universitat de Les Illes Balears, Health Research Institute of the Balearic Islands (IdISBa), Ctra. Valldemossa Km 7.5, 07122 Palma, Spain
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6
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Waite KA, Vontz G, Lee SY, Roelofs J. Proteasome condensate formation is driven by multivalent interactions with shuttle factors and ubiquitin chains. Proc Natl Acad Sci U S A 2024; 121:e2310756121. [PMID: 38408252 DOI: 10.1073/pnas.2310756121] [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: 06/26/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024] Open
Abstract
Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome condensates in yeast depends on ubiquitin chains together with the proteasome shuttle factors Rad23 and Dsk2. These shuttle factors colocalize to these condensates. Strains deleted for the third shuttle factor gene, DDI1, show proteasome condensates in the absence of cellular stress, consistent with the accumulation of substrates with long K48-linked ubiquitin chains that accumulate in this mutant. We propose a model where the long K48-linked ubiquitin chains function as a scaffold for the ubiquitin-binding domains of the shuttle factors and the proteasome, allowing for the multivalent interactions that further drive condensate formation. Indeed, we determined different intrinsic ubiquitin receptors of the proteasome-Rpn1, Rpn10, and Rpn13-and the Ubl domains of Rad23 and Dsk2 are critical under different condensate-inducing conditions. In all, our data support a model where the cellular accumulation of substrates with long ubiquitin chains, potentially due to reduced cellular energy, allows for proteasome condensate formation. This suggests that proteasome condensates are not simply for proteasome storage, but function to sequester soluble ubiquitinated substrates together with inactive proteasomes.
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Affiliation(s)
- Kenrick A Waite
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Gabrielle Vontz
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Stella Y Lee
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Jeroen Roelofs
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160
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7
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Lin CY, Wu KY, Chi LM, Tang YH, Huang HJ, Lai CH, Tsai CN, Tsai CL. Starvation-inactivated MTOR triggers cell migration via a ULK1-SH3PXD2A/TKS5-MMP14 pathway in ovarian carcinoma. Autophagy 2023; 19:3151-3168. [PMID: 37505094 PMCID: PMC10621272 DOI: 10.1080/15548627.2023.2239633] [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: 11/16/2022] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
ABBREVIATIONS AMPK: AMP-activated protein kinase; CHX: cycloheximide; RAD001: everolimus; HBSS: Hanks' balanced salt solution; LC-MS/MS: liquid chromatography-mass spectrometry/mass spectrometry; MMP14: matrix metallopeptidase 14; MTOR: mechanistic target of rapamycin kinase; MAPK: mitogen-activated protein kinase; RB1CC1/FIP200: RB1 inducible coiled-coil 1; PtdIns3P: phosphatidylinositol-3-phosphate; PX: phox homology; SH3: Src homology 3; SH3PXD2A/TKS5: SH3 and PX domains 2A; SH3PXD2A-[6A]: S112A S142A S146A S147A S175A S348A mutant; ULK1: unc-51 like autophagy activating kinase 1.
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Affiliation(s)
- Chiao-Yun Lin
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Taoyuan City, Guishan District, Taiwan
| | - Kai-Yun Wu
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Taoyuan City, Guishan District, Taiwan
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Medical Center And Chang Gung University, Taoyuan City, Guishan District, Taiwan
| | - Lang-Ming Chi
- Molecular Medicine Research Center, Chang Gung University, Taoyuan City, Guishan District, Taiwan
| | - Yun-Hsin Tang
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Taoyuan City, Guishan District, Taiwan
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Medical Center And Chang Gung University, Taoyuan City, Guishan District, Taiwan
| | - Huei-Jean Huang
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Taoyuan City, Guishan District, Taiwan
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Medical Center And Chang Gung University, Taoyuan City, Guishan District, Taiwan
| | - Chyong-Huey Lai
- Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Taoyuan City, Guishan District, Taiwan
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Medical Center And Chang Gung University, Taoyuan City, Guishan District, Taiwan
| | - Chi-Neu Tsai
- Graduate Institute of Clinical Medical Science, Chang-Gung University, Taoyuan City, Guishan District, Taiwan
- Department of Surgery, New Taipei Municipal Tucheng Hospital, New Taipei City, Tucheng District, Taiwan
| | - Chia-Lung Tsai
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Taoyuan City, Guishan District, Taiwan
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8
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Li J, Wang H. Autophagy-dependent ferroptosis in infectious disease. J Transl Int Med 2023; 11:355-362. [PMID: 38130644 PMCID: PMC10732494 DOI: 10.2478/jtim-2023-0099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Autophagy is the initial defense response of the host against pathogens. Autophagy can be either non-selective or selective. It selectively targets the degradation of autophagic substrates through the sorting and transportation of autophagic receptor proteins. However, excessive autophagy activity will trigger cell death especially ferroptosis, which was characterized by the accumulation of lipid peroxide and free iron. Several certain types of selective autophagy degrade antioxidant systems and ferritin. Here, we summarized the latest researches of autophagy in infection and discuss the regulatory mechanisms and signaling pathways of autophagy-dependent ferroptosis.
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Affiliation(s)
- Jiarou Li
- Department of Critical Care Medicine, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin150086, Heilongjiang Province, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin150086, Heilongjiang Province, China
| | - Hongliang Wang
- Department of Critical Care Medicine, The Second Affiliated Hospital of Harbin Medical University, 246 Xuefu Road, Nangang District, Harbin150086, Heilongjiang Province, China
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9
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Hua Z. Deciphering the protein ubiquitylation system in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6487-6504. [PMID: 37688404 DOI: 10.1093/jxb/erad354] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 09/07/2023] [Indexed: 09/10/2023]
Abstract
Protein ubiquitylation is a post-translational modification (PTM) process that covalently modifies a protein substrate with either mono-ubiquitin moieties or poly-ubiquitin chains often at the lysine residues. In Arabidopsis, bioinformatic predictions have suggested that over 5% of its proteome constitutes the protein ubiquitylation system. Despite advancements in functional genomic studies in plants, only a small fraction of this bioinformatically predicted system has been functionally characterized. To expand our understanding about the regulatory function of protein ubiquitylation to that rivalling several other major systems, such as transcription regulation and epigenetics, I describe the status, issues, and new approaches of protein ubiquitylation studies in plant biology. I summarize the methods utilized in defining the ubiquitylation machinery by bioinformatics, identifying ubiquitylation substrates by proteomics, and characterizing the ubiquitin E3 ligase-substrate pathways by functional genomics. Based on the functional and evolutionary analyses of the F-box gene superfamily, I propose a deleterious duplication model for the large expansion of this family in plant genomes. Given this model, I present new perspectives of future functional genomic studies on the plant ubiquitylation system to focus on core and active groups of ubiquitin E3 ligase genes.
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Affiliation(s)
- Zhihua Hua
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
- Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
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10
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Zhang H, Han Y, Xiao W, Gao Y, Sui Z, Ren P, Meng F, Tang P, Yu Z. USP4 promotes the proliferation, migration, and invasion of esophageal squamous cell carcinoma by targeting TAK1. Cell Death Dis 2023; 14:730. [PMID: 37949874 PMCID: PMC10638297 DOI: 10.1038/s41419-023-06259-0] [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: 02/13/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
Ubiquitin-specific protease 4 (USP4) represents a potential oncogene involved in various human cancers. Nevertheless, the biological roles and precise mechanism of USP4 in esophageal squamous cell carcinoma (ESCC) progression are not understood. Here, USP4 expression was found to be markedly upregulated in ESCC tumor tissues and cells. Loss- and gain-of-function assays suggested that USP4 silencing inhibited ESCC cell proliferation, migration, and invasion, while USP4 overexpression promoted these behaviors. Consistently, USP4 silencing repressed tumor growth and metastasis in an ESCC nude mouse model in vivo. As a target molecule of USP4, transforming growth factor-β-activated kinase 1 (TAK1) also showed high expression in ESCC. Moreover, we observed that USP4 specifically interacted with TAK1 and stabilized TAK1 protein levels via deubiquitination in ESCC cells. Importantly, USP4 promotes ESCC proliferation, migration, and invasion via the MEK/ERK signaling pathway and can be inhibited by U0126. Neutral red (NR), an inhibitor of USP4 can suppress ESCC progression in vitro and in vivo. Overall, this study revealed that USP4/TAK1 plays crucial roles in ESCC progression by modulating proliferation, migration, and invasion, and USP4 might be a potential therapeutic target in ESCC.
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Affiliation(s)
- Hongdian Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China
| | - Youming Han
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China
- Binhai Hospital of Tianjin Medical University General Hospital, Tianjin, 300456, China
| | - Wanyi Xiao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China
| | - Yongyin Gao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China
| | - Zhilin Sui
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, 518116, China
| | - Peng Ren
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China
| | - Fanbiao Meng
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China.
| | - Peng Tang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China.
| | - Zhentao Yu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Digestive Cancer of Tianjin, Tianjin, 300060, China.
- National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and PeKing Union Medical College, Shenzhen, 518116, China.
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11
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Zhou Y, Xu K, Gao H, Yao W, Zhang Y, Zhang Y, Azhar Hussain M, Wang F, Yang X, Li H. Comparative Proteomic Analysis of Two Wild Soybean ( Glycine soja) Genotypes Reveals Positive Regulation of Saline-Alkaline Stress Tolerance by Tonoplast Transporters. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:14109-14124. [PMID: 37749803 DOI: 10.1021/acs.jafc.3c02111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Soil saline-alkalization is a significant constraint for soybean production. Owing to higher genetic diversity of wild soybean, we compared the proteomic landscape of saline-alkaline stress-tolerant (SWBY032) and stress-sensitive (SWLJ092) wild soybean (Glycine soja) strains under saline and saline-alkaline stress. Out of 346 differentially expressed proteins (DEPs) specifically involved in saline-alkaline stress, 159 and 133 DEPs were identified in only SWLJ092 and SWBY032, respectively. Functional annotations revealed that more ribosome proteins were downregulated in SWLJ092, whereas more membrane transporters were upregulated in SWBY032. Moreover, protein-protein interaction analysis of 133 DEPs revealed that 14 protein-synthesis- and 2 TCA-cycle-related DEPs might alter saline-alkaline tolerance by affecting protein synthesis and amino acid metabolism. Furthermore, we confirmed G. soja tonoplast intrinsic protein (GsTIP2-1 and GsTIP2-2), inositol transporter (GsINT1), sucrose transport protein (GsSUC4), and autoinhibited Ca2+-ATPase (GsACA11) as tonoplast transporters can synergistically improve saline-alkaline tolerance in soybean, possibly by relieving the inhibition of protein synthesis and amino acid metabolism. Overall, our findings provided a foundation for molecular breeding of a saline-alkaline stress-tolerant soybean.
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Affiliation(s)
- Yonggang Zhou
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Keheng Xu
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
| | - Hongtao Gao
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Wenbo Yao
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Yinhe Zhang
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Yuntong Zhang
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Muhammad Azhar Hussain
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570288, China
| | - Fawei Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China
| | - Xinquan Yang
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- School of Chemistry and Chemical Engineering, Guangzhou University, Guangzhou 510006, China
| | - Haiyan Li
- Sanya Nanfan Research Institute of Hainan University, Sanya 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
- College of Tropical Crops, Hainan University, Haikou 570288, China
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12
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Zhang YF, Huang J, Zhang WX, Liu YH, Wang X, Song J, Jin CY, Zhang SY. Tubulin degradation: Principles, agents, and applications. Bioorg Chem 2023; 139:106684. [PMID: 37356337 DOI: 10.1016/j.bioorg.2023.106684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/27/2023]
Abstract
The microtubule system plays an important role in the mitosis and growth of eukaryotic cells, and it is considered as an appealing and highly successful molecular target for cancer treatment. In fact, microtubule targeting agents, such as paclitaxel and vinblastine, have been approved by FDA for tumor therapy, which have achieved significant therapeutic effects and sales performance. At present, microtubule targeting agents mainly include microtubule-destabilizing agents, microtubule-stabilizing agents, and a few tubulin degradation agents. Although there are few reports about tubulin degradation agents at present, tubulin degradation agents show great potential in overcoming multidrug resistance and reducing neurotoxicity. In addition, some natural drugs could specifically degrade tubulin in tumor cells, but have no effect in normal cells, thus showing a good biosafety profile. Therefore, tubulin degradation agents might exhibit a better application. Currently, some small molecules have been designed to promote tubulin degradation with potent antiproliferative activities, showing the potential for cancer treatment. In this work, we reviewed the reports on tubulin degradation, and focused on the degradation mechanism and important functional groups of chemically synthesized compounds, hoping to provide help for the degradation design of tubulin.
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Affiliation(s)
- Yi-Fan Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Jiao Huang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Wei-Xin Zhang
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Yun-He Liu
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China
| | - Xiao Wang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jian Song
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Cheng-Yun Jin
- School of Pharmaceutical Sciences, Institute of Drug Discovery & Development, Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou 450001, China.
| | - Sai-Yang Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
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13
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Dao TP, Rajendran A, Galagedera SKK, Haws W, Castañeda CA. Short N-terminal disordered regions and the proline-rich domain are major regulators of phase transitions for full-length UBQLN1, UBQLN2 and UBQLN4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559790. [PMID: 37808720 PMCID: PMC10557701 DOI: 10.1101/2023.09.27.559790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Highly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2 and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2 and UBQLN4 exhibit distinct phase behaviors in vitro. Strikingly, UBQLN4 phase separates at a much lower saturation concentration than UBQLN1. However, neither UBQLN1 nor UBQLN4 phase separates with a strong temperature dependence, unlike UBQLN2. We determined that the temperature-dependent phase behavior of UBQLN2 stems from its unique proline-rich (Pxx) region, which is absent in the other UBQLNs. We found that the short N-terminal disordered regions of UBQLN1, UBQLN2 and UBQLN4 inhibit UBQLN phase separation via electrostatics interactions. Charge variants of the N-terminal regions exhibit altered phase behaviors. Consistent with the sensitivity of UBQLN phase separation to the composition of the N-terminal regions, epitope tags placed on the N-termini of the UBQLNs tune phase separation. Overall, our in vitro results have important implications for studies of UBQLNs in cells, including the identification of phase separation as a potential mechanism to distinguish the cellular roles of UBQLNs, and the need to apply caution when using epitope tags to prevent experimental artifacts.
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Affiliation(s)
- Thuy P. Dao
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Anitha Rajendran
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | | | - William Haws
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
| | - Carlos A. Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, NY 13244, USA
- Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, NY 13244, USA
- BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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14
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Davis C, Spaller BL, Choi E, Kurrasch J, Chong H, Elsasser S, Finley D, Matouschek A. A strict requirement in proteasome substrates for spacing between ubiquitin tag and degradation initiation elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552540. [PMID: 37609285 PMCID: PMC10441315 DOI: 10.1101/2023.08.08.552540] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Proteins are typically targeted to the proteasome for degradation through the attachment of ubiquitin chains and the proteasome initiates degradation at a disordered region within the target protein. Yet some proteins with ubiquitin chains and disordered regions escape degradation. Here we investigate how the position of the ubiquitin chain on the target protein relative to the disordered region modulates degradation and show that the distance between the two determines whether a protein is degraded efficiently. This distance depends on the type of the degradation tag and is likely a result of the separation on the proteasome between the receptor that binds the tag and the site that engages the disordered region.
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15
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Waite KA, Vontz G, Lee SY, Roelofs J. Proteasome condensate formation is driven by multivalent interactions with shuttle factors and K48-linked ubiquitin chains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.546446. [PMID: 37425862 PMCID: PMC10326979 DOI: 10.1101/2023.06.25.546446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Stress conditions can cause the relocalization of proteasomes to condensates in yeast and mammalian cells. The interactions that facilitate the formation of proteasome condensates, however, are unclear. Here, we show that the formation of proteasome condensates in yeast depends on long K48-linked ubiquitin chains together with the proteasome shuttle factors Rad23 and Dsk2. These shuttle factors colocalize to these condensates. Strains deleted for the third shuttle factor gene, DDI1 , show proteasome condensates in the absence of cellular stress, consistent with the accumulation of substrates with long K48-linked ubiquitin chains that accumulate in this mutant. We propose a model where the long K48-linked ubiquitin chains function as a scaffold for the ubiquitin binding domains of the shuttle factors and the proteasome, allowing for the multivalent interactions that further drive condensate formation. Indeed, we determined different intrinsic ubiquitin receptors of the proteasome (Rpn1, Rpn10, and Rpn13) are critical under different condensate inducing conditions. In all, our data support a model where the cellular accumulation of substrates with long ubiquitin chains, potentially due to reduced cellular energy, allows for proteasome condensate formation. This suggests that proteasome condensates are not simply for proteasome storage, but function to sequester soluble ubiquitinated substrates together with inactive proteasomes. Significance Stress conditions can cause the relocalization of proteasomes to condensates in yeast as well as mammalian cells. Our work shows that the formation of proteasome condensates in yeast depends on long K48-linked ubiquitin chains, the proteasome binding shuttle factors Rad23 and Dsk2 and proteasome intrinsic ubiquitin receptors. Here, different receptors are critical for different condensate inducers. These results indicate distinct condensates can form with specific functionality. Our identification of key factors involved in the process is crucial for understanding the function of proteasome relocalization to condensates. We propose that cellular accumulation of substrates with long ubiquitin chains results in the formation of condensates comprising those ubiquitinated substrates, proteasomes, and proteasome shuttle factors, where the ubiquitin chains serve as the scaffold for condensate formation.
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16
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Makaros Y, Raiff A, Timms RT, Wagh AR, Gueta MI, Bekturova A, Guez-Haddad J, Brodsky S, Opatowsky Y, Glickman MH, Elledge SJ, Koren I. Ubiquitin-independent proteasomal degradation driven by C-degron pathways. Mol Cell 2023; 83:1921-1935.e7. [PMID: 37201526 PMCID: PMC10237035 DOI: 10.1016/j.molcel.2023.04.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 03/13/2023] [Accepted: 04/25/2023] [Indexed: 05/20/2023]
Abstract
Although most eukaryotic proteins are targeted for proteasomal degradation by ubiquitination, a subset have been demonstrated to undergo ubiquitin-independent proteasomal degradation (UbInPD). However, little is known about the molecular mechanisms driving UbInPD and the degrons involved. Utilizing the GPS-peptidome approach, a systematic method for degron discovery, we found thousands of sequences that promote UbInPD; thus, UbInPD is more prevalent than currently appreciated. Furthermore, mutagenesis experiments revealed specific C-terminal degrons required for UbInPD. Stability profiling of a genome-wide collection of human open reading frames identified 69 full-length proteins subject to UbInPD. These included REC8 and CDCA4, proteins which control proliferation and survival, as well as mislocalized secretory proteins, suggesting that UbInPD performs both regulatory and protein quality control functions. In the context of full-length proteins, C termini also play a role in promoting UbInPD. Finally, we found that Ubiquilin family proteins mediate the proteasomal targeting of a subset of UbInPD substrates.
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Affiliation(s)
- Yaara Makaros
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Anat Raiff
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Richard T Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, Cambridgeshire CB2 0AW, UK
| | - Ajay R Wagh
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Mor Israel Gueta
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Aizat Bekturova
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Julia Guez-Haddad
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Sagie Brodsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yarden Opatowsky
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Michael H Glickman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel.
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17
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Yin SS, Chen C, Liu Z, Liu SL, Guo JH, Zhang C, Zhang QW, Gao FH. Isoalantolactone mediates the degradation of BCR-ABL protein in imatinib-resistant CML cells by down-regulating survivin. Cell Cycle 2023; 22:1407-1420. [PMID: 37202916 PMCID: PMC10281474 DOI: 10.1080/15384101.2023.2209963] [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: 02/09/2022] [Revised: 11/02/2022] [Accepted: 02/10/2023] [Indexed: 05/20/2023] Open
Abstract
Isoalantolactone (Iso) is a bioactive lactone isolated from the root of Inula helenium L, which has been reported to have many pharmacological effects. To investigate the role and mechanism of isoalantolactone in chronic myeloid leukemia (CML), we first investigated isoalantolactone's anti-proliferative effects on imatinib-sensitive and imatinib-resistant CML cells by CCK8. Flow cytometry was used to detect isoalantolactone-induced cell apoptosis. Survivin was overexpressed in KBM5 and KBM5T315I cells using the lentivirus vector pSIN-3×flag-PURO. In KBM5 and KBM5T315I cells, shRNA was used to knockdown survivin. Cellular Thermal Shift Assay (CETSA) was used to detect the interaction between isoalantolactone and survivin. The ubiquitin of survivin induced by isoalantolactone was detected through immunoprecipitation. Quantitative polymerase-chain reaction (Q-PCR) and western blotting were used to detect the levels of mRNA and protein. Isoalantolactone inhibits the proliferation and promotes apoptosis of imatinib-resistant CML cells. Although isoalantolactone inhibits the proteins of BCR-ABL and survivin, it cannot inhibit survivin and BCR-ABL mRNA levels. Simultaneously, it was shown that isoalantolactone can degrade survivin protein by increasing ubiquitination. It was demonstrated that isoalantolactone-induced survivin mediated downregulation of BCR-ABL protein. It was also revealed that isoalantolactone triggered BCR-ABL protein degradation via caspase-3. Altogether, isoalantolactone inhibits survivin through the ubiquitin proteasome pathway, and mediates BCR-ABL downregulation in a caspase-3 dependent manner. These data suggest that isoalantolactone is a natural compound, which can be used as a potential drug to treat TKI-resistant CML.
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MESH Headings
- Humans
- Imatinib Mesylate/pharmacology
- Imatinib Mesylate/therapeutic use
- Survivin
- Caspase 3
- Drug Resistance, Neoplasm
- Cell Proliferation
- Fusion Proteins, bcr-abl
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Apoptosis
- RNA, Messenger
- Ubiquitins/pharmacology
- Ubiquitins/therapeutic use
- Cell Line, Tumor
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Affiliation(s)
- Shan-Shan Yin
- Department of Oncology, Shanghai 9th People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chen Chen
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Wangfujing, Dongcheng District, Beijing, China
| | - Zhen Liu
- Department of Oncology, Shanghai 9th People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shan-Ling Liu
- Department of Clinical Laboratory, The First Hospital of Changsha City, Changsha, China
| | - Jia-Hui Guo
- Department of Oncology, Shanghai 9th People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Zhang
- Department of Geriatrics, Shanghai ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Quan-Wu Zhang
- Department of Pathology, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Feng-Hou Gao
- Department of Oncology, Shanghai 9th People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Raffeiner M, Zhu S, González-Fuente M, Üstün S. Interplay between autophagy and proteasome during protein turnover. TRENDS IN PLANT SCIENCE 2023; 28:698-714. [PMID: 36801193 DOI: 10.1016/j.tplants.2023.01.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 05/13/2023]
Abstract
Protein homeostasis is epitomized by an equilibrium between protein biosynthesis and degradation: the 'life and death' of proteins. Approximately one-third of newly synthesized proteins are degraded. As such, protein turnover is required to maintain cellular integrity and survival. Autophagy and the ubiquitin-proteasome system (UPS) are the two principal degradation pathways in eukaryotes. Both pathways orchestrate many cellular processes during development and upon environmental stimuli. Ubiquitination of degradation targets is used as a 'death' signal by both processes. Recent findings revealed a direct functional link between both pathways. Here, we summarize key findings in the field of protein homeostasis, with an emphasis on the newly revealed crosstalk between both degradation machineries and how it is decided which pathway facilitates target degradation.
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Affiliation(s)
- Margot Raffeiner
- Eberhard-Karls-Universität Tübingen, Zentrum für Molekular Biologie der Pflanzen, 72076 Tübingen, Germany; Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany
| | - Shanshuo Zhu
- Eberhard-Karls-Universität Tübingen, Zentrum für Molekular Biologie der Pflanzen, 72076 Tübingen, Germany; Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany
| | - Manuel González-Fuente
- Eberhard-Karls-Universität Tübingen, Zentrum für Molekular Biologie der Pflanzen, 72076 Tübingen, Germany; Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany
| | - Suayib Üstün
- Eberhard-Karls-Universität Tübingen, Zentrum für Molekular Biologie der Pflanzen, 72076 Tübingen, Germany; Faculty of Biology & Biotechnology, Ruhr-University of Bochum, 44780 Bochum, Germany.
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19
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Majid N, Khan RH. Protein aggregation: Consequences, mechanism, characterization and inhibitory strategies. Int J Biol Macromol 2023; 242:125123. [PMID: 37270122 DOI: 10.1016/j.ijbiomac.2023.125123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/01/2023] [Accepted: 05/25/2023] [Indexed: 06/05/2023]
Abstract
Proteins play a major role in the regulation of various cellular functions including the synthesis of structural components. But proteins are stable under physiological conditions only. A slight variation in environmental conditions can cost them huge in terms of conformational stability ultimately leading to aggregation. Under normal conditions, aggregated proteins are degraded or removed from the cell by a quality control system including ubiquitin-proteasomal machinery and autophagy. But they are burdened under diseased conditions or are impaired by the aggregated proteins leading to the generation of toxicity. The misfolding and aggregation of protein such as amyloid-β, α-synuclein, human lysozyme etc., are responsible for certain diseases including Alzheimer, Parkinson, and non- neuropathic systemic amyloidosis respectively. Extensive research has been done to find the therapeutics for such diseases but till now we have got only symptomatic treatment that will reduce the disease severity but will not target the initial formation of nucleus responsible for disease progression and propagation. Hence there is an urgent need to develop the drugs targeting the cause of the disease. For this, a wide knowledge related to misfolding and aggregation under the same heading is required as described in this review alongwith the strategies hypothesized and implemented till now. This will contribute a lot to the work of researchers in the field of neuroscience.
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Affiliation(s)
- Nabeela Majid
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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20
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Hao X, Sun J, Zhong L, Baudry M, Bi X. UBE3A deficiency-induced autophagy is associated with activation of AMPK-ULK1 and p53 pathways. Exp Neurol 2023; 363:114358. [PMID: 36849003 PMCID: PMC10073344 DOI: 10.1016/j.expneurol.2023.114358] [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: 12/27/2022] [Revised: 02/03/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
Angelman Syndrome (AS) is a neurodevelopmental disorder caused by deficiency of the maternally expressed UBE3A gene. The UBE3A proteins functions both as an E3 ligase in the ubiquitin-proteasome system (UPS), and as a transcriptional co-activator for steroid hormone receptors. Here we investigated the effects of UBE3A deficiency on autophagy in the cerebellum of AS mice and in COS1 cells. Numbers and size of LC3- and LAMP2-immunopositive puncta were increased in cerebellar Purkinje cells of AS mice, as compared to wildtype mice. Western blot analysis showed an increase in the conversion of LC3I to LC3II in AS mice, as expected from increased autophagy. Levels of active AMPK and of one of its substrates, ULK1, a factor involved in autophagy initiation, were also increased. Colocalization of LC3 with LAMP2 was increased and p62 levels were decreased, indicating an increase in autophagy flux. UBE3A deficiency was also associated with reduced levels of phosphorylated p53 in the cytosol and increased levels in nuclei, which favors autophagy induction. UBE3A siRNA knockdown in COS-1 cells resulted in increased size and intensity of LC3-immunopositive puncta and increased the LC3 II/I ratio, as compared to control siRNA-treated cells, confirming the results found in the cerebellum of AS mice. These results indicate that UBE3A deficiency enhances autophagic activity through activation of the AMPK-ULK1 pathway and alterations in p53.
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Affiliation(s)
- Xiaoning Hao
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Jiandong Sun
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Li Zhong
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Michel Baudry
- College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Xiaoning Bi
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA.
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21
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Kim SH, Nichols KD, Anderson EN, Liu Y, Ramesh N, Jia W, Kuerbis CJ, Scalf M, Smith LM, Pandey UB, Tibbetts RS. Axon guidance genes modulate neurotoxicity of ALS-associated UBQLN2. eLife 2023; 12:e84382. [PMID: 37039476 PMCID: PMC10147378 DOI: 10.7554/elife.84382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
Mutations in the ubiquitin (Ub) chaperone Ubiquilin 2 (UBQLN2) cause X-linked forms of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) through unknown mechanisms. Here, we show that aggregation-prone, ALS-associated mutants of UBQLN2 (UBQLN2ALS) trigger heat stress-dependent neurodegeneration in Drosophila. A genetic modifier screen implicated endolysosomal and axon guidance genes, including the netrin receptor, Unc-5, as key modulators of UBQLN2 toxicity. Reduced gene dosage of Unc-5 or its coreceptor Dcc/frazzled diminished neurodegenerative phenotypes, including motor dysfunction, neuromuscular junction defects, and shortened lifespan, in flies expressing UBQLN2ALS alleles. Induced pluripotent stem cells (iPSCs) harboring UBQLN2ALS knockin mutations exhibited lysosomal defects while inducible motor neurons (iMNs) expressing UBQLN2ALS alleles exhibited cytosolic UBQLN2 inclusions, reduced neurite complexity, and growth cone defects that were partially reversed by silencing of UNC5B and DCC. The combined findings suggest that altered growth cone dynamics are a conserved pathomechanism in UBQLN2-associated ALS/FTD.
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Affiliation(s)
- Sang Hwa Kim
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Kye D Nichols
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Yining Liu
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Nandini Ramesh
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Weiyan Jia
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Connor J Kuerbis
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin-MadisonMadisonUnited States
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical CenterPittsburghUnited States
| | - Randal S Tibbetts
- Department of Human Oncology, University of Wisconsin School of Medicine and Public HealthMadisonUnited States
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22
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Wang Z, Li T, Zhang X, Feng J, Liu Z, Shan W, Joosten MHAJ, Govers F, Du Y. A Phytophthora infestans RXLR effector targets a potato ubiquitin-like domain-containing protein to inhibit the proteasome activity and hamper plant immunity. THE NEW PHYTOLOGIST 2023; 238:781-797. [PMID: 36653957 DOI: 10.1111/nph.18749] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Ubiquitin-like domain-containing proteins (UDPs) are involved in the ubiquitin-proteasome system because of their ability to interact with the 26S proteasome. Here, we identified potato StUDP as a target of the Phytophthora infestans RXLR effector Pi06432 (PITG_06432), which supresses the salicylic acid (SA)-related immune pathway. By overexpressing and silencing of StUDP in potato, we show that StUDP negatively regulates plant immunity against P. infestans. StUDP interacts with, and destabilizes, the 26S proteasome subunit that is referred to as REGULATORY PARTICLE TRIPLE-A ATP-ASE (RPT) subunit StRPT3b. This destabilization represses the proteasome activity. Proteomic analysis and Western blotting show that StUDP decreases the stability of the master transcription factor SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (SARD1) in SA biosynthesis. StUDP negatively regulates the SA signalling pathway by repressing the proteasome activity and destabilizing StSARD1, leading to a decreased expression of the SARD1-targeted gene ISOCHORISMATE SYNTHASE 1 and thereby a decrease in SA content. Pi06432 stabilizes StUDP, and it depends on StUDP to destabilize StRPT3b and thereby supress the proteasome activity. Our study reveals that the P. infestans effector Pi06432 targets StUDP to hamper the homeostasis of the proteasome by the degradation of the proteasome subunit StRPT3b and thereby suppresses SA-related immunity.
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Affiliation(s)
- Ziwei Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, Shaanxi, 712100, China
| | - Xiaojiang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jiashu Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhuting Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Weixing Shan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Matthieu H A J Joosten
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Yu Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Shaanxi Engineering Research Center for Vegetables, Yangling, Shaanxi, 712100, China
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23
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Zhang J, Cao L, Gao A, Ren R, Yu L, Li Q, Liu Y, Qi W, Hou Y, Sui W, Su G, Zhang Y, Zhang C, Zhang M. E3 ligase RNF99 negatively regulates TLR-mediated inflammatory immune response via K48-linked ubiquitination of TAB2. Cell Death Differ 2023; 30:966-978. [PMID: 36681779 PMCID: PMC10070438 DOI: 10.1038/s41418-023-01115-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/23/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
Innate immunity is the first line to defend against pathogenic microorganisms, and Toll-like receptor (TLR)-mediated inflammatory responses are an essential component of innate immunity. However, the regulatory mechanisms of TLRs in innate immunity remain unperfected. We found that the expression of E3 ligase Ring finger protein 99 (RNF99) decreased significantly in peripheral blood monocytes from patients infected with Gram negative bacteria (G-) and macrophages stimulated by TLRs ligands, indicating the role of RNF99. We also demonstrated for the first time, the protective role of RNF99 against LPS-induced septic shock and dextran sodium sulfate (DSS)-induced colitis using RNF99 knockout mice (RNF99-/-) and bone marrow-transplanted mice. In vitro experiments revealed that RNF99 deficiency significantly promoted TLR-mediated inflammatory cytokine expression and activated the NF-κB and MAPK pathways in macrophages. Mechanistically, in both macrophages and HEK293 cell line with TLR4 stably transfection, RNF99 interacted with and degraded TAK1-binding protein (TAB) 2, a regulatory protein of the kinase TAK1, via the lysine (K)48-linked ubiquitin-proteasomal pathway on lysine 611 of TAB2, which further regulated the TLR-mediated inflammatory response. Overall, these findings indicated the physiological significance of RNF99 in macrophages in regulating TLR-mediated inflammatory reactions. It provided new insight into TLRs signal transduction, and offered a novel approach for preventing bacterial infections, endotoxin shock, and other inflammatory ills.
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Affiliation(s)
- Jie Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lei Cao
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Amy Gao
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Ruiqing Ren
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Liwen Yu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Qian Li
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yapeng Liu
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Wenqian Qi
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yonghao Hou
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Wenhai Sui
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Guohai Su
- Cardiovascular Disease Research Center, Jinan Central Hospital, Shandong First Medical University, Jinan, Shandong, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
- Cardiovascular Disease Research Center, Jinan Central Hospital, Shandong First Medical University, Jinan, Shandong, China
| | - Cheng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Cardiovascular Disease Research Center, Jinan Central Hospital, Shandong First Medical University, Jinan, Shandong, China.
| | - Meng Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
- Cardiovascular Disease Research Center, Jinan Central Hospital, Shandong First Medical University, Jinan, Shandong, China.
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24
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Tsui H, van Kampen SJ, Han SJ, Meraviglia V, van Ham WB, Casini S, van der Kraak P, Vink A, Yin X, Mayr M, Bossu A, Marchal GA, Monshouwer-Kloots J, Eding J, Versteeg D, de Ruiter H, Bezstarosti K, Groeneweg J, Klaasen SJ, van Laake LW, Demmers JAA, Kops GJPL, Mummery CL, van Veen TAB, Remme CA, Bellin M, van Rooij E. Desmosomal protein degradation as an underlying cause of arrhythmogenic cardiomyopathy. Sci Transl Med 2023; 15:eadd4248. [PMID: 36947592 DOI: 10.1126/scitranslmed.add4248] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023]
Abstract
Arrhythmogenic cardiomyopathy (ACM) is an inherited progressive cardiac disease. Many patients with ACM harbor mutations in desmosomal genes, predominantly in plakophilin-2 (PKP2). Although the genetic basis of ACM is well characterized, the underlying disease-driving mechanisms remain unresolved. Explanted hearts from patients with ACM had less PKP2 compared with healthy hearts, which correlated with reduced expression of desmosomal and adherens junction (AJ) proteins. These proteins were also disorganized in areas of fibrotic remodeling. In vitro data from human-induced pluripotent stem cell-derived cardiomyocytes and microtissues carrying the heterozygous PKP2 c.2013delC pathogenic mutation also displayed impaired contractility. Knockin mice carrying the equivalent heterozygous Pkp2 c.1755delA mutation recapitulated changes in desmosomal and AJ proteins and displayed cardiac dysfunction and fibrosis with age. Global proteomics analysis of 4-month-old heterozygous Pkp2 c.1755delA hearts indicated involvement of the ubiquitin-proteasome system (UPS) in ACM pathogenesis. Inhibition of the UPS in mutant mice increased area composita proteins and improved calcium dynamics in isolated cardiomyocytes. Additional proteomics analyses identified lysine ubiquitination sites on the desmosomal proteins, which were more ubiquitinated in mutant mice. In summary, we show that a plakophilin-2 mutation can lead to decreased desmosomal and AJ protein expression through a UPS-dependent mechanism, which preceded cardiac remodeling. These findings suggest that targeting protein degradation and improving desmosomal protein stability may be a potential therapeutic strategy for the treatment of ACM.
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Affiliation(s)
- Hoyee Tsui
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Sebastiaan Johannes van Kampen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Su Ji Han
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Viviana Meraviglia
- Department of Anatomy and Embryology, University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Willem B van Ham
- Department of Medical Physiology, University Medical Center Utrecht, 3584 CM, Netherlands
| | - Simona Casini
- Department of Clinical and Experimental Cardiology, University Medical Center Amsterdam, 1105 AZ, Netherlands
| | - Petra van der Kraak
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Netherlands
| | - Aryan Vink
- Department of Pathology, University Medical Center Utrecht, 3584 CX, Netherlands
| | - Xiaoke Yin
- James Black Centre, King's College, University of London, WC2R 2LS London, UK
| | - Manuel Mayr
- James Black Centre, King's College, University of London, WC2R 2LS London, UK
| | - Alexandre Bossu
- Department of Medical Physiology, University Medical Center Utrecht, 3584 CM, Netherlands
| | - Gerard A Marchal
- Department of Clinical and Experimental Cardiology, University Medical Center Amsterdam, 1105 AZ, Netherlands
| | - Jantine Monshouwer-Kloots
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Joep Eding
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Danielle Versteeg
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Hesther de Ruiter
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus Medical Center Rotterdam, 3015 CN, Netherlands
| | - Judith Groeneweg
- Department of Cardiology, University Medical Center Utrecht, 3584 CX, Netherlands
| | - Sjoerd J Klaasen
- Oncode Institute, Hubrecht Institute, Royal Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Linda W van Laake
- Department of Cardiology, University Medical Center Utrecht, 3584 CX, Netherlands
| | - Jeroen A A Demmers
- Proteomics Center, Erasmus Medical Center Rotterdam, 3015 CN, Netherlands
| | - Geert J P L Kops
- Oncode Institute, Hubrecht Institute, Royal Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
| | - Christine L Mummery
- Department of Anatomy and Embryology, University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Toon A B van Veen
- Department of Medical Physiology, University Medical Center Utrecht, 3584 CM, Netherlands
| | - Carol Ann Remme
- Department of Clinical and Experimental Cardiology, University Medical Center Amsterdam, 1105 AZ, Netherlands
| | - Milena Bellin
- Department of Anatomy and Embryology, University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Eva van Rooij
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT, Netherlands
- Department of Cardiology, University Medical Center Utrecht, 3584 CX, Netherlands
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25
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Wang YX, Lin SR, Xu LZ, Ye YY, Qi PZ, Wang WF, Buttino I, Li HF, Guo BY. Comparative transcriptomic analysis revealed changes in multiple signaling pathways involved in protein degradation in the digestive gland of Mytilus coruscus during high-temperatures. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 46:101060. [PMID: 36731219 DOI: 10.1016/j.cbd.2023.101060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 01/28/2023]
Abstract
As a result of global warming, the Mytilus coruscus living attached in the intertidal zone experience extreme and fluctuating changes in temperature, and extreme temperature changes are causing mass mortality of intertidal species. This study explores the transcriptional response of M. coruscus at different temperatures (18 °C, 26 °C, and 33 °C) and different times (0, 12, and 24 h) of action by analyzing the potential temperature of the intertidal zone. In response to high temperatures, several signaling pathways in M. coruscus, ribosome, endocytosis, endoplasmic reticulum stress, protein degradation, and lysosomes, interact to counter the adverse effects of high temperatures on protein homeostasis. Increased expression of key genes, including heat shock proteins (Hsp70, Hsp20, and Hsp110), Lysosome-associated membrane glycoprotein (LAMP), endoplasmic reticulum chaperone (BiP), and baculoviral IAP repeat-containing protein 7 (BIRC7), may further mitigate the effects of heat stress and delay mortality in M. coruscus. These results reveal changes in multiple signaling pathways involved in protein degradation during high-temperature stress, which will contribute to our overall understanding of the molecular mechanisms underlying the response of M. coruscus to high-temperature stress.
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Affiliation(s)
- Yu-Xia Wang
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Shuang-Rui Lin
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Le-Zhong Xu
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Ying-Ying Ye
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Peng-Zhi Qi
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Wei-Feng Wang
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China
| | - Isabella Buttino
- Italian Institute for Environmental Protection and Research ISPRA, Via del Cedro n.38, 57122 Livorno, Italy
| | - Hong-Fei Li
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China.
| | - Bao-Ying Guo
- National Engineering Research Center for Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022 Zhoushan, China.
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26
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Gómez-Tortosa E, Baradaran-Heravi Y, Dillen L, Choudhury NR, Agüero Rabes P, Pérez-Pérez J, Kocoglu C, Sainz MJ, Ruiz González A, Téllez R, Cremades-Jimeno L, Cárdaba B, Van Broeckhoven C, Michlewski G, van der Zee J. TRIM25 mutation (p.C168*), coding for an E3 ubiquitin ligase, is a cause of early-onset autosomal dominant dementia with amyloid load and parkinsonism. Alzheimers Dement 2022. [PMID: 36576960 DOI: 10.1002/alz.12913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/27/2022] [Accepted: 11/10/2022] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Patients with familial early-onset dementia (EOD) pose a unique opportunity for gene identification studies. METHODS We present the phenotype and whole-exome sequencing (WES) study of an autosomal dominant EOD family. Candidate genes were examined in a set of dementia cases and controls (n = 3712). Western blotting was conducted of the wild-type and mutant protein of the final candidate. RESULTS Age at disease onset was 60 years (range 56 to 63). The phenotype comprised mixed amnestic and behavioral features, and parkinsonism. Cerebrospinal fluid and plasma biomarkers, and a positron emission tomography amyloid study suggested Alzheimer's disease. WES and the segregation pattern pointed to a nonsense mutation in the TRIM25 gene (p.C168*), coding for an E3 ubiquitin ligase, which was absent in the cohorts studied. Protein studies supported a loss-of-function mechanism. DISCUSSION This study supports a new physiopathological mechanism for brain amyloidosis. Furthermore, it extends the role of E3 ubiquitin ligases dysfunction in the development of neurodegenerative diseases. HIGHLIGHTS A TRIM25 nonsense mutation (p.C168*) is associated with autosomal dominant early-onset dementia and parkinsonism with biomarkers suggestive of Alzheimer's disease. TRIM25 protein studies support that the mutation exerts its effect through loss of function. TRIM25, an E3 ubiquitin ligase, is known for its role in the innate immune response but this is the first report of association with neurodegeneration. The role of TRIM25 dysfunction in development of amyloidosis and neurodegeneration merits a new line of research.
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Affiliation(s)
| | - Yalda Baradaran-Heravi
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Lubina Dillen
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Nila Roy Choudhury
- Infection Medicine, University of Edinburgh, The Chancellor's Building, Edinburgh, UK
| | | | | | - Cemile Kocoglu
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - M José Sainz
- Department of Neurology, Fundación Jiménez Díaz, Madrid, Spain
| | | | - Raquel Téllez
- Department of Immunology, Fundación Jiménez Díaz, Madrid, Spain
| | | | - Blanca Cárdaba
- Department of Immunology, Fundación Jiménez Díaz, Madrid, Spain
| | -
- Department of Neurology, Fundación Jiménez Díaz, Madrid, Spain
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Gracjan Michlewski
- Infection Medicine, University of Edinburgh, The Chancellor's Building, Edinburgh, UK.,Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Julie van der Zee
- Neurodegenerative Brain Diseases, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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27
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Sparks A, Kelly CJ, Saville MK. Ubiquitin receptors play redundant roles in the proteasomal degradation of the p53 repressor MDM2. FEBS Lett 2022; 596:2746-2767. [PMID: 35735670 PMCID: PMC9796813 DOI: 10.1002/1873-3468.14436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/01/2022] [Accepted: 06/05/2022] [Indexed: 01/07/2023]
Abstract
Much remains to be determined about the participation of ubiquitin receptors in proteasomal degradation and their potential as therapeutic targets. Suppression of the ubiquitin receptor S5A/PSMD4/hRpn10 alone stabilises p53/TP53 but not the key p53 repressor MDM2. Here, we observed S5A and the ubiquitin receptors ADRM1/PSMD16/hRpn13 and RAD23A and B functionally overlap in MDM2 degradation. We provide further evidence that degradation of only a subset of ubiquitinated proteins is sensitive to S5A knockdown because ubiquitin receptor redundancy is commonplace. p53 can be upregulated by S5A modulation while degradation of substrates with redundant receptors is maintained. Our observations and analysis of Cancer Dependency Map (DepMap) screens show S5A depletion/loss substantially reduces cancer cell line viability. This and selective S5A dependency of proteasomal substrates make S5A a target of interest for cancer therapy.
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Affiliation(s)
| | - Christopher J. Kelly
- School of MedicineUniversity of DundeeUK,Institute of Infection, Immunity and InflammationUniversity of GlasgowUK
| | - Mark K. Saville
- School of MedicineUniversity of DundeeUK,Silver River EditingDundeeUK
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28
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OMA1-mediated integrated stress response protects against ferroptosis in mitochondrial cardiomyopathy. Cell Metab 2022; 34:1875-1891.e7. [PMID: 36113464 DOI: 10.1016/j.cmet.2022.08.017] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/24/2022] [Accepted: 08/19/2022] [Indexed: 01/11/2023]
Abstract
Cardiomyopathy and heart failure are common manifestations in mitochondrial disease caused by deficiencies in the oxidative phosphorylation (OXPHOS) system of mitochondria. Here, we demonstrate that the cardiac-specific loss of the assembly factor Cox10 of the cytochrome c oxidase causes mitochondrial cardiomyopathy in mice, which is associated with OXPHOS deficiency, lysosomal defects, and an aberrant mitochondrial morphology. Activation of the mitochondrial peptidase Oma1 in Cox10-/- mice results in mitochondrial fragmentation and induction of the integrated stress response (ISR) along the Oma1-Dele1-Atf4 signaling axis. Ablation of Oma1 or Dele1 in Cox10-/- mice aggravates cardiomyopathy. ISR inhibition impairs the cardiac glutathione metabolism, limits the selenium-dependent accumulation of the glutathione peroxidase Gpx4, and increases lipid peroxidation in the heart, ultimately culminating in ferroptosis. Our results demonstrate a protective role of the Oma1-Dele1-mediated ISR in mitochondrial cardiomyopathy and link ferroptosis to OXPHOS deficiency and mitochondrial disease.
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29
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Liu CX, Wang B, Zhu WP, Xu YF, Yang YY, Qian XH. An Endoplasmic Reticulum (ER)‐Targeting DNA Nanodevice for Autophagy‐Dependent Degradation of Proteins in Membrane‐Bound Organelles. Angew Chem Int Ed Engl 2022; 61:e202205509. [DOI: 10.1002/anie.202205509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Caixia X. Liu
- Shanghai Key Laboratory of Chemical Biology School of Pharmacy East China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Bin Wang
- Shanghai Key Laboratory of Chemical Biology School of Pharmacy East China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Weiping P. Zhu
- Shanghai Key Laboratory of Chemical Biology School of Pharmacy East China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism School of Pharmacy East China University of Science and Technology 130 Mei Long Road Shanghai 200237 China
| | - Yufang F. Xu
- Shanghai Key Laboratory of Chemical Biology School of Pharmacy East China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Yangyang Y. Yang
- Shanghai Key Laboratory of Chemical Biology School of Pharmacy East China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
| | - Xuhong H. Qian
- Shanghai Key Laboratory of Chemical Biology School of Pharmacy East China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
- State Key Laboratory of Bioreactor Engineering East China University of Science and Technology 130 Meilong Road Shanghai 200237 P.R. China
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30
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Park SH, Jeong JS, Zhou Y, Binte Mustafa NF, Chua NH. Deubiquitination of BES1 by UBP12/UBP13 promotes brassinosteroid signaling and plant growth. PLANT COMMUNICATIONS 2022; 3:100348. [PMID: 35706355 PMCID: PMC9483116 DOI: 10.1016/j.xplc.2022.100348] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 05/26/2023]
Abstract
As a key transcription factor in the brassinosteroid (BR) signaling pathway, the activity and expression of BES1 (BRI1-EMS-SUPPRESSOR 1) are stringently regulated. BES1 degradation is mediated by ubiquitin-related 26S proteasomal and autophagy pathways, which attenuate and terminate BR signaling; however, the opposing deubiquitinases (DUBs) are still unknown. Here, we showed that the ubp12-2w/13-3 double mutant phenocopies the BR-deficient dwarf mutant, suggesting that the two DUBs UBP12/UBP13 antagonize ubiquitin-mediated degradation to stabilize BES1. These two DUBs can trim tetraubiquitin with K46 and K63 linkages in vitro. UBP12/BES1 and UBP13/BES1 complexes are localized in both cytosol and nuclei. UBP12/13 can deubiquitinate polyubiquitinated BES1 in vitro and in planta, and UBP12 interacts with and deubiquitinates both inactive, phosphorylated BES1 and active, dephosphorylated BES1 in vivo. UBP12 overexpression in BES1OE plants significantly enhances cell elongation in hypocotyls and petioles and increases the ratio of leaf length to width compared with BES1OE or UBP12OE plants. Hypocotyl elongation and etiolation result from elevated BES1 levels because BES1 degradation is retarded by UBP12 in darkness or in light with BR. Protein degradation inhibitor experiments show that the majority of BES1 can be degraded by either the proteasomal or the autophagy pathway, but a minor BES1 fraction remains pathway specific. In conclusion, UBP12/UBP13 deubiquitinate BES1 to stabilize the latter as a positive regulator for BR responses.
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Affiliation(s)
- Su-Hyun Park
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Jin Seo Jeong
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Yu Zhou
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nur Fatimah Binte Mustafa
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore 117604, Singapore.
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31
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Crosstalk between Biomolecular Condensates and Proteostasis. Cells 2022; 11:cells11152415. [PMID: 35954258 PMCID: PMC9368065 DOI: 10.3390/cells11152415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 12/23/2022] Open
Abstract
Proper homeostasis of the proteome, referred to as proteostasis, is maintained by chaperone-dependent refolding of misfolded proteins and by protein degradation via the ubiquitin-proteasome system and the autophagic machinery. This review will discuss a crosstalk between biomolecular condensates and proteostasis, whereby the crowding of proteostasis factors into macromolecular assemblies is often established by phase separation of membraneless biomolecular condensates. Specifically, ubiquitin and other posttranslational modifications come into play as agents of phase separation, essential for the formation of condensates and for ubiquitin-proteasome system activity. Furthermore, an intriguing connection associates malfunction of the same pathways to the accumulation of misfolded and ubiquitinated proteins in aberrant condensates, the formation of protein aggregates, and finally, to the pathogenesis of neurodegenerative diseases. The crosstalk between biomolecular condensates and proteostasis is an emerging theme in cellular and disease biology and further studies will focus on delineating specific molecular pathways involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases.
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Dao TP, Yang Y, Presti MF, Cosgrove MS, Hopkins JB, Ma W, Loh SN, Castañeda CA. Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains. EMBO Rep 2022; 23:e55056. [PMID: 35762418 PMCID: PMC9346500 DOI: 10.15252/embr.202255056] [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: 03/15/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
Ubiquitin‐binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48‐ and K63‐linked polyubiquitin chains, respectively. UBQLN2 comprises self‐associating regions that drive its homotypic liquid–liquid phase separation (LLPS). Specific interactions between one of these regions and ubiquitin inhibit UBQLN2 LLPS. Here, we show that, unlike ubiquitin, the effects of multivalent polyubiquitin chains on UBQLN2 LLPS are highly dependent on chain types. Specifically, K11‐Ub4 and K48‐Ub4 chains generally inhibit UBQLN2 LLPS, whereas K63‐Ub4, M1‐Ub4 chains, and a designed tetrameric ubiquitin construct significantly enhance LLPS. We demonstrate that these opposing effects stem from differences in chain conformations but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin‐binding surface promote UBQLN2 LLPS by enabling a switch between homotypic to partially heterotypic LLPS that is driven by both UBQLN2 self‐interactions and interactions between multiple UBQLN2 units with each polyubiquitin chain. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic LLPS with ubiquitin‐binding shuttles and adaptors.
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Affiliation(s)
- Thuy P Dao
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
| | - Yiran Yang
- Department of Chemistry Syracuse University Syracuse NY USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Michael S Cosgrove
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Jesse B Hopkins
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Weikang Ma
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Sciences Illinois Institute of Technology Chicago IL USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology SUNY Upstate Medical University Syracuse NY USA
| | - Carlos A Castañeda
- Departments of Biology and Chemistry Syracuse University Syracuse NY USA
- Interdisciplinary Neuroscience Program Syracuse University Syracuse NY USA
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33
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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34
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Liu C, Wang B, Zhu W, Xu Y, Yang Y, Qian X. An ER‐targeting DNA Nanodevice for Autophagy‐dependent Degradation of Proteins in Membrane‐bound Organelles. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Caixia Liu
- East China University of Science and Technology School of Pharmacy CHINA
| | - Bin Wang
- East China University of Science and Technology School of Pharmacy Shanghai CHINA
| | - Weiping Zhu
- East China University of Science and Technology School of Pharmacy CHINA
| | - Yufang Xu
- East China University of Science and Technology School of Pharmacy School of Pharmacy CHINA
| | - Yangyang Yang
- East China University of Science and Technology School of Pharmacy Meilong Road 130 200237 Shanghai CHINA
| | - Xuhong Qian
- East China University of Science and Technology School of Pharmacy CHINA
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35
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Gan D, Ying J, Zhao Y. Prebiotic Chemistry: The Role of Trimetaphosphate in Prebiotic Chemical Evolution. Front Chem 2022; 10:941228. [PMID: 35910738 PMCID: PMC9326000 DOI: 10.3389/fchem.2022.941228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 11/22/2022] Open
Abstract
Life’s origins have always been a scientific puzzle. Understanding the production of biomolecules is crucial for understanding the evolution of life on Earth. Numerous studies on trimetaphosphate have been conducted in the field of prebiotic chemistry. However, its role in prebiotic chemistry has been documented infrequently in the review literature. The goal of this thesis is to review the role of trimetaphosphate in the early Earth’s biomolecule synthesis and phosphorylation. Additionally, various trimetaphosphate-mediated reaction pathways are discussed, as well as the role of trimetaphosphate in prebiotic chemistry. Finally, in our opinion, interactions between biomolecules should be considered in prebiotic synthesis scenarios since this may result in some advances in subsequent research on this subject. The research establishes an essential and opportune foundation for an in-depth examination of the “mystery of life".
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Affiliation(s)
- Dingwei Gan
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- *Correspondence: Jianxi Ying,
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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36
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Ma X, Ru Y, Luo Y, Kuai L, Chen QL, Bai Y, Liu YQ, Chen J, Luo Y, Song JK, Zhou M, Li B. Post-Translational Modifications in Atopic Dermatitis: Current Research and Clinical Relevance. Front Cell Dev Biol 2022; 10:942838. [PMID: 35874824 PMCID: PMC9301047 DOI: 10.3389/fcell.2022.942838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022] Open
Abstract
Atopic dermatitis (AD) is a chronic and relapsing cutaneous disorder characterized by compromised immune system, excessive inflammation, and skin barrier disruption. Post-translational modifications (PTMs) are covalent and enzymatic modifications of proteins after their translation, which have been reported to play roles in inflammatory and allergic diseases. However, less attention has been paid to the effect of PTMs on AD. This review summarized the knowledge of six major classes (including phosphorylation, acetylation, ubiquitination, SUMOylation, glycosylation, o-glycosylation, and glycation) of PTMs in AD pathogenesis and discussed the opportunities for disease management.
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Affiliation(s)
- Xin Ma
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Shanghai Skin Disease Hospital of Tongji University, Shanghai, China
| | - Yi Ru
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ying Luo
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Le Kuai
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Qi-Long Chen
- Shanghai Skin Disease Hospital of Tongji University, Shanghai, China
| | - Yun Bai
- Shanghai Skin Disease Hospital of Tongji University, Shanghai, China
| | - Ye-Qiang Liu
- Shanghai Skin Disease Hospital of Tongji University, Shanghai, China
| | - Jia Chen
- Shanghai Skin Disease Hospital of Tongji University, Shanghai, China
| | - Yue Luo
- Shanghai Skin Disease Hospital of Tongji University, Shanghai, China
| | - Jian-Kun Song
- Shanghai Skin Disease Hospital of Tongji University, Shanghai, China
| | - Mi Zhou
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Mi Zhou, ; Bin Li,
| | - Bin Li
- Shanghai Skin Disease Hospital of Tongji University, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Mi Zhou, ; Bin Li,
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37
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The PH Domain and C-Terminal polyD Motif of Phafin2 Exhibit a Unique Concurrence in Animals. MEMBRANES 2022; 12:membranes12070696. [PMID: 35877899 PMCID: PMC9324892 DOI: 10.3390/membranes12070696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 01/27/2023]
Abstract
Phafin2, a member of the Phafin family of proteins, contributes to a plethora of cellular activities including autophagy, endosomal cargo transportation, and macropinocytosis. The PH and FYVE domains of Phafin2 play key roles in membrane binding, whereas the C-terminal poly aspartic acid (polyD) motif specifically autoinhibits the PH domain binding to the membrane phosphatidylinositol 3-phosphate (PtdIns3P). Since the Phafin2 FYVE domain also binds PtdIns3P, the role of the polyD motif remains unclear. In this study, bioinformatics tools and resources were employed to determine the concurrence of the PH-FYVE module with the polyD motif among Phafin2 and PH-, FYVE-, or polyD-containing proteins from bacteria to humans. FYVE was found to be an ancient domain of Phafin2 and is related to proteins that are present in both prokaryotes and eukaryotes. Interestingly, the polyD motif only evolved in Phafin2 and PH- or both PH-FYVE-containing proteins in animals. PolyD motifs are absent in PH domain-free FYVE-containing proteins, which usually display cellular trafficking or autophagic functions. Moreover, the prediction of the Phafin2-interacting network indicates that Phafin2 primarily cross-talks with proteins involved in autophagy, protein trafficking, and neuronal function. Taken together, the concurrence of the polyD motif with the PH domain may be associated with complex cellular functions that evolved specifically in animals.
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38
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Smalley S, Hellmann H. Review: Exploring possible approaches using ubiquitylation and sumoylation pathways in modifying plant stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 319:111275. [PMID: 35487671 DOI: 10.1016/j.plantsci.2022.111275] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
Abstract
Ubiquitin and similar proteins, such as SUMO, are utilized by plants to modify target proteins to rapidly change their stability and activity in cells. This review will provide an overview of these crucial protein interactions with a focus on ubiquitylation and sumoylation in plants and how they contribute to stress tolerance. The work will also explore possibilities to use these highly conserved pathways for novel approaches to generate more robust crop plants better fit to cope with abiotic and biotic stress situations.
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Affiliation(s)
- Samuel Smalley
- Washington State University, Pullman, WA 99164, United States
| | - Hanjo Hellmann
- Washington State University, Pullman, WA 99164, United States.
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39
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Liu F, Morderer D, Wren MC, Vettleson-Trutza SA, Wang Y, Rabichow BE, Salemi MR, Phinney BS, Oskarsson B, Dickson DW, Rossoll W. Proximity proteomics of C9orf72 dipeptide repeat proteins identifies molecular chaperones as modifiers of poly-GA aggregation. Acta Neuropathol Commun 2022; 10:22. [PMID: 35164882 PMCID: PMC8842533 DOI: 10.1186/s40478-022-01322-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
The most common inherited cause of two genetically and clinico-pathologically overlapping neurodegenerative diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), is the presence of expanded GGGGCC intronic hexanucleotide repeats in the C9orf72 gene. Aside from haploinsufficiency and toxic RNA foci, another non-exclusive disease mechanism is the non-canonical translation of the repeat RNA into five different dipeptide repeat proteins (DPRs), which form neuronal inclusions in affected patient brains. While evidence from cellular and animal models supports a toxic gain-of-function of pathologic poly-GA, poly-GR, and poly-PR aggregates in promoting deposition of TDP-43 pathology and neurodegeneration in affected brain areas, the relative contribution of DPRs to the disease process in c9FTD/ALS patients remains unclear. Here we have used the proximity-dependent biotin identification (BioID) proximity proteomics approach to investigate the formation and collective composition of DPR aggregates using cellular models. While interactomes of arginine rich poly-GR and poly-PR aggregates overlapped and were enriched for nucleolar and ribosomal proteins, poly-GA aggregates demonstrated a distinct association with proteasomal components, molecular chaperones (HSPA1A/HSP70, HSPA8/HSC70, VCP/p97), co-chaperones (BAG3, DNAJA1A) and other factors that regulate protein folding and degradation (SQSTM1/p62, CALR, CHIP/STUB1). Experiments in cellular models of poly-GA pathology show that molecular chaperones and co-chaperones are sequestered to the periphery of dense cytoplasmic aggregates, causing depletion from their typical cellular localization. Their involvement in the pathologic process is confirmed in autopsy brain tissue, where HSPA8, BAG3, VCP, and its adapter protein UBXN6 show a close association with poly-GA aggregates in the frontal cortex, temporal cortex, and hippocampus of c9FTLD and c9ALS cases. The association of heat shock proteins and co-chaperones with poly-GA led us to investigate their potential role in reducing its aggregation. We identified HSP40 co-chaperones of the DNAJB family as potent modifiers that increased the solubility of poly-GA, highlighting a possible novel therapeutic avenue and a central role of molecular chaperones in the pathogenesis of human C9orf72-linked diseases.
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40
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TDP-43 pathology: from noxious assembly to therapeutic removal. Prog Neurobiol 2022; 211:102229. [DOI: 10.1016/j.pneurobio.2022.102229] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/08/2021] [Accepted: 01/26/2022] [Indexed: 02/08/2023]
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41
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Takanashi Y, Kahyo T, Kamamoto S, Zhang H, Chen B, Ping Y, Mizuno K, Kawase A, Koizumi K, Satou M, Funai K, Shiiya N, Setou M. Ubiquitin-like 3 as a new protein-sorting factor for small extracellular vesicles. Cell Struct Funct 2022; 47:1-18. [PMID: 35197392 PMCID: PMC10511055 DOI: 10.1247/csf.21078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 11/11/2022] Open
Abstract
Ubiquitin-like 3 (UBL3) is a well-conserved ubiquitin-like protein (UBL) in eukaryotes and regulates the ubiquitin cascade, but the significant roles of UBL3 in cellular processes remained unknown. Recently, UBL3 was elucidated to be a post-translational modification factor that promotes protein sorting to small extracellular vesicles (sEVs). Proteins sorted into sEVs have been studied as etiologies of sEV-related diseases. Also, there have been attempts to construct drug delivery systems (DDSs) by loading proteins into sEVs. In this review, we introduce the new concept that UBL3 has a critical role in the protein-sorting system and compare structure conservation between UBL3 and other UBLs from an evolutionary perspective. We conclude with future perspectives for the utility of UBL3 in sEV-related diseases and DDS.Key words: UBL3, small extracellular vesicles, protein sorting, ubiquitin-like protein, post-translational modification.
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Affiliation(s)
- Yusuke Takanashi
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
- First Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tomoaki Kahyo
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Sae Kamamoto
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Hengsen Zhang
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Bin Chen
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Yashuang Ping
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kiyomichi Mizuno
- First Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Akikazu Kawase
- First Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kei Koizumi
- First Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Masanori Satou
- First Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kazuhito Funai
- First Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Norihiko Shiiya
- First Department of Surgery, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
| | - Mitsutoshi Setou
- Department of Cellular and Molecular Anatomy, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
- International Mass Imaging Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
- Department of Systems Molecular Anatomy, Institute for Medical Photonics Research, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi Ward, Hamamatsu, Shizuoka 431-3192, Japan
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Lin KH, Ali A, Kuo CH, Yang PC, Kumar VB, Padma VV, Lo JF, Huang CY, Kuo WW. Carboxyl terminus of HSP70-interacting protein attenuates advanced glycation end products-induced cardiac injuries by promoting NFκB proteasomal degradation. J Cell Physiol 2021; 237:1888-1901. [PMID: 34958118 DOI: 10.1002/jcp.30660] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 11/06/2021] [Accepted: 12/03/2021] [Indexed: 12/13/2022]
Abstract
Advanced glycation end products (AGEs), which are highly reactive molecules resulting from persistent high-glucose levels, can lead to the generation of oxidative stress and cardiac complications. The carboxyl terminus of HSP70 interacting protein (CHIP) has been demonstrated to have a protective role in several diseases, including cardiac complications; however, the role in preventing AGE-induced cardiac damages remains poorly understood. Here, we found that elevated AGE levels impaired cardiac CHIP expression in streptozotocin-induced diabetes and high-fat diet-administered animals, representing AGE exposure models. We used the TUNEL assay, hematoxylin and eosin, Masson's trichrome staining, and western blotting to prove that cardiac injuries were induced in diabetic animals and AGE-treated cardiac cells. Interestingly, our results collectively indicated that CHIP overexpression significantly rescued the AGE-induced cardiac injuries and promoted cell survival. Moreover, CHIP knockdown-mediated stabilization of nuclear factor κB (NFκB) was attenuated by overexpressing CHIP in the cells. Furthermore, co-immunoprecipitation and immunoblot assay revealed that CHIP promotes the ubiquitination and proteasomal degradation of AGE-induced NFκB. Importantly, fluorescence microscopy, a luciferase reporter assay, electrophoretic mobility shift assay, and subcellular fractionation further demonstrated that CHIP overexpression inhibits AGE-induced NFκB nuclear translocation, reduced its binding ability with the promoter sequences of the receptor of AGE, consequently inhibiting the translocation of the receptor AGE to the cell membrane for its proper function. Overall, our current study findings suggest that CHIP can target NFκB for ubiquitin-mediated proteasomal degradation, and thereby potentially rescue AGE-induced cardiac damages.
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Affiliation(s)
- Kuan-Ho Lin
- College of Medicine, China Medical University, Taichung, Taiwan.,Department of Emergency Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Ayaz Ali
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
| | - Chia-Hua Kuo
- Department of Sports Sciences, University of Taipei, Taipei, Taiwan
| | - Pei-Chen Yang
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan
| | | | | | - Jeng-Fan Lo
- Department of Dentistry, National Yang-Ming University, Taipei, Taiwan.,Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan.,Genome Research Centre, National Yang-Ming University, Taipei, Taiwan.,Cancer Progression Centre of Excellence, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Yang Huang
- Department of Biotechnology, Asia University, Taichung, Taiwan.,Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.,Cardiovascular and Mitochondrial Related Disease Research Center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan.,Centre of General Education, Buddhist Tzu Chi Medical Foundation, Tzu Chi University of Science and Technology, Hualien, Taiwan.,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Wei-Wen Kuo
- Department of Biological Science and Technology, China Medical University, Taichung, Taiwan.,Ph.D. Program for Biotechnology Industry, China Medical University, Taichung, Taiwan
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43
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Hanley SE, Willis SD, Cooper KF. Snx4-assisted vacuolar targeting of transcription factors defines a new autophagy pathway for controlling ATG expression. Autophagy 2021; 17:3547-3565. [PMID: 33678121 PMCID: PMC8632336 DOI: 10.1080/15548627.2021.1877934] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/14/2021] [Indexed: 12/18/2022] Open
Abstract
Autophagy, in part, is controlled by the repression and activation of autophagy-related (ATG) genes. Here, we describe a new selective autophagy pathway that targets functional transcriptional regulators to control their activity. This pathway is activated in response to nitrogen starvation and recycles transcriptional activators (Msn2 and Rim15) and a repressor (Ssn2/Med13) of ATG expression. Further analysis of Ssn2/Med13 vacuolar proteolysis revealed that this pathway utilizes the core autophagic machinery. However, it is independent of known nucleophagy mechanisms, receptor proteins, and the scaffold protein Atg11. Instead, Ssn2/Med13 exits the nucleus through the nuclear pore complex (NPC) and associates with the cytoplasmic nucleoporin Gle1, a member of the RNA remodeling complex. Dbp5 and Nup159, that act in concert with Gle1, are also required for Ssn2/Med13 clearance. Ssn2/Med13 is retrieved from the nuclear periphery and degraded by Atg17-initiated phagophores anchored to the vacuole. Efficient transfer to phagophores depends on the sorting nexin heterodimer Snx4/Atg24-Atg20, which binds to Atg17, and relocates to the perinucleus following nitrogen starvation. To conclude, this pathway defines a previously undescribed autophagy mechanism that targets select transcriptional regulators for rapid vacuolar proteolysis, utilizing the RNA remodeling complex, the sorting nexin heterodimer Snx4-Atg20, Atg17, and the core autophagic machinery. It is physiologically relevant as this Snx4-assisted vacuolar targeting pathway permits cells to fine-tune the autophagic response by controlling the turnover of both positive and negative regulators of ATG transcription.Abbreviations: AIM: Atg8 interacting motif; ATG: autophagy-related; CKM: CDK8 kinase module; IDR: intrinsically disordered region; IP6: phosphoinositide inositol hexaphosphate; NPC: nuclear pore complex; PAS: phagophore assembly site; UPS: ubiquitin-proteasomal system.
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Affiliation(s)
- Sara E. Hanley
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Stephen D. Willis
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
| | - Katrina F. Cooper
- Department of Molecular Biology, Graduate School of Biomedical Sciences, Rowan University, Stratford, NJ, USA
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Wang HQ, Yang SW, Gao Y, Liu YJ, Li X, Ai QD, Lin MY, Yang YT, Zeng Q, Zhang Y, Wang ZZ, Chen NH. Novel antidepressant mechanism of ginsenoside Rg1: Regulating biosynthesis and degradation of connexin43. JOURNAL OF ETHNOPHARMACOLOGY 2021; 278:114212. [PMID: 34087399 DOI: 10.1016/j.jep.2021.114212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Panax ginseng C. A. Meyer is a valuable medicinal herb and "alternative" remedy for the prevention and treatment of depression. Dysfunction of connexin43 (Cx43)-gap junction in astrocytes is predisposed to the precipitation of depression. Ginsenoside Rg1 (Rg1), the main bioactive constituent extracted from ginseng, is efficacious in the management of depression by upregulating the content of Cx43. Our previous results indicated that pretreatment with Rg1 significantly improved Cx43-gap junction in corticosterone (CORT)-treated astrocytes. However, the antidepressant mechanism underlying how Rg1 upregulates Cx43-gap junction in astrocytes hasn't been proposed. AIM OF THE STUDY To dissect the mechanisms of Rg1 controlling Cx43 levels in primary astrocytes. METHODS We examined the changes of the level of Cx43 mRNA, the degradation of Cx43, as well as the ubiquitin-proteasomal and autophagy-lysosomal degradation pathways of Cx43 followed by Rg1 prior to CORT in rat primary astrocytes isolated from prefrontal cortex and hippocampus. Furthermore, the recognized method of scrape loading/dye transfer was performed to detect Cx43-gap junctional function, an essencial indicator of the antidepressant effect. RESULTS Pretreatment with Rg1 could reverse CORT-induced downregulation of Cx43 biosynthesis, acceleration of Cx43 degradation, and upregulation of two Cx43 degradation pathways in primary astrocytes. CONCLUSION The findings in the present study provide the first evidence highlighting that Rg1 increases Cx43 protein levels through the upregulation of Cx43 mRNA and downregulation of Cx43 degradation, which may be attributed to the effect of Rg1 on the ubiquitin-proteasomal and autophagy-lysosomal degradation pathways of Cx43.
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Affiliation(s)
- Hui-Qin Wang
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China; State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Song-Wei Yang
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China
| | - Yan Gao
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Ying-Jiao Liu
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China
| | - Xun Li
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China
| | - Qi-Di Ai
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China
| | - Mei-Yu Lin
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China
| | - Yan-Tao Yang
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China
| | - Qi Zeng
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China
| | - Yi Zhang
- Department of Anatomy, School of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 102488, China
| | - Zhen-Zhen Wang
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Nai-Hong Chen
- Hunan University of Chinese Medicine & Hunan Engineering Technology Center of Standardization and Function of Chinese Herbal Decoction Pieces, Changsha, 410208, Hunan, China; State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica & Neuroscience Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
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Sun-Wang JL, Yarritu-Gallego A, Ivanova S, Zorzano A. The ubiquitin-proteasome system and autophagy: self-digestion for metabolic health. Trends Endocrinol Metab 2021; 32:594-608. [PMID: 34034951 DOI: 10.1016/j.tem.2021.04.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 01/02/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a global health challenge. Therefore, understanding the molecular mechanisms underlying the pathophysiology of T2DM is key to improving current therapies. Loss of protein homeostasis leads to the accumulation of damaged proteins in cells, which results in tissue dysfunction. The elimination of damaged proteins occurs through the ubiquitin-proteasome system (UPS) and autophagy. In this review, we describe the mutual regulation between the UPS and autophagy and the involvement of these two proteolytic systems in metabolic dysregulation, insulin resistance, and T2DM. We propose that alterations in the UPS or autophagy contribute to triggering insulin resistance and the development of T2DM. In addition, these two pathways emerge as promising therapeutic targets for improving insulin resistance.
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Affiliation(s)
- Jia Liang Sun-Wang
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain.
| | - Alex Yarritu-Gallego
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany; Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany
| | - Saška Ivanova
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain
| | - Antonio Zorzano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Departament de Bioquímica i Biomedicina Molecular, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain; CIBER de Diabetes y Enfermedades Metabólicas Asociadas, Barcelona, Spain.
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Saffari-Chaleshtori J, Asadi-Samani M, Rasouli M, Shafiee SM. Autophagy and Ubiquitination as Two Major Players in Colorectal Cancer: A Review on Recent Patents. Recent Pat Anticancer Drug Discov 2021; 15:143-153. [PMID: 32603286 DOI: 10.2174/1574892815666200630103626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND As one of the most commonly diagnosed cancers among men and women, Colorectal Cancer (CRC) leads to high rates of morbidity and mortality across the globe. Recent anti- CRC therapies are now targeting specific signaling pathways involved in colorectal carcinogenesis. Ubiquitin Proteasome System (UPS) and autophagy are two main protein quality control systems, which play major roles in the carcinogenesis of colorectal cancer. A balanced function of these two pathways is necessary for the regulation of cell proliferation and cell death. OBJECTIVE In this systematic review, we discuss the available evidence regarding the roles of autophagy and ubiquitination in progression and inhibition of CRC. METHODS The search terms "colorectal cancer" or "colon cancer" or "colorectal carcinoma" or "colon carcinoma" in combination with "ubiquitin proteasome" and "autophagy" were searched in PubMed, Web of Science, and Scopus databases, and also Google Patents (https://patents.google .com) from January 2000 to Feb 2020. RESULTS The most important factors involved in UPS and autophagy have been investigated. There are many important factors involved in UPS and autophagy but this systematic review shows the studies that have mostly focused on the role of ATG, 20s proteasome and mTOR in CRC, and the more important factors such as ATG8, FIP200, and TIGAR factors that are effective in the regulation of autophagy in CRC cells have not been yet investigated. CONCLUSION The most important factors involved in UPS and autophagy such as ATG, 20s proteasome and mTOR, ATG8, FIP200, and TIGAR can be considered in drug therapy for controlling or activating autophagy.
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Affiliation(s)
- Javad Saffari-Chaleshtori
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Majid Asadi-Samani
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Maryam Rasouli
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sayed Mohammad Shafiee
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Yu Y, Xiao L, Ren Z, Zhu G, Wang W, Jia Y, Peng A, Wang X. Glucose-induced decrease of cystathionine β-synthase mediates renal injuries. FASEB J 2021; 35:e21576. [PMID: 33864412 DOI: 10.1096/fj.202002696rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/30/2022]
Abstract
Exogenous hydrogen sulfide (H2 S) protects kidneys from diabetic injuries in animal models. In order to explore the role of endogenous H2 S in diabetic nephropathy, we determined the renal H2S producing enzymes in vivo and in vitro. In diabetic mice, H2 S levels in blood and kidney were decreased while cystathionine β-synthase (CBS), mainly located in mouse renal proximal convoluted tubules (PCT), was reduced selectively. In cultured mouse PCT cells treated with high glucose, CBS protein and activity was reduced while ubiquitinated CBS was increased, which was abolished by a proteasome inhibitor MG132 at 1 hour; high glucose drove CBS colocalized with proteasome 26S subunit ATPase6, indicating an involvement of ubiquitination proteasome degradation. At 48 hours, high glucose also selectively decreased CBS protein, concentration-dependently, but increased the ubiquitination of CBS; silence of CBS by siRNA increased nitrotyrosine, a marker for protein oxidative injury. Nitrotyrosine was also increased by high glucose treatments. The increases of nitrotyrosine either by cbs-siRNA or by glucose were restored by GYY4137, indicating that the H2 S donor may protect kidney from oxidative injury induced by CBS deficiency. In diabetic kidneys, ubiquitinated CBS and nitrotyrosine were increased but restored by GYY4137. The treatment also ameliorated albuminuria and renal morphologic changes in diabetic mice. Our findings suggest that high glucose induces reduction of renal CBS protein and activity in vivo and in vitro that is critical to the pathogenesis of diabetic kidney disease.
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Affiliation(s)
- Yanting Yu
- Department of Nephrology, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China.,The Core Laboratory, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Leijuan Xiao
- Department of Nephrology, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiyun Ren
- The Core Laboratory, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Gangyi Zhu
- The Core Laboratory, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Weiwan Wang
- The Core Laboratory, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Yutao Jia
- Department of Nephrology, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
| | - Ai Peng
- Department of Nephrology and Rheumatology, Affiliated Shanghai Tenth Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Xiaoyan Wang
- Department of Nephrology, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China.,The Core Laboratory, Nanjing BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, China
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Coxsackievirus B3 Exploits the Ubiquitin-Proteasome System to Facilitate Viral Replication. Viruses 2021; 13:v13071360. [PMID: 34372566 PMCID: PMC8310229 DOI: 10.3390/v13071360] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 01/18/2023] Open
Abstract
Infection by RNA viruses causes extensive cellular reorganization, including hijacking of membranes to create membranous structures termed replication organelles, which support viral RNA synthesis and virion assembly. In this study, we show that infection with coxsackievirus B3 entails a profound impairment of the protein homeostasis at virus-utilized membranes, reflected by an accumulation of ubiquitinylated proteins, including K48-linked polyubiquitin conjugates, known to direct proteins to proteasomal degradation. The enrichment of membrane-bound ubiquitin conjugates is attributed to the presence of the non-structural viral proteins 2B and 3A, which are known to perturb membrane integrity and can cause an extensive rearrangement of cellular membranes. The locally increased abundance of ubiquitinylated proteins occurs without an increase of oxidatively damaged proteins. During the exponential phase of replication, the oxidative damage of membrane proteins is even diminished, an effect we attribute to the recruitment of glutathione, which is known to be required for the formation of infectious virus particles. Furthermore, we show that the proteasome contributes to the processing of viral precursor proteins. Taken together, we demonstrate how an infection with coxsackievirus B3 affects the cellular protein and redox homeostasis locally at the site of viral replication and virus assembly.
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Blasiak J, Szczepanska J, Fila M, Pawlowska E, Kaarniranta K. Potential of Telomerase in Age-Related Macular Degeneration-Involvement of Senescence, DNA Damage Response and Autophagy and a Key Role of PGC-1α. Int J Mol Sci 2021; 22:ijms22137194. [PMID: 34281248 PMCID: PMC8268995 DOI: 10.3390/ijms22137194] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 02/07/2023] Open
Abstract
Age-related macular degeneration (AMD), the main cause of vision loss in the elderly, is associated with oxidation in the retina cells promoting telomere attrition. Activation of telomerase was reported to improve macular functions in AMD patients. The catalytic subunit of human telomerase (hTERT) may directly interact with proteins important for senescence, DNA damage response, and autophagy, which are impaired in AMD. hTERT interaction with mTORC1 (mTOR (mechanistic target of rapamycin) complex 1) and PINK1 (PTEN-induced kinase 1) activates macroautophagy and mitophagy, respectively, and removes cellular debris accumulated over AMD progression. Ectopic expression of telomerase in retinal pigment epithelium (RPE) cells lengthened telomeres, reduced senescence, and extended their lifespan. These effects provide evidence for the potential of telomerase in AMD therapy. Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) may be involved in AMD pathogenesis through decreasing oxidative stress and senescence, regulation of vascular endothelial growth factor (VEGF), and improving autophagy. PGC-1α and TERT form an inhibitory positive feedback loop. In conclusion, telomerase activation and its ectopic expression in RPE cells, as well as controlled clinical trials on the effects of telomerase activation in AMD patients, are justified and should be assisted by PGC-1α modulators to increase the therapeutic potential of telomerase in AMD.
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Affiliation(s)
- Janusz Blasiak
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
- Correspondence: (J.B.); (K.K.)
| | - Joanna Szczepanska
- Department of Pediatric Dentistry, Medical University of Lodz, 92-216 Lodz, Poland;
| | - Michal Fila
- Department of Developmental Neurology and Epileptology, Polish Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland;
| | - Elzbieta Pawlowska
- Department of Orthodontics, Medical University of Lodz, 92-217 Lodz, Poland;
| | - Kai Kaarniranta
- Department of Ophthalmology, University of Eastern Finland, 70210 Kuopio, Finland
- Department of Ophthalmology, Kuopio University Hospital, 70210 Kuopio, Finland
- Correspondence: (J.B.); (K.K.)
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Zheng T, Galagedera SKK, Castañeda CA. Previously uncharacterized interactions between the folded and intrinsically disordered domains impart asymmetric effects on UBQLN2 phase separation. Protein Sci 2021; 30:1467-1481. [PMID: 34029402 DOI: 10.1002/pro.4128] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 02/06/2023]
Abstract
Shuttle protein UBQLN2 functions in protein quality control (PQC) by binding to proteasomal receptors and ubiquitinated substrates via its N-terminal ubiquitin-like (UBL) and C-terminal ubiquitin-associated (UBA) domains, respectively. Between these two folded domains are low-complexity STI1-I and STI1-II regions, connected by disordered linkers. The STI1 regions bind other components, such as HSP70, that are important to the PQC functions of UBQLN2. We recently determined that the STI1-II region enables UBQLN2 to undergo liquid-liquid phase separation (LLPS) to form liquid droplets in vitro and biomolecular condensates in cells. However, how the interplay between the folded (UBL/UBA) domains and the intrinsically disordered regions mediates phase separation is largely unknown. Using engineered domain deletion constructs, we found that removing the UBA domain inhibits UBQLN2 LLPS while removing the UBL domain enhances LLPS, suggesting that UBA and UBL domains contribute asymmetrically in modulating UBQLN2 LLPS. To explain these differential effects, we interrogated the interactions that involve the UBA and UBL domains across the entire UBQLN2 molecule using nuclear magnetic resonance spectroscopy. To our surprise, aside from well-studied canonical UBL:UBA interactions, there also exist moderate interactions between the UBL and several disordered regions, including STI1-I and residues 555-570, the latter of which is a known contributor to UBQLN2 LLPS. Our findings are essential for the understanding of both the molecular driving forces of UBQLN2 LLPS and the effects of ligand binding to UBL, UBA, or disordered regions on the phase behavior and physiological functions of UBQLN2.
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Affiliation(s)
- Tongyin Zheng
- Department of Chemistry, Syracuse University, Syracuse, New York, USA
| | | | - Carlos A Castañeda
- Departments of Biology and Chemistry, Syracuse University, Syracuse, New York, USA.,Interdisciplinary Neuroscience Program, Syracuse University, Syracuse, New York, USA.,BioInspired Institute, Syracuse University, Syracuse, New York, USA
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