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Kotewicz KM, Zhang M, Kim S, Martin MS, Chowdhury AR, Tai A, Scheck RA, Isberg RR. Sde Proteins Coordinate Ubiquitin Utilization and Phosphoribosylation to Promote Establishment and Maintenance of the Legionella Replication Vacuole. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.07.553534. [PMID: 38645023 PMCID: PMC11030226 DOI: 10.1101/2023.09.07.553534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The Legionella pneumophila Sde family of translocated proteins promotes host tubular endoplasmic reticulum (ER) rearrangements that are tightly linked to phosphoribosyl-ubiquitin (pR-Ub) modification of Reticulon 4 (Rtn4). Sde proteins have two additional activities of unclear relevance to the infection process: K63 linkage-specific deubiquitination and phosphoribosyl modification of polyubiquitin (pR-Ub). We show here that the deubiquitination activity (DUB) stimulates ER rearrangements while pR-Ub protects the replication vacuole from cytosolic surveillance by autophagy. Loss of DUB activity was tightly linked to lowered pR-Ub modification of Rtn4, consistent with the DUB activity fueling the production of pR-Ub-Rtn4. In parallel, phosphoribosyl modification of polyUb, in a region of the protein known as the isoleucine patch, prevented binding by the autophagy adapter p62. An inability of Sde mutants to modify polyUb resulted in immediate p62 association, a critical precursor to autophagic attack. The ability of Sde WT to block p62 association decayed quickly after bacterial infection, as predicted by the presence of previously characterized L. pneumophila effectors that inactivate Sde and remove polyUb. In sum, these results show that the accessory Sde activities act to stimulate ER rearrangements and protect from host innate immune sensing in a temporal fashion.
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Affiliation(s)
- Kristin M Kotewicz
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
- Current address: Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Mengyun Zhang
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
- Current address: Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Seongok Kim
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Meghan S Martin
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA, 02155, USA
| | - Atish Roy Chowdhury
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Albert Tai
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
| | - Rebecca A Scheck
- Department of Chemistry, Tufts University, 62 Talbot Ave, Medford, MA, 02155, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, 150 Harrison Ave., Boston, MA 02111, USA
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2
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Kurusu R, Morishita H, Komatsu M. p62 bodies: cytosolic zoning by phase separation. J Biochem 2024; 175:141-146. [PMID: 37948628 DOI: 10.1093/jb/mvad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Abstract
Cellular zoning or partitioning is critical in preventing macromolecules from random diffusion and orchestrating the spatiotemporal dynamics of biochemical reactions. Along with membranous organelles, membraneless organelles contribute to the precise regulation of biochemical reactions inside cells. In response to environmental cues, membraneless organelles rapidly form through liquid-liquid phase separation, sequester certain proteins and RNAs, mediate specific reactions and dissociate. Among membraneless organelles, ubiquitin-positive condensates, namely, p62 bodies, maintain cellular homeostasis through selective autophagy of themselves to contribute to intracellular quality control. p62 bodies also activate the anti-oxidative stress response regulated by the KEAP1-NRF2 system. In this review, we present an overview of recent advancements in cellular and molecular biology related to p62 bodies, highlighting their dynamic nature and functions.
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Affiliation(s)
- Reo Kurusu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Hideaki Morishita
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
- Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masaaki Komatsu
- Department of Physiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
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3
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Feng J, Li Y, Zhang Y, Sun S, Sun J, Xu Q, Ji X, Liu Y, Wan Q. Endothelium-specific deletion of p62 causes organ fibrosis and cardiac dysfunction. J Transl Med 2024; 22:161. [PMID: 38365674 PMCID: PMC10870664 DOI: 10.1186/s12967-024-04946-w] [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: 11/10/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND The autophagy adapter SQSTM1/p62 is crucial for maintaining homeostasis in various organs and cells due to its protein-protein interaction domains and involvement in diverse physiological and pathological processes. Vascular endothelium cells play a unique role in vascular biology and contribute to vascular health. METHODS Using the Cre-loxP system, we generated mice with endothelium cell-specific knockout of p62 mediated by Tek (Tek receptor tyrosine kinase)-cre to investigate the essential role of p62 in the endothelium. In vitro, we employed protein mass spectrometry and IPA to identify differentially expressed proteins upon knockdown of p62. Immunoprecipitation assays were conducted to demonstrate the interaction between p62 and FN1 or LAMC2 in human umbilical vein endothelium cells (HUVECs). Additionally, we identified the degradation pathway of FN1 and LAMC2 using the autophagy inhibitor 3-methyladenine (3-MA) or proteasome inhibitor MG132. Finally, the results of immunoprecipitation demonstrated that the interaction between p62 and LAMC2 was abolished in the PB1 truncation group of p62, while the interaction between p62 and FN1 was abolished in the UBA truncation group of p62. RESULTS Our findings revealed that p62 Endo mice exhibited heart, lung, and kidney fibrosis compared to littermate controls, accompanied by severe cardiac dysfunction. Immunoprecipitation assays provided evidence of p62 acting as an autophagy adapter in the autophagy-lysosome pathway for FN1 and LAMC2 degradation respectively through PB1 and UBA domain with these proteins rather than proteasome system. CONCLUSIONS Our study demonstrates that defects in p62 within endothelium cells induce multi-organ fibrosis and cardiac dysfunction in mice. Our findings indicate that FN1 and LAMC2, as markers of (EndoMT), have detrimental effects on HUVECs and elucidate the autophagy-lysosome degradation mechanism of FN1 and LAMC2.
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Affiliation(s)
- Jing Feng
- Key Laboratory of Cell Metabolism in Medical and Health of Shandong Provincial Health Commission, Jinan Central Hospital, Shandong University, Jinan, 250021, Shandong, China
- Qingdao Central Hospital, Shandong University, Qingdao, 266042, Shandong, China
| | - Yan Li
- Department of Pulmonary and Critical Care Medicine, The Second Hospital of Shandong University, Jinan, 250033, Shandong, China
| | - Yu Zhang
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Shengnan Sun
- Key Laboratory of Cell Metabolism in Medical and Health of Shandong Provincial Health Commission, Jinan Central Hospital, Shandong University, Jinan, 250021, Shandong, China
| | - Jian Sun
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
- Shandong Key Laboratory of Infections Respiratory Disease, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China
| | - Quanlin Xu
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China
- Shandong Key Laboratory of Infections Respiratory Disease, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China
| | - Xingzhao Ji
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Shandong Key Laboratory of Infections Respiratory Disease, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China.
| | - Yi Liu
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Jinan, 250021, Shandong, China.
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
- Shandong Key Laboratory of Infections Respiratory Disease, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China.
| | - Qiang Wan
- Key Laboratory of Cell Metabolism in Medical and Health of Shandong Provincial Health Commission, Jinan Central Hospital, Shandong University, Jinan, 250021, Shandong, China.
- Key Laboratory of Cell Metabolism in Medical and Health of Shandong Provincial Health Commission, Central Hospital Affiliated to Shandong First Medical University, Jinan, 250021, Shandong, China.
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4
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Hwang I, Kim BS, Lee HY, Cho SW, Lee SE, Ahn JY. PA2G4/EBP1 ubiquitination by PRKN/PARKIN promotes mitophagy protecting neuron death in cerebral ischemia. Autophagy 2024; 20:365-379. [PMID: 37712850 PMCID: PMC10813645 DOI: 10.1080/15548627.2023.2259215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023] Open
Abstract
Cerebral ischemia induces massive mitochondrial damage, leading to neuronal death. The elimination of damaged mitochondria via mitophagy is critical for neuroprotection. Here we show that the level of PA2G4/EBP1 (proliferation-associated 2G4) was notably increased early during transient middle cerebral artery occlusion and prevented neuronal death by eliciting cerebral ischemia-reperfusion (IR)-induced mitophagy. Neuron-specific knockout of Pa2g4 increased infarct volume and aggravated neuron loss with impaired mitophagy and was rescued by introduction of adeno-associated virus serotype 2 expressing PA2G4/EBP1. We determined that PA2G4/EBP1 is ubiquitinated on lysine 376 by PRKN/PARKIN on the damaged mitochondria and interacts with receptor protein SQSTM1/p62 for mitophagy induction. Thus, our study suggests that PA2G4/EBP1 ubiquitination following cerebral IR-injury promotes mitophagy induction, which may be implicated in neuroprotection.Abbreviations: AAV: adeno-associated virus; ACTB: actin beta; BNIP3L/NIX: BCL2 interacting protein 3 like; CA1: Cornu Ammonis 1; CASP3: caspase 3; CCCP: carbonyl cyanide m-chlorophenyl hydrazone; DMSO: dimethyl sulfoxide; PA2G4/EBP1: proliferation-associated 2G4; FUNDC1: FUN14 domain containing 1; IB: immunoblotting; ICC: immunocytochemistry; IHC: immunohistochemistry; IP: immunoprecipitation; MCAO: middle cerebral artery occlusion; MEF: mouse embryonic fibroblast; OGD: oxygen-glucose deprivation; PRKN/PARKIN: parkin RBR E3 ubiquitin protein ligase; PINK1: PTEN induced kinase 1; RBFOX3/NeuN: RNA binding fox-1 homolog 3; SQSTM1/p62: sequestosome 1; TIMM23: translocase of inner mitochondrial membrane 23; TOMM20: translocase of outer mitochondrial membrane 20; TUBB: tubulin beta class I; WT: wild-type.
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Affiliation(s)
- Inwoo Hwang
- Department of Molecular Cell Biology, Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Byeong-Seong Kim
- Department of Molecular Cell Biology, Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Ho Yun Lee
- Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sung-Woo Cho
- Department of Biochemistry and Molecular Biology, University of Ulsan, College of Medicine, Seoul, Korea
| | - Seung Eun Lee
- Research Animal Resources Center, Korea Institute of Science and Technology, Seongbuk-gu, Republic of Korea
| | - Jee-Yin Ahn
- Department of Molecular Cell Biology, Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
- Single Cell Network Research Center, Sungkyunkwan University School of Medicine, Suwon, Korea
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
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Mei L, Chen X, Wei F, Huang X, Liu L, Yao J, Chen J, Luo X, Wang Z, Yang A. Tethering ATG16L1 or LC3 induces targeted autophagic degradation of protein aggregates and mitochondria. Autophagy 2023; 19:2997-3013. [PMID: 37424101 PMCID: PMC10549199 DOI: 10.1080/15548627.2023.2234797] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/11/2023] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) based on the ubiquitin-proteasome system have made great progress in the field of drug discovery. There is mounting evidence that the accumulation of aggregation-prone proteins or malfunctioning organelles is associated with the occurrence of various age-related neurodegenerative disorders and cancers. However, PROTACs are inefficient for the degradation of such large targets due to the narrow entrance channel of the proteasome. Macroautophagy (hereafter referred to as autophagy) is known as a self-degradative process involved in the degradation of bulk cytoplasmic components or specific cargoes that are sequestered into autophagosomes. In the present study, we report the development of a generalizable strategy for the targeted degradation of large targets. Our results suggested that tethering large target models to phagophore-associated ATG16L1 or LC3 induced targeted autophagic degradation of the large target models. Furthermore, we successfully applied this autophagy-targeting degradation strategy to the targeted degradation of HTT65Q aggregates and mitochondria. Specifically, chimeras consisting of polyQ-binding peptide 1 (QBP) and ATG16L1-binding peptide (ABP) or LC3-interacting region (LIR) induced targeted autophagic degradation of pathogenic HTT65Q aggregates; and the chimeras consisting of mitochondria-targeting sequence (MTS) and ABP or LIR promoted targeted autophagic degradation of dysfunctional mitochondria, hence ameliorating mitochondrial dysfunction in a Parkinson disease cell model and protecting cells from apoptosis induced by the mitochondrial stress agent FCCP. Therefore, this study provides a new strategy for the selective proteolysis of large targets and enrich the toolkit for autophagy-targeting degradation.Abbreviations: ABP: ATG16L1-binding peptide; ATG16L1: autophagy related 16 like 1; ATTEC: autophagy-tethering compound; AUTAC: autophagy-targeting chimera; AUTOTAC: autophagy-targeting chimera; Baf A1: bafilomycin A1; BCL2: BCL2 apoptosis regulator; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CASP3: caspase 3; CPP: cell-penetrating peptide; CQ: chloroquine phosphate; DAPI: 4',6-diamidino-2-phenylindole; DCM: dichloromethane; DMF: N,N-dimethylformamide; DMSO: dimethyl sulfoxide; EBSS: Earle's balanced salt solution; FCCP: carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone; FITC: fluorescein-5-isothiocyanate; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HEK293: human embryonic kidney 293; HEK293T: human embryonic kidney 293T; HPLC: high-performance liquid chromatography; HRP: horseradish peroxidase; HTT: huntingtin; LIR: LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MFF: mitochondrial fission factor; MTS: mitochondria-targeting sequence; NBR1: NBR1 autophagy cargo receptor; NLRX1: NLR family member X1; OPTN: optineurin; P2A: self-cleaving 2A peptide; PB1: Phox and Bem1p; PBS: phosphate-buffered saline; PE: phosphatidylethanolamine; PINK1: PTEN induced kinase 1; PRKN: parkin RBR E3 ubiquitin protein ligase; PROTACs: proteolysis-targeting chimeras; QBP: polyQ-binding peptide 1; SBP: streptavidin-binding peptide; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SPATA33: spermatogenesis associated 33; TIMM23: translocase of inner mitochondrial membrane 23; TMEM59: transmembrane protein 59; TOMM20: translocase of outer mitochondrial membrane 20; UBA: ubiquitin-associated; WT: wild type.
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Affiliation(s)
- Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Fujing Wei
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Xunguang Luo
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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6
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Isberg R, Kotewicz K, Zheng M, Kim S, Tai A. Sde Proteins Coordinate Ubiquitin Utilization and Phosphoribosylation to Promote Establishment and Maintenance of the Legionella Replication Vacuole. RESEARCH SQUARE 2023:rs.3.rs-3269310. [PMID: 37790456 PMCID: PMC10543313 DOI: 10.21203/rs.3.rs-3269310/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The Legionella pneumophilaSde family of translocated proteins promote host tubular endoplasmic reticulum (ER) rearrangements that are tightly linked to phosphoribosyl-ubiquitin (pR-Ub) modification of Reticulon 4 (Rtn4). Sde proteins have two additional activities of unclear relevance to the infection process: K63 linkage-specific deubiquitination and phosphoribosyl modification of polyubiquitin (pR-Ub). We show here that the deubiquitination activity (DUB) stimulates ER rearrangements while pR-Ub protects the replication vacuole from cytosolic surveillance by autophagy. Loss of DUB activity was tightly linked to lowered pR-Ub modification of Rtn4, consistent with the DUB activity fueling the production of pR-Ub-Rtn4. In parallel, phosphoribosyl modification of polyUb, in a region of the protein known as the isoleucine patch, caused an absolute block in binding by the autophagy adapter p62. An inability of Sde mutants to modify polyUb resulted in immediate p62 association, a critical precursor to autophagic attack. The ability of Sde WT to block p62 association decayed quickly after bacterial infection, as predicted by the presence of previously characterized L. pneumophila effectors that inactivate Sde and remove polyUb. In sum, these results show that the accessory Sde activities act to stimulate ER rearrangements and protect from host innate immune sensing in a temporal fashion.
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7
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Hou XN, Tang C. The pros and cons of ubiquitination on the formation of protein condensates. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1084-1098. [PMID: 37294105 PMCID: PMC10423694 DOI: 10.3724/abbs.2023096] [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: 12/30/2022] [Accepted: 03/19/2023] [Indexed: 06/10/2023] Open
Abstract
Ubiquitination, a post-translational modification that attaches one or more ubiquitin (Ub) molecules to another protein, plays a crucial role in the phase-separation processes. Ubiquitination can modulate the formation of membrane-less organelles in two ways. First, a scaffold protein drives phase separation, and Ub is recruited to the condensates. Second, Ub actively phase-separates through the interactions with other proteins. Thus, the role of ubiquitination and the resulting polyUb chains ranges from bystanders to active participants in phase separation. Moreover, long polyUb chains may be the primary driving force for phase separation. We further discuss that the different roles can be determined by the lengths and linkages of polyUb chains which provide preorganized and multivalent binding platforms for other client proteins. Together, ubiquitination adds a new layer of regulation for the flow of material and information upon cellular compartmentalization of proteins.
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Affiliation(s)
- Xue-Ni Hou
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Chun Tang
- Beijing National Laboratory for Molecular SciencesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
- Center for Quantitate BiologyPKU-Tsinghua Center for Life ScienceAcademy for Advanced Interdisciplinary StudiesPeking UniversityBeijing100871China
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8
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Shim SM, Choi HR, Kwon SC, Kim HY, Sung KW, Jung EJ, Mun SR, Bae TH, Kim DH, Son YS, Jung CH, Lee J, Lee MJ, Park JW, Kwon YT. The Cys-N-degron pathway modulates pexophagy through the N-terminal oxidation and arginylation of ACAD10. Autophagy 2023; 19:1642-1661. [PMID: 36184612 PMCID: PMC10262816 DOI: 10.1080/15548627.2022.2126617] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/02/2022] Open
Abstract
In the N-degron pathway, N-recognins recognize cognate substrates for degradation via the ubiquitin (Ub)-proteasome system (UPS) or the autophagy-lysosome system (hereafter autophagy). We have recently shown that the autophagy receptor SQSTM1/p62 (sequestosome 1) is an N-recognin that binds the N-terminal arginine (Nt-Arg) as an N-degron to modulate autophagic proteolysis. Here, we show that the N-degron pathway mediates pexophagy, in which damaged peroxisomal fragments are degraded by autophagy under normal and oxidative stress conditions. This degradative process initiates when the Nt-Cys of ACAD10 (acyl-CoA dehydrogenase family, member 10), a receptor in pexophagy, is oxidized into Cys sulfinic (CysO2) or sulfonic acid (CysO3) by ADO (2-aminoethanethiol (cysteamine) dioxygenase). Under oxidative stress, the Nt-Cys of ACAD10 is chemically oxidized by reactive oxygen species (ROS). The oxidized Nt-Cys2 is arginylated by ATE1-encoded R-transferases, generating the RCOX N-degron. RCOX-ACAD10 marks the site of pexophagy via the interaction with PEX5 and binds the ZZ domain of SQSTM1/p62, recruiting LC3+-autophagic membranes. In mice, knockout of either Ate1 responsible for Nt-arginylation or Sqstm1/p62 leads to increased levels of peroxisomes. In the cells from patients with peroxisome biogenesis disorders (PBDs), characterized by peroxisomal loss due to uncontrolled pexophagy, inhibition of either ATE1 or SQSTM1/p62 was sufficient to recover the level of peroxisomes. Our results demonstrate that the Cys-N-degron pathway generates an N-degron that regulates the removal of damaged peroxisomal membranes along with their contents. We suggest that tannic acid, a commercially available drug on the market, has a potential to treat PBDs through its activity to inhibit ATE1 R-transferases.Abbreviations: ACAA1, acetyl-Coenzyme A acyltransferase 1; ACAD, acyl-Coenzyme A dehydrogenase; ADO, 2-aminoethanethiol (cysteamine) dioxygenase; ATE1, arginyltransferase 1; CDO1, cysteine dioxygenase type 1; ER, endoplasmic reticulum; LIR, LC3-interacting region; MOXD1, monooxygenase, DBH-like 1; NAC, N-acetyl-cysteine; Nt-Arg, N-terminal arginine; Nt-Cys, N-terminal cysteine; PB1, Phox and Bem1p; PBD, peroxisome biogenesis disorder; PCO, plant cysteine oxidase; PDI, protein disulfide isomerase; PTS, peroxisomal targeting signal; R-COX, Nt-Arg-CysOX; RNS, reactive nitrogen species; ROS, reactive oxygen species; SNP, sodium nitroprusside; UBA, ubiquitin-associated; UPS, ubiquitinproteasome system.
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Affiliation(s)
- Sang Mi Shim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ha Rim Choi
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Soon Chul Kwon
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Hye Yeon Kim
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Ki Woon Sung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
| | - Eui Jung Jung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Su Ran Mun
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Tae Hyun Bae
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Dong Hyun Kim
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Korea
| | - Yeon Sung Son
- Neuroscience Research Institute, Medical Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Chan Hoon Jung
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jihoon Lee
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
| | - Min Jae Lee
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Joo-Won Park
- Department of Biochemistry, College of Medicine, Ewha Womans University, Seoul, Republic of Korea
| | - Yong Tae Kwon
- Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Cellular Degradation Biology Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
- AUTOTAC Bio Inc., Seoul, Republic of Korea
- Ischemic/Hypoxic Disease Institute, College of Medicine, Seoul National University, Seoul, Republic of Korea
- SNU Dementia Research Center, College of Medicine, Seoul National University, Seoul, Republic of Korea
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9
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Carvalho PPD, Alves NA. Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues. J Biomol Struct Dyn 2022; 40:11719-11728. [PMID: 34486937 PMCID: PMC8425439 DOI: 10.1080/07391102.2021.1965028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrícia P. D. Carvalho
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,CONTACT Patrícia P. D. Carvalho ;
| | - Nelson A. Alves
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,Nelson Alves
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10
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Abstract
Cellular homeostasis requires the swift and specific removal of damaged material. Selective autophagy represents a major pathway for the degradation of such cargo material. This is achieved by the sequestration of the cargo within double-membrane vesicles termed autophagosomes, which form de novo around the cargo and subsequently deliver their content to lysosomes for degradation. The importance of selective autophagy is exemplified by the various neurodegenerative diseases associated with defects in this pathway, including Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal dementia. It has become evident that cargo receptors are acting as Swiss army knives in selective autophagy by recognizing the cargo, orchestrating the recruitment of the machinery for autophagosome biogenesis, and closely aligning the membrane with the cargo. Furthermore, cargo receptors sequester ubiquitinated proteins into larger condensates upstream of autophagy induction. Here, we review recent insights into the mechanisms of action of cargo receptors in selective autophagy by focusing on the roles of sequestosome-like cargo receptors in the degradation of misfolded, ubiquitinated proteins and damaged mitochondria. We also highlight at which steps defects in their function result in the accumulation of harmful material and how this knowledge may guide the design of future therapies.
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Affiliation(s)
- Elias Adriaenssens
- Max Perutz Labs, Vienna BioCenter, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Luca Ferrari
- Max Perutz Labs, Vienna BioCenter, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
| | - Sascha Martens
- Max Perutz Labs, Vienna BioCenter, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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11
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DiRusso CJ, Dashtiahangar M, Gilmore TD. Scaffold proteins as dynamic integrators of biological processes. J Biol Chem 2022; 298:102628. [PMID: 36273588 PMCID: PMC9672449 DOI: 10.1016/j.jbc.2022.102628] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 11/15/2022] Open
Abstract
Scaffold proteins act as molecular hubs for the docking of multiple proteins to organize efficient functional units for signaling cascades. Over 300 human proteins have been characterized as scaffolds, acting in a variety of signaling pathways. While the term scaffold implies a static, supportive platform, it is now clear that scaffolds are not simply inert docking stations but can undergo conformational changes that affect their dependent signaling pathways. In this review, we catalog scaffold proteins that have been shown to undergo actionable conformational changes, with a focus on the role that conformational change plays in the activity of the classic yeast scaffold STE5, as well as three human scaffold proteins (KSR, NEMO, SHANK3) that are integral to well-known signaling pathways (RAS, NF-κB, postsynaptic density). We also discuss scaffold protein conformational changes vis-à-vis liquid-liquid phase separation. Changes in scaffold structure have also been implicated in human disease, and we discuss how aberrant conformational changes may be involved in disease-related dysregulation of scaffold and signaling functions. Finally, we discuss how understanding these conformational dynamics will provide insight into the flexibility of signaling cascades and may enhance our ability to treat scaffold-associated diseases.
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12
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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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13
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Turco E, Savova A, Gere F, Ferrari L, Romanov J, Schuschnig M, Martens S. Reconstitution defines the roles of p62, NBR1 and TAX1BP1 in ubiquitin condensate formation and autophagy initiation. Nat Commun 2021; 12:5212. [PMID: 34471133 PMCID: PMC8410870 DOI: 10.1038/s41467-021-25572-w] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/13/2021] [Indexed: 01/02/2023] Open
Abstract
The autophagic degradation of misfolded and ubiquitinated proteins is important for cellular homeostasis. In this process, which is governed by cargo receptors, ubiquitinated proteins are condensed into larger structures and subsequently become targets for the autophagy machinery. Here we employ in vitro reconstitution and cell biology to define the roles of the human cargo receptors p62/SQSTM1, NBR1 and TAX1BP1 in the selective autophagy of ubiquitinated substrates. We show that p62 is the major driver of ubiquitin condensate formation. NBR1 promotes condensate formation by equipping the p62-NBR1 heterooligomeric complex with a high-affinity UBA domain. Additionally, NBR1 recruits TAX1BP1 to the ubiquitin condensates formed by p62. While all three receptors interact with FIP200, TAX1BP1 is the main driver of FIP200 recruitment and thus the autophagic degradation of p62-ubiquitin condensates. In summary, our study defines the roles of all three receptors in the selective autophagy of ubiquitin condensates.
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Affiliation(s)
- Eleonora Turco
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
| | - Adriana Savova
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Flora Gere
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Luca Ferrari
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Julia Romanov
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Martina Schuschnig
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Sascha Martens
- Max Perutz Labs, University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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14
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Root J, Merino P, Nuckols A, Johnson M, Kukar T. Lysosome dysfunction as a cause of neurodegenerative diseases: Lessons from frontotemporal dementia and amyotrophic lateral sclerosis. Neurobiol Dis 2021; 154:105360. [PMID: 33812000 PMCID: PMC8113138 DOI: 10.1016/j.nbd.2021.105360] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 03/16/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are fatal neurodegenerative disorders that are thought to exist on a clinical and pathological spectrum. FTD and ALS are linked by shared genetic causes (e.g. C9orf72 hexanucleotide repeat expansions) and neuropathology, such as inclusions of ubiquitinated, misfolded proteins (e.g. TAR DNA-binding protein 43; TDP-43) in the CNS. Furthermore, some genes that cause FTD or ALS when mutated encode proteins that localize to the lysosome or modulate endosome-lysosome function, including lysosomal fusion, cargo trafficking, lysosomal acidification, autophagy, or TFEB activity. In this review, we summarize evidence that lysosomal dysfunction, caused by genetic mutations (e.g. C9orf72, GRN, MAPT, TMEM106B) or toxic-gain of function (e.g. aggregation of TDP-43 or tau), is an important pathogenic disease mechanism in FTD and ALS. Further studies into the normal function of many of these proteins are required and will help uncover the mechanisms that cause lysosomal dysfunction in FTD and ALS. Mutations or polymorphisms in genes that encode proteins important for endosome-lysosome function also occur in other age-dependent neurodegenerative diseases, including Alzheimer's (e.g. APOE, PSEN1, APP) and Parkinson's (e.g. GBA, LRRK2, ATP13A2) disease. A more complete understanding of the common and unique features of lysosome dysfunction across the spectrum of neurodegeneration will help guide the development of therapies for these devastating diseases.
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Affiliation(s)
- Jessica Root
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Paola Merino
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Austin Nuckols
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Michelle Johnson
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia
| | - Thomas Kukar
- Department of Pharmacology and Chemical Biology, Emory University, School of Medicine, Atlanta 30322, Georgia; Center for Neurodegenerative Disease, Emory University, School of Medicine, Atlanta 30322, Georgia; Department of Neurology, Emory University, School of Medicine, Atlanta 30322, Georgia.
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15
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Lei L, Wu Z, Winklhofer KF. Protein quality control by the proteasome and autophagy: A regulatory role of ubiquitin and liquid-liquid phase separation. Matrix Biol 2021; 100-101:9-22. [DOI: 10.1016/j.matbio.2020.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022]
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16
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The high stability of the three-helix bundle UBA domain of p62 protein as revealed by molecular dynamics simulations. J Mol Model 2021; 27:102. [PMID: 33665744 DOI: 10.1007/s00894-021-04698-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
The ubiquitin-associated (UBA) domain is an important motif in the modulation of many molecular functionalities. It has been mainly associated with ubiquitin-mediated proteolysis, a multistep mechanism in which undesirable proteins are tagged with polyubiquitin chains for degradation in the proteasome complex. Comparison among UBA domains reveals a quite small structural variability, displaying an overall fold with a tightly packed three-helix bundle, and a common conserved hydrophobic patch on their surface that is important for ubiquitin binding. Mutations in the UBA domain, mainly in the highly conserved hydrophobic patch, induce conformational instabilities, which can be related to weak affinity for ubiquitin. This raises the question whether such hydrophobic patch presents conserved structural arrangement for selective recognition and protein binding. A concern that led us to investigate the stability of the p62-UBA domain as a case study regarding its structural arrangement as a function of temperature and two NaCl concentrations. Our results reveal that the temperature range and ionic strengths considered in this work produced a negligible effect on the three-helix bundle fold of p62-UBA domain.
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17
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Molecular Mechanisms of Senescence and Implications for the Treatment of Myeloid Malignancies. Cancers (Basel) 2021; 13:cancers13040612. [PMID: 33557090 PMCID: PMC7913823 DOI: 10.3390/cancers13040612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 01/30/2021] [Accepted: 02/01/2021] [Indexed: 01/07/2023] Open
Abstract
Senescence is a cellular state that is involved in aging-associated diseases but may also prohibit the development of pre-cancerous lesions and tumor growth. Senescent cells are actively secreting chemo- and cytokines, and this senescence-associated secretory phenotype (SASP) can contribute to both early anti-tumorigenic and long-term pro-tumorigenic effects. Recently, complex mechanisms of cellular senescence and their influence on cellular processes have been defined in more detail and, therefore, facilitate translational development of targeted therapies. In this review, we aim to discuss major molecular pathways involved in cellular senescence and potential therapeutic strategies, with a specific focus on myeloid malignancies.
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18
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Lopez-Reyes RG, Quinet G, Gonzalez-Santamarta M, Larrue C, Sarry JE, Rodriguez MS. Inhibition of the proteasome and proteaphagy enhances apoptosis in FLT3-ITD-driven acute myeloid leukemia. FEBS Open Bio 2020; 11:48-60. [PMID: 33410599 PMCID: PMC7780102 DOI: 10.1002/2211-5463.12950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/15/2020] [Accepted: 08/12/2020] [Indexed: 12/05/2022] Open
Abstract
Acute myeloid leukaemia (AML) is a clonal disorder that affects hematopoietic stem cells or myeloid progenitors. One of the most common mutations that results in AML occurs in the gene encoding fms‐like tyrosine kinase 3 (FLT3). Previous studies have demonstrated that AML cells expressing FLT3‐internal tandem duplication (ITD) are more sensitive to the proteasome inhibitor bortezomib (Bz) than FLT3 wild‐type cells, with this cytotoxicity being mediated by autophagy (Atg). Here, we show that proteasome inhibition with Bz results in modest but consistent proteaphagy in MOLM‐14 leukemic cells expressing the FLT3‐ITD mutation, but not in OCI‐AML3 leukemic cells with wild‐type FLT3. Chemical inhibition of Atg with bafilomycin A simultaneously blocked proteaphagy and resulted in the accumulation of the p62 Atg receptor in Bz‐treated MOLM‐14 cells. The use of ubiquitin traps revealed that ubiquitin plays an important role in proteasome‐Atg cross‐talk. The p62 inhibitor verteporfin blocked proteaphagy and, importantly, resulted in accumulation of high molecular weight forms of p62 and FLT3‐ITD in Bz‐treated MOLM‐14 cells. Both Atg inhibitors enhanced Bz‐induced apoptosis in FLT3‐ITD‐driven leukemic cells, highlighting the therapeutic potential of these treatments.
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Affiliation(s)
- Rosa G Lopez-Reyes
- Institute of Advanced Technology and Life Sciences (ITAV), IPBS-Centre de la Recherche Scientifique (CNRS), Université Toulouse III Paul Sabatier, Toulouse, France.,Cancer Research Center of Toulouse Unité Mixte de Recherche (UMR) 1037 INSERM, ERL 5294 Centre de la Recherche Scientifique (CNRS), Toulouse, France
| | - Grégoire Quinet
- Institute of Advanced Technology and Life Sciences (ITAV), IPBS-Centre de la Recherche Scientifique (CNRS), Université Toulouse III Paul Sabatier, Toulouse, France
| | - Maria Gonzalez-Santamarta
- Institute of Advanced Technology and Life Sciences (ITAV), IPBS-Centre de la Recherche Scientifique (CNRS), Université Toulouse III Paul Sabatier, Toulouse, France
| | - Clément Larrue
- Cancer Research Center of Toulouse Unité Mixte de Recherche (UMR) 1037 INSERM, ERL 5294 Centre de la Recherche Scientifique (CNRS), Toulouse, France
| | - Jean-Emmanuel Sarry
- Cancer Research Center of Toulouse Unité Mixte de Recherche (UMR) 1037 INSERM, ERL 5294 Centre de la Recherche Scientifique (CNRS), Toulouse, France
| | - Manuel S Rodriguez
- Institute of Advanced Technology and Life Sciences (ITAV), IPBS-Centre de la Recherche Scientifique (CNRS), Université Toulouse III Paul Sabatier, Toulouse, France
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19
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Cytoplasmic Cargo Receptor p62 Inhibits Avibirnavirus Replication by Mediating Autophagic Degradation of Viral Protein VP2. J Virol 2020; 94:JVI.01255-20. [PMID: 32967959 PMCID: PMC7925189 DOI: 10.1128/jvi.01255-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/05/2020] [Indexed: 12/25/2022] Open
Abstract
Avibirnavirus causes severe immunosuppression and mortality in young chickens. VP2, the capsid protein of avibirnavirus, is responsible for virus assembly, maturation, and replication. Previous study showed that avibirnavirus particles could be engulfed into the autophagosome and degradation of virus particles took apart. Selective autophagy is a highly specific and regulated degradation pathway for the clearance of damaged or unwanted cytosolic components and superfluous organelles as well as invading microbes. However, whether and how selective autophagy removes avibirnavirus capsids is largely unknown. Here, we have shown that selective autophagy specifically clears ubiquitinated avibirnavirus protein VP2 by p62 recognition and that p62 is an inhibitor of avibirnavirus replication, highlighting the role of p62 as a potential drug target for mediating the removal of ubiquitinated virus components from cells. Selective autophagy regulates the degradation of cytoplasmic cargos, such as damaged organelles, invading pathogens, and aggregated proteins. Furthermore, autophagy is capable of degrading avibirnavirus, but the mechanism responsible for this process is unclear. Here, we show that autophagy cargo receptor p62 regulates the degradation of the avibirnavirus capsid protein VP2. Binding of p62 to VP2 enhances autophagic induction and promotes autophagic degradation of viral protein VP2. Further study showed that the interaction of p62 with viral protein VP2 is dependent on ubiquitination at the K411 site of VP2 and the ubiquitin-associated domain of p62. Mutation analysis showed that the K411R mutation of viral protein VP2 prohibits its p62-mediated degradation. Consistent with this finding, p62 lacking the ubiquitin-associated domain or the LC3-interacting region no longer promoted the degradation of VP2. Virus production revealed that the knockout of p62 but not the overexpression of p62 promotes the replication of avibirnavirus. Collectively, our findings suggest that p62 mediates selective autophagic degradation of avibirnavirus protein VP2 in a ubiquitin-dependent manner and is an inhibitor of avibirnavirus replication. IMPORTANCE Avibirnavirus causes severe immunosuppression and mortality in young chickens. VP2, the capsid protein of avibirnavirus, is responsible for virus assembly, maturation, and replication. Previous study showed that avibirnavirus particles could be engulfed into the autophagosome and degradation of virus particles took apart. Selective autophagy is a highly specific and regulated degradation pathway for the clearance of damaged or unwanted cytosolic components and superfluous organelles as well as invading microbes. However, whether and how selective autophagy removes avibirnavirus capsids is largely unknown. Here, we have shown that selective autophagy specifically clears ubiquitinated avibirnavirus protein VP2 by p62 recognition and that p62 is an inhibitor of avibirnavirus replication, highlighting the role of p62 as a potential drug target for mediating the removal of ubiquitinated virus components from cells.
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20
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Johnston HE, Samant RS. Alternative systems for misfolded protein clearance: life beyond the proteasome. FEBS J 2020; 288:4464-4487. [PMID: 33135311 DOI: 10.1111/febs.15617] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/15/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
Protein misfolding is a major driver of ageing-associated frailty and disease pathology. Although all cells possess multiple, well-characterised protein quality control systems to mitigate the toxicity of misfolded proteins, how they are integrated to maintain protein homeostasis ('proteostasis') in health-and how their disintegration contributes to disease-is still an exciting and fast-paced area of research. Under physiological conditions, the predominant route for misfolded protein clearance involves ubiquitylation and proteasome-mediated degradation. When the capacity of this route is overwhelmed-as happens during conditions of acute environmental stress, or chronic ageing-related decline-alternative routes for protein quality control are activated. In this review, we summarise our current understanding of how proteasome-targeted misfolded proteins are retrafficked to alternative protein quality control routes such as juxta-nuclear sequestration and selective autophagy when the ubiquitin-proteasome system is compromised. We also discuss the molecular determinants of these alternative protein quality control systems, attempt to clarify distinctions between various cytoplasmic spatial quality control inclusion bodies (e.g., Q-bodies, p62 bodies, JUNQ, aggresomes, and aggresome-like induced structures 'ALIS'), and speculate on emerging concepts in the field that we hope will spur future research-with the potential to benefit the rational development of healthy ageing strategies.
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Affiliation(s)
| | - Rahul S Samant
- Signalling Programme, The Babraham Institute, Cambridge, UK
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21
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Xu L, Zhang Y, Li YM, Lu XF. Total chemical synthesis of the phosphorylated p62 UBA domain reveals that Ser 407Pi but not Ser 403Pi enhances ubiquitin binding. Org Biomol Chem 2020; 18:8709-8715. [PMID: 33084718 DOI: 10.1039/d0ob01906b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
As an autophagic adaptor, p62 specifically targets ubiquitinated proteins to an autophagosome for lysosomal degradation through a critical ubiquitin-associated (UBA) domain. Recent research studies reported that the Ser403 and Ser407 sites on the UBA domain were modified by phosphorylation, increasing the binding affinity between p62 and ubiquitin (Ub). However, the exact role of each phosphorylation site in the regulation of the UBA domain and Ub binding remains unclear. In this text, we applied total chemical synthesis to prepare four types of phosphorylated UBAs, among which the bisphosphorylated UBA was successfully synthesized via the pseudo-dipeptide unit and auxiliary-mediated hydrazide-based native chemical ligation (NCL). Isothermal titration calorimetry (ITC) assays showed that the phosphorylation at S407 enhanced the binding affinity between UBA and Ub, while that at S403 did not. It was suggested that phosphorylation at S407 might be important for promoting the interplay between the UBA domain and Ub, whereas phosphorylation at S403 was not directly involved in this interaction.
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Affiliation(s)
- Ling Xu
- Department of Anesthesiology (High-Tech Branch), the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230027, China
| | - Yan Zhang
- Department of Anesthesiology (High-Tech Branch), the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230027, China
| | - Yi-Ming Li
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Xian-Fu Lu
- Department of Anesthesiology (High-Tech Branch), the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230027, China
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22
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Chen K, Chen J, Wang L, Yang J, Xiao F, Wang X, Yuan J, Wang L, He Y. Parkin ubiquitinates GATA4 and attenuates the GATA4/GAS1 signaling and detrimental effects on diabetic nephropathy. FASEB J 2020; 34:8858-8875. [PMID: 32436607 DOI: 10.1096/fj.202000053r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/13/2020] [Accepted: 05/05/2020] [Indexed: 01/26/2023]
Abstract
Renal tubular injury contributes to the progression of diabetic nephropathy (DN). This study explored the role and mechanisms of E3-ubiquitin ligase Parkin in the renal tubular injury of DN. We found that Parkin expression gradually decreased and was inversely associated with IL-6, TGF-β1, and GATA4 expression in the kidney during the progression of DN. Parkin over-expression (OE) reduced inflammation, fibrosis, premature senescence of renal tubular epithelial cells (RTECs), and improved renal function while Parkin knockout (KO) had opposite effects in DN mice. Parkin-OE decreased GATA4 protein, but not its mRNA transcripts in the kidney of DN mice and high glucose (HG)-treated RTECs. Immunoprecipitation indicated that Parkin directly interacted with GATA4 in DN kidney. Parkin-OE enhanced GATA4 ubiquitination. Furthermore, Parkin-KO upregulated growth arrest-specific gene 1 (GAS1) expression in renal tubular tissues of DN mice and GATA4-OE enhanced the HG-upregulated GAS1 expression in RTECs. Conversely, GAS1-OE mitigated the effect of Parkin-OE on HG-induced P21, IL-6, and TGF-β1 expression in RTECs. These results indicate that Parkin inhibits the progression of DN by promoting GATA4 ubiquitination and downregulating the GATA4/GAS1 signaling to inhibit premature senescence, inflammation, and fibrosis in DN mice. Thus, these findings uncover new mechanisms underlying the action of Parkin during the process of DN.
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Affiliation(s)
- Kehong Chen
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Jia Chen
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Ling Wang
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Jie Yang
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Fei Xiao
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Xianyue Wang
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Junjie Yuan
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Limin Wang
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
| | - Yani He
- Department of Nephrology, Daping Hospital, Army Medical University, Chongqing, China
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23
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Abstract
Autophagy is a conserved and fundamental cellular process mainly to recycle or eliminate dysfunctional cellular organelles or proteins. As a response to cellular stress, autophagy is used as a defense mechanism to combat the infection with pathogenic bacteria. However, many intracellular bacteria have developed diverse mechanisms to evade recognition, to manipulate the autophagic pathway, and to hijack the autophagosomal compartment for replication. In this review, we discuss recent understandings on how bacteria interact with host autophagy.
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Affiliation(s)
- Yao-Wen Wu
- a Department of Chemistry, Umeå Centre for Microbial Research , Umeå University , Umeå , Sweden.,b Chemical Genomics Centre of the Max Planck Society , Dortmund , Germany.,c Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Fu Li
- a Department of Chemistry, Umeå Centre for Microbial Research , Umeå University , Umeå , Sweden.,b Chemical Genomics Centre of the Max Planck Society , Dortmund , Germany.,c Max Planck Institute of Molecular Physiology , Dortmund , Germany
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24
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Jeong SJ, Zhang X, Rodriguez-Velez A, Evans TD, Razani B. p62/ SQSTM1 and Selective Autophagy in Cardiometabolic Diseases. Antioxid Redox Signal 2019; 31:458-471. [PMID: 30588824 PMCID: PMC6653798 DOI: 10.1089/ars.2018.7649] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Significance: p62/SQSTM1 is a multifunctional scaffolding protein involved in the regulation of various signaling pathways as well as autophagy. In particular, p62/SQSTM1 serves as an essential adaptor to identify and deliver specific organelles and protein aggregates to autophagosomes for degradation, a process known as selective autophagy. Critical Issues: With the emergence of autophagy as a critical process in cellular metabolism and the development of cardiometabolic diseases, it is increasingly important to understand p62's role in the integration of signaling and autophagic pathways. Recent Advances: This review first discusses the features that make p62/SQSTM1 an ideal chaperone in integrating signaling pathways with autophagy and details the current understanding of its diverse roles in selective autophagy processes. Distinct and overlapping roles of other chaperones with similar functions are then discussed in the context of p62/SQSTM1. Finally, the recent literature focusing on p62 and selective autophagy in metabolism and the spectrum of cardiometabolic diseases including atherosclerosis, fatty liver disease, and obesity is evaluated. Future Directions: A comprehensive understanding of the nuanced roles p62/SQSTM1 plays in mediating distinct autophagy pathways would provide new insights into the mechanisms of this critical degradative pathway. This will, in turn, facilitate our understanding of cardiovascular and cardiometabolic disease pathology and the development of novel autophagy-modulating therapeutic strategies.
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Affiliation(s)
- Se-Jin Jeong
- 1 Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Xiangyu Zhang
- 1 Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Astrid Rodriguez-Velez
- 1 Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Trent D Evans
- 1 Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Babak Razani
- 1 Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri.,2 Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.,3 John Cochran VA Medical Center, St. Louis, Missouri
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25
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Palmisano NJ, Meléndez A. Autophagy in C. elegans development. Dev Biol 2019; 447:103-125. [PMID: 29709599 PMCID: PMC6204124 DOI: 10.1016/j.ydbio.2018.04.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 03/19/2018] [Accepted: 04/12/2018] [Indexed: 12/11/2022]
Abstract
Autophagy involves the sequestration of cytoplasmic contents in a double-membrane structure referred to as the autophagosome and the degradation of its contents upon delivery to lysosomes. Autophagy activity has a role in multiple biological processes during the development of the nematode Caenorhabditis elegans. Basal levels of autophagy are required to remove aggregate prone proteins, paternal mitochondria, and spermatid-specific membranous organelles. During larval development, autophagy is required for the remodeling that occurs during dauer development, and autophagy can selectively degrade components of the miRNA-induced silencing complex, and modulate miRNA-mediated silencing. Basal levels of autophagy are important in synapse formation and in the germ line, to promote the proliferation of proliferating stem cells. Autophagy activity is also required for the efficient removal of apoptotic cell corpses by promoting phagosome maturation. Finally, autophagy is also involved in lipid homeostasis and in the aging process. In this review, we first describe the molecular complexes involved in the process of autophagy, its regulation, and mechanisms for cargo recognition. In the second section, we discuss the developmental contexts where autophagy has been shown to be important. Studies in C. elegans provide valuable insights into the physiological relevance of this process during metazoan development.
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Affiliation(s)
- Nicholas J Palmisano
- Biology Department, Queens College, CUNY, Flushing, NY, USA; Biology Ph.D. Program, The Graduate Center of the City University of New York, NK, USA
| | - Alicia Meléndez
- Biology Department, Queens College, CUNY, Flushing, NY, USA; Biology Ph.D. Program, The Graduate Center of the City University of New York, NK, USA; Biochemistry Ph.D. Program, The Graduate Center of the City University of New York, NY, USA.
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26
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The Roles of Ubiquitin-Binding Protein Shuttles in the Degradative Fate of Ubiquitinated Proteins in the Ubiquitin-Proteasome System and Autophagy. Cells 2019; 8:cells8010040. [PMID: 30634694 PMCID: PMC6357184 DOI: 10.3390/cells8010040] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 12/24/2018] [Accepted: 01/03/2019] [Indexed: 12/15/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) and autophagy are the two major intracellular protein quality control (PQC) pathways that are responsible for cellular proteostasis (homeostasis of the proteome) by ensuring the timely degradation of misfolded, damaged, and unwanted proteins. Ubiquitination serves as the degradation signal in both these systems, but substrates are precisely targeted to one or the other pathway. Determining how and when cells target specific proteins to these two alternative PQC pathways and control the crosstalk between them are topics of considerable interest. The ubiquitin (Ub) recognition code based on the type of Ub-linked chains on substrate proteins was believed to play a pivotal role in this process, but an increasing body of evidence indicates that the PQC pathway choice is also made based on other criteria. These include the oligomeric state of the Ub-binding protein shuttles, their conformation, protein modifications, and the presence of motifs that interact with ATG8/LC3/GABARAP (autophagy-related protein 8/microtubule-associated protein 1A/1B-light chain 3/GABA type A receptor-associated protein) protein family members. In this review, we summarize the current knowledge regarding the Ub recognition code that is bound by Ub-binding proteasomal and autophagic receptors. We also discuss how cells can modify substrate fate by modulating the structure, conformation, and physical properties of these receptors to affect their shuttling between both degradation pathways.
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27
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Sharma V, Verma S, Seranova E, Sarkar S, Kumar D. Selective Autophagy and Xenophagy in Infection and Disease. Front Cell Dev Biol 2018; 6:147. [PMID: 30483501 PMCID: PMC6243101 DOI: 10.3389/fcell.2018.00147] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/10/2018] [Indexed: 12/29/2022] Open
Abstract
Autophagy, a cellular homeostatic process, which ensures cellular survival under various stress conditions, has catapulted to the forefront of innate defense mechanisms during intracellular infections. The ability of autophagy to tag and target intracellular pathogens toward lysosomal degradation is central to this key defense function. However, studies involving the role and regulation of autophagy during intracellular infections largely tend to ignore the housekeeping function of autophagy. A growing number of evidences now suggest that the housekeeping function of autophagy, rather than the direct pathogen degradation function, may play a decisive role to determine the outcome of infection and immunological balance. We discuss herein the studies that establish the homeostatic and anti-inflammatory function of autophagy, as well as role of bacterial effectors in modulating and coopting these functions. Given that the core autophagy machinery remains largely the same across diverse cargos, how selectivity plays out during intracellular infection remains intriguing. We explore here, the contrasting role of autophagy adaptors being both selective as well as pleotropic in functions and discuss whether E3 ligases could bring in the specificity to cargo selectivity.
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Affiliation(s)
- Vartika Sharma
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Surbhi Verma
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Elena Seranova
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sovan Sarkar
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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28
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Danieli A, Martens S. p62-mediated phase separation at the intersection of the ubiquitin-proteasome system and autophagy. J Cell Sci 2018; 131:131/19/jcs214304. [PMID: 30287680 DOI: 10.1242/jcs.214304] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The degradation of misfolded proteins is essential for cellular homeostasis. Misfolded proteins are normally degraded by the ubiquitin-proteasome system (UPS), and selective autophagy serves as a backup mechanism when the UPS is overloaded. Selective autophagy mediates the degradation of harmful material by its sequestration within double-membrane organelles called autophagosomes. The selectivity of autophagic processes is mediated by cargo receptors, which link the cargo to the autophagosomal membrane. The p62 cargo receptor (SQSTM1) has a main function during the degradation of misfolded, ubiquitylated proteins by selective autophagy; here it functions to phase separate these proteins into larger condensates and tether them to the autophagosomal membrane. Recent work has given us crucial insights into the mechanism of action of the p62 cargo receptor during selective autophagy and how its activity can be integrated with the UPS. We will discuss these recent insights in the context of protein quality control and the emerging concept of cellular organization mediated by phase transitions.
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Affiliation(s)
- Alberto Danieli
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
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29
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Kocaturk NM, Gozuacik D. Crosstalk Between Mammalian Autophagy and the Ubiquitin-Proteasome System. Front Cell Dev Biol 2018; 6:128. [PMID: 30333975 PMCID: PMC6175981 DOI: 10.3389/fcell.2018.00128] [Citation(s) in RCA: 271] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
Autophagy and the ubiquitin-proteasome system (UPS) are the two major intracellular quality control and recycling mechanisms that are responsible for cellular homeostasis in eukaryotes. Ubiquitylation is utilized as a degradation signal by both systems, yet, different mechanisms are in play. The UPS is responsible for the degradation of short-lived proteins and soluble misfolded proteins whereas autophagy eliminates long-lived proteins, insoluble protein aggregates and even whole organelles (e.g., mitochondria, peroxisomes) and intracellular parasites (e.g., bacteria). Both the UPS and selective autophagy recognize their targets through their ubiquitin tags. In addition to an indirect connection between the two systems through ubiquitylated proteins, recent data indicate the presence of connections and reciprocal regulation mechanisms between these degradation pathways. In this review, we summarize these direct and indirect interactions and crosstalks between autophagy and the UPS, and their implications for cellular stress responses and homeostasis.
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Affiliation(s)
- Nur Mehpare Kocaturk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Devrim Gozuacik
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
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30
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Autophagy differentially regulates TNF receptor Fn14 by distinct mammalian Atg8 proteins. Nat Commun 2018; 9:3744. [PMID: 30218067 PMCID: PMC6138730 DOI: 10.1038/s41467-018-06275-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 07/26/2018] [Indexed: 02/07/2023] Open
Abstract
Autophagy, a conserved membrane trafficking process, sequesters cytoplasmic components into autophagosomes and targets them for lysosomal degradation. The TNF receptor Fn14 participates in multiple intracellular signaling pathways and is strongly induced upon tissue injury and solid tumorigenesis. While Fn14 is a short-lived protein, the regulation of its levels is largely obscure. Here we uncover a role for autophagy in Fn14 turnover, wherein specific core autophagy Atg8 proteins play distinct roles: Fn14 accumulates in the ERGIC in absence of GABARAP but within endosomes in the vicinity of autophagic membranes in absence of GATE-16. Moreover, GABARAP regulates overall cellular levels of Fn14, whereas GATE-16 regulates TWEAK signaling by Fn14 and thereby NF-κB activity. These findings not only implicate different Atg8 proteins in distinct roles within the mechanism of selective autophagic regulation of Fn14, but may also provide a more general view of their role in mediating autophagosome biogenesis from different membrane sources.
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31
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Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter. Nat Commun 2018; 9:3291. [PMID: 30120248 PMCID: PMC6098011 DOI: 10.1038/s41467-018-05825-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 07/27/2018] [Indexed: 02/06/2023] Open
Abstract
p62/SQSTM1 is the key autophagy adapter protein and the hub of multi-cellular signaling. It was recently reported that autophagy and N-end rule pathways are linked via p62. However, the exact recognition mode of degrading substrates and regulation of p62 in the autophagic pathway remain unknown. Here, we present the complex structures between the ZZ-domain of p62 and various type-1 and type-2 N-degrons. The binding mode employed in the interaction of the ZZ-domain with N-degrons differs from that employed by classic N-recognins. It was also determined that oligomerization via the PB1 domain can control functional affinity to the R-BiP substrate. Unexpectedly, we found that self-oligomerization and disassembly of p62 are pH-dependent. These findings broaden our understanding of the functional repertoire of the N-end rule pathway and provide an insight into the regulation of p62 during the autophagic pathway. The autophagy adapter p62/SQSTM1 plays a key role in selective autophagy and also recognizes N-end rule substrates. Here the authors provide molecular insights into p62 N-end rule substrate recognition by solving the structures of the p62 ZZ-domain in complex with various type 1 and type 2 degrons and also show the pH dependent oligomerization of p62.
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32
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Cabe M, Rademacher DJ, Karlsson AB, Cherukuri S, Bakowska JC. PB1 and UBA domains of p62 are essential for aggresome-like induced structure formation. Biochem Biophys Res Commun 2018; 503:2306-2311. [PMID: 29966650 DOI: 10.1016/j.bbrc.2018.06.153] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/27/2018] [Indexed: 11/26/2022]
Abstract
ALIS are large, transient, cytosolic aggregates that serve as storage compartments for ubiquitin-tagged defective ribosomal products. We determined the importance of the protein p62 in the formation of ALIS and demonstrated that two domains of p62-PB1 and UBA-are essential for ALIS assembly. Those two major binding domains of p62, also known as sequestosome 1, were shown to play a critical role in the formation of autophagosomes or cytoplasmic aggregates. Specifically, the PB1 domain is essential for self-oligomerization, and the UBA domain allows p62 to bind to polyubiquitin chains or ubiquitinated proteins. After stimulation of RAW 264.7 macrophages with lipopolysaccharide, we observed a significant decrease in the number of cells with ALIS. Importantly, cells overexpressing either a PB1 mutant or UBA-deleted p62 construct also exhibited a substantially diminished number of cells containing ALIS. Since both p62 and ubiquitin are found in ALIS, we evaluated the dynamics of YFP-tagged p62 in ALIS. In contrast to the findings of a previous study that evaluated GFP-tagged ubiquitin motility in ALIS, we determined that YFP-tagged p62 has very limited mobility. Lastly, we determined that GST-tagged full-length p62 binds to Lys-63-linked polyubiquitin chains but not to Lys-48-linked chains. Overall, our findings provide insight on the essential role that p62, particularly its PB1 and UBA domains, has in the formation of ALIS.
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Affiliation(s)
- Maleen Cabe
- Department of Molecular Pharmacology and Therapeutics, Loyola University Chicago, Maywood, IL 60153, USA
| | - David J Rademacher
- Core Imaging Facility and Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL 60153, USA
| | - Amelia B Karlsson
- Department of Molecular Pharmacology and Therapeutics, Loyola University Chicago, Maywood, IL 60153, USA
| | - Srinivas Cherukuri
- Department of Molecular Pharmacology and Therapeutics, Loyola University Chicago, Maywood, IL 60153, USA
| | - Joanna C Bakowska
- Department of Molecular Pharmacology and Therapeutics, Loyola University Chicago, Maywood, IL 60153, USA.
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33
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Mishra R, Upadhyay A, Prajapati VK, Mishra A. Proteasome-mediated proteostasis: Novel medicinal and pharmacological strategies for diseases. Med Res Rev 2018; 38:1916-1973. [DOI: 10.1002/med.21502] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/13/2018] [Accepted: 04/04/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Ribhav Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
| | - Vijay Kumar Prajapati
- Department of Biochemistry; School of Life Sciences; Central University of Rajasthan; Rajasthan India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
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34
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Nibe Y, Oshima S, Kobayashi M, Maeyashiki C, Matsuzawa Y, Otsubo K, Matsuda H, Aonuma E, Nemoto Y, Nagaishi T, Okamoto R, Tsuchiya K, Nakamura T, Nakada S, Watanabe M. Novel polyubiquitin imaging system, PolyUb-FC, reveals that K33-linked polyubiquitin is recruited by SQSTM1/p62. Autophagy 2018; 14:347-358. [PMID: 29164995 DOI: 10.1080/15548627.2017.1407889] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Ubiquitin chains are formed with 8 structurally and functionally distinct polymers. However, the functions of each polyubiquitin remain poorly understood. We developed a polyubiquitin-mediated fluorescence complementation (PolyUb-FC) assay using Kusabira Green (KG) as a split fluorescent protein. The PolyUb-FC assay has the advantage that monoubiquitination is nonfluorescent and chain-specific polyubiquitination can be directly visualized in living cells without using antibodies. We applied the PolyUb-FC assay to examine K33-linked polyubiquitin. We demonstrated that SQSTM1/p62 puncta colocalized with K33-linked polyubiquitin and this interaction was modulated by the ZRANB1/TRABID-K29 and -K33 linkage-specific deubiquitinase (DUB). We further showed that the colocalization of K33-linked polyubiquitin and MAP1LC3/LC3 (microtubule associated protein 1 light chain 3) puncta was impaired by SQSTM1/p62 deficiency. Taken together, these findings provide novel insights into how atypical polyubiquitin is recruited by SQSTM1/p62. Finally, we developed an inducible-PolyUb-FC system for visualizing chain-specific polyubiquitin. The PolyUb-FC will be a useful tool for analyzing the dynamics of atypical polyubiquitin chain generation.
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Affiliation(s)
- Yoichi Nibe
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Shigeru Oshima
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Masanori Kobayashi
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Chiaki Maeyashiki
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Yu Matsuzawa
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Kana Otsubo
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Hiroki Matsuda
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Emi Aonuma
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Yasuhiro Nemoto
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Takashi Nagaishi
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Ryuichi Okamoto
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan.,b Center for Stem Cell and Regenerative Medicine , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Kiichiro Tsuchiya
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Tetsuya Nakamura
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan.,c Department of Advanced Therapeutics for GI Diseases , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
| | - Shinichiro Nakada
- d Department of Bioregulation and Cellular Response, Graduate School of Medicine , Osaka University , Osaka , Japan
| | - Mamoru Watanabe
- a Department of Gastroenterology and Hepatology , Graduate School , Tokyo Medical and Dental University (TMDU) , Tokyo , Japan
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35
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Zaffagnini G, Savova A, Danieli A, Romanov J, Tremel S, Ebner M, Peterbauer T, Sztacho M, Trapannone R, Tarafder AK, Sachse C, Martens S. p62 filaments capture and present ubiquitinated cargos for autophagy. EMBO J 2018; 37:embj.201798308. [PMID: 29343546 PMCID: PMC5830917 DOI: 10.15252/embj.201798308] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 01/03/2018] [Accepted: 01/03/2018] [Indexed: 12/14/2022] Open
Abstract
The removal of misfolded, ubiquitinated proteins is an essential part of the protein quality control. The ubiquitin-proteasome system (UPS) and autophagy are two interconnected pathways that mediate the degradation of such proteins. During autophagy, ubiquitinated proteins are clustered in a p62-dependent manner and are subsequently engulfed by autophagosomes. However, the nature of the protein substrates targeted for autophagy is unclear. Here, we developed a reconstituted system using purified components and show that p62 and ubiquitinated proteins spontaneously coalesce into larger clusters. Efficient cluster formation requires substrates modified with at least two ubiquitin chains longer than three moieties and is based on p62 filaments cross-linked by the substrates. The reaction is inhibited by free ubiquitin, K48-, and K63-linked ubiquitin chains, as well as by the autophagosomal marker LC3B, suggesting a tight cross talk with general proteostasis and autophagosome formation. Our study provides mechanistic insights on how substrates are channeled into autophagy.
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Affiliation(s)
- Gabriele Zaffagnini
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Adriana Savova
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Alberto Danieli
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Julia Romanov
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Shirley Tremel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Ebner
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Thomas Peterbauer
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Martin Sztacho
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Riccardo Trapannone
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Abul K Tarafder
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
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36
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Lee A, Rayner SL, Gwee SSL, De Luca A, Shahheydari H, Sundaramoorthy V, Ragagnin A, Morsch M, Radford R, Galper J, Freckleton S, Shi B, Walker AK, Don EK, Cole NJ, Yang S, Williams KL, Yerbury JJ, Blair IP, Atkin JD, Molloy MP, Chung RS. Pathogenic mutation in the ALS/FTD gene, CCNF, causes elevated Lys48-linked ubiquitylation and defective autophagy. Cell Mol Life Sci 2018; 75:335-354. [PMID: 28852778 PMCID: PMC11105586 DOI: 10.1007/s00018-017-2632-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/29/2017] [Accepted: 08/23/2017] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative disorders that have common molecular and pathogenic characteristics, such as aberrant accumulation and ubiquitylation of TDP-43; however, the mechanisms that drive this process remain poorly understood. We have recently identified CCNF mutations in familial and sporadic ALS and FTD patients. CCNF encodes cyclin F, a component of an E3 ubiquitin-protein ligase (SCFcyclin F) complex that is responsible for ubiquitylating proteins for degradation by the ubiquitin-proteasome system. In this study, we examined the ALS/FTD-causing p.Ser621Gly (p.S621G) mutation in cyclin F and its effect upon downstream Lys48-specific ubiquitylation in transfected Neuro-2A and SH-SY5Y cells. Expression of mutant cyclin FS621G caused increased Lys48-specific ubiquitylation of proteins in neuronal cells compared to cyclin FWT. Proteomic analysis of immunoprecipitated Lys48-ubiquitylated proteins from mutant cyclin FS621G-expressing cells identified proteins that clustered within the autophagy pathway, including sequestosome-1 (p62/SQSTM1), heat shock proteins, and chaperonin complex components. Examination of autophagy markers p62, LC3, and lysosome-associated membrane protein 2 (Lamp2) in cells expressing mutant cyclin FS621G revealed defects in the autophagy pathway specifically resulting in impairment in autophagosomal-lysosome fusion. This finding highlights a potential mechanism by which cyclin F interacts with p62, the receptor responsible for transporting ubiquitylated substrates for autophagic degradation. These findings demonstrate that ALS/FTD-causing mutant cyclin FS621G disrupts Lys48-specific ubiquitylation, leading to accumulation of substrates and defects in the autophagic machinery. This study also demonstrates that a single missense mutation in cyclin F causes hyper-ubiquitylation of proteins that can indirectly impair the autophagy degradation pathway, which is implicated in ALS pathogenesis.
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Affiliation(s)
- Albert Lee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia.
- Australian Proteome Analysis Facility, Macquarie University, Research Park Drive, North Ryde, NSW, 2109, Australia.
| | - Stephanie L Rayner
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Research Park Drive, North Ryde, NSW, 2109, Australia
| | - Serene S L Gwee
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Alana De Luca
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Hamideh Shahheydari
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Vinod Sundaramoorthy
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Audrey Ragagnin
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Marco Morsch
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Rowan Radford
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Jasmin Galper
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Sarah Freckleton
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Bingyang Shi
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Adam K Walker
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Emily K Don
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Nicholas J Cole
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Shu Yang
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, School of Biological Sciences, University of Wollongong, Northfields Avenue, Wollongong, NSW, 2522, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
| | - Julie D Atkin
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Melbourne, VIC, 3086, Australia
| | - Mark P Molloy
- Australian Proteome Analysis Facility, Macquarie University, Research Park Drive, North Ryde, NSW, 2109, Australia
- Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Research Park Drive, North Ryde, NSW, 2109, Australia
| | - Roger S Chung
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, 2 Technology Place, North Ryde, NSW, 2109, Australia
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Heath RJ, Goel G, Baxt LA, Rush JS, Mohanan V, Paulus GLC, Jani V, Lassen KG, Xavier RJ. RNF166 Determines Recruitment of Adaptor Proteins during Antibacterial Autophagy. Cell Rep 2017; 17:2183-2194. [PMID: 27880896 DOI: 10.1016/j.celrep.2016.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 09/13/2016] [Accepted: 10/26/2016] [Indexed: 02/08/2023] Open
Abstract
Xenophagy is a form of selective autophagy that involves the targeting and elimination of intracellular pathogens through several recognition, recruitment, and ubiquitination events. E3 ubiquitin ligases control substrate selectivity in the ubiquitination cascade; however, systematic approaches to map the role of E3 ligases in antibacterial autophagy have been lacking. We screened more than 600 putative human E3 ligases, identifying E3 ligases that are required for adaptor protein recruitment and LC3-bacteria colocalization, critical steps in antibacterial autophagy. An unbiased informatics approach pinpointed RNF166 as a key gene that interacts with the autophagy network and controls the recruitment of ubiquitin as well as the autophagy adaptors p62 and NDP52 to bacteria. Mechanistic studies demonstrated that RNF166 catalyzes K29- and K33-linked polyubiquitination of p62 at residues K91 and K189. Thus, our study expands the catalog of E3 ligases that mediate antibacterial autophagy and identifies a critical role for RNF166 in this process.
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Affiliation(s)
- Robert J Heath
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Gautam Goel
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Leigh A Baxt
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jason S Rush
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vishnu Mohanan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Geraldine L C Paulus
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vijay Jani
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kara G Lassen
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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Mazzucco AE, Smogorzewska A, Kang C, Luo J, Schlabach MR, Xu Q, Patel R, Elledge SJ. Genetic interrogation of replicative senescence uncovers a dual role for USP28 in coordinating the p53 and GATA4 branches of the senescence program. Genes Dev 2017; 31:1933-1938. [PMID: 29089421 PMCID: PMC5710139 DOI: 10.1101/gad.304857.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/19/2017] [Indexed: 11/25/2022]
Abstract
In this study, Mazzucco et al. describe a panel of genetic screens to identify genes required for replicative senescence and uncover a role in senescence for the potent tumor suppressor and ATM substrate USP28. Their findings suggest a role for ubiquitination in senescence and imply a common node downstream from ATM that links the TP53 and GATA4 branches of the senescence response. Senescence is a terminal differentiation program that halts the growth of damaged cells and must be circumvented for cancer to arise. Here we describe a panel of genetic screens to identify genes required for replicative senescence. We uncover a role in senescence for the potent tumor suppressor and ATM substrate USP28. USP28 controls activation of both the TP53 branch and the GATA4/NFkB branch that controls the senescence-associated secretory phenotype (SASP). These results suggest a role for ubiquitination in senescence and imply a common node downstream from ATM that links the TP53 and GATA4 branches of the senescence response.
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Affiliation(s)
- Anna E Mazzucco
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Agata Smogorzewska
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.,The Rockefeller University, New York, New York 10065, USA
| | - Chanhee Kang
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,School of Biological Sciences, Seoul National University, Seoul 08826, South Korea
| | - Ji Luo
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Michael R Schlabach
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.,KSQ Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Qikai Xu
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Rupesh Patel
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
| | - Stephen J Elledge
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
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39
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CaMKII-mediated Beclin 1 phosphorylation regulates autophagy that promotes degradation of Id and neuroblastoma cell differentiation. Nat Commun 2017; 8:1159. [PMID: 29079782 PMCID: PMC5660092 DOI: 10.1038/s41467-017-01272-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 09/02/2017] [Indexed: 01/11/2023] Open
Abstract
Autophagy is a degradative pathway that delivers cellular components to the lysosome for degradation. The role of autophagy in cell differentiation is poorly understood. Here we show that CaMKII can directly phosphorylate Beclin 1 at Ser90 to promote K63-linked ubiquitination of Beclin 1 and activation of autophagy. Meanwhile, CaMKII can also promote K63-linked ubiquitination of inhibitor of differentiation 1/2 (Id-1/2) by catalyzing phosphorylation of Id proteins and recruiting TRAF-6. Ubiquitinated Id-1/Id-2 can then bind to p62 and be transported to autolysosomes for degradation. Id degradation promotes the differentiation of neuroblastoma cells and reduces the proportion of stem-like cells. Our study proposes a mechanism by which autophagic degradation of Id proteins can regulate cell differentiation. This suggests that targeting of CaMKII and the regulation of autophagic degradation of Id may be an effective therapeutic strategy to induce cell differentiation in neuroblastoma. Neuroblastoma cell differentiation is regulated by Id proteins. Here, the authors show that CaMKII-mediated phosphorylation of Beclin 1 can activate K63-linked ubiquitination and autophagic degradation of Id proteins uncovering a role for autophagy in cell differentiation.
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40
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Molecular Mechanisms Responsible for Increased Vulnerability of the Ageing Oocyte to Oxidative Damage. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2017; 2017:4015874. [PMID: 29312475 PMCID: PMC5664291 DOI: 10.1155/2017/4015874] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/03/2017] [Indexed: 12/23/2022]
Abstract
In their midthirties, women experience a decline in fertility, coupled to a pronounced increase in the risk of aneuploidy, miscarriage, and birth defects. Although the aetiology of such pathologies are complex, a causative relationship between the age-related decline in oocyte quality and oxidative stress (OS) is now well established. What remains less certain are the molecular mechanisms governing the increased vulnerability of the aged oocyte to oxidative damage. In this review, we explore the reduced capacity of the ageing oocyte to mitigate macromolecular damage arising from oxidative insults and highlight the dramatic consequences for oocyte quality and female fertility. Indeed, while oocytes are typically endowed with a comprehensive suite of molecular mechanisms to moderate oxidative damage and thus ensure the fidelity of the germline, there is increasing recognition that the efficacy of such protective mechanisms undergoes an age-related decline. For instance, impaired reactive oxygen species metabolism, decreased DNA repair, reduced sensitivity of the spindle assembly checkpoint, and decreased capacity for protein repair and degradation collectively render the aged oocyte acutely vulnerable to OS and limits their capacity to recover from exposure to such insults. We also highlight the inadequacies of our current armoury of assisted reproductive technologies to combat age-related female infertility, emphasising the need for further research into mechanisms underpinning the functional deterioration of the ageing oocyte.
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41
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Tan XL, Pan M, Zheng Y, Gao S, Liang LJ, Li YM. Sortase-mediated chemical protein synthesis reveals the bidentate binding of bisphosphorylated p62 with K63 diubiquitin. Chem Sci 2017; 8:6881-6887. [PMID: 29147513 PMCID: PMC5636944 DOI: 10.1039/c7sc02937c] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 08/03/2017] [Indexed: 12/21/2022] Open
Abstract
Phosphorylation of S403 or S407 of the autophagic receptor protein p62 has recently been discovered to enhance the binding of p62 with ubiquitinated protein substrates to upregulate selective autophagy. To elucidate the molecular mechanism of how phosphorylation regulates the recruitment of ubiquitinated proteins, we report the first chemical synthesis of homogeneously phosphorylated p62, which enables the setting up of accurate in vitro systems for biochemical studies. Our synthesis employs the technology of sortase A-mediated protein hydrazide ligation, which successfully affords three types of phosphorylated p62 at the multi-milligram scale. Quantitative biochemical measurements show that the binding affinity of S403/S407-bisphosphorylated p62 to K63 diubiquitin is significantly higher than that of mono-phosphorylated p62. This finding suggests that phosphorylated S403 and S407 sites should bind to different epitopes on the ubiquitin chain. Furthermore, glutamate mutation is found to give a significantly impaired binding affinity, implying the necessity of using chemically synthesized phosphorylated p62 for the biochemical study of selective autophagy.
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Affiliation(s)
- Xiang-Long Tan
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China.,School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China .
| | - Man Pan
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yong Zheng
- School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China . .,High Magnetic Field Laboratory , Chinese Academy of Sciences , Hefei 230031 , China
| | - Shuai Gao
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Lu-Jun Liang
- Tsinghua-Peking Center for Life Sciences , Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Department of Chemistry , Tsinghua University , Beijing 100084 , China
| | - Yi-Ming Li
- School of Biological and Medical Engineering , Hefei University of Technology , Hefei , Anhui 230009 , China .
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42
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Ottaviani D, Marin O, Arrigoni G, Franchin C, Vilardell J, Sandre M, Li W, Parfitt DA, Pinna LA, Cheetham ME, Ruzzene M. Protein kinase CK2 modulates HSJ1 function through phosphorylation of the UIM2 domain. Hum Mol Genet 2017; 26:611-623. [PMID: 28031292 PMCID: PMC5409130 DOI: 10.1093/hmg/ddw420] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 11/13/2022] Open
Abstract
HSJ1 (DNAJB2), a member of the DNAJ family of molecular chaperones, is a key player in neuronal proteostasis maintenance. It binds ubiquitylated proteins through its Ubiquitin Interacting Motifs (UIMs) and facilitates their delivery to the proteasome for degradation. Mutations in the DNAJB2 gene lead to inherited neuropathies such as Charcot-Marie-Tooth type-2, distal hereditary motor neuropathies, spinal muscular atrophy with parkinsonism and the later stages can resemble amyotrophic lateral sclerosis. HSJ1 overexpression can reduce aggregation of neurodegeneration-associated proteins in vitro and in vivo; however, the regulation of HSJ1 function is little understood. Here we show that CK2, a ubiquitous and constitutively active protein kinase, phosphorylates HSJ1 within its second UIM, at the dominant site Ser250 and the hierarchical site Ser247. A phospho-HSJ1 specific antibody confirmed phosphorylation of endogenous HSJ1a and HSJ1b. A tandem approach of phospho-site mutation and treatment with CK2 specific inhibitors demonstrated that phosphorylation at these sites is accompanied by a reduced ability of HSJ1 to bind ubiquitylated clients and to exert its chaperone activity. Our results disclose a novel interplay between ubiquitin- and phosphorylation-dependent signalling, and represent the first report of a regulatory mechanism for UIM-dependent function. They also suggest that CK2 inhibitors could release the full neuroprotective potential of HSJ1, and deserve future interest as therapeutic strategies for neurodegenerative disease.
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Affiliation(s)
- Daniele Ottaviani
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| | - Oriano Marin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129 Padova, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129 Padova, Italy
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, Via G. Orus 2/B, 35129 Padova, Italy
| | - Jordi Vilardell
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| | - Michele Sandre
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| | - Wenwen Li
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - David A. Parfitt
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Lorenzo A. Pinna
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
| | | | - Maria Ruzzene
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b 35131 Padova, Italy
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43
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Feng L, Zhang J, Zhu N, Ding Q, Zhang X, Yu J, Qiang W, Zhang Z, Ma Y, Huang D, Shen Y, Fang S, Yu Y, Wang H, Shen Y. Ubiquitin ligase SYVN1/HRD1 facilitates degradation of the SERPINA1 Z variant/α-1-antitrypsin Z variant via SQSTM1/p62-dependent selective autophagy. Autophagy 2017; 13:686-702. [PMID: 28121484 PMCID: PMC5388218 DOI: 10.1080/15548627.2017.1280207] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
SERPINA1/AAT/α-1-antitrypsin (serpin family A member 1) deficiency (SERPINA1/ AAT-D) is an autosomal recessive disorder characterized by the retention of misfolded SERPINA1/AAT in the endoplasmic reticulum (ER) of hepatocytes and a significant reduction of serum SERPINA1/AAT level. The Z variant of SERPINA1/AAT, containing a Glu342Lys (E342K) mutation (SERPINA1E342K/ATZ), the most common form of SERPINA1/AAT-D, is prone to misfolding and polymerization, which retains it in the ER of hepatocytes and leads to liver injury. Both proteasome and macroautophagy/autophagy pathways are responsible for disposal of SERPINA1E342K/ATZ after it accumulates in the ER. However, the mechanisms by which SERPINA1E342K/ATZ is selectively degraded by autophagy remain unknown. Here, we showed that ER membrane-spanning ubiquitin ligase (E3) SYVN1/HRD1 enhances the degradation of SERPINA1E342K/ATZ through the autophagy-lysosome pathway. We found that SYVN1 promoted SERPINA1E342K/ATZ, especially Triton X 100-insoluble SERPINA1E342K/ATZ clearance. However, the effect of SYVN1 in SERPINA1E342K/ATZ clearance was impaired after autophagy inhibition, as well as in autophagy-related 5 (atg5) knockout cells. On the contrary, autophagy induction enhanced SYVN1-mediated SERPINA1E342K/ATZ degradation. Further study showed that SYVN1 mediated SERPINA1E342K/ATZ ubiquitination, which is required for autophagic degradation of SERPINA1E342K/ATZ by promoting the interaction between SERPINA1E342K/ATZ and SQSTM1/p62 for formation of the autophagy complex. Interestingly, SYVN1-mediated lysine 48 (K48)-linked polyubiquitin chains that conjugated onto SERPINA1E342K/ATZ might predominantly bind to the ubiquitin-associated (UBA) domain of SQSTM1 and couple the ubiquitinated SERPINA1E342K/ATZ to the lysosome for degradation. In addition, autophagy inhibition attenuated the suppressive effect of SYVN1 on SERPINA1E342K/ATZ cytotoxicity, and the autophagy inducer rapamycin enhanced the suppressive effect of SYVN1 on SERPINA1E342K/ATZ-induced cell apoptosis. Therefore, this study proved that SYVN1 enhances SERPINA1E342K/ATZ degradation through SQSTM1-dependent autophagy and attenuates SERPINA1E342K/ATZ cytotoxicity.
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Affiliation(s)
- Lijie Feng
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Jin Zhang
- b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Na Zhu
- b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China.,c The 4th Affiliated Hospital, Anhui Medical University , Hefei, Anhui , China
| | - Qian Ding
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Xiaojie Zhang
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Jishuang Yu
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Weimin Qiang
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Zhetao Zhang
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Yuyang Ma
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Dake Huang
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China
| | - Yujun Shen
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Shengyun Fang
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China.,d Center for Biomedical Engineering and Technology , University of Maryland , Baltimore , MD , USA
| | - Yifan Yu
- e Actuarial Science, School of Continuing Education , Columbia University , New York , NY , USA
| | - Haiping Wang
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
| | - Yuxian Shen
- a School of Basic Medical Sciences , Anhui Medical University , Hefei, Anhui , China.,b Institute of Biopharmaceuticals, Anhui Medical University , Hefei, Anhui , China
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44
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Liu WJ, Ye L, Huang WF, Guo LJ, Xu ZG, Wu HL, Yang C, Liu HF. p62 links the autophagy pathway and the ubiqutin-proteasome system upon ubiquitinated protein degradation. Cell Mol Biol Lett 2016; 21:29. [PMID: 28536631 PMCID: PMC5415757 DOI: 10.1186/s11658-016-0031-z] [Citation(s) in RCA: 580] [Impact Index Per Article: 72.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 12/07/2016] [Indexed: 01/19/2023] Open
Abstract
The ubiquitin–proteasome system (UPS) and autophagy are two distinct and interacting proteolytic systems. They play critical roles in cell survival under normal conditions and during stress. An increasing body of evidence indicates that ubiquitinated cargoes are important markers of degradation. p62, a classical receptor of autophagy, is a multifunctional protein located throughout the cell and involved in many signal transduction pathways, including the Keap1–Nrf2 pathway. It is involved in the proteasomal degradation of ubiquitinated proteins. When the cellular p62 level is manipulated, the quantity and location pattern of ubiquitinated proteins change with a considerable impact on cell survival. Altered p62 levels can even lead to some diseases. The proteotoxic stress imposed by proteasome inhibition can activate autophagy through p62 phosphorylation. A deficiency in autophagy may compromise the ubiquitin–proteasome system, since overabundant p62 delays delivery of the proteasomal substrate to the proteasome despite proteasomal catalytic activity being unchanged. In addition, p62 and the proteasome can modulate the activity of HDAC6 deacetylase, thus influencing the autophagic degradation.
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Affiliation(s)
- Wei Jing Liu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China.,Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, 100700 China
| | - Lin Ye
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Wei Fang Huang
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Lin Jie Guo
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Zi Gan Xu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Hong Luan Wu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Chen Yang
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
| | - Hua Feng Liu
- The Institute of Nephrology, Guangdong Medical University, Zhanjiang, Guangdong 524001 China
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45
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Clough B, Wright JD, Pereira PM, Hirst EM, Johnston AC, Henriques R, Frickel EM. K63-Linked Ubiquitination Targets Toxoplasma gondii for Endo-lysosomal Destruction in IFNγ-Stimulated Human Cells. PLoS Pathog 2016; 12:e1006027. [PMID: 27875583 PMCID: PMC5119857 DOI: 10.1371/journal.ppat.1006027] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/26/2016] [Indexed: 12/03/2022] Open
Abstract
Toxoplasma gondii is the most common protozoan parasitic infection in man. Gamma interferon (IFNγ) activates haematopoietic and non-haematopoietic cells to kill the parasite and mediate host resistance. IFNγ-driven host resistance pathways and parasitic virulence factors are well described in mice, but a detailed understanding of pathways that kill Toxoplasma in human cells is lacking. Here we show, that contrary to the widely held belief that the Toxoplasma vacuole is non-fusogenic, in an immune-stimulated environment, the vacuole of type II Toxoplasma in human cells is able to fuse with the host endo-lysosomal machinery leading to parasite death by acidification. Similar to murine cells, we find that type II, but not type I Toxoplasma vacuoles are targeted by K63-linked ubiquitin in an IFNγ-dependent manner in non-haematopoetic primary-like human endothelial cells. Host defence proteins p62 and NDP52 are subsequently recruited to the type II vacuole in distinct, overlapping microdomains with a loss of IFNγ-dependent restriction in p62 knocked down cells. Autophagy proteins Atg16L1, GABARAP and LC3B are recruited to <10% of parasite vacuoles and show no parasite strain preference, which is consistent with inhibition and enhancement of autophagy showing no effect on parasite replication. We demonstrate that this differs from HeLa human epithelial cells, where type II Toxoplasma are restricted by non-canonical autophagy leading to growth stunting that is independent of lysosomal acidification. In contrast to mouse cells, human vacuoles do not break. In HUVEC, the ubiquitinated vacuoles are targeted for destruction in acidified LAMP1-positive endo-lysosomal compartments. Consequently, parasite death can be prevented by inhibiting host ubiquitination and endosomal acidification. Thus, K63-linked ubiquitin recognition leading to vacuolar endo-lysosomal fusion and acidification is an important, novel virulence-driven Toxoplasma human host defence pathway. Toxoplasma gondii is an intracellular parasite that can invade nucleated cells of any warm-blooded animal into a compartment known as a parasitophorous vacuole (PV). The production of gamma interferon (IFNγ) drives the restriction and killing of Toxoplasma. It is not fully known how the parasite inside the PV is eliminated in human cells, although its fate depends on the cell type into which it invades. In IFNγ-stimulated epithelial HeLa cells for instance growth of type II parasites is restricted 24h post-infection by employing the cellular autophagy pathway. Distinctly, we show here that in human endothelial cells the parasite is destroyed by fusion of the PV with the cell’s endo-lysosomal pathway as early as 6h post-infection. This process, which is at odds with the normally non-fusogenic nature of the PV, is dependent on IFNγ. Parasite death follows Lysine63-linked ubiquitination of the PV and is specific to type II Toxoplasma. Our results demonstrate for the first time that vacuolar acidification leading to parasite death is central to controlling infection by Toxoplasma in human endothelial cells.
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Affiliation(s)
- Barbara Clough
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, United Kingdom
| | - Joseph D. Wright
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, United Kingdom
| | - Pedro M. Pereira
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, United Kingdom
| | - Elizabeth M. Hirst
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, United Kingdom
| | - Ashleigh C. Johnston
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, United Kingdom
| | - Ricardo Henriques
- MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, United Kingdom
| | - Eva-Maria Frickel
- Host-Toxoplasma Interaction Laboratory, The Francis Crick Institute, United Kingdom
- * E-mail:
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46
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Abstract
Autophagy is a process tightly regulated by various autophagy-related proteins. It is generally classified into non-selective and selective autophagy. Whereas non-selective autophagy is triggered when the cell is under starvation, selective autophagy is involved in eliminating dysfunctional organelles, misfolded and/or ubiquitylated proteins, and intracellular pathogens. These components are recognized by autophagy receptors and delivered to phagophores. Several selective autophagy receptors have been identified and characterized. They usually have some common domains, such as LC3-interacting- region (LIR) motif, a specific cargo interacting (ubiquitin-dependent or ubiquitin-independent) domain. Recently, structural data of these autophagy receptors has been described, which provides an insight of their function in the selective autophagic process. In this review, we summarize the most up-to-date findings about the structure-function of autophagy receptors that regulates selective autophagy.
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Affiliation(s)
- Byeong-Won Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Do Hoon Kwon
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul 02841, Korea
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47
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Xie X, Li F, Wang Y, Wang Y, Lin Z, Cheng X, Liu J, Chen C, Pan L. Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2. Autophagy 2016; 11:1775-89. [PMID: 26506893 DOI: 10.1080/15548627.2015.1082025] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The autophagy receptor CALCOCO2/NDP52 functions as a bridging adaptor and plays an essential role in the selective autophagic degradation of invading pathogens by specifically recognizing ubiquitin-coated intracellular pathogens and subsequently targeting them to the autophagic machinery; thereby it is required for innate immune defense against a range of infectious pathogens in mammals. However, the mechanistic basis underlying CALCOCO2-mediated specific recognition of ubiqutinated pathogens is still unknown. Here, using biochemical and structural analyses, we demonstrated that the cargo-binding region of CALCOCO2 contains a dynamic unconventional zinc finger as well as a C2H2-type zinc-finger, and only the C2H2-type zinc finger specifically recognizes mono-ubiquitin or poly-ubiquitin chains. In addition to elucidating the specific ubiquitin recognition mechanism of CALCOCO2, the structure of the CALCOCO2 C2H2-type zinc finger in complex with mono-ubiquitin also uncovers a unique zinc finger-binding mode for ubiquitin. Our findings provide mechanistic insight into how CALCOCO2 targets ubiquitin-decorated pathogens for autophagic degradations.
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Affiliation(s)
- Xingqiao Xie
- a State Key Laboratory of Bioorganic and Natural Products Chemistry
| | - Faxiang Li
- a State Key Laboratory of Bioorganic and Natural Products Chemistry.,b Interdisciplinary Research Center on Biology and Chemistry
| | - Yuanyuan Wang
- d Unit of Pathogenic Fungal Infection and Host Immunity; Institut Pasteur of Shanghai; Chinese Academy of Science ; Shanghai , China
| | - Yingli Wang
- a State Key Laboratory of Bioorganic and Natural Products Chemistry
| | - Zhijie Lin
- e Division of Life Science, State Key Laboratory of Molecular Neuroscience; Hong Kong University of Science and Technology ; Kowloon , Hong Kong , China
| | - Xiaofang Cheng
- a State Key Laboratory of Bioorganic and Natural Products Chemistry.,b Interdisciplinary Research Center on Biology and Chemistry
| | - Jianping Liu
- a State Key Laboratory of Bioorganic and Natural Products Chemistry
| | - Changbin Chen
- d Unit of Pathogenic Fungal Infection and Host Immunity; Institut Pasteur of Shanghai; Chinese Academy of Science ; Shanghai , China
| | - Lifeng Pan
- a State Key Laboratory of Bioorganic and Natural Products Chemistry.,c Collaborative Innovation Center of Chemistry for Life Sciences; Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences ; Shanghai , China
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48
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Suwansa-Ard S, Kankuan W, Thongbuakaew T, Saetan J, Kornthong N, Kruangkum T, Khornchatri K, Cummins SF, Isidoro C, Sobhon P. Transcriptomic analysis of the autophagy machinery in crustaceans. BMC Genomics 2016; 17:587. [PMID: 27506197 PMCID: PMC4979118 DOI: 10.1186/s12864-016-2996-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 08/04/2016] [Indexed: 01/31/2023] Open
Abstract
Background The giant freshwater prawn, Macrobrachium rosenbergii, is a decapod crustacean that is commercially important as a food source. Farming of commercial crustaceans requires an efficient management strategy because the animals are easily subjected to stress and diseases during the culture. Autophagy, a stress response process, is well-documented and conserved in most animals, yet it is poorly studied in crustaceans. Results In this study, we have performed an in silico search for transcripts encoding autophagy-related (Atg) proteins within various tissue transcriptomes of M. rosenbergii. Basic Local Alignment Search Tool (BLAST) search using previously known Atg proteins as queries revealed 41 transcripts encoding homologous M. rosenbergii Atg proteins. Among these Atg proteins, we selected commonly used autophagy markers, including Beclin 1, vacuolar protein sorting (Vps) 34, microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B), p62/sequestosome 1 (SQSTM1), and lysosomal-associated membrane protein 1 (Lamp-1) for further sequence analyses using comparative alignment and protein structural prediction. We found that crustacean autophagy marker proteins contain conserved motifs typical of other animal Atg proteins. Western blotting using commercial antibodies raised against human Atg marker proteins indicated their presence in various M. rosenbergii tissues, while immunohistochemistry localized Atg marker proteins within ovarian tissue, specifically late stage oocytes. Conclusions This study demonstrates that the molecular components of autophagic process are conserved in crustaceans, which is comparable to autophagic process in mammals. Furthermore, it provides a foundation for further studies of autophagy in crustaceans that may lead to more understanding of the reproduction- and stress-related autophagy, which will enable the efficient aquaculture practices. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2996-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saowaros Suwansa-Ard
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Wilairat Kankuan
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,Laboratory of Molecular Pathology, Department of Health Sciences, Amedeo Avogadro University, Novara, Italy
| | - Tipsuda Thongbuakaew
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand.,School of Medicine, Walailak University, Nakhon Si Thammarat, Thailand
| | - Jirawat Saetan
- Department of Anatomy, Faculty of Science, Prince of Songkla University, Hatyai, Songkhla, Thailand
| | - Napamanee Kornthong
- Chulabhorn International College of Medicine, Thammsat University, Klongluang, Phathumthani, Thailand
| | - Thanapong Kruangkum
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kanjana Khornchatri
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Scott F Cummins
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, QLD, Australia
| | - Ciro Isidoro
- Laboratory of Molecular Pathology, Department of Health Sciences, Amedeo Avogadro University, Novara, Italy.
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand. .,Faculty of Allied Health Sciences, Burapha University, Chonburi, Thailand.
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49
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Scott D, Garner TP, Long J, Strachan J, Mistry SC, Bottrill AR, Tooth DJ, Searle MS, Oldham NJ, Layfield R. Mass spectrometry insights into a tandem ubiquitin-binding domain hybrid engineered for the selective recognition of unanchored polyubiquitin. Proteomics 2016; 16:1961-9. [DOI: 10.1002/pmic.201600067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/18/2016] [Accepted: 03/29/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Daniel Scott
- School of Life Sciences; Queen's Medical Centre; University of Nottingham; Nottingham UK
- School of Chemistry; University Park; University of Nottingham; Nottingham UK
| | - Tom P Garner
- Department of Biochemistry; Albert Einstein College of Medicine of Yeshiva University; Bronx NY USA
| | - Jed Long
- School of Chemistry; University Park; University of Nottingham; Nottingham UK
- Centre for Biomolecular Sciences; University Park; University of Nottingham; Nottingham UK
| | - Jo Strachan
- Institute of Cell Biology; University of Edinburgh; Edinburgh UK
| | - Sharad C. Mistry
- Protein & Nucleic Acid Chemistry Laboratory; University of Leicester; Leicester UK
| | - Andrew R. Bottrill
- Protein & Nucleic Acid Chemistry Laboratory; University of Leicester; Leicester UK
| | - David J. Tooth
- School of Life Sciences; Queen's Medical Centre; University of Nottingham; Nottingham UK
| | - Mark S. Searle
- School of Chemistry; University Park; University of Nottingham; Nottingham UK
- Centre for Biomolecular Sciences; University Park; University of Nottingham; Nottingham UK
| | - Neil J. Oldham
- School of Chemistry; University Park; University of Nottingham; Nottingham UK
| | - Rob Layfield
- School of Life Sciences; Queen's Medical Centre; University of Nottingham; Nottingham UK
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50
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Delineating the relationship between amyotrophic lateral sclerosis and frontotemporal dementia: Sequence and structure-based predictions. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1742-54. [PMID: 27318084 DOI: 10.1016/j.bbadis.2016.06.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 05/19/2016] [Accepted: 06/14/2016] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are related neurodegenerative disorders which are characterized by a rapid decline in cognitive and motor functions, and short survival. Both syndromes may be present within the same family or even in the same person. The genetic findings for both diseases also support the existence of a continuum, with mutations in the same genes being found in patients with ALS, FTD or FTD/ALS. Little is known about the molecular mechanisms underlying the differences in mutations of the same protein causing either ALS or FTD. Here, we shed light on 348 ALS and FTD missense mutations in 14 genes focusing on genic intolerance and protein stability based on available 3D structures. Using EvoTol, we prioritized the disease-causing genes and their domain. The most intolerant genes predicted by EvoTol are SQSTM1 and OPTN which are involved in protein homeostasis. Further, using ENCoM (Elastic Network Contact Model) that predicts stability based on vibrational entropy, we predicted that most of the missense mutations with destabilizing energies are in the structural regions that control the protein-protein interaction, and only a few mutations affect protein folding. We found a trend that energy changes are higher for ALS compared to FTD mutations. The stability of the ALS mutants correlated well with the duration of disease progression as compared to FTD-ALS mutants. This study provides a comprehensive understanding of the mechanism of ALS and illustrates the significance of structure-energy based studies in differentiating ALS and FTD mutations.
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