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Sadhukhan T, Bagh MB, Appu AP, Mondal A, Zhang W, Liu A, Mukherjee AB. In a mouse model of INCL reduced S-palmitoylation of cytosolic thioesterase APT1 contributes to microglia proliferation and neuroinflammation. J Inherit Metab Dis 2021; 44:1051-1069. [PMID: 33739454 DOI: 10.1002/jimd.12379] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/13/2021] [Accepted: 03/17/2021] [Indexed: 01/19/2023]
Abstract
S-palmitoylation is a reversible posttranslational modification in which a 16-carbon saturated fatty acid (generally palmitate) is attached to specific cysteine residues in polypeptides via thioester linkage. Dynamic S-palmitoylation (palmitoylation-depalmitoylation), like phosphorylation-dephosphorylation, regulates the function of numerous proteins, especially in the brain. While a family of 23 palmitoyl-acyl transferases (PATS), commonly known as ZDHHCs, catalyze S-palmitoylation of proteins, the thioesterases, localized either in the cytoplasm (eg, APT1) or in the lysosome (eg, PPT1) mediate depalmitoylation. Previously, we reported that APT1 requires dynamic S-palmitoylation for shuttling between the cytosol and the plasma membrane. APT1 depalmitoylated H-Ras to regulate its signaling pathway that stimulates cell proliferation. Although we demonstrated that APT1 catalyzed its own depalmitoylation, the ZDHHC(s) that S-palmitoylated APT1 had remained unidentified. We report here that ZDHHC5 and ZDHHC23 catalyze APT1 S-palmitoylation. Intriguingly, lysosomal Ppt1-deficiency in Cln1-/- mouse, a reliable animal model of INCL, markedly reduced ZDHHC5 and ZDHHC23 levels. Remarkably, in the brain of these mice decreased ZDHHC5 and ZDHHC23 levels suppressed membrane-bound APT1, thereby, increasing plasma membrane-localized H-Ras, which activated its signaling pathway stimulating microglia proliferation. Increased inflammatory cytokines produced by microglia together with increased complement C1q level contributed to the transformation of astrocytes to neurotoxic A1 phenotype. Importantly, neuroinflammation was ameliorated by treatment of Cln1-/- mice with a PPT1-mimetic small molecule, N-tert(Butyl)hydroxylamine (NtBuHA). Our results revealed a novel pathway to neuropathology in an INCL mouse model and uncovered a previously unrecognized mechanism of the neuroprotective actions of NtBuHA and its potential as a drug target.
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Affiliation(s)
- Tamal Sadhukhan
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Maria B Bagh
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Abhilash P Appu
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Avisek Mondal
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
| | - Wei Zhang
- Biostatistics and Bioinformatics Branch (HNT72), Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Aiyi Liu
- Biostatistics and Bioinformatics Branch (HNT72), Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - Anil B Mukherjee
- Section on Developmental Genetics, Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, Maryland, USA
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52
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Chen JJ, Fan Y, Boehning D. Regulation of Dynamic Protein S-Acylation. Front Mol Biosci 2021; 8:656440. [PMID: 33981723 PMCID: PMC8107437 DOI: 10.3389/fmolb.2021.656440] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Protein S-acylation is the reversible addition of fatty acids to the cysteine residues of target proteins. It regulates multiple aspects of protein function, including the localization to membranes, intracellular trafficking, protein interactions, protein stability, and protein conformation. This process is regulated by palmitoyl acyltransferases that have the conserved amino acid sequence DHHC at their active site. Although they have conserved catalytic cores, DHHC enzymes vary in their protein substrate selection, lipid substrate preference, and regulatory mechanisms. Alterations in DHHC enzyme function are associated with many human diseases, including cancers and neurological conditions. The removal of fatty acids from acylated cysteine residues is catalyzed by acyl protein thioesterases. Notably, S-acylation is now known to be a highly dynamic process, and plays crucial roles in signaling transduction in various cell types. In this review, we will explore the recent findings on protein S-acylation, the enzymatic regulation of this process, and discuss examples of dynamic S-acylation.
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53
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Abrami L, Audagnotto M, Ho S, Marcaida MJ, Mesquita FS, Anwar MU, Sandoz PA, Fonti G, Pojer F, Peraro MD, van der Goot FG. Palmitoylated acyl protein thioesterase APT2 deforms membranes to extract substrate acyl chains. Nat Chem Biol 2021; 17:438-447. [PMID: 33707782 PMCID: PMC7610442 DOI: 10.1038/s41589-021-00753-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/27/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023]
Abstract
Many biochemical reactions require controlled recruitment of proteins to membranes. This is largely regulated by posttranslational modifications. A frequent one is S-acylation, which consists of the addition of acyl chains and can be reversed by poorly understood acyl protein thioesterases (APTs). Using a panel of computational and experimental approaches, we dissect the mode of action of the major cellular thioesterase APT2 (LYPLA2). We show that soluble APT2 is vulnerable to proteasomal degradation, from which membrane binding protects it. Interaction with membranes requires three consecutive steps: electrostatic attraction, insertion of a hydrophobic loop and S-acylation by the palmitoyltransferases ZDHHC3 or ZDHHC7. Once bound, APT2 is predicted to deform the lipid bilayer to extract the acyl chain bound to its substrate and capture it in a hydrophobic pocket to allow hydrolysis. This molecular understanding of APT2 paves the way to understand the dynamics of APT2-mediated deacylation of substrates throughout the endomembrane system.
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Affiliation(s)
- Laurence Abrami
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Martina Audagnotto
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Sylvia Ho
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Maria Jose Marcaida
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | | | - Muhammad U. Anwar
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Patrick A. Sandoz
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Giulia Fonti
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Florence Pojer
- Protein Production and Structure Core Facility, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, EPFL, Lausanne, Switzerland,Corresponding Authors: F. Gisou van der Goot () and Matteo Dal Peraro ()
| | - F. Gisou van der Goot
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland,Corresponding Authors: F. Gisou van der Goot () and Matteo Dal Peraro ()
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54
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Busquets-Hernández C, Triola G. Palmitoylation as a Key Regulator of Ras Localization and Function. Front Mol Biosci 2021; 8:659861. [PMID: 33816563 PMCID: PMC8010249 DOI: 10.3389/fmolb.2021.659861] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/22/2021] [Indexed: 11/27/2022] Open
Abstract
Ras proteins require membrane association for proper function. This process is tightly regulated by reversible palmitoylation that controls not only the distribution over different subcellular compartments but also Ras compartmentalization within membrane subdomains. As a result, there is a growing interest in protein palmitoylation and the enzymes that control this process. In this minireview, we discuss how palmitoylation affects the localization and function of Ras proteins. A better understanding of the regulatory mechanism controlling protein lipidation is expected to provide new insights into the functional role of these modifications and may ultimately lead to the development of novel therapeutic approaches.
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Affiliation(s)
| | - Gemma Triola
- Department of Biological Chemistry, Laboratory of Chemical Biology, Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Barcelona, Spain
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55
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Abstract
S-palmitoylation is a reversible posttranslational lipid modification of proteins. It controls protein activity, stability, trafficking and protein–protein interactions. Recent global profiling of immune cells and targeted analysis have identified many S-palmitoylated immunity-associated proteins. Here, we review S-palmitoylated immune receptors and effectors, and their dynamic regulation at cellular membranes to generate specific and balanced immune responses. We also highlight how this understanding can drive therapeutic advances to pharmacologically modulate immune responses.
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Affiliation(s)
- Tandrila Das
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA.,Departments of Immunology and Microbiology, Chemistry, Scripps Research, La Jolla, CA 92037, USA
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56
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Main A, Fuller W. Protein S-Palmitoylation: advances and challenges in studying a therapeutically important lipid modification. FEBS J 2021; 289:861-882. [PMID: 33624421 DOI: 10.1111/febs.15781] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022]
Abstract
The lipid post-translational modification S-palmitoylation is a vast developing field, with the modification itself and the enzymes that catalyse the reversible reaction implicated in a number of diseases. In this review, we discuss the past and recent advances in the experimental tools used in this field, including pharmacological tools, animal models and techniques to understand how palmitoylation controls protein localisation and function. Additionally, we discuss the obstacles to overcome in order to advance the field, particularly to the point at which modulating palmitoylation may be achieved as a therapeutic strategy.
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Affiliation(s)
- Alice Main
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - William Fuller
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
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57
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Losada de la Lastra A, Hassan S, Tate EW. Deconvoluting the biology and druggability of protein lipidation using chemical proteomics. Curr Opin Chem Biol 2021; 60:97-112. [PMID: 33221680 DOI: 10.1016/j.cbpa.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 01/13/2023]
Abstract
Lipids are indispensable cellular building blocks, and their post-translational attachment to proteins makes them important regulators of many biological processes. Dysfunction of protein lipidation is also implicated in many pathological states, yet its systematic analysis presents significant challenges. Thanks to innovations in chemical proteomics, lipidation can now be readily studied by metabolic tagging using functionalized lipid analogs, enabling global profiling of lipidated substrates using mass spectrometry. This has spearheaded the first deconvolution of their full scope in a range of contexts, from cells to pathogens and multicellular organisms. Protein N-myristoylation, S-acylation, and S-prenylation are the most well-studied lipid post-translational modifications because of their extensive contribution to the regulation of diverse cellular processes. In this review, we focus on recent advances in the study of these post-translational modifications, with an emphasis on how novel mass spectrometry methods have elucidated their roles in fundamental biological processes.
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Affiliation(s)
- Ana Losada de la Lastra
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Sarah Hassan
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Wood Lane, London, W12 0BZ, UK.
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58
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Ji B, Skup M. Roles of palmitoylation in structural long-term synaptic plasticity. Mol Brain 2021; 14:8. [PMID: 33430908 PMCID: PMC7802216 DOI: 10.1186/s13041-020-00717-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/15/2020] [Indexed: 11/30/2022] Open
Abstract
Long-term potentiation (LTP) and long-term depression (LTD) are important cellular mechanisms underlying learning and memory processes. N-Methyl-d-aspartate receptor (NMDAR)-dependent LTP and LTD play especially crucial roles in these functions, and their expression depends on changes in the number and single channel conductance of the major ionotropic glutamate receptor α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) located on the postsynaptic membrane. Structural changes in dendritic spines comprise the morphological platform and support for molecular changes in the execution of synaptic plasticity and memory storage. At the molecular level, spine morphology is directly determined by actin cytoskeleton organization within the spine and indirectly stabilized and consolidated by scaffold proteins at the spine head. Palmitoylation, as a uniquely reversible lipid modification with the ability to regulate protein membrane localization and trafficking, plays significant roles in the structural and functional regulation of LTP and LTD. Altered structural plasticity of dendritic spines is also considered a hallmark of neurodevelopmental disorders, while genetic evidence strongly links abnormal brain function to impaired palmitoylation. Numerous studies have indicated that palmitoylation contributes to morphological spine modifications. In this review, we have gathered data showing that the regulatory proteins that modulate the actin network and scaffold proteins related to AMPAR-mediated neurotransmission also undergo palmitoylation and play roles in modifying spine architecture during structural plasticity.
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Affiliation(s)
- Benjun Ji
- Nencki Institute of Experimental Biology, 02-093, Warsaw, Poland.
| | - Małgorzata Skup
- Nencki Institute of Experimental Biology, 02-093, Warsaw, Poland.
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59
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Nagarajan SR, Butler LM, Hoy AJ. The diversity and breadth of cancer cell fatty acid metabolism. Cancer Metab 2021; 9:2. [PMID: 33413672 PMCID: PMC7791669 DOI: 10.1186/s40170-020-00237-2] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Tumor cellular metabolism exhibits distinguishing features that collectively enhance biomass synthesis while maintaining redox balance and cellular homeostasis. These attributes reflect the complex interactions between cell-intrinsic factors such as genomic-transcriptomic regulation and cell-extrinsic influences, including growth factor and nutrient availability. Alongside glucose and amino acid metabolism, fatty acid metabolism supports tumorigenesis and disease progression through a range of processes including membrane biosynthesis, energy storage and production, and generation of signaling intermediates. Here, we highlight the complexity of cellular fatty acid metabolism in cancer, the various inputs and outputs of the intracellular free fatty acid pool, and the numerous ways that these pathways influence disease behavior.
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Affiliation(s)
- Shilpa R Nagarajan
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Churchill Hospital, Oxford, UK
| | - Lisa M Butler
- Adelaide Medical School and Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, SA, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Andrew J Hoy
- Discipline of Physiology, School of Medical Sciences, Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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60
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Tewari R, Shayahati B, Fan Y, Akimzhanov AM. T cell receptor-dependent S-acylation of ZAP-70 controls activation of T cells. J Biol Chem 2021; 296:100311. [PMID: 33482200 PMCID: PMC7949058 DOI: 10.1016/j.jbc.2021.100311] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 02/06/2023] Open
Abstract
ZAP-70 is a tyrosine kinase essential for T cell immune responses. Upon engagement of the T cell receptor (TCR), ZAP-70 is recruited to the specialized plasma membrane domains, becomes activated, and is released to phosphorylate its laterally segregated targets. A shift in ZAP-70 distribution at the plasma membrane is recognized as a critical step in TCR signal transduction and amplification. However, the molecular mechanism supporting stimulation-dependent plasma membrane compartmentalization of ZAP-70 remains poorly understood. In this study, we identified previously uncharacterized lipidation (S-acylation) of ZAP-70 using Acyl-Biotin Exchange assay, a technique that selectively captures S-acylated proteins. We found that this posttranslational modification of ZAP-70 is dispensable for its enzymatic activity. However, the lipidation-deficient mutant of ZAP-70 failed to propagate the TCR pathway suggesting that S-acylation is essential for ZAP-70 interaction with its protein substrates. The kinetics of ZAP-70 S-acylation were consistent with TCR signaling events indicating that agonist-induced S-acylation is a part of the signaling mechanism controlling T cell activation and function. Taken together, our results suggest that TCR-induced S-acylation of ZAP-70 can serve as a critical regulator of T cell-mediated immunity.
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Affiliation(s)
- Ritika Tewari
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Bieerkehazhi Shayahati
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Ying Fan
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA; Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, USA
| | - Askar M Akimzhanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA.
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61
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McClafferty H, Runciman H, Shipston MJ. Site-specific deacylation by ABHD17a controls BK channel splice variant activity. J Biol Chem 2020; 295:16487-16496. [PMID: 32913120 PMCID: PMC7864050 DOI: 10.1074/jbc.ra120.015349] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/26/2020] [Indexed: 12/15/2022] Open
Abstract
S-Acylation, the reversible post-translational lipid modification of proteins, is an important mechanism to control the properties and function of ion channels and other polytopic transmembrane proteins. However, although increasing evidence reveals the role of diverse acyl protein transferases (zDHHC) in controlling ion channel S-acylation, the acyl protein thioesterases that control ion channel deacylation are very poorly defined. Here we show that ABHD17a (α/β-hydrolase domain-containing protein 17a) deacylates the stress-regulated exon domain of large conductance voltage- and calcium-activated potassium (BK) channels inhibiting channel activity independently of effects on channel surface expression. Importantly, ABHD17a deacylates BK channels in a site-specific manner because it has no effect on the S-acylated S0-S1 domain conserved in all BK channels that controls membrane trafficking and is deacylated by the acyl protein thioesterase Lypla1. Thus, distinct S-acylated domains in the same polytopic transmembrane protein can be regulated by different acyl protein thioesterases revealing mechanisms for generating both specificity and diversity for these important enzymes to control the properties and functions of ion channels.
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Affiliation(s)
- Heather McClafferty
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Hamish Runciman
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael J Shipston
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh, United Kingdom.
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62
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Gök C, Fuller W. Topical review: Shedding light on molecular and cellular consequences of NCX1 palmitoylation. Cell Signal 2020; 76:109791. [DOI: 10.1016/j.cellsig.2020.109791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 01/21/2023]
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63
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Abstract
Protein S-acylation (commonly known as palmitoylation) is a widespread reversible lipid modification, which plays critical roles in regulating protein localization, activity, stability, and complex formation. The deregulation of protein S-acylation contributes to many diseases such as cancer and neurodegenerative disorders. The past decade has witnessed substantial progress in proteomic analysis of protein S-acylation, which significantly advanced our understanding of S-acylation biology. In this review, we summarized the techniques for the enrichment of S-acylated proteins or peptides, critically reviewed proteomic studies of protein S-acylation at eight different levels, and proposed major challenges for the S-acylproteomics field. In summary, proteome-scale analysis of protein S-acylation comes of age and will play increasingly important roles in discovering new disease mechanisms, biomarkers, and therapeutic targets.
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Affiliation(s)
- Yang Wang
- Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095, United States
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64
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Diskin C, Ryan TAJ, O'Neill LAJ. Modification of Proteins by Metabolites in Immunity. Immunity 2020; 54:19-31. [PMID: 33220233 DOI: 10.1016/j.immuni.2020.09.014] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/31/2020] [Accepted: 09/15/2020] [Indexed: 12/14/2022]
Abstract
Immunometabolism has emerged as a key focus for immunologists, with metabolic change in immune cells becoming as important a determinant for specific immune effector responses as discrete signaling pathways. A key output for these changes involves post-translational modification (PTM) of proteins by metabolites. Products of glycolysis and Krebs cycle pathways can mediate these events, as can lipids, amino acids, and polyamines. A rich and diverse set of PTMs in macrophages and T cells has been uncovered, altering phenotype and modulating immunity and inflammation in different contexts. We review the recent findings in this area and speculate whether they could be of use in the effort to develop therapeutics for immune-related diseases.
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Affiliation(s)
- C Diskin
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - T A J Ryan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland
| | - L A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Ireland.
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65
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Yang X, Chatterjee V, Ma Y, Zheng E, Yuan SY. Protein Palmitoylation in Leukocyte Signaling and Function. Front Cell Dev Biol 2020; 8:600368. [PMID: 33195285 PMCID: PMC7655920 DOI: 10.3389/fcell.2020.600368] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Palmitoylation is a post-translational modification (PTM) based on thioester-linkage between palmitic acid and the cysteine residue of a protein. This covalent attachment of palmitate is reversibly and dynamically regulated by two opposing sets of enzymes: palmitoyl acyltransferases containing a zinc finger aspartate-histidine-histidine-cysteine motif (PAT-DHHCs) and thioesterases. The reversible nature of palmitoylation enables fine-tuned regulation of protein conformation, stability, and ability to interact with other proteins. More importantly, the proper function of many surface receptors and signaling proteins requires palmitoylation-meditated partitioning into lipid rafts. A growing number of leukocyte proteins have been reported to undergo palmitoylation, including cytokine/chemokine receptors, adhesion molecules, pattern recognition receptors, scavenger receptors, T cell co-receptors, transmembrane adaptor proteins, and signaling effectors including the Src family of protein kinases. This review provides the latest findings of palmitoylated proteins in leukocytes and focuses on the functional impact of palmitoylation in leukocyte function related to adhesion, transmigration, chemotaxis, phagocytosis, pathogen recognition, signaling activation, cytotoxicity, and cytokine production.
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Affiliation(s)
- Xiaoyuan Yang
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Victor Chatterjee
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Yonggang Ma
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Ethan Zheng
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Sarah Y Yuan
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,Department of Surgery, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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66
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Jin J, Zhi X, Wang X, Meng D. Protein palmitoylation and its pathophysiological relevance. J Cell Physiol 2020; 236:3220-3233. [PMID: 33094504 DOI: 10.1002/jcp.30122] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/25/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022]
Abstract
Protein palmitoylation, in which C16 fatty acid chains are attached to cysteine residues via a reversible thioester linkage, is one of the most common lipid modifications and plays important roles in regulating protein stability, subcellular localization, membrane trafficking, interactions with effector proteins, enzymatic activity, and a variety of other cellular processes. Moreover, the unique reversibility of palmitoylation allows proteins to be rapidly shuttled between biological membranes and cytoplasmic substrates in a process usually controlled by a member of the DHHC family of protein palmitoyl transferases (PATs). Notably, mutations in PATs are closely related to a variety of human diseases, such as cancer, neurological disorders, and immune deficiency conditions. In addition to PATs, intracellular palmitoylation dynamics are also regulated by the interplay between distinct posttranslational modifications, including ubiquitination and phosphorylation. Understanding the specific mechanisms of palmitoylation may reveal novel potential therapeutic targets for many human diseases.
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Affiliation(s)
- Jiayu Jin
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, Fudan University, Shanghai, China
| | - Xiuling Zhi
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, Fudan University, Shanghai, China
| | - Xinhong Wang
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, Fudan University, Shanghai, China
| | - Dan Meng
- Shanghai Key Laboratory of Bioactive Small Molecules, Department of Physiology and Pathophysiology, Fudan University, Shanghai, China
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García-Ibáñez Y, Riesco-Eizaguirre G, Santisteban P, Casar B, Crespo P. RAS Subcellular Localization Inversely Regulates Thyroid Tumor Growth and Dissemination. Cancers (Basel) 2020; 12:cancers12092588. [PMID: 32927904 PMCID: PMC7565207 DOI: 10.3390/cancers12092588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
Simple Summary RAS mutations occur frequently in thyroid tumors, but the extent to which they are associated to tumor aggressiveness is still uncertain. HRAS proteins occupy different subcellular localizations, from which they regulate distinct biochemical processes. Herein, we demonstrate that the capacity of HRAS-transformed thyroid cells to extravasate and invade distant organs is orchestrated by HRAS subcellular localization, by a mechanism dependent on VEGF-B secretion. Interestingly, aggressiveness inversely correlates with tumor size. Moreover, we have identified the acyl protein thioesterase APT-1, a regulator of HRAS sublocalization, as a determinant of thyroid tumor growth versus dissemination. As such, alterations in APT-1 expression levels can dramatically affect the behavior of thyroid tumors. In this respect, APT-1 levels could serve as a biomarker that may help in the stratification of HRAS mutant thyroid tumors based on their aggressiveness. Abstract RAS mutations are the second most common genetic alteration in thyroid tumors. However, the extent to which they are associated with the most aggressive phenotypes is still controversial. Regarding their malignancy, the majority of RAS mutant tumors are classified as undetermined, which complicates their clinical management and can lead to undesired under- or overtreatment. Using the chick embryo spontaneous metastasis model, we herein demonstrate that the aggressiveness of HRAS-transformed thyroid cells, as determined by the ability to extravasate and metastasize at distant organs, is orchestrated by HRAS subcellular localization. Remarkably, aggressiveness inversely correlates with tumor size. In this respect, we also show that RAS site-specific capacity to regulate tumor growth and dissemination is dependent on VEGF-B secretion. Furthermore, we have identified the acyl protein thioesterase APT-1 as a determinant of thyroid tumor growth versus dissemination. We show that alterations in APT-1 expression levels can dramatically affect the behavior of thyroid tumors, based on its role as a regulator of HRAS sublocalization at distinct plasma membrane microdomains. In agreement, APT-1 emerges in thyroid cancer clinical samples as a prognostic factor. As such, APT-1 levels could serve as a biomarker that could help in the stratification of HRAS mutant thyroid tumors based on their aggressiveness.
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Affiliation(s)
- Yaiza García-Ibáñez
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, E-39011 Cantabria, Spain; (Y.G.-I.); (B.C.)
| | - Garcilaso Riesco-Eizaguirre
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid. E-28029 Madrid, Spain; (G.R.-E.); (P.S.)
- Departamento de Endocrinología y Nutrición, Hospital Universitario de Móstoles, E-28935 Madrid, Spain
- Departamento de Endocrinología Molecular, Universidad Francisco de Vitoria, E-28223 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Pilar Santisteban
- Instituto de Investigaciones Biomédicas “Alberto Sols”, Consejo Superior de Investigaciones Científicas -Universidad Autónoma de Madrid. E-28029 Madrid, Spain; (G.R.-E.); (P.S.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Berta Casar
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, E-39011 Cantabria, Spain; (Y.G.-I.); (B.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Piero Crespo
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Cantabria. Santander, E-39011 Cantabria, Spain; (Y.G.-I.); (B.C.)
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence:
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Liu H, Yan P, Ren J, Wu C, Yuan W, Rao M, Zhang Z, Kong E. Identifying the Potential Substrates of the Depalmitoylation Enzyme Acyl-protein Thioesterase 1. Curr Mol Med 2020; 19:364-375. [PMID: 30914023 DOI: 10.2174/1566524019666190325143412] [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: 11/07/2018] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 01/03/2023]
Abstract
BACKGROUND The homeostasis of palmitoylation and depalmitoylation is involved in various cellular processes, the disruption of which induces severe physiological consequences. Acyl-protein thioesterase (APT) and palmitoyl-protein thioesterases (PPT) catalyze the depalmitoylation process. The natural mutation in human PPT1 caused neurodegenerative disease, yet the understanding of APT1 remains to be elucidated. While the deletion of APT1 in mice turned out to be potentially embryonically lethal, the decoding of its function strictly relied on the identification of its substrates. OBJECTIVE To determine the potential substrates of APT1 by using the generated human APT1 knockout cell line. METHODS The combined techniques of palmitoyl-protein enrichment and massspectrometry were used to analyze the different proteins. Palmitoyl-proteins both in HEK293T and APT1-KO cells were extracted by resin-assisted capture (RAC) and data independent acquisition (DIA) quantitative method of proteomics for data collection. RESULTS In total, 382 proteins were identified. The gene ontology classification segregated these proteins into diverse biological pathways e.g. endoplasmic reticulum process and ubiquitin-mediated proteolysis. A few potential substrates were selected for verification; indeed, major proteins were palmitoylated. Importantly, their levels of palmitoylation were clearly changed in APT1-KO cells. Interestingly, the proliferation of APT1-KO cells escalated dramatically as compared to that of the WT cells, which could be rescued by APT1 overexpression. CONCLUSION Our study provides a large scale of potential substrates of APT1, thus facilitating the understanding of its intervened molecular functions.
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Affiliation(s)
- Huicong Liu
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Peipei Yan
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Junyan Ren
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Can Wu
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Wei Yuan
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Muding Rao
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Zhongjian Zhang
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Eryan Kong
- Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
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69
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Abstract
RAS was identified as a human oncogene in the early 1980s and subsequently found to be mutated in nearly 30% of all human cancers. More importantly, RAS plays a central role in driving tumor development and maintenance. Despite decades of effort, there remain no FDA approved drugs that directly inhibit RAS. The prevalence of RAS mutations in cancer and the lack of effective anti-RAS therapies stem from RAS' core role in growth factor signaling, unique structural features, and biochemistry. However, recent advances have brought promising new drugs to clinical trials and shone a ray of hope in the field. Here, we will exposit the details of RAS biology that illustrate its key role in cell signaling and shed light on the difficulties in therapeutically targeting RAS. Furthermore, past and current efforts to develop RAS inhibitors will be discussed in depth.
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Affiliation(s)
- J Matthew Rhett
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States
| | - Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States.
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70
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Weller PF, Wang H, Melo RCN. The Charcot-Leyden crystal protein revisited-A lysopalmitoylphospholipase and more. J Leukoc Biol 2020; 108:105-112. [PMID: 32272499 DOI: 10.1002/jlb.3mr0320-319rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/08/2020] [Accepted: 03/12/2020] [Indexed: 12/30/2022] Open
Abstract
The Charcot-Leyden crystal protein (CLC-P), a constituent of human and not mouse eosinophils, is one of the most abundant proteins within human eosinophils. It has a propensity to form crystalline structures, Charcot-Leyden crystals, which are hallmarks in their distinctive extracellular crystalline forms as markers of eosinophilic inflammation. The functions of CLC-P within eosinophils have been uncertain. Although the action of CLC-P as a lysophospholipase has been questioned, assays of chromatographically purified CLC-P and crystal-derived CLC-P as well as studies of transfected recombinant CLC-P have consistently documented that CLC-P endogenously expresses lysophospholipase activity, releasing free palmitate from substrate lysopalmitoylphosphatidylcholine. Rather than acting solely as a hydrolytic enzyme to release palmitate from a lysolipid substrate, some other lysophospholipases function more dominantly as acyl-protein thioesterases (APTs), enzymes that catalyze the removal of thioester-linked, long chain fatty acids, such as palmitate, from cysteine residues of proteins. As such APTs participate in palmitoylation, a post-translational modification that can affect membrane localization, vesicular transport, and secretion. CLC-P has attributes of an APT. Thus, whereas CLC-P expresses inherent lysophospholipase activity, like some other lysophospholipase enzymes, it likely also functions in regulating the dynamic palmitoylation cycle, including, given its dominant subplasmalemmal location, at the human eosinophil's plasma membrane.
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Affiliation(s)
- Peter F Weller
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Haibin Wang
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Rossana C N Melo
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.,Laboratory of Cellular Biology, Department of Biology, ICB, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
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71
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Neviani V, van Deventer S, Wörner TP, Xenaki KT, van de Waterbeemd M, Rodenburg RNP, Wortel IMN, Kuiper JK, Huisman S, Granneman J, van Bergen En Henegouwen PMP, Heck AJR, van Spriel AB, Gros P. Site-specific functionality and tryptophan mimicry of lipidation in tetraspanin CD9. FEBS J 2020; 287:5323-5344. [PMID: 32181977 PMCID: PMC7818406 DOI: 10.1111/febs.15295] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/19/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022]
Abstract
Lipidation of transmembrane proteins regulates many cellular activities, including signal transduction, cell–cell communication, and membrane trafficking. However, how lipidation at different sites in a membrane protein affects structure and function remains elusive. Here, using native mass spectrometry we determined that wild‐type human tetraspanins CD9 and CD81 exhibit nonstochastic distributions of bound acyl chains. We revealed CD9 lipidation at its three most frequent lipidated sites suffices for EWI‐F binding, while cysteine‐to‐alanine CD9 mutations markedly reduced binding of EWI‐F. EWI‐F binding by CD9 was rescued by mutating all or, albeit to a lesser extent, only the three most frequently lipidated sites into tryptophans. These mutations did not affect the nanoscale distribution of CD9 in cell membranes, as shown by super‐resolution microscopy using a CD9‐specific nanobody. Thus, these data demonstrate site‐specific, possibly conformation‐dependent, functionality of lipidation in tetraspanin CD9 and identify tryptophan mimicry as a possible biochemical approach to study site‐specific transmembrane‐protein lipidation.
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Affiliation(s)
- Viviana Neviani
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Sjoerd van Deventer
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Tobias P Wörner
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Katerina T Xenaki
- Cell Biology, Department of Biology, Utrecht University, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Remco N P Rodenburg
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Inge M N Wortel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Jeroen K Kuiper
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Sofie Huisman
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Joke Granneman
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | | | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Annemiek B van Spriel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Piet Gros
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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72
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Wang Y, Lu H, Fang C, Xu J. Palmitoylation as a Signal for Delivery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1248:399-424. [DOI: 10.1007/978-981-15-3266-5_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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73
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Gök C, Fuller W. Regulation of NCX1 by palmitoylation. Cell Calcium 2020; 86:102158. [PMID: 31935590 DOI: 10.1016/j.ceca.2019.102158] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/28/2019] [Accepted: 12/29/2019] [Indexed: 11/17/2022]
Abstract
Palmitoylation (S-acylation) is the reversible conjugation of a fatty acid (usually C16 palmitate) to intracellular cysteine residues of proteins via a thioester linkage. Palmitoylation anchors intracellular regions of proteins to membranes because the palmitoylated cysteine is recruited to the lipid bilayer. NCX1 is palmitoylated at a single cysteine in its large regulatory intracellular loop. The presence of an amphipathic α-helix immediately adjacent to the NCX1 palmitoylation site is required for NCX1 palmitoylation. The NCX1 palmitoylation site is conserved through most metazoan phlya. Although palmitoylation does not regulate the normal forward or reverse ion transport modes of NCX1, NCX1 palmitoylation is required for its inactivation: sodium-dependent inactivation and inactivation by PIP2 depletion are significantly impaired for unpalmitoylatable NCX1. Here we review the role of palmitoylation in regulating NCX1 activity, and highlight future questions that must be addressed to fully understand the importance of this regulatory mechanism for sodium and calcium transport in cardiac muscle.
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Affiliation(s)
- Caglar Gök
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - William Fuller
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK. https://twitter.com@FullerLabGlas
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74
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Therapeutic targeting of protein S-acylation for the treatment of disease. Biochem Soc Trans 2019; 48:281-290. [DOI: 10.1042/bst20190707] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
The post-translational modification protein S-acylation (commonly known as palmitoylation) plays a critical role in regulating a wide range of biological processes including cell growth, cardiac contractility, synaptic plasticity, endocytosis, vesicle trafficking, membrane transport and biased-receptor signalling. As a consequence, zDHHC-protein acyl transferases (zDHHC-PATs), enzymes that catalyse the addition of fatty acid groups to specific cysteine residues on target proteins, and acyl proteins thioesterases, proteins that hydrolyse thioester linkages, are important pharmaceutical targets. At present, no therapeutic drugs have been developed that act by changing the palmitoylation status of specific target proteins. Here, we consider the role that palmitoylation plays in the development of diseases such as cancer and detail possible strategies for selectively manipulating the palmitoylation status of specific target proteins, a necessary first step towards developing clinically useful molecules for the treatment of disease.
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75
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Gadalla MR, Veit M. Toward the identification of ZDHHC enzymes required for palmitoylation of viral protein as potential drug targets. Expert Opin Drug Discov 2019; 15:159-177. [PMID: 31809605 DOI: 10.1080/17460441.2020.1696306] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Introduction: S-acylation is the attachment of fatty acids not only to cysteines of cellular, but also of viral proteins. The modification is often crucial for the protein´s function and hence for virus replication. Transfer of fatty acids is mediated by one or several of the 23 members of the ZDHHC family of proteins. Since their genes are linked to various human diseases, they represent drug targets.Areas covered: The authors explore whether targeting acylation of viral proteins might be a strategy to combat viral diseases. Many human pathogens contain S-acylated proteins; the ZDHHCs involved in their acylation are currently identified. Based on the 3D structure of two ZDHHCs, the regulation and the biochemistry of the palmitolyation reaction and the lipid and protein substrate specificities are discussed. The authors then speculate how ZDHHCs might recognize S-acylated membrane proteins of Influenza virus.Expert opinion: Although many viral diseases can now be treated, the available drugs bind to viral proteins that rapidly mutate and become resistant. To develop inhibitors for the genetically more stable cellular ZDHHCs, their binding sites for viral substrates need to be identified. If only a few cellular proteins are recognized by the same binding site, development of specific inhibitors may have therapeutic potential.
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Affiliation(s)
- Mohamed Rasheed Gadalla
- Institute of Virology, Free University Berlin, Berlin, Germany.,Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Michael Veit
- Institute of Virology, Free University Berlin, Berlin, Germany
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76
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Sada R, Kimura H, Fukata Y, Fukata M, Yamamoto H, Kikuchi A. Dynamic palmitoylation controls the microdomain localization of the DKK1 receptors CKAP4 and LRP6. Sci Signal 2019; 12:12/608/eaat9519. [PMID: 31744930 DOI: 10.1126/scisignal.aat9519] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dickkopf1 (DKK1) was originally identified as an antagonist of Wnt signaling that binds to and induces the clathrin-mediated endocytosis of the Wnt coreceptors low-density lipoprotein receptor-related proteins 5 and 6 (LRP5/6). DKK1 also binds to cytoskeleton-associated protein 4 (CKAP4), which was originally identified as an endoplasmic reticulum (ER) protein but also functions at the plasma membrane as a receptor for various ligands. The DKK1-CKAP4 pathway is activated in several human cancers and promotes cell proliferation by activating signaling through the kinases PI3K and AKT. We found that both CKAP4 and LRP6 primarily localized to detergent-resistant membrane (DRM) fractions of the plasma membrane in a palmitoylation-dependent manner and that palmitoylation of CKAP4 was required for it to promote cell proliferation. DKK1 induced the depalmitoylation of both CKAP4 and LRP6 by acylprotein thioesterases (APTs), resulting in their translocation to the non-DRM fractions. Moreover, DKK1-dependent depalmitoylation of both receptors required activation of the PI3K-AKT pathway. DKK1 simultaneously bound CKAP4 and LRP6, resulting in the formation of a ternary complex. LRP5/6 knockdown decreased DKK1-dependent AKT activation and cancer cell proliferation through CKAP4, whereas CKAP4 knockdown did not affect DKK1-dependent inhibition of Wnt signaling through LRP5/6. These results indicate that the palmitoylation states of CKAP4 and LRP6 play important roles in their signaling and that LRP5/6 enhance DKK1-CKAP4 signaling.
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Affiliation(s)
- Ryota Sada
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Hirokazu Kimura
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Yuko Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki 444-8787, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki 444-8787, Japan
| | - Masaki Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki 444-8787, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki 444-8787, Japan
| | - Hideki Yamamoto
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan.
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77
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Azizi SA, Kathayat RS, Dickinson BC. Activity-Based Sensing of S-Depalmitoylases: Chemical Technologies and Biological Discovery. Acc Chem Res 2019; 52:3029-3038. [PMID: 31577124 DOI: 10.1021/acs.accounts.9b00354] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
While lipids were first appreciated as a critical hydrophobic barrier, our understanding of their roles at the cellular and organismal levels continues to grow. Not only are they important independent operators, providing a platform for both static and dynamic organization and communication within the cell, they also exert significant effects via the chemical modification of proteins. Addition of a lipid post-translational modification (PTM) alters protein hydrophobicity and behavior, with distinct consequences for subcellular trafficking, localization, intra- and intermolecular interactions, and stability. One of the most abundant and widespread protein lipidation events is S-acylation, installation of a long-chain lipid to the thiol of a cysteine side chain through a thioester linkage. S-Acylation is often referred to as S-palmitoylation, due to the prevalence of palmitate as the lipid modification. Unlike many lipid PTMs, S-acylation is enzymatically reversible, enabling the cell to tune proteome-wide properties through dynamic alterations in protein lipidation status. While much has been uncovered about the molecular effects of S-acylation and its implications for physiology, current biochemical and chemical methods only assess substrate lipidation levels or steady-state levels of enzyme activity. Yet, the writer protein acyl transferases (PATs) and eraser acyl protein thioesterases (APTs) are dynamically active, responsible for sometimes-rapid changes in S-palmitoylation status of target proteins. Thus, to understand the full scope, significance, and subtlety of S-deacylation and its regulation in the cell, it is necessary to observe the timing and cellular geography of regulatory enzyme activities. In this Account, we review the chemical tools developed by our group to selectively visualize and perturb the activity of APTs in live cells, highlighting the biological insights gained from their application. To visualize APT activity, we masked fluorogenic molecules with thioacylated, peptide-based APT substrate mimetics; APT activity and thus thiol deprotection releases a fluorescent product in the turn-on depalmitoylation probes (DPPs), while in ratiometric depalmitoylation probes (RDPs) the emission of the parent fluorophore is altered. Application of these probes in live cells reveals that APT activity is sensitive to cell signaling events and metabolic disturbances. Additionally, as indicated above, the location of regulatory enzymes is critical in lipid signaling, and one organelle of particular interest, due to its role in maintaining cellular homeostasis and its legion of lipidated proteins, is the mitochondria. Therefore, we developed a class of spatially constrained mitoDPPs to visualize mitochondrial APT activity as well as a selective inhibitor of mitochondrial deacylation activity, mitoFP. With these tools, we identify two mitochondrial S-depalmitoylases and connect mitochondrial S-depalmitoylation to redox buffering capacity. Moreover, some of the changes in activity observed are specific to the mitochondria, confirming spatial as well as temporal regulation of eraser protein activity. Overall, this chemical toolkit for S-depalmitoylase activity, imaging reagents and a targeted inhibitor, will continue to illuminate the regulatory mechanisms and roles of S-depalmitoylation within the complex homeostatic networks of the cell.
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Affiliation(s)
- Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, Illinois 60637, United States
| | - Rahul S. Kathayat
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Bryan C. Dickinson
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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78
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Cao Y, Qiu T, Kathayat RS, Azizi SA, Thorne AK, Ahn D, Fukata Y, Fukata M, Rice PA, Dickinson BC. ABHD10 is an S-depalmitoylase affecting redox homeostasis through peroxiredoxin-5. Nat Chem Biol 2019; 15:1232-1240. [PMID: 31740833 PMCID: PMC6871660 DOI: 10.1038/s41589-019-0399-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 09/30/2019] [Indexed: 12/12/2022]
Abstract
S-palmitoylation is a reversible lipid post-translational modification that has been observed on mitochondrial proteins, but both the regulation and functional consequences of mitochondrial S-palmitoylation are poorly understood. Here, we show that perturbing the “erasers” of S-palmitoylation, acyl protein thioesterases (APTs), with either pan-active inhibitors or a new mitochondrial-targeted APT inhibitor, diminishes the antioxidant buffering capacity of mitochondria. Surprisingly, this effect was not mediated by the only known mitochondrial APT, but rather by a resident mitochondrial protein with no known endogenous function, ABHD10. We show that ABHD10 is a new member of the APT family of regulatory proteins and identify peroxiredoxin 5 (PRDX5), a key antioxidant protein, as the first target of ABHD10 S-depalmitoylase activity. We then discover that ABHD10 regulates the S-palmitoylation status of the nucleophilic active site residue of PRDX5, providing a direct mechanistic connection between ABHD10-mediated S-depalmitoylation of PRDX5 and its antioxidant capacity.
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Affiliation(s)
- Yang Cao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Tian Qiu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Rahul S Kathayat
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.,Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL, USA
| | - Anneke K Thorne
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Daniel Ahn
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
| | - Yuko Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
| | - Masaki Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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79
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Effects of Post-translational Modifications on Membrane Localization and Signaling of Prostanoid GPCR-G Protein Complexes and the Role of Hypoxia. J Membr Biol 2019; 252:509-526. [PMID: 31485700 DOI: 10.1007/s00232-019-00091-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/17/2019] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in the adaptive responses to cellular stresses such as hypoxia. In addition to influencing cellular gene expression profiles, hypoxic microenvironments can perturb membrane protein localization, altering GPCR effector scaffolding and altering downstream signaling. Studies using proteomics approaches have revealed significant regulation of GPCR and G proteins by their state of post-translational modification. The aim of this review is to examine the effects of post-translational modifications on membrane localization and signaling of GPCR-G protein complexes, with an emphasis on vascular prostanoid receptors, and to highlight what is known about the effect of cellular hypoxia on these mechanisms. Understanding post-translational modifications of protein targets will help to define GPCR targets in treatment of disease, and to inform research into mechanisms of hypoxic cellular responses.
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80
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Palmeira JDF, Argañaraz GA, de Oliveira GXLM, Argañaraz ER. Physiological relevance of ACOT8-Nef interaction in HIV infection. Rev Med Virol 2019; 29:e2057. [PMID: 31179598 DOI: 10.1002/rmv.2057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 11/06/2022]
Abstract
During human immunodeficiency virus (HIV) infection, Nef viral protein plays a crucial role in viral pathogenesis and progression of acquired immunodeficiency syndrome. Nef is expressed in the early stages of infection and alters the cellular environment increasing infectivity, viral replication, and the evasion of host immune response through several mechanisms. Nef has numerous functional domains that allow it to interact with a number of proteins, interfering with intracellular traffic. Among these proteins, human peroxisomal thioesterase 8, ACOT8, has been shown to be an important cellular partner of Nef. It has been suggested that this interaction may be involved in Nef-dependent endocytosis and also in the modulation of lipid composition in membrane rafts. However, the actual role of this interaction, as well as the mechanisms involved, has not yet been fully elucidated. In this review, we focused on the interplay between Nef and ACOT8 proteins, highlighting the possible physiological relevance in HIV infection.
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Affiliation(s)
| | - Gustavo A Argañaraz
- Laboratory of Molecular Neurovirology, Faculty of Health Science, University of Brasília, Brazil
| | | | - Enrique R Argañaraz
- Laboratory of Molecular Neurovirology, Faculty of Health Science, University of Brasília, Brazil
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81
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Targeting MC1R depalmitoylation to prevent melanomagenesis in redheads. Nat Commun 2019; 10:877. [PMID: 30787281 PMCID: PMC6382811 DOI: 10.1038/s41467-019-08691-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 01/24/2019] [Indexed: 11/23/2022] Open
Abstract
Some genetic melanocortin-1 receptor (MC1R) variants responsible for human red hair color (RHC-variants) are consequently associated with increased melanoma risk. Although MC1R signaling is critically dependent on its palmitoylation primarily mediated by the ZDHHC13 protein-acyl transferase, whether increasing MC1R palmitoylation represents a viable therapeutic target to limit melanomagenesis in redheads is unknown. Here we identify a specific and efficient in vivo strategy to induce MC1R palmitoylation for therapeutic benefit. We validate the importance of ZDHHC13 to MC1R signaling in vivo by targeted expression of ZDHHC13 in C57BL/6J-MC1RRHC mice and subsequently inhibit melanomagenesis. By identifying APT2 as the MC1R depalmitoylation enzyme, we are able to demonstrate that administration of the selective APT2 inhibitor ML349 treatment efficiently increases MC1R signaling and represses UVB-induced melanomagenesis in vitro and in vivo. Targeting APT2, therefore, represents a preventive/therapeutic strategy to reduce melanoma risk, especially in individuals with red hair. Melanocortin-1 receptor is a palmitoylated protein and variants of the receptor are associated with red hair colour and susceptibility to melanoma. Here, the authors describe a method to enhance the palmitoylation of the receptor, which can inhibit melanomagenesis in mice.
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82
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Systematic Screening of Depalmitoylating Enzymes and Evaluation of Their Activities by the Acyl-PEGyl Exchange Gel-Shift (APEGS) Assay. Methods Mol Biol 2019; 2009:83-98. [PMID: 31152397 DOI: 10.1007/978-1-4939-9532-5_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Palmitoylation is a reversible posttranslational lipid modification of proteins involved in a wide range of cellular functions. More than a thousand proteins are estimated to be palmitoylated. In neurons, PSD-95, a major postsynaptic scaffold protein, requires palmitoylation for its specific accumulation at the synapse and dynamically cycles between palmitoylated and depalmitoylated states. Although palmitoylating enzymes of PSD-95 have been well characterized, little is known about the depalmitoylating enzymes (e.g., thioesterases for palmitoylated PSD-95). An elegant pharmacological analysis has suggested that subsets of α/β hydrolase domain (ABHD)-containing proteins of the metabolic serine hydrolase superfamily involve thioesterases for palmitoylated proteins. Here, we describe a systematic method to screen the ABHD serine hydrolase genes, which unveiled ABHD17 as the depalmitoylating enzyme for PSD-95. Furthermore, we introduce the acyl-PEGyl exchange gel-shift (APEGS) method that enables quantification of palmitoylation levels/stoichiometries on proteins in various biological samples and can be used to monitor the dynamic depalmitoylation process of proteins.
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83
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Abstract
Palmitoylation or S-acylation is the posttranslational attachment of fatty acids to cysteine residues and is common among integral and peripheral membrane proteins. Palmitoylated proteins have been found in every eukaryotic cell type examined (yeast, insect, and vertebrate cells), as well as in viruses grown in these cells. The exact functions of protein palmitoylation are not well understood. Intrinsically hydrophilic proteins, especially signaling molecules, are anchored by long-chain fatty acids to the cytoplasmic face of the plasma membrane. Palmitoylation may also promote targeting to membrane subdomains enriched in glycosphingolipids and cholesterol or affect protein-protein interactions.This chapter describes (1) a standard protocol for metabolic labeling of palmitoylated proteins and also the procedures to prove a covalent and ester-type linkage of the fatty acids, (2) a simple method to analyze the fatty acid content of S-acylated proteins, (3) two methods to analyze dynamic palmitoylation for a given protein, and (4) protocols to study cell-free palmitoylation of proteins.
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Affiliation(s)
- Larisa Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Ludwig Krabben
- Freie Universität Berlin, Fachbereich Veterinärmedizin, Zentrum für Infektionsmedizin, Institut für Virologie, Berlin, Germany
| | - Marina Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Michael Veit
- Freie Universität Berlin, Fachbereich Veterinärmedizin, Zentrum für Infektionsmedizin, Institut für Virologie, Berlin, Germany.
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84
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Amara N, Foe IT, Onguka O, Garland M, Bogyo M. Synthetic Fluorogenic Peptides Reveal Dynamic Substrate Specificity of Depalmitoylases. Cell Chem Biol 2018; 26:35-47.e7. [PMID: 30393067 DOI: 10.1016/j.chembiol.2018.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/21/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022]
Abstract
Palmitoylation is a post-translational modification involving the thioesterification of cysteine residues with a 16-carbon-saturated fatty acid. Little is known about rates of depalmitoylation or the parameters that dictate these rates. Here we report a modular strategy to synthesize quenched fluorogenic substrates for the specific detection of depalmitoylase activity and for mapping the substrate specificity of individual depalmitoylases. We demonstrate that human depalmitoylases APT1 and APT2, and TgPPT1 from the parasite Toxoplasma gondii, have distinct specificities that depend on amino acid residues distal to the palmitoyl cysteine. This information informs the design of optimal and non-optimal substrates as well as isoform-selective substrates to detect the activity of a specific depalmitoylase in complex proteomes. In addition to providing tools for studying depalmitoylases, our findings identify a previously unrecognized mechanism for regulating steady-state levels of distinct palmitoylation sites by sequence-dependent control of depalmitoylation rates.
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Affiliation(s)
- Neri Amara
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian T Foe
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ouma Onguka
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Megan Garland
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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85
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Ahearn I, Zhou M, Philips MR. Posttranslational Modifications of RAS Proteins. Cold Spring Harb Perspect Med 2018; 8:cshperspect.a031484. [PMID: 29311131 DOI: 10.1101/cshperspect.a031484] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The three human RAS genes encode four proteins that play central roles in oncogenesis by acting as binary molecular switches that regulate signaling pathways for growth and differentiation. Each is subject to a set of posttranslational modifications (PTMs) that modify their activity or are required for membrane targeting. The enzymes that catalyze the various PTMs are potential targets for anti-RAS drug discovery. The PTMs of RAS proteins are the focus of this review.
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Affiliation(s)
- Ian Ahearn
- Department of Medicine, Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016
| | - Mo Zhou
- Department of Medicine, Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016
| | - Mark R Philips
- Department of Medicine, Perlmutter Cancer Center, New York University School of Medicine, New York, New York 10016
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86
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Ampah KK, Greaves J, Shun-Shion AS, Asnawi AW, Lidster JA, Chamberlain LH, Collins MO, Peden AA. S-acylation regulates the trafficking and stability of the unconventional Q-SNARE STX19. J Cell Sci 2018; 131:jcs.212498. [PMID: 30254024 DOI: 10.1242/jcs.212498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 09/17/2018] [Indexed: 12/19/2022] Open
Abstract
STX19 is an unusual Qa-SNARE as it lacks a C-terminal transmembrane domain. However, it is efficiently targeted to post-Golgi membranes. Here, we set out to determine the intracellular localisation of endogenous STX19 and elucidate the mechanism by which it is targeted to membranes. We have found that a pool of STX19 is localised to tubular recycling endosomes where it colocalises with MICAL-L1 and Rab8 (which has Rab8a and Rab8b forms). Using a combination of genetic, biochemical and cell-based approaches, we have identified that STX19 is S-acylated at its C-terminus and is a substrate for several Golgi-localised S-acyltransferases, suggesting that STX19 is initially S-acylated at the Golgi before trafficking to the plasma membrane and endosomes. Surprisingly, we have found that S-acylation is a key determinant in targeting STX19 to tubular recycling endosomes, suggesting that S-acylation may play a general role in directing proteins to this compartment. In addition, S-acylation also protects STX19 from proteosomal degradation, indicating that S-acylation regulates the function of STX19 at multiple levels.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Khamal K Ampah
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Jennifer Greaves
- Faculty of Health and Life Sciences, Coventry University, Science and Health Building, 20 Whitefriars Street, Coventry CV1 2DS, UK
| | - Amber S Shun-Shion
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Asral W Asnawi
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK.,Faculty of Medicine and Health Sciences, University Sains Islam Malaysia, 55700 Kuala Lumpur, Malaysia
| | - Jessica A Lidster
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Mark O Collins
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK.,Faculty of Science, Mass Spectrometry Centre, University of Sheffield, Brook Hill Road, Sheffield S3 7HF, UK
| | - Andrew A Peden
- Department of Biomedical Science, Centre for Membrane Interactions and Dynamics, University of Sheffield, Firth Court, Sheffield S10 2TN, UK
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87
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Ko PJ, Dixon SJ. Protein palmitoylation and cancer. EMBO Rep 2018; 19:embr.201846666. [PMID: 30232163 DOI: 10.15252/embr.201846666] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/24/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
Protein S-palmitoylation is a reversible post-translational modification that alters the localization, stability, and function of hundreds of proteins in the cell. S-palmitoylation is essential for the function of both oncogenes (e.g., NRAS and EGFR) and tumor suppressors (e.g., SCRIB, melanocortin 1 receptor). In mammalian cells, the thioesterification of palmitate to internal cysteine residues is catalyzed by 23 Asp-His-His-Cys (DHHC)-family palmitoyl S-acyltransferases while the removal of palmitate is catalyzed by serine hydrolases, including acyl-protein thioesterases (APTs). These enzymes modulate the function of important oncogenes and tumor suppressors and often display altered expression patterns in cancer. Targeting S-palmitoylation or the enzymes responsible for palmitoylation dynamics may therefore represent a candidate therapeutic strategy for certain cancers.
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Affiliation(s)
- Pin-Joe Ko
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA, USA
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88
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Zaballa ME, van der Goot FG. The molecular era of protein S-acylation: spotlight on structure, mechanisms, and dynamics. Crit Rev Biochem Mol Biol 2018; 53:420-451. [DOI: 10.1080/10409238.2018.1488804] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- María-Eugenia Zaballa
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - F. Gisou van der Goot
- Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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89
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Smith MA, Phillips WK, Rabin PL, Johnson RJ. A dynamic loop provides dual control over the catalytic and membrane binding activity of a bacterial serine hydrolase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:925-932. [PMID: 29857162 DOI: 10.1016/j.bbapap.2018.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/11/2018] [Accepted: 05/24/2018] [Indexed: 10/16/2022]
Abstract
The bacterial acyl protein thioesterase (APT) homologue FTT258 from the gram-negative pathogen Francisella tularensis exists in equilibrium between a closed and open state. Interconversion between these two states is dependent on structural rearrangement of a dynamic loop overlapping its active site. The dynamics and structural properties of this loop provide a simple model for how the catalytic activity of FTT258 could be spatiotemporally regulated within the cell. Herein, we characterized the dual roles of this dynamic loop in controlling its catalytic and membrane binding activity. Using a comprehensive library of loop variants, we determined the relative importance of each residue in the loop to these two biological functions. For the catalytic activity, a centrally located tryptophan residue (Trp66) was essential, with the resulting alanine variant showing complete ablation of enzyme activity. Detailed analysis of Trp66 showed that its hydrophobicity in combination with spatial arrangement defined its essential role in catalysis. Substitution of other loop residues congregated along the N-terminal side of the loop also significantly impacted catalytic activity, indicating a critical role for this loop in controlling catalytic activity. For membrane binding, the centrally located hydrophobic residues played a surprising minor role in membrane binding. Instead general electrostatic interactions regulated membrane binding with positively charged residues bracketing the dynamic loop controlling membrane binding. Overall for FTT258, this dynamic loop dually controlled its biological activities through distinct residues within the loop and this regulation provides a new model for the spatiotemporal control over FTT258 and potentially homologous APT function.
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Affiliation(s)
- Mackenzie A Smith
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208, USA
| | - Whitney K Phillips
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208, USA
| | - Perry L Rabin
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208, USA
| | - R Jeremy Johnson
- Department of Chemistry and Biochemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208, USA.
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90
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De I, Sadhukhan S. Emerging Roles of DHHC-mediated Protein S-palmitoylation in Physiological and Pathophysiological Context. Eur J Cell Biol 2018; 97:319-338. [DOI: 10.1016/j.ejcb.2018.03.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/14/2018] [Accepted: 03/16/2018] [Indexed: 02/08/2023] Open
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91
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Howie J, Wypijewski KJ, Plain F, Tulloch LB, Fraser NJ, Fuller W. Greasing the wheels or a spanner in the works? Regulation of the cardiac sodium pump by palmitoylation. Crit Rev Biochem Mol Biol 2018; 53:175-191. [PMID: 29424237 DOI: 10.1080/10409238.2018.1432560] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The ubiquitous sodium/potassium ATPase (Na pump) is the most abundant primary active transporter at the cell surface of multiple cell types, including ventricular myocytes in the heart. The activity of the Na pump establishes transmembrane ion gradients that control numerous events at the cell surface, positioning it as a key regulator of the contractile and metabolic state of the myocardium. Defects in Na pump activity and regulation elevate intracellular Na in cardiac muscle, playing a causal role in the development of cardiac hypertrophy, diastolic dysfunction, arrhythmias and heart failure. Palmitoylation is the reversible conjugation of the fatty acid palmitate to specific protein cysteine residues; all subunits of the cardiac Na pump are palmitoylated. Palmitoylation of the pump's accessory subunit phospholemman (PLM) by the cell surface palmitoyl acyl transferase DHHC5 leads to pump inhibition, possibly by altering the relationship between the pump catalytic α subunit and specifically bound membrane lipids. In this review, we discuss the functional impact of PLM palmitoylation on the cardiac Na pump and the molecular basis of recognition of PLM by its palmitoylating enzyme DHHC5, as well as effects of palmitoylation on Na pump cell surface abundance in the cardiac muscle. We also highlight the numerous unanswered questions regarding the cellular control of this fundamentally important regulatory process.
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Affiliation(s)
- Jacqueline Howie
- a Institute of Cardiovascular and Medical Sciences , University of Glasgow , Glasgow , UK
| | | | - Fiona Plain
- b Molecular and Clinical Medicine , University of Dundee , Dundee , UK
| | - Lindsay B Tulloch
- b Molecular and Clinical Medicine , University of Dundee , Dundee , UK
| | - Niall J Fraser
- b Molecular and Clinical Medicine , University of Dundee , Dundee , UK
| | - William Fuller
- a Institute of Cardiovascular and Medical Sciences , University of Glasgow , Glasgow , UK
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92
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Won SJ, Cheung See Kit M, Martin BR. Protein depalmitoylases. Crit Rev Biochem Mol Biol 2018; 53:83-98. [PMID: 29239216 PMCID: PMC6009847 DOI: 10.1080/10409238.2017.1409191] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 12/13/2022]
Abstract
Protein depalmitoylation describes the removal of thioester-linked long chain fatty acids from cysteine residues in proteins. For many S-palmitoylated proteins, this process is promoted by acyl protein thioesterase enzymes, which catalyze thioester hydrolysis to solubilize and displace substrate proteins from membranes. The closely related enzymes acyl protein thioesterase 1 (APT1; LYPLA1) and acyl protein thioesterase 2 (APT2; LYPLA2) were initially identified from biochemical assays as G protein depalmitoylases, yet later were shown to accept a number of S-palmitoylated protein and phospholipid substrates. Leveraging the development of isoform-selective APT inhibitors, several studies report distinct roles for APT enzymes in growth factor and hormonal signaling. Recent crystal structures of APT1 and APT2 reveal convergent acyl binding channels, suggesting additional factors beyond acyl chain recognition mediate substrate selection. In addition to APT enzymes, the ABHD17 family of hydrolases contributes to the depalmitoylation of Ras-family GTPases and synaptic proteins. Overall, enzymatic depalmitoylation ensures efficient membrane targeting by balancing the palmitoylation cycle, and may play additional roles in signaling, growth, and cell organization. In this review, we provide a perspective on the biochemical, structural, and cellular analysis of protein depalmitoylases, and outline opportunities for future studies of systems-wide analysis of protein depalmitoylation.
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Affiliation(s)
- Sang Joon Won
- a Program in Chemical Biology , University of Michigan , Ann Arbor , MI , USA
| | | | - Brent R Martin
- a Program in Chemical Biology , University of Michigan , Ann Arbor , MI , USA
- b Department of Chemistry , University of Michigan , Ann Arbor , MI , USA
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93
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Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes. Nat Commun 2018; 9:334. [PMID: 29362370 PMCID: PMC5780395 DOI: 10.1038/s41467-017-02655-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/18/2017] [Indexed: 01/25/2023] Open
Abstract
The reversible modification of cysteine residues by thioester formation with palmitate (S-palmitoylation) is an abundant lipid post-translational modification (PTM) in mammalian systems. S-palmitoylation has been observed on mitochondrial proteins, providing an intriguing potential connection between metabolic lipids and mitochondrial regulation. However, it is unknown whether and/or how mitochondrial S-palmitoylation is regulated. Here we report the development of mitoDPPs, targeted fluorescent probes that measure the activity levels of “erasers” of S-palmitoylation, acyl-protein thioesterases (APTs), within mitochondria of live cells. Using mitoDPPs, we discover active S-depalmitoylation in mitochondria, in part mediated by APT1, an S-depalmitoylase previously thought to reside in the cytosol and on the Golgi apparatus. We also find that perturbation of long-chain acyl-CoA cytoplasm and mitochondrial regulatory proteins, respectively, results in selective responses from cytosolic and mitochondrial S-depalmitoylases. Altogether, this work reveals that mitochondrial S-palmitoylation is actively regulated by “eraser” enzymes that respond to alterations in mitochondrial lipid homeostasis. S-palmitoylation regulation has been studied mostly in the cytosol and its role in mitochondria is unclear. Here the authors develop fluorescent mitochondria-targeted probes and find that depalmitoylation occurs in mitochondria and it’s influenced by alterations in mitochondrial lipid homeostasis.
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94
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Sobocińska J, Roszczenko-Jasińska P, Ciesielska A, Kwiatkowska K. Protein Palmitoylation and Its Role in Bacterial and Viral Infections. Front Immunol 2018; 8:2003. [PMID: 29403483 PMCID: PMC5780409 DOI: 10.3389/fimmu.2017.02003] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 12/26/2017] [Indexed: 12/11/2022] Open
Abstract
S-palmitoylation is a reversible, enzymatic posttranslational modification of proteins in which palmitoyl chain is attached to a cysteine residue via a thioester linkage. S-palmitoylation determines the functioning of proteins by affecting their association with membranes, compartmentalization in membrane domains, trafficking, and stability. In this review, we focus on S-palmitoylation of proteins, which are crucial for the interactions of pathogenic bacteria and viruses with the host. We discuss the role of palmitoylated proteins in the invasion of host cells by bacteria and viruses, and those involved in the host responses to the infection. We highlight recent data on protein S-palmitoylation in pathogens and their hosts obtained owing to the development of methods based on click chemistry and acyl-biotin exchange allowing proteomic analysis of protein lipidation. The role of the palmitoyl moiety present in bacterial lipopolysaccharide and lipoproteins, contributing to infectivity and affecting recognition of bacteria by innate immune receptors, is also discussed.
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Affiliation(s)
- Justyna Sobocińska
- Laboratory of Molecular Membrane Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Paula Roszczenko-Jasińska
- Laboratory of Molecular Membrane Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Anna Ciesielska
- Laboratory of Molecular Membrane Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Kwiatkowska
- Laboratory of Molecular Membrane Biology, Department of Cell Biology, Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
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95
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Stypulkowski E, Asangani IA, Witze ES. The depalmitoylase APT1 directs the asymmetric partitioning of Notch and Wnt signaling during cell division. Sci Signal 2018; 11:eaam8705. [PMID: 29295957 PMCID: PMC5914505 DOI: 10.1126/scisignal.aam8705] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Asymmetric cell division results in two distinctly fated daughter cells. A molecular hallmark of asymmetric division is the unequal partitioning of cell fate determinants. We have previously established that growth factor signaling promotes protein depalmitoylation to foster polarized protein localization, which, in turn, drives migration and metastasis. We report protein palmitoylation as a key mechanism for the asymmetric partitioning of the cell fate determinants Numb and β-catenin through the activity of the depalmitoylating enzyme APT1. Using point mutations, we showed that specific palmitoylated residues on Numb were required for its asymmetric localization. By live-cell imaging, we showed that reciprocal interactions between APT1 and the Rho family GTPase CDC42 promoted the asymmetric localization of Numb and β-catenin to the plasma membrane. This, in turn, restricted Notch- or Wnt-responsive transcriptional activity to one daughter cell. Moreover, we showed that altering APT1 abundance changed the transcriptional signatures of MDA-MB-231 triple receptor-negative breast cancer cells, similar to changes in Notch and β-catenin-mediated Wnt signaling. We also showed that loss of APT1 depleted a specific subpopulation of tumorigenic cells in colony formation assays. Together, our findings suggest that APT1-mediated depalmitoylation is a major mechanism of asymmetric cell division that maintains Notch- and Wnt-associated protein dynamics, gene expression, and cellular functions.
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Affiliation(s)
- Ewa Stypulkowski
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Irfan A Asangani
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric S Witze
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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96
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Abstract
The small GTPase Rab7 is the main regulator of membrane trafficking at late endosomes. This small GTPase regulates endosome-to-trans Golgi Network trafficking of sorting receptors, membrane fusion of late endosomes to lysosomes, and autophagosomes to lysosomes during autophagy. Rab7, like all Rab GTPases, binds downstream effectors coordinating several divergent pathways. How cells regulate these interactions and downstream functions is not well understood. Recent evidence suggests that Rab7 function can be modulated by the combination of several post-translational modifications that facilitate interactions with one effector while preventing binding to another one. In this review, we discuss recent data on how phosphorylation, palmitoylation and ubiquitination modulate the ability of this small GTPase to orchestrate membrane trafficking at the late endosomes.
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Affiliation(s)
- Graziana Modica
- Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Laval, Québec, Canada H7V 1B7
| | - Stephane Lefrancois
- Centre INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Laval, Québec, Canada H7V 1B7.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada H3A 0C7
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97
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Jiang H, Zhang X, Chen X, Aramsangtienchai P, Tong Z, Lin H. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 2018; 118:919-988. [PMID: 29292991 DOI: 10.1021/acs.chemrev.6b00750] [Citation(s) in RCA: 283] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein lipidation, including cysteine prenylation, N-terminal glycine myristoylation, cysteine palmitoylation, and serine and lysine fatty acylation, occurs in many proteins in eukaryotic cells and regulates numerous biological pathways, such as membrane trafficking, protein secretion, signal transduction, and apoptosis. We provide a comprehensive review of protein lipidation, including descriptions of proteins known to be modified and the functions of the modifications, the enzymes that control them, and the tools and technologies developed to study them. We also highlight key questions about protein lipidation that remain to be answered, the challenges associated with answering such questions, and possible solutions to overcome these challenges.
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Affiliation(s)
- Hong Jiang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiaoyu Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiao Chen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Pornpun Aramsangtienchai
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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98
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Segal-Salto M, Hansson K, Sapir T, Kaplan A, Levy T, Schweizer M, Frotscher M, James P, Reiner O. Proteomics insights into infantile neuronal ceroid lipofuscinosis (CLN1) point to the involvement of cilia pathology in the disease. Hum Mol Genet 2017; 26:1678. [PMID: 28334871 DOI: 10.1093/hmg/ddx074] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/20/2017] [Indexed: 01/23/2023] Open
Abstract
Mutations in the depalmitoylation enzyme, palmitoyl protein thioesterase (PPT1), result in the early onset neurodegenerative disease known as Infantile Neuronal Ceroid Lipofuscinosis. Here, we provide proteomic evidence suggesting that PPT1 deficiency could be considered as a ciliopathy. Analysis of membrane proteins from brain enriched for acylated proteins from neonate Ppt1 knock out and control mice revealed a list of 88 proteins with differential expression levels. Amongst them, we identified Rab3IP, which regulates ciliogenesis in concert with Rab8 and Rab11. Immunostaining analysis revealed that PPT1 is localized in the cilia. Indeed, an unbiased proteomics analysis on isolated cilia revealed 660 proteins, which differed in their abundance levels between wild type and Ppt1 knock out. We demonstrate here that Rab3IP, Rab8 and Rab11 are palmitoylated, and that palmitoylation of Rab11 is required for correct intracellular localization. Cells and brain preparations from Ppt1-/- mice exhibited fewer cells with cilia and abnormally longer cilia, with both acetylated tubulin and Rab3IP wrongly distributed along the length of cilia. Most importantly, the analysis revealed a difference in the distribution and levels of the modified proteins in cilia in the retina of mutant mice versus the wildtype, which may be important in the early neurodegenerative phenotype. Overall, our results suggest a novel link between palmitoylated proteins, cilial organization and the pathophysiology of Neuronal Ceroid Lipofuscinosis.
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Affiliation(s)
- Michal Segal-Salto
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Karin Hansson
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden and BTK, Åbo Academy University, Turku, Finland
| | - Tamar Sapir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Anna Kaplan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Talia Levy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michaela Schweizer
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Frotscher
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter James
- Department of Immunotechnology, Lund University, Medicon Village, Lund, Sweden and BTK, Åbo Academy University, Turku, Finland
| | - Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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99
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Daniotti JL, Pedro MP, Valdez Taubas J. The role of S-acylation in protein trafficking. Traffic 2017; 18:699-710. [DOI: 10.1111/tra.12510] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/16/2017] [Accepted: 08/20/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Jose L. Daniotti
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET; Universidad Nacional de Córdoba; Córdoba Argentina
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Maria P. Pedro
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET; Universidad Nacional de Córdoba; Córdoba Argentina
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Javier Valdez Taubas
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET; Universidad Nacional de Córdoba; Córdoba Argentina
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas; Universidad Nacional de Córdoba; Córdoba Argentina
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100
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Substrate selectivity in the zDHHC family of S-acyltransferases. Biochem Soc Trans 2017; 45:751-758. [PMID: 28620036 DOI: 10.1042/bst20160309] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 02/07/2023]
Abstract
S-acylation is a reversible lipid modification occurring on cysteine residues mediated by a family of membrane-bound 'zDHHC' enzymes. S-acylation predominantly results in anchoring of soluble proteins to membrane compartments or in the trafficking of membrane proteins to different compartments. Recent work has shown that although S-acylation of some proteins may involve very weak interactions with zDHHC enzymes, a pool of zDHHC enzymes exhibit strong and specific interactions with substrates, thereby recruiting them for S-acylation. For example, the ankyrin-repeat domains of zDHHC17 and zDHHC13 interact specifically with unstructured consensus sequences present in some proteins, thus contributing to substrate specificity of these enzymes. In addition to this new information on zDHHC enzyme protein substrate specificity, recent work has also identified marked differences in selectivity of zDHHC enzymes for acyl-CoA substrates and has started to unravel the underlying molecular basis for this lipid selectivity. This review will focus on the protein and acyl-CoA selectivity of zDHHC enzymes.
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