1
|
Forrester MT, Egol JR, Tata A, Tata PR, Foster MW. Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.23.586403. [PMID: 38585928 PMCID: PMC10996552 DOI: 10.1101/2024.03.23.586403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Proteins undergo reversible S-acylation via a thioester linkage in vivo. S-palmitoylation, modification by C16:0 fatty acid, is a common S-acylation that mediates critical protein-membrane and protein-protein interactions. The most widely used S-acylation assays, including acyl-biotin exchange and acyl resin-assisted capture, utilize blocking of free Cys thiols, hydroxylamine-dependent cleavage of the thioester and subsequent labeling of nascent thiol. These assays generally require >500 micrograms of protein input material per sample and numerous reagent removal and washing steps, making them laborious and ill-suited for high throughput and low input applications. To overcome these limitations, we devised "Acyl-Trap", a suspension trap-based assay that utilizes a thiol-reactive quartz to enable buffer exchange and hydroxylamine-mediated S-acyl enrichment. We show that the method is compatible with protein-level detection of S-acylated proteins (e.g. H-Ras) as well as S-acyl site identification and quantification using "on trap" isobaric labeling and LC-MS/MS from as little as 20 micrograms of protein input. In mouse brain, Acyl-Trap identified 279 reported sites of S-acylation and 1298 previously unreported putative sites. Also described are conditions for long-term hydroxylamine storage, which streamlines the assay. More generally, Acyl-Trap serves as a proof-of-concept for PTM-tailored suspension traps suitable for both traditional protein detection and chemoproteomic workflows.
Collapse
Affiliation(s)
- Michael T Forrester
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jacob R Egol
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Purushothama Rao Tata
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Matthew W Foster
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC, 27710, USA
| |
Collapse
|
2
|
Ni H, Wang Y, Yao K, Wang L, Huang J, Xiao Y, Chen H, Liu B, Yang CY, Zhao J. Cyclical palmitoylation regulates TLR9 signalling and systemic autoimmunity in mice. Nat Commun 2024; 15:1. [PMID: 38169466 PMCID: PMC10762000 DOI: 10.1038/s41467-023-43650-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024] Open
Abstract
Toll-like receptor 9 (TLR9) recognizes self-DNA and plays intricate roles in systemic lupus erythematosus (SLE). However, the molecular mechanism regulating the endosomal TLR9 response is incompletely understood. Here, we report that palmitoyl-protein thioesterase 1 (PPT1) regulates systemic autoimmunity by removing S-palmitoylation from TLR9 in lysosomes. PPT1 promotes the secretion of IFNα by plasmacytoid dendritic cells (pDCs) and TNF by macrophages. Genetic deficiency in or chemical inhibition of PPT1 reduces anti-nuclear antibody levels and attenuates nephritis in B6.Sle1yaa mice. In healthy volunteers and patients with SLE, the PPT1 inhibitor, HDSF, reduces IFNα production ex vivo. Mechanistically, biochemical and mass spectrometry analyses demonstrated that TLR9 is S-palmitoylated at C258 and C265. Moreover, the protein acyltransferase, DHHC3, palmitoylates TLR9 in the Golgi, and regulates TLR9 trafficking to endosomes. Subsequent depalmitoylation by PPT1 facilitates the release of TLR9 from UNC93B1. Our results reveal a posttranslational modification cycle that controls TLR9 response and autoimmunity.
Collapse
Affiliation(s)
- Hai Ni
- Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yinuo Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Yao
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ling Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiancheng Huang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yongfang Xiao
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongyao Chen
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bo Liu
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China.
| | - Cliff Y Yang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, China.
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China.
| | - Jijun Zhao
- Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
| |
Collapse
|
3
|
Gu M, Jiang H, Tan M, Yu L, Xu N, Li Y, Wu H, Hou Q, Dai C. Palmitoyltransferase DHHC9 and acyl protein thioesterase APT1 modulate renal fibrosis through regulating β-catenin palmitoylation. Nat Commun 2023; 14:6682. [PMID: 37865665 PMCID: PMC10590414 DOI: 10.1038/s41467-023-42476-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 10/12/2023] [Indexed: 10/23/2023] Open
Abstract
palmitoylation, a reversible post-translational modification, is initiated by the DHHC family of palmitoyltransferases and reversed by several acyl protein thioesterases. However, the role and mechanisms for protein palmitoylation in renal fibrosis have not been elucidated. Here we show protein palmitoylation and DHHC9 were downregulated in the fibrotic kidneys of mouse models and chronic kidney disease (CKD) patients. Ablating DHHC9 in tubular cells aggravated, while inducing DHHC9 overexpression with adeno-DHHC9 transfection or iproniazid treatment protected against kidney fibrosis in male mouse models. Mechanistically, DHHC9 palmitoylated β-catenin, thereby promoted its ubiquitination and degradation. Additionally, acyl protein thioesterase 1 (APT1) was induced in the fibrotic kidneys, which depalmitoylated β-catenin, increased its abundance and nuclear translocation. Ablating tubular APT1 or inhibiting APT1 with ML348 markedly protected against unilateral ureter obstruction (UUO) or ischemia/reperfusion injury (IRI)-induced kidney fibrosis in male mice. This study reveals the regulatory mechanism of protein palmitoylation in kidney fibrosis.
Collapse
Affiliation(s)
- Mengru Gu
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
- Department of Clinical Genetics, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Hanlu Jiang
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Mengzhu Tan
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Long Yu
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Ning Xu
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Ying Li
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Han Wu
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Qing Hou
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China
| | - Chunsun Dai
- Center for Kidney Diseases, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China.
- Department of Clinical Genetics, the Second Affiliated Hospital of Nanjing Medical University; Nanjing, China, 210009, 262 North Zhongshan Road, Nanjing, Jiangsu, China.
| |
Collapse
|
4
|
Hurst CH, Turnbull D, Xhelilaj K, Myles S, Pflughaupt RL, Kopischke M, Davies P, Jones S, Robatzek S, Zipfel C, Gronnier J, Hemsley PA. S-acylation stabilizes ligand-induced receptor kinase complex formation during plant pattern-triggered immune signaling. Curr Biol 2023; 33:1588-1596.e6. [PMID: 36924767 DOI: 10.1016/j.cub.2023.02.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 01/20/2023] [Accepted: 02/21/2023] [Indexed: 03/17/2023]
Abstract
Plant receptor kinases are key transducers of extracellular stimuli, such as the presence of beneficial or pathogenic microbes or secreted signaling molecules. Receptor kinases are regulated by numerous post-translational modifications.1,2,3 Here, using the immune receptor kinases FLS24 and EFR,5 we show that S-acylation at a cysteine conserved in all plant receptor kinases is crucial for function. S-acylation involves the addition of long-chain fatty acids to cysteine residues within proteins, altering their biochemical properties and behavior within the membrane environment.6 We observe S-acylation of FLS2 at C-terminal kinase domain cysteine residues within minutes following the perception of its ligand, flg22, in a BAK1 co-receptor and PUB12/13 ubiquitin ligase-dependent manner. We demonstrate that S-acylation is essential for FLS2-mediated immune signaling and resistance to bacterial infection. Similarly, mutating the corresponding conserved cysteine residue in EFR suppressed elf18-triggered signaling. Analysis of unstimulated and activated FLS2-containing complexes using microscopy, detergents, and native membrane DIBMA nanodiscs indicates that S-acylation stabilizes, and promotes retention of, activated receptor kinase complexes at the plasma membrane to increase signaling efficiency.
Collapse
Affiliation(s)
- Charlotte H Hurst
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Dionne Turnbull
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Kaltra Xhelilaj
- ZMBP Universität Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany
| | - Sally Myles
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Robin L Pflughaupt
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Michaela Kopischke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paul Davies
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Susan Jones
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Cyril Zipfel
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK; Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Julien Gronnier
- ZMBP Universität Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany; Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8008 Zurich, Switzerland
| | - Piers A Hemsley
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.
| |
Collapse
|
5
|
Buffa V, Adamo G, Picciotto S, Bongiovanni A, Romancino DP. A Simple, Semi-Quantitative Acyl Biotin Exchange-Based Method to Detect Protein S-Palmitoylation Levels. MEMBRANES 2023; 13:361. [PMID: 36984748 PMCID: PMC10053657 DOI: 10.3390/membranes13030361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
Protein S-palmitoylation is a reversible post-translational lipidation in which palmitic acid (16:0) is added to protein cysteine residue by a covalent thioester bond. This modification plays an active role in membrane targeting of soluble proteins, protein-protein interaction, protein trafficking, and subcellular localization. Moreover, palmitoylation is related to different diseases, such as neurodegenerative pathologies, cancer, and developmental defects. The aim of this research is to provide a straightforward and sensitive procedure to detect protein palmitoylation based on Acyl Biotin Exchange (ABE) chemistry. Our protocol setup consists of co-immunoprecipitation of native proteins (i.e., CD63), followed by the direct detection of palmitoylation on proteins immobilized on polyvinylidene difluoride (PVDF) membranes. With respect to the conventional ABE-based protocol, we optimized and validated a rapid semi-quantitative assay that is shown to be significantly more sensitive and highly reproducible.
Collapse
Affiliation(s)
- Valentina Buffa
- Institute for Research and Biomedical Innovation (IRIB), National Research Council (CNR), Via Ugo La Malfa, 153-90146 Palermo, Italy
- Integrare UMR_S951 Genethon, Inserm, University of Evry, Université Paris Saclay Genethon, 91000 Evry, France
| | - Giorgia Adamo
- Institute for Research and Biomedical Innovation (IRIB), National Research Council (CNR), Via Ugo La Malfa, 153-90146 Palermo, Italy
| | - Sabrina Picciotto
- Institute for Research and Biomedical Innovation (IRIB), National Research Council (CNR), Via Ugo La Malfa, 153-90146 Palermo, Italy
| | - Antonella Bongiovanni
- Institute for Research and Biomedical Innovation (IRIB), National Research Council (CNR), Via Ugo La Malfa, 153-90146 Palermo, Italy
| | - Daniele P. Romancino
- Institute for Research and Biomedical Innovation (IRIB), National Research Council (CNR), Via Ugo La Malfa, 153-90146 Palermo, Italy
| |
Collapse
|
6
|
Ma T, Fu S, Wang K, Wang Y, Wu J, Zhou X. Palmitoylation Is Indispensable for Remorin to Restrict Tobacco Mosaic Virus Cell-to-Cell Movement in Nicotiana benthamiana. Viruses 2022; 14:1324. [PMID: 35746795 PMCID: PMC9227848 DOI: 10.3390/v14061324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
Remorin (REM) is a plant-specific plasma membrane-associated protein regulating plasmodesmata plasticity and restricting viral cell-to-cell movement. Here, we show that palmitoylation is broadly present in group 1 remorin proteins in Nicotiana benthamiana and is crucial for plasma membrane localization and accumulation. By screening the four members of N. benthamiana group 1 remorin proteins, we found that only NbREM1.5 could significantly hamper tobacco mosaic virus (TMV) cell-to-cell movement. We further showed that NbREM1.5 interacts with the movement protein of TMV in vivo and interferes with its function of expanding the plasmodesmata size exclusion limit. We also demonstrated that palmitoylation is indispensable for NbREM1.5 to hamper plasmodesmata permeability and inhibit TMV cell-to-cell movement.
Collapse
Affiliation(s)
- Tingting Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Shuai Fu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Kun Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Yaqin Wang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (T.M.); (S.F.); (K.W.); (Y.W.); (J.W.)
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| |
Collapse
|
7
|
Kumar M, Carr P, Turner SR. An atlas of Arabidopsis protein S-acylation reveals its widespread role in plant cell organization and function. NATURE PLANTS 2022. [PMID: 35681017 DOI: 10.1101/2020.05.12.090415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
S-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterized, largely as a result of the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. To address this gap in our knowledge, we used an optimized acyl-resin-assisted capture assay to perform a comprehensive analysis of plant protein S-acylation from six separate tissues. In our high- and medium-confidence groups, we identified 1,849 cysteines modified by S-acylation, which were located in 1,640 unique peptides from 1,094 different proteins. This represents around 6% of the detectable Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm the S-acylation of a number of proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity and are all predicted to possess a RING-type zinc finger at their amino terminus composed of eight cysteines. For CESA8, we find evidence for S-acylation of these cysteines that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING-type domain, the same region of CESA8 appears to have evolved a very different structure. Together, the data suggest that this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrating the importance of further work in this area.
Collapse
Affiliation(s)
- Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Carr
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Holiferm, Manchester, UK
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| |
Collapse
|
8
|
Kumar M, Carr P, Turner SR. An atlas of Arabidopsis protein S-acylation reveals its widespread role in plant cell organization and function. NATURE PLANTS 2022; 8:670-681. [PMID: 35681017 DOI: 10.1038/s41477-022-01164-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/04/2022] [Indexed: 05/28/2023]
Abstract
S-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterized, largely as a result of the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. To address this gap in our knowledge, we used an optimized acyl-resin-assisted capture assay to perform a comprehensive analysis of plant protein S-acylation from six separate tissues. In our high- and medium-confidence groups, we identified 1,849 cysteines modified by S-acylation, which were located in 1,640 unique peptides from 1,094 different proteins. This represents around 6% of the detectable Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm the S-acylation of a number of proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity and are all predicted to possess a RING-type zinc finger at their amino terminus composed of eight cysteines. For CESA8, we find evidence for S-acylation of these cysteines that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING-type domain, the same region of CESA8 appears to have evolved a very different structure. Together, the data suggest that this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrating the importance of further work in this area.
Collapse
Affiliation(s)
- Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Carr
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Holiferm, Manchester, UK
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| |
Collapse
|
9
|
Elliot Murphy R, Banerjee A. In vitro reconstitution of substrate S-acylation by the zDHHC family of protein acyltransferases. Open Biol 2022; 12:210390. [PMID: 35414257 PMCID: PMC9006032 DOI: 10.1098/rsob.210390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/21/2022] [Indexed: 01/09/2023] Open
Abstract
Protein S-acylation, more commonly known as protein palmitoylation, is a biological process defined by the covalent attachment of long chain fatty acids onto cysteine residues of a protein, effectively altering the local hydrophobicity and influencing its stability, localization and overall function. Observed ubiquitously in all eukaryotes, this post translational modification is mediated by the 23-member family of zDHHC protein acyltransferases in mammals. There are thousands of proteins that are S-acylated and multiple zDHHC enzymes can potentially act on a single substrate. Since its discovery, numerous methods have been developed for the identification of zDHHC substrates and the individual members of the family that catalyse their acylation. Despite these recent advances in assay development, there is a persistent gap in knowledge relating to zDHHC substrate specificity and recognition, that can only be thoroughly addressed through in vitro reconstitution. Herein, we will review the various methods currently available for reconstitution of protein S-acylation for the purposes of identifying enzyme-substrate pairs with a particular emphasis on the advantages and disadvantages of each approach.
Collapse
Affiliation(s)
- R. Elliot Murphy
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anirban Banerjee
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
10
|
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: 47] [Impact Index Per Article: 15.7] [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.
Collapse
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
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
A STAT3 palmitoylation cycle promotes T H17 differentiation and colitis. Nature 2020; 586:434-439. [PMID: 33029007 DOI: 10.1038/s41586-020-2799-2] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 07/10/2020] [Indexed: 02/05/2023]
Abstract
Cysteine palmitoylation (S-palmitoylation) is a reversible post-translational modification that is installed by the DHHC family of palmitoyltransferases and is reversed by several acyl protein thioesterases1,2. Although thousands of human proteins are known to undergo S-palmitoylation, how this modification is regulated to modulate specific biological functions is poorly understood. Here we report that the key T helper 17 (TH17) cell differentiation stimulator, STAT33,4, is subject to reversible S-palmitoylation on cysteine 108. DHHC7 palmitoylates STAT3 and promotes its membrane recruitment and phosphorylation. Acyl protein thioesterase 2 (APT2, also known as LYPLA2) depalmitoylates phosphorylated STAT3 (p-STAT3) and enables it to translocate to the nucleus. This palmitoylation-depalmitoylation cycle enhances STAT3 activation and promotes TH17 cell differentiation; perturbation of either palmitoylation or depalmitoylation negatively affects TH17 cell differentiation. Overactivation of TH17 cells is associated with several inflammatory diseases, including inflammatory bowel disease (IBD). In a mouse model, pharmacological inhibition of APT2 or knockout of Zdhhc7-which encodes DHHC7-relieves the symptoms of IBD. Our study reveals not only a potential therapeutic strategy for the treatment of IBD but also a model through which S-palmitoylation regulates cell signalling, which might be broadly applicable for understanding the signalling functions of numerous S-palmitoylation events.
Collapse
|
13
|
S-acylation in plants: an expanding field. Biochem Soc Trans 2020; 48:529-536. [DOI: 10.1042/bst20190703] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/10/2020] [Accepted: 03/11/2020] [Indexed: 02/07/2023]
Abstract
S-acylation is a common yet poorly understood fatty acid-based post-translational modification of proteins in all eukaryotes, including plants. While exact roles for S-acylation in protein function are largely unknown the reversibility of S-acylation indicates that it is likely able to play a regulatory role. As more studies reveal the roles of S-acylation within the cell it is becoming apparent that how S-acylation affects proteins is conceptually different from other reversible modifications such as phosphorylation or ubiquitination; a new mind-set is therefore required to fully integrate these data into our knowledge of plant biology. This review aims to highlight recent advances made in the function and enzymology of S-acylation in plants, highlights current and emerging technologies for its study and suggests future avenues for investigation.
Collapse
|
14
|
Hurst CH, Wright KM, Turnbull D, Leslie K, Jones S, Hemsley PA. Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function. Sci Rep 2019; 9:12818. [PMID: 31492958 PMCID: PMC6731221 DOI: 10.1038/s41598-019-49302-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 01/24/2023] Open
Abstract
S-acylation is a common post-translational modification of membrane protein cysteine residues with many regulatory roles. S-acylation adjacent to transmembrane domains has been described in the literature as affecting diverse protein properties including turnover, trafficking and microdomain partitioning. However, all of these data are derived from mammalian and yeast systems. Here we examine the role of S-acylation adjacent to the transmembrane domain of the plant pathogen perceiving receptor-like kinase FLS2. Surprisingly, S-acylation of FLS2 adjacent to the transmembrane domain is not required for either FLS2 trafficking or signalling function. Expanding this analysis to the wider plant receptor-like kinase family we find that S-acylation adjacent to receptor-like kinase domains is common, affecting ~25% of Arabidopsis receptor-like kinases, but poorly conserved between orthologues through evolution. This suggests that S-acylation of receptor-like kinases at this site is likely the result of chance mutation leading to cysteine occurrence. As transmembrane domains followed by cysteine residues are common motifs for S-acylation to occur, and many S-acyl transferases appear to have lax substrate specificity, we propose that many receptor-like kinases are fortuitously S-acylated once chance mutation has introduced a cysteine at this site. Interestingly some receptor-like kinases show conservation of S-acylation sites between orthologues suggesting that S-acylation has come to play a role and has been positively selected for during evolution. The most notable example of this is in the ERECTA-like family where S-acylation of ERECTA adjacent to the transmembrane domain occurs in all ERECTA orthologues but not in the parental ERECTA-like clade. This suggests that ERECTA S-acylation occurred when ERECTA emerged during the evolution of angiosperms and may have contributed to the neo-functionalisation of ERECTA from ERECTA-like proteins.
Collapse
Affiliation(s)
- Charlotte H Hurst
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK.,Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Kathryn M Wright
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Dionne Turnbull
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Kerry Leslie
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK.,Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Susan Jones
- Information and Computer Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Piers A Hemsley
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK. .,Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
| |
Collapse
|
15
|
Determination of Protein S-Acylation State by Enhanced Acyl-Switch Methods. Methods Mol Biol 2019. [PMID: 31152391 DOI: 10.1007/978-1-4939-9532-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
S-Acylation is increasingly being recognized as an important dynamic posttranslational modification of cysteine residues in proteins. Various approaches have been described for assaying protein S-acylation with acyl-switch approaches being the most common and accessible. However, these approaches can be time-consuming with low reproducibility as a result of multiple protein precipitation/resuspension cleanup steps. Here we present a faster, cleaner, and more sensitive acyl-switch approach for detecting the S-acylation state of any protein, from any cell or tissue type, that can be detected by western blotting. In the case of acyl-RAC, the procedure is now performed without protein precipitation, greatly increasing speed and improving sample handling in the assay. This also allows for more samples to be processed simultaneously and opens the way for medium-throughput assays. Overall, maleimide scavenging improves the reliability of determination and quantification of protein S-acylation state by acyl-switch methods.
Collapse
|
16
|
Abrami L, Denhardt-Eriksson RA, Hatzimanikatis V, van der Goot FG. Dynamic Radiolabeling of S-Palmitoylated Proteins. Methods Mol Biol 2019; 2009:111-127. [PMID: 31152399 DOI: 10.1007/978-1-4939-9532-5_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Proteins can be radiolabeled either during synthesis, typically using 35S-cysteine/methionine (35S-Cys/Met), or after synthesis, by adding a radiolabeled posttranslational modification. Here we describe how protein S-palmitoylation, and its dynamics, can be monitored by 3H-palmitate labeling and how the importance of S-palmitoylation in protein biogenesis and turnover can be investigated using 35S-Cys/Met pulse-chase metabolic labeling. Proteins frequently have multiple palmitoylation sites. The importance thereof on the design and interpretation of metabolic labeling experiments is discussed.
Collapse
Affiliation(s)
- Laurence Abrami
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Robin A Denhardt-Eriksson
- Global Health Institute, Laboratory of Computational Systems Biotechnology, EPFL, Lausanne, Switzerland
| | | | | |
Collapse
|
17
|
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.
Collapse
|
18
|
Hurst CH, Turnbull D, Myles SM, Leslie K, Keinath NF, Hemsley PA. Variable Effects of C-Terminal Fusions on FLS2 Function: Not All Epitope Tags Are Created Equal. PLANT PHYSIOLOGY 2018; 177:522-531. [PMID: 29686160 PMCID: PMC6001324 DOI: 10.1104/pp.17.01700] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/06/2018] [Indexed: 05/26/2023]
Abstract
Receptor-like kinases (RLKs) are the largest family of proteins in plants and are responsible for perceiving the vast majority of extracellular stimuli. Thus, RLKs function in diverse processes, including sensing pathogen attacks, regulating symbiotic interactions, transducing hormone and peptide signals, and monitoring cell wall status. However, despite their fundamental role in plant biology, very few antibodies are available against RLKs, which necessitates the use of epitope tags and fluorescent protein fusions in biochemical analyses such as immunoblot analysis and intracellular visualization. Epitope tags are widely used and are typically assumed to be benign, with no influence on protein function. FLAGELLIN SENSITIVE2 (FLS2) is the receptor for bacterial flagellin and often is used as a model for RLK function. Previous work implies that carboxyl-terminal epitope fusions to FLS2 maintain protein function. Here, a detailed complementation analysis of Arabidopsis (Arabidopsis thaliana) fls2 mutant plants expressing various FLS2 C-terminal epitope fusions revealed highly variable and unpredictable FLS2-mediated signaling outputs. In addition, only one out of four FLS2 epitope fusions maintained the ability to inhibit plant growth in response to flg22 treatment comparable to that in the wild type or control untagged transgenic lines. These results raise concerns over the widespread use of RLK epitope tag fusions for functional studies. Many of the subtleties of FLS2 function, and by extension those of other RLKs, may have been overlooked or inappropriately interpreted through the use of RLK epitope tag fusions.
Collapse
Affiliation(s)
- Charlotte H Hurst
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Dionne Turnbull
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Sally M Myles
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
| | - Kerry Leslie
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Nana F Keinath
- Department of Plant Developmental Biology, Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Piers A Hemsley
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| |
Collapse
|
19
|
Thinon E, Fernandez JP, Molina H, Hang HC. Selective Enrichment and Direct Analysis of Protein S-Palmitoylation Sites. J Proteome Res 2018; 17:1907-1922. [PMID: 29575903 PMCID: PMC6104640 DOI: 10.1021/acs.jproteome.8b00002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
S-Fatty-acylation is the covalent attachment of long chain fatty acids, predominately palmitate (C16:0, S-palmitoylation), to cysteine (Cys) residues via a thioester linkage on proteins. This post-translational and reversible lipid modification regulates protein function and localization in eukaryotes and is important in mammalian physiology and human diseases. While chemical labeling methods have improved the detection and enrichment of S-fatty-acylated proteins, mapping sites of modification and characterizing the endogenously attached fatty acids are still challenging. Here, we describe the integration and optimization of fatty acid chemical reporter labeling with hydroxylamine-mediated enrichment of S-fatty-acylated proteins and direct tagging of modified Cys residues to selectively map lipid modification sites. This afforded improved enrichment and direct identification of many protein S-fatty-acylation sites compared to previously described methods. Notably, we directly identified the S-fatty-acylation sites of IFITM3, an important interferon-stimulated inhibitor of virus entry, and we further demonstrated that the highly conserved Cys residues are primarily modified by palmitic acid. The methods described here should facilitate the direct analysis of protein S-fatty-acylation sites and their endogenously attached fatty acids in diverse cell types and activation states important for mammalian physiology and diseases.
Collapse
Affiliation(s)
- Emmanuelle Thinon
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, 1 Midland Road, Kings Cross, London NW1 1AT, UK
| | - Joseph P. Fernandez
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, New York, USA
| | - Howard C. Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| |
Collapse
|