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Tsumagari K, Isobe Y, Imami K, Arita M. Exploring protein lipidation by mass spectrometry-based proteomics. J Biochem 2024; 175:225-233. [PMID: 38102731 PMCID: PMC10908362 DOI: 10.1093/jb/mvad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/13/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Protein lipidation is a common co- or post-translational modification that plays a crucial role in regulating the localization, interaction and function of cellular proteins. Dysregulation of lipid modifications can lead to various diseases, including cancer, neurodegenerative diseases and infectious diseases. Therefore, the identification of proteins undergoing lipidation and their lipidation sites should provide insights into many aspects of lipid biology, as well as providing potential targets for therapeutic strategies. Bottom-up proteomics using liquid chromatography/tandem mass spectrometry is a powerful technique for the global analysis of protein lipidation. Here, we review proteomic methods for profiling protein lipidation, focusing on the two major approaches: the use of chemical probes, such as lipid alkyne probes, and the use of enrichment techniques for endogenous lipid-modified peptides. The challenges facing these methods and the prospects for developing them further to achieve a comprehensive analysis of lipid modifications are discussed.
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Affiliation(s)
- Kazuya Tsumagari
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yosuke Isobe
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Koshi Imami
- Proteome Homeostasis Research Unit, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Integrative Genomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo 105-8512, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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2
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Talwadekar M, Khatri S, Balaji C, Chakraborty A, Basak NP, Kamat SS, Kolthur-Seetharam U. Metabolic transitions regulate global protein fatty acylation. J Biol Chem 2024; 300:105563. [PMID: 38101568 PMCID: PMC10808961 DOI: 10.1016/j.jbc.2023.105563] [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: 06/29/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Intermediary metabolites and flux through various pathways have emerged as key determinants of post-translational modifications. Independently, dynamic fluctuations in their concentrations are known to drive cellular energetics in a bi-directional manner. Notably, intracellular fatty acid pools that drastically change during fed and fasted states act as precursors for both ATP production and fatty acylation of proteins. Protein fatty acylation is well regarded for its role in regulating structure and functions of diverse proteins; however, the effect of intracellular concentrations of fatty acids on protein modification is less understood. In this regard, we unequivocally demonstrate that metabolic contexts, viz. fed and fasted states, dictate the extent of global fatty acylation. Moreover, we show that presence or absence of glucose that influences cellular and mitochondrial uptake/utilization of fatty acids and affects palmitoylation and oleoylation, which is consistent with their intracellular abundance in fed and fasted states. Employing complementary approaches including click-chemistry, lipidomics, and imaging, we show the top-down control of cellular metabolic state. Importantly, our results establish the crucial role of mitochondria and retrograde signaling components like SIRT4, AMPK, and mTOR in orchestrating protein fatty acylation at a whole cell level. Specifically, pharmacogenetic perturbations that alter either mitochondrial functions and/or retrograde signaling affect protein fatty acylation. Besides illustrating the cross-talk between carbohydrate and lipid metabolism in mediating bulk post-translational modification, our findings also highlight the involvement of mitochondrial energetics.
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Affiliation(s)
- Manasi Talwadekar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Subhash Khatri
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Chinthapalli Balaji
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Arnab Chakraborty
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Nandini-Pal Basak
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research, Pune, India.
| | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India; Tata Institute of Fundamental Research, Hyderabad, India.
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3
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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.
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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
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4
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Dennis KMJH, Heather LC. Post-translational palmitoylation of metabolic proteins. Front Physiol 2023; 14:1122895. [PMID: 36909239 PMCID: PMC9998952 DOI: 10.3389/fphys.2023.1122895] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Numerous cellular proteins are post-translationally modified by addition of a lipid group to their structure, which dynamically influences the proteome by increasing hydrophobicity of proteins often impacting protein conformation, localization, stability, and binding affinity. These lipid modifications include myristoylation and palmitoylation. Palmitoylation involves a 16-carbon saturated fatty acyl chain being covalently linked to a cysteine thiol through a thioester bond. Palmitoylation is unique within this group of modifications, as the addition of the palmitoyl group is reversible and enzyme driven, rapidly affecting protein targeting, stability and subcellular trafficking. The palmitoylation reaction is catalyzed by a large family of Asp-His-His-Cys (DHHCs) motif-containing palmitoyl acyltransferases, while the reverse reaction is catalyzed by acyl-protein thioesterases (APTs), that remove the acyl chain. Palmitoyl-CoA serves an important dual purpose as it is not only a key metabolite fueling energy metabolism, but is also a substrate for this PTM. In this review, we discuss protein palmitoylation in regulating substrate metabolism, focusing on membrane transport proteins and kinases that participate in substrate uptake into the cell. We then explore the palmitoylation of mitochondrial proteins and the palmitoylation regulatory enzymes, a less explored field for potential lipid metabolic regulation.
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Affiliation(s)
- Kaitlyn M J H Dennis
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Lisa C Heather
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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5
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Dorn RS, Prescher JA. Bioorthogonal Phosphines: Then and Now. Isr J Chem 2022. [DOI: 10.1002/ijch.202200070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert S. Dorn
- Departments of Chemistry University of California Irvine California 92697 United States
| | - Jennifer A. Prescher
- Departments of Chemistry University of California Irvine California 92697 United States
- Molecular Biology & Biochemistry University of California Irvine California 92697 United States
- Pharmaceutical Sciences University of California Irvine California 92697 United States
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6
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Pei X, Li KY, Shen Y, Li JT, Lei MZ, Fang CY, Lu HJ, Yang HJ, Wen W, Yin M, Qu J, Lei QY. Palmitoylation of MDH2 by ZDHHC18 activates mitochondrial respiration and accelerates ovarian cancer growth. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2017-2030. [PMID: 35366151 DOI: 10.1007/s11427-021-2048-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/16/2021] [Indexed: 12/22/2022]
Abstract
Epithelial ovarian cancer (EOC) exhibits strong dependency on the tricarboxylic acid (TCA) cycle and oxidative phosphorylation to fuel anabolic process. Here, we show that malate dehydrogenase 2 (MDH2), a key enzyme of the TCA cycle, is palmitoylated at cysteine 138 (C138) residue, resulting in increased activity of MDH2. We next identify that ZDHHC18 acts as a palmitoyltransferase of MDH2. Glutamine deprivation enhances MDH2 palmitoylation by increasing the binding between ZDHHC18 and MDH2. MDH2 silencing represses mitochondrial respiration as well as ovarian cancer cell proliferation both in vitro and in vivo. Intriguingly, re-expression of wild-type MDH2, but not its palmitoylation-deficient C138S mutant, sustains mitochondrial respiration and restores the growth as well as clonogenic capability of ovarian cancer cells. Notably, MDH2 palmitoylation level is elevated in clinical cancer samples from patients with high-grade serous ovarian cancer. These observations suggest that MDH2 palmitoylation catalyzed by ZDHHC18 sustains mitochondrial respiration and promotes the malignancy of ovarian cancer, yielding possibilities of targeting ZDHHC18-mediated MDH2 palmitoylation in the treatment of EOC.
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Affiliation(s)
- Xuan Pei
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Kai-Yue Li
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yuan Shen
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jin-Tao Li
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ming-Zhu Lei
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Cai-Yun Fang
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hao-Jie Lu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Hui-Juan Yang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Wenyu Wen
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200032, China
| | - Miao Yin
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jia Qu
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Qun-Ying Lei
- Fudan University Shanghai Cancer Center & Institutes of Biomedical Sciences; Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; The Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China. .,State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200032, China.
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7
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Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJC, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid—a Naturally Occurring 1,2‐Cyclopropene Fatty Acid—by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates**. Angew Chem Int Ed Engl 2022; 61:e202207640. [PMID: 35838324 PMCID: PMC9546306 DOI: 10.1002/anie.202207640] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Indexed: 12/25/2022]
Abstract
In the field of lipid research, bioorthogonal chemistry has made the study of lipid uptake and processing in living systems possible, whilst minimising biological properties arising from detectable pendant groups. To allow the study of unsaturated free fatty acids in live cells, we here report the use of sterculic acid, a 1,2‐cyclopropene‐containing oleic acid analogue, as a bioorthogonal probe. We show that this lipid can be readily taken up by dendritic cells without toxic side effects, and that it can subsequently be visualised using an inverse electron‐demand Diels–Alder reaction with quenched tetrazine‐fluorophore conjugates. In addition, the lipid can be used to identify changes in protein oleoylation after immune cell activation. Finally, this reaction can be integrated into a multiplexed bioorthogonal reaction workflow by combining it with two sequential copper‐catalysed Huisgen ligation reactions. This allows for the study of multiple biomolecules in the cell simultaneously by multimodal confocal imaging.
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Affiliation(s)
- Kristine Bertheussen
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Merel van de Plassche
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Iakovia Ttofi
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Alexi J. C. Sarris
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Herman S. Overkleeft
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Mario van der Stelt
- Department of Molecular Physiology Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Sander I. van Kasteren
- Department of Bio-Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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8
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Bertheussen K, van de Plassche M, Bakkum T, Gagestein B, Ttofi I, Sarris AJ, Overkleeft HS, van der Stelt M, van Kasteren SI. Live‐Cell Imaging of Sterculic Acid – a Naturally Occurring 1,2‐Cyclopropene Fatty Acid – by Bioorthogonal Reaction with Turn‐On Tetrazine‐Fluorophore Conjugates. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kristine Bertheussen
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | | | - Thomas Bakkum
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Berend Gagestein
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Iakovia Ttofi
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Alexi J.C. Sarris
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Herman S. Overkleeft
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Mario van der Stelt
- Leiden University: Universiteit Leiden Leiden Institute of Chemistry NETHERLANDS
| | - Sander Izaak van Kasteren
- Leiden University Leiden Institute of Chemistry Gorlaeus LaboratoryEinsteinweg 55 2333 CC Leiden NETHERLANDS
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9
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Mooli RGR, Ramakrishnan SK. Emerging Role of Hepatic Ketogenesis in Fatty Liver Disease. Front Physiol 2022; 13:946474. [PMID: 35860662 PMCID: PMC9289363 DOI: 10.3389/fphys.2022.946474] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD), the most common chronic liver diseases, arise from non-alcoholic fatty liver (NAFL) characterized by excessive fat accumulation as triglycerides. Although NAFL is benign, it could progress to non-alcoholic steatohepatitis (NASH) manifested with inflammation, hepatocyte damage and fibrosis. A subset of NASH patients develops end-stage liver diseases such as cirrhosis and hepatocellular carcinoma. The pathogenesis of NAFLD is highly complex and strongly associated with perturbations in lipid and glucose metabolism. Lipid disposal pathways, in particular, impairment in condensation of acetyl-CoA derived from β-oxidation into ketogenic pathway strongly influence the hepatic lipid loads and glucose metabolism. Current evidence suggests that ketogenesis dispose up to two-thirds of the lipids entering the liver, and its dysregulation significantly contribute to the NAFLD pathogenesis. Moreover, ketone body administration in mice and humans shows a significant improvement in NAFLD. This review focuses on hepatic ketogenesis and its role in NAFLD pathogenesis. We review the possible mechanisms through which impaired hepatic ketogenesis may promote NAFLD progression. Finally, the review sheds light on the therapeutic implications of a ketogenic diet in NAFLD.
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10
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Protein Lipidation Types: Current Strategies for Enrichment and Characterization. Int J Mol Sci 2022; 23:ijms23042365. [PMID: 35216483 PMCID: PMC8880637 DOI: 10.3390/ijms23042365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/18/2022] [Accepted: 02/18/2022] [Indexed: 12/04/2022] Open
Abstract
Post-translational modifications regulate diverse activities of a colossal number of proteins. For example, various types of lipids can be covalently linked to proteins enzymatically or non-enzymatically. Protein lipidation is perhaps not as extensively studied as protein phosphorylation, ubiquitination, or glycosylation although it is no less significant than these modifications. Evidence suggests that proteins can be attached by at least seven types of lipids, including fatty acids, lipoic acids, isoprenoids, sterols, phospholipids, glycosylphosphatidylinositol anchors, and lipid-derived electrophiles. In this review, we summarize types of protein lipidation and methods used for their detection, with an emphasis on the conjugation of proteins with polyunsaturated fatty acids (PUFAs). We discuss possible reasons for the scarcity of reports on PUFA-modified proteins, limitations in current methodology, and potential approaches in detecting PUFA modifications.
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11
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Rosier K, McDevitt MT, Smet J, Floyd BJ, Verschoore M, Marcaida MJ, Bingman CA, Lemmens I, Dal Peraro M, Tavernier J, Cravatt BF, Gounko NV, Vints K, Monnens Y, Bhalla K, Aerts L, Rashan EH, Vanlander AV, Van Coster R, Régal L, Pagliarini DJ, Creemers JW. Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function. iScience 2021; 24:103460. [PMID: 34888501 PMCID: PMC8634043 DOI: 10.1016/j.isci.2021.103460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Deficiency of the serine hydrolase prolyl endopeptidase-like (PREPL) causes a recessive metabolic disorder characterized by neonatal hypotonia, feeding difficulties, and growth hormone deficiency. The pathophysiology of PREPL deficiency and the physiological substrates of PREPL remain largely unknown. In this study, we connect PREPL with mitochondrial gene expression and oxidative phosphorylation by analyzing its protein interactors. We demonstrate that the long PREPLL isoform localizes to mitochondria, whereas PREPLS remains cytosolic. Prepl KO mice showed reduced mitochondrial complex activities and disrupted mitochondrial gene expression. Furthermore, mitochondrial ultrastructure was abnormal in a PREPL-deficient patient and Prepl KO mice. In addition, we reveal that PREPL has (thio)esterase activity and inhibition of PREPL by Palmostatin M suggests a depalmitoylating function. We subsequently determined the crystal structure of PREPL, thereby providing insight into the mechanism of action. Taken together, PREPL is a (thio)esterase rather than a peptidase and PREPLL is involved in mitochondrial homeostasis.
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Affiliation(s)
- Karen Rosier
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Molly T. McDevitt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joél Smet
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Brendan J. Floyd
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Maxime Verschoore
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Maria J. Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irma Lemmens
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jan Tavernier
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Benjamin F. Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia V. Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Yenthe Monnens
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Kritika Bhalla
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Laetitia Aerts
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arnaud V. Vanlander
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Luc Régal
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Neurology and Metabolism, UZ Brussel, Brussels, Belgium
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Departments of Cell Biology and Physiology, Biochemistry and Molecular Biophysics, and Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - John W.M. Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
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12
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Qu M, Zhou X, Wang X, Li H. Lipid-induced S-palmitoylation as a Vital Regulator of Cell Signaling and Disease Development. Int J Biol Sci 2021; 17:4223-4237. [PMID: 34803494 PMCID: PMC8579454 DOI: 10.7150/ijbs.64046] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Accepted: 09/20/2021] [Indexed: 12/29/2022] Open
Abstract
Lipid metabolites are emerging as pivotal regulators of protein function and cell signaling. The availability of intracellular fatty acid is tightly regulated by glycolipid metabolism and may affect human body through many biological mechanisms. Recent studies have demonstrated palmitate, either from exogenous fatty acid uptake or de novo fatty acid synthesis, may serve as the substrate for protein palmitoylation and regulate protein function via palmitoylation. Palmitoylation, the most-studied protein lipidation, encompasses the reversible covalent attachment of palmitate moieties to protein cysteine residues. It controls various cellular physiological processes and alters protein stability, conformation, localization, membrane association and interaction with other effectors. Dysregulation of palmitoylation has been implicated in a plethora of diseases, such as metabolic syndrome, cancers, neurological disorders and infections. Accordingly, it could be one of the molecular mechanisms underlying the impact of palmitate metabolite on cellular homeostasis and human diseases. Herein, we explore the relationship between lipid metabolites and the regulation of protein function through palmitoylation. We review the current progress made on the putative role of palmitate in altering the palmitoylation of key proteins and thus contributing to the pathogenesis of various diseases, among which we focus on metabolic disorders, cancers, inflammation and infections, neurodegenerative diseases. We also highlight the opportunities and new therapeutics to target palmitoylation in disease development.
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Affiliation(s)
- Mengyuan Qu
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuan Zhou
- National Clinical Research Center for Infectious Disease; Department of liver Diseases, Shenzhen Third People's Hospital, Shenzhen, China
| | - Xiaotong Wang
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Honggang Li
- Institute of Reproductive Health/Center of Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Wuhan Tongji Reproductive Medicine Hospital, Wuhan, China
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13
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Suazo KF, Park KY, Distefano MD. A Not-So-Ancient Grease History: Click Chemistry and Protein Lipid Modifications. Chem Rev 2021; 121:7178-7248. [PMID: 33821625 PMCID: PMC8820976 DOI: 10.1021/acs.chemrev.0c01108] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein lipid modification involves the attachment of hydrophobic groups to proteins via ester, thioester, amide, or thioether linkages. In this review, the specific click chemical reactions that have been employed to study protein lipid modification and their use for specific labeling applications are first described. This is followed by an introduction to the different types of protein lipid modifications that occur in biology. Next, the roles of click chemistry in elucidating specific biological features including the identification of lipid-modified proteins, studies of their regulation, and their role in diseases are presented. A description of the use of protein-lipid modifying enzymes for specific labeling applications including protein immobilization, fluorescent labeling, nanostructure assembly, and the construction of protein-drug conjugates is presented next. Concluding remarks and future directions are presented in the final section.
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Affiliation(s)
- Kiall F. Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Keun-Young Park
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455 USA
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14
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Nalbantoglu S, Karadag A. Metabolomics bridging proteomics along metabolites/oncometabolites and protein modifications: Paving the way toward integrative multiomics. J Pharm Biomed Anal 2021; 199:114031. [PMID: 33857836 DOI: 10.1016/j.jpba.2021.114031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 02/08/2023]
Abstract
Systems biology adopted functional and integrative multiomics approaches enable to discover the whole set of interacting regulatory components such as genes, transcripts, proteins, metabolites, and metabolite dependent protein modifications. This interactome build up the midpoint of protein-protein/PTM, protein-DNA/RNA, and protein-metabolite network in a cell. As the key drivers in cellular metabolism, metabolites are precursors and regulators of protein post-translational modifications [PTMs] that affect protein diversity and functionality. The precisely orchestrated core pattern of metabolic networks refer to paradigm 'metabolites regulate PTMs, PTMs regulate enzymes, and enzymes modulate metabolites' through a multitude of feedback and feed-forward pathway loops. The concept represents a flawless PTM-metabolite-enzyme(protein) regulomics underlined in reprogramming cancer metabolism. Immense interconnectivity of those biomolecules in their spectacular network of intertwined metabolic pathways makes integrated proteomics and metabolomics an excellent opportunity, and the central component of integrative multiomics framework. It will therefore be of significant interest to integrate global proteome and PTM-based proteomics with metabolomics to achieve disease related altered levels of those molecules. Thereby, present update aims to highlight role and analysis of interacting metabolites/oncometabolites, and metabolite-regulated PTMs loop which may function as translational monitoring biomarkers along the reprogramming continuum of oncometabolism.
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Affiliation(s)
- Sinem Nalbantoglu
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey.
| | - Abdullah Karadag
- TUBITAK Marmara Research Center, Gene Engineering and Biotechnology Institute, Molecular, Oncology Laboratory, Gebze, Kocaeli, Turkey
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15
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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: 49] [Impact Index Per Article: 16.3] [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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16
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Tripathi P, Zhu Z, Qin H, Elsherbini A, Crivelli SM, Roush E, Wang G, Spassieva SD, Bieberich E. Palmitoylation of acetylated tubulin and association with ceramide-rich platforms is critical for ciliogenesis. J Lipid Res 2021; 62:100021. [PMID: 33380429 PMCID: PMC7903138 DOI: 10.1194/jlr.ra120001190] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/19/2020] [Accepted: 12/30/2020] [Indexed: 11/21/2022] Open
Abstract
Microtubules are polymers composed of αβ-tubulin subunits that provide structure to cells and play a crucial role in in the development and function of neuronal processes and cilia, microtubule-driven extensions of the plasma membrane that have sensory (primary cilia) or motor (motile cilia) functions. To stabilize microtubules in neuronal processes and cilia, α tubulin is modified by the posttranslational addition of an acetyl group, or acetylation. We discovered that acetylated tubulin in microtubules interacts with the membrane sphingolipid, ceramide. However, the molecular mechanism and function of this interaction are not understood. Here, we show that in human induced pluripotent stem cell-derived neurons, ceramide stabilizes microtubules, which indicates a similar function in cilia. Using proximity ligation assays, we detected complex formation of ceramide with acetylated tubulin in Chlamydomonas reinhardtii flagella and cilia of human embryonic kidney (HEK293T) cells, primary cultured mouse astrocytes, and ependymal cells. Using incorporation of palmitic azide and click chemistry-mediated addition of fluorophores, we show that a portion of acetylated tubulin is S-palmitoylated. S-palmitoylated acetylated tubulin is colocalized with ceramide-rich platforms in the ciliary membrane, and it is coimmunoprecipitated with Arl13b, a GTPase that mediates transport of proteins into cilia. Inhibition of S-palmitoylation with 2-bromo palmitic acid or inhibition of ceramide biosynthesis with fumonisin B1 reduces formation of the Arl13b-acetylated tubulin complex and its transport into cilia, concurrent with impairment of ciliogenesis. Together, these data show, for the first time, that ceramide-rich platforms mediate membrane anchoring and interaction of S-palmitoylated proteins that are critical for cilium formation, stabilization, and function.
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Affiliation(s)
- Priyanka Tripathi
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Zhihui Zhu
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Haiyan Qin
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Ahmed Elsherbini
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Simone M Crivelli
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA; Veterans Affairs Medical Center, Lexington, KY, USA
| | - Emily Roush
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Guanghu Wang
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Stefka D Spassieva
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA
| | - Erhard Bieberich
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY, USA; Veterans Affairs Medical Center, Lexington, KY, USA.
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17
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Main A, Robertson-Gray O, Fuller W. Cyclophilin D palmitoylation and permeability transition: a new twist in the tale of myocardial ischaemia-reperfusion injury. Cardiovasc Res 2021; 117:15-17. [PMID: 32449761 PMCID: PMC7797206 DOI: 10.1093/cvr/cvaa149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Alice Main
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Olivia Robertson-Gray
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - William Fuller
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, Sir James Black Building, University of Glasgow, Glasgow G12 8QQ, UK
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18
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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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19
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Zhou L, Zhou M, Gritsenko MA, Stacey G. Selective Enrichment Coupled with Proteomics to Identify S-Acylated Plasma Membrane Proteins in Arabidopsis. ACTA ACUST UNITED AC 2020; 5:e20119. [PMID: 32976704 DOI: 10.1002/cppb.20119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein S-acylation, predominately in the form of palmitoylation, is a reversible lipid post-translational modification on cysteines that plays important roles in protein localization, trafficking, activity, and complex assembly. The functions and regulatory mechanisms of S-acylation have been extensively studied in mammals owing to remarkable development of high-resolution proteomics and the discovery of the S-acylation-related enzymes. However, the advancement of S-acylation studies in plants lags behind that in mammals, mainly due to the lack of knowledge about proteins responsible for this process, such as protein acyltransferases and their substrates. In this article, a set of systematic protocols to study global S-acylation in Arabidopsis seedlings is described. The procedures are presented in detail, including preparation of Arabidopsis seedlings, enrichment of plasma membrane (PM) proteins, ensuing enrichment of S-acylated proteins/peptides based on the acyl-biotin exchange method, and large-scale identification of S-acylated proteins/peptides via mass spectrometry. This approach enables researchers to study S-acylation of PM proteins in plants in a systematic and straightforward way. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of Arabidopsis seedling materials Basic Protocol 2: Isolation and enrichment of plasma membrane proteins Support Protocol 1: Determination of protein concentration using BCA assay Basic Protocol 3: Enrichment of S-acylated proteins by acyl-biotin exchange method Support Protocol 2: Protein precipitation by methanol/chloroform method Basic Protocol 4: Trypsin digestion and proteomic analysis Alternate Protocol: Pre-resin digestion and peptide-level enrichment.
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Affiliation(s)
- Lijuan Zhou
- Division of Plant Sciences, C.S. Bond Life Science Center, University of Missouri, Columbia, Missouri
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington
| | - Marina A Gritsenko
- Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Gary Stacey
- Division of Plant Sciences, C.S. Bond Life Science Center, University of Missouri, Columbia, Missouri.,Division of Biochemistry, C.S. Bond Life Science Center, University of Missouri, Columbia, Missouri
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20
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Jiang T, Laughlin ST. Enzyme- or light-triggered cyclopropenes for bioorthogonal ligation. Methods Enzymol 2020; 641:1-34. [PMID: 32713519 DOI: 10.1016/bs.mie.2020.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Since first reported at the beginning of the 21st century, bioorthogonal reactions have become powerful tools for investigating biological systems. Here, we review several classic and current bioorthogonal reactions, including the Staudinger-Bertozzi ligation, strain-promoted azide-alkyne cycloaddition (SPAAC), 1,3-dipolar cycloaddition, and tetrazine-alkene ligation. We discuss the capabilities and limitations of the subset of current bioorthogonal reactions that can be "turned on" by exposure to light or an enzyme. Finally, we focus on our recently developed turn-on cyclopropenes, which can be activated for reaction with tetrazines by exposure to light or enzymes, like nitroreductase, depending on the modular reaction caging group appended to the cyclopropene. We discuss the caged cyclopropene's molecular design and synthesis, and we discuss experiments to evaluate and verify reactivity both in vitro and in vivo.
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Affiliation(s)
- Ting Jiang
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States
| | - Scott T Laughlin
- Department of Chemistry, Stony Brook University, Stony Brook, NY, United States; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, United States.
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21
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Maksimovic I, Zheng Q, Trujillo MN, Galligan JJ, David Y. An Azidoribose Probe to Track Ketoamine Adducts in Histone Ribose Glycation. J Am Chem Soc 2020; 142:9999-10007. [PMID: 32390412 PMCID: PMC8052992 DOI: 10.1021/jacs.0c01325] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Reactive cellular metabolites can modify macromolecules and form adducts known as nonenzymatic covalent modifications (NECMs). The dissection of the mechanisms, regulation, and consequences of NECMs, such as glycation, has been challenging due to the complex and often ambiguous nature of the adducts formed. Specific chemical tools are required to directly track the formation of these modifications on key targets in order to uncover their underlying physiological importance. Here, we present the novel chemoenzymatic synthesis of an active azido-modified ribose analog, 5-azidoribose (5-AR), as well as the synthesis of an inactive control derivative, 1-azidoribose (1-AR), and their application toward understanding protein ribose-glycation in vitro and in cellulo. With these new probes we found that, similar to methylglyoxal (MGO) glycation, ribose glycation specifically accumulates on histones. In addition to fluorescent labeling, we demonstrate the utility of the probe in enriching modified targets, which were identified by label-free quantitative proteomics and high-resolution MS/MS workflows. Finally, we establish that the known oncoprotein and hexose deglycase, fructosamine 3-kinase (FN3K), recognizes and facilitates the removal of 5-AR glycation adducts in live cells, supporting the dynamic regulation of ribose glycation as well as validating the probe as a new platform to monitor FN3K activity. Altogether, we demonstrate this probe's utilities to uncover ribose-glycation and deglycation events as well as track FN3K activity toward establishing its potential as a new cancer vulnerability.
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Affiliation(s)
- Igor Maksimovic
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Qingfei Zheng
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Marissa N Trujillo
- Department of Pharmaocology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - James J Galligan
- Department of Pharmaocology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Yael David
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Pharmacology, Weill Cornell Medicine, New York, New York 10065, United States
- Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York 10065, United States
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22
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Affiliation(s)
- Christin Bednarek
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Ilona Wehl
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Nicole Jung
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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23
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Tewari R, West SJ, Shayahati B, Akimzhanov AM. Detection of Protein S-Acylation using Acyl-Resin Assisted Capture. J Vis Exp 2020. [PMID: 32338654 DOI: 10.3791/61016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Protein S-acylation, also referred to as S-palmitoylation, is a reversible post-translational modification of cysteine residues with long-chain fatty acids via a labile thioester bond. S-acylation, which is emerging as a widespread regulatory mechanism, can modulate almost all aspects of the biological activity of proteins, from complex formation to protein trafficking and protein stability. The recent progress in understanding of the biological function of protein S-acylation was achieved largely due to the development of novel biochemical tools allowing robust and sensitive detection of protein S-acylation in a variety of biological samples. Here, we describe acyl resin-assisted capture (Acyl-RAC), a recently developed method based on selective capture of endogenously S-acylated proteins by thiol-reactive Sepharose beads. Compared to existing approaches, Acyl-RAC requires fewer steps and can yield more reliable results when coupled with mass spectrometry for identification of novel S-acylation targets. A major limitation in this technique is the lack of ability to discriminate between fatty acid species attached to cysteines via the same thioester bond.
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Affiliation(s)
- Ritika Tewari
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UT Health
| | - Savannah J West
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UT Health; MD Anderson UT Health Graduate School
| | - Bieerkehazi Shayahati
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UT Health
| | - Askar M Akimzhanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UT Health;
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24
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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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25
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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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26
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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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27
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Zareba-Koziol M, Bartkowiak-Kaczmarek A, Figiel I, Krzystyniak A, Wojtowicz T, Bijata M, Wlodarczyk J. Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins. Mol Cell Proteomics 2019; 18:1916-1938. [PMID: 31311849 PMCID: PMC6773552 DOI: 10.1074/mcp.ra119.001581] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/12/2019] [Indexed: 11/06/2022] Open
Abstract
The precise regulation of synaptic integrity is critical for neuronal network connectivity and proper brain function. Essential aspects of the activity and localization of synaptic proteins are regulated by posttranslational modifications. S-palmitoylation is a reversible covalent modification of the cysteine with palmitate. It modulates affinity of the protein for cell membranes and membranous compartments. Intracellular palmitoylation dynamics are regulated by crosstalk with other posttranslational modifications, such as S-nitrosylation. S-nitrosylation is a covalent modification of cysteine thiol by nitric oxide and can modulate protein functions. Therefore, simultaneous identification of endogenous site-specific proteomes of both cysteine modifications under certain biological conditions offers new insights into the regulation of functional pathways. Still unclear, however, are the ways in which this crosstalk is affected in brain pathology, such as stress-related disorders. Using a newly developed mass spectrometry-based approach Palmitoylation And Nitrosylation Interplay Monitoring (PANIMoni), we analyzed the endogenous S-palmitoylation and S-nitrosylation of postsynaptic density proteins at the level of specific single cysteine in a mouse model of chronic stress. Among a total of 813 S-PALM and 620 S-NO cysteine sites that were characterized on 465 and 360 proteins, respectively, we sought to identify those that were differentially affected by stress. Our data show involvement of S-palmitoylation and S-nitrosylation crosstalk in the regulation of 122 proteins including receptors, scaffolding proteins, regulatory proteins and cytoskeletal components. Our results suggest that atypical crosstalk between the S-palmitoylation and S-nitrosylation interplay of proteins involved in synaptic transmission, protein localization and regulation of synaptic plasticity might be one of the main events associated with chronic stress disorder, leading to destabilization in synaptic networks.
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Affiliation(s)
- Monika Zareba-Koziol
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland.
| | - Anna Bartkowiak-Kaczmarek
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Izabela Figiel
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Adam Krzystyniak
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Tomasz Wojtowicz
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Monika Bijata
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland
| | - Jakub Wlodarczyk
- Laboratory of Cell Biophysics, Nencki Institute of Experimental Biology, Polish Academy of Science, 02-093 Warsaw, Poland.
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Zhou B, Wang Y, Yan Y, Mariscal J, Di Vizio D, Freeman MR, Yang W. Low-Background Acyl-Biotinyl Exchange Largely Eliminates the Coisolation of Non- S-Acylated Proteins and Enables Deep S-Acylproteomic Analysis. Anal Chem 2019; 91:9858-9866. [PMID: 31251020 PMCID: PMC7451198 DOI: 10.1021/acs.analchem.9b01520] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein S-acylation (also called palmitoylation) is a common post-translational modification whose deregulation plays a key role in the pathogenesis of many diseases. Acyl-biotinyl exchange (ABE), a widely used method for the enrichment of S-acylated proteins, has the potential of capturing the entire S-acylproteome in any type of biological sample. Here, we showed that current ABE methods suffer from a high background arising from the coisolation of non-S-acylated proteins. The background can be substantially reduced by an additional blockage of residual free cysteine residues with 2,2'-dithiodipyridine prior to the biotin-HPDP reaction. Coupling the low-background ABE (LB-ABE) method with label-free proteomics, 2 895 high-confidence candidate S-acylated proteins (including 1 591 known S-acylated proteins) were identified from human prostate cancer LNCaP cells, representing so-far the largest S-acylproteome data set identified in a single study. Immunoblotting analysis confirmed the S-acylation of five known and five novel prostate cancer-related S-acylated proteins in LNCaP cells and suggested that their S-acylation levels were about 0.6-1.8%. In summary, the LB-ABE method largely eliminates the coisolation of non-S-acylated proteins and enables deep S-acylproteomic analysis. It is expected to facilitate a much more comprehensive and accurate quantification of S-acylproteomes than previous ABE methods.
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Affiliation(s)
- Bo Zhou
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Yang Wang
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Yiwu Yan
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Javier Mariscal
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Dolores Di Vizio
- Division of Cancer Biology and Therapeutics, Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
- Department of Pathology and Laboratory Medicine, 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
| | - Michael R. Freeman
- Division of Cancer Biology and Therapeutics, 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
| | - Wei Yang
- Division of Cancer Biology and Therapeutics, 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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Takahara M, Wakabayashi R, Fujimoto N, Minamihata K, Goto M, Kamiya N. Enzymatic Cell‐Surface Decoration with Proteins using Amphiphilic Lipid‐Fused Peptide Substrates. Chemistry 2019; 25:7315-7321. [DOI: 10.1002/chem.201900370] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/03/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Mari Takahara
- Department of Materials Science & Chemical EngineeringNational Institute of Technology, Kitakyushu College 5-20-1 Shii, Kokuraminamiku Kitakyushu 802-0985 Japan
| | - Rie Wakabayashi
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| | - Naoki Fujimoto
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| | - Kosuke Minamihata
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| | - Masahiro Goto
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
- Division of Biotechnology, Center for Future ChemistryKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
| | - Noriho Kamiya
- Department of Applied ChemistryGraduate School of EngineeringKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
- Division of Biotechnology, Center for Future ChemistryKyushu University 744 Motooka, Nishiku Fukuoka 819-0395 Japan
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30
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Zhang Z, Zhang HY, Zhang Y, Li H. Inactivation of the Ras/MAPK/PPARγ signaling axis alleviates diabetic mellitus-induced erectile dysfunction through suppression of corpus cavernosal endothelial cell apoptosis by inhibiting HMGCS2 expression. Endocrine 2019; 63:615-631. [PMID: 30460485 DOI: 10.1007/s12020-018-1810-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/30/2018] [Indexed: 01/30/2023]
Abstract
PURPOSE Diabetic mellitus-induced erectile dysfunction (DMED) represents a significant complication associated with diabetes mellitus (DM) that greatly affects human life quality. Various reports have highlighted the involvement of mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2) in the regulation of mitochondrial fatty acid oxidation, which has also been linked with DM. Through bioinformatics analysis, HMGCS2 was determined to be a novel target among DM patients suffering from erectile dysfunction (ED), and enriched in the Ras/ERK/PPAR signaling axis. Owing to the fact that the key mechanism HMGCS2 involved in DM remains largely unknown, we set out to investigate the role of the Ras/MAPK/PPARγ signaling axis and HMGCS2 in the corpus cavernosal endothelial cells (CCECs) of rats with DMED. METHODS Firstly, bioinformatics analysis was used to screen out differentially expressed genes in DMED. Then, to investigate the influence of the Ras/MAPK/PPARγ signaling axis and HMGCS2 on DMED, a rat model of DMED was established and injected with Simvastatin and si-Hmgcs2. The individual expression patterns of Ras, MAPK, PPARγ and HMGCS2 were determined by RT-qPCR, immunohistochemistry and western blot analysis methods. Afterwards, to investigate the mechanism of Ras/MAPK/PPARγ signaling axis and HMGCS2, CCECs were isolated from DMED rats and transfected with agonists and inhibitors of the Ras/MAPK/PPARγ signaling axis and siRNA of HMGCS2, with their respective functions in apoptosis and impairment of CCECs evaluated using TUNEL staining and flow cytometry. RESULTS Microarray analysis and KEGG pathway enrichment analysis revealed that Ras/ERK/PPAR signaling axis mediated HMGCS2 in DMED. Among the DMED rats, the Ras/MAPK/PPAR signaling axis was also activated while the expression of HMGCS2 was upregulated. The activation of Ras was determined to be capable of upregulating ERK expression which resulted in the inhibition of the transcription of PPARγ and subsequent upregulation of HMGCS2 expression. The inhibited activation of the Ras/ERK/PPAR signaling axis and silencing HMGCS2 were observed to provide an alleviatory effect on the injury of DMED while acting to inhibit the apoptosis of CCECs. CONCLUSION Collectively, the key findings suggested that suppression of the Ras/MAPK/PPARγ signaling axis could downregulate expression of HMGCS2, so as to alleviate DMED. This study defines the potential treatment for DMED through inhibition of the Ras/MAPK/PPARγ signaling axis and silencing HMGCS2.
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Affiliation(s)
- Zhuo Zhang
- Department of Urology, China-Japan Union Hospital of Jilin University, 130000, Changchun, P.R. China
| | - Hai-Yan Zhang
- Department of Gastrointestinal Surgery, China-Japan Union Hospital of Jilin University, 130000, Changchun, P.R. China
| | - Ying Zhang
- Department of Pathology, China-Japan Union Hospital of Jilin University, 130000, Changchun, P.R. China
| | - Hai Li
- Department of Urology, China-Japan Union Hospital of Jilin University, 130000, Changchun, P.R. China.
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31
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Greaves J, Tomkinson NCO. Detection of Heterogeneous Protein S-Acylation in Cells. Methods Mol Biol 2019; 2009:13-33. [PMID: 31152392 DOI: 10.1007/978-1-4939-9532-5_2] [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] [Indexed: 06/09/2023]
Abstract
The use of synthetically synthesized azide and alkyne fatty acid analogs coupled with bioorthogonal Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition reaction-based detection methods to study protein S-acylation reactions has replaced the traditional method of using in vivo metabolic radiolabeling with tritiated palmitic acid and has greatly facilitated our understanding of this essential cellular process. Here, we describe the chemical synthesis of myristic (C:14), palmitic (C16:0), and stearic (C18:0) acid-azide probes and detail how they may be utilized as chemical reporters for the analysis of S-acylation of exogenously expressed proteins in cells.
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Affiliation(s)
- Jennifer Greaves
- Faculty of Health and Life Sciences, Centre for Sport, Exercise and Life Sciences, Coventry University, Coventry, UK.
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
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32
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Abstract
Dynamic and reversible protein S-acylation, most commonly occurring as S-palmitoylation, plays an important role in protein/membrane association and the regulation of intracellular signaling via cycles of palmitoylation and depalmitoylation. Direct analysis of protein S-acylation by mass spectrometry (MS) offers several benefits over indirect detection methods in that it can definitively determine the location and nature of the acyl modification, and is not prone to false discoveries. However, characterization of acyl proteins is challenging because of the tendency of acyl loss during sample preparation and tandem MS analysis. In this chapter, we present a sample preparation protocol that preserves labile acyl modifications and an LC-MS/MS workflow for detection of S-acylation with high confidence and sensitivity.
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Affiliation(s)
- Yuhuan Ji
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Cheng Lin
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA.
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33
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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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Abstract
Click chemistry has emerged as a powerful tool in our arsenal for unlocking new biology. This includes its utility in both chemical biology and drug discovery. An emerging application of click chemistry is in the development of biochemical assays for high-throughput screening to identify new chemical probes and drug leads. This Feature Article will discuss the advancements in click chemistry that were necessary for the development of a new class of biochemical assay, catalytic enzyme-linked click chemistry assay or cat-ELCCA. Inspired by enzyme immunoassays, cat-ELCCA was designed as a click chemistry-based amplification assay where bioorthogonally-tagged analytes and enzymes are used in place of the enzyme-linked secondary antibodies used in immunoassays. The result is a robust assay format with demonstrated applicability in several important areas of biology and drug discovery, including post-translational modifications, pre-microRNA maturation, and protein-protein and RNA-protein interactions. Through the use of cat-ELCCA and other related click chemistry-based assays, new chemical probes for interrogating promising drug targets have been discovered. These examples will be discussed, in addition to a future outlook on the impact of this approach in probe and drug discovery.
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Affiliation(s)
- Amanda L Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, 1600 Huron Parkway, NCRC B520, Ann Arbor, Michigan 48109, USA.
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35
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Zaręba-Kozioł M, Figiel I, Bartkowiak-Kaczmarek A, Włodarczyk J. Insights Into Protein S-Palmitoylation in Synaptic Plasticity and Neurological Disorders: Potential and Limitations of Methods for Detection and Analysis. Front Mol Neurosci 2018; 11:175. [PMID: 29910712 PMCID: PMC5992399 DOI: 10.3389/fnmol.2018.00175] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 05/09/2018] [Indexed: 12/20/2022] Open
Abstract
S-palmitoylation (S-PALM) is a lipid modification that involves the linkage of a fatty acid chain to cysteine residues of the substrate protein. This common posttranslational modification (PTM) is unique among other lipid modifications because of its reversibility. Hence, like phosphorylation or ubiquitination, it can act as a switch that modulates various important physiological pathways within the cell. Numerous studies revealed that S-PALM plays a crucial role in protein trafficking and function throughout the nervous system. Notably, the dynamic turnover of palmitate on proteins at the synapse may provide a key mechanism for rapidly changing synaptic strength. Indeed, palmitate cycling on postsynaptic density-95 (PSD-95), the major postsynaptic density protein at excitatory synapses, regulates the number of synaptic α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs) and thus affects synaptic transmission. Accumulating evidence suggests a relationship between impairments in S-PALM and severe neurological disorders. Therefore, determining the precise levels of S-PALM may be essential for understanding the ways in which this PTM is regulated in the brain and controls synaptic dynamics. Protein S-PALM can be characterized using metabolic labeling methods and biochemical tools. Both approaches are discussed herein in the context of specific methods and their advantages and disadvantages. This review clearly shows progress in the field, which has led to the development of new, more sensitive techniques that enable the detection of palmitoylated proteins and allow predictions of potential palmitate binding sites. Unfortunately, one significant limitation of these approaches continues to be the inability to use them in living cells.
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Affiliation(s)
- Monika Zaręba-Kozioł
- Laboratory of Cell Biophysics, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Izabela Figiel
- Laboratory of Cell Biophysics, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Anna Bartkowiak-Kaczmarek
- Laboratory of Cell Biophysics, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Włodarczyk
- Laboratory of Cell Biophysics, Department of Molecular and Cellular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
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Yao CH, Liu GY, Wang R, Moon SH, Gross RW, Patti GJ. Identifying off-target effects of etomoxir reveals that carnitine palmitoyltransferase I is essential for cancer cell proliferation independent of β-oxidation. PLoS Biol 2018; 16:e2003782. [PMID: 29596410 PMCID: PMC5892939 DOI: 10.1371/journal.pbio.2003782] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 04/10/2018] [Accepted: 02/22/2018] [Indexed: 02/06/2023] Open
Abstract
It has been suggested that some cancer cells rely upon fatty acid oxidation (FAO) for energy. Here we show that when FAO was reduced approximately 90% by pharmacological inhibition of carnitine palmitoyltransferase I (CPT1) with low concentrations of etomoxir, the proliferation rate of various cancer cells was unaffected. Efforts to pharmacologically inhibit FAO more than 90% revealed that high concentrations of etomoxir (200 μM) have an off-target effect of inhibiting complex I of the electron transport chain. Surprisingly, however, when FAO was reduced further by genetic knockdown of CPT1, the proliferation rate of these same cells decreased nearly 2-fold and could not be restored by acetate or octanoic acid supplementation. Moreover, CPT1 knockdowns had altered mitochondrial morphology and impaired mitochondrial coupling, whereas cells in which CPT1 had been approximately 90% inhibited by etomoxir did not. Lipidomic profiling of mitochondria isolated from CPT1 knockdowns showed depleted concentrations of complex structural and signaling lipids. Additionally, expression of a catalytically dead CPT1 in CPT1 knockdowns did not restore mitochondrial coupling. Taken together, these results suggest that transport of at least some long-chain fatty acids into the mitochondria by CPT1 may be required for anabolic processes that support healthy mitochondrial function and cancer cell proliferation independent of FAO.
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Affiliation(s)
- Cong-Hui Yao
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gao-Yuan Liu
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Bioorganic and Molecular Pharmacology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rencheng Wang
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sung Ho Moon
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Bioorganic and Molecular Pharmacology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Richard W. Gross
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Bioorganic and Molecular Pharmacology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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37
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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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38
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Gao X, Hannoush RN. A Decade of Click Chemistry in Protein Palmitoylation: Impact on Discovery and New Biology. Cell Chem Biol 2017; 25:236-246. [PMID: 29290622 DOI: 10.1016/j.chembiol.2017.12.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/10/2017] [Accepted: 11/30/2017] [Indexed: 12/17/2022]
Abstract
Protein palmitoylation plays diverse roles in regulating the trafficking, stability, and activity of cellular proteins. The advent of click chemistry has propelled the field of protein palmitoylation forward by providing specific, sensitive, rapid, and easy-to-handle methods for studying protein palmitoylation. This year marks the 10th anniversary since the first click chemistry-based fatty acid probes for detecting protein lipid modifications were reported. The goal of this review is to highlight key biological advancements in the field of protein palmitoylation during the past 10 years. In particular, we discuss the impact of click chemistry on enabling protein palmitoylation proteomics methods, uncovering novel lipid modifications on proteins and elucidating their functions, as well as the development of non-radioactive biochemical and enzymatic assays. In addition, this review provides context for building and exploring new research avenues in protein palmitoylation through the use of clickable fatty acid probes.
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Affiliation(s)
- Xinxin Gao
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA
| | - Rami N Hannoush
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, CA, USA.
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Shen LF, Chen YJ, Liu KM, Haddad ANS, Song IW, Roan HY, Chen LY, Yen JJY, Chen YJ, Wu JY, Chen YT. Role of S-Palmitoylation by ZDHHC13 in Mitochondrial function and Metabolism in Liver. Sci Rep 2017; 7:2182. [PMID: 28526873 PMCID: PMC5438363 DOI: 10.1038/s41598-017-02159-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 04/12/2017] [Indexed: 11/17/2022] Open
Abstract
Palmitoyltransferase (PAT) catalyses protein S-palmitoylation which adds 16-carbon palmitate to specific cysteines and contributes to various biological functions. We previously reported that in mice, deficiency of Zdhhc13, a member of the PAT family, causes severe phenotypes including amyloidosis, alopecia, and osteoporosis. Here, we show that Zdhhc13 deficiency results in abnormal liver function, lipid abnormalities, and hypermetabolism. To elucidate the molecular mechanisms underlying these disease phenotypes, we applied a site-specific quantitative approach integrating an alkylating resin-assisted capture and mass spectrometry-based label-free strategy for studying the liver S-palmitoylome. We identified 2,190 S-palmitoylated peptides corresponding to 883 S-palmitoylated proteins. After normalization using the membrane proteome with TMT10-plex labelling, 400 (31%) of S-palmitoylation sites on 254 proteins were down-regulated in Zdhhc13-deficient mice, representing potential ZDHHC13 substrates. Among these, lipid metabolism and mitochondrial dysfunction proteins were overrepresented. MCAT and CTNND1 were confirmed to be specific ZDHHC13 substrates. Furthermore, we found impaired mitochondrial function in hepatocytes of Zdhhc13-deficient mice and Zdhhc13-knockdown Hep1–6 cells. These results indicate that ZDHHC13 is an important regulator of mitochondrial activity. Collectively, our study allows for a systematic view of S-palmitoylation for identification of ZDHHC13 substrates and demonstrates the role of ZDHHC13 in mitochondrial function and metabolism in liver.
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Affiliation(s)
- Li-Fen Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kai-Ming Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Amir N Saleem Haddad
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - I-Wen Song
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsiao-Yuh Roan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Li-Ying Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Jeffrey J Y Yen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Jer-Yuarn Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yuan-Tsong Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan. .,Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, United States of America.
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40
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Chen BJ, Lam TC, Liu LQ, To CH. Post-translational modifications and their applications in eye research (Review). Mol Med Rep 2017; 15:3923-3935. [PMID: 28487982 DOI: 10.3892/mmr.2017.6529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 02/22/2017] [Indexed: 02/05/2023] Open
Abstract
Gene expression is the process by which genetic information is used for the synthesis of a functional gene product, and ultimately regulates cell function. The increase of biological complexity from genome to proteome is vast, and the post-translational modification (PTM) of proteins contribute to this complexity. The study of protein expression and PTMs has attracted attention in the post‑genomic era. Due to the limited capability of conventional biochemical techniques in the past, large‑scale PTM studies were technically challenging. The introduction of effective protein separation methods, specific PTM purification strategies and advanced mass spectrometers has enabled the global profiling of PTMs and the identification of a targeted PTM within the proteome. The present review provides an overview of current proteomic technologies being applied in eye research, with a particular focus on studies of PTMs in ocular tissues and ocular diseases.
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Affiliation(s)
- Bing-Jie Chen
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
| | - Long-Qian Liu
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chi-Ho To
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
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41
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Issa H, Huc-Claustre E, Reddad T, Bonadé Bottino N, Tropis M, Houssin C, Daffé M, Bayan N, Dautin N. Click-chemistry approach to study mycoloylated proteins: Evidence for PorB and PorC porins mycoloylation in Corynebacterium glutamicum. PLoS One 2017; 12:e0171955. [PMID: 28199365 PMCID: PMC5310785 DOI: 10.1371/journal.pone.0171955] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/27/2017] [Indexed: 01/23/2023] Open
Abstract
Protein mycoloylation is a recently identified, new form of protein acylation. This post-translational modification consists in the covalent attachment of mycolic acids residues to serine. Mycolic acids are long chain, α-branched, β-hydroxylated fatty acids that are exclusively found in the cell envelope of Corynebacteriales, a bacterial order that includes important genera such as Mycobacterium, Nocardia or Corynebacterium. So far, only 3 mycoloylated proteins have been identified: PorA, PorH and ProtX from C. glutamicum. Whereas the identity and function of ProtX is unknown, PorH and PorA associate to form a membrane channel, the activity of which is dependent upon PorA mycoloylation. However, the exact role of mycoloylation and the generality of this phenomenon are still unknown. In particular, the identity of other mycoloylated proteins, if any, needs to be determined together with establishing whether such modification occurs in Corynebacteriales genera other than Corynebacterium. Here, we tested whether a metabolic labeling and click-chemistry approach could be used to detect mycoloylated proteins. Using a fatty acid alkyne analogue, we could indeed label PorA, PorH and ProtX and determine ProtX mycoloylation site. Importantly, we also show that two other porins from C. glutamicum, PorB and PorC are mycoloylated.
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Affiliation(s)
- Hanane Issa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
- Holy Spirit University of Kaslik (USEK), Jounieh, Mount Lebanon, Lebanon
| | | | - Thamila Reddad
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nolwenn Bonadé Bottino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Maryelle Tropis
- Institute of Pharmacology and Structural Biology (IPBS), UMR 5089, France
| | - Christine Houssin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Mamadou Daffé
- Institute of Pharmacology and Structural Biology (IPBS), UMR 5089, France
| | - Nicolas Bayan
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nathalie Dautin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
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Meyer M, Kovács AD, Pearce DA. Decreased sensitivity of palmitoyl protein thioesterase 1-deficient neurons to chemical anoxia. Metab Brain Dis 2017; 32:275-279. [PMID: 27722792 PMCID: PMC5335868 DOI: 10.1007/s11011-016-9919-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/03/2016] [Indexed: 01/12/2023]
Abstract
Infantile CLN1 disease, also known as infantile neuronal ceroid lipofuscinosis, is a fatal childhood neurodegenerative disorder caused by mutations in the CLN1 gene. CLN1 encodes a soluble lysosomal enzyme, palmitoyl protein thioesterase 1 (PPT1), and it is still unclear why neurons are selectively vulnerable to the loss of PPT1 enzyme activity in infantile CLN1 disease. To examine the effects of PPT1 deficiency on several well-defined neuronal signaling and cell death pathways, different toxic insults were applied in cerebellar granule neuron cultures prepared from wild type (WT) and palmitoyl protein thioesterase 1-deficient (Ppt1 -/- ) mice, a model of infantile CLN1 disease. Glutamate uptake inhibition by t-PDC (L-trans-pyrrolidine-2,4-dicarboxylic acid) or Zn2+-induced general mitochondrial dysfunction caused similar toxicity in WT and Ppt1 -/- cultures. Ppt1 -/- neurons, however, were more sensitive to mitochondrial complex I inhibition by MPP+ (1-methyl-4-phenylpyridinium), and had significantly decreased sensitivity to chemical anoxia induced by the mitochondrial complex IV inhibitor, sodium azide. Our results indicate that PPT1 deficiency causes alterations in the mitochondrial respiratory chain.
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Affiliation(s)
- Meredith Meyer
- Sanford Children's Health Research Center, Sanford Research, 2301 E. 60th Street, Sioux Falls, SD, 57104, USA
| | - Attila D Kovács
- Sanford Children's Health Research Center, Sanford Research, 2301 E. 60th Street, Sioux Falls, SD, 57104, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota Sioux Falls, Sioux Falls, SD, 57104, USA
| | - David A Pearce
- Sanford Children's Health Research Center, Sanford Research, 2301 E. 60th Street, Sioux Falls, SD, 57104, USA.
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota Sioux Falls, Sioux Falls, SD, 57104, USA.
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43
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Gao H, Sun W, Song Z, Yu Y, Wang L, Chen X, Zhang Q. A Method to Generate and Analyze Modified Myristoylated Proteins. Chembiochem 2017; 18:324-330. [PMID: 27925692 DOI: 10.1002/cbic.201600608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Indexed: 11/07/2022]
Abstract
Covalent lipid modification of proteins is essential to their cellular localizations and functions. Engineered lipid motifs, coupled with bio-orthogonal chemistry, have been utilized to identify myristoylated or palmitoylated proteins in cells. However, whether modified proteins have similar properties as endogenous ones has not been well investigated mainly due to lack of methods to generate and analyze purified proteins. We have developed a method that utilizes metabolic interference and mass spectrometry to produce and analyze modified, myristoylated small GTPase ADP-ribosylation factor 1 (Arf1). The capacities of these recombinant proteins to bind liposomes and load and hydrolyze GTP were measured and compared with the unmodified myristoylated Arf1. The ketone-modified myristoylated Arf1 could be further labeled by fluorophore-coupled hydrazine and subsequently visualized through fluorescence imaging. This methodology provides an effective model system to characterize lipid-modified proteins with additional functions before applying them to cellular systems.
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Affiliation(s)
- Huanyao Gao
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Wei Sun
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Zhiquan Song
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Yanbao Yu
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Li Wang
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, School of Medicine, The University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA
| | - Qisheng Zhang
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, 125 Mason Farm Road, Chapel Hill, NC, 27599, USA
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44
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Li Y, Qi B. Progress toward Understanding Protein S-acylation: Prospective in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:346. [PMID: 28392791 PMCID: PMC5364179 DOI: 10.3389/fpls.2017.00346] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Accepted: 02/28/2017] [Indexed: 05/02/2023]
Abstract
S-acylation, also known as S-palmitoylation or palmitoylation, is a reversible post-translational lipid modification in which long chain fatty acid, usually the 16-carbon palmitate, covalently attaches to a cysteine residue(s) throughout the protein via a thioester bond. It is involved in an array of important biological processes during growth and development, reproduction and stress responses in plant. S-acylation is a ubiquitous mechanism in eukaryotes catalyzed by a family of enzymes called Protein S-Acyl Transferases (PATs). Since the discovery of the first PAT in yeast in 2002 research in S-acylation has accelerated in the mammalian system and followed by in plant. However, it is still a difficult field to study due to the large number of PATs and even larger number of putative S-acylated substrate proteins they modify in each genome. This is coupled with drawbacks in the techniques used to study S-acylation, leading to the slower progress in this field compared to protein phosphorylation, for example. In this review we will summarize the discoveries made so far based on knowledge learnt from the characterization of protein S-acyltransferases and the S-acylated proteins, the interaction mechanisms between PAT and its specific substrate protein(s) in yeast and mammals. Research in protein S-acylation and PATs in plants will also be covered although this area is currently less well studied in yeast and mammalian systems.
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45
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Reddy KD, Malipeddi J, DeForte S, Pejaver V, Radivojac P, Uversky VN, Deschenes RJ. Physicochemical sequence characteristics that influence S-palmitoylation propensity. J Biomol Struct Dyn 2016; 35:2337-2350. [PMID: 27498722 DOI: 10.1080/07391102.2016.1217275] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Over the past 30 years, several hundred eukaryotic proteins spanning from yeast to man have been shown to be S-palmitoylated. This post-translational modification involves the reversible addition of a 16-carbon saturated fatty acyl chain onto the cysteine residue of a protein where it regulates protein membrane association and distribution, conformation, and stability. However, the large-scale proteome-wide discovery of new palmitoylated proteins has been hindered by the difficulty of identifying a palmitoylation consensus sequence. Using a bioinformatics approach, we show that the enrichment of hydrophobic and basic residues, the cellular context of the protein, and the structural features of the residues surrounding the palmitoylated cysteine all influence the likelihood of palmitoylation. We developed a new palmitoylation predictor that incorporates these identified features, and this predictor achieves a Matthews Correlation Coefficient of .74 using 10-fold cross validation, and significantly outperforms existing predictors on unbiased testing sets. This demonstrates that palmitoylation sites can be predicted with accuracy by taking into account not only physiochemical properties of the modified cysteine and its surrounding residues, but also structural parameters and the subcellular localization of the modified cysteine. This will allow for improved predictions of palmitoylated residues in uncharacterized proteins. A web-based version of this predictor is currently under development.
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Affiliation(s)
- Krishna D Reddy
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA
| | - Jashwanth Malipeddi
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA
| | - Shelly DeForte
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA
| | - Vikas Pejaver
- c Department of Computer Science and Informatics , Indiana University , Bloomington , IN 47405 , USA
| | - Predrag Radivojac
- c Department of Computer Science and Informatics , Indiana University , Bloomington , IN 47405 , USA
| | - Vladimir N Uversky
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA.,b Johnnie B. Byrd Alzheimer's Research Institute , University of South Florida , Tampa , FL 33612 , USA
| | - Robert J Deschenes
- a Department of Molecular Medicine , University of South Florida , 12901 Bruce B. Downs Blvd., MDC 07, Tampa , FL 33612 , USA
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46
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Foe IT, Child MA, Majmudar JD, Krishnamurthy S, van der Linden WA, Ward GE, Martin BR, Bogyo M. Global Analysis of Palmitoylated Proteins in Toxoplasma gondii. Cell Host Microbe 2016; 18:501-11. [PMID: 26468752 DOI: 10.1016/j.chom.2015.09.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/25/2015] [Accepted: 09/16/2015] [Indexed: 02/01/2023]
Abstract
Post-translational modifications (PTMs) such as palmitoylation are critical for the lytic cycle of the protozoan parasite Toxoplasma gondii. While palmitoylation is involved in invasion, motility, and cell morphology, the proteins that utilize this PTM remain largely unknown. Using a chemical proteomic approach, we report a comprehensive analysis of palmitoylated proteins in T. gondii, identifying a total of 282 proteins, including cytosolic, membrane-associated, and transmembrane proteins. From this large set of palmitoylated targets, we validate palmitoylation of proteins involved in motility (myosin light chain 1, myosin A), cell morphology (PhIL1), and host cell invasion (apical membrane antigen 1, AMA1). Further studies reveal that blocking AMA1 palmitoylation enhances the release of AMA1 and other invasion-related proteins from apical secretory organelles, suggesting a previously unrecognized role for AMA1. These findings suggest that palmitoylation is ubiquitous throughout the T. gondii proteome and reveal insights into the biology of this important human pathogen.
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Affiliation(s)
- Ian T Foe
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew A Child
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jaimeen D Majmudar
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shruthi Krishnamurthy
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | | | - Gary E Ward
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA
| | - Brent R Martin
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, 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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47
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Fang C, Zhang X, Zhang L, Gao X, Yang P, Lu H. Identification of Palmitoylated Transitional Endoplasmic Reticulum ATPase by Proteomic Technique and Pan Antipalmitoylation Antibody. J Proteome Res 2016; 15:956-62. [PMID: 26865113 DOI: 10.1021/acs.jproteome.5b00979] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein palmitoylation plays a significant role in a wide range of biological processes such as cell signal transduction, metabolism, apoptosis, and carcinogenesis. For high-throughput analysis of protein palmitoylation, approaches based on the acyl-biotin exchange or metabolic labeling of azide/alkynyl-palmitate analogs are commonly used. No palmitoylation antibody has been reported. Here, the palmitoylated proteome of human colon cancer cell lines SW480 was analyzed via a TS-6B-based method. In total, 151 putative palmitoylated sites on 92 proteins, including 100 novel sites, were identified. Except for 3 known palmitoylated transmembrane proteins, ATP1A1, ZDHHC5, and PLP2, some important proteins including kinases, ion channels, receptors, and cytoskeletal proteins were also identified, such as CLIC1, PGK1, PPIA, FKBP4, exportin-2, etc. More importantly, the pan antipalmitoylation antibody was developed and verified for the first time. Our homemade pan antipalmitoylation antiserum could differentiate well protein palmitoylation from mouse brain membrane fraction and SW480 cells, which affords a new technique for analyzing protein palmitoylation by detecting the palmitic acid moiety directly. Furthermore, the candidate protein transitional endoplasmic reticulum ATPase (VCP) identified in SW480 cells was validated to be palmitoylated by Western blotting with anti-VCP antibody and the homemade pan antipalmitoylation antibody.
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Affiliation(s)
- Caiyun Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, China
| | - Xiaoqin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, China
| | - Lei Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, China
| | - Xing Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, China
| | - Haojie Lu
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University , Shanghai 200433, China
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48
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Identification of new palmitoylated proteins in Toxoplasma gondii. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:400-8. [PMID: 26825284 DOI: 10.1016/j.bbapap.2016.01.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 12/15/2015] [Accepted: 01/04/2016] [Indexed: 01/23/2023]
Abstract
Protein palmitoylation has been shown to be an important post-translational modification in eukaryotic cells. This modification alters the localization and/or the function of the targeted protein. In recent years, protein palmitoylation has risen in importance in apicomplexan parasites as well. In Toxoplasma gondii, some proteins have been reported to be modified by palmitate. With the development of new techniques that allow the isolation of palmitoylated proteins, this significant post-translational modification has begun to be studied in more detail in T. gondii. Here we describe the palmitoylome of the tachyzoite stage of T. gondii using a combination of the acyl-biotin exchange chemistry method and mass spectrometry analysis. We identified 401 proteins found in multiple cellular compartments, with a wide range of functions that vary from metabolic processes, gliding and host-cell invasion to even regulation of transcription and translation. Besides, we found that more rhoptry proteins than the ones already described for Toxoplasma are palmitoylated, suggesting an important role for this modification in the invasion mechanism of the host-cell. This study documents that protein palmitoylation is a common modification in T. gondii that could have an impact on different cellular processes.
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49
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Ourailidou ME, Zwinderman MRH, Dekker FJ. Bioorthogonal metabolic labelling with acyl-CoA reporters: targeting protein acylation. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00446b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bioorthogonal labels in protein acylation: advantages and disadvantages of metaBO(W)lic tagging with acyl-CoA(RROWS).
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Affiliation(s)
- Maria. E. Ourailidou
- Pharmaceutical Gene Modulation
- Groningen Research Institute of Pharmacy (GRIP)
- University of Groningen
- 9713 AV Groningen
- The Netherlands
| | - Martijn R. H. Zwinderman
- Pharmaceutical Gene Modulation
- Groningen Research Institute of Pharmacy (GRIP)
- University of Groningen
- 9713 AV Groningen
- The Netherlands
| | - Frank J. Dekker
- Pharmaceutical Gene Modulation
- Groningen Research Institute of Pharmacy (GRIP)
- University of Groningen
- 9713 AV Groningen
- The Netherlands
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50
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Fukata Y, Murakami T, Yokoi N, Fukata M. Local Palmitoylation Cycles and Specialized Membrane Domain Organization. CURRENT TOPICS IN MEMBRANES 2015; 77:97-141. [PMID: 26781831 DOI: 10.1016/bs.ctm.2015.10.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Palmitoylation is an evolutionally conserved lipid modification of proteins. Dynamic and reversible palmitoylation controls a wide range of molecular and cellular properties of proteins including the protein trafficking, protein function, protein stability, and specialized membrane domain organization. However, technical difficulties in (1) detection of palmitoylated substrate proteins and (2) purification and enzymology of palmitoylating enzymes have prevented the progress in palmitoylation research, compared with that in phosphorylation research. The recent development of proteomic and chemical biology techniques has unexpectedly expanded the known complement of palmitoylated proteins in various species and tissues/cells, and revealed the unique occurrence of palmitoylated proteins in membrane-bound organelles and specific membrane compartments. Furthermore, identification and characterization of DHHC (Asp-His-His-Cys) palmitoylating enzyme-substrate pairs have contributed to elucidating the regulatory mechanisms and pathophysiological significance of protein palmitoylation. Here, we review the recent progress in protein palmitoylation at the molecular, cellular, and in vivo level and discuss how locally regulated palmitoylation machinery works for dynamic nanoscale organization of membrane domains.
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Affiliation(s)
- Yuko Fukata
- Division of Membrane Physiology, Department of Cell Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Tatsuro Murakami
- Division of Membrane Physiology, Department of Cell Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Norihiko Yokoi
- Division of Membrane Physiology, Department of Cell Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Masaki Fukata
- Division of Membrane Physiology, Department of Cell Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan; Department of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
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