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    Proteome-Scale Analysis of Protein S-Acylation Comes of Age
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    • Yang Wang
      Yang Wang
      Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
      More by Yang Wang
    • Wei Yang*
      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
      *Tel: +1 (310)423-7142. Email: [email protected]
      More by Wei Yang
      Orcidhttp://orcid.org/0000-0003-2575-3570
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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2021, 20, 1, 14–26
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    https://doi.org/10.1021/acs.jproteome.0c00409
    Published November 30, 2020
    Copyright © 2020 American Chemical Society
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    Abstract

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    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.

    Copyright © 2020 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00409.

    • Supporting Table S1: A list of ABE-related methods for the enrichment of S-acylated proteins; Supporting Table S2: A list of MLCC-related methods for the enrichment of S-acylated proteins; Supporting Table S3: A list of quantitative S-acylproteomics studies to identify S-acylated proteins and/or S-acylation sites; Supporting Table S4: A list of comparative S-acylproteomics studies; Supporting Table S5: A list of temporal S-acylproteomics studies; Supporting Table S6: A list of proteomic studies of S-acylation cross-talk with other post-translational modifications; Supporting Table S7: A list of proteomic studies of S-acylprotein complexes; Supporting Table S8: A list of human PAT-substrate pairs in the SwissPalm database (v3); Supporting Table S9: A list of mouse PAT-substrate pairs in the SwissPalm database (v3); Supporting Table S10: A list of human APT-substrate pairs in the SwissPalm database (v3); Supporting Table S11: A list of mouse APT-substrate pairs in the SwissPalm database (v3); Supporting Table S12: A list of proteomic studies of PAT/APT substrates; Supporting Table S13: A list of proteomic studies of PAT/APT-binding partners; Supporting Table S14: A list of proteomic studies of the off-targets of PAT/APT inhibitors (XLSX)

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    This article is cited by 28 publications.

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    2. Michael T. Forrester, Jacob R. Egol, Aleksandra Tata, Purushothama Rao Tata, Matthew W. Foster. Analysis of Protein Cysteine Acylation Using a Modified Suspension Trap (Acyl-Trap). Journal of Proteome Research 2024, 23 (8) , 3716-3725. https://doi.org/10.1021/acs.jproteome.4c00225
    3. Jian Cai, Ming Song, Ming Li, Michael Merchant, Frederick Benz, Craig McClain, Jon Klein. Site-Specific Identification of Protein S-Acylation by IodoTMT0 Labeling and Immobilized Anti-TMT Antibody Resin Enrichment. Journal of Proteome Research 2024, 23 (2) , 673-683. https://doi.org/10.1021/acs.jproteome.3c00525
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    8. Dan Cao, Wenxuan Sun, Xinyi Li, Lian Jian, Xinran Zhou, Ann M. Bode, Xiangjian Luo. The role of novel protein acylations in cancer. European Journal of Pharmacology 2024, 979 , 176841. https://doi.org/10.1016/j.ejphar.2024.176841
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    17. Francisco S. Mesquita, Laurence Abrami, Arthur Samurkas, F. Gisou van der Goot. S‐acylation: an orchestrator of the life cycle and function of membrane proteins. The FEBS Journal 2024, 291 (1) , 45-56. https://doi.org/10.1111/febs.16972
    18. Oliver Quinn, Manoj Kumar, Simon Turner. The role of lipid-modified proteins in cell wall synthesis and signaling. Plant Physiology 2023, 194 (1) , 51-66. https://doi.org/10.1093/plphys/kiad491
    19. Zhaoli Chen, Xiaogang Bai, Xiangyang Li, Bingshan Zeng, Bing Hu. Selection of Reference Genes for Gene Expression Analysis in Acacia melanoxylon under Different Conditions. Forests 2023, 14 (11) , 2245. https://doi.org/10.3390/f14112245
    20. Jing Cai, Jun Cui, Liqiu Wang. S‐palmitoylation regulates innate immune signaling pathways: molecular mechanisms and targeted therapies. European Journal of Immunology 2023, 53 (10) https://doi.org/10.1002/eji.202350476
    21. Mingli Li, Leisi Zhang, Chun-Wei Chen. Diverse Roles of Protein Palmitoylation in Cancer Progression, Immunity, Stemness, and Beyond. Cells 2023, 12 (18) , 2209. https://doi.org/10.3390/cells12182209
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    23. Liqiu Wang, Jing Cai, Xin Zhao, Ling Ma, Ping Zeng, Lingli Zhou, Yukun Liu, Shuai Yang, Zhe Cai, Song Zhang, Liang Zhou, Jiahui Yang, Tao Liu, Shouheng Jin, Jun Cui. Palmitoylation prevents sustained inflammation by limiting NLRP3 inflammasome activation through chaperone-mediated autophagy. Molecular Cell 2023, 83 (2) , 281-297.e10. https://doi.org/10.1016/j.molcel.2022.12.002
    24. Yinghan Zhang, Yazhuo Hu, Zhitao Han, Yan Geng, Zheng Xia, Yongsheng Zhou, Zhenfu Wang, Yuanyuan Wang, Eryan Kong, Xiaoning Wang, Jianjun Jia, Honghong Zhang, . Cattle Encephalon Glycoside and Ignotin Ameliorate Palmitoylation of PSD-95 and Enhance Expression of Synaptic Proteins in the Frontal Cortex of a APPswe/PS1dE9 Mouse Model of Alzheimer’s Disease. Journal of Alzheimer's Disease 2022, 88 (1) , 141-154. https://doi.org/10.3233/JAD-220009
    25. Marc-Antoine Millette, Sarah Roy, Christian Salesse. Farnesylation and lipid unsaturation are critical for the membrane binding of the C-terminal segment of G-Protein Receptor Kinase 1. Colloids and Surfaces B: Biointerfaces 2022, 211 , 112315. https://doi.org/10.1016/j.colsurfb.2021.112315
    26. Jeroen Guns, Sam Vanherle, Jerome J. A. Hendriks, Jeroen F. J. Bogie. Protein Lipidation by Palmitate Controls Macrophage Function. Cells 2022, 11 (3) , 565. https://doi.org/10.3390/cells11030565
    27. Yiwu Yan, Su Yeon Yeon, Chen Qian, Sungyong You, Wei Yang. On the Road to Accurate Protein Biomarkers in Prostate Cancer Diagnosis and Prognosis: Current Status and Future Advances. International Journal of Molecular Sciences 2021, 22 (24) , 13537. https://doi.org/10.3390/ijms222413537
    28. Jessica J. Chen, Ying Fan, Darren Boehning. Regulation of Dynamic Protein S-Acylation. Frontiers in Molecular Biosciences 2021, 8 https://doi.org/10.3389/fmolb.2021.656440
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    Journal of Proteome Research

    Cite this: J. Proteome Res. 2021, 20, 1, 14–26
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jproteome.0c00409
    Published November 30, 2020
    Copyright © 2020 American Chemical Society
    Request reuse permissions

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