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Abstract
S-palmitoylation is a reversible posttranslational lipid modification of proteins. It controls protein activity, stability, trafficking and protein–protein interactions. Recent global profiling of immune cells and targeted analysis have identified many S-palmitoylated immunity-associated proteins. Here, we review S-palmitoylated immune receptors and effectors, and their dynamic regulation at cellular membranes to generate specific and balanced immune responses. We also highlight how this understanding can drive therapeutic advances to pharmacologically modulate immune responses.
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Affiliation(s)
- Tandrila Das
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA
| | - Jacob S Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Howard C Hang
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, NY 10065, USA.,Departments of Immunology and Microbiology, Chemistry, Scripps Research, La Jolla, CA 92037, USA
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52
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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: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/01/2021] [Accepted: 02/22/2021] [Indexed: 12/11/2022]
Abstract
The lipid post-translational modification S-palmitoylation is a vast developing field, with the modification itself and the enzymes that catalyse the reversible reaction implicated in a number of diseases. In this review, we discuss the past and recent advances in the experimental tools used in this field, including pharmacological tools, animal models and techniques to understand how palmitoylation controls protein localisation and function. Additionally, we discuss the obstacles to overcome in order to advance the field, particularly to the point at which modulating palmitoylation may be achieved as a therapeutic strategy.
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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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53
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Li S, Yu K, Wu G, Zhang Q, Wang P, Zheng J, Liu ZX, Wang J, Gao X, Cheng H. pCysMod: Prediction of Multiple Cysteine Modifications Based on Deep Learning Framework. Front Cell Dev Biol 2021; 9:617366. [PMID: 33732693 PMCID: PMC7959776 DOI: 10.3389/fcell.2021.617366] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
Abstract
Thiol groups on cysteines can undergo multiple post-translational modifications (PTMs), acting as a molecular switch to maintain redox homeostasis and regulating a series of cell signaling transductions. Identification of sophistical protein cysteine modifications is crucial for dissecting its underlying regulatory mechanism. Instead of a time-consuming and labor-intensive experimental method, various computational methods have attracted intense research interest due to their convenience and low cost. Here, we developed the first comprehensive deep learning based tool pCysMod for multiple protein cysteine modification prediction, including S-nitrosylation, S-palmitoylation, S-sulfenylation, S-sulfhydration, and S-sulfinylation. Experimentally verified cysteine sites curated from literature and sites collected by other databases and predicting tools were integrated as benchmark dataset. Several protein sequence features were extracted and united into a deep learning model, and the hyperparameters were optimized by particle swarm optimization algorithms. Cross-validations indicated our model showed excellent robustness and outperformed existing tools, which was able to achieve an average AUC of 0.793, 0.807, 0.796, 0.793, and 0.876 for S-nitrosylation, S-palmitoylation, S-sulfenylation, S-sulfhydration, and S-sulfinylation, demonstrating pCysMod was stable and suitable for protein cysteine modification prediction. Besides, we constructed a comprehensive protein cysteine modification prediction web server based on this model to benefit the researches finding the potential modification sites of their interested proteins, which could be accessed at http://pcysmod.omicsbio.info. This work will undoubtedly greatly promote the study of protein cysteine modification and contribute to clarifying the biological regulation mechanisms of cysteine modification within and among the cells.
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Affiliation(s)
- Shihua Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Kai Yu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guandi Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Panqin Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Jian Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jichao Wang
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xinjiao Gao
- MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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54
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Battu A, Purushotham R, Dey P, Vamshi SS, Kaur R. An aspartyl protease-mediated cleavage regulates structure and function of a flavodoxin-like protein and aids oxidative stress survival. PLoS Pathog 2021; 17:e1009355. [PMID: 33630938 PMCID: PMC7943015 DOI: 10.1371/journal.ppat.1009355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/09/2021] [Accepted: 02/02/2021] [Indexed: 11/30/2022] Open
Abstract
A family of eleven glycosylphosphatidylinositol-anchored aspartyl proteases, commonly referred to as CgYapsins, regulate a myriad of cellular processes in the pathogenic yeast Candida glabrata, but their protein targets are largely unknown. Here, using the immunoprecipitation-mass spectrometry approach, we identify the flavodoxin-like protein (Fld-LP), CgPst2, to be an interactor of one of the aspartyl protease CgYps1. We also report the presence of four Fld-LPs in C. glabrata, which are required for survival in kidneys in the murine model of systemic candidiasis. We further demonstrated that of four Fld-LPs, CgPst2 was solely required for menadione detoxification. CgPst2 was found to form homo-oligomers, and contribute to cellular NADH:quinone oxidoreductase activity. CgYps1 cleaved CgPst2 at the C-terminus, and this cleavage was pivotal to oligomerization, activity and function of CgPst2. The arginine-174 residue in CgPst2 was essential for CgYps1-mediated cleavage, with alanine substitution of the arginine-174 residue also leading to elevated activity and oligomerization of CgPst2. Finally, we demonstrate that menadione treatment led to increased CgPst2 and CgYps1 protein levels, diminished CgYps1-CgPst2 interaction, and enhanced CgPst2 cleavage and activity, thereby implicating CgYps1 in activating CgPst2. Altogether, our findings of proteolytic cleavage as a key regulatory determinant of CgPst2, which belongs to the family of highly conserved, electron-carrier flavodoxin-fold-containing proteins, constituting cellular oxidative stress defense system in diverse organisms, unveil a hidden regulatory layer of environmental stress response mechanisms.
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Affiliation(s)
- Anamika Battu
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate studies, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Rajaram Purushotham
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Partha Dey
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - S. Surya Vamshi
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Rupinder Kaur
- Laboratory of Fungal Pathogenesis, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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55
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Woodley KT, Collins MO. Regulation and function of the palmitoyl-acyltransferase ZDHHC5. FEBS J 2021; 288:6623-6634. [PMID: 33415776 DOI: 10.1111/febs.15709] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/19/2020] [Accepted: 01/06/2021] [Indexed: 01/22/2023]
Abstract
Protein palmitoylation (S-acylation) has emerged as an important player in a range of cellular processes, and as a result, the palmitoyl-acyltransferase (PAT) enzymes which mediate this modification have entered into the spotlight. Palmitoyltransferase ZDHHC5 (ZDHHC5) is among the more unique members of the PAT family as it is mainly localised to the plasma membrane and contains an extended cytoplasmic domain with several regulatory features. ZDHHC5 plays a vital role in a wide range of processes in different cell types. In this review, we offer a summary of the functions of ZDHHC5 in synaptic plasticity, cardiac function, cell adhesion and fatty acid uptake, among other processes. We also explore recent work has revealed several mechanisms to control the activity, localisation and function of ZDHHC5.
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Affiliation(s)
- Keith T Woodley
- Department of Biomedical Science & Centre for Membrane Interactions and Dynamics (CMIAD), Firth Court, Western Bank, University of Sheffield, UK.,Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, UK
| | - Mark O Collins
- Department of Biomedical Science & Centre for Membrane Interactions and Dynamics (CMIAD), Firth Court, Western Bank, University of Sheffield, UK
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56
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Wang P, Zhang Q, Li S, Cheng B, Xue H, Wei Z, Shao T, Liu ZX, Cheng H, Wang Z. iCysMod: an integrative database for protein cysteine modifications in eukaryotes. Brief Bioinform 2021; 22:6066620. [PMID: 33406221 DOI: 10.1093/bib/bbaa400] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 01/06/2023] Open
Abstract
As important post-translational modifications, protein cysteine modifications (PCMs) occurring at cysteine thiol group play critical roles in the regulation of various biological processes in eukaryotes. Due to the rapid advancement of high-throughput proteomics technologies, a large number of PCM events have been identified but remain to be curated. Thus, an integrated resource of eukaryotic PCMs will be useful for the research community. In this work, we developed an integrative database for protein cysteine modifications in eukaryotes (iCysMod), which curated and hosted 108 030 PCM events for 85 747 experimentally identified sites on 31 483 proteins from 48 eukaryotes for 8 types of PCMs, including oxidation, S-nitrosylation (-SNO), S-glutathionylation (-SSG), disulfide formation (-SSR), S-sulfhydration (-SSH), S-sulfenylation (-SOH), S-sulfinylation (-SO2H) and S-palmitoylation (-S-palm). Then, browse and search options were provided for accessing the dataset, while various detailed information about the PCM events was well organized for visualization. With human dataset in iCysMod, the sequence features around the cysteine modification sites for each PCM type were analyzed, and the results indicated that various types of PCMs presented distinct sequence recognition preferences. Moreover, different PCMs can crosstalk with each other to synergistically orchestrate specific biological processes, and 37 841 PCM events involved in 119 types of PCM co-occurrences at the same cysteine residues were finally obtained. Taken together, we anticipate that the database of iCysMod would provide a useful resource for eukaryotic PCMs to facilitate related researches, while the online service is freely available at http://icysmod.omicsbio.info.
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Affiliation(s)
- Panqin Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Qingfeng Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shihua Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ben Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Han Xue
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhen Wei
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Tian Shao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Ze-Xian Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Han Cheng
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
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57
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Tewari R, Shayahati B, Fan Y, Akimzhanov AM. T cell receptor-dependent S-acylation of ZAP-70 controls activation of T cells. J Biol Chem 2021; 296:100311. [PMID: 33482200 PMCID: PMC7949058 DOI: 10.1016/j.jbc.2021.100311] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/21/2020] [Accepted: 01/14/2021] [Indexed: 02/06/2023] Open
Abstract
ZAP-70 is a tyrosine kinase essential for T cell immune responses. Upon engagement of the T cell receptor (TCR), ZAP-70 is recruited to the specialized plasma membrane domains, becomes activated, and is released to phosphorylate its laterally segregated targets. A shift in ZAP-70 distribution at the plasma membrane is recognized as a critical step in TCR signal transduction and amplification. However, the molecular mechanism supporting stimulation-dependent plasma membrane compartmentalization of ZAP-70 remains poorly understood. In this study, we identified previously uncharacterized lipidation (S-acylation) of ZAP-70 using Acyl-Biotin Exchange assay, a technique that selectively captures S-acylated proteins. We found that this posttranslational modification of ZAP-70 is dispensable for its enzymatic activity. However, the lipidation-deficient mutant of ZAP-70 failed to propagate the TCR pathway suggesting that S-acylation is essential for ZAP-70 interaction with its protein substrates. The kinetics of ZAP-70 S-acylation were consistent with TCR signaling events indicating that agonist-induced S-acylation is a part of the signaling mechanism controlling T cell activation and function. Taken together, our results suggest that TCR-induced S-acylation of ZAP-70 can serve as a critical regulator of T cell-mediated immunity.
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Affiliation(s)
- Ritika Tewari
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Bieerkehazhi Shayahati
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Ying Fan
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA; Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, USA
| | - Askar M Akimzhanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA.
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58
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Patwardhan A, Cheng N, Trejo J. Post-Translational Modifications of G Protein-Coupled Receptors Control Cellular Signaling Dynamics in Space and Time. Pharmacol Rev 2021; 73:120-151. [PMID: 33268549 PMCID: PMC7736832 DOI: 10.1124/pharmrev.120.000082] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are a large family comprising >800 signaling receptors that regulate numerous cellular and physiologic responses. GPCRs have been implicated in numerous diseases and represent the largest class of drug targets. Although advances in GPCR structure and pharmacology have improved drug discovery, the regulation of GPCR function by diverse post-translational modifications (PTMs) has received minimal attention. Over 200 PTMs are known to exist in mammalian cells, yet only a few have been reported for GPCRs. Early studies revealed phosphorylation as a major regulator of GPCR signaling, whereas later reports implicated a function for ubiquitination, glycosylation, and palmitoylation in GPCR biology. Although our knowledge of GPCR phosphorylation is extensive, our knowledge of the modifying enzymes, regulation, and function of other GPCR PTMs is limited. In this review we provide a comprehensive overview of GPCR post-translational modifications with a greater focus on new discoveries. We discuss the subcellular location and regulatory mechanisms that control post-translational modifications of GPCRs. The functional implications of newly discovered GPCR PTMs on receptor folding, biosynthesis, endocytic trafficking, dimerization, compartmentalized signaling, and biased signaling are also provided. Methods to detect and study GPCR PTMs as well as PTM crosstalk are further highlighted. Finally, we conclude with a discussion of the implications of GPCR PTMs in human disease and their importance for drug discovery. SIGNIFICANCE STATEMENT: Post-translational modification of G protein-coupled receptors (GPCRs) controls all aspects of receptor function; however, the detection and study of diverse types of GPCR modifications are limited. A thorough understanding of the role and mechanisms by which diverse post-translational modifications regulate GPCR signaling and trafficking is essential for understanding dysregulated mechanisms in disease and for improving and refining drug development for GPCRs.
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Affiliation(s)
- Anand Patwardhan
- Department of Pharmacology and the Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California
| | - Norton Cheng
- Department of Pharmacology and the Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California
| | - JoAnn Trejo
- Department of Pharmacology and the Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California
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59
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Zhang J, Peng Q, Zhao W, Sun W, Yang J, Liu N. Proteomics in Influenza Research: The Emerging Role of Posttranslational Modifications. J Proteome Res 2020; 20:110-121. [PMID: 33348980 DOI: 10.1021/acs.jproteome.0c00778] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Influenza viruses continue evolving and have the ability to cause a global pandemic, so it is very important to elucidate its pathogenesis and find new treatment methods. In recent years, proteomics has made important contributions to describing the dynamic interaction between influenza viruses and their hosts, especially in posttranslational regulation of a variety of key biological processes. Protein posttranslational modifications (PTMs) increase the diversity of functionality of the organismal proteome and affect almost all aspects of pathogen biology, primarily by regulating the structure, function, and localization of the modified proteins. Considerable technical achievements in mass spectrometry-based proteomics have been made in a large number of proteome-wide surveys of PTMs in many different organisms. Herein we specifically focus on the proteomic studies regarding a variety of PTMs that occur in both the influenza viruses, mainly influenza A viruses (IAVs), and their hosts, including phosphorylation, ubiquitination and ubiquitin-like modification, glycosylation, methylation, acetylation, and some types of acylation. Integration of these data sets provides a unique scenery of the global regulation and interplay of different PTMs during the interaction between IAVs and their hosts. Various techniques used to globally profiling these PTMs, mostly MS-based approaches, are discussed regarding their increasing roles in mechanical regulation of interaction between influenza viruses and their hosts.
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Affiliation(s)
- Jinming Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Qisheng Peng
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Weizheng Zhao
- Clinical Medical College, Jilin University, Changchun 130021, PR China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Jingbo Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Central Laboratory, Jilin University Second Hospital, Jilin University, Changchun 130062, PR China
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60
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Leyland B, Zarka A, Didi-Cohen S, Boussiba S, Khozin-Goldberg I. High Resolution Proteome of Lipid Droplets Isolated from the Pennate Diatom Phaeodactylum tricornutum (Bacillariophyceae) Strain pt4 provides mechanistic insights into complex intracellular coordination during nitrogen deprivation. JOURNAL OF PHYCOLOGY 2020; 56:1642-1663. [PMID: 32779202 DOI: 10.1111/jpy.13063] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 05/14/2020] [Accepted: 07/12/2020] [Indexed: 05/08/2023]
Abstract
Lipid droplets (LDs) are an organelle conserved amongst all eukaryotes, consisting of a neutral lipid core surrounded by a polar lipid monolayer. Many species of microalgae accumulate LDs in response to stress conditions, such as nitrogen starvation. Here, we report the isolation and proteomic profiling of LD proteins from the model oleaginous pennate diatom Phaeodactylum tricornutum, strain Pt4 (UTEX 646). We also provide a quantitative description of LD morphological ontogeny, and fatty acid content. Novel cell disruption and LD isolation methods, combined with suspension-trapping and nanoflow liquid chromatography coupled to high resolution mass spectrometry, yielded an unprecedented number of LD proteins. Predictive annotation of the LD proteome suggests a broad assemblage of proteins with diverse functions, including lipid metabolism and vesicle trafficking, as well as ribosomal and proteasomal machinery. These proteins provide mechanistic insights into LD processes, and evidence for interactions between LDs and other organelles. We identify for the first time several key steps in diatom LD-associated triacylglycerol biosynthesis. Bioinformatic analyses of the LD proteome suggests multiple protein targeting mechanisms, including amphipathic helices, post-translational modifications, and translocation machinery. This work corroborates recent findings from other strains of P. tricornutum, other diatoms, and other eukaryotic organisms, suggesting that the fundamental proteins orchestrating LDs are conserved, and represent an ancient component of the eukaryotic endomembrane system. We postulate a comprehensive model of nitrogen starvation-induced diatom LDs on a molecular scale, and provide a wealth of candidates for metabolic engineering, with the potential to eventually customize LD contents.
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Affiliation(s)
- Ben Leyland
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus, Be'er Sheva, 84990, Israel
| | - Aliza Zarka
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus, Be'er Sheva, 84990, Israel
| | - Shoshana Didi-Cohen
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus, Be'er Sheva, 84990, Israel
| | - Sammy Boussiba
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus, Be'er Sheva, 84990, Israel
| | - Inna Khozin-Goldberg
- The Microalgal Biotechnology Laboratory, The French Associates Institute for Agriculture and Biotechnology, Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boker Campus, Be'er Sheva, 84990, Israel
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61
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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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62
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Salaun C, Locatelli C, Zmuda F, Cabrera González J, Chamberlain LH. Accessory proteins of the zDHHC family of S-acylation enzymes. J Cell Sci 2020; 133:133/22/jcs251819. [PMID: 33203738 DOI: 10.1242/jcs.251819] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Almost two decades have passed since seminal work in Saccharomyces cerevisiae identified zinc finger DHHC domain-containing (zDHHC) enzymes as S-acyltransferases. These enzymes are ubiquitous in the eukarya domain, with 23 distinct zDHHC-encoding genes in the human genome. zDHHC enzymes mediate the bulk of S-acylation (also known as palmitoylation) reactions in cells, transferring acyl chains to cysteine thiolates, and in so-doing affecting the stability, localisation and function of several thousand proteins. Studies using purified components have shown that the minimal requirements for S-acylation are an appropriate zDHHC enzyme-substrate pair and fatty acyl-CoA. However, additional proteins including GCP16 (also known as Golga7), Golga7b, huntingtin and selenoprotein K, have been suggested to regulate the activity, stability and trafficking of certain zDHHC enzymes. In this Review, we discuss the role of these accessory proteins as essential components of the cellular S-acylation system.
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Affiliation(s)
- Christine Salaun
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Carolina Locatelli
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Filip Zmuda
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
| | - Juan Cabrera González
- Fac. de Ciencias Químicas, Universidad Complutense, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, UK
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63
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Yi L, Zheng C. The emerging roles of ZDHHCs-mediated protein palmitoylation in the antiviral innate immune responses. Crit Rev Microbiol 2020; 47:34-43. [PMID: 33100085 DOI: 10.1080/1040841x.2020.1835821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Post-translational modifications (PTMs) play a pivotal role in expanding functional protein diversity. During viral infection, pathogen-associated molecular patterns derived from viruses are recognized by pattern recognition receptors present in the membrane surface and the cytoplasm of infected cells, which subsequently induces the antiviral innate immunity to protect the host from the invading viruses. Fatty acylation modification is identified as a post-translation lipid modification process. Mounting evidence is presented that lipid modification functions as a novel regulatory mechanism of antiviral innate immunity. In mammalian cells, DHHC (Asp-His-His-Cys) domain is indispensable for most of the palmitoylation modification, which belongs to fatty acylation. ZDHHC family proteins are composed of 23 members in human cells. In this review, we will summarize the recent findings of the regulatory mechanism of the palmitoylation in the process of host antiviral innate immunity against viruses.
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Affiliation(s)
- Li Yi
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
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64
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Li Y, Wang S, Chen Y, Li M, Dong X, Hang HC, Peng T. Site-specific chemical fatty-acylation for gain-of-function analysis of protein S-palmitoylation in live cells. Chem Commun (Camb) 2020; 56:13880-13883. [PMID: 33094750 DOI: 10.1039/d0cc06073a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein S-palmitoylation, or S-fatty-acylation, regulates many fundamental cellular processes in eukaryotes. Herein, we present a chemical fatty-acylation approach that involves site-specific incorporation of cycloalkyne-containing unnatural amino acids and subsequent bioorthogonal reactions with fatty-acyl tetrazines to install fatty-acylation mimics at target protein sites, allowing gain-of-function analysis of S-palmitoylation in live cells.
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Affiliation(s)
- Yumeng Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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65
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Kesidis A, Depping P, Lodé A, Vaitsopoulou A, Bill RM, Goddard AD, Rothnie AJ. Expression of eukaryotic membrane proteins in eukaryotic and prokaryotic hosts. Methods 2020; 180:3-18. [DOI: 10.1016/j.ymeth.2020.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/05/2020] [Accepted: 06/08/2020] [Indexed: 12/15/2022] Open
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66
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Plain F, Howie J, Kennedy J, Brown E, Shattock MJ, Fraser NJ, Fuller W. Control of protein palmitoylation by regulating substrate recruitment to a zDHHC-protein acyltransferase. Commun Biol 2020; 3:411. [PMID: 32737405 PMCID: PMC7395175 DOI: 10.1038/s42003-020-01145-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/15/2020] [Indexed: 12/18/2022] Open
Abstract
Although palmitoylation regulates numerous cellular processes, as yet efforts to manipulate this post-translational modification for therapeutic gain have proved unsuccessful. The Na-pump accessory sub-unit phospholemman (PLM) is palmitoylated by zDHHC5. Here, we show that PLM palmitoylation is facilitated by recruitment of the Na-pump α sub-unit to a specific site on zDHHC5 that contains a juxtamembrane amphipathic helix. Site-specific palmitoylation and GlcNAcylation of this helix increased binding between the Na-pump and zDHHC5, promoting PLM palmitoylation. In contrast, disruption of the zDHHC5-Na-pump interaction with a cell penetrating peptide reduced PLM palmitoylation. Our results suggest that by manipulating the recruitment of specific substrates to particular zDHHC-palmitoyl acyl transferases, the palmitoylation status of individual proteins can be selectively altered, thus opening the door to the development of molecular modulators of protein palmitoylation for the treatment of disease.
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Affiliation(s)
- Fiona Plain
- School of Medicine, University of Dundee, Dundee, UK
| | - Jacqueline Howie
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Jennifer Kennedy
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Elaine Brown
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Michael J Shattock
- Cardiovascular Division, The Rayne Institute, King's College London, London, UK
| | | | - William Fuller
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
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Platelets in Healthy and Disease States: From Biomarkers Discovery to Drug Targets Identification by Proteomics. Int J Mol Sci 2020; 21:ijms21124541. [PMID: 32630608 PMCID: PMC7352998 DOI: 10.3390/ijms21124541] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/15/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Platelets are a heterogeneous small anucleate blood cell population with a central role both in physiological haemostasis and in pathological states, spanning from thrombosis to inflammation, and cancer. Recent advances in proteomic studies provided additional important information concerning the platelet biology and the response of platelets to several pathophysiological pathways. Platelets circulate systemically and can be easily isolated from human samples, making proteomic application very interesting for characterizing the complexity of platelet functions in health and disease as well as for identifying and quantifying potential platelet proteins as biomarkers and novel antiplatelet therapeutic targets. To date, the highly dynamic protein content of platelets has been studied in resting and activated platelets, and several subproteomes have been characterized including platelet-derived microparticles, platelet granules, platelet releasates, platelet membrane proteins, and specific platelet post-translational modifications. In this review, a critical overview is provided on principal platelet proteomic studies focused on platelet biology from signaling to granules content, platelet proteome changes in several diseases, and the impact of drugs on platelet functions. Moreover, recent advances in quantitative platelet proteomics are discussed, emphasizing the importance of targeted quantification methods for more precise, robust and accurate quantification of selected proteins, which might be used as biomarkers for disease diagnosis, prognosis and therapy, and their strong clinical impact in the near future.
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68
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Stix R, Lee CJ, Faraldo-Gómez JD, Banerjee A. Structure and Mechanism of DHHC Protein Acyltransferases. J Mol Biol 2020; 432:4983-4998. [PMID: 32522557 DOI: 10.1016/j.jmb.2020.05.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 01/01/2023]
Abstract
S-acylation, whereby a fatty acid chain is covalently linked to a cysteine residue by a thioester linkage, is the most prevalent kind of lipid modification of proteins. Thousands of proteins are targets of this post-translational modification, which is catalyzed by a family of eukaryotic integral membrane enzymes known as DHHC protein acyltransferases (DHHC-PATs). Our knowledge of the repertoire of S-acylated proteins has been rapidly expanding owing to development of the chemoproteomic techniques. There has also been an increasing number of reports in the literature documenting the importance of S-acylation in human physiology and disease. Recently, the first atomic structures of two different DHHC-PATs were determined using X-ray crystallography. This review will focus on the insights gained into the molecular mechanism of DHHC-PATs from these structures and highlight representative data from the biochemical literature that they help explain.
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Affiliation(s)
- Robyn Stix
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chul-Jin Lee
- Unit on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - José D Faraldo-Gómez
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anirban Banerjee
- Unit on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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69
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Reina S, Pittalà MGG, Guarino F, Messina A, De Pinto V, Foti S, Saletti R. Cysteine Oxidations in Mitochondrial Membrane Proteins: The Case of VDAC Isoforms in Mammals. Front Cell Dev Biol 2020; 8:397. [PMID: 32582695 PMCID: PMC7287182 DOI: 10.3389/fcell.2020.00397] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 04/29/2020] [Indexed: 12/16/2022] Open
Abstract
Cysteine residues are reactive amino acids that can undergo several modifications driven by redox reagents. Mitochondria are the source of an abundant production of radical species, and it is surprising that such a large availability of highly reactive chemicals is compatible with viable and active organelles, needed for the cell functions. In this work, we review the results highlighting the modifications of cysteines in the most abundant proteins of the outer mitochondrial membrane (OMM), that is, the voltage-dependent anion selective channel (VDAC) isoforms. This interesting protein family carries several cysteines exposed to the oxidative intermembrane space (IMS). Through mass spectrometry (MS) analysis, cysteine posttranslational modifications (PTMs) were precisely determined, and it was discovered that such cysteines can be subject to several oxidization degrees, ranging from the disulfide bridge to the most oxidized, the sulfonic acid, one. The large spectra of VDAC cysteine oxidations, which is unique for OMM proteins, indicate that they have both a regulative function and a buffering capacity able to counteract excess of mitochondrial reactive oxygen species (ROS) load. The consequence of these peculiar cysteine PTMs is discussed.
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Affiliation(s)
- Simona Reina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Maria Gaetana Giovanna Pittalà
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Francesca Guarino
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Angela Messina
- Section of Molecular Biology, Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Salvatore Foti
- Organic Mass Spectrometry Laboratory, Department of Chemical Sciences, University of Catania, Catania, Italy
| | - Rosaria Saletti
- Organic Mass Spectrometry Laboratory, Department of Chemical Sciences, University of Catania, Catania, Italy
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70
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Dogga SK, Frénal K. Two palmitoyl acyltransferases involved sequentially in the biogenesis of the inner membrane complex of Toxoplasma gondii. Cell Microbiol 2020; 22:e13212. [PMID: 32329212 DOI: 10.1111/cmi.13212] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 01/05/2023]
Abstract
The phylum Apicomplexa includes a number of significant human pathogens like Toxoplasma gondii and Plasmodium species. These obligate intracellular parasites possess a membranous structure, the inner membrane complex (IMC), composed of flattened vesicles apposed to the plasma membrane. Numerous proteins associated with the IMC are anchored via a lipid post-translational modification termed palmitoylation. This acylation is catalysed by multi-membrane spanning protein S-acyl-transferases (PATs) containing a catalytic Asp-His-His-Cys (DHHC) motif, commonly referred to as DHHCs. Contrasting the redundancy observed in other organisms, several PATs are essential for T. gondii tachyzoite survival; 2 of them, TgDHHC2 and TgDHHC14 being IMC-resident. Disruption of either of these TgDHHCs results in a rapid collapse of the IMC in the developing daughter cells leading to dramatic morphological defects of the parasites while the impact on the other organelles is limited to their localisation but not to their biogenesis. The acyl-transferase activity of TgDHHC2 and TgDHHC14 is involved sequentially in the formation of the sub-compartments of the IMC. Investigation of proteins known to be palmitoylated and localised to these sub-compartments identified TgISP1/3 as well as TgIAP1/2 to lose their membrane association revealing them as likely substrates of TgDHHC2, while these proteins are not impacted by TgDHHC14 depletion.
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Affiliation(s)
- Sunil Kumar Dogga
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karine Frénal
- Department of Microbiology and Molecular Medicine, CMU, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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71
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Philippe JM, Jenkins PM. Spatial organization of palmitoyl acyl transferases governs substrate localization and function. Mol Membr Biol 2020; 35:60-75. [PMID: 31969037 DOI: 10.1080/09687688.2019.1710274] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein palmitoylation is a critical posttranslational modification that regulates protein trafficking, localization, stability, sorting and function. In mammals, addition of this lipid modification onto proteins is mediated by a family of 23 palmitoyl acyl transferases (PATs). PATs often palmitoylate substrates in a promiscuous manner, precluding our understanding of how these enzymes achieve specificity for their substrates. Despite generous efforts to identify consensus motifs defining PAT-substrate specificity, it remains to be determined whether additional factors beyond interaction motifs, such as local palmitoylation, participate in PAT-substrate selection. In this review, we emphasize the role of local palmitoylation, in which substrates are palmitoylated and trapped in the same subcellular compartments as their PATs, as a mechanism of enzyme-substrate specificity. We focus here on non-Golgi-localized PATs, as physical proximity to their substrates enables them to engage in local palmitoylation, compared to Golgi PATs, which often direct trafficking of their substrates elsewhere. PAT subcellular localization may be an under-recognized, yet important determinant of PAT-substrate specificity that may work in conjunction or completely independently of interaction motifs. We also discuss some current hypotheses about protein motifs that contribute to localization of non-Golgi-localized PATs, important for the downstream targeting of their substrates.
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Affiliation(s)
- Julie M Philippe
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Paul M Jenkins
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA.,Department of Psychiatry, University of Michigan Medical School, Ann Arbor, MI, USA
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72
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Gundersen CB. Cysteine string proteins. Prog Neurobiol 2020; 188:101758. [DOI: 10.1016/j.pneurobio.2020.101758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/06/2020] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
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73
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Shirakawa R, Goto‐Ito S, Goto K, Wakayama S, Kubo H, Sakata N, Trinh DA, Yamagata A, Sato Y, Masumoto H, Cheng J, Fujimoto T, Fukai S, Horiuchi H. A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus. EMBO J 2020; 39:e104120. [PMID: 32128853 PMCID: PMC7156963 DOI: 10.15252/embj.2019104120] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/22/2020] [Accepted: 01/31/2020] [Indexed: 01/08/2023] Open
Abstract
Protein prenylation is essential for many cellular processes including signal transduction, cytoskeletal reorganization, and membrane trafficking. Here, we identify a novel type of protein prenyltransferase, which we named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of RabGGTase. Using a biotinylated geranylgeranyl analogue, we identified the Golgi SNARE protein Ykt6 as a substrate of GGTase-III. GGTase-III transfers a geranylgeranyl group to mono-farnesylated Ykt6, generating doubly prenylated Ykt6. The crystal structure of GGTase-III in complex with Ykt6 provides structural basis for Ykt6 double prenylation. In GGTase-III-deficient cells, Ykt6 remained in a singly prenylated form, and the Golgi SNARE complex assembly was severely impaired. Consequently, the Golgi apparatus was structurally disorganized, and intra-Golgi protein trafficking was delayed. Our findings reveal a fourth type of protein prenyltransferase that generates geranylgeranyl-farnesyl Ykt6. Double prenylation of Ykt6 is essential for the structural and functional organization of the Golgi apparatus.
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Affiliation(s)
- Ryutaro Shirakawa
- Department of Molecular and Cellular BiologyInstitute of Development, Aging and CancerTohoku UniversitySendaiJapan
| | - Sakurako Goto‐Ito
- Institute for Quantitative BiosciencesThe University of TokyoTokyoJapan
- Synchrotron Radiation Research OrganizationThe University of TokyoTokyoJapan
| | - Kota Goto
- Department of Molecular and Cellular BiologyInstitute of Development, Aging and CancerTohoku UniversitySendaiJapan
| | - Shonosuke Wakayama
- Department of Molecular and Cellular BiologyInstitute of Development, Aging and CancerTohoku UniversitySendaiJapan
| | - Haremaru Kubo
- Department of Molecular and Cellular BiologyInstitute of Development, Aging and CancerTohoku UniversitySendaiJapan
| | - Natsumi Sakata
- Department of Molecular and Cellular BiologyInstitute of Development, Aging and CancerTohoku UniversitySendaiJapan
| | - Duc Anh Trinh
- Department of Molecular and Cellular BiologyInstitute of Development, Aging and CancerTohoku UniversitySendaiJapan
| | - Atsushi Yamagata
- Institute for Quantitative BiosciencesThe University of TokyoTokyoJapan
- Synchrotron Radiation Research OrganizationThe University of TokyoTokyoJapan
| | - Yusuke Sato
- Institute for Quantitative BiosciencesThe University of TokyoTokyoJapan
- Synchrotron Radiation Research OrganizationThe University of TokyoTokyoJapan
- Present address:
Center for Research on Green Sustainable ChemistryTottori UniversityTottoriJapan
| | - Hiroshi Masumoto
- Biomedical Research Support CenterNagasaki University School of MedicineNagasakiJapan
| | - Jinglei Cheng
- Department of Anatomy and Molecular Cell BiologyNagoya University Graduate School of MedicineNagoyaJapan
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old AgeJuntendo University Graduate School of MedicineTokyoJapan
| | - Shuya Fukai
- Institute for Quantitative BiosciencesThe University of TokyoTokyoJapan
- Synchrotron Radiation Research OrganizationThe University of TokyoTokyoJapan
| | - Hisanori Horiuchi
- Department of Molecular and Cellular BiologyInstitute of Development, Aging and CancerTohoku UniversitySendaiJapan
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74
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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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75
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Ning W, Jiang P, Guo Y, Wang C, Tan X, Zhang W, Peng D, Xue Y. GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins. Brief Bioinform 2020; 22:1836-1847. [PMID: 32248222 DOI: 10.1093/bib/bbaa038] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/19/2020] [Accepted: 02/25/2020] [Indexed: 12/12/2022] Open
Abstract
As an important reversible lipid modification, S-palmitoylation mainly occurs at specific cysteine residues in proteins, participates in regulating various biological processes and is associated with human diseases. Besides experimental assays, computational prediction of S-palmitoylation sites can efficiently generate helpful candidates for further experimental consideration. Here, we reviewed the current progress in the development of S-palmitoylation site predictors, as well as training data sets, informative features and algorithms used in these tools. Then, we compiled a benchmark data set containing 3098 known S-palmitoylation sites identified from small- or large-scale experiments, and developed a new method named data quality discrimination (DQD) to distinguish data quality weights (DQWs) between the two types of the sites. Besides DQD and our previous methods, we encoded sequence similarity values into images, constructed a deep learning framework of convolutional neural networks (CNNs) and developed a novel algorithm of graphic presentation system (GPS) 6.0. We further integrated nine additional types of sequence-based and structural features, implemented parallel CNNs (pCNNs) and designed a new predictor called GPS-Palm. Compared with other existing tools, GPS-Palm showed a >31.3% improvement of the area under the curve (AUC) value (0.855 versus 0.651) for general prediction of S-palmitoylation sites. We also produced two species-specific predictors, with corresponding AUC values of 0.900 and 0.897 for predicting human- and mouse-specific sites, respectively. GPS-Palm is free for academic research at http://gpspalm.biocuckoo.cn/.
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Affiliation(s)
- Wanshan Ning
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Peiran Jiang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Yaping Guo
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Chenwei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Xiaodan Tan
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Weizhi Zhang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Di Peng
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, Ezhou 436044, China
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76
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Pan Y, Xiao Y, Pei Z, Cummins TR. S-Palmitoylation of the sodium channel Nav1.6 regulates its activity and neuronal excitability. J Biol Chem 2020; 295:6151-6164. [PMID: 32161114 DOI: 10.1074/jbc.ra119.012423] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/10/2020] [Indexed: 12/12/2022] Open
Abstract
S-Palmitoylation is a reversible post-translational lipid modification that dynamically regulates protein functions. Voltage-gated sodium channels are subjected to S-palmitoylation and exhibit altered functions in different S-palmitoylation states. Our aim was to investigate whether and how S-palmitoylation regulates Nav1.6 channel function and to identify S-palmitoylation sites that can potentially be pharmacologically targeted. Acyl-biotin exchange assay showed that Nav1.6 is modified by S-palmitoylation in the mouse brain and in a Nav1.6 stable HEK 293 cell line. Using whole-cell voltage clamp, we discovered that enhancing S-palmitoylation with palmitic acid increases Nav1.6 current, whereas blocking S-palmitoylation with 2-bromopalmitate reduces Nav1.6 current and shifts the steady-state inactivation in the hyperpolarizing direction. Three S-palmitoylation sites (Cys1169, Cys1170, and Cys1978) were identified. These sites differentially modulate distinct Nav1.6 properties. Interestingly, Cys1978 is exclusive to Nav1.6 among all Nav isoforms and is evolutionally conserved in Nav1.6 among most species. Cys1978 S-palmitoylation regulates current amplitude uniquely in Nav1.6. Furthermore, we showed that eliminating S-palmitoylation at specific sites alters Nav1.6-mediated excitability in dorsal root ganglion neurons. Therefore, our study reveals S-palmitoylation as a potential isoform-specific mechanism to modulate Nav activity and neuronal excitability in physiological and diseased conditions.
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Affiliation(s)
- Yanling Pan
- Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Yucheng Xiao
- Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202
| | - Zifan Pei
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202
| | - Theodore R Cummins
- Program in Medical Neuroscience, Paul and Carole Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, Indiana 46202; Department of Biology, School of Science, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, Indiana 46202.
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77
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Gadalla MR, Abrami L, van der Goot FG, Veit M. Hemagglutinin of Influenza A, but not of Influenza B and C viruses is acylated by ZDHHC2, 8, 15 and 20. Biochem J 2020; 477:285-303. [PMID: 31872235 DOI: 10.1042/bcj20190752] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/15/2019] [Accepted: 12/23/2019] [Indexed: 02/05/2023]
Abstract
Hemagglutinin (HA), a glycoprotein of Influenza A viruses and its proton channel M2 are site-specifically modified with fatty acids. Whereas two cysteines in the short cytoplasmic tail of HA contain only palmitate, stearate is exclusively attached to one cysteine located at the cytoplasmic border of the transmembrane region (TMR). M2 is palmitoylated at a cysteine positioned in an amphiphilic helix near the TMR. The enzymes catalyzing acylation of HA and M2 have not been identified, but zinc finger DHHC domain-containing (ZDHHC) palmitoyltransferases are candidates. We used a siRNA library to knockdown expression of each of the 23 human ZDHHCs in HA-expressing HeLa cells. siRNAs against ZDHHC2 and 8 had the strongest effect on acylation of HA as demonstrated by Acyl-RAC and confirmed by 3H-palmitate labeling. CRISPR/Cas9 knockout of ZDHHC2 and 8 in HAP1 cells, but also of the phylogenetically related ZDHHCs 15 and 20 strongly reduced acylation of group 1 and group 2 HAs and of M2, but individual ZDHHCs exhibit slightly different substrate preferences. These ZDHHCs co-localize with HA at membranes of the exocytic pathway in a human lung cell line. ZDHHC2, 8, 15 and 20 are not required for acylation of the HA-esterase-fusion protein of Influenza C virus that contains only stearate at one transmembrane cysteine. Knockout of these ZDHHCs also did not compromise acylation of HA of Influenza B virus that contains two palmitoylated cysteines in its cytoplasmic tail. Results are discussed with respect to the acyl preferences and possible substrate recognition features of the identified ZDHHCs.
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Affiliation(s)
- Mohamed Rasheed Gadalla
- Institute of Virology, Free University Berlin, 14163 Berlin, Germany
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
| | - Laurence Abrami
- Global Health Institute, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - F Gisou van der Goot
- Global Health Institute, Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michael Veit
- Institute of Virology, Free University Berlin, 14163 Berlin, Germany
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78
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Lu H, Fang C. Methodology for Detecting Protein Palmitoylation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1248:425-430. [PMID: 32185720 DOI: 10.1007/978-981-15-3266-5_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
It is well established that palmitoylation plays a key role in the regulation of immune checkpoints, but the technical challenges in detecting protein palmitoylation have significantly prohibited further researches in this field. Till now, different approaches have been proposed, such as mutagenesis, antibody-based methods, bioinformatic prediction, "palmitate-centric" approaches, and "cysteine-centric" approaches. Of specific importance, high-throughput methods that allow the unbiased discovery of palmitoylation in the whole proteome should be further improved and employed. This chapter will summarize the methodological progresses for detecting protein palmitoylation, aiming to facilitate future researches in the lipid modification of immune checkpoint proteins.
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Affiliation(s)
- Haojie Lu
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, China.
| | - Caiyun Fang
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200438, China
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79
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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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80
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A novel ER membrane protein Ehg1/May24 plays a critical role in maintaining multiple nutrient permeases in yeast under high-pressure perturbation. Sci Rep 2019; 9:18341. [PMID: 31797992 PMCID: PMC6892922 DOI: 10.1038/s41598-019-54925-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 11/19/2019] [Indexed: 12/24/2022] Open
Abstract
Previously, we isolated 84 deletion mutants in Saccharomyces cerevisiae auxotrophic background that exhibited hypersensitive growth under high hydrostatic pressure and/or low temperature. Here, we observed that 24 deletion mutants were rescued by the introduction of four plasmids (LEU2, HIS3, LYS2, and URA3) together to grow at 25 MPa, thereby suggesting close links between the genes and nutrient uptake. Most of the highly ranked genes were poorly characterized, including MAY24/YPR153W. May24 appeared to be localized in the endoplasmic reticulum (ER) membrane. Therefore, we designated this gene as EHG (ER-associated high-pressure growth gene) 1. Deletion of EHG1 led to reduced nutrient transport rates and decreases in the nutrient permease levels at 25 MPa. These results suggest that Ehg1 is required for the stability and functionality of the permeases under high pressure. Ehg1 physically interacted with nutrient permeases Hip1, Bap2, and Fur4; however, alanine substitutions for Pro17, Phe19, and Pro20, which were highly conserved among Ehg1 homologues in various yeast species, eliminated interactions with the permeases as well as the high-pressure growth ability. By functioning as a novel chaperone that facilitated coping with high-pressure-induced perturbations, Ehg1 could exert a stabilizing effect on nutrient permeases when they are present in the ER.
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81
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Sharma S, Ahmed M, Akhter Y. Fungal acetyltransferases structures, mechanisms and inhibitors: A review. Int J Biol Macromol 2019; 157:626-640. [PMID: 31786301 DOI: 10.1016/j.ijbiomac.2019.11.214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
Acetylation of proteins is vital and mediate many processes within the cells like protein interactions, intercellular localization, protein stability, transcriptional regulation, enzyme activity and many more. Acetylation, an evolutionarily conserved process, attracted more attention due to its key regulatory role in many cellular processes and its effect on proteome and metabolome. In eukaryotes, protein acetylation also contribute to the epigenetic regulation of gene expression. Acetylation involves the transfer of acetyl group from donor acetyl coenzyme A to a suitable acceptor molecule and the reaction is catalyzed by acetyltransferase enzymes. The review focuses on current understanding of different acetyltransferase families: their discovery, structure and catalytic mechanism in fungal species. Fungal acetyltransferases use divergent catalytic mechanisms and carry out catalysis in a substrate-specific manner. The studies have explored different fungal acetyltransferases in relation to secondary metabolite production and the fungal pathogenesis. Although, the functions and catalytic mechanism of acetyltransferases are well known, however further enhanced knowledge may improve their utilization in various applications of biotechnology.
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Affiliation(s)
- Shikha Sharma
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Mushtaq Ahmed
- School of Earth and Environmental Sciences, Central University of Himachal Pradesh, Shahpur, District-Kangra, Himachal Pradesh 176206, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, VidyaVihar, Raebareli Road, Lucknow, Uttar Pradesh 226025, India.
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82
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Sada R, Kimura H, Fukata Y, Fukata M, Yamamoto H, Kikuchi A. Dynamic palmitoylation controls the microdomain localization of the DKK1 receptors CKAP4 and LRP6. Sci Signal 2019; 12:12/608/eaat9519. [PMID: 31744930 DOI: 10.1126/scisignal.aat9519] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Dickkopf1 (DKK1) was originally identified as an antagonist of Wnt signaling that binds to and induces the clathrin-mediated endocytosis of the Wnt coreceptors low-density lipoprotein receptor-related proteins 5 and 6 (LRP5/6). DKK1 also binds to cytoskeleton-associated protein 4 (CKAP4), which was originally identified as an endoplasmic reticulum (ER) protein but also functions at the plasma membrane as a receptor for various ligands. The DKK1-CKAP4 pathway is activated in several human cancers and promotes cell proliferation by activating signaling through the kinases PI3K and AKT. We found that both CKAP4 and LRP6 primarily localized to detergent-resistant membrane (DRM) fractions of the plasma membrane in a palmitoylation-dependent manner and that palmitoylation of CKAP4 was required for it to promote cell proliferation. DKK1 induced the depalmitoylation of both CKAP4 and LRP6 by acylprotein thioesterases (APTs), resulting in their translocation to the non-DRM fractions. Moreover, DKK1-dependent depalmitoylation of both receptors required activation of the PI3K-AKT pathway. DKK1 simultaneously bound CKAP4 and LRP6, resulting in the formation of a ternary complex. LRP5/6 knockdown decreased DKK1-dependent AKT activation and cancer cell proliferation through CKAP4, whereas CKAP4 knockdown did not affect DKK1-dependent inhibition of Wnt signaling through LRP5/6. These results indicate that the palmitoylation states of CKAP4 and LRP6 play important roles in their signaling and that LRP5/6 enhance DKK1-CKAP4 signaling.
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Affiliation(s)
- Ryota Sada
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Hirokazu Kimura
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Yuko Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki 444-8787, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki 444-8787, Japan
| | - Masaki Fukata
- Division of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki 444-8787, Japan.,Department of Physiological Sciences, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki 444-8787, Japan
| | - Hideki Yamamoto
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Akira Kikuchi
- Department of Molecular Biology and Biochemistry, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan.
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83
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Kordyukova LV, Serebryakova MV, Khrustalev VV, Veit M. Differential S-Acylation of Enveloped Viruses. Protein Pept Lett 2019; 26:588-600. [PMID: 31161979 DOI: 10.2174/0929866526666190603082521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/11/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022]
Abstract
Post-translational modifications often regulate protein functioning. Covalent attachment of long chain fatty acids to cysteine residues via a thioester linkage (known as protein palmitoylation or S-acylation) affects protein trafficking, protein-protein and protein-membrane interactions. This post-translational modification is coupled to membrane fusion or virus assembly and may affect viral replication in vitro and thus also virus pathogenesis in vivo. In this review we outline modern methods to study S-acylation of viral proteins and to characterize palmitoylproteomes of virus infected cells. The palmitoylation site predictor CSS-palm is critically tested against the Class I enveloped virus proteins. We further focus on identifying the S-acylation sites directly within acyl-peptides and the specific fatty acid (e.g, palmitate, stearate) bound to them using MALDI-TOF MS-based approaches. The fatty acid heterogeneity/ selectivity issue attracts now more attention since the recently published 3D-structures of two DHHC-acyl-transferases gave a hint how this might be achieved.
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Affiliation(s)
- Larisa V Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Vladislav V Khrustalev
- Department of General Chemistry, Belarusian State Medical University, Minsk 220116, Belarus
| | - Michael Veit
- Institut für Virologie, Vet.-Med. Faculty, Free University Berlin, Berlin 14163, Germany
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84
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Abstract
We review the mechanisms responsible for amino acid homeostasis in Saccharomyces cerevisiae and other fungi. Amino acid homeostasis is essential for cell growth and survival. Hence, the de novo synthesis reactions, metabolic conversions, and transport of amino acids are tightly regulated. Regulation varies from nitrogen pool sensing to control by individual amino acids and takes place at the gene (transcription), protein (posttranslational modification and allostery), and vesicle (trafficking and endocytosis) levels. The pools of amino acids are controlled via import, export, and compartmentalization. In yeast, the majority of the amino acid transporters belong to the APC (amino acid-polyamine-organocation) superfamily, and the proteins couple the uphill transport of amino acids to the electrochemical proton gradient. Although high-resolution structures of yeast amino acid transporters are not available, homology models have been successfully exploited to determine and engineer the catalytic and regulatory functions of the proteins. This has led to a further understanding of the underlying mechanisms of amino acid sensing and subsequent downregulation of transport. Advances in optical microscopy have revealed a new level of regulation of yeast amino acid transporters, which involves membrane domain partitioning. The significance and the interrelationships of the latest discoveries on amino acid homeostasis are put in context.
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85
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Xiong X, Lee CF, Li W, Yu J, Zhu L, Kim Y, Zhang H, Sun H. Acid Sphingomyelinase regulates the localization and trafficking of palmitoylated proteins. Biol Open 2019; 8:bio.040311. [PMID: 31142470 PMCID: PMC6826292 DOI: 10.1242/bio.040311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In human, loss of acid sphingomyelinase (ASM/SMPD1) causes Niemann–Pick disease, type A. ASM hydrolyzes sphingomyelins to produce ceramides but protein targets of ASM remain largely unclear. Our mass spectrometry-based proteomic analyses have identified >100 proteins associated with the ASM-dependent, detergent-resistant membrane microdomains (lipid rafts), with >60% of these proteins being palmitoylated, including SNAP23, Src-family kinases Yes and Lyn, and Ras and Rab family small GTPases. Inactivation of ASM abolished the presence of these proteins in the plasma membrane, with many of them trapped in the Golgi. While palmitoylation inhibitors and palmitoylation mutants phenocopied the effects of ASM inactivation, we demonstrated that ASM is required for the transport of palmitoylated proteins, such as SNAP23 and Lyn, from the Golgi to the plasma membrane without affecting palmitoylation directly. Importantly, ASM delivered extracellularly can regulate the trafficking of SNAP23 from the Golgi to the plasma membrane. Our studies suggest that ASM, acting at the plasma membrane to produce ceramides, regulates the localization and trafficking of the palmitoylated proteins. Summary: Acid sphingomyelinase (ASM) regulates palmitoylated protein trafficking and localization.
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Affiliation(s)
- Xiahui Xiong
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154-4003, USA
| | - Chia-Fang Lee
- Protea Biosciences, 1311 Pineview drive, Morgantown, West Virginia, USA
| | - Wenjing Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154-4003, USA
| | - Jiekai Yu
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154-4003, USA
| | - Linyu Zhu
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154-4003, USA
| | - Yongsoon Kim
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154-4003, USA
| | - Hui Zhang
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154-4003, USA
| | - Hong Sun
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV 89154-4003, USA
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86
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Hurst CH, Wright KM, Turnbull D, Leslie K, Jones S, Hemsley PA. Juxta-membrane S-acylation of plant receptor-like kinases is likely fortuitous and does not necessarily impact upon function. Sci Rep 2019; 9:12818. [PMID: 31492958 PMCID: PMC6731221 DOI: 10.1038/s41598-019-49302-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/22/2019] [Indexed: 01/24/2023] Open
Abstract
S-acylation is a common post-translational modification of membrane protein cysteine residues with many regulatory roles. S-acylation adjacent to transmembrane domains has been described in the literature as affecting diverse protein properties including turnover, trafficking and microdomain partitioning. However, all of these data are derived from mammalian and yeast systems. Here we examine the role of S-acylation adjacent to the transmembrane domain of the plant pathogen perceiving receptor-like kinase FLS2. Surprisingly, S-acylation of FLS2 adjacent to the transmembrane domain is not required for either FLS2 trafficking or signalling function. Expanding this analysis to the wider plant receptor-like kinase family we find that S-acylation adjacent to receptor-like kinase domains is common, affecting ~25% of Arabidopsis receptor-like kinases, but poorly conserved between orthologues through evolution. This suggests that S-acylation of receptor-like kinases at this site is likely the result of chance mutation leading to cysteine occurrence. As transmembrane domains followed by cysteine residues are common motifs for S-acylation to occur, and many S-acyl transferases appear to have lax substrate specificity, we propose that many receptor-like kinases are fortuitously S-acylated once chance mutation has introduced a cysteine at this site. Interestingly some receptor-like kinases show conservation of S-acylation sites between orthologues suggesting that S-acylation has come to play a role and has been positively selected for during evolution. The most notable example of this is in the ERECTA-like family where S-acylation of ERECTA adjacent to the transmembrane domain occurs in all ERECTA orthologues but not in the parental ERECTA-like clade. This suggests that ERECTA S-acylation occurred when ERECTA emerged during the evolution of angiosperms and may have contributed to the neo-functionalisation of ERECTA from ERECTA-like proteins.
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Affiliation(s)
- Charlotte H Hurst
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK.,Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Kathryn M Wright
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Dionne Turnbull
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK
| | - Kerry Leslie
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK.,Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.,Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Susan Jones
- Information and Computer Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Piers A Hemsley
- Division of Plant Science, School of Life Science, University of Dundee (at JHI), Invergowrie, Dundee, DD2 5DA, UK. .,Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
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87
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Abstract
Over the past decade the number and variety of protein post-translational modifications that have been detected and characterized in bacteria have rapidly increased. Most post-translational protein modifications occur in a relatively low number of bacterial proteins in comparison with eukaryotic proteins, and most of the modified proteins carry low, substoichiometric levels of modification; therefore, their structural and functional analysis is particularly challenging. The number of modifying enzymes differs greatly among bacterial species, and the extent of the modified proteome strongly depends on environmental conditions. Nevertheless, evidence is rapidly accumulating that protein post-translational modifications have vital roles in various cellular processes such as protein synthesis and turnover, nitrogen metabolism, the cell cycle, dormancy, sporulation, spore germination, persistence and virulence. Further research of protein post-translational modifications will fill current gaps in the understanding of bacterial physiology and open new avenues for treatment of infectious diseases.
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88
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Chen JJ, Marsden AN, Scott CA, Akimzhanov AM, Boehning D. DHHC5 Mediates β-Adrenergic Signaling in Cardiomyocytes by Targeting Gα Proteins. Biophys J 2019; 118:826-835. [PMID: 31547976 PMCID: PMC7036738 DOI: 10.1016/j.bpj.2019.08.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023] Open
Abstract
S-palmitoylation is a reversible posttranslational modification that plays an important role in regulating protein localization, trafficking, and stability. Recent studies have shown that some proteins undergo extremely rapid palmitoylation/depalmitoylation cycles after cellular stimulation supporting a direct signaling role for this posttranslational modification. Here, we investigated whether β-adrenergic stimulation of cardiomyocytes led to stimulus-dependent palmitoylation of downstream signaling proteins. We found that β-adrenergic stimulation led to rapidly increased Gαs and Gαi palmitoylation. The kinetics of palmitoylation was temporally consistent with the downstream production of cAMP and contractile responses. We identified the plasma membrane-localized palmitoyl acyltransferase DHHC5 as an important mediator of the stimulus-dependent palmitoylation in cardiomyocytes. Knockdown of DHHC5 showed that this enzyme is necessary for palmitoylation of Gαs, Gαi, and functional responses downstream of β-adrenergic stimulation. A palmitoylation assay with purified components revealed that Gαs and Gαi are direct substrates of DHHC5. Finally, we provided evidence that the C-terminal tail of DHHC5 can be palmitoylated in response to stimulation and such modification is important for its dynamic localization and function in the plasma membrane. Our results reveal that DHHC5 is a central regulator of signaling downstream of β-adrenergic receptors in cardiomyocytes.
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Affiliation(s)
- Jessica J Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas
| | - Autumn N Marsden
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas
| | - C Anthony Scott
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Askar M Akimzhanov
- Department of Biochemistry and Molecular Biology, McGovern Medical School at UTHealth, Houston, Texas
| | - Darren Boehning
- Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, New Jersey.
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89
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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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90
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Werner N, Ramirez-Sarmiento CA, Agosin E. Protein engineering of carotenoid cleavage dioxygenases to optimize β-ionone biosynthesis in yeast cell factories. Food Chem 2019; 299:125089. [PMID: 31319343 DOI: 10.1016/j.foodchem.2019.125089] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 10/26/2022]
Abstract
Synthesis of β-ionone in recombinant Saccharomyces cerevisiae is limited by the efficiency of Carotenoid Cleavage Dioxygenases (CCD), membrane-tethered enzymes catalyzing the last step in the pathway. We performed in silico design and membrane affinity analysis, focused on single-point mutations of PhCCD1 to improve membrane anchoring. The resulting constructs were tested in a β-carotene hyper-producing strain by comparing colony pigmentation against colonies transformed with native PhCCD1 and further analyzed by β-ionone quantification via RP-HPLC. Two single-point mutants increased β-ionone yields almost 3-fold when compared to native PhCCD1. We also aimed to improve substrate accessibility of PhCCD1 through the amino-terminal addition of membrane destination peptides directed towards the endoplasmic reticulum or plasma membrane. Yeast strains expressing peptide-PhCCD1 constructs showed β-ionone yields up to 4-fold higher than the strain carrying the native enzyme. Our results demonstrate that protein engineering of CCDs significantly increases the yield of β-ionone synthesized by metabolically engineered yeast.
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Affiliation(s)
- Nicole Werner
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile.
| | - César A Ramirez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile.
| | - Eduardo Agosin
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile.
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91
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Abstract
Cell nutrition, detoxification, signalling, homeostasis and response to drugs, processes related to cell growth, differentiation and survival are all mediated by plasma membrane (PM) proteins called transporters. Despite their distinct fine structures, mechanism of function, energetic requirements, kinetics and substrate specificities, all transporters are characterized by a main hydrophobic body embedded in the PM as a series of tightly packed, often intertwined, α-helices that traverse the lipid bilayer in a zigzag mode, connected with intracellular or extracellular loops and hydrophilic N- and C-termini. Whereas longstanding genetic, biochemical and biophysical evidence suggests that specific transmembrane segments, and also their connecting loops, are responsible for substrate recognition and transport dynamics, emerging evidence also reveals the functional importance of transporter N- and C-termini, in respect to transport catalysis, substrate specificity, subcellular expression, stability and signalling. This review highlights selected prototypic examples of transporters in which their termini play important roles in their functioning.
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Affiliation(s)
- Emmanuel Mikros
- Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis, 15771 Athens, Greece
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
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92
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Ernst AM, Toomre D, Bogan JS. Acylation - A New Means to Control Traffic Through the Golgi. Front Cell Dev Biol 2019; 7:109. [PMID: 31245373 PMCID: PMC6582194 DOI: 10.3389/fcell.2019.00109] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022] Open
Abstract
The Golgi is well known to act as center for modification and sorting of proteins for secretion and delivery to other organelles. A key sorting step occurs at the trans-Golgi network and is mediated by protein adapters. However, recent data indicate that sorting also occurs much earlier, at the cis-Golgi, and uses lipid acylation as a novel means to regulate anterograde flux. Here, we examine an emerging role of S-palmitoylation/acylation as a mechanism to regulate anterograde routing. We discuss the critical Golgi-localized DHHC S-palmitoyltransferase enzymes that orchestrate this lipid modification, as well as their diverse protein clients (e.g., MAP6, SNAP25, CSP, LAT, β-adrenergic receptors, GABA receptors, and GLUT4 glucose transporters). Critically, for integral membrane proteins, S-acylation can act as new a “self-sorting” signal to concentrate these cargoes in rims of Golgi cisternae, and to promote their rapid traffic through the Golgi or, potentially, to bypass the Golgi. We discuss this mechanism and examine its potential relevance to human physiology and disease, including diabetes and neurodegenerative diseases.
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Affiliation(s)
- Andreas M Ernst
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Derek Toomre
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Jonathan S Bogan
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, United States.,Section of Endocrinology and Metabolism, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, United States
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93
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Rif1 S-acylation mediates DNA double-strand break repair at the inner nuclear membrane. Nat Commun 2019; 10:2535. [PMID: 31182712 PMCID: PMC6557901 DOI: 10.1038/s41467-019-10349-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 05/08/2019] [Indexed: 12/29/2022] Open
Abstract
Rif1 is involved in telomere homeostasis, DNA replication timing, and DNA double-strand break (DSB) repair pathway choice from yeast to human. The molecular mechanisms that enable Rif1 to fulfill its diverse roles remain to be determined. Here, we demonstrate that Rif1 is S-acylated within its conserved N-terminal domain at cysteine residues C466 and C473 by the DHHC family palmitoyl acyltransferase Pfa4. Rif1 S-acylation facilitates the accumulation of Rif1 at DSBs, the attenuation of DNA end-resection, and DSB repair by non-homologous end-joining (NHEJ). These findings identify S-acylation as a posttranslational modification regulating DNA repair. S-acylated Rif1 mounts a localized DNA-damage response proximal to the inner nuclear membrane, revealing a mechanism of compartmentalized DSB repair pathway choice by sequestration of a fatty acylated repair factor at the inner nuclear membrane.
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94
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Enrichment of S-Palmitoylated Proteins for Mass Spectrometry Analysis. Methods Mol Biol 2019. [PMID: 31152396 DOI: 10.1007/978-1-4939-9532-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
As the 10-year anniversary of their first introduction approaches, alkynyl fatty acids have revolutionized the analysis of S-palmitoylation dynamics, acting as functional mimics incorporated into native modification sites in cultured cells. The alkyne functional group provides a robust handle for bioorthogonal Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) to reporter-linked azides, forming a stable conjugate for enrichment for mass spectrometry analysis or in-gel fluorescence. Importantly, metabolic labeling enables time-dependent analysis of S-palmitoylation dynamics, which can be used to profile incorporation and turnover rates across the proteome. Here we present a protocol for cell labeling, click chemistry conjugation, enrichment, and isobaric tandem mass tag labeling for quantitative mass spectrometry analysis of protein S-palmitoylation.
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95
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Wang Z, Schey KL. Proteomic Analysis of S-Palmitoylated Proteins in Ocular Lens Reveals Palmitoylation of AQP5 and MP20. Invest Ophthalmol Vis Sci 2019; 59:5648-5658. [PMID: 30489624 PMCID: PMC6266727 DOI: 10.1167/iovs.18-25312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The purpose of this study was to characterize the palmitoyl-proteome in lens fiber cells. S-palmitoylation is the most common form of protein S-acylation and the reversible nature of this modification functions as a molecular switch to regulate many biological processes. This modification could play important roles in regulating protein functions and protein–protein interactions in the lens. Methods The palmitoyl-proteome of bovine lens fiber cells was investigated by combining acyl-biotin exchange (ABE) chemistry and mass-spectrometry analysis. Due to the possibility of false-positive results from ABE experiment, a method was also developed for direct detection of palmitoylated peptides by mass spectrometry for validating palmitoylation of lens proteins MP20 and AQP5. Palmitoylation levels on AQP5 in different regions of the lens were quantified after iodoacetamide (IAA)-palmitate exchange. Results The ABE experiment identified 174 potential palmitoylated proteins. These proteins include 39 well-characterized palmitoylated proteins, 92 previously reported palmitoylated proteins in other tissues, and 43 newly identified potential palmitoylated proteins including two important transmembrane proteins in the lens, AQP5 and MP20. Further analysis by direct detection of palmitoylated peptides confirmed palmitoylation of AQP5 on C6 and palmitoylation of MP20 on C159. Palmitoylation of AQP5 was found to only occur in a narrow region of the inner lens cortex and does not occur in the lens epithelium, in the lens outer cortex, or in the lens nucleus. Conclusions AQP5 and MP20 are among 174 palmitoylated proteins found in bovine lens fiber cells. This modification to AQP5 and MP20 may play a role in their translocation from the cytoplasm to cell membranes during fiber cell differentiation.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States
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96
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Palmitoylation in apicomplexan parasites: from established regulatory roles to putative new functions. Mol Biochem Parasitol 2019; 230:16-23. [PMID: 30978365 DOI: 10.1016/j.molbiopara.2019.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 03/17/2019] [Accepted: 04/07/2019] [Indexed: 01/28/2023]
Abstract
This minireview aims to provide a comprehensive synthesis on protein palmitoylation in apicomplexan parasites and higher eukaryotes where most of the data is available. Apicomplexan parasites encompass numerous obligate intracellular parasites with significant health risk to animals and humans. Protein palmitoylation is a widespread post-translational modification that plays important regulatory roles in several physiological and pathological states. Functional studies demonstrate that many processes important for parasites are regulated by protein palmitoylation. Structural analyses suggest that enzymes responsible for the palmitoylation process have a conserved architecture in eukaryotes although there are particular differences which could be related to their substrate specificities. Interestingly, with the publication of T. gondii and P. falciparum palmitoylomes new possible regulatory functions are unveiled. Here we focus our discussion on data from both palmitoylomes that suggest that palmitoylation of nuclear proteins regulate different chromatin-related processes such as nucleosome assembly and stability, transcription, translation and DNA repair.
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97
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Sullivan A, Wallace RL, Wellington R, Luo X, Capaldi AP. Multilayered regulation of TORC1-body formation in budding yeast. Mol Biol Cell 2019; 30:400-410. [PMID: 30485160 PMCID: PMC6589571 DOI: 10.1091/mbc.e18-05-0297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/08/2018] [Accepted: 11/20/2018] [Indexed: 02/05/2023] Open
Abstract
The target of rapamycin kinase complex 1 (TORC1) regulates cell growth and metabolism in eukaryotes. In Saccharomyces cerevisiae, TORC1 activity is known to be controlled by the conserved GTPases, Gtr1/2, and movement into and out of an inactive agglomerate/body. However, it is unclear whether/how these regulatory steps are coupled. Here we show that active Gtr1/2 is a potent inhibitor of TORC1-body formation, but cells missing Gtr1/2 still form TORC1-bodies in a glucose/nitrogen starvation-dependent manner. We also identify 13 new activators of TORC1-body formation and show that seven of these proteins regulate the Gtr1/2-dependent repression of TORC1-body formation, while the remaining proteins drive the subsequent steps in TORC1 agglomeration. Finally, we show that the conserved phosphatidylinositol-3-phosphate (PI(3)P) binding protein, Pib2, forms a complex with TORC1 and overrides the Gtr1/2-dependent repression of TORC1-body formation during starvation. These data provide a unified, systems-level model of TORC1 regulation in yeast.
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Affiliation(s)
- Arron Sullivan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
| | - Ryan L. Wallace
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
| | - Rachel Wellington
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
| | - Xiangxia Luo
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
| | - Andrew P. Capaldi
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721-0206
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98
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Weill U, Arakel EC, Goldmann O, Golan M, Chuartzman S, Munro S, Schwappach B, Schuldiner M. Toolbox: Creating a systematic database of secretory pathway proteins uncovers new cargo for COPI. Traffic 2019. [PMID: 29527758 PMCID: PMC5947560 DOI: 10.1111/tra.12560] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A third of yeast genes encode for proteins that function in the endomembrane system. However, the precise localization for many of these proteins is still uncertain. Here, we visualized a collection of ~500 N‐terminally, green fluorescent protein (GFP), tagged proteins of the yeast Saccharomyces cerevisiae. By co‐localizing them with 7 known markers of endomembrane compartments we determined the localization for over 200 of them. Using this approach, we create a systematic database of the various secretory compartments and identify several new residents. Focusing in, we now suggest that Lam5 resides in contact sites between the endoplasmic reticulum and the late Golgi. Additionally, analysis of interactions between the COPI coat and co‐localizing proteins from our screen identifies a subset of proteins that are COPI‐cargo. In summary, our approach defines the protein roster within each compartment enabling characterization of the physical and functional organization of the endomembrane system and its components.
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Affiliation(s)
- Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eric C Arakel
- Universitätsmedizin Göttingen Institut für Molekularbiologie Humboldtallee 23, D-37073 Göttingen, Germany
| | - Omer Goldmann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Matan Golan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Silvia Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Blanche Schwappach
- Universitätsmedizin Göttingen Institut für Molekularbiologie Humboldtallee 23, D-37073 Göttingen, Germany.,Max-Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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99
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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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100
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Pinto SM, Subbannayya Y, Prasad TSK. Functional Proteomic Analysis to Characterize Signaling Crosstalk. Methods Mol Biol 2019; 1871:197-224. [PMID: 30276742 DOI: 10.1007/978-1-4939-8814-3_14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The biological activities of a cell are determined by its response to external stimuli. The signals are transduced from either intracellular or extracellular milieu through networks of multi-protein complexes and post-translational modifications of proteins (PTMs). Most PTMs including phosphorylation, acetylation, ubiquitination, and SUMOylation, among others, modulate activities of proteins and regulate biological processes such as proliferation, differentiation, as well as host pathogen interaction. Conventionally, reverse genetics analysis and single molecule-based studies were employed to identify and characterize the function of PTMs and enzyme-substrate networks regulated by them. With the advent of high-throughput technologies, it is now possible to identify and quantify thousands of PTM sites in a single experiment. Here, we discuss recent advances in enrichment strategies of various PTMs. We also describe a method for the identification and relative quantitation of proteins using a tandem mass tag labeling approach combined with serial enrichment of phosphorylation, acetylation and succinylation using antibody enrichment strategy.
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Affiliation(s)
- Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India.
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