1
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Ocasio CA, Baggelaar MP, Sipthorp J, Losada de la Lastra A, Tavares M, Volarić J, Soudy C, Storck EM, Houghton JW, Palma-Duran SA, MacRae JI, Tomić G, Carr L, Downward J, Eggert US, Tate EW. A palmitoyl transferase chemical-genetic system to map ZDHHC-specific S-acylation. Nat Biotechnol 2024; 42:1548-1558. [PMID: 38191663 PMCID: PMC11471619 DOI: 10.1038/s41587-023-02030-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/13/2023] [Indexed: 01/10/2024]
Abstract
The 23 human zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S-acyltransferases catalyze long-chain S-acylation at cysteine residues across an extensive network of hundreds of proteins important for normal physiology or dysregulated in disease. Here we present a technology to directly map the protein substrates of a specific ZDHHC at the whole-proteome level, in intact cells. Structure-guided engineering of paired ZDHHC 'hole' mutants and 'bumped' chemically tagged fatty acid probes enabled probe transfer to specific protein substrates with excellent selectivity over wild-type ZDHHCs. Chemical-genetic systems were exemplified for five human ZDHHCs (3, 7, 11, 15 and 20) and applied to generate de novo ZDHHC substrate profiles, identifying >300 substrates and S-acylation sites for new functionally diverse proteins across multiple cell lines. We expect that this platform will elucidate S-acylation biology for a wide range of models and organisms.
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Affiliation(s)
| | - Marc P Baggelaar
- The Francis Crick Institute, London, UK
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, London, UK
- Utrecht University, Biomolecular Mass Spectrometry & Proteomics Group, Utrecht, The Netherlands
| | - James Sipthorp
- The Francis Crick Institute, London, UK
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, London, UK
| | - Ana Losada de la Lastra
- The Francis Crick Institute, London, UK
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, London, UK
| | - Manuel Tavares
- The Francis Crick Institute, London, UK
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, London, UK
| | - Jana Volarić
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, London, UK
| | | | - Elisabeth M Storck
- King's College London, Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences and Department of Chemistry, London, UK
| | | | - Susana A Palma-Duran
- The Francis Crick Institute, London, UK
- Department of Food Science, Research Center in Food and Development A.C., Hermosillo, Mexico
| | | | | | | | | | - Ulrike S Eggert
- King's College London, Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences and Department of Chemistry, London, UK
| | - Edward W Tate
- The Francis Crick Institute, London, UK.
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, London, UK.
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2
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Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024; 31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Proteins are responsible for most intracellular functions, which they perform as part of higher-order molecular complexes, located within defined subcellular niches. Localization is both dynamic and context specific and mislocalization underlies a multitude of diseases. It is thus vital to be able to measure the components of higher-order protein complexes and their subcellular location dynamically in order to fully understand cell biological processes. Here, we review the current range of highly complementary approaches that determine the subcellular organization of the proteome. We discuss the scale and resolution at which these approaches are best employed and the caveats that should be taken into consideration when applying them. We also look to the future and emerging technologies that are paving the way for a more comprehensive understanding of the functional roles of protein isoforms, which is essential for unraveling the complexities of cell biology and the development of disease treatments.
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Affiliation(s)
- Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte Hutchings
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kishor D Ingole
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Suyeon Kim
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Mehul V Makwana
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kieran J A McCaskie
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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3
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Boutin C, Clément C, Rivoal J. Post-Translational Modifications to Cysteine Residues in Plant Proteins and Their Impact on the Regulation of Metabolism and Signal Transduction. Int J Mol Sci 2024; 25:9845. [PMID: 39337338 PMCID: PMC11432348 DOI: 10.3390/ijms25189845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 08/21/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Cys is one of the least abundant amino acids in proteins. However, it is often highly conserved and is usually found in important structural and functional regions of proteins. Its unique chemical properties allow it to undergo several post-translational modifications, many of which are mediated by reactive oxygen, nitrogen, sulfur, or carbonyl species. Thus, in addition to their role in catalysis, protein stability, and metal binding, Cys residues are crucial for the redox regulation of metabolism and signal transduction. In this review, we discuss Cys post-translational modifications (PTMs) and their role in plant metabolism and signal transduction. These modifications include the oxidation of the thiol group (S-sulfenylation, S-sulfinylation and S-sulfonylation), the formation of disulfide bridges, S-glutathionylation, persulfidation, S-cyanylation S-nitrosation, S-carbonylation, S-acylation, prenylation, CoAlation, and the formation of thiohemiacetal. For each of these PTMs, we discuss the origin of the modifier, the mechanisms involved in PTM, and their reversibility. Examples of the involvement of Cys PTMs in the modulation of protein structure, function, stability, and localization are presented to highlight their importance in the regulation of plant metabolic and signaling pathways.
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Affiliation(s)
- Charlie Boutin
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Camille Clément
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Rue Sherbrooke est, Montréal, QC H1X 2B2, Canada
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4
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Forrester MT, Egol JR, Ozbay S, Singh R, Tata PR. Topology-Driven Discovery of Transmembrane Protein S-Palmitoylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.08.611865. [PMID: 39282397 PMCID: PMC11398512 DOI: 10.1101/2024.09.08.611865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Protein S-palmitoylation is a reversible lipophilic posttranslational modification regulating a diverse number of signaling pathways. Within transmembrane proteins (TMPs), S-palmitoylation is implicated in conditions from inflammatory disorders to respiratory viral infections. Many small-scale experiments have observed S-palmitoylation at juxtamembrane Cys residues. However, most large-scale S-palmitoyl discovery efforts rely on trypsin-based proteomics within which hydrophobic juxtamembrane regions are likely underrepresented. Machine learning- by virtue of its freedom from experimental constraints - is particularly well suited to address this discovery gap surrounding TMP S-palmitoylation. Utilizing a UniProt-derived feature set, a gradient boosted machine learning tool (TopoPalmTree) was constructed and applied to a holdout dataset of viral S-palmitoylated proteins. Upon application to the mouse TMP proteome, 1591 putative S-palmitoyl sites (i.e. not listed in SwissPalm or UniProt) were identified. Two lung-expressed S-palmitoyl candidates (synaptobrevin Vamp5 and water channel Aquaporin-5) were experimentally assessed. Finally, TopoPalmTree was used for rational design of an S-palmitoyl site on KDEL-Receptor 2. This readily interpretable model aligns the innumerable small-scale experiments observing juxtamembrane S-palmitoylation into a proteomic tool for TMP S-palmitoyl discovery and design, thus facilitating future investigations of this important modification.
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Affiliation(s)
- Michael T. Forrester
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University School of Medicine, Durham, NC 27710
| | - Jacob R. Egol
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710
| | - Sinan Ozbay
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710
| | - Rohit Singh
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710
| | - Purushothama Rao Tata
- Division of Pulmonary, Allergy and Critical Care Medicine, Duke University School of Medicine, Durham, NC 27710
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710
- Duke Regeneration Center, Duke University School of Medicine, Durham, NC 27710
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5
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Nie L, Fei C, Fan Y, Dang F, Zhao Z, Zhu T, Wu X, Dai T, Balasubramanian A, Pan J, Hu Y, Luo HR, Wei W, Chen J. Consecutive palmitoylation and phosphorylation orchestrates NLRP3 membrane trafficking and inflammasome activation. Mol Cell 2024; 84:3336-3353.e7. [PMID: 39173637 DOI: 10.1016/j.molcel.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/16/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024]
Abstract
NLRP3 inflammasome activation, essential for cytokine secretion and pyroptosis in response to diverse stimuli, is closely associated with various diseases. Upon stimulation, NLRP3 undergoes subcellular membrane trafficking and conformational rearrangements, preparing itself for inflammasome assembly at the microtubule-organizing center (MTOC). Here, we elucidate an orchestrated mechanism underlying these ordered processes using human and murine cells. Specifically, NLRP3 undergoes palmitoylation at two sites by palmitoyl transferase zDHHC1, facilitating its trafficking between subcellular membranes, including the mitochondria, trans-Golgi network (TGN), and endosome. This dynamic trafficking culminates in the localization of NLRP3 to the MTOC, where LATS1/2, pre-recruited to MTOC during priming, phosphorylates NLRP3 to further facilitate its interaction with NIMA-related kinase 7 (NEK7), ultimately leading to full NLRP3 activation. Consistently, Zdhhc1-deficiency mitigated LPS-induced inflammation and conferred protection against mortality in mice. Altogether, our findings provide valuable insights into the regulation of NLRP3 membrane trafficking and inflammasome activation, governed by palmitoylation and phosphorylation events.
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Affiliation(s)
- Li Nie
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China.
| | - Chenjie Fei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China
| | - Yizeng Fan
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, P.R. China
| | - Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Ziyue Zhao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China
| | - Tingfang Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China
| | - Xiangyu Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China
| | - Ting Dai
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China
| | - Arumugam Balasubramanian
- Department of Pathology, Dana-Farber/Harvard Cancer Center, Harvard Medical School, Department of Laboratory Medicine, Boston Children's Hospital, Enders Research Building, Room 811, Boston, MA 02115, USA
| | - Jing Pan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China
| | - Yang Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China
| | - Hongbo R Luo
- Department of Pathology, Dana-Farber/Harvard Cancer Center, Harvard Medical School, Department of Laboratory Medicine, Boston Children's Hospital, Enders Research Building, Room 811, Boston, MA 02115, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo 315211, P.R. China; Key Laboratory of Aquacultural Biotechnology of Ministry of Education, Ningbo University, Ningbo 315211, P.R. China.
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6
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Cannon AE, Horn PJ. The Molecular Frequency, Conservation and Role of Reactive Cysteines in Plant Lipid Metabolism. PLANT & CELL PHYSIOLOGY 2024; 65:826-844. [PMID: 38113384 DOI: 10.1093/pcp/pcad163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/21/2023] [Accepted: 12/18/2023] [Indexed: 12/21/2023]
Abstract
Cysteines (Cys) are chemically reactive amino acids containing sulfur that play diverse roles in plant biology. Recent proteomics investigations in Arabidopsis thaliana have revealed the presence of thiol post-translational modifications (PTMs) in several Cys residues. These PTMs are presumed to impact protein structure and function, yet mechanistic data regarding the specific Cys susceptible to modification and their biochemical relevance remain limited. To help address these limitations, we have conducted a wide-ranging analysis by integrating published datasets encompassing PTM proteomics (comparing S-sulfenylation, persulfidation, S-nitrosylation and S-acylation), genomics and protein structures, with a specific focus on proteins involved in plant lipid metabolism. The prevalence and distribution of modified Cys residues across all analyzed proteins is diverse and multifaceted. Nevertheless, by combining an evaluation of sequence conservation across 100+ plant genomes with AlphaFold-generated protein structures and physicochemical predictions, we have unveiled structural propensities associated with Cys modifications. Furthermore, we have identified discernible patterns in lipid biochemical pathways enriched with Cys PTMs, notably involving beta-oxidation, jasmonic acid biosynthesis, fatty acid biosynthesis and wax biosynthesis. These collective findings provide valuable insights for future investigations targeting the mechanistic foundations of Cys modifications and the regulation of modified proteins in lipid metabolism and other metabolic pathways.
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Affiliation(s)
- Ashley E Cannon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
| | - Patrick J Horn
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA
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7
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Susa KJ, Kruse AC, Blacklow SC. Tetraspanins: structure, dynamics, and principles of partner-protein recognition. Trends Cell Biol 2024; 34:509-522. [PMID: 37783654 PMCID: PMC10980598 DOI: 10.1016/j.tcb.2023.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/18/2023] [Accepted: 09/07/2023] [Indexed: 10/04/2023]
Abstract
Tetraspanins are a large, highly conserved family of four-pass transmembrane (TM) proteins that play critical roles in a variety of essential cellular functions, including cell migration, protein trafficking, maintenance of membrane integrity, and regulation of signal transduction. Tetraspanins carry out these biological functions primarily by interacting with partner proteins. Here, we summarize significant advances that have revealed fundamental principles underpinning structure-function relationships in tetraspanins. We first review the structural features of tetraspanin ectodomains and full-length apoproteins, and then discuss how recent structural studies of tetraspanin complexes have revealed plasticity in partner-protein recognition that enables tetraspanins to bind to remarkably different protein families, viral proteins, and antibody fragments. Finally, we discuss major questions and challenges that remain in studying tetraspanin complexes.
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Affiliation(s)
- Katherine J Susa
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158, USA.
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Stephen C Blacklow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA.
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8
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Wu R, Ji G, Chen W, Zhang L, Fang C, Lu H. Simultaneous and site-specific profiling of heterogeneity and turnover in protein S-acylation by intact S-acylated peptide analysis with a cleavable bioorthogonal tag. Analyst 2024; 149:1111-1120. [PMID: 38170640 DOI: 10.1039/d3an02059b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Protein S-acylation is an important lipid modification characteristic for heterogeneity in the acyl chain and dynamicity in the acylation/deacylation cycle. Most S-acylproteomic research has been limited by indirect identification of modified proteins/peptides without attached fatty acids, resulting in the failure to precisely characterize S-acylated sites with attached fatty acids. The study of S-acylation turnover is still limited at the protein level. Herein, aiming to site-specifically profile both the heterogeneity and the turnover of S-acylation, we first developed a site-specific strategy for intact S-acylated peptide analysis by introducing an acid cleavable bioorthogonal tag into a metabolic labelling method (ssMLCC). The cleavable bioorthogonal tag allowed for the selective enrichment and efficient MS analysis of intact S-acylated peptides so that S-acylated sites and their attached fatty acids could be directly analysed, enabling the precise mapping of S-acylated sites, as well as circumventing false positives from previous studies. Moreover, 606 S-palmitoylated (C16:0) sites of 441 proteins in HeLa cells were identified. All types of S-acylated peptides were further characterized by an open search, providing site-specific profiling of acyl chain heterogeneity, including S-myristoylation, S-palmitoylation, S-palmitoleylation, and S-oleylation. Furthermore, site-specific monitoring of S-palmitoylation turnover was achieved by coupling with pulse-chase methods, facilitating the detailed observation of the dynamic event at each site in multi-palmitoylated proteins, and 85 rapidly cycling palmitoylated sites in 79 proteins were identified. This study provided a strategy for the precise and comprehensive analysis of protein S-acylation based on intact S-acylated peptide analysis, contributing to the further understanding of its complexity and biological functions.
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Affiliation(s)
- Roujun Wu
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, P. R. China.
| | - Guanghui Ji
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, P. R. China.
| | - Weiyu Chen
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, P. R. China.
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Caiyun Fang
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, P. R. China.
| | - Haojie Lu
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, P. R. China.
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
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9
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Aßfalg M, Güner G, Müller SA, Breimann S, Langosch D, Muhle-Goll C, Frishman D, Steiner H, Lichtenthaler SF. Cleavage efficiency of the intramembrane protease γ-secretase is reduced by the palmitoylation of a substrate's transmembrane domain. FASEB J 2024; 38:e23442. [PMID: 38275103 DOI: 10.1096/fj.202302152r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/20/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024]
Abstract
The intramembrane protease γ-secretase has broad physiological functions, but also contributes to Notch-dependent tumors and Alzheimer's disease. While γ-secretase cleaves numerous membrane proteins, only few nonsubstrates are known. Thus, a fundamental open question is how γ-secretase distinguishes substrates from nonsubstrates and whether sequence-based features or post-translational modifications of membrane proteins contribute to substrate recognition. Using mass spectrometry-based proteomics, we identified several type I membrane proteins with short ectodomains that were inefficiently or not cleaved by γ-secretase, including 'pituitary tumor-transforming gene 1-interacting protein' (PTTG1IP). To analyze the mechanism preventing cleavage of these putative nonsubstrates, we used the validated substrate FN14 as a backbone and replaced its transmembrane domain (TMD), where γ-cleavage occurs, with the one of nonsubstrates. Surprisingly, some nonsubstrate TMDs were efficiently cleaved in the FN14 backbone, demonstrating that a cleavable TMD is necessary, but not sufficient for cleavage by γ-secretase. Cleavage efficiencies varied by up to 200-fold. Other TMDs, including that of PTTG1IP, were still barely cleaved within the FN14 backbone. Pharmacological and mutational experiments revealed that the PTTG1IP TMD is palmitoylated, which prevented cleavage by γ-secretase. We conclude that the TMD sequence of a membrane protein and its palmitoylation can be key factors determining substrate recognition and cleavage efficiency by γ-secretase.
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Affiliation(s)
- Marlene Aßfalg
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Gökhan Güner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephan A Müller
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Stephan Breimann
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Department of Bioinformatics, School of Life Sciences, Technical University of Munich, Freising, Germany
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
| | | | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Harald Steiner
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Biomedical Center (BMC), Division of Metabolic Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Stefan F Lichtenthaler
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Neuroproteomics, School of Medicine and Health, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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10
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Wibbe N, Ebnet K. Cell Adhesion at the Tight Junctions: New Aspects and New Functions. Cells 2023; 12:2701. [PMID: 38067129 PMCID: PMC10706136 DOI: 10.3390/cells12232701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Tight junctions (TJ) are cell-cell adhesive structures that define the permeability of barrier-forming epithelia and endothelia. In contrast to this seemingly static function, TJs display a surprisingly high molecular complexity and unexpected dynamic regulation, which allows the TJs to maintain a barrier in the presence of physiological forces and in response to perturbations. Cell-cell adhesion receptors play key roles during the dynamic regulation of TJs. They connect individual cells within cellular sheets and link sites of cell-cell contacts to the underlying actin cytoskeleton. Recent findings support the roles of adhesion receptors in transmitting mechanical forces and promoting phase separation. In this review, we discuss the newly discovered functions of cell adhesion receptors localized at the TJs and their role in the regulation of the barrier function.
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Affiliation(s)
- Nicolina Wibbe
- Institute-Associated Research Group "Cell Adhesion and Cell Polarity", Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
| | - Klaus Ebnet
- Institute-Associated Research Group "Cell Adhesion and Cell Polarity", Institute of Medical Biochemistry, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Münster, D-48419 Münster, Germany
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11
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Thomas P, Pang Y, Kelder J. Membrane progesterone receptors on the cell membrane: A review highlighting potential export motifs in mPRα regulating its trafficking to the cell surface. Steroids 2023; 199:109295. [PMID: 37558174 DOI: 10.1016/j.steroids.2023.109295] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
Substantial progress has been made in our understanding of the nongenomic actions, ligand binding, intracellular signaling pathways, and functions of membrane progesterone receptors (mPRs) in reproductive and nonreproductive tissues since their discovery 20 years ago. The five mPRs are members of the progestin adipoQ receptor (PAQR) family which also includes adiponectin receptors (AdipoRs). However, unlike AdipoRs, the 3-D structures of mPRs are unknown, and their structural characteristics remain poorly understood. The mechanisms regulating mPR functions and their trafficking to the cell surface have received little attention and have not been systematically reviewed. This paper summarizes some structural aspects of mPRs, including the ligand binding pocket of mPRα recently derived from homology modeling with AdipoRs, and the proposed topology of mPRs from the preponderance of positively charged amino acid residues in their intracellular domains. The mechanisms of trafficking membrane receptors to the cell surface are discussed, including the amino acid motifs involved with their export to the cell surface, the roles of adaptor proteins, and post-translational glycosylation and palmitoylation modifications that promote cell surface expression and retention. Evidence for similar mechanisms regulating the expression and functions of mPRs on the cell surface is discussed, including the identification of potential export motifs on mPRα required for its trafficking to the cell membrane. Collectively, these results have identified several potential mechanisms regulating the expression and functions of mPRs on the cell membrane for further investigation.
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Affiliation(s)
- Peter Thomas
- University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA.
| | - Yefei Pang
- University of Texas at Austin Marine Science Institute, 750 Channel View Drive, Port Aransas, TX 78373, USA
| | - Jan Kelder
- Theoretical & Computational Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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12
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Salaun C, Tomkinson NCO, Chamberlain LH. The endoplasmic reticulum-localized enzyme zDHHC6 mediates S-acylation of short transmembrane constructs from multiple type I and II membrane proteins. J Biol Chem 2023; 299:105201. [PMID: 37660915 PMCID: PMC10520890 DOI: 10.1016/j.jbc.2023.105201] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023] Open
Abstract
In this study, we investigated the S-acylation of two host cell proteins important for viral infection: TMPRSS2 (transmembrane serine protease 2), which cleaves severe acute respiratory syndrome coronavirus 2 spike to facilitate viral entry, and bone marrow stromal antigen 2, a general viral restriction factor. We found that both proteins were S-acylated by zDHHC6, an S-acyltransferase enzyme localized at the endoplasmic reticulum, in coexpression experiments. Mutagenic analysis revealed that zDHHC6 modifies a single cysteine in each protein, which are in proximity to the transmembrane domains (TMDs). For TMPRSS2, the modified cysteine is positioned two residues into the TMD, whereas the modified cysteine in bone marrow stromal antigen 2 has a cytosolic location two amino acids upstream of the TMD. Cysteine swapping revealed that repositioning the target cysteine of TMPRSS2 further into the TMD substantially reduced S-acylation by zDHHC6. Interestingly, zDHHC6 efficiently S-acylated truncated forms of these proteins that contained only the TMDs and short juxtamembrane regions. The ability of zDHHC6 to modify short TMD sequences was also seen for the transferrin receptor (another type II membrane protein) and for five different type I membrane protein constructs, including cluster of differentiation 4. Collectively, the results of this study show that zDHHC6 can modify diverse membrane proteins (type I and II) and requires only the presence of the TMD and target cysteine for efficient S-acylation. Thus, zDHHC6 may be a broad specificity S-acyltransferase specialized for the modification of a diverse set of transmembrane proteins at the endoplasmic reticulum.
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Affiliation(s)
- Christine Salaun
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom.
| | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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13
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Harada K, Sho R, Takakura H, Yokoyama E, Koyama R, Yamamoto Y, Adachi N, Tanaka S, Hide I, Sakai N. S-Palmitoylation of the serotonin transporter promotes its cell surface expression and serotonin uptake. Biochem Biophys Res Commun 2023; 662:58-65. [PMID: 37099811 DOI: 10.1016/j.bbrc.2023.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/28/2023]
Abstract
The neurotransmitter serotonin (5-HT) is transported back into serotonergic neurons by the serotonin transporter (SERT). SERT is a main target of antidepressants, and much effort has therefore focused on finding relationships between SERT and depression. However, it is not fully understood how SERT is regulated at the cellular level. Here, we report post-translational regulation of SERT by S-palmitoylation, in which palmitate is covalently attached to cysteine residues of proteins. Using AD293 cells (a human embryonic kidney 293-derived cell line with improved cell adherence) transiently transfected with FLAG-tagged human SERT, we observed S-palmitoylation of immature SERT containing high-mannose type N-glycans or no N-glycan, which is presumed to be localized in the early secretory pathway, such as the endoplasmic reticulum. Mutational analysis by alanine substitutions shows that S-palmitoylation of immature SERT occurs at least at Cys-147 and Cys-155, juxtamembrane cysteine residues within the first intracellular loop. Furthermore, mutation of Cys-147 reduced cellular uptake of a fluorescent SERT substrate that mimics 5-HT without decreasing SERT on the cell surface. On the other hand, combined mutation of Cys-147 and Cys-155 inhibited SERT surface expression and reduced the uptake of the 5-HT mimic. Thus, S-palmitoylation of Cys-147 and Cys-155 is important for both the cell surface expression and 5-HT uptake capacity of SERT. Given the importance of S-palmitoylation in brain homeostasis, further investigation of SERT S-palmitoylation could provide new insights into the treatment of depression.
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Affiliation(s)
- Kana Harada
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
| | - Ryoma Sho
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Hiromiki Takakura
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Eri Yokoyama
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Reika Koyama
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Yuka Yamamoto
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Naoko Adachi
- Laboratory of Molecular Pharmacology, Biosignal Research Center, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan
| | - Shigeru Tanaka
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Izumi Hide
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Norio Sakai
- Department of Molecular and Pharmacological Neuroscience, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
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14
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Hashimoto Y, Greene C, Munnich A, Campbell M. The CLDN5 gene at the blood-brain barrier in health and disease. Fluids Barriers CNS 2023; 20:22. [PMID: 36978081 PMCID: PMC10044825 DOI: 10.1186/s12987-023-00424-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
The CLDN5 gene encodes claudin-5 (CLDN-5) that is expressed in endothelial cells and forms tight junctions which limit the passive diffusions of ions and solutes. The blood-brain barrier (BBB), composed of brain microvascular endothelial cells and associated pericytes and end-feet of astrocytes, is a physical and biological barrier to maintain the brain microenvironment. The expression of CLDN-5 is tightly regulated in the BBB by other junctional proteins in endothelial cells and by supports from pericytes and astrocytes. The most recent literature clearly shows a compromised BBB with a decline in CLDN-5 expression increasing the risks of developing neuropsychiatric disorders, epilepsy, brain calcification and dementia. The purpose of this review is to summarize the known diseases associated with CLDN-5 expression and function. In the first part of this review, we highlight the recent understanding of how other junctional proteins as well as pericytes and astrocytes maintain CLDN-5 expression in brain endothelial cells. We detail some drugs that can enhance these supports and are being developed or currently in use to treat diseases associated with CLDN-5 decline. We then summarise mutagenesis-based studies which have facilitated a better understanding of the physiological role of the CLDN-5 protein at the BBB and have demonstrated the functional consequences of a recently identified pathogenic CLDN-5 missense mutation from patients with alternating hemiplegia of childhood. This mutation is the first gain-of-function mutation identified in the CLDN gene family with all others representing loss-of-function mutations resulting in mis-localization of CLDN protein and/or attenuated barrier function. Finally, we summarize recent reports about the dosage-dependent effect of CLDN-5 expression on the development of neurological diseases in mice and discuss what cellular supports for CLDN-5 regulation are compromised in the BBB in human diseases.
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Affiliation(s)
- Yosuke Hashimoto
- Trinity College Dublin, Smurfit Institute of Genetics, Dublin, D02 VF25, Ireland.
| | - Chris Greene
- Trinity College Dublin, Smurfit Institute of Genetics, Dublin, D02 VF25, Ireland
| | - Arnold Munnich
- Institut Imagine, INSERM UMR1163, Université Paris Cité, Paris, F-75015, France
- Departments of Pediatric Neurology and Medical Genetics, Hospital Necker Enfants Malades, Université Paris Cité, Paris, F-75015, France
| | - Matthew Campbell
- Trinity College Dublin, Smurfit Institute of Genetics, Dublin, D02 VF25, Ireland.
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15
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Kuo CWS, Dobi S, Gök C, Da Silva Costa A, Main A, Robertson-Gray O, Baptista-Hon D, Wypijewski KJ, Costello H, Hales TG, MacQuaide N, Smith GL, Fuller W. Palmitoylation of the pore-forming subunit of Ca(v)1.2 controls channel voltage sensitivity and calcium transients in cardiac myocytes. Proc Natl Acad Sci U S A 2023; 120:e2207887120. [PMID: 36745790 PMCID: PMC9963536 DOI: 10.1073/pnas.2207887120] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 12/07/2022] [Indexed: 02/08/2023] Open
Abstract
Mammalian voltage-activated L-type Ca2+ channels, such as Ca(v)1.2, control transmembrane Ca2+ fluxes in numerous excitable tissues. Here, we report that the pore-forming α1C subunit of Ca(v)1.2 is reversibly palmitoylated in rat, rabbit, and human ventricular myocytes. We map the palmitoylation sites to two regions of the channel: The N terminus and the linker between domains I and II. Whole-cell voltage clamping revealed a rightward shift of the Ca(v)1.2 current-voltage relationship when α1C was not palmitoylated. To examine function, we expressed dihydropyridine-resistant α1C in human induced pluripotent stem cell-derived cardiomyocytes and measured Ca2+ transients in the presence of nifedipine to block the endogenous channels. The transients generated by unpalmitoylatable channels displayed a similar activation time course but significantly reduced amplitude compared to those generated by wild-type channels. We thus conclude that palmitoylation controls the voltage sensitivity of Ca(v)1.2. Given that the identified Ca(v)1.2 palmitoylation sites are also conserved in most Ca(v)1 isoforms, we propose that palmitoylation of the pore-forming α1C subunit provides a means to regulate the voltage sensitivity of voltage-activated Ca2+ channels in excitable cells.
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Affiliation(s)
- Chien-Wen S. Kuo
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
| | - Sara Dobi
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
| | - Caglar Gök
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
| | - Ana Da Silva Costa
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
| | - Alice Main
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
| | - Olivia Robertson-Gray
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
| | - Daniel Baptista-Hon
- Division of Systems Medicine, Institute of Academic Anaesthesia, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
- Center for Biomedicine and Innovations, Faculty of Medicine, Macau University of Science and Technology, Macau SAR, 999078China
| | | | - Hannah Costello
- Division of Systems Medicine, Institute of Academic Anaesthesia, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Tim G. Hales
- Division of Systems Medicine, Institute of Academic Anaesthesia, School of Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - Niall MacQuaide
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
| | - Godfrey L. Smith
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
| | - William Fuller
- School of Cardiovascular and Metabolic Health, University of Glasgow, GlasgowG12 8QQ, UK
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16
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Butler L, Locatelli C, Allagioti D, Lousa I, Lemonidis K, Tomkinson NCO, Salaun C, Chamberlain LH. S-acylation of Sprouty and SPRED proteins by the S-acyltransferase zDHHC17 involves a novel mode of enzyme-substrate interaction. J Biol Chem 2023; 299:102754. [PMID: 36442513 PMCID: PMC9800311 DOI: 10.1016/j.jbc.2022.102754] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/27/2022] Open
Abstract
S-acylation is an essential post-translational modification, which is mediated by a family of 23 zDHHC enzymes in humans. Several thousand proteins are modified by S-acylation; however, we lack a detailed understanding of how enzyme-substrate recognition and specificity is achieved. Previous work showed that the ankyrin repeat domain of zDHHC17 (ANK17) recognizes a short linear motif, known as the zDHHC ANK binding motif (zDABM) in substrate protein SNAP25, as a mechanism of substrate recruitment prior to S-acylation. Here, we investigated the S-acylation of the Sprouty and SPRED family of proteins by zDHHC17. Interestingly, although Sprouty-2 (Spry2) contains a zDABM that interacts with ANK17, this mode of binding is dispensable for S-acylation, and indeed removal of the zDABM does not completely ablate binding to zDHHC17. Furthermore, the related SPRED3 protein interacts with and is efficiently S-acylated by zDHHC17, despite lacking a zDABM. We undertook mutational analysis of SPRED3 to better understand the basis of its zDABM-independent interaction with zDHHC17. This analysis found that the cysteine-rich SPR domain of SPRED3, which is the defining feature of all Sprouty and SPRED proteins, interacts with zDHHC17. Surprisingly, the interaction with SPRED3 was independent of ANK17. Our mutational analysis of Spry2 was consistent with the SPR domain of this protein containing a zDHHC17-binding site, and Spry2 also showed detectable binding to a zDHHC17 mutant lacking the ANK domain. Thus, zDHHC17 can recognize its substrates through zDABM-dependent and/or zDABM-independent mechanisms, and some substrates display more than one mode of binding to this enzyme.
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Affiliation(s)
- Liam Butler
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Carolina Locatelli
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Despoina Allagioti
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Irina Lousa
- UCIBIO, REQUIMTE, Laboratory of Biochemistry, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Kimon Lemonidis
- School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Nicholas C O Tomkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Christine Salaun
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom.
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17
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Berselli A, Benfenati F, Maragliano L, Alberini G. Multiscale modelling of claudin-based assemblies: a magnifying glass for novel structures of biological interfaces. Comput Struct Biotechnol J 2022; 20:5984-6010. [DOI: 10.1016/j.csbj.2022.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/03/2022] Open
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18
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Fujiwara S, Nguyen TP, Furuse K, Fukazawa Y, Otani T, Furuse M. Tight junction formation by a claudin mutant lacking the COOH-terminal PDZ domain-binding motif. Ann N Y Acad Sci 2022; 1516:85-94. [PMID: 35945631 DOI: 10.1111/nyas.14881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Claudin-based tight junctions (TJs) are formed at the most apical part of cell-cell contacts in epithelial cells. Previous studies suggest that scaffolding proteins ZO-1 and ZO-2 (ZO proteins) determine the location of TJs by interacting with claudins, but this idea is not conclusive. To address the role of the ZO proteins binding to claudins at TJs, a COOH-terminal PDZ domain binding motif-deleted claudin-3 mutant, which lacks the ZO protein binding, was stably expressed in claudin-deficient MDCK cells. The COOH-terminus-deleted claudin-3 was localized at the apicolateral region similar to full-length claudin-3. Consistently, freeze-fracture electron microscopy revealed that the COOH-terminus-deleted claudin-3-expressing cells reconstituted belts of TJs at the most apical region of the lateral membrane and restored functional epithelial barriers. These results suggest that the interaction of claudins with ZO proteins is not a prerequisite for TJ formation at the most apical part of cell-cell contacts.
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Affiliation(s)
- Sachiko Fujiwara
- Division of Cell Structure, National Institute for Physiological Sciences, Okazaki, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Thanh Phuong Nguyen
- Division of Cell Structure, National Institute for Physiological Sciences, Okazaki, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Kyoko Furuse
- Division of Cell Structure, National Institute for Physiological Sciences, Okazaki, Japan
| | - Yugo Fukazawa
- Division of Brain Structure and Function, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
- Life Science Innovation Center, University of Fukui, Fukui, Japan
| | - Tetsuhisa Otani
- Division of Cell Structure, National Institute for Physiological Sciences, Okazaki, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Mikio Furuse
- Division of Cell Structure, National Institute for Physiological Sciences, Okazaki, Japan
- Department of Physiological Sciences, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki, Japan
- Nagoya University Graduate School of Medicine, Aichi, Japan
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19
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Gal J, Bondada V, Mashburn CB, Rodgers DW, Croall DE, Geddes JW. S-acylation regulates the membrane association and activity of Calpain-5. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119298. [PMID: 35643222 DOI: 10.1016/j.bbamcr.2022.119298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Calpain-5 (CAPN5) is a member of the calpain family of calcium-activated neutral thiol proteases. CAPN5 is partly membrane associated, despite its lack of a transmembrane domain. Unlike classical calpains, CAPN5 contains a C-terminal C2 domain. C2 domains often have affinity to lipids, mediating membrane association. We recently reported that the C2 domain of CAPN5 was essential for its membrane association and the activation of its autolytic activity. However, despite the removal of the C2 domain by autolysis, the N-terminal fragment of CAPN5 remained membrane associated. S-acylation, also referred to as S-palmitoylation, is a reversible post-translational lipid modification of cysteine residues that promotes membrane association of soluble proteins. In the present study several S-acylated cysteine residues were identified in CAPN5 with the acyl-PEG exchange method. Data reported here demonstrate that CAPN5 is S-acylated on up to three cysteine residues including Cys-4 and Cys-512, and likely Cys-507. The D589N mutation in a potential calcium binding loop within the C2 domain interfered with the S-acylation of CAPN5, likely preventing initial membrane association. Mutating specific cysteine residues of CAPN5 interfered with both its membrane association and the activation of CAPN5 autolysis. Taken together, our results suggest that the S-acylation of CAPN5 is critical for its membrane localization which appears to favor its enzymatic activity.
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Affiliation(s)
- Jozsef Gal
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
| | - Vimala Bondada
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA
| | - Charles B Mashburn
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA
| | - David W Rodgers
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA
| | - Dorothy E Croall
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - James W Geddes
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
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20
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Berselli A, Alberini G, Benfenati F, Maragliano L. Computational Assessment of Different Structural Models for Claudin-5 Complexes in Blood-Brain Barrier Tight Junctions. ACS Chem Neurosci 2022; 13:2140-2153. [PMID: 35816296 PMCID: PMC9976285 DOI: 10.1021/acschemneuro.2c00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The blood-brain barrier (BBB) strictly regulates the exchange of ions and molecules between the blood and the central nervous system. Tight junctions (TJs) are multimeric structures that control the transport through the paracellular spaces between the adjacent brain endothelial cells of the BBB. Claudin-5 (Cldn5) proteins are essential for TJ formation and assemble into multiprotein complexes via cis-interactions within the same cell membrane and trans-interactions across two contiguous cells. Despite the relevant biological function of Cldn5 proteins and their role as targets of brain drug delivery strategies, the molecular details of their assembly within TJs are still unclear. Two different structural models have been recently introduced, in which Cldn5 dimers belonging to opposite cells join to generate paracellular pores. However, a comparison of these models in terms of ionic transport features is still lacking. In this work, we used molecular dynamics simulations and free energy (FE) calculations to assess the two Cldn5 pore models and investigate the thermodynamic properties of water and physiological ions permeating through them. Despite different FE profiles, both structures present single/multiple FE barriers to ionic permeation, while being permissive to water flux. These results reveal that both models are compatible with the physiological role of Cldn5 TJ strands. By identifying the protein-protein surface at the core of TJ Cldn5 assemblies, our computational investigation provides a basis for the rational design of synthetic peptides and other molecules capable of opening paracellular pores in the BBB.
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Affiliation(s)
- Alessandro Berselli
- Center
for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, Genova 16132, Italy
- Department
of Experimental Medicine, Università
Degli Studi di Genova, Viale Benedetto XV, 3, Genova 16132, Italy
| | - Giulio Alberini
- Center
for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, Genova 16132, Italy
- IRCCS
Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, Genova 16132, Italy
| | - Fabio Benfenati
- Center
for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, Genova 16132, Italy
- IRCCS
Ospedale Policlinico San Martino, Largo Rosanna Benzi, 10, Genova 16132, Italy
| | - Luca Maragliano
- Center
for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi, 10, Genova 16132, Italy
- Department
of Life and Environmental Sciences, Polytechnic
University of Marche, Via Brecce Bianche, Ancona 60131, Italy
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21
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Wild AR, Hogg PW, Flibotte S, Nasseri GG, Hollman RB, Abazari D, Haas K, Bamji SX. Exploring the expression patterns of palmitoylating and de-palmitoylating enzymes in the mouse brain using the curated RNA-seq database BrainPalmSeq. eLife 2022; 11:e75804. [PMID: 35819139 PMCID: PMC9365392 DOI: 10.7554/elife.75804] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Protein S-palmitoylation is a reversible post-translational lipid modification that plays a critical role in neuronal development and plasticity, while dysregulated S-palmitoylation underlies a number of severe neurological disorders. Dynamic S-palmitoylation is regulated by a large family of ZDHHC palmitoylating enzymes, their accessory proteins, and a small number of known de-palmitoylating enzymes. Here, we curated and analyzed expression data for the proteins that regulate S-palmitoylation from publicly available RNAseq datasets, providing a comprehensive overview of their distribution in the mouse nervous system. We developed a web-tool that enables interactive visualization of the expression patterns for these proteins in the nervous system (http://brainpalmseq.med.ubc.ca/), and explored this resource to find region and cell-type specific expression patterns that give insight into the function of palmitoylating and de-palmitoylating enzymes in the brain and neurological disorders. We found coordinated expression of ZDHHC enzymes with their accessory proteins, de-palmitoylating enzymes and other brain-expressed genes that included an enrichment of S-palmitoylation substrates. Finally, we utilized ZDHHC expression patterns to predict and validate palmitoylating enzyme-substrate interactions.
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Affiliation(s)
- Angela R Wild
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Peter W Hogg
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Stephane Flibotte
- Life Sciences Institute Bioinformatics Facility, University of British ColumbiaVancouverCanada
| | - Glory G Nasseri
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Rocio B Hollman
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Danya Abazari
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Kurt Haas
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
| | - Shernaz X Bamji
- Department of Cellular and Physiological Sciences, Life Sciences Institute and Djavad Mowafaghian Centre for Brain Health, University of British ColumbiaVancouverCanada
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22
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Ma Z, Shi S, Ren M, Pang C, Zhan Y, An H, Sun F. Molecular Mechanism of CD44 Homodimerization Modulated by Palmitoylation and Membrane Environments. Biophys J 2022; 121:2671-2683. [PMID: 35733341 DOI: 10.1016/j.bpj.2022.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 04/21/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022] Open
Abstract
The homodimerization of CD44 plays a key role in an intercellular-to-extracellular signal transduction and tumor progression. Acylated modification and specific membrane environments have been reported to mediate translocation and oligomerization of CD44, however, the underlying molecular mechanism remains elusive. In this study, extensive molecular dynamics simulations are performed to characterize the dimerization of palmitoylated CD44 variants in different bilayer environments. CD44 forms homodimer depending on the cysteines on the juxta-membrane domains, and the dimerization efficiency and packing configurations are defected by their palmitoylated modifications. In the phase-segregated (raft included) membrane, homodimerization of the palmitoylated CD44 is hardly observed, whereas PIP2 addition compensates to realize dimerization. However, the structure of CD44 homodimer formed in the phase-segregated bilayer turns susceptive and PIP2 addition allows for an extensive conformation of the cytoplasmic domain, a proposal prerequisite to access the cytoskeleton linker proteins. The results unravel a delicate competitive relationship between PIP2, lipid raft and palmitoylation in mediating protein homodimerization, which helps to clarify the dynamic dimer conformations and involved cellular signaling of the CD44 likewise proteins.
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Affiliation(s)
- Ziyi Ma
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Sai Shi
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
| | - Meina Ren
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Chunli Pang
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China
| | - Yong Zhan
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China
| | - Hailong An
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China; State Key Laboratory of Reliability and Intelligence of Electrical Equipment, Hebei University of Technology, Tianjin 300401, China; Key Laboratory of Electromagnetic Field and Electrical Apparatus Reliability of Hebei Province, Hebei University of Technology, Tianjin 300401, China.
| | - Fude Sun
- Key Laboratory of Molecular Biophysics, Hebei Province, Institute of Biophysics, School of Health Science & Biomedical Engineering, Hebei University of Technology, Tianjin, 300401, China.
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23
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Kumar M, Carr P, Turner SR. An atlas of Arabidopsis protein S-acylation reveals its widespread role in plant cell organization and function. NATURE PLANTS 2022. [PMID: 35681017 DOI: 10.1101/2020.05.12.090415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
S-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterized, largely as a result of the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. To address this gap in our knowledge, we used an optimized acyl-resin-assisted capture assay to perform a comprehensive analysis of plant protein S-acylation from six separate tissues. In our high- and medium-confidence groups, we identified 1,849 cysteines modified by S-acylation, which were located in 1,640 unique peptides from 1,094 different proteins. This represents around 6% of the detectable Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm the S-acylation of a number of proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity and are all predicted to possess a RING-type zinc finger at their amino terminus composed of eight cysteines. For CESA8, we find evidence for S-acylation of these cysteines that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING-type domain, the same region of CESA8 appears to have evolved a very different structure. Together, the data suggest that this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrating the importance of further work in this area.
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Affiliation(s)
- Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Carr
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Holiferm, Manchester, UK
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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24
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Tian Y, Zeng H, Wu J, Huang J, Gao Q, Tang D, Cai L, Liao Z, Wang Y, Liu X, Lin J. Screening DHHCs of S-acylated proteins using an OsDHHC cDNA library and bimolecular fluorescence complementation in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1763-1780. [PMID: 35411551 DOI: 10.1111/tpj.15769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/30/2022] [Accepted: 04/07/2022] [Indexed: 05/28/2023]
Abstract
S-acylation is an important lipid modification that primarily involves DHHC proteins (DHHCs) and associated S-acylated proteins. No DHHC-S-acylated protein pair has been reported so far in rice (Oryza sativa L.) and the molecular mechanisms underlying S-acylation in plants are largely unknown. We constructed an OsDHHC cDNA library for screening corresponding pairs of DHHCs and S-acylated proteins using bimolecular fluorescence complementation assays. Five DHHC-S-acylated protein pairs (OsDHHC30-OsCBL2, OsDHHC30-OsCBL3, OsDHHC18-OsNOA1, OsDHHC13-OsNAC9, and OsDHHC14-GSD1) were identified in rice. Among the pairs, OsCBL2 and OsCBL3 were S-acylated by OsDHHC30 in yeast and rice. The localization of OsCBL2 and OsCBL3 in the endomembrane depended on S-acylation mediated by OsDHHC30. Meanwhile, all four OsDHHCs screened complemented the thermosensitive phenotype of an akr1 yeast mutant, and their DHHC motifs were required for S-acyltransferase activity. Overexpression of OsDHHC30 in rice plants improved their salt and oxidative tolerance. Together, these results contribute to our understanding of the molecular mechanism underlying S-acylation in plants.
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Affiliation(s)
- Ye Tian
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Hui Zeng
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Jicai Wu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Jian Huang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Qiang Gao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Dongying Tang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Lipeng Cai
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Zhaoyi Liao
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Yan Wang
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Xuanming Liu
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
| | - Jianzhong Lin
- Hunan Province Key Laboratory of Plant Functional Genomics and Developmental Regulation, State Key Laboratory of Chemo/Biosensing and Chemometrics, National Center of Technology Innovation for Saline-Alkali Tolerant Rice, College of Biology, Hunan University, Changsha, 410082, Hunan, China
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25
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Kumar M, Carr P, Turner SR. An atlas of Arabidopsis protein S-acylation reveals its widespread role in plant cell organization and function. NATURE PLANTS 2022; 8:670-681. [PMID: 35681017 DOI: 10.1038/s41477-022-01164-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 05/04/2022] [Indexed: 05/28/2023]
Abstract
S-acylation is the addition of a fatty acid to a cysteine residue of a protein. While this modification may profoundly alter protein behaviour, its effects on the function of plant proteins remains poorly characterized, largely as a result of the lack of basic information regarding which proteins are S-acylated and where in the proteins the modification occurs. To address this gap in our knowledge, we used an optimized acyl-resin-assisted capture assay to perform a comprehensive analysis of plant protein S-acylation from six separate tissues. In our high- and medium-confidence groups, we identified 1,849 cysteines modified by S-acylation, which were located in 1,640 unique peptides from 1,094 different proteins. This represents around 6% of the detectable Arabidopsis proteome and suggests an important role for S-acylation in many essential cellular functions including trafficking, signalling and metabolism. To illustrate the potential of this dataset, we focus on cellulose synthesis and confirm the S-acylation of a number of proteins known to be involved in cellulose synthesis and trafficking of the cellulose synthase complex. In the secondary cell walls, cellulose synthesis requires three different catalytic subunits (CESA4, CESA7 and CESA8) that all exhibit striking sequence similarity and are all predicted to possess a RING-type zinc finger at their amino terminus composed of eight cysteines. For CESA8, we find evidence for S-acylation of these cysteines that is incompatible with any role in coordinating metal ions. We show that while CESA7 may possess a RING-type domain, the same region of CESA8 appears to have evolved a very different structure. Together, the data suggest that this study represents an atlas of S-acylation in Arabidopsis that will facilitate the broader study of this elusive post-translational modification in plants as well as demonstrating the importance of further work in this area.
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Affiliation(s)
- Manoj Kumar
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Paul Carr
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Holiferm, Manchester, UK
| | - Simon R Turner
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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26
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Renna SA, Michael JV, Kong X, Ma L, Ma P, Nieman MT, Edelstein LC, McKenzie SE. Human and mouse PAR4 are functionally distinct receptors: Studies in novel humanized mice. J Thromb Haemost 2022; 20:1236-1247. [PMID: 35152546 DOI: 10.1111/jth.15669] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 08/31/2023]
Abstract
BACKGROUND Human and mouse platelets both express protease-activated receptor (PAR) 4 but sequence alignment reveals differences in several functional domains. These differences may result in functional disparities between the receptors which make it difficult to translate PAR4 studies using mice to human platelet physiology. OBJECTIVES To generate transgenic mice that express human, but not mouse, PAR4 and directly compare human and mouse PAR4 function in the same platelet environment. METHODS Transgenic mice were made using a genomic clone of the F2RL3 gene (encoding PAR4) and backcrossed with Par4 KO mice. For certain experiments, mice were bred with GRK6 KO mice. Tail bleeding time and platelet function in response to PAR4-activating peptide were assessed. RESULTS Human F2RL3 was successfully integrated into the mouse genome, transgenic mice were crossed to the mPar4 KO background (PAR4 tg/KO), and PAR4 was functionally expressed on platelets. Compared to WT, PAR4 tg/KO mice exhibited shortened tail bleeding time and their platelets were more responsive to PAR4-AP as assessed by α-granule release and integrin activation. The opposite was observed with thrombin. Knocking out GRK6 had no effect on human PAR4-expressing platelets, unlike mouse Par4-expressing platelets. PAR4 tg/KO platelets exhibited greater Ca2+ area under the curve and more robust extracellular vesicle release than WT stimulated with PAR4-AP. CONCLUSION These data suggest that (1) human PAR4- and mouse Par4-mediated signaling are different and (2) the feedback regulation mechanisms of human and mouse PAR4 are different. These functional differences are important to consider when interpreting PAR4 studies done with mice.
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Affiliation(s)
- Stephanie A Renna
- Department of Medicine, The Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - James V Michael
- Department of Medicine, The Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Xianguo Kong
- Department of Medicine, The Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Lin Ma
- Department of Medicine, The Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Peisong Ma
- Department of Medicine, The Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Marvin T Nieman
- Department of Medicine, The Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Leonard C Edelstein
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
| | - Steven E McKenzie
- Department of Medicine, The Cardeza Foundation for Hematologic Research, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, USA
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27
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Kuzmin A, Orekhov P, Astashkin R, Gordeliy V, Gushchin I. Structure and dynamics of the SARS-CoV-2 envelope protein monomer. Proteins 2022; 90:1102-1114. [PMID: 35119706 DOI: 10.1002/prot.26317] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/09/2022] [Accepted: 01/31/2022] [Indexed: 12/11/2022]
Abstract
Coronaviruses, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), present an ongoing threat to human wellbeing. Consequently, elucidation of molecular determinants of their function and interaction with the host is an important task. Whereas some of the coronaviral proteins are extensively characterized, others remain understudied. Here, we use molecular dynamics simulations to analyze the structure and dynamics of the SARS-CoV-2 envelope (E) protein (a viroporin) in the monomeric form. The protein consists of the hydrophobic α-helical transmembrane domain (TMD) and amphiphilic α-helices H2 and H3, connected by flexible linkers. We show that TMD has a preferable orientation in the membrane, while H2 and H3 reside at the membrane surface. Orientation of H2 is strongly influenced by palmitoylation of cysteines Cys40, Cys43, and Cys44. Glycosylation of Asn66 affects the orientation of H3. We also observe that the monomeric E protein both generates and senses the membrane curvature, preferably localizing with the C-terminus at the convex regions of the membrane; the protein in the pentameric form displays these properties as well. Localization to curved regions may be favorable for assembly of the E protein oligomers, whereas induction of curvature may facilitate the budding of the viral particles. The presented results may be helpful for a better understanding of the function of the coronaviral E protein and viroporins in general, and for overcoming the ongoing SARS-CoV-2 pandemic.
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Affiliation(s)
- Alexander Kuzmin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Roman Astashkin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Valentin Gordeliy
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.,Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.,JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
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28
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Local and substrate-specific S-palmitoylation determines subcellular localization of Gαo. Nat Commun 2022; 13:2072. [PMID: 35440597 PMCID: PMC9018777 DOI: 10.1038/s41467-022-29685-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Peripheral membrane proteins (PMPs) associate with cellular membranes through post-translational modifications like S-palmitoylation. The Golgi apparatus is generally viewed as the transitory station where palmitoyl acyltransferases (PATs) modify PMPs, which are then transported to their ultimate destinations such as the plasma membrane (PM). However, little substrate specificity among the many PATs has been determined. Here we describe the inherent partitioning of Gαo - α-subunit of heterotrimeric Go proteins - to PM and Golgi, independent from Golgi-to-PM transport. A minimal code within Gαo N-terminus governs its compartmentalization and re-coding produces G protein versions with shifted localization. We establish the S-palmitoylation at the outer nuclear membrane assay ("SwissKASH") to probe substrate specificity of PATs in intact cells. With this assay, we show that PATs localizing to different membrane compartments display remarkable substrate selectivity, which is the basis for PMP compartmentalization. Our findings uncover a mechanism governing protein localization and establish the basis for innovative drug discovery.
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29
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Pan S, Chen R. Pathological implication of protein post-translational modifications in cancer. Mol Aspects Med 2022; 86:101097. [PMID: 35400524 PMCID: PMC9378605 DOI: 10.1016/j.mam.2022.101097] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/07/2023]
Abstract
Protein post-translational modifications (PTMs) profoundly influence protein functions and play crucial roles in essentially all cell biological processes. The diverse realm of PTMs and their crosstalk is linked to many critical signaling events involved in neoplastic transformation, carcinogenesis and metastasis. The pathological roles of various PTMs are implicated in all aspects of cancer hallmark functions, cancer metabolism and regulation of tumor microenvironment. Study of PTMs has become an important area in cancer research to understand cancer biology and discover novel biomarkers and therapeutic targets. With a limited scope, this review attempts to discuss some PTMs of high frequency with recognized importance in cancer biology, including phosphorylation, acetylation, glycosylation, palmitoylation and ubiquitination, as well as their implications in clinical applications. These protein modifications are among the most abundant PTMs and profoundly implicated in carcinogenesis.
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30
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Ramadan AA, Mayilsamy K, McGill AR, Ghosh A, Giulianotti MA, Donow HM, Mohapatra SS, Mohapatra S, Chandran B, Deschenes RJ, Roy A. Identification of SARS-CoV-2 Spike Palmitoylation Inhibitors That Results in Release of Attenuated Virus with Reduced Infectivity. Viruses 2022; 14:v14030531. [PMID: 35336938 PMCID: PMC8950683 DOI: 10.3390/v14030531] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/25/2022] [Accepted: 03/02/2022] [Indexed: 02/02/2023] Open
Abstract
The spike proteins of enveloped viruses are transmembrane glycoproteins that typically undergo post-translational attachment of palmitate on cysteine residues on the cytoplasmic facing tail of the protein. The role of spike protein palmitoylation in virus biogenesis and infectivity is being actively studied as a potential target of novel antivirals. Here, we report that palmitoylation of the first five cysteine residues of the C-terminal cysteine-rich domain of the SARS-CoV-2 S protein are indispensable for infection, and palmitoylation-deficient spike mutants are defective in membrane fusion. The DHHC9 palmitoyltransferase interacts with and palmitoylates the spike protein in the ER and Golgi and knockdown of DHHC9 results in reduced fusion and infection of SARS-CoV-2. Two bis-piperazine backbone-based DHHC9 inhibitors inhibit SARS-CoV-2 S protein palmitoylation and the resulting progeny virion particles released are defective in fusion and infection. This establishes these palmitoyltransferase inhibitors as potential new intervention strategies against SARS-CoV-2.
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Affiliation(s)
- Ahmed A. Ramadan
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
| | - Karthick Mayilsamy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Department of Veterans Affairs, James A Haley Veterans Hospital, Tampa, FL 33612, USA
| | - Andrew R. McGill
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Department of Veterans Affairs, James A Haley Veterans Hospital, Tampa, FL 33612, USA
- Department of Internal Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Anandita Ghosh
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
| | - Marc A. Giulianotti
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (M.A.G.); (H.M.D.)
| | - Haley M. Donow
- Center for Translational Science, Florida International University, Port St. Lucie, FL 34987, USA; (M.A.G.); (H.M.D.)
| | - Shyam S. Mohapatra
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Department of Veterans Affairs, James A Haley Veterans Hospital, Tampa, FL 33612, USA
- Department of Internal Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Subhra Mohapatra
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Department of Veterans Affairs, James A Haley Veterans Hospital, Tampa, FL 33612, USA
| | - Bala Chandran
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
| | - Robert J. Deschenes
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Correspondence: (R.J.D.); (A.R.); Tel.: +1-(813)-974-6393 (R.J.D.); +1-(813)-974-5540 (A.R.)
| | - Arunava Roy
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA; (A.A.R.); (K.M.); (A.R.M.); (A.G.); (S.S.M.); (S.M.); (B.C.)
- Correspondence: (R.J.D.); (A.R.); Tel.: +1-(813)-974-6393 (R.J.D.); +1-(813)-974-5540 (A.R.)
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Qu H, Jin Q, Quan C. CLDN6: From Traditional Barrier Function to Emerging Roles in Cancers. Int J Mol Sci 2021; 22:ijms222413416. [PMID: 34948213 PMCID: PMC8705207 DOI: 10.3390/ijms222413416] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/06/2021] [Accepted: 12/12/2021] [Indexed: 02/07/2023] Open
Abstract
Claudins (CLDNs) are the most important tight junction proteins, which are mainly expressed in endothelial cells or epithelial cells in a tissue-specific manner. As a member of the CLDNs family, CLDN6 is highly expressed in fetal tissues such as the stomach, pancreas, lung, and kidney, but is not expressed in corresponding adult tissues. The expression of CLDN6 is regulated by a variety of factors, including but not limited to stimuli and transcription factors, DNA methylation, and post-translational modifications. CLDN6 has been found to have a key role in the formation of barriers, especially the lung epithelial barrier and the epidermal permeability barrier (EPB). Importantly, the roles of CLDN6 in cancers have gained focus and are being investigated in recent years. Strong evidence indicates that the altered expression of CLDN6 is linked to the development of various cancers. Malignant phenotypes of tumors affected by CLDN6 include proliferation and apoptosis, migration and invasion, and drug resistance, which are regulated by CLDN6-mediated key signaling pathways. Given the important role in tumors and its low or no expression in normal tissues, CLDN6 is an ideal target for tumor therapy. This review aims to provide an overview of the structure and regulation of CLDN6, and its traditional barrier function, with a special emphasis on its emerging roles in cancers, including its impact on the malignant phenotypes, signal-modulating effects, the prognosis of tumor patients, and clinical applications in cancers.
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A bioorthogonal chemical reporter for fatty acid synthase-dependent protein acylation. J Biol Chem 2021; 297:101272. [PMID: 34606827 PMCID: PMC8551652 DOI: 10.1016/j.jbc.2021.101272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 02/07/2023] Open
Abstract
Mammalian cells acquire fatty acids (FAs) from dietary sources or via de novo palmitate production by fatty acid synthase (FASN). Although most cells express FASN at low levels, it is upregulated in cancers of the breast, prostate, and liver, among others, and is required during the replication of many viruses, such as dengue virus, hepatitis C, HIV-1, hepatitis B, and severe acute respiratory syndrome coronavirus 2, among others. The precise role of FASN in disease pathogenesis is poorly understood, and whether de novo FA synthesis contributes to host or viral protein acylation has been traditionally difficult to study. Here, we describe a cell-permeable and click chemistry-compatible alkynyl acetate analog (alkynyl acetic acid or 5-hexynoic acid [Alk-4]) that functions as a reporter of FASN-dependent protein acylation. In an FASN-dependent manner, Alk-4 selectively labels the cellular protein interferon-induced transmembrane protein 3 at its known palmitoylation sites, a process that is essential for the antiviral activity of the protein, and the HIV-1 matrix protein at its known myristoylation site, a process that is required for membrane targeting and particle assembly. Alk-4 metabolic labeling also enabled biotin-based purification and identification of more than 200 FASN-dependent acylated cellular proteins. Thus, Alk-4 is a useful bioorthogonal tool to selectively probe FASN-mediated protein acylation in normal and diseased states.
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33
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Hashimoto Y, Campbell M, Tachibana K, Okada Y, Kondoh M. Claudin-5: A Pharmacological Target to Modify the Permeability of the Blood-Brain Barrier. Biol Pharm Bull 2021; 44:1380-1390. [PMID: 34602546 DOI: 10.1248/bpb.b21-00408] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Claudin-5 is the dominant tight junction protein in brain endothelial cells and exclusively limits the paracellular permeability of molecules larger than 400 Da across the blood-brain barrier (BBB). Its pathological impairment or sustained down-regulation has been shown to lead to the progression of psychiatric and neurological disorders, whereas its expression under physiological conditions prevents the passage of drugs across the BBB. While claudin-5 enhancers could potentially act as vascular stabilizers to treat neurological diseases, claudin-5 inhibitors could function as delivery systems to enhance the brain uptake of hydrophilic small-molecular-weight drugs. Therefore, the effects of claudin-5 manipulation on modulating the BBB in different neurological diseases requires further examination. To manipulate claudin-5 expression levels and function, several claudin-5 modulating molecules have been developed. In this review, we first describe the molecular, cellular and pathological aspects of claudin-5 to highlight the mechanisms of claudin-5 enhancers/inhibitors. We then discuss recently developed claudin-5 enhancers/inhibitors and new methods to discover these molecules.
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Affiliation(s)
| | | | | | - Yoshiaki Okada
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Masuo Kondoh
- Graduate School of Pharmaceutical Sciences, Osaka University
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34
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Wu D, Robinson CV. Connecting ‘multi-omics’ approaches to endogenous protein complexes. TRENDS IN CHEMISTRY 2021. [DOI: 10.1016/j.trechm.2021.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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35
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Chen JJ, Fan Y, Boehning D. Regulation of Dynamic Protein S-Acylation. Front Mol Biosci 2021; 8:656440. [PMID: 33981723 PMCID: PMC8107437 DOI: 10.3389/fmolb.2021.656440] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022] Open
Abstract
Protein S-acylation is the reversible addition of fatty acids to the cysteine residues of target proteins. It regulates multiple aspects of protein function, including the localization to membranes, intracellular trafficking, protein interactions, protein stability, and protein conformation. This process is regulated by palmitoyl acyltransferases that have the conserved amino acid sequence DHHC at their active site. Although they have conserved catalytic cores, DHHC enzymes vary in their protein substrate selection, lipid substrate preference, and regulatory mechanisms. Alterations in DHHC enzyme function are associated with many human diseases, including cancers and neurological conditions. The removal of fatty acids from acylated cysteine residues is catalyzed by acyl protein thioesterases. Notably, S-acylation is now known to be a highly dynamic process, and plays crucial roles in signaling transduction in various cell types. In this review, we will explore the recent findings on protein S-acylation, the enzymatic regulation of this process, and discuss examples of dynamic S-acylation.
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36
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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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37
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Zhang T, Gaffrey MJ, Li X, Qian WJ. Characterization of cellular oxidative stress response by stoichiometric redox proteomics. Am J Physiol Cell Physiol 2020; 320:C182-C194. [PMID: 33264075 DOI: 10.1152/ajpcell.00040.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The thiol redox proteome refers to all proteins whose cysteine thiols are subjected to various redox-dependent posttranslational modifications (PTMs) including S-glutathionylation (SSG), S-nitrosylation (SNO), S-sulfenylation (SOH), and S-sulfhydration (SSH). These modifications can impact various aspects of protein function such as activity, binding, conformation, localization, and interactions with other molecules. To identify novel redox proteins in signaling and regulation, it is highly desirable to have robust redox proteomics methods that can provide global, site-specific, and stoichiometric quantification of redox PTMs. Mass spectrometry (MS)-based redox proteomics has emerged as the primary platform for broad characterization of thiol PTMs in cells and tissues. Herein, we review recent advances in MS-based redox proteomics approaches for quantitative profiling of redox PTMs at physiological or oxidative stress conditions and highlight some recent applications. Considering the relative maturity of available methods, emphasis will be on two types of modifications: 1) total oxidation (i.e., all reversible thiol modifications), the level of which represents the overall redox state, and 2) S-glutathionylation, a major form of reversible thiol oxidation. We also discuss the significance of stoichiometric measurements of thiol PTMs as well as future perspectives toward a better understanding of cellular redox regulatory networks in cells and tissues.
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Affiliation(s)
- Tong Zhang
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Matthew J Gaffrey
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Xiaolu Li
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.,Bioproducts Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
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38
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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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39
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Barth M, Schmidt C. Native mass spectrometry-A valuable tool in structural biology. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4578. [PMID: 32662584 DOI: 10.1002/jms.4578] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Proteins and the complexes they form with their ligands are the players of cellular action. Their function is directly linked with their structure making the structural analysis of protein-ligand complexes essential. Classical techniques of structural biology include X-ray crystallography, nuclear magnetic resonance spectroscopy and recently distinguished cryo-electron microscopy. However, protein-ligand complexes are often dynamic and heterogeneous and consequently challenging for these techniques. Alternative approaches are therefore needed and gained importance during the last decades. One alternative is native mass spectrometry, which is the analysis of intact protein complexes in the gas phase. To achieve this, sample preparation and instrument conditions have to be optimised. Native mass spectrometry then reveals stoichiometry, protein interactions and topology of protein assemblies. Advanced techniques such as ion mobility and high-resolution mass spectrometry further add to the range of applications and deliver information on shape and microheterogeneity of the complexes. In this tutorial, we explain the basics of native mass spectrometry including sample requirements, instrument modifications and interpretation of native mass spectra. We further discuss the developments of native mass spectrometry and provide example spectra and applications.
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Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
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40
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Zmuda F, Chamberlain LH. Regulatory effects of post-translational modifications on zDHHC S-acyltransferases. J Biol Chem 2020; 295:14640-14652. [PMID: 32817054 PMCID: PMC7586229 DOI: 10.1074/jbc.rev120.014717] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
The human zDHHC S-acyltransferase family comprises 23 enzymes that mediate the S-acylation of a multitude of cellular proteins, including channels, receptors, transporters, signaling molecules, scaffolds, and chaperones. This reversible post-transitional modification (PTM) involves the attachment of a fatty acyl chain, usually derived from palmitoyl-CoA, to specific cysteine residues on target proteins, which affects their stability, localization, and function. These outcomes are essential to control many processes, including synaptic transmission and plasticity, cell growth and differentiation, and infectivity of viruses and other pathogens. Given the physiological importance of S-acylation, it is unsurprising that perturbations in this process, including mutations in ZDHHC genes, have been linked to different neurological pathologies and cancers, and there is growing interest in zDHHC enzymes as novel drug targets. Although zDHHC enzymes control a diverse array of cellular processes and are associated with major disorders, our understanding of these enzymes is surprisingly incomplete, particularly with regard to the regulatory mechanisms controlling these enzymes. However, there is growing evidence highlighting the role of different PTMs in this process. In this review, we discuss how PTMs, including phosphorylation, S-acylation, and ubiquitination, affect the stability, localization, and function of zDHHC enzymes and speculate on possible effects of PTMs that have emerged from larger screening studies. Developing a better understanding of the regulatory effects of PTMs on zDHHC enzymes will provide new insight into the intracellular dynamics of S-acylation and may also highlight novel approaches to modulate S-acylation for clinical gain.
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Affiliation(s)
- Filip Zmuda
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
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41
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Yuan M, Chen X, Sun Y, Jiang L, Xia Z, Ye K, Jiang H, Yang B, Ying M, Cao J, He Q. ZDHHC12-mediated claudin-3 S-palmitoylation determines ovarian cancer progression. Acta Pharm Sin B 2020; 10:1426-1439. [PMID: 32963941 PMCID: PMC7488353 DOI: 10.1016/j.apsb.2020.03.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/18/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
The membrane protein claudin-3 (CLDN3) is critical for the formation and maintenance of tight junction and its high expression has been implicated in dictating malignant progression in various cancers. However, the post-translational modification of CLDN3 and its biological function remains poorly understood. Here, we report that CLDN3 is positively correlated with ovarian cancer progression both in vitro and in vivo. Of interest, CLDN3 undergoes S-palmitoylation on three juxtamembrane cysteine residues, which contribute to the accurate plasma membrane localization and protein stability of CLDN3. Moreover, the deprivation of S-palmitoylation in CLDN3 significantly abolishes its tumorigenic promotion effect in ovarian cancer cells. By utilizing the co-immunoprecipitation assay, we further identify ZDHHC12 as a CLDN3-targating palmitoyltransferase from 23 ZDHHC family proteins. Furthermore, the knockdown of ZDHHC12 also significantly inhibits CLDN3 accurate membrane localization, protein stability and ovarian cancer cells tumorigenesis. Thus, our work reveals S-palmitoylation as a novel regulatory mechanism that modulates CLDN3 function, which implies that targeting ZDHHC12-mediated CLDN3 S-palmitoylation might be a potential strategy for ovarian cancer therapy.
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Affiliation(s)
- Meng Yuan
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaobing Chen
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yitang Sun
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Li Jiang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhongni Xia
- Tongde Hospital of Zhejiang Province, Hangzhou 310012, China
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Hong Jiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 100098, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Meidan Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ji Cao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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42
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Orinska Z, Hagemann PM, Halova I, Draber P. Tetraspanins in the regulation of mast cell function. Med Microbiol Immunol 2020; 209:531-543. [PMID: 32507938 PMCID: PMC7395004 DOI: 10.1007/s00430-020-00679-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/06/2020] [Indexed: 12/13/2022]
Abstract
Mast cells (MCs) are long-living immune cells highly specialized in the storage and release of different biologically active compounds and are involved in the regulation of innate and adaptive immunity. MC degranulation and replacement of MC granules are accompanied by active membrane remodelling. Tetraspanins represent an evolutionary conserved family of transmembrane proteins. By interacting with lipids and other membrane and intracellular proteins, they are involved in organisation of membrane protein complexes and act as "molecular facilitators" connecting extracellular and cytoplasmic signaling elements. MCs express different tetraspanins and MC degranulation is accompanied by changes in membrane organisation. Therefore, tetraspanins are very likely involved in the regulation of MC exocytosis and membrane reorganisation after degranulation. Antiviral response and production of exosomes are further aspects of MC function characterized by dynamic changes of membrane organization. In this review, we pay a particular attention to tetraspanin gene expression in different human and murine MC populations, discuss tetraspanin involvement in regulation of key MC signaling complexes, and analyze the potential contribution of tetraspanins to MC antiviral response and exosome production. In-depth knowledge of tetraspanin-mediated molecular mechanisms involved in different aspects of the regulation of MC response will be beneficial for patients with allergies, characterized by overwhelming MC reactions.
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Affiliation(s)
- Zane Orinska
- Division of Experimental Pneumology, Research Center Borstel, Leibniz Lungenzentrum, Airway Research Center North, German Center for Lung Research (DZL), Borstel, Germany.
| | - Philipp M Hagemann
- Division of Experimental Pneumology, Research Center Borstel, Leibniz Lungenzentrum, Airway Research Center North, German Center for Lung Research (DZL), Borstel, Germany
| | - Ivana Halova
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Draber
- Department of Signal Transduction, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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43
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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44
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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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45
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Meoli L, Günzel D. Channel functions of claudins in the organization of biological systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183344. [PMID: 32442419 DOI: 10.1016/j.bbamem.2020.183344] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/27/2020] [Accepted: 05/05/2020] [Indexed: 02/07/2023]
Abstract
Claudins are tight junction proteins mostly appreciated in their function of paracellular barrier-formation. Compared to a virtual absence of any tight junctions, their paracellular sealing role certainly stands out. Yet, it was recognized immediately after the discovery of the first claudins, that some members of the claudin protein family were able to convey size and charge selectivity to the paracellular pathway. Thus, paracellular permeability can be fine-tuned according to the physiological needs of a tissue by inserting these channel-forming claudins into tight junction strands. Precise permeability adjustment is further suggested by the presence of numerous isoforms of channel-forming claudins (claudin-10b-, -15-, -16-like isoforms) in various vertebrate taxa. Moreover, their expression and localization are controlled by multiple transcriptional and posttranslational mechanisms. Consequently, mutation or dysregulation of channel-forming claudins can cause severe diseases. The present review therefore aims at providing an up-to-date report of the current research on these aspects of channel-forming claudins and their possible implications on future developments.
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Affiliation(s)
- Luca Meoli
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology, Rheumatology, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany
| | - Dorothee Günzel
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology, Rheumatology, Charité - Universitätsmedizin Berlin, 12203 Berlin, Germany.
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46
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Potential Plasticity of the Mannoprotein Repertoire Associated to Mycobacterium tuberculosis Virulence Unveiled by Mass Spectrometry-Based Glycoproteomics. Molecules 2020; 25:molecules25102348. [PMID: 32443484 PMCID: PMC7287972 DOI: 10.3390/molecules25102348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/04/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
To date, Mycobacterium tuberculosis (Mtb) remains the world’s greatest infectious killer. The rise of multidrug-resistant strains stresses the need to identify new therapeutic targets to fight the epidemic. We previously demonstrated that bacterial protein-O-mannosylation is crucial for Mtb infectiousness, renewing the interest of the bacterial-secreted mannoproteins as potential drug-targetable virulence factors. The difficulty of inventorying the mannoprotein repertoire expressed by Mtb led us to design a stringent multi-step workflow for the reliable identification of glycosylated peptides by large-scale mass spectrometry-based proteomics. Applied to the differential analyses of glycoproteins secreted by the wild-type Mtb strain—and by its derived mutant invalidated for the protein-O-mannosylating enzyme PMTub—this approach led to the identification of not only most already known mannoproteins, but also of yet-unknown mannosylated proteins. In addition, analysis of the glycoproteome expressed by the isogenic recombinant Mtb strain overexpressing the PMTub gene revealed an unexpected mannosylation of proteins, with predicted or demonstrated functions in Mtb growth and interaction with the host cell. Since in parallel, a transient increased expression of the PMTub gene has been observed in the wild-type bacilli when infecting macrophages, our results strongly suggest that the Mtb mannoproteome may undergo adaptive regulation during infection of the host cells. Overall, our results provide deeper insights into the complexity of the repertoire of mannosylated proteins expressed by Mtb, and open the way to novel opportunities to search for still-unexploited potential therapeutic targets.
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Palmitoylation of the K ATP channel Kir6.2 subunit promotes channel opening by regulating PIP 2 sensitivity. Proc Natl Acad Sci U S A 2020; 117:10593-10602. [PMID: 32332165 DOI: 10.1073/pnas.1918088117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A physiological role for long-chain acyl-CoA esters to activate ATP-sensitive K+ (KATP) channels is well established. Circulating palmitate is transported into cells and converted to palmitoyl-CoA, which is a substrate for palmitoylation. We found that palmitoyl-CoA, but not palmitic acid, activated the channel when applied acutely. We have altered the palmitoylation state by preincubating cells with micromolar concentrations of palmitic acid or by inhibiting protein thioesterases. With acyl-biotin exchange assays we found that Kir6.2, but not sulfonylurea receptor (SUR)1 or SUR2, was palmitoylated. These interventions increased the KATP channel mean patch current, increased the open time, and decreased the apparent sensitivity to ATP without affecting surface expression. Similar data were obtained in transfected cells, rat insulin-secreting INS-1 cells, and isolated cardiac myocytes. Kir6.2ΔC36, expressed without SUR, was also positively regulated by palmitoylation. Mutagenesis of Kir6.2 Cys166 prevented these effects. Clinical variants in KCNJ11 that affect Cys166 had a similar gain-of-function phenotype, but was more pronounced. Molecular modeling studies suggested that palmitoyl-C166 and selected large hydrophobic mutations make direct hydrophobic contact with Kir6.2-bound PIP2 Patch-clamp studies confirmed that palmitoylation of Kir6.2 at Cys166 enhanced the PIP2 sensitivity of the channel. Physiological relevance is suggested since palmitoylation blunted the regulation of KATP channels by α1-adrenoreceptor stimulation. The Cys166 residue is conserved in some other Kir family members (Kir6.1 and Kir3, but not Kir2), which are also subject to regulated palmitoylation, suggesting a general mechanism to control the open state of certain Kir channels.
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Neviani V, van Deventer S, Wörner TP, Xenaki KT, van de Waterbeemd M, Rodenburg RNP, Wortel IMN, Kuiper JK, Huisman S, Granneman J, van Bergen En Henegouwen PMP, Heck AJR, van Spriel AB, Gros P. Site-specific functionality and tryptophan mimicry of lipidation in tetraspanin CD9. FEBS J 2020; 287:5323-5344. [PMID: 32181977 PMCID: PMC7818406 DOI: 10.1111/febs.15295] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/19/2020] [Accepted: 03/13/2020] [Indexed: 12/18/2022]
Abstract
Lipidation of transmembrane proteins regulates many cellular activities, including signal transduction, cell–cell communication, and membrane trafficking. However, how lipidation at different sites in a membrane protein affects structure and function remains elusive. Here, using native mass spectrometry we determined that wild‐type human tetraspanins CD9 and CD81 exhibit nonstochastic distributions of bound acyl chains. We revealed CD9 lipidation at its three most frequent lipidated sites suffices for EWI‐F binding, while cysteine‐to‐alanine CD9 mutations markedly reduced binding of EWI‐F. EWI‐F binding by CD9 was rescued by mutating all or, albeit to a lesser extent, only the three most frequently lipidated sites into tryptophans. These mutations did not affect the nanoscale distribution of CD9 in cell membranes, as shown by super‐resolution microscopy using a CD9‐specific nanobody. Thus, these data demonstrate site‐specific, possibly conformation‐dependent, functionality of lipidation in tetraspanin CD9 and identify tryptophan mimicry as a possible biochemical approach to study site‐specific transmembrane‐protein lipidation.
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Affiliation(s)
- Viviana Neviani
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Sjoerd van Deventer
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Tobias P Wörner
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Katerina T Xenaki
- Cell Biology, Department of Biology, Utrecht University, The Netherlands
| | - Michiel van de Waterbeemd
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Remco N P Rodenburg
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Inge M N Wortel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Jeroen K Kuiper
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Sofie Huisman
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Joke Granneman
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | | | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Department of Chemistry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands
| | - Annemiek B van Spriel
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud UMC, Nijmegen, The Netherlands
| | - Piet Gros
- Crystal and Structural Chemistry, Department of Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
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Oda Y, Sugawara T, Fukata Y, Izumi Y, Otani T, Higashi T, Fukata M, Furuse M. The extracellular domain of angulin-1 and palmitoylation of its cytoplasmic region are required for angulin-1 assembly at tricellular contacts. J Biol Chem 2020; 295:4289-4302. [PMID: 32079676 PMCID: PMC7105312 DOI: 10.1074/jbc.ra119.010491] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 02/13/2020] [Indexed: 12/13/2022] Open
Abstract
Tricellular tight junctions (tTJs) create paracellular barriers at tricellular contacts (TCs), where the vertices of three polygonal epithelial cells meet. tTJs are marked by the enrichment of two types of membrane proteins, tricellulin and angulin family proteins. However, how TC geometry is recognized for tTJ formation remains unknown. In the present study, we examined the molecular mechanism for the assembly of angulin-1 at the TCs. We found that clusters of cysteine residues in the juxtamembrane region within the cytoplasmic domain of angulin-1 are highly palmitoylated. Mutagenesis analyses of the cysteine residues in this region revealed that palmitoylation is essential for localization of angulin-1 at TCs. Consistently, suppression of Asp-His-His-Cys motif-containing palmitoyltransferases expressed in EpH4 cells significantly impaired the TC localization of angulin-1. Cholesterol depletion from the plasma membrane of cultured epithelial cells hampered the localization of angulin-1 at TCs, suggesting the existence of a lipid membrane microdomain at TCs that attracts highly palmitoylated angulin-1. Furthermore, the extracellular domain of angulin-1 was also required for its TC localization, irrespective of the intracellular palmitoylation. Taken together, our findings suggest that both angulin-1's extracellular domain and palmitoylation of its cytoplasmic region are required for its assembly at TCs.
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Affiliation(s)
- Yukako Oda
- Division of Cell Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Taichi Sugawara
- Division of Cell Structure, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Yuko Fukata
- Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka Myodaiji, Okazaki, Aichi 444-8585, Japan; Division of Membrane Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Yasushi Izumi
- Division of Cell Structure, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Tetsuhisa Otani
- Division of Cell Structure, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Tomohito Higashi
- Division of Cell Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
| | - Masaki Fukata
- Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka Myodaiji, Okazaki, Aichi 444-8585, Japan; Division of Membrane Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Mikio Furuse
- Division of Cell Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; Division of Cell Structure, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Physiological Sciences, School of Life Science, Graduate University for Advanced Studies, SOKENDAI, 38 Nishigonaka Myodaiji, Okazaki, Aichi 444-8585, Japan.
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50
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Assembly of Tight Junction Strands: Claudin-10b and Claudin-3 Form Homo-Tetrameric Building Blocks that Polymerise in a Channel-Independent Manner. J Mol Biol 2020; 432:2405-2427. [DOI: 10.1016/j.jmb.2020.02.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/12/2020] [Accepted: 02/28/2020] [Indexed: 02/03/2023]
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