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Busquets-Hernández C, Ribó S, Gratacós-Batlle E, Carbajo D, Tsiotsia A, Blanco-Canosa JB, Chamberlain LH, Triola G. Quantitative analysis of protein lipidation and acyl-CoAs reveals substrate preferences of the S-acylation machinery. Chem Sci 2024; 15:12845-12855. [PMID: 39148806 PMCID: PMC11322976 DOI: 10.1039/d4sc02235a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 07/08/2024] [Indexed: 08/17/2024] Open
Abstract
Protein palmitoylation or S-acylation has emerged as a key regulator of cellular processes. Increasing evidence shows that this modification is not restricted to palmitate but it can include additional fatty acids, raising the possibility that differential S-acylation contributes to the fine-tuning of protein activity. However, methods to profile the acyl moieties attached to proteins are scarce. Herein, we report a method for the identification and quantification of lipids bound to proteins that relies on hydroxylamine treatment and mass spectrometry analysis of fatty acid hydroxamates. This method has enabled unprecedented and extensive profiling of the S-acylome in different cell lines and tissues and has shed light on the substrate specificity of some S-acylating enzymes. Moreover, we could extend it to quantify also the acyl-CoAs, which are thioesters formed between a fatty acid and a coenzyme A, overcoming many of the previously described challenges for the detection of such species. Importantly, the simultaneous analysis of the lipid fraction and the proteome allowed us to establish, for the first time, a direct correlation between the endogenous levels of acyl-CoAs and the S-acylation profile of its proteome.
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Affiliation(s)
- Carla Busquets-Hernández
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Silvia Ribó
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Esther Gratacós-Batlle
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Daniel Carbajo
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Alexandra Tsiotsia
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Juan B Blanco-Canosa
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde Glasgow UK
| | - Gemma Triola
- Department of Biological Chemistry, Institute for Advanced Chemistry of Catalonia (IQAC-CSIC) Barcelona Spain
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2
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Cai J, Song M, Li M, Merchant M, Benz F, McClain C, Klein J. Site-Specific Identification of Protein S-Acylation by IodoTMT0 Labeling and Immobilized Anti-TMT Antibody Resin Enrichment. J Proteome Res 2024; 23:673-683. [PMID: 38157263 DOI: 10.1021/acs.jproteome.3c00525] [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] [Indexed: 01/03/2024]
Abstract
Protein S-acylation is a reversible post-translational modification (PTM). It is present on diverse proteins and has important roles in regulating protein function. Aminolysis with hydroxylamine is widely used in the global identification of the PTM. However, the identification is indirect. Distinct criteria have been used for identification, and the false discovery rate has not been addressed. Here, we report a site-specific method for S-acylation identification based on tagging of S-acylation sites with iodoTMT0. Efforts to improve the performance of the method and confidence of identification are discussed, highlighting the importance of reducing contaminant peptides and keeping the recovery rate consistent between aliquots with or without hydroxylamine treatment. With very stringent criteria, presumptive S-acylation sites of 269, 684, 695, and 780 were identified from HK2 cells, HK11 cells, mouse brain, and mouse liver samples, respectively. Among them, the newly identified protein S-acylation sites are equivalent to 34% of human and 24% of mouse S-acylation sites reported previously. In addition, false-positive rates for S-acylation identification and S-acylation abundances were estimated. Significant differences in S-acylation abundance were found from different samples (from 0.08% in HK2 cells to 0.76% in mouse brain), and the false-positive rates were significantly higher for samples with a low abundance of S-acylation.
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Affiliation(s)
- Jian Cai
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky 40292, United States
| | - Ming Song
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center, University of Louisville, Louisville, Kentucky 40292, United States
| | - Ming Li
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky 40292, United States
| | - Michael Merchant
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky 40292, United States
| | - Frederick Benz
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky 40202, United States
| | - Craig McClain
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky 40292, United States
- Hepatobiology and Toxicology Center, University of Louisville, Louisville, Kentucky 40292, United States
- Department of Pharmacology and Toxicology, University of Louisville School of Medicine, Louisville, Kentucky 40202, United States
- Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky 40292, United States
- Alcohol Research Center, University of Louisville, Louisville, Kentucky 40202, United States
| | - Jon Klein
- Division of Nephrology and Hypertension, Department of Medicine, University of Louisville School of Medicine, Louisville, Kentucky 40292, United States
- Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky 40292, United States
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3
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Sun Q, Xing X, Wang H, Wan K, Fan R, Liu C, Wang Y, Wu W, Wang Y, Wang R. SCD1 is the critical signaling hub to mediate metabolic diseases: Mechanism and the development of its inhibitors. Biomed Pharmacother 2024; 170:115586. [PMID: 38042113 DOI: 10.1016/j.biopha.2023.115586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 12/04/2023] Open
Abstract
Metabolic diseases, featured with dysregulated energy homeostasis, have become major global health challenges. Patients with metabolic diseases have high probability to manifest multiple complications in lipid metabolism, e.g. obesity, insulin resistance and fatty liver. Therefore, targeting the hub genes in lipid metabolism may systemically ameliorate the metabolic diseases, along with the complications. Stearoyl-CoA desaturase 1(SCD1) is a key enzyme that desaturates the saturated fatty acids (SFAs) derived from de novo lipogenesis or diet to generate monounsaturated fatty acids (MUFAs). SCD1 maintains the metabolic and tissue homeostasis by responding to, and integrating the multiple layers of endogenous stimuli, which is mediated by the synthesized MUFAs. It critically regulates a myriad of physiological processes, including energy homeostasis, development, autophagy, tumorigenesis and inflammation. Aberrant transcriptional and epigenetic activation of SCD1 regulates AMPK/ACC, SIRT1/PGC1α, NcDase/Wnt, etc, and causes aberrant lipid accumulation, thereby promoting the progression of obesity, non-alcoholic fatty liver, diabetes and cancer. This review critically assesses the integrative mechanisms of the (patho)physiological functions of SCD1 in metabolic homeostasis, inflammation and autophagy. For translational perspective, potent SCD1 inhibitors have been developed to treat various types of cancer. We thus discuss the multidisciplinary advances that greatly accelerate the development of SCD1 new inhibitors. In conclusion, besides cancer treatment, SCD1 may serve as the promising target to combat multiple metabolic complications simultaneously.
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Affiliation(s)
- Qin Sun
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Xiaorui Xing
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Huanyu Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Kang Wan
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Ruobing Fan
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Cheng Liu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Yongjian Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Wenyi Wu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China
| | - Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China.
| | - Ru Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, China.
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4
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Kalantary-Charvadeh A, Hosseini V, Mehdizadeh A, Nazari Soltan Ahmad S, Rahbarghazi R, Nozad Charoudeh H, Nouri M, Darabi M. The porcupine inhibitor WNT974 provokes ectodermal lineage differentiation of human embryonic stem cells. Cell Biochem Funct 2022; 40:359-368. [PMID: 35445405 DOI: 10.1002/cbf.3700] [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: 12/01/2021] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 11/08/2022]
Abstract
Porcupine (Porcn) enzyme plays an essential role in Wnt signaling activation. Stearoyl-CoA desaturase-1 (SCD1) is required to provide Porcn substrates. The aim of this study was to determine the effect of a novel Porcn inhibitor on the fate of human embryonic stem cells (hESCs) and the reliance of Porcn on SCD1 activity. hESCs were cultured on a feeder layer or Matrigel-coated plates. Small molecules WNT974 (LGK-974) and CAY10566 were used to inhibit Porcn and SCD1 activity, respectively. We assessed the effect of Porcn inhibition on viability, expression of Wnt signaling targets, pluripotency markers, proliferation, differentiation, and protein fatty acylation. hESCs' conditioned medium (CM) containing secreted Wnt proteins were applied in rescue experiments. To examine the catalytic dependency of Porcn on SCD1, the results of combined inhibitor treatment were compared with the SCD1 inhibitor alone. LGK-974 at the selected concentrations showed mild effects on hESCs viability, but significantly reduced messenger RNA and protein expression of Wnt signaling targets (Axin-2 and c-Myc) and pluripotency markers (OCT-4 and SOX-2) (p < .05). Adding 1 μM of Porcn inhibitor reduced proliferation (p = .03) and enhanced differentiation capacity into ectodermal progenitors (p = .02), which were reverted by CM. Click chemistry reaction did not show significant alteration in protein fatty acylation upon LGK-974 treatment. Moreover, combined inhibitor treatment caused no further substantial reduction in Wnt signaling targets, pluripotency markers, and protein fatty acylation relative to CAY10566-treated cultures. The substrate availability for Porcn activity is regulated by SCD1 and targeting Porcn by LGK-974 prompts the transition of hESCs from self-renewal state to ectodermal lineage.
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Affiliation(s)
- Ashkan Kalantary-Charvadeh
- Department of Biochemistry and Clinical Laboratories, Tabriz University of Medical Sciences, Tabriz, Iran.,Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Hosseini
- Molecular Medicine Research Center, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Mehdizadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Nazari Soltan Ahmad
- Department of Biochemistry and Clinical Laboratories, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hojjatollah Nozad Charoudeh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Nouri
- Department of Biochemistry and Clinical Laboratories, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Darabi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Molecular Cell Biology Laboratory, Internal Medicine IV, University of Heidelberg, Heidelberg, Germany
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Kalantary-Charvadeh A, Hosseini V, Mehdizadeh A, Darabi M. Application of porcupine inhibitors in stem cell fate determination. Chem Biol Drug Des 2020; 96:1052-1068. [PMID: 32419352 DOI: 10.1111/cbdd.13704] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 04/27/2020] [Accepted: 05/03/2020] [Indexed: 02/06/2023]
Abstract
Porcupine (Porcn), a membrane-bound O-acyltransferase, is an endoplasmic reticulum-located protein that has catalytic activity. Porcn is involved in post-translational lipid modification of wingless-Int (Wnt) proteins and serves as an indispensable step in the Wnt proper secretion and signaling. Small-molecule inhibitors targeting Porcn catalytic function in vitro and in vivo are of great interest not only for treating cancer and fibrotic disorders but also in the field of regenerative medicine. Although a number of studies have been conducted, the exact role of Porcn in stem cell fate is not entirely clear. In some cases, Porcn inhibition declined differentiation rate, and in others, it induced stem cell differentiation toward specific lineages. In this review, we first elaborated the Porcn catalytic activity and its inhibitors. Then, we discussed about the recently reported results of Porcn inhibitors in stem cells self-renewal and differentiation.
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Affiliation(s)
- Ashkan Kalantary-Charvadeh
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Hosseini
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Mehdizadeh
- Endocrine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Masoud Darabi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Schulte-Zweckel J, Dwivedi M, Brockmeyer A, Janning P, Winter R, Triola G. A hydroxylamine probe for profiling S-acylated fatty acids on proteins. Chem Commun (Camb) 2019; 55:11183-11186. [PMID: 31465055 DOI: 10.1039/c9cc05989j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Reversible S-palmitoylation is a key regulatory mechanism of protein function and localization. There is increasing evidence that S-acylation is not restricted to palmitate but it includes shorter, longer, and unsaturated fatty acids. However, the diversity of this protein modification has not been fully explored. Herein, we report a chemical probe that combined with MS-based analysis allows the rapid detection and quantification of fatty acids linked to proteins. We have used this approach to profile the S-acylome and to show that the oncogene N-Ras is heterogeneously acylated with palmitate and palmitoleate. Studies on protein distribution in membrane subdomains with semisynthetic proteins revealed that unsaturated N-Ras presents an increased tendency toward clustering and higher insertion kinetic rate constants.
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Affiliation(s)
- Janine Schulte-Zweckel
- Department of Chemical Biology, Max-Planck-Institute of molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
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7
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Issue Highlights. IUBMB Life 2019. [DOI: 10.1002/iub.2025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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