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Xiao J, Niu L, Tong Z, Jin S, Wang X, Liu X, Xiao C, Fan H. Chemical acylation of pea protein isolate hydrolysate with fatty acid N-hydroxysuccinimide esters: Effect on structure and functional properties. Food Chem 2024; 443:138495. [PMID: 38277937 DOI: 10.1016/j.foodchem.2024.138495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/07/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024]
Abstract
Applications of pea protein in the food industry have been greatly restricted by its poor functional properties. In order to solve this problem, a novel technique combining enzymatic hydrolysis and fatty acid acylation has been applied in this work to construct a pea protein-fatty acid covalent complex that aims to improve its functional properties. The processed pea protein with increased water solubility tends to decrease the chance of self-aggregation. Additionally, emulsifying and antioxidant properties have also been found after this process. On top of that, the modified pea protein has been characterized by Fourier transform infrared and circular dichroism spectroscopy. These results demonstrate that these properties were mainly caused by the acylation of the amino group from hydrolyzed pea protein and the carboxyl group from the fatty acid. The enzymatic hydrolysis/fatty acid acylation research provides insights into manufacturing high-quality functional lipoproteins from inexpensive pea protein for the food industry.
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Affiliation(s)
- Jing Xiao
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, PR China
| | - Li Niu
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, PR China
| | - Zongbo Tong
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, PR China
| | - Shuxiu Jin
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, PR China
| | - Xiaomei Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, PR China
| | - Xuebo Liu
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, PR China
| | - Chunxia Xiao
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, PR China.
| | - Huafang Fan
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, PR China.
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2
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Cai Y, Chang C, Liao R. Overcoming the detrimental O- acylation in TMTpro labeling improves the proteome depth and quantification precision. Anal Chim Acta 2024; 1304:342538. [PMID: 38637049 DOI: 10.1016/j.aca.2024.342538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND With the advent of proline-based reporter isobaric Tandem Mass Tag (TMTpro) reagents, the sample multiplexing capacity of tandem mass tags (TMTs) has been expanded, and up to 18 samples can be quantified in a multiplexed manner. Like classic TMT reagents, TMTpro reagents contain a tertiary amine group, which markedly enhances their reactivity toward hydroxyl groups and results in O-acylation of serine, threonine and tyrosine residues. This overlabeling significantly compromises proteome analysis in terms of depth and precision. In particular, the reactivity of hydroxyl-containing residues can be dramatically enhanced when coexisting with a histidine in the same peptides, leading to a severe systematic bias against the analysis of these peptides. Although some protocols using a reduced molar excess of TMT under alkaline conditions can alleviate overlabeling of histidine-free peptides to some extent, they have a limited effect on histidyl- and hydroxyl-containing peptides. RESULTS Here, we report a novel TMTpro labeling method that overcomes detrimental overlabeling while providing high labeling efficiency of amines. Additionally, our method is cost-effective, as it requires only half the amount of TMTpro reagents recommended by the reagent manufacturer. In a deep-scale analysis of a yeast/human two-proteome model sample, we compared our method with a typical alkaline labeling method using a reduced molar excess of TMTpro. Even at a depth of over 10,000 proteins, our method detected 23.7% more unique peptides and 8.7% more protein groups compared to the alkaline labeling method. Moreover, our method significantly improved the quantitative precision due to the reduced variability in labeling and increased protein sequence coverage. This substantially enhanced the statistical power of our method for detecting differentially abundant proteins, providing an average of 13% more yeast proteins that reached statistical significance. SIGNIFCANCE We presented a novel TMTpro labeling method that overcomes the detrimental O-acylation and thus significantly improves the depth and quantitative precision for proteome analysis.
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Affiliation(s)
- Yan Cai
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Chenchen Chang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China
| | - Rijing Liao
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200125, China.
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3
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De Marchi L, Salemi L, Bellumori M, Chignola R, Mainente F, Santisteban Soto DV, Fierri I, Ciulu M, Zoccatelli G. Thermal degradation of red cabbage (Brassica oleracea L. var. Capitata f. rubra) anthocyanins in a water model extract under accelerated shelf-life testing. Food Chem 2024; 440:138272. [PMID: 38159318 DOI: 10.1016/j.foodchem.2023.138272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/28/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024]
Abstract
Red cabbage (RC) represents a source of anthocyanins acylated with hydroxycinnamic acids (HCA) that are described to enhance their stability. Nevertheless, data about their thermal degradation are still controversial. Our aim was to comprehensively analyse the degradation kinetics of individual RC anthocyanins in a model aqueous extract treated at 40 °C × 30 days to simulate severe but realistic storage conditions. Free anthocyanins and radical-scavenging capacity showed different kinetics. The results confirm the high stability of RC anthocyanins (t1/2: 16.4-18.4 days), although HPLC analyses of each molecule displayed distinct kinetics with t1/2 from 12.6 to 35.1 days. In particular, the sinapoyl acylation negatively affected the stability of the anthocyanins, while the forms monoacylated with glycosyl p-coumaric and ferulic acids exhibited higher stability. In conclusion, our results indicate that acylation is not a prerogative of stability, as this is instead more dependent on specific acylation patterns and the glycosylation of HCA.
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Affiliation(s)
- Laura De Marchi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Laura Salemi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Maria Bellumori
- Department of NEUROFARBA, University of Florence, Via Ugo Schiff, 6, 50019 Sesto F.no, Florence, Italy
| | - Roberto Chignola
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Federica Mainente
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | | | - Ilaria Fierri
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Marco Ciulu
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Gianni Zoccatelli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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4
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Seipp K, Grölz V, Glass H, Quraishi E, Vierengel N, Opatz T. Total Synthesis of (±)-Oxacyclododecindione. J Org Chem 2024; 89:5746-5763. [PMID: 38597924 DOI: 10.1021/acs.joc.4c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Racemic total synthesis of the natural product oxacyclododecindione, isolated in 2008 as the first member of the oxacyclododecindione family, is reported. Studies toward this molecule commenced with a biomimetic late-stage C-H oxidation starting from 14-deoxyoxacyclododecindione as a known precursor. This provided insights into the reactivity of the macrolactone class but did not permit the synthesis of the target natural product. Based on these results, a synthetic strategy through intramolecular Friedel-Crafts acylation combined with Barton decarboxylation to introduce the tertiary alcohol, a major challenge in previous synthetic efforts, was envisioned. This resulted in an 11-step racemic total synthesis of (±)-oxacyclododecindione, renowned for its potent anti-inflammatory and antifibrotic activities.
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Affiliation(s)
- Kevin Seipp
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Vincent Grölz
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Hagen Glass
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Elisabeth Quraishi
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Nina Vierengel
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128 Mainz, Germany
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5
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Sheikhi M, Nemayandeh N, Shirangi M. Peptide Acylation in Aliphatic Polyesters: a Review of Mechanisms and Inhibition Strategies. Pharm Res 2024; 41:765-778. [PMID: 38504074 DOI: 10.1007/s11095-024-03682-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
Biodegradable polyesters are widely employed in the development of controlled release systems for peptide drugs. However, one of the challenges in developing a polyester-based delivery system for peptides is the acylation reaction between peptides and polymers. Peptide acylation is an important factor that affects formulation stability and can occur during storage, in vitro release, and after drug administration. This review focuses on the mechanisms and parameters that influence the rate of peptide acylation within polyesters. Furthermore, it discusses reported strategies to minimize the acylation reaction.
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Affiliation(s)
- Mojgan Sheikhi
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Science Tehran, Tehran, Iran
| | - Nasrin Nemayandeh
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Science Tehran, Tehran, Iran
| | - Mehrnoosh Shirangi
- Department of Drug and Food Control, Faculty of Pharmacy, Tehran University of Medical Science Tehran, Tehran, Iran.
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6
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Zhang CC, Li Y, Jiang CY, Le QM, Liu X, Ma L, Wang FF. O-GlcN Acylation mediates H 2O 2-induced apoptosis through regulation of STAT3 and FOXO1. Acta Pharmacol Sin 2024; 45:714-727. [PMID: 38191912 PMCID: PMC10943090 DOI: 10.1038/s41401-023-01218-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
The O-linked-β-N-acetylglucosamine (O-GlcNAc) glycosylation (O-GlcNAcylation) is a critical post-translational modification that couples the external stimuli to intracellular signal transduction networks. However, the critical protein targets of O-GlcNAcylation in oxidative stress-induced apoptosis remain to be elucidated. Here, we show that treatment with H2O2 inhibited O-GlcNAcylation, impaired cell viability, increased the cleaved caspase 3 and accelerated apoptosis of neuroblastoma N2a cells. The O-GlcNAc transferase (OGT) inhibitor OSMI-1 or the O-GlcNAcase (OGA) inhibitor Thiamet-G enhanced or inhibited H2O2-induced apoptosis, respectively. The total and phosphorylated protein levels, as well as the promoter activities of signal transducer and activator of transcription factor 3 (STAT3) and Forkhead box protein O 1 (FOXO1) were suppressed by OSMI-1. In contrast, overexpressing OGT or treating with Thiamet-G increased the total protein levels of STAT3 and FOXO1. Overexpression of STAT3 or FOXO1 abolished OSMI-1-induced apoptosis. Whereas the anti-apoptotic effect of OGT and Thiamet-G in H2O2-treated cells was abolished by either downregulating the expression or activity of endogenous STAT3 or FOXO1. These results suggest that STAT3 or FOXO1 are the potential targets of O-GlcNAcylation involved in the H2O2-induced apoptosis of N2a cells.
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Affiliation(s)
- Chen-Chun Zhang
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Yuan Li
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Chang-You Jiang
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Qiu-Min Le
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Xing Liu
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Lan Ma
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China
| | - Fei-Fei Wang
- School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurology, Pharmacology Research Center, Huashan Hospital, Fudan University, Shanghai, 200032, China.
- Research Unit of Addiction Memory, Chinese Academy of Medical Sciences (2021RU009), Shanghai, 200032, China.
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7
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Haas BC, Lim NK, Jermaks J, Gaster E, Guo MC, Malig TC, Werth J, Zhang H, Toste FD, Gosselin F, Miller SJ, Sigman MS. Enantioselective Sulfonimidamide Acylation via a Cinchona Alkaloid-Catalyzed Desymmetrization: Scope, Data Science, and Mechanistic Investigation. J Am Chem Soc 2024; 146:8536-8546. [PMID: 38480482 PMCID: PMC10990064 DOI: 10.1021/jacs.4c00374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Methods to access chiral sulfur(VI) pharmacophores are of interest in medicinal and synthetic chemistry. We report the desymmetrization of unprotected sulfonimidamides via asymmetric acylation with a cinchona-phosphinate catalyst. The desired products are formed in excellent yield and enantioselectivity with no observed bis-acylation. A data-science-driven approach to substrate scope evaluation was coupled to high throughput experimentation (HTE) to facilitate statistical modeling in order to inform mechanistic studies. Reaction kinetics, catalyst structural studies, and density functional theory (DFT) transition state analysis elucidated the turnover-limiting step to be the collapse of the tetrahedral intermediate and provided key insights into the catalyst-substrate structure-activity relationships responsible for the origin of the enantioselectivity. This study offers a reliable method for accessing enantioenriched sulfonimidamides to propel their application as pharmacophores and serves as an example of the mechanistic insight that can be gleaned from integrating data science and traditional physical organic techniques.
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Affiliation(s)
- Brittany C Haas
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ngiap-Kie Lim
- Department of Synthetic Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Janis Jermaks
- Department of Synthetic Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Eden Gaster
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Melody C Guo
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Thomas C Malig
- Department of Synthetic Molecule Analytical Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Jacob Werth
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Haiming Zhang
- Department of Synthetic Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Francis Gosselin
- Department of Synthetic Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Scott J Miller
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Matthew S Sigman
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
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8
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Mosheim JR, Ruggieri F, Humeau C, Hance P, Willand N, Hilbert JL, Heuson E, Froidevaux R. Biocatalytic Regioselective O- acylation of Sesquiterpene Lactones from Chicory: A Pathway to Novel Ester Derivatives. Chembiochem 2024; 25:e202300722. [PMID: 38235523 DOI: 10.1002/cbic.202300722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 01/17/2024] [Indexed: 01/19/2024]
Abstract
We report the first biocatalytic modification of sesquiterpene lactones (STLs) found in the chicory plants, specifically lactucin (Lc), 11β,13-dihydrolactucin (DHLc), lactucopicrin (Lp), and 11β,13-dihydrolactucopicrin (DHLp). The selective O-acylation of their primary alcohol group was carried out by the lipase B from Candida antarctica (CAL-B) using various aliphatic vinyl esters as acyl donors. Perillyl alcohol, a simpler monoterpenoid, served as a model to set up the desired O-acetylation reaction by comparing the use of acetic acid and vinyl acetate as acyl donors. Similar conditions were then applied to DHLc, where five novel ester chains were selectively introduced onto the primary alcohol group, with conversions going from >99 % (acetate and propionate) to 69 % (octanoate). The synthesis of the corresponding O-acetyl esters of Lc, Lp, and DHLp was also successfully achieved with near-quantitative conversion. Molecular docking simulations were then performed to elucidate the preferred enzyme-substrate binding modes in the acylation reactions with STLs, as well as to understand their interactions with crucial amino acid residues at the active site. Our methodology enables the selective O-acylation of the primary alcohol group in four different STLs, offering possibilities for synthesizing novel derivatives with significant potential applications in pharmaceuticals or as biocontrol agents.
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Affiliation(s)
- J Rodriguez Mosheim
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - Institut Charles Viollette, Lille, France
| | - F Ruggieri
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - Institut Charles Viollette, Lille, France
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - C Humeau
- Univ. Lorraine, CNRS, UMR 7274 - Laboratoire Réactions et Génie des Procédés, -, F-54000, Nancy, France
| | - P Hance
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - Institut Charles Viollette, Lille, France
- Joint Laboratory University of Lille-Florimond-Desprez CHIC41Health, F-59655, Villeuneve d'Ascq, France
| | - N Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - J L Hilbert
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - Institut Charles Viollette, Lille, France
- Joint Laboratory University of Lille-Florimond-Desprez CHIC41Health, F-59655, Villeuneve d'Ascq, France
| | - E Heuson
- Univ. Lille, CNRS, Centrale Lille, Univ. Artois, UMR 8181-UCCS-, Unité de Catalyse et Chimie du Solide, F-59000, Lille, France
| | - R Froidevaux
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394 - Institut Charles Viollette, Lille, France
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9
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Kulich I, Schmid J, Teplova A, Qi L, Friml J. Rapid translocation of NGR proteins driving polarization of PIN-activating D6 protein kinase during root gravitropism. eLife 2024; 12:RP91523. [PMID: 38441122 PMCID: PMC10942638 DOI: 10.7554/elife.91523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Root gravitropic bending represents a fundamental aspect of terrestrial plant physiology. Gravity is perceived by sedimentation of starch-rich plastids (statoliths) to the bottom of the central root cap cells. Following gravity perception, intercellular auxin transport is redirected downwards leading to an asymmetric auxin accumulation at the lower root side causing inhibition of cell expansion, ultimately resulting in downwards bending. How gravity-induced statoliths repositioning is translated into asymmetric auxin distribution remains unclear despite PIN auxin efflux carriers and the Negative Gravitropic Response of roots (NGR) proteins polarize along statolith sedimentation, thus providing a plausible mechanism for auxin flow redirection. In this study, using a functional NGR1-GFP construct, we visualized the NGR1 localization on the statolith surface and plasma membrane (PM) domains in close proximity to the statoliths, correlating with their movements. We determined that NGR1 binding to these PM domains is indispensable for NGR1 functionality and relies on cysteine acylation and adjacent polybasic regions as well as on lipid and sterol PM composition. Detailed timing of the early events following graviperception suggested that both NGR1 repolarization and initial auxin asymmetry precede the visible PIN3 polarization. This discrepancy motivated us to unveil a rapid, NGR-dependent translocation of PIN-activating AGCVIII kinase D6PK towards lower PMs of gravity-perceiving cells, thus providing an attractive model for rapid redirection of auxin fluxes following gravistimulation.
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Affiliation(s)
- Ivan Kulich
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Julia Schmid
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | | | - Linlin Qi
- Institute of Science and Technology AustriaKlosterneuburgAustria
| | - Jiří Friml
- Institute of Science and Technology AustriaKlosterneuburgAustria
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10
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Akhmadi A, Yeskendir A, Dey N, Mussakhmetov A, Shatkenova Z, Kulyyassov A, Andreeva A, Utepbergenov D. DJ-1 protects proteins from acylation by catalyzing the hydrolysis of highly reactive cyclic 3-phosphoglyceric anhydride. Nat Commun 2024; 15:2004. [PMID: 38443379 PMCID: PMC10915168 DOI: 10.1038/s41467-024-46391-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/26/2024] [Indexed: 03/07/2024] Open
Abstract
Mutations in the human PARK7 gene that encodes protein DJ-1 lead to familial Parkinsonism due to loss of dopaminergic neurons. However, the molecular function of DJ-1 underpinning its cytoprotective effects are unclear. Recently, DJ-1 has been shown to prevent acylation of amino groups of proteins and metabolites by 1,3-bisphosphoglycerate. This acylation is indirect and thought to proceed via the formation of an unstable intermediate, presumably a cyclic 3-phosphoglyceric anhydride (cPGA). Several lines of evidence indicate that DJ-1 destroys cPGA, however this enzymatic activity has not been directly demonstrated. Here, we report simple and effective procedures for synthesis and quantitation of cPGA and present a comprehensive characterization of this highly reactive acylating electrophile. We demonstrate that DJ-1 is an efficient cPGA hydrolase with kcat/Km = 5.9 × 106 M-1s-1. Experiments with DJ-1-null cells reveal that DJ-1 protects against accumulation of 3-phosphoglyceroyl-lysine residues in proteins. Our results establish a definitive cytoprotective function for DJ-1 that uses catalytic hydrolysis of cPGA to mitigate the damage from this glycolytic byproduct.
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Affiliation(s)
- Aizhan Akhmadi
- Ph.D. Program in Life Sciences, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Adilkhan Yeskendir
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
- Master Program, School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Nelly Dey
- Master Program, School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Arman Mussakhmetov
- National Center for Biotechnology, Astana, 010000, Kazakhstan
- Ph.D. Program in Biology, L.N. Gumilyov Eurasian National University, Astana, 010000, Kazakhstan
| | - Zariat Shatkenova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | | | - Anna Andreeva
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan
| | - Darkhan Utepbergenov
- Department of Chemistry, School of Sciences and Humanities, Nazarbayev University, Astana, 010000, Kazakhstan.
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11
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Kadokawa JI. An overview on acylation methods of α-chitin. Int J Biol Macromol 2024; 262:130166. [PMID: 38360241 DOI: 10.1016/j.ijbiomac.2024.130166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/28/2024] [Accepted: 02/11/2024] [Indexed: 02/17/2024]
Abstract
This article overviews the acylation methods of α-chitin developed over the last four decades. The acylation of polysaccharides has been identified as a useful approach for conferring properties such as thermoplasticity. Owing to the poor solubility of α-chitin, its acylation using acid anhydrides and acyl chlorides has been traditionally investigated under heterogeneous conditions in strong acidic media. Although chitin chains depolymerize under acidic conditions, the resultant derivatives exhibit certain properties and functions. Solvents, such as LiCl/N,N-dimethyladcetamide, ionic liquids, and deep eutectic solvents, are suitable for α-chitin dissolution; therefore, acylation methods for α-chitin under homogeneous conditions have been developed using these solvents as reaction media. The functional materialization of the resultant derivatives was achieved by introducing appropriate substituents and controlling their ratios.
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Affiliation(s)
- Jun-Ichi Kadokawa
- Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan.
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12
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Zhang Z, Li X, Cao C. Octanoic acid-rich enteral nutrition attenuated hypercatabolism through the acylated ghrelin-POMC pathway in endotoxemic rats. Nutrition 2024; 119:112329. [PMID: 38215672 DOI: 10.1016/j.nut.2023.112329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/02/2023] [Accepted: 12/12/2023] [Indexed: 01/14/2024]
Abstract
OBJECTIVES Metabolic disorders and no response to intravenous nutrition because of sepsis have been urgent problems for clinical nutrition support. Enteral nutrition (EN) has been an important clinical therapeutic measure in septic patients; however, simple EN has not demonstrated good performance. This study aimed to investigate the effects of different concentrations of octanoic acid (OA)-rich EN on hypercatabolism in endotoxemic rats and test whether OA-rich EN could attenuate hypercatabolism through the acylated ghrelin-proopiomelanocortin (POMC) pathway. METHODS Rats were randomly divided into six groups: sham, lipopolysaccharide (LPS), LPS + EN and LPS + EN + OA (0.25, 0.5, and 1 g/kg, respectively) groups to investigate the effects of different concentrations of OA-rich EN on hypercatabolism in endotoxemic rats. The rats were then randomly divided into four groups: sham, LPS, LPS + OA, and LPS + OA + Go-CoA-Tat, to test whether OA-rich EN attenuated hypercatabolism through the acylated ghrelin-POMC pathway. Rats received nutrition support via a gastric tube for 3 d (100 kcal/kg daily). Insulin resistance, muscle protein synthesis and atrophy, inflammatory cytokines, ghrelin in circulation and hypothalamus, ghrelin O-acyltransferase (GOAT), and the adenosine 5'-monophosphate-activated protein kinase (AMPK)-autophagy-POMC pathway were measured. RESULTS Compared with simple EN, OA-rich EN promoted the acylation of ghrelin in a dose-dependent manner and attenuated POMC-mediated hypercatabolism in endotoxemic rats. Inhibition of GOAT activity decreased the level of acylated ghrelin and aggravated POMC-mediated hypercatabolism conferred by OA-rich EN. CONCLUSIONS OA-rich EN could increase the level of acylated ghrelin and attenuate hypercatabolism through the acylated ghrelin-POMC pathway compared with simple EN in endotoxemic rats.
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Affiliation(s)
- Zihao Zhang
- Department of General Surgery, the Second Affiliated Hospital of Soochow University, Suzhou, China; Department of Anesthesiology, the Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaohua Li
- Department of General Surgery, the Second Affiliated Hospital of Soochow University, Suzhou, China; Department of Thyroid and Breast Surgery, Suzhou Wuzhong People's Hospital, Suzhou, China
| | - Chun Cao
- Department of General Surgery, the Second Affiliated Hospital of Soochow University, Suzhou, China.
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13
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Hu S, Chen Y, Tao X, He R, Ju X, Wang Z. Enhanced emulsification performance and interfacial properties of Janus-like rapeseed cruciferin through asymmetric acylation modification. Int J Biol Macromol 2024; 260:129467. [PMID: 38237834 DOI: 10.1016/j.ijbiomac.2024.129467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Plant protein emulsifiers, particularly rapeseed protein isolate with its superior amino acid composition and predominantly globular protein, have captured significant interest in the food industry. Nonetheless, the application of these proteins has been stymied by their lackluster emulsification properties. Addressing this challenge, our study implements an innovative asymmetric acylation technique to modify the surface of rapeseed cruciferin (RC), morphing it into a structure resembling Janus nanoparticles. This alteration amplifies the emulsification prowess of RC by a remarkable 2.7 times compared to its natural form, and 1.43 times over its conventionally acylated counterpart. The asymmetrically acylated RC, marked by a distinctive three-phase contact angle of 90.4°, manifests an outstanding amphiphilic character. Moreover, it surpasses both the natural and conventionally acylated RC in terms of diffusion, penetration, and rearrangement rates, as well as protein concentration at the oil-water interface. Compared to commonly used emulsifiers in the food industry, such as lecithin and soy protein, the asymmetrically acylated RC stands out, stabilizing emulsions with the tiniest particle size and effectively staving off emulsion stratification over a longer duration. This study underscores that asymmetric acylation serves as a reliable methodology for producing efficient plant protein emulsifiers, considerably amplifying their utility in the food industry.
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Affiliation(s)
- Shengqing Hu
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Yao Chen
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Xuan Tao
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Rong He
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Xingrong Ju
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Zhigao Wang
- College of Food Science and Engineering, Collaborative Innovation Center for Modern Grain Circulation and Safety, Key Laboratory of Grains and Oils Quality Control and Processing, Nanjing University of Finance and Economics, Nanjing 210023, China.
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14
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Abstract
Lysine acylation, a type of posttranslational protein modification sensitive to cellular metabolic states, influences the functions of target proteins involved in diverse cellular processes. Particularly, lysine butyrylation, crotonylation, β-hydroxybutyrylation, and 2-hydroxyisobutyrylation, four types of four-carbon acylations, are modulated by intracellular concentrations of their respective acyl-CoAs and sensitive to alterations of nutrient metabolism induced by cellular and/or environmental signals. In this review, we discussed the metabolic pathways producing these four-carbon acyl-CoAs, the regulation of lysine acylation and deacylation, and the functions of individual lysine acylation.
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Affiliation(s)
- Yi Fang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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15
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Xu Y, Ding K, Peng T. Chemical Proteomics Reveals N ε-Fatty- Acylation of Septins by Rho Inactivation Domain (RID) of the Vibrio MARTX Toxin to Alter Septin Localization and Organization. Mol Cell Proteomics 2024; 23:100730. [PMID: 38311109 PMCID: PMC10924143 DOI: 10.1016/j.mcpro.2024.100730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/16/2024] [Accepted: 01/31/2024] [Indexed: 02/06/2024] Open
Abstract
Vibrio species, the Gram-negative bacterial pathogens causing cholera and sepsis, produce multiple secreted virulence factors for infection and pathogenesis. Among these is the multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin that releases several critical effector domains with distinct functions inside eukaryotic host cells. One such effector domain, the Rho inactivation domain (RID), has been discovered to catalyze long-chain Nε-fatty-acylation on lysine residues of Rho GTPases, causing inactivation of Rho GTPases and disruption of the host actin cytoskeleton. However, whether RID modifies other host proteins to exert additional functions remains to be determined. Herein, we describe the integration of bioorthogonal chemical labeling and quantitative proteomics to globally profile the target proteins modified by RID in living cells. More than 246 proteins are identified as new RID substrates, including many involved in GTPase regulation, cytoskeletal organization, and cell division. We demonstrate that RID extensively Nε-fatty-acylates septin proteins, the fourth cytoskeletal component of mammalian cells with important roles in diverse cellular processes. While affinity purification and mass spectrometry analysis show that RID-mediated Nε-fatty-acylation does not affect septin-septin interactions, this modification increases the membrane association of septins and confers localization to detergent-resistant membrane rafts. As a result, the filamentous assembly and organization of septins are disrupted by RID-mediated Nε-fatty-acylation, further contributing to cytoskeletal and mitotic defects that phenocopy the effects of septin depletion. Overall, our work greatly expands the substrate scope and function of RID and demonstrates the role of RID-mediated Nε-fatty-acylation in manipulating septin localization and organization.
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Affiliation(s)
- Yaxin Xu
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ke Ding
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Tao Peng
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China; Shenzhen Bay Laboratory, Institute of Chemical Biology, Shenzhen, China.
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16
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Néré R, Kouba S, Carreras-Sureda A, Demaurex N. S- acylation of Ca2+ transport proteins: molecular basis and functional consequences. Biochem Soc Trans 2024; 52:407-421. [PMID: 38348884 PMCID: PMC10903462 DOI: 10.1042/bst20230818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/29/2024]
Abstract
Calcium (Ca2+) regulates a multitude of cellular processes during fertilization and throughout adult life by acting as an intracellular messenger to control effector functions in excitable and non-excitable cells. Changes in intracellular Ca2+ levels are driven by the co-ordinated action of Ca2+ channels, pumps, and exchangers, and the resulting signals are shaped and decoded by Ca2+-binding proteins to drive rapid and long-term cellular processes ranging from neurotransmission and cardiac contraction to gene transcription and cell death. S-acylation, a lipid post-translational modification, is emerging as a critical regulator of several important Ca2+-handling proteins. S-acylation is a reversible and dynamic process involving the attachment of long-chain fatty acids (most commonly palmitate) to cysteine residues of target proteins by a family of 23 proteins acyltransferases (zDHHC, or PATs). S-acylation modifies the conformation of proteins and their interactions with membrane lipids, thereby impacting intra- and intermolecular interactions, protein stability, and subcellular localization. Disruptions of S-acylation can alter Ca2+ signalling and have been implicated in the development of pathologies such as heart disease, neurodegenerative disorders, and cancer. Here, we review the recent literature on the S-acylation of Ca2+ transport proteins of organelles and of the plasma membrane and highlight the molecular basis and functional consequence of their S-acylation as well as the therapeutic potential of targeting this regulation for diseases caused by alterations in cellular Ca2+ fluxes.
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Affiliation(s)
- Raphaël Néré
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Sana Kouba
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Amado Carreras-Sureda
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Nicolas Demaurex
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
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17
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Gonzalez-Alfonso JL, Alonso C, Poveda A, Ubiparip Z, Ballesteros AO, Desmet T, Jiménez-Barbero J, Coderch L, Plou FJ. Strategy for the Enzymatic Acylation of the Apple Flavonoid Phloretin Based on Prior α-Glucosylation. J Agric Food Chem 2024; 72:4325-4333. [PMID: 38350922 PMCID: PMC10905995 DOI: 10.1021/acs.jafc.3c09261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/29/2024] [Accepted: 02/01/2024] [Indexed: 02/15/2024]
Abstract
The acylation of flavonoids serves as a means to alter their physicochemical properties, enhance their stability, and improve their bioactivity. Compared with natural flavonoid glycosides, the acylation of nonglycosylated flavonoids presents greater challenges since they contain fewer reactive sites. In this work, we propose an efficient strategy to solve this problem based on a first α-glucosylation step catalyzed by a sucrose phosphorylase, followed by acylation using a lipase. The method was applied to phloretin, a bioactive dihydrochalcone mainly present in apples. Phloretin underwent initial glucosylation at the 4'-OH position, followed by subsequent (and quantitative) acylation with C8, C12, and C16 acyl chains employing an immobilized lipase from Thermomyces lanuginosus. Electrospray ionization-mass spectrometry (ESI-MS) and two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) confirmed that the acylation took place at 6-OH of glucose. The water solubility of C8 acyl glucoside closely resembled that of aglycone, but for C12 and C16 derivatives, it was approximately 3 times lower. Compared with phloretin, the radical scavenging capacity of the new derivatives slightly decreased with 2,2-diphenyl-1-picrylhydrazyl (DPPH) and was similar to 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS•+). Interestingly, C12 acyl-α-glucoside displayed an enhanced (3-fold) transdermal absorption (using pig skin biopsies) compared to phloretin and its α-glucoside.
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Affiliation(s)
| | - Cristina Alonso
- Institute
of Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18–26, 08034 Barcelona, Spain
| | - Ana Poveda
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), 48160 Derio, Spain
| | - Zorica Ubiparip
- Centre
for Synthetic Biology (CSB), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Antonio O. Ballesteros
- Institute
of Catalysis and Petrochemistry (ICP-CSIC), Marie Curie 2, 28049 Madrid, Spain
| | - Tom Desmet
- Centre
for Synthetic Biology (CSB), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), 48160 Derio, Spain
- Basque
Foundation for Science, 48009 Bilbao, Spain
| | - Luisa Coderch
- Institute
of Advanced Chemistry of Catalonia (IQAC-CSIC), Jordi Girona 18–26, 08034 Barcelona, Spain
| | - Francisco J. Plou
- Institute
of Catalysis and Petrochemistry (ICP-CSIC), Marie Curie 2, 28049 Madrid, Spain
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18
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Hu H, Hu W, Guo AD, Zhai L, Ma S, Nie HJ, Zhou BS, Liu T, Jia X, Liu X, Yao X, Tan M, Chen XH. Spatiotemporal and direct capturing global substrates of lysine-modifying enzymes in living cells. Nat Commun 2024; 15:1465. [PMID: 38368419 PMCID: PMC10874396 DOI: 10.1038/s41467-024-45765-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/04/2024] [Indexed: 02/19/2024] Open
Abstract
Protein-modifying enzymes regulate the dynamics of myriad post-translational modification (PTM) substrates. Precise characterization of enzyme-substrate associations is essential for the molecular basis of cellular function and phenotype. Methods for direct capturing global substrates of protein-modifying enzymes in living cells are with many challenges, and yet largely unexplored. Here, we report a strategy to directly capture substrates of lysine-modifying enzymes via PTM-acceptor residue crosslinking in living cells, enabling global profiling of substrates of PTM-enzymes and validation of PTM-sites in a straightforward manner. By integrating enzymatic PTM-mechanisms, and genetically encoding residue-selective photo-crosslinker into PTM-enzymes, our strategy expands the substrate profiles of both bacterial and mammalian lysine acylation enzymes, including bacterial lysine acylases PatZ, YiaC, LplA, TmcA, and YjaB, as well as mammalian acyltransferases GCN5 and Tip60, leading to discovery of distinct yet functionally important substrates and acylation sites. The concept of direct capturing substrates of PTM-enzymes via residue crosslinking may extend to the other types of amino acid residues beyond lysine, which has the potential to facilitate the investigation of diverse types of PTMs and substrate-enzyme interactive proteomics.
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Affiliation(s)
- Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wei Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - An-Di Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
| | - Song Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hui-Jun Nie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bin-Shan Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Tianxian Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xinglong Jia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xing Liu
- MOE Key Laboratory for Cellular Dynamics and Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Xuebiao Yao
- MOE Key Laboratory for Cellular Dynamics and Hefei National Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong, 528400, China.
| | - Xiao-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
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19
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Liu F, Qu PY, Li JP, Yang LN, Geng YJ, Lu JY, Zhang Y, Li S. Arabidopsis protein S-acyl transferases positively mediate BR signaling through S- acylation of BSK1. Proc Natl Acad Sci U S A 2024; 121:e2322375121. [PMID: 38315835 PMCID: PMC10873554 DOI: 10.1073/pnas.2322375121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 02/07/2024] Open
Abstract
Protein S-acyl transferases (PATs) catalyze S-acylation, a reversible post-translational modification critical for membrane association, trafficking, and stability of substrate proteins. Many plant proteins are potentially S-acylated but few have corresponding PATs identified. By using genomic editing, confocal imaging, pharmacological, genetic, and biochemical assays, we demonstrate that three Arabidopsis class C PATs positively regulate BR signaling through S-acylation of BRASSINOSTEROID-SIGNALING KINASE1 (BSK1). PAT19, PAT20, and PAT22 associate with the plasma membrane (PM) and the trans-Golgi network/early endosome (TGN/EE). Functional loss of all three genes results in a plethora of defects, indicative of reduced BR signaling and rescued by enhanced BR signaling. PAT19, PAT20, and PAT22 interact with BSK1 and are critical for the S-acylation of BSK1, and for BR signaling. The PM abundance of BSK1 was reduced by functional loss of PAT19, PAT20, and PAT22 whereas abolished by its S-acylation-deficient point mutations, suggesting a key role of S-acylation in its PM targeting. Finally, an active BR analog induces vacuolar trafficking and degradation of PAT19, PAT20, or PAT22, suggesting that the S-acylation of BSK1 by the three PATs serves as a negative feedback module in BR signaling.
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Affiliation(s)
- Fei Liu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Peng-Yu Qu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Ji-Peng Li
- College of Life Sciences, Shandong Agricultural University, Tai’an271018, China
| | - Li-Na Yang
- College of Life Sciences, Shandong Agricultural University, Tai’an271018, China
| | - Yuan-Jun Geng
- College of Life Sciences, Shandong Agricultural University, Tai’an271018, China
| | - Jin-Yu Lu
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Yan Zhang
- Frontiers Science Center for Cell Responses, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Sha Li
- College of Life Sciences, Shandong Agricultural University, Tai’an271018, China
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Shi H, Cui W, Qin Y, Chen L, Yu T, Lv J. A glimpse into novel acylations and their emerging role in regulating cancer metastasis. Cell Mol Life Sci 2024; 81:76. [PMID: 38315203 PMCID: PMC10844364 DOI: 10.1007/s00018-023-05104-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
Metastatic cancer is a major cause of cancer-related mortality; however, the complex regulation process remains to be further elucidated. A large amount of preliminary investigations focus on the role of epigenetic mechanisms in cancer metastasis. Notably, the posttranslational modifications were found to be critically involved in malignancy, thus attracting considerable attention. Beyond acetylation, novel forms of acylation have been recently identified following advances in mass spectrometry, proteomics technologies, and bioinformatics, such as propionylation, butyrylation, malonylation, succinylation, crotonylation, 2-hydroxyisobutyrylation, lactylation, among others. These novel acylations play pivotal roles in regulating different aspects of energy mechanism and mediating signal transduction by covalently modifying histone or nonhistone proteins. Furthermore, these acylations and their modifying enzymes show promise regarding the diagnosis and treatment of tumors, especially tumor metastasis. Here, we comprehensively review the identification and characterization of 11 novel acylations, and the corresponding modifying enzymes, highlighting their significance for tumor metastasis. We also focus on their potential application as clinical therapeutic targets and diagnostic predictors, discussing the current obstacles and future research prospects.
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Affiliation(s)
- Huifang Shi
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Weigang Cui
- Central Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Yan Qin
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Lei Chen
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China
| | - Tao Yu
- Center for Regenerative Medicine, Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China.
- Department of Cardiac Ultrasound, The Affiliated Hospital of Qingdao University, No. 16 Jiangsu Road, Qingdao, 266000, China.
| | - Jie Lv
- Clinical Laboratory, The Rizhao People's Hospital Affiliated to Jining Medical University, No. 126 Taian Road, Rizhao, 276826, Shandong, China.
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [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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23
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Zýka J, Prouza V, Habanová N, Pohl R, Parkan K. The synthesis and characterization of electron-poor glycosylamines and derived glycosylamides. Carbohydr Res 2024; 536:109023. [PMID: 38242070 DOI: 10.1016/j.carres.2024.109023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/26/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024]
Abstract
This paper describes a unified approach toward diglycosylamines using methanolic ammonia. All the glycosylamines prepared have been fully characterized, and their anomeric configuration has been determined. The article presents a novel method for the N-acylation of diglycosylamines and other electron-poor glycosylamines, which employs nitromethane as a solvent in carboxylic anhydride acylation under acidic conditions. The feasibility of this transformation is represented by a wide range of reaction substrates. All glycosylamides are formed solely with β-configuration. These two reactions constitute a simple and effective route to the synthesis of a novel class of compounds with an N-glycosidic linkage.
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Affiliation(s)
- Jakub Zýka
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 166 10, Prague, Czech Republic
| | - Vít Prouza
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 166 10, Prague, Czech Republic
| | - Nina Habanová
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 166 10, Prague, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 166 10, Prague, Czech Republic
| | - Kamil Parkan
- Department of Chemistry of Natural Compounds, University of Chemistry and Technology, Prague, Technická 5, 166 28, Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo Nám. 2, 166 10, Prague, Czech Republic.
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24
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Li W, Ye T, Ye W, Liang J, Wang W, Han D, Liu X, Huang L, Ouyang Y, Liao J, Chen T, Yang C, Lai J. S- acylation of a non-secreted peptide controls plant immunity via secreted-peptide signal activation. EMBO Rep 2024; 25:489-505. [PMID: 38177916 PMCID: PMC10897394 DOI: 10.1038/s44319-023-00029-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 11/25/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Small peptides modulate multiple processes in plant cells, but their regulation by post-translational modification remains unclear. ROT4 (ROTUNDIFOLIA4) belongs to a family of Arabidopsis non-secreted small peptides, but knowledge on its molecular function and how it is regulated is limited. Here, we find that ROT4 is S-acylated in plant cells. S-acylation is an important form of protein lipidation, yet so far it has not been reported to regulate small peptides in plants. We show that this modification is essential for the plasma membrane association of ROT4. Overexpression of S-acylated ROT4 results in a dramatic increase in immune gene expression. S-acylation of ROT4 enhances its interaction with BSK5 (BRASSINOSTEROID-SIGNALING KINASE 5) to block the association between BSK5 and PEPR1 (PEP RECEPTOR1), a receptor kinase for secreted plant elicitor peptides (PEPs), thereby activating immune signaling. Phenotype analysis indicates that S-acylation is necessary for ROT4 functions in pathogen resistance, PEP response, and the regulation of development. Collectively, our work reveals an important role for S-acylation in the cross-talk of non-secreted and secreted peptide signaling in plant immunity.
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Affiliation(s)
- Wenliang Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Tushu Ye
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Weixian Ye
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jieyi Liang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Wen Wang
- Key Laboratory of Laser Life Science, MOE Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Danlu Han
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Xiaoshi Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Liting Huang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Youwei Ouyang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Jianwei Liao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Tongsheng Chen
- Key Laboratory of Laser Life Science, MOE Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
| | - Jianbin Lai
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou, 510631, China.
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25
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Zhang B, Yu Y, Fox BW, Liu Y, Thirumalaikumar VP, Skirycz A, Lin H, Schroeder FC. Amino acid and protein specificity of protein fatty acylation in C. elegans. Proc Natl Acad Sci U S A 2024; 121:e2307515121. [PMID: 38252833 PMCID: PMC10835129 DOI: 10.1073/pnas.2307515121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Protein lipidation plays critical roles in regulating protein function and localization. However, the chemical diversity and specificity of fatty acyl group utilization have not been investigated using untargeted approaches, and it is unclear to what extent structures and biosynthetic origins of S-acyl moieties differ from N- and O-fatty acylation. Here, we show that fatty acylation patterns in Caenorhabditis elegans differ markedly between different amino acid residues. Hydroxylamine capture revealed predominant cysteine S-acylation with 15-methylhexadecanoic acid (isoC17:0), a monomethyl branched-chain fatty acid (mmBCFA) derived from endogenous leucine catabolism. In contrast, enzymatic protein hydrolysis showed that N-terminal glycine was acylated almost exclusively with straight-chain myristic acid, whereas lysine was acylated preferentially with two different mmBCFAs and serine was acylated promiscuously with a broad range of fatty acids, including eicosapentaenoic acid. Global profiling of fatty acylated proteins using a set of click chemistry-capable alkyne probes for branched- and straight-chain fatty acids uncovered 1,013 S-acylated proteins and 510 hydroxylamine-resistant N- or O-acylated proteins. Subsets of S-acylated proteins were labeled almost exclusively by either a branched-chain or a straight-chain probe, demonstrating acylation specificity at the protein level. Acylation specificity was confirmed for selected examples, including the S-acyltransferase DHHC-10. Last, homology searches for the identified acylated proteins revealed a high degree of conservation of acylation site patterns across metazoa. Our results show that protein fatty acylation patterns integrate distinct branches of lipid metabolism in a residue- and protein-specific manner, providing a basis for mechanistic studies at both the amino acid and protein levels.
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Affiliation(s)
- Bingsen Zhang
- Boyce Thompson Institute, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Yan Yu
- Boyce Thompson Institute, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Bennett W. Fox
- Boyce Thompson Institute, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | - Yinong Liu
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
| | | | | | - Hening Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
- HHMI, Cornell University, Ithaca, NY14853
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - Frank C. Schroeder
- Boyce Thompson Institute, Cornell University, Ithaca, NY14853
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY14853
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26
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Xiao L, Fang L, Kool ET. 2'-OH as a universal handle for studying intracellular RNAs. Cell Chem Biol 2024; 31:110-124. [PMID: 37992716 PMCID: PMC10841764 DOI: 10.1016/j.chembiol.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/28/2023] [Accepted: 10/29/2023] [Indexed: 11/24/2023]
Abstract
RNA plays pivotal roles in most cellular processes, serving as both the traditional carrier of genetic information and as a key regulator of cellular functions. The advent of chemical technologies has contributed critically to the analysis of cellular RNA structures, functions, and interactions. Many of these methods and molecules involve the utilization of chemically reactive handles in RNAs, either introduced externally or inherent within the polymer itself. Among these handles, the 2'-hydroxyl (2'-OH) group has emerged as an exceptionally well-suited and general chemical moiety for the modification and profiling of RNAs in intracellular studies. In this review, we provide an overview of the recent advancements in intracellular applications of acylation at the 2'-OH group of RNA. We outline progress made in probing RNA structure and interactomes, controlling RNA function, RNA imaging, and analyzing RNA-small molecule interactions, all achieved in living cells through this simple chemical handle on the biopolymer.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA.
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27
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Aleshin VA, Kaehne T, Maslova MV, Graf AV, Bunik VI. Posttranslational Acylations of the Rat Brain Transketolase Discriminate the Enzyme Responses to Inhibitors of ThDP-Dependent Enzymes or Thiamine Transport. Int J Mol Sci 2024; 25:917. [PMID: 38255994 PMCID: PMC10815635 DOI: 10.3390/ijms25020917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/23/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Transketolase (TKT) is an essential thiamine diphosphate (ThDP)-dependent enzyme of the non-oxidative branch of the pentose phosphate pathway, with the glucose-6P flux through the pathway regulated in various medically important conditions. Here, we characterize the brain TKT regulation by acylation in rats with perturbed thiamine-dependent metabolism, known to occur in neurodegenerative diseases. The perturbations are modeled by the administration of oxythiamine inhibiting ThDP-dependent enzymes in vivo or by reduced thiamine availability in the presence of metformin and amprolium, inhibiting intracellular thiamine transporters. Compared to control rats, chronic administration of oxythiamine does not significantly change the modification level of the two detected TKT acetylation sites (K6 and K102) but doubles malonylation of TKT K499, concomitantly decreasing 1.7-fold the level of demalonylase sirtuin 5. The inhibitors of thiamine transporters do not change average levels of TKT acylation or sirtuin 5. TKT structures indicate that the acylated residues are distant from the active sites. The acylations-perturbed electrostatic interactions may be involved in conformational shifts and/or the formation of TKT complexes with other proteins or nucleic acids. Acetylation of K102 may affect the active site entrance/exit and subunit interactions. Correlation analysis reveals that the action of oxythiamine is characterized by significant negative correlations of K499 malonylation or K6 acetylation with TKT activity, not observed upon the action of the inhibitors of thiamine transport. However, the transport inhibitors induce significant negative correlations between the TKT activity and K102 acetylation or TKT expression, absent in the oxythiamine group. Thus, perturbations in the ThDP-dependent catalysis or thiamine transport manifest in the insult-specific patterns of the brain TKT malonylation and acetylations.
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Affiliation(s)
- Vasily A. Aleshin
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Thilo Kaehne
- Institute of Experimental Internal Medicine, Otto von Guericke University, 39106 Magdeburg, Germany;
| | - Maria V. Maslova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Anastasia V. Graf
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia;
| | - Victoria I. Bunik
- Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia; (V.A.A.); (A.V.G.)
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
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28
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Longin H, Broeckaert N, Langen M, Hari R, Kramarska A, Oikarinen K, Hendrix H, Lavigne R, van Noort V. FLAMS: Find Lysine Acylations and other Modification Sites. Bioinformatics 2024; 40:btae005. [PMID: 38195744 PMCID: PMC10783949 DOI: 10.1093/bioinformatics/btae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/04/2023] [Accepted: 01/08/2024] [Indexed: 01/11/2024] Open
Abstract
SUMMARY Today, hundreds of post-translational modification (PTM) sites are routinely identified at once, but the comparison of new experimental datasets to already existing ones is hampered by the current inability to search most PTM databases at the protein residue level. We present FLAMS (Find Lysine Acylations and other Modification Sites), a Python3-based command line and web-tool that enables researchers to compare their PTM sites to the contents of the CPLM, the largest dedicated protein lysine modification database, and dbPTM, the most comprehensive general PTM database, at the residue level. FLAMS can be integrated into PTM analysis pipelines, allowing researchers to quickly assess the novelty and conservation of PTM sites across species in newly generated datasets, aiding in the functional assessment of sites and the prioritization of sites for further experimental characterization. AVAILABILITY AND IMPLEMENTATION FLAMS is implemented in Python3, and freely available under an MIT license. It can be found as a command line tool at https://github.com/hannelorelongin/FLAMS, pip and conda; and as a web service at https://www.biw.kuleuven.be/m2s/cmpg/research/CSB/tools/flams/.
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Affiliation(s)
- Hannelore Longin
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven 3001, Belgium
| | - Nand Broeckaert
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven 3001, Belgium
| | - Maarten Langen
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
| | - Roshan Hari
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
| | - Anna Kramarska
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
| | - Kasper Oikarinen
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
| | - Hanne Hendrix
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven 3001, Belgium
| | - Rob Lavigne
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven 3001, Belgium
| | - Vera van Noort
- KU Leuven, Department of Microbial and Molecular Systems, Computational Systems Biology, Leuven 3001, Belgium
- Leiden University, Institute of Biology Leiden (IBL), Leiden 2333 BE, The Netherlands
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29
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Dunkelmann DL, Piedrafita C, Dickson A, Liu KC, Elliott TS, Fiedler M, Bellini D, Zhou A, Cervettini D, Chin JW. Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism. Nature 2024; 625:603-610. [PMID: 38200312 PMCID: PMC10794150 DOI: 10.1038/s41586-023-06897-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 11/23/2023] [Indexed: 01/12/2024]
Abstract
The genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1-3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4-6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs-this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-L-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs in Escherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several β-amino acids, α,α-disubstituted-amino acids and β-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of β-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers.
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Affiliation(s)
| | - Carlos Piedrafita
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Alexandre Dickson
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kim C Liu
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Thomas S Elliott
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marc Fiedler
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Dom Bellini
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew Zhou
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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30
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Mesquita FS, Abrami L, Samurkas A, van der Goot FG. S- acylation: an orchestrator of the life cycle and function of membrane proteins. FEBS J 2024; 291:45-56. [PMID: 37811679 DOI: 10.1111/febs.16972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/06/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
S-acylation is a covalent post-translational modification of proteins with fatty acids, achieved by enzymatic attachment via a labile thioester bond. This modification allows for dynamic control of protein properties and functions in association with cell membranes. This lipid modification regulates a substantial portion of the human proteome and plays an increasingly recognized role throughout the lifespan of affected proteins. Recent technical advancements have propelled the S-acylation field into a 'molecular era', unveiling new insights into its mechanistic intricacies and far-reaching implications. With a striking increase in the number of studies on this modification, new concepts are indeed emerging on the roles of S-acylation in specific cell biology processes and features. After a brief overview of the enzymes involved in S-acylation, this viewpoint focuses on the importance of S-acylation in the homeostasis, function, and coordination of integral membrane proteins. In particular, we put forward the hypotheses that S-acylation is a gatekeeper of membrane protein folding and turnover and a regulator of the formation and dynamics of membrane contact sites.
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Affiliation(s)
| | - Laurence Abrami
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Arthur Samurkas
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
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31
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Talwadekar M, Khatri S, Balaji C, Chakraborty A, Basak NP, Kamat SS, Kolthur-Seetharam U. Metabolic transitions regulate global protein fatty acylation. J Biol Chem 2024; 300:105563. [PMID: 38101568 PMCID: PMC10808961 DOI: 10.1016/j.jbc.2023.105563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Intermediary metabolites and flux through various pathways have emerged as key determinants of post-translational modifications. Independently, dynamic fluctuations in their concentrations are known to drive cellular energetics in a bi-directional manner. Notably, intracellular fatty acid pools that drastically change during fed and fasted states act as precursors for both ATP production and fatty acylation of proteins. Protein fatty acylation is well regarded for its role in regulating structure and functions of diverse proteins; however, the effect of intracellular concentrations of fatty acids on protein modification is less understood. In this regard, we unequivocally demonstrate that metabolic contexts, viz. fed and fasted states, dictate the extent of global fatty acylation. Moreover, we show that presence or absence of glucose that influences cellular and mitochondrial uptake/utilization of fatty acids and affects palmitoylation and oleoylation, which is consistent with their intracellular abundance in fed and fasted states. Employing complementary approaches including click-chemistry, lipidomics, and imaging, we show the top-down control of cellular metabolic state. Importantly, our results establish the crucial role of mitochondria and retrograde signaling components like SIRT4, AMPK, and mTOR in orchestrating protein fatty acylation at a whole cell level. Specifically, pharmacogenetic perturbations that alter either mitochondrial functions and/or retrograde signaling affect protein fatty acylation. Besides illustrating the cross-talk between carbohydrate and lipid metabolism in mediating bulk post-translational modification, our findings also highlight the involvement of mitochondrial energetics.
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Affiliation(s)
- Manasi Talwadekar
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Subhash Khatri
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Chinthapalli Balaji
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Arnab Chakraborty
- Department of Biology, Indian Institute of Science Education and Research, Pune, India
| | - Nandini-Pal Basak
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Siddhesh S Kamat
- Department of Biology, Indian Institute of Science Education and Research, Pune, India.
| | - Ullas Kolthur-Seetharam
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India; Tata Institute of Fundamental Research, Hyderabad, India.
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Guo P, Niu Z, Zhang D, Zhao F, Li J, Lu T, Qin X, Liu S, Li Z, Li Y, Li S. Potential impact of cuproptosis-related genes on tumor immunity in esophageal carcinoma. Aging (Albany NY) 2023; 15:15535-15556. [PMID: 38159255 PMCID: PMC10781504 DOI: 10.18632/aging.205391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/07/2023] [Indexed: 01/03/2024]
Abstract
Cuproptosis involves a direct interaction with the tricarboxylic acid (TCA) lipid acylation components. This process intricately intersects with post-transcriptional lipid acylation (LA) and is linked to mitochondrial respiration and LA metabolism. Copper ions form direct bonds with acylated DLAT, promoting DLAT oligomerization, reducing Fe-S cluster proteins, and inducing a protein-triggered toxic stress response that culminates in cell demise. Simultaneously, the importance of immune contexture in cancer progression and treatment has significantly increased. We assessed the expression of cuproptosis-related genes (CRGs) across TCGA and validated our findings using the GEO data. Consensus clustering divided esophageal cancer (ESCA) patients into two clusters based on the expression of 7 CRGs. We evaluated the expression of immune checkpoint inhibitor (ICI) targets and calculated the elevated tumor mutational burden (TMB). Weighted gene co-expression network analysis (WGCNA) identified genes associated with the expression of CRGs and immunity. Cluster 1 exhibited increased immune infiltration, higher expression of ICI targets, higher TMB, and a higher incidence of deficiency in mismatch repair-microsatellite instability-high status. WGCNA analysis identified 14 genes associated with the expression of CRGs and immune scores. ROC analysis revealed specific hub genes with strong predictive capabilities. The expression levels of SLC6A3, MITD1, and PDHA1 varied across different pathological stages; CCS, LIPT2, PDHB, and PDHA1 showed variation in response to radiation therapy; MITD1 and PDHA1 exhibited differences related to the pathological M stages of ESCA. CRGs influence the immune contexture and can potentially transform cold tumors into hot tumors in ESCA patients.
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Affiliation(s)
- Pengfei Guo
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Graduate school of Hebei Medical University, Shijiazhuang, China
| | - Zemiao Niu
- Graduate school of Hebei Medical University, Shijiazhuang, China
| | - Dengfeng Zhang
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Graduate school of Hebei Medical University, Shijiazhuang, China
| | - Fangchao Zhao
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Graduate school of Hebei Medical University, Shijiazhuang, China
| | - Jing Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
- Graduate school of Hebei Medical University, Shijiazhuang, China
| | - Tianxing Lu
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xuebo Qin
- Department of Thoracic Surgery, Hebei Chest Hospital, Shijiazhuang, China
| | - Shiquan Liu
- Department of Thoracic Surgery, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Zhirong Li
- Clinical Laboratory Center, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yishuai Li
- Department of Thoracic Surgery, Hebei Chest Hospital, Shijiazhuang, China
| | - Shujun Li
- Department of Thoracic Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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Shioi R, Xiao L, Fang L, Kool ET. Efficient post-synthesis incorporation and conjugation of reactive ketones in RNA via 2'- acylation. Chem Commun (Camb) 2023; 60:232-235. [PMID: 38054242 PMCID: PMC10745195 DOI: 10.1039/d3cc05123d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Despite the broad utility of ketones in bioconjugation, few methods exist to introduce them into RNA. Here we develop highly reactive 2'-OH acylating reagents containing strained-ring ketones, and employ them as versatile labeling handles for RNA.
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Affiliation(s)
- Ryuta Shioi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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34
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Fang L, Kool ET. Reactivity-based RNA profiling for analyzing transcriptome interactions of small molecules in human cells. STAR Protoc 2023; 4:102670. [PMID: 37917579 PMCID: PMC10643522 DOI: 10.1016/j.xpro.2023.102670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/06/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
Protein-targeted small-molecule drugs may unintentionally bind intracellular RNA, contributing to drug toxicity. Moreover, new drugs are actively sought for intentionally targeting RNA. Here, we present a protocol to globally profile RNA-drug interactions in human cells using acylating probes and next-generation sequencing. We describe steps for cell culture, target acylation, library preparation, and sequencing. Detailed bioinformatic analyses identify drug-binding RNA loci in ∼16,000 poly(A)+ human transcripts. This streamlined workflow identifies RNA-drug interactions at single-nucleotide resolution, revealing widespread transcriptome interactions of drugs. For complete details on the use and execution of this protocol, please refer to Fang et al.1.
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Affiliation(s)
- Linglan Fang
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA.
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35
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Bhattacharya A, Tanwar L, Fracassi A, Brea RJ, Salvador-Castell M, Khanal S, Sinha SK, Devaraj NK. Chemoselective Esterification of Natural and Prebiotic 1,2-Amino Alcohol Amphiphiles in Water. J Am Chem Soc 2023; 145:27149-27159. [PMID: 38039527 PMCID: PMC10722506 DOI: 10.1021/jacs.3c12038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
In cells, a vast number of membrane lipids are formed by the enzymatic O-acylation of polar head groups with acylating agents such as fatty acyl-CoAs. Although such ester-containing lipids appear to be a requirement for life on earth, it is unclear if similar types of lipids could have spontaneously formed in the absence of enzymatic machinery at the origin of life. There are few examples of enzyme-free esterification of amphiphiles in water and none that can occur in water at physiological pH using biochemically relevant acylating agents. Here we report the unexpected chemoselective O-acylation of 1,2-amino alcohol amphiphiles in water directed by Cu(II) and several other transition metal ions. In buffers containing Cu(II) ions, mixing biological 1,2-amino alcohol amphiphiles such as sphingosylphosphorylcholine with biochemically relevant acylating agents, namely, acyl adenylates and acyl-CoAs, leads to the formation of the O-acylation product with high selectivity. The resulting O-acylated sphingolipids self-assemble into vesicles with markedly different biophysical properties than those formed from their N-acyl counterparts. We also demonstrate that Cu(II) can direct the O-acylation of alternative 1,2-amino alcohols, including prebiotically relevant 1,2-amino alcohol amphiphiles, suggesting that simple mechanisms for aqueous esterification may have been prevalent on earth before the evolution of enzymes.
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Affiliation(s)
- Ahanjit Bhattacharya
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Lalita Tanwar
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Alessandro Fracassi
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Roberto J. Brea
- Biomimetic
Membrane Chemistry (BioMemChem) Group, Centro de Investigacións
Científicas Avanzadas (CICA), Universidade
da Coruña, Rúa As Carballeiras, 15701, A Coruña, Spain
| | - Marta Salvador-Castell
- Department
of Physics, University of California, San
Diego, La Jolla, California 92093, United States
| | - Satyam Khanal
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
| | - Sunil K. Sinha
- Department
of Physics, University of California, San
Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department
of Chemistry and Biochemistry, University
of California, San Diego, La Jolla, California 92093, United States
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Tang H, Wang R, Pang S, Han W, Zhang Q, Fang Q, Chen X, Huang Q, Qiu D, Zhou R, Li L. Native ApxIIA secreted by Actinobacillus pleuropneumoniae induces apoptosis in porcine alveolar macrophages dependent on concentration and acylation. Vet Microbiol 2023; 287:109908. [PMID: 37952264 DOI: 10.1016/j.vetmic.2023.109908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023]
Abstract
Actinobacillus pleuropneumoniae is an important swine respiratory pathogen causing substantial economic losses to the global pig industry. The Apx toxins of A. pleuropneumoniae belong to the RTX toxin family and are major virulence factors. In addition to hemolysis and/or cytotoxicity via pore-forming activity, RTX toxins, such as ApxIA of A. pleuropneumoniae, have been reported to cause other effects on target cells, e.g., apoptosis. A. pleuropneumoniae ApxIIA is expressed by most serotypes and has moderate hemolytic and cytotoxic activities. In this study, porcine alveolar macrophages (3D4/21) were stimulated with different concentrations of purified native ApxIIA from the serotype 7 strain AP76 which only secretes ApxIIA. By observation of nuclear condensation via fluorescent staining and detection of apoptosis and necrosis by flow cytometry, it was found that high and low concentrations of native ApxIIA mainly caused necrosis or apoptosis of 3D4/21 cells, respectively. ApxIIA purified from an AP76 mutant with a deleted acetyltransferase gene (apxIIC) did not induce necrosis nor apoptosis. Western blot analysis using specific antibodies showed that a cleaved caspase 3 and activated capase 9 was detected after treatment of cells with a low concentration of native ApxIIA, while general or specific inhibitors of caspase 3, 8, 9 blocked these effects. ApxIIA-induced apoptosis of macrophages may be a mechanism of A. pleuropneumoniae to escape host immune clearance.
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Affiliation(s)
- Hao Tang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Rong Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Siqi Pang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Weiyao Han
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Qiuhong Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Qiong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Xiabing Chen
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Sciences, Wuhan, Hubei 430070, China
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei 430070, China
| | - Dexin Qiu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei 430070, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China; International Research Center for Animal Disease, Ministry of Science and Technology of the People's Republic of China, Wuhan, Hubei 430070, China.
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37
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Ronchetti R, Pannone LA, Cerra B, Camaioni E, Lopopolo G, Attolino E, Gioiello A. Multi-Gram Scale Synthesis and Characterization of Mometasone Furoate EP Impurity C. Molecules 2023; 28:7859. [PMID: 38067588 PMCID: PMC10708511 DOI: 10.3390/molecules28237859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Mometasone furoate is a synthetic corticosteroid used in the treatment of skin inflammatory conditions, hay fever and asthma. The industrial manufacturing routes to mometasone furoate are generally accompanied by the formation of numerous process impurities that need to be detected and quantified, as requested by regulatory authorities. The ready availability of such impurities in the required quantity and purity is therefore essential for toxicological studies, analytical method development and process validation. Herein, we report the multi-gram scale preparation of 21'-chloro-(16'α-methyl-3',11',20'-trioxo-pregna-1',4'-dien-17'-yl)-furan-2-carboxylate (mometasone furoate EP impurity C), one of the known impurities of mometasone furoate. This study also includes the systematic investigation of the final acylation step, as well as the characterization of the difuroate enol ether intermediate and its conversion to the target impurity C.
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Affiliation(s)
- Riccardo Ronchetti
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06122 Perugia, Italy; (R.R.); (L.A.P.); (E.C.); (A.G.)
| | - Luigi Alfonso Pannone
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06122 Perugia, Italy; (R.R.); (L.A.P.); (E.C.); (A.G.)
| | - Bruno Cerra
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06122 Perugia, Italy; (R.R.); (L.A.P.); (E.C.); (A.G.)
| | - Emidio Camaioni
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06122 Perugia, Italy; (R.R.); (L.A.P.); (E.C.); (A.G.)
| | - Gianfranco Lopopolo
- Research & Development Department, Newchem SpA, Via Roveggia, 47, 37136 Verona, Italy; (G.L.); (E.A.)
| | - Emanuele Attolino
- Research & Development Department, Newchem SpA, Via Roveggia, 47, 37136 Verona, Italy; (G.L.); (E.A.)
| | - Antimo Gioiello
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06122 Perugia, Italy; (R.R.); (L.A.P.); (E.C.); (A.G.)
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38
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Abdellattif MH, Hamed EO, Elhoseni NKR, Assy MG, Emwas AHM, Jaremko M, Celik I, Titi A, Kumar Yadav K, Elgendy MS, Shehab WS. Synthesis of novel pyrazolone candidates with studying some biological activities and in-silico studies. Sci Rep 2023; 13:19170. [PMID: 37932273 PMCID: PMC10628256 DOI: 10.1038/s41598-023-43575-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 09/26/2023] [Indexed: 11/08/2023] Open
Abstract
Pyranopyrazole derivatives have a vital role in the class of organic compounds because of their broad spectrum of biological and pharmacological importance. Our current goal is the [3 + 3] cycloaddition of benzoyl isothiocyanate and pyrazolone 1 to undergo oxidation cyclization, producing pyrazoloxadiazine 3. The diol 5 was obtained as a condensation of two equivalents of 1 with thiophene-2-carboxaldehyde in acetic acid above the sodium acetate mixture. When the condensation was carried out in piperidine under fusion, unsaturated ketone 4 was obtained. The pyrazolo pyran derivative 11 resulted from the [3 + 3] cycloaddition of 1 and cinnamic acid, while the Pyrone derivative was prepared by acylation of 12 with two equivalents of acetic anhydride. Phthalic anhydride undergoes arylation using zinc chloride as a catalyst. The cyclic keto acid 23 was synthesized by the action of succinic anhydride on 12 in the acetic medium, while the latter reacted with cinnamic acid, leading to pyrazole derivative 24. All of these reactions were through the Michael reaction mechanism. All the tested compounds showed good antimicrobial activity against pathogenic microorganisms; newly synthesized compounds were also screened for their antioxidant activity. Rational studies were carried out by the ABTs method to allow a broader choice of activities. In addition, similar off-compounds were conducted. Molecular docking studies with the CB-Dock server and MD simulations were created with the default settings of the Solution Builder on the CHARMM-GUI server at 150 nm. A good correlation was obtained between the experimental results and the theoretical bioavailability predictions using POM theory.
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Affiliation(s)
- Magda H Abdellattif
- Department of Chemistry, Sciences College, Taif University, P. O. Box 11099, 21944, Taif, Saudi Arabia.
| | - Eman O Hamed
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Nourhan Kh R Elhoseni
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Mohamed G Assy
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Abdul-Hamid M Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - Mariusz Jaremko
- Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, 38039, Turkey
| | - Abderrahim Titi
- Laboratory of Applied and Environmental Chemistry (LCAE), Mohamed First University, Oujda, Morocco
| | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal, 462044, India
- Department of Civil and Environmental Engineering, Faculty of Engineering, PSU Energy Systems Research Institute, Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Marwa S Elgendy
- Department of Chemistry, Faculty of Sciences, Alazhar University (Girls), Cairo, Egypt
| | - Wesam S Shehab
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt.
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Anwar MU, van der Goot FG. Refining S- acylation: Structure, regulation, dynamics, and therapeutic implications. J Cell Biol 2023; 222:e202307103. [PMID: 37756661 PMCID: PMC10533364 DOI: 10.1083/jcb.202307103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
With a limited number of genes, cells achieve remarkable diversity. This is to a large extent achieved by chemical posttranslational modifications of proteins. Amongst these are the lipid modifications that have the unique ability to confer hydrophobicity. The last decade has revealed that lipid modifications of proteins are extremely frequent and affect a great variety of cellular pathways and physiological processes. This is particularly true for S-acylation, the only reversible lipid modification. The enzymes involved in S-acylation and deacylation are only starting to be understood, and the list of proteins that undergo this modification is ever-increasing. We will describe the state of knowledge on the enzymes that regulate S-acylation, from their structure to their regulation, how S-acylation influences target proteins, and finally will offer a perspective on how alterations in the balance between S-acylation and deacylation may contribute to disease.
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Affiliation(s)
- Muhammad U. Anwar
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - F. Gisou van der Goot
- Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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40
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Meng X, Templeton C, Clementi C, Veit M. The role of an amphiphilic helix and transmembrane region in the efficient acylation of the M2 protein from influenza virus. Sci Rep 2023; 13:18928. [PMID: 37919373 PMCID: PMC10622425 DOI: 10.1038/s41598-023-45945-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023] Open
Abstract
Protein palmitoylation, a cellular process occurring at the membrane-cytosol interface, is orchestrated by members of the DHHC enzyme family and plays a pivotal role in regulating various cellular functions. The M2 protein of the influenza virus, which is acylated at a membrane-near amphiphilic helix serves as a model for studying the intricate signals governing acylation and its interaction with the cognate enzyme, DHHC20. We investigate it here using both experimental and computational assays. We report that altering the biophysical properties of the amphiphilic helix, particularly by shortening or disrupting it, results in a substantial reduction in M2 palmitoylation, but does not entirely abolish the process. Intriguingly, DHHC20 exhibits an augmented affinity for some M2 mutants compared to the wildtype M2. Molecular dynamics simulations unveil interactions between amino acids of the helix and the catalytically significant DHHC and TTXE motifs of DHHC20. Our findings suggest that the binding of M2 to DHHC20, while not highly specific, is mediated by requisite contacts, possibly instigating the transfer of fatty acids. A comprehensive comprehension of protein palmitoylation mechanisms is imperative for the development of DHHC-specific inhibitors, holding promise for the treatment of diverse human diseases.
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Affiliation(s)
- Xiaorong Meng
- Institute of Virology, Veterinary Faculty, Freie Universität Berlin, Berlin, Germany
| | - Clark Templeton
- Theoretical and Computational Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Cecilia Clementi
- Theoretical and Computational Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Michael Veit
- Institute of Virology, Veterinary Faculty, Freie Universität Berlin, Berlin, Germany.
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41
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Lyu X, Kanda R, Tsuda S, Hashimoto Y, Fujii T, Kashiwagi K. Novel Carboxylation Method for Polyetheretherketone (PEEK) Surface Modification Using Friedel-Crafts Acylation. Int J Mol Sci 2023; 24:15651. [PMID: 37958636 PMCID: PMC10650194 DOI: 10.3390/ijms242115651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Recently, polyetheretherketone (PEEK) has shown promising dental applications. Surface treatment is essential for dental applications owing to its poor surface energy and wettability; however, no consensus on an effective treatment method has been achieved. In this study, we attempted to carboxylate PEEK sample surfaces via Friedel-Crafts acylation using succinic anhydride and AlBr3. The possibility of further chemical modifications using carboxyl groups was examined. The samples were subjected to dehydration-condensation reactions with 1H,1H-pentadecafluorooctylamine and N,N'-dicyclohexylcarbodiimide. Furthermore, the sample's surface properties at each reaction stage were evaluated. An absorption band in the 3300-3500 cm-1 wavenumber region was observed. Additionally, peak suggestive of COOH was observed in the sample spectra. Secondary modification diminished the absorption band in 3300-3500 cm-1 and a clear F1s signal was observed. Thus, Friedel-Crafts acylation with succinic anhydride produced carboxyl groups on the PEEK sample surfaces. Further chemical modification of the carboxyl groups by dehydration-condensation reactions is also possible. Thus, a series of reactions can be employed to impart desired chemical structures to PEEK surfaces.
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Affiliation(s)
- Xinghui Lyu
- Department of Fixed Prosthodontics and Occlusion, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata 573-1121, Osaka, Japan; (X.L.); (T.F.); (K.K.)
| | - Ryuhei Kanda
- Division of Creative and Integrated Medicine, Advanced Medicine Research Center, Translational Research Institute for Medical Innovation (TRIMI), Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata 573-1121, Osaka, Japan;
| | - Susumu Tsuda
- Department of Chemistry, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata 573-1121, Osaka, Japan;
| | - Yoshiya Hashimoto
- Division of Creative and Integrated Medicine, Advanced Medicine Research Center, Translational Research Institute for Medical Innovation (TRIMI), Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata 573-1121, Osaka, Japan;
- Department of Biomaterial, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata 573-1121, Osaka, Japan
| | - Takamasa Fujii
- Department of Fixed Prosthodontics and Occlusion, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata 573-1121, Osaka, Japan; (X.L.); (T.F.); (K.K.)
| | - Kosuke Kashiwagi
- Department of Fixed Prosthodontics and Occlusion, Osaka Dental University, 8-1 Kuzuhahanazonocho, Hirakata 573-1121, Osaka, Japan; (X.L.); (T.F.); (K.K.)
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Angala SK, Carreras-Gonzalez A, Huc-Claustre E, Anso I, Kaur D, Jones V, Palčeková Z, Belardinelli JM, de Sousa-d'Auria C, Shi L, Slama N, Houssin C, Quémard A, McNeil M, Guerin ME, Jackson M. Acylation of glycerolipids in mycobacteria. Nat Commun 2023; 14:6694. [PMID: 37872138 PMCID: PMC10593935 DOI: 10.1038/s41467-023-42478-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/12/2023] [Indexed: 10/25/2023] Open
Abstract
We report on the existence of two phosphatidic acid biosynthetic pathways in mycobacteria, a classical one wherein the acylation of the sn-1 position of glycerol-3-phosphate (G3P) precedes that of sn-2 and another wherein acylations proceed in the reverse order. Two unique acyltransferases, PlsM and PlsB2, participate in both pathways and hold the key to the unusual positional distribution of acyl chains typifying mycobacterial glycerolipids wherein unsaturated substituents principally esterify position sn-1 and palmitoyl principally occupies position sn-2. While PlsM selectively transfers a palmitoyl chain to the sn-2 position of G3P and sn-1-lysophosphatidic acid (LPA), PlsB2 preferentially transfers a stearoyl or oleoyl chain to the sn-1 position of G3P and an oleyl chain to sn-2-LPA. PlsM is the first example of an sn-2 G3P acyltransferase outside the plant kingdom and PlsB2 the first example of a 2-acyl-G3P acyltransferase. Both enzymes are unique in their ability to catalyze acyl transfer to both G3P and LPA.
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Affiliation(s)
- Shiva Kumar Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Ana Carreras-Gonzalez
- Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain
- Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
| | - Emilie Huc-Claustre
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Itxaso Anso
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, 48903, Spain
| | - Devinder Kaur
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
- New England Newborn Screening Program, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Victoria Jones
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Zuzana Palčeková
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Juan M Belardinelli
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Célia de Sousa-d'Auria
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Libin Shi
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Nawel Slama
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Christine Houssin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Annaïk Quémard
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, UPS, Université Toulouse III - Paul Sabatier, Toulouse, France
| | - Michael McNeil
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Marcelo E Guerin
- Unidad de Biofisica, Centro Mixto Consejo Superior de Investigaciones Cientificas - Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC-UPV/EHU), Barrio Sarriena s/n, Leioa, Bizkaia, 48940, Spain
- Departamento de Bioquímica, Universidad del País Vasco, Leioa, Spain
- Structural Glycobiology Laboratory, Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, Bizkaia, 48903, Spain
- IKERBASQUE, Basque Foundation for Science, 48009, Bilbao, Spain
- Structural Glycobiology Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona Science Park, c/Baldiri Reixac 4-8, Tower R, 08028, Barcelona, Catalonia, Spain
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA.
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Teo S, Bossio A, Stamatakou E, Pascual-Vargas P, Jones ME, Schuhmacher LN, Salinas PC. S- acylation of the Wnt receptor Frizzled-5 by zDHHC5 controls its cellular localization and synaptogenic activity in the rodent hippocampus. Dev Cell 2023; 58:2063-2079.e9. [PMID: 37557176 DOI: 10.1016/j.devcel.2023.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 05/05/2023] [Accepted: 07/18/2023] [Indexed: 08/11/2023]
Abstract
Proper localization of receptors for synaptic organizing factors is crucial for synapse formation. Wnt proteins promote synapse assembly through Frizzled (Fz) receptors. In hippocampal neurons, the surface and synaptic localization of Fz5 is regulated by neuronal activity, but the mechanisms involved remain poorly understood. Here, we report that all Fz receptors can be post-translationally modified by S-acylation and that Fz5 is S-acylated on three C-terminal cysteines by zDHHC5. S-acylation is essential for Fz5 localization to the cell surface, axons, and presynaptic sites. Notably, S-acylation-deficient Fz5 is internalized faster, affecting its association with signalosome components at the cell surface. S-acylation-deficient Fz5 also fails to activate canonical and divergent canonical Wnt pathways. Fz5 S-acylation levels are regulated by the pattern of neuronal activity. In vivo studies demonstrate that S-acylation-deficient Fz5 expression fails to induce presynaptic assembly. Our studies show that S-acylation of Frizzled receptors is a mechanism controlling their localization and function.
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Affiliation(s)
- Samuel Teo
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Alessandro Bossio
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Eleanna Stamatakou
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Patricia Pascual-Vargas
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Megan E Jones
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Laura-Nadine Schuhmacher
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Patricia C Salinas
- Department of Cell and Developmental Biology, Division of Biosciences, University College London, London WC1E 6BT, UK.
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Zhang L, Shi X, Qiu H, Liu S, Yang T, Li X, Liu X. Protein modification by short-chain fatty acid metabolites in sepsis: a comprehensive review. Front Immunol 2023; 14:1171834. [PMID: 37869005 PMCID: PMC10587562 DOI: 10.3389/fimmu.2023.1171834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 09/15/2023] [Indexed: 10/24/2023] Open
Abstract
Sepsis is a major life-threatening syndrome of organ dysfunction caused by a dysregulated host response due to infection. Dysregulated immunometabolism is fundamental to the onset of sepsis. Particularly, short-chain fatty acids (SCFAs) are gut microbes derived metabolites serving to drive the communication between gut microbes and the immune system, thereby exerting a profound influence on the pathophysiology of sepsis. Protein post-translational modifications (PTMs) have emerged as key players in shaping protein function, offering novel insights into the intricate connections between metabolism and phenotype regulation that characterize sepsis. Accumulating evidence from recent studies suggests that SCFAs can mediate various PTM-dependent mechanisms, modulating protein activity and influencing cellular signaling events in sepsis. This comprehensive review discusses the roles of SCFAs metabolism in sepsis associated inflammatory and immunosuppressive disorders while highlights recent advancements in SCFAs-mediated lysine acylation modifications, such as substrate supplement and enzyme regulation, which may provide new pharmacological targets for the treatment of sepsis.
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Affiliation(s)
- Liang Zhang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Xinhui Shi
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Hongmei Qiu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Sijia Liu
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Ting Yang
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Xiaoli Li
- Department of Pharmacology, College of Pharmacy, Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Drug Metabolism, Chongqing, China
- Key Laboratory for Biochemistry and Molecular Pharmacology of Chongqing, Chongqing, China
| | - Xin Liu
- Medical Research Center, Southwest Hospital, Third Military Medical University, Chongqing, China
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Huang X, Yao J, Liu L, Chen J, Mei L, Huangfu J, Luo D, Wang X, Lin C, Chen X, Yang Y, Ouyang S, Wei F, Wang Z, Zhang S, Xiang T, Neculai D, Sun Q, Kong E, Tate EW, Yang A. S- acylation of p62 promotes p62 droplet recruitment into autophagosomes in mammalian autophagy. Mol Cell 2023; 83:3485-3501.e11. [PMID: 37802024 PMCID: PMC10552648 DOI: 10.1016/j.molcel.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 06/22/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023]
Abstract
p62 is a well-characterized autophagy receptor that recognizes and sequesters specific cargoes into autophagosomes for degradation. p62 promotes the assembly and removal of ubiquitinated proteins by forming p62-liquid droplets. However, it remains unclear how autophagosomes efficiently sequester p62 droplets. Herein, we report that p62 undergoes reversible S-acylation in multiple human-, rat-, and mouse-derived cell lines, catalyzed by zinc-finger Asp-His-His-Cys S-acyltransferase 19 (ZDHHC19) and deacylated by acyl protein thioesterase 1 (APT1). S-acylation of p62 enhances the affinity of p62 for microtubule-associated protein 1 light chain 3 (LC3)-positive membranes and promotes autophagic membrane localization of p62 droplets, thereby leading to the production of small LC3-positive p62 droplets and efficient autophagic degradation of p62-cargo complexes. Specifically, increasing p62 acylation by upregulating ZDHHC19 or by genetic knockout of APT1 accelerates p62 degradation and p62-mediated autophagic clearance of ubiquitinated proteins. Thus, the protein S-acylation-deacylation cycle regulates p62 droplet recruitment to the autophagic membrane and selective autophagic flux, thereby contributing to the control of selective autophagic clearance of ubiquitinated proteins.
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Affiliation(s)
- Xue Huang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jia Yao
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Lu Liu
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jing Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Ligang Mei
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Jingjing Huangfu
- Institute of Psychiatry and Neuroscience, Xinxiang Key Laboratory of Protein Palmitoylation and Major Human Diseases, Xinxiang Medical University, Xinxiang, China
| | - Dong Luo
- School of Pharmacy, Chongqing University, Chongqing 401331, China
| | - Xinyi Wang
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China; Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Changhai Lin
- School of Life Sciences, Chongqing University, Chongqing 401331, China; Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Xiaorong Chen
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Yi Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Sheng Ouyang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Fujing Wei
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhuolin Wang
- School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Shaolin Zhang
- School of Pharmacy, Chongqing University, Chongqing 401331, China
| | - Tingxiu Xiang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Dante Neculai
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Qiming Sun
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang, China; Department of Biochemistry and Department of Cardiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Eryan Kong
- Institute of Psychiatry and Neuroscience, Xinxiang Key Laboratory of Protein Palmitoylation and Major Human Diseases, Xinxiang Medical University, Xinxiang, China
| | - Edward W Tate
- Department of Chemistry, Imperial College London, 82 Wood Lane, London W12 0BZ, UK
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing 401331, China.
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Li Y, Xu M, Zhai H, Yang C, Yang J, Ke Z, Chen W, Ou J, Sha Z, Xiao Q. Lipopolysaccharide (LPS) extracted from Bacteroides vulgatus effectively prevents LPS extracted from Escherichia coli from inducing epithelial‑mesenchymal transition. Mol Med Rep 2023; 28:195. [PMID: 37681466 PMCID: PMC10502948 DOI: 10.3892/mmr.2023.13082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/09/2023] [Indexed: 09/09/2023] Open
Abstract
Pathological epithelial‑mesenchymal transition (EMT) has been shown to fulfill a key role in the development and progression of a variety of lung diseases. It has been demonstrated that the inflammatory microenvironment is a decisive factor in inducing pathological EMT. Hexacylated lipopolysaccharide (LPS) [or proacylated lipopolysaccharide (P‑LPS), which functions as proinflammatory lipopolysaccharide] is one of the most effective Toll‑like receptor 4 (TLR4) agonists. Furthermore, the pentacylated and tetracylated form of lipopolysaccharide (or A‑LPS, which functions as anti‑inflammatory lipopolysaccharide) has been shown to elicit competitive antagonistic effects against the pro‑inflammatory activity of P‑LPS. At present, it remains unclear whether LPS extracted from Bacteroides vulgatus (BV‑LPS) can prevent LPS extracted from Escherichia coli (EC‑LPS) from inducing pathological EMT. In the present study, A549 cells and C57BL/6 mice lung tissue were both induced by EC‑LPS (P‑LPS) and BV‑LPS (A‑LPS), either alone or in combination. The anticipated anti‑inflammatory effects of BV‑LPS were analyzed by examining the lung coefficient, lung pathology, A549 cell morphology and expression levels both of the inflammatory cytokines, IL‑1β, IL‑6 and TNF‑α and of the EMT signature proteins, epithelial cadherin (E‑cadherin), α‑smooth muscle actin (α‑SMA) and vimentin. In addition, the expression levels of TLR4, bone morphogenic protein and activin membrane‑bound inhibitor (BAMBI) and Snail were detected and the possible mechanism underlying how BV‑LPS may prevent EC‑LPS‑induced EMT was analyzed. The results obtained showed that the morphology of the A549 cells was significantly polarized, the lung index was significantly increased, the alveolar structure was collapsed and the expression levels of IL‑1β, IL‑6, TNF‑α, α‑SMA, vimentin, TLR4 and Snail in both lung tissue and A549 cells were significantly increased, whereas those of E‑cadherin and BAMBI were significantly decreased. Treatment with BV‑LPS in combination with EC‑LPS was found to reverse these changes. In conclusion, the present study demonstrated that BV‑LPS is able to effectively prevent EC‑LPS‑induced EMT in A549 cells and in mouse lung tissue and furthermore, the underlying mechanism may be associated with inhibition of the TLR4/BAMBI/Snail signaling pathway.
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Affiliation(s)
- Yuping Li
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Mengdan Xu
- Shizhen College, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550200, P.R. China
| | - Haiying Zhai
- The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550000, P.R. China
| | - Changfu Yang
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Jiaotong Yang
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Zunli Ke
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Wanhao Chen
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Jiangqin Ou
- The First Affiliated Hospital, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550000, P.R. China
| | - Zongge Sha
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
| | - Qiaoqiao Xiao
- Basic Medical School, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, P.R. China
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47
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Azizi SA, Qiu T, Brookes NE, Dickinson BC. Regulation of ERK2 activity by dynamic S- acylation. Cell Rep 2023; 42:113135. [PMID: 37715953 PMCID: PMC10591828 DOI: 10.1016/j.celrep.2023.113135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 09/18/2023] Open
Abstract
Extracellular signal-regulated kinases (ERK1/2) are key effector proteins of the mitogen-activated protein kinase pathway, choreographing essential processes of cellular physiology. Here, we discover that ERK1/2 are subject to S-acylation, a reversible lipid modification of cysteine residues, at C271/C254. The levels of ERK1/2 S-acylation are modulated by epidermal growth factor (EGF) signaling, mirroring its phosphorylation dynamics, and acylation-deficient ERK2 displays altered phosphorylation patterns. We show that ERK1/2 S-acylation is mediated by "writer" protein acyl transferases (PATs) and "eraser" acyl protein thioesterases (APTs) and that chemical inhibition of either lipid addition or removal alters ERK1/2's EGF-triggered transcriptional program. Finally, in a mouse model of metabolic syndrome, we find that ERK1/2 lipidation levels correlate with alterations in ERK1/2 lipidation writer/eraser expression, solidifying a link between ERK1/2 activity, ERK1/2 lipidation, and organismal health. This study describes how lipidation regulates ERK1/2 and offers insight into the role of dynamic S-acylation in cell signaling more broadly.
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Affiliation(s)
- Saara-Anne Azizi
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA; Medical Scientist Training Program, Pritzker School of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Tian Qiu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Noah E Brookes
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Bryan C Dickinson
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.
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Habazaki M, Mizumoto S, Kajino H, Kujirai T, Kurumizaka H, Kawashima SA, Yamatsugu K, Kanai M. A chemical catalyst enabling histone acylation with endogenous acyl-CoA. Nat Commun 2023; 14:5790. [PMID: 37737243 PMCID: PMC10517024 DOI: 10.1038/s41467-023-41426-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/29/2023] [Indexed: 09/23/2023] Open
Abstract
Life emerges from a network of biomolecules and chemical reactions catalyzed by enzymes. As enzyme abnormalities are often connected to various diseases, a chemical catalyst promoting physiologically important intracellular reactions in place of malfunctional endogenous enzymes would have great utility in understanding and treating diseases. However, research into such small-molecule chemical enzyme surrogates remains limited, due to difficulties in developing a reactive catalyst capable of activating inert cellular metabolites present at low concentrations. Herein, we report a small-molecule catalyst, mBnA, as a surrogate for a histone acetyltransferase. A hydroxamic acid moiety of suitable electronic characteristics at the catalytic site, paired with a thiol-thioester exchange process, enables mBnA to activate endogenous acyl-CoAs present in low concentrations and promote histone lysine acylations in living cells without the addition of exogenous acyl donors. An enzyme surrogate utilizing cellular metabolites will be a unique tool for elucidation of and synthetic intervention in the chemistry of life and disease.
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Affiliation(s)
- Misuzu Habazaki
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shinsuke Mizumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hidetoshi Kajino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Shigehiro A Kawashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Kenzo Yamatsugu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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49
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Ji G, Wu R, Zhang L, Yao J, Zhang C, Zhang X, Liu Z, Liu Y, Wang T, Fang C, Lu H. Global Analysis of Endogenously Intact S-Acylated Peptides Reveals Localization Differentiation of Heterogeneous Lipid Chains in Mammalian Cells. Anal Chem 2023; 95:13055-13063. [PMID: 37611173 DOI: 10.1021/acs.analchem.3c01484] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
S-acylation is a widespread lipidation form in eukaryotes in which various fatty acids can be covalently attached to specific cysteine residues. However, due to the low reactivity of the lipid moieties and lack of specific antibodies, purification of intact S-acylated peptides remains challenging. Here, we developed a pretreatment method for direct separation and global analysis of endogenously intact S-acylated peptides by nanographite fluoride-based solid-phase extraction (nGF-SPE), together with the investigation and optimization of the enrichment procedure as well as the LC-MS/MS analysis process. Consequently, we performed the first global profiling of endogenously intact S-acylated peptides, with 701 S-palmitoylated peptides from HeLa cell lysates in a restricted search. Furthermore, coupling the nGF-SPE method with open search mode, altogether 1119 intact S-acylated peptides were identified with the attached palmitate, palmitoleate, myristate, and octanoate chain, respectively, providing a global insight into the endogenously heterogeneous modification state. Notably, we found and validated that S-palmitoleoylation (C16:1) provided less affinity toward lipid rafts compared with S-palmitoylation (C16:0). This study developed the first straightforward way to characterize endogenously intact S-acylated peptides on a proteome-wide scale, providing the modified residues together with their attached lipid moieties simultaneously, which paves the way for further understanding of protein S-acylation.
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Affiliation(s)
- Guanghui Ji
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, P. R. China
| | - Roujun Wu
- 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
| | - Jun Yao
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Cheng Zhang
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, P. R. China
| | - Xiaoqin Zhang
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, P. R. China
| | - Zhiyong Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Yang Liu
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, P. R. China
| | - Ting Wang
- Department of Chemistry and Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200433, 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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Abstract
The presence of a hydroxyl group at the 2'-position in its ribose makes RNA susceptible to hydrolysis. Stabilization of RNAs for storage, transport and biological application thus remains a serious challenge, particularly for larger RNAs that are not accessible by chemical synthesis. Here we present reversible 2'-OH acylation as a general strategy to preserve RNA of any length or origin. High-yield polyacylation of 2'-hydroxyls ('cloaking') by readily accessible acylimidazole reagents effectively shields RNAs from both thermal and enzymatic degradation. Subsequent treatment with water-soluble nucleophilic reagents removes acylation adducts quantitatively ('uncloaking') and recovers a remarkably broad range of RNA functions, including reverse transcription, translation and gene editing. Furthermore, we show that certain α-dimethylamino- and α-alkoxy- acyl adducts are spontaneously removed in human cells, restoring messenger RNA translation with extended functional half-lives. These findings support the potential of reversible 2'-acylation as a simple and general molecular solution for enhancing RNA stability and provide mechanistic insights for stabilizing RNA regardless of length or origin.
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Affiliation(s)
- Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA.
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