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Suazo KF, Mishra V, Maity S, Auger SA, Justyna K, Petre AM, Ottoboni L, Ongaro J, Corti SP, Lotti F, Przedborski S, Distefano MD. Improved synthesis and application of an alkyne-functionalized isoprenoid analogue to study the prenylomes of motor neurons, astrocytes and their stem cell progenitors. Bioorg Chem 2024; 147:107365. [PMID: 38636436 DOI: 10.1016/j.bioorg.2024.107365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
Protein prenylation is one example of a broad class of post-translational modifications where proteins are covalently linked to various hydrophobic moieties. To globally identify and monitor levels of all prenylated proteins in a cell simultaneously, our laboratory and others have developed chemical proteomic approaches that rely on the metabolic incorporation of isoprenoid analogues bearing bio-orthogonal functionality followed by enrichment and subsequent quantitative proteomic analysis. Here, several improvements in the synthesis of the alkyne-containing isoprenoid analogue C15AlkOPP are reported to improve synthetic efficiency. Next, metabolic labeling with C15AlkOPP was optimized to obtain useful levels of metabolic incorporation of the probe in several types of primary cells. Those conditions were then used to study the prenylomes of motor neurons (ES-MNs), astrocytes (ES-As), and their embryonic stem cell progenitors (ESCs), which allowed for the identification of 54 prenylated proteins from ESCs, 50 from ES-MNs, and 84 from ES-As, representing all types of prenylation. Bioinformatic analysis revealed specific enriched pathways, including nervous system development, chemokine signaling, Rho GTPase signaling, and adhesion. Hierarchical clustering showed that most enriched pathways in all three cell types are related to GTPase activity and vesicular transport. In contrast, STRING analysis showed significant interactions in two populations that appear to be cell type dependent. The data provided herein demonstrates that robust incorporation of C15AlkOPP can be obtained in ES-MNs and related primary cells purified via magnetic-activated cell sorting allowing the identification and quantification of numerous prenylated proteins. These results suggest that metabolic labeling with C15AlkOPP should be an effective approach for investigating the role of prenylated proteins in primary cells in both normal cells and disease pathologies, including ALS.
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Affiliation(s)
- Kiall F Suazo
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Vartika Mishra
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA.
| | - Sanjay Maity
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Shelby A Auger
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Katarzyna Justyna
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Alexandru M Petre
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Linda Ottoboni
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy.
| | - Jessica Ongaro
- Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefania P Corti
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, Università degli Studi di Milano, Milan, Italy; Neurology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
| | - Francesco Lotti
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA.
| | - Serge Przedborski
- Center for Motor Neuron Biology and Diseases, Department of Neurology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Pathology & Cell Biology. Columbia University Irving Medical Center. New York, NY 10032, USA; Department of Neuroscience, Pathology, and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Mark D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
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Fu J, Li S, Xu M, Zhang D, Chen L. Changes in physicochemical properties and formation process of colloidal nanoparticles (CNPs) during the lamb soup stewing. Food Chem 2024; 442:138290. [PMID: 38219561 DOI: 10.1016/j.foodchem.2023.138290] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/16/2024]
Abstract
Colloidal nanoparticles (CNPs), as carriers of nutrients, naturally exist in food or form during cooking. In this study, the colloidal properties, structures, rheological properties, and chemical composition location of CNPs were analyzed during 15 min to 5 h lamb soup stewing. With the increasing stewing time, the particle size and absolute value of the zeta potential of CNPs increased, indicating that CNPs became more stable. As the stewing time increased, the blue-shifted Fourier transform infrared spectroscopy absorption peaks and the red-shifted fluorescence spectroscopy absorption peaks certificated the structural changes in CNPs. And α-helix and β-turn content decreased, while β-sheet and random coil content increased in processing, potentially resulting in the opening CNPs structures. In addition, our findings revealed that proteins were encapsulated within the lipids in the inner part, while carbohydrates were dispersed in the outermost layers of the CNPs with a phospholipid bilayer.
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Affiliation(s)
- Jianing Fu
- Institute of Food Science and Technology, Chinese Academy of Agriculture Sciences, Key Laboratory of Agro-Products Quality & Safety Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, China; The College of Food Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Shaobo Li
- Institute of Food Science and Technology, Chinese Academy of Agriculture Sciences, Key Laboratory of Agro-Products Quality & Safety Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Meizhen Xu
- Institute of Food Science and Technology, Chinese Academy of Agriculture Sciences, Key Laboratory of Agro-Products Quality & Safety Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Dequan Zhang
- Institute of Food Science and Technology, Chinese Academy of Agriculture Sciences, Key Laboratory of Agro-Products Quality & Safety Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, China
| | - Li Chen
- Institute of Food Science and Technology, Chinese Academy of Agriculture Sciences, Key Laboratory of Agro-Products Quality & Safety Harvest, Storage, Transportation, Management and Control, Ministry of Agriculture and Rural Affairs, Beijing 100193, China.
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Kundu S, Rohokale R, Lin C, Chen S, Biswas S, Guo Z. Bifunctional glycosphingolipid (GSL) probes to investigate GSL-interacting proteins in cell membranes. J Lipid Res 2024; 65:100570. [PMID: 38795858 DOI: 10.1016/j.jlr.2024.100570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/28/2024] Open
Abstract
Glycosphingolipids (GSLs) are abundant glycolipids on cells and essential for cell recognition, adhesion, signal transduction, and so on. However, their lipid anchors are not long enough to cross the membrane bilayer. To transduce transmembrane signals, GSLs must interact with other membrane components, whereas such interactions are difficult to investigate. To overcome this difficulty, bifunctional derivatives of II3-β-N-acetyl-D-galactosamine-GA2 (GalNAc-GA2) and β-N-acetyl-D-glucosamine-ceramide (GlcNAc-Cer) were synthesized as probes to explore GSL-interacting membrane proteins in live cells. Both probes contain photoreactive diazirine in the lipid moiety, which can crosslink with proximal membrane proteins upon photoactivation, and clickable alkyne in the glycan to facilitate affinity tag addition for crosslinked protein pull-down and characterization. The synthesis is highlighted by the efficient assembly of simple glycolipid precursors followed by on-site lipid remodeling. These probes were employed to profile GSL-interacting membrane proteins in HEK293 cells. The GalNAc-GA2 probe revealed 312 distinct proteins, with GlcNAc-Cer probe-crosslinked proteins as controls, suggesting the potential influence of the glycan on GSL functions. Many of the proteins identified with the GalNAc-GA2 probe are associated with GSLs, and some have been validated as being specific to this probe. The versatile probe design and experimental protocols are anticipated to be widely applicable to GSL research.
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Affiliation(s)
- Sayan Kundu
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Rajendra Rohokale
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Chuwei Lin
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Sixue Chen
- Department of Biology, Genetics Institute, University of Florida, Gainesville, FL, USA; Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Shayak Biswas
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL, USA.
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Uematsu M, Baskin JM. Chemical Approaches for Measuring and Manipulating Lipids at the Organelle Level. Cold Spring Harb Perspect Biol 2023; 15:a041407. [PMID: 37604586 PMCID: PMC10691496 DOI: 10.1101/cshperspect.a041407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
As the products of complex and often redundant metabolic pathways, lipids are challenging to measure and perturb using genetic tools. Yet by virtue of being the major constituents of cellular membranes, lipids are highly regulated in space and time. Chemists have stepped into this methodological void, developing an array of techniques for the precise quantification and manipulation of lipids at the subcellular, organelle level. Here, we survey the landscape of these methods. For measuring lipids, we summarize the use of metabolic labeling and click chemistry tagging, photoaffinity labeling, isotopic tagging for Raman microscopy, and chemoenzymatic labeling for tracking lipid production and interorganelle transport. For perturbing lipids, we describe synthetic photocaged lipids and membrane editing approaches using optogenetic enzymes for precise manipulation of lipid signaling. Collectively, these chemical and biochemical tools are revealing phenomena and mechanisms underlying lipid functions at the subcellular level.
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Affiliation(s)
- Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
| | - Jeremy M Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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Zhu W, Su H, Wei Y, Huang Y, Chen S, Shi Y, Long Y, Qiu Y, Wei J. Asiatic acid ameliorates rifampicin- and isoniazid-induced liver injury in vivo by regulating sphingolipid metabolism and mitogen-activated protein kinase signalling pathways. Basic Clin Pharmacol Toxicol 2023; 133:402-417. [PMID: 37272388 DOI: 10.1111/bcpt.13909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 05/25/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
In this study, we aimed to determine whether asiatic acid (AA) exerts any therapeutic effects on rifampicin (RFP)- and isoniazid (INH)-induced liver injury and elucidate the underlying mechanisms. Briefly, liver injury in mice was induced via RFP and INH administration. We investigated the effects and potential action mechanisms of AA on liver injury using transcriptomics, metabolomics and various examinations. We found that AA significantly ameliorated the pathological changes in liver tissues and decreased the transaminase activity, inflammation and oxidative stress damage. Transcriptomics revealed 147 differentially expressed genes (DEGs) between the AA and model groups that were enriched in metabolic and mitogen-activated protein kinase (MAPK) signalling pathways. Metabolomics revealed 778 differentially expressed metabolites between the AA and model groups. Furthermore, integrated transcriptomics and metabolomics analyses revealed strong correlations between DEGs and differentially expressed metabolites and indicated that AA regulates the sphingolipid metabolism by inhibiting the expression of delta 4-desaturase, sphingolipid 1. Experimental results confirmed that AA inhibited the MAPK signalling pathway. In summary, AA inhibits inflammation and oxidative stress damage by regulating the sphingolipid metabolism pathway and blocking the MAPK signalling pathway, thereby relieving the RFP/INH-induced liver injury.
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Affiliation(s)
- Wuchang Zhu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
- Pharmacy Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hongmei Su
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Yuanyuan Wei
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Yushen Huang
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Siyun Chen
- Pharmacy Department, The People's Hospital of Hezhou, Hezhou, China
| | - Yanxia Shi
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Yan Long
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Yue Qiu
- Pharmaceutical College, Guangxi Medical University, Nanning, China
| | - Jinbin Wei
- Pharmaceutical College, Guangxi Medical University, Nanning, China
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Kraouia M, Nartea A, Maoloni A, Osimani A, Garofalo C, Fanesi B, Ismaiel L, Aquilanti L, Pacetti D. Sea Fennel ( Crithmum maritimum L.) as an Emerging Crop for the Manufacturing of Innovative Foods and Nutraceuticals. Molecules 2023; 28:4741. [PMID: 37375298 DOI: 10.3390/molecules28124741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Sea fennel (Crithmum maritimum L.) is a perennial, strongly aromatic herb that has been used since ancient times in cuisine and folk medicine due to its renowned properties. Recently described as a "cash" crop, sea fennel is an ideal candidate for the promotion of halophyte agriculture in the Mediterranean basin due to its acknowledged adaptation to the Mediterranean climate, its resilience to risks/shocks related to climate changes, and its exploitability in food and non-food applications, which generates an alternative source of employment in rural areas. The present review provides insight into the nutritional and functional traits of this new crop as well as its exploitation in innovative food and nutraceutical applications. Various previous studies have fully demonstrated the high biological and nutritional potential of sea fennel, highlighting its high content of bioactive compounds, including polyphenols, carotenoids, ω-3 and ω-6 essential fatty acids, minerals, vitamins, and essential oils. Moreover, in previous studies, this aromatic halophyte showed good potential for application in the manufacturing of high-value foods, including both fermented and unfermented preserves, sauces, powders, and spices, herbal infusions and decoctions, and even edible films, as well as nutraceuticals. Further research efforts are needed to fully disclose the potential of this halophyte in view of its full exploitation by the food and nutraceutical industries.
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Affiliation(s)
- Maryem Kraouia
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
| | - Ancuta Nartea
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
| | - Antonietta Maoloni
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
| | - Andrea Osimani
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
| | - Cristiana Garofalo
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
| | - Benedetta Fanesi
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
| | - Lama Ismaiel
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
| | - Lucia Aquilanti
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
| | - Deborah Pacetti
- Department of Agricultural, Food and Environmental Sciences (D3A), Università Politecnica delle Marche (UNIVPM), 60131 Ancona, Italy
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Abstract
Lipids are key components of all organisms. We are well educated in their use as fuel and their essential role to form membranes. We also know much about their biosynthesis and metabolism. We are also aware that most lipids have signaling character meaning that a change in their concentration or location constitutes a signal that helps a living cell to respond to changes in the environment or to fulfill its specific function ranging from secretion to cell division. What is much less understood is how lipids change location in cells over time and what other biomolecules they interact with at each stage of their lifetime. Due to the large number of often quite similar lipid species and the sometimes very short lifetime of signaling lipids, we need highly specific tools to manipulate and visualize lipids and lipid-protein interactions. If successfully applied, these tools provide fabulous opportunities for discovery.In this Account, I summarize the development of synthetic tools from our lab that were designed to address crucial properties that allow them to function as tools in live cell experiments. Techniques to change the concentration of lipids by adding a small molecule or by light are described and complemented by examples of biological findings made when applying the tools. This ranges from chemical dimerizer-based systems to synthetic "caged" lipid derivatives. Furthermore, I discuss the problem of locating a lipid in an intact cell. Synthetic molecular probes are described that help to unravel the lipid location and to determine their binding proteins. These location studies require in-cell lipid tagging by click chemistry, photo-cross-linking to prevent further movement and the "caging" groups to avoid premature metabolism. The combination of these many technical features in a single tool allows for the analysis of not only lipid fluxes through metabolism but also lipid transport from one membrane to another as well as revealing the lipid interactome in a cell-dependent manner. This latter point is crucial because with these multifunctional tools in combination with lipidomics we can now address differences in healthy versus diseased cells and ultimately find the changes that are essential for disease development and new therapeutics that prevent these changes.
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Affiliation(s)
- Carsten Schultz
- Department of Chemical Physiology and
Biochemistry, Oregon Health & Science
University, Portland, Oregon 97239, United States
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