1
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Klińska-Bąchor S, Demski K, Gong Y, Banaś A. Biochemical characterization of acyl-CoA:diacylglycerol acyltransferase2 from the diatom Phaeodactylum tricornutum and its potential effect on LC-PUFAs biosynthesis in planta. BMC Plant Biol 2024; 24:309. [PMID: 38649801 PMCID: PMC11036593 DOI: 10.1186/s12870-024-05014-7] [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: 01/08/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), belonging to ω-3 long-chain polyunsaturated fatty acids (ω3-LC-PUFAs), are essential components of human diet. They are mainly supplemented by marine fish consumption, although their native producers are oleaginous microalgae. Currently, increasing demand for fish oils is insufficient to meet the entire global needs, which puts pressure on searching for the alternative solutions. One possibility may be metabolic engineering of plants with an introduced enzymatic pathway producing ω3-LC-PUFAs. RESULT In this study we focused on the acyl-CoA:diacylglycerol acyltransferase2b (PtDGAT2b) from the diatom Phaeodactylum tricornutum, an enzyme responsible for triacylglycerol (TAG) biosynthesis via acyl-CoA-dependent pathway. Gene encoding PtDGAT2b, incorporated into TAG-deficient yeast strain H1246, was used to confirm its activity and conduct biochemical characterization. PtDGAT2b exhibited a broad acyl-CoA preference with both di-16:0-DAG and di-18:1-DAG, whereas di-18:1-DAG was favored. The highest preference for acyl donors was observed for 16:1-, 10:0- and 12:0-CoA. PtDGAT2b also very efficiently utilized CoA-conjugated ω-3 LC-PUFAs (stearidonic acid, eicosatetraenoic acid and EPA). Additionally, verification of the potential role of PtDGAT2b in planta, through its transient expression in tobacco leaves, indicated increased TAG production with its relative amount increasing to 8%. Its co-expression with the gene combinations aimed at EPA biosynthesis led to, beside elevated TAG accumulation, efficient accumulation of EPA which constituted even 25.1% of synthesized non-native fatty acids (9.2% of all fatty acids in TAG pool). CONCLUSIONS This set of experiments provides a comprehensive biochemical characterization of DGAT enzyme from marine microalgae. Additionally, this study elucidates that PtDGAT2b can be used successfully in metabolic engineering of plants designed to obtain a boosted TAG level, enriched not only in ω-3 LC-PUFAs but also in medium-chain and ω-7 fatty acids.
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Affiliation(s)
- Sylwia Klińska-Bąchor
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland.
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
| | - Kamil Demski
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Yangmin Gong
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Antoni Banaś
- Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
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2
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Zhou Y, Lv R, Ye RD, Ren R, Yu L. The 3-hydroxyacyl-CoA dehydratase 1/2 form complex with trans-2-enoyl-CoA reductase involved in substrates transfer in very long chain fatty acid elongation. Biochem Biophys Res Commun 2024; 704:149588. [PMID: 38422897 DOI: 10.1016/j.bbrc.2024.149588] [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: 01/20/2024] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 03/02/2024]
Abstract
Very long-chain fatty acids (VLCFAs) are fatty acids with a carbon chain length greater than 18 carbons (>C18) and exhibit various functions, such as in skin barrier formation, liver homeostasis, myelin maintenance, spermatogenesis, retinal function, and anti-inflammation. VLCFAs are absorbed by dietary or elongated from endogenous hexadecanoyl acids (C16). Similar to long-chain fatty acid synthesis, VLCFAs elongation begins with acyl-CoA and malonyl-CoA as sources, and the length of the acyl chain is extended by two carbon units in each cycle. However, the VLCFAs elongation machinery is located in ER membrane and consists of four components, FA elongase (ELOVL), 3-ketoacyl-CoA reductase (KAR), 3-hydroxyacyl-CoA dehydratase (HACD), and trans-2-enoyl-CoA reductase (TECR), which is different with the long-chain fatty acid machinery fatty acid synthase (FAS) complex. Although the critical components in the elongation cycle are identified, the detailed catalytic and regulation mechanisms are still poorly understood. Here, we focused on the structural and biochemical analysis of TECR-associated VLCFA elongation reactions. Firstly, we identified a stable complex of human HACD2-TECR based on extensive in vitro characterizations. Combining computational modeling and biochemical analysis, we confirmed the critical interactions between TECR and HACD1/2. Then, we proposed the putative substrate binding sites and catalytic residues for TECR and HACD2. Besides, we revealed the structural similarities of HACD with ELOVLs and proposed the possible competition mechanism of TECR-associated complex formation.
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Affiliation(s)
- Youli Zhou
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Rui Lv
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Richard D Ye
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, 518172, China
| | - Ruobing Ren
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Leiye Yu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China.
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3
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Zeaiter N, Belot L, Cunin V, Nahed RA, Tokarska-Schlattner M, Le Gouellec A, Petosa C, Khochbin S, Schlattner U. Acetyl-CoA synthetase (ACSS2) does not generate butyryl- and crotonyl-CoA. Mol Metab 2024; 81:101903. [PMID: 38369012 PMCID: PMC10906504 DOI: 10.1016/j.molmet.2024.101903] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/05/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024] Open
Abstract
Acetyl and other acyl groups from different short-chain fatty acids (SCFA) competitively modify histones at various lysine sites. To fully understand the functional significance of such histone acylation, a key epigenetic mechanism, it is crucial to characterize the cellular sources of the corresponding acyl-CoA molecules required for the lysine modification. Like acetate, SCFAs such as propionate, butyrate and crotonate are thought to be the substrates used to generate the corresponding acyl-CoAs by enzymes known as acyl-CoA synthetases. The acetyl-CoA synthetase, ACSS2, which produces acetyl-CoA from acetate in the nucleocytoplasmic compartment, has been proposed to also mediate the synthesis of acyl-CoAs such as butyryl- and crotonyl-CoA from the corresponding SCFAs. This idea is now widely accepted and is sparking new research projects. However, based on our direct in vitro experiments with purified or recombinant enzymes and structural considerations, we demonstrate that ACSS2 is unable to mediate the generation of non-acetyl acyl-CoAs like butyryl- and crotonyl-CoA. It is therefore essential to re-examine published data and corresponding discussions in the light of this new finding.
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Affiliation(s)
- Nour Zeaiter
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France
| | - Laura Belot
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Valérie Cunin
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, 38000 Grenoble, France
| | - Roland Abi Nahed
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France
| | | | - Audrey Le Gouellec
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, 38000 Grenoble, France
| | - Carlo Petosa
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Saadi Khochbin
- Univ. Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France.
| | - Uwe Schlattner
- Univ. Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; Institut Universitaire de France, Paris, France.
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4
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Wang W, Wang P, Zhu L, Liu B, Wei Q, Hou Y, Li X, Hu Y, Li W, Wang Y, Jiang C, Yang G, Wang J. An optimized fluorescent biosensor for monitoring long-chain fatty acyl-CoAs metabolism in vivo. Biosens Bioelectron 2024; 247:115935. [PMID: 38128319 DOI: 10.1016/j.bios.2023.115935] [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: 10/17/2023] [Revised: 12/07/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Long-chain fatty acyl-CoAs (LCACoAs) are intermediates in lipid metabolism that exert a wide range of cellular functions. However, our knowledge about the subcellular distribution and regulatory impacts of LCACoAs is limited by a lack of methods for detecting LCACoAs in living cells and tissues. Here, we report our development of LACSerHR, a genetically encoded fluorescent biosensor that enables precise measurement of subtle fluctuations in the levels of endogenous LCACoAs in vivo. LACSerHR significantly improve the fluorescent brightness and analyte affinity, in vitro and in vivo testing showcased LACSerHR's large dynamic range. We demonstrate LACSerHR's capacity for real-time evaluation of LCACoA levels in specific subcellular compartments, for example in response to disruption of ACSL enzyme function in HEK293T cells. Moreover, we show the application of LACSerHR for sensitive measurement of elevated LCACoA levels in the livers of mouse models for two common metabolic diseases (NAFLD and type 2 diabetes). Thus, our LACSerHR sensor is a powerful, broadly applicable tool for studying LCACoAs metabolism and disease.
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Affiliation(s)
- Weibo Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China; National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, PR China
| | - Pengcheng Wang
- Center of Basic Medical Research, Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, 100191, PR China
| | - Lixin Zhu
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China
| | - Bingjie Liu
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China
| | - Qingpeng Wei
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China
| | - Yongkang Hou
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China
| | - Xi Li
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China
| | - Yufei Hu
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China
| | - Wenzhe Li
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China
| | - Yuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China
| | - Changtao Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, 100191, PR China
| | - Guangfu Yang
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, PR China.
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology, School of Pharmaceutical Sciences Peking University, Beijing, 100191, PR China.
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5
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Ducrot L, López IL, Orrego AH, López-Gallego F. Coenzyme A Thioester Intermediates as Platform Molecules in Cell-Free Chemical Biomanufacturing. Chembiochem 2024; 25:e202300673. [PMID: 37994376 DOI: 10.1002/cbic.202300673] [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: 09/30/2023] [Revised: 11/06/2023] [Indexed: 11/24/2023]
Abstract
The in vitro synthesis of Coenzyme A (CoA)-thioester intermediates opens new avenues to transform simple molecules into more complex and multifunctional ones by assembling cell-free biosynthetic cascades. In this review, we have systematically cataloged known CoA-dependent enzyme reactions that have been successfully implemented in vitro. To faciliate their identification, we provide their UniProt ID when available. Based on this catalog, we have organized enzymes into three modules: activation, modification, and removal. i) The activation module includes enzymes capable of fusing CoA with organic molecules. ii) The modification module includes enzymes capable of catalyzing chemical modifications in the structure of acyl-CoA intermediates. And iii) the removal module includes enzymes able to remove the CoA and release an organic molecule different from the one activated in the upstream. Based on these reactions, we constructed a reaction network that summarizes the most relevant CoA-dependent biosynthetic pathways reported until today. From the information available in the articles, we have plotted the total turnover number of CoA as a function of the product titer, observing a positive correlation between both parameters. Therefore, the success of a CoA-dependent in vitro pathway depends on its ability to regenerate CoA, but also to regenerate other cofactors such as NAD(P)H and ATP.
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Affiliation(s)
- Laurine Ducrot
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Idania L López
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Alejandro H Orrego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
| | - Fernando López-Gallego
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, Donostia-San Sebastián, 20014, Spain
- Ikerbasque, Basque Foundation for Science, 48009, Bilbao, Spain
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6
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Rahman AA, Butcko AJ, Songyekutu E, Granneman JG, Mottillo EP. Direct effects of adipocyte lipolysis on AMPK through intracellular long-chain acyl-CoA signaling. Sci Rep 2024; 14:19. [PMID: 38167670 PMCID: PMC10761689 DOI: 10.1038/s41598-023-50903-w] [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: 09/21/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024] Open
Abstract
Long-chain acyl-CoAs (LC-acyl-CoAs) are important intermediary metabolites and are also thought to function as intracellular signaling molecules; however, the direct effects of LC-acyl-CoAs have been difficult to determine in real-time and dissociate from Protein Kinase A (PKA) signaling. Here, we examined the direct role of lipolysis in generating intracellular LC-acyl-CoAs and activating AMPK in white adipocytes by pharmacological activation of ABHD5 (also known as CGI-58), a lipase co-activator. Activation of lipolysis in 3T3-L1 adipocytes independent of PKA with synthetic ABHD5 ligands, resulted in greater activation of AMPK compared to receptor-mediated activation with isoproterenol, a β-adrenergic receptor agonist. Importantly, the effect of pharmacological activation of ABHD5 on AMPK activation was blocked by inhibiting ATGL, the rate-limiting enzyme for triacylglycerol hydrolysis. Utilizing a novel FRET sensor to detect intracellular LC-acyl-CoAs, we demonstrate that stimulation of lipolysis in 3T3-L1 adipocytes increased the production of LC-acyl-CoAs, an effect which was blocked by inhibition of ATGL. Moreover, ATGL inhibition blocked AMPKβ1 S108 phosphorylation, a site required for allosteric regulation. Increasing intracellular LC-acyl-CoAs by removal of BSA in the media and pharmacological inhibition of DGAT1 and 2 resulted in greater activation of AMPK. Finally, inhibiting LC-acyl-CoA generation reduced activation of AMPK; however, did not lower energy charge. Overall, results demonstrate that lipolysis in white adipocytes directly results in allosteric activation of AMPK through the generation of LC-acyl-CoAs.
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Affiliation(s)
- Abir A Rahman
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital, 6135 Woodward Ave., Detroit, MI, 48202, USA
| | - Andrew J Butcko
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital, 6135 Woodward Ave., Detroit, MI, 48202, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Emmanuel Songyekutu
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - James G Granneman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48202, USA
| | - Emilio P Mottillo
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital, 6135 Woodward Ave., Detroit, MI, 48202, USA.
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48202, USA.
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7
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Neves D, Meinen D, Alter TB, Blank LM, Ebert BE. Expanding Pseudomonas taiwanensis VLB120's acyl-CoA portfolio: Propionate production in mineral salt medium. Microb Biotechnol 2024; 17:e14309. [PMID: 37537795 PMCID: PMC10832534 DOI: 10.1111/1751-7915.14309] [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: 02/13/2023] [Revised: 06/06/2023] [Accepted: 06/25/2023] [Indexed: 08/05/2023] Open
Abstract
As one of the main precursors, acetyl-CoA leads to the predominant production of even-chain products. From an industrial biotechnology perspective, extending the acyl-CoA portfolio of a cell factory is vital to producing industrial relevant odd-chain alcohols, acids, ketones and polyketides. The bioproduction of odd-chain molecules can be facilitated by incorporating propionyl-CoA into the metabolic network. The shortest pathway for propionyl-CoA production, which relies on succinyl-CoA catabolism encoded by the sleeping beauty mutase operon, was evaluated in Pseudomonas taiwanensis VLB120. A single genomic copy of the sleeping beauty mutase genes scpA, argK and scpB combined with the deletion of the methylcitrate synthase PVLB_08385 was sufficient to observe propionyl-CoA accumulation in this Pseudomonas. The chassis' capability for odd-chain product synthesis was assessed by expressing an acyl-CoA hydrolase, which enabled propionate synthesis. Three fed-batch strategies during bioreactor fermentations were benchmarked for propionate production, in which a maximal propionate titre of 2.8 g L-1 was achieved. Considering that the fermentations were carried out in mineral salt medium under aerobic conditions and that a single genome copy drove propionyl-CoA production, this result highlights the potential of Pseudomonas to produce propionyl-CoA derived, odd-chain products.
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Affiliation(s)
- Dário Neves
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
| | - Daniel Meinen
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
| | - Tobias B. Alter
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
| | - Lars M. Blank
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
| | - Birgitta E. Ebert
- Institute of Applied Microbiology‐iAMB, Aachen Biology and Biotechnology‐ABBtRWTH Aachen UniversityAachenGermany
- Australian Institute for Bioengineering and Nanotechnology (AIBN)The University of QueenslandBrisbaneQueenslandAustralia
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8
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Zhou HL, Grimmett ZW, Venetos NM, Stomberski CT, Qian Z, McLaughlin PJ, Bansal PK, Zhang R, Reynolds JD, Premont RT, Stamler JS. An enzyme that selectively S-nitrosylates proteins to regulate insulin signaling. Cell 2023; 186:5812-5825.e21. [PMID: 38056462 PMCID: PMC10794992 DOI: 10.1016/j.cell.2023.11.009] [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: 03/28/2023] [Revised: 09/01/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023]
Abstract
Acyl-coenzyme A (acyl-CoA) species are cofactors for numerous enzymes that acylate thousands of proteins. Here, we describe an enzyme that uses S-nitroso-CoA (SNO-CoA) as its cofactor to S-nitrosylate multiple proteins (SNO-CoA-assisted nitrosylase, SCAN). Separate domains in SCAN mediate SNO-CoA and substrate binding, allowing SCAN to selectively catalyze SNO transfer from SNO-CoA to SCAN to multiple protein targets, including the insulin receptor (INSR) and insulin receptor substrate 1 (IRS1). Insulin-stimulated S-nitrosylation of INSR/IRS1 by SCAN reduces insulin signaling physiologically, whereas increased SCAN activity in obesity causes INSR/IRS1 hypernitrosylation and insulin resistance. SCAN-deficient mice are thus protected from diabetes. In human skeletal muscle and adipose tissue, SCAN expression increases with body mass index and correlates with INSR S-nitrosylation. S-nitrosylation by SCAN/SNO-CoA thus defines a new enzyme class, a unique mode of receptor tyrosine kinase regulation, and a revised paradigm for NO function in physiology and disease.
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Affiliation(s)
- Hua-Lin Zhou
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zachary W Grimmett
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Nicholas M Venetos
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Colin T Stomberski
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Zhaoxia Qian
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Precious J McLaughlin
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Puneet K Bansal
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rongli Zhang
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - James D Reynolds
- Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Anesthesiology and Perioperative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Richard T Premont
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jonathan S Stamler
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Institute for Transformative Molecular Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA; Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
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9
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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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10
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Li X, Karpac J. A distinct Acyl-CoA binding protein (ACBP6) shapes tissue plasticity during nutrient adaptation in Drosophila. Nat Commun 2023; 14:7599. [PMID: 37989752 PMCID: PMC10663470 DOI: 10.1038/s41467-023-43362-4] [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: 12/08/2022] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
Nutrient availability is a major selective force in the evolution of metazoa, and thus plasticity in tissue function and morphology is shaped by adaptive responses to nutrient changes. Utilizing Drosophila, we reveal that distinct calibration of acyl-CoA metabolism, mediated by Acbp6 (Acyl-CoA binding-protein 6), is critical for nutrient-dependent tissue plasticity. Drosophila Acbp6, which arose by evolutionary duplication and binds acyl-CoA to tune acetyl-CoA metabolism, is required for intestinal resizing after nutrient deprivation through activating intestinal stem cell proliferation from quiescence. Disruption of acyl-CoA metabolism by Acbp6 attenuation drives aberrant 'switching' of metabolic networks in intestinal enterocytes during nutrient adaptation, impairing acetyl-CoA metabolism and acetylation amid intestinal resizing. We also identified STAT92e, whose function is influenced by acetyl-CoA levels, as a key regulator of acyl-CoA and nutrient-dependent changes in stem cell activation. These findings define a regulatory mechanism, shaped by acyl-CoA metabolism, that adjusts proliferative homeostasis to coordinately regulate tissue plasticity during nutrient adaptation.
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Affiliation(s)
- Xiaotong Li
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, Bryan, TX, USA
| | - Jason Karpac
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, Bryan, TX, USA.
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11
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Tan L, Martinez SA, Lorenzi PL, Karlstaedt A. Quantitative Analysis of Acetyl-CoA, Malonyl-CoA, and Succinyl-CoA in Myocytes. J Am Soc Mass Spectrom 2023; 34:2567-2574. [PMID: 37812744 DOI: 10.1021/jasms.3c00278] [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] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Several analytical challenges make it difficult to accurately measure coenzyme A (CoA) metaboforms, including insufficient stability and a lack of available metabolite standards. Consequently, our understanding of CoA biology and the modulation of human diseases may be nascent. CoA's serve as lipid precursors, energy intermediates, and mediators of post-translational modifications of proteins. Here, we present a liquid chromatography-mass spectrometry (LC-MS) approach to measure malonyl-CoA, acetyl-CoA, and succinyl-CoA in complex biological samples. Additionally, we evaluated workflows to increase sample stability. We used reference standards to optimize CoA assay sensitivity and test CoA metabolite stability as a function of the reconstitution solvent. We show that using glass instead of plastic sample vials decreases CoA signal loss and improves the sample stability. We identify additives that improve CoA stability and facilitate accurate analysis of CoA species across large sample sets. We apply our optimized workflow to biological samples of skeletal muscle cells cultured under hypoxic and normoxia conditions. Together, our workflow improves the detection and identification of CoA species through targeted analysis in complex biological samples.
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Affiliation(s)
- Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Sara A Martinez
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Philip L Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, United States
| | - Anja Karlstaedt
- Department of Cardiology, Smidt Heart Institute, Los Angeles, California 90048, United States
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12
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Lancaster MS, Kim B, Doud EH, Tate MD, Sharify AD, Gao H, Chen D, Simpson E, Gillespie P, Chu X, Miller MJ, Wang Y, Liu Y, Mosley AL, Kim J, Graham BH. Loss of succinyl-CoA synthetase in mouse forebrain results in hypersuccinylation with perturbed neuronal transcription and metabolism. Cell Rep 2023; 42:113241. [PMID: 37819759 PMCID: PMC10683835 DOI: 10.1016/j.celrep.2023.113241] [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: 08/08/2022] [Revised: 08/24/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023] Open
Abstract
Lysine succinylation is a subtype of protein acylation associated with metabolic regulation of succinyl-CoA in the tricarboxylic acid cycle. Deficiency of succinyl-CoA synthetase (SCS), the tricarboxylic acid cycle enzyme catalyzing the interconversion of succinyl-CoA to succinate, results in mitochondrial encephalomyopathy in humans. This report presents a conditional forebrain-specific knockout (KO) mouse model of Sucla2, the gene encoding the ATP-specific beta isoform of SCS, resulting in postnatal deficiency of the entire SCS complex. Results demonstrate that accumulation of succinyl-CoA in the absence of SCS leads to hypersuccinylation within the murine cerebral cortex. Specifically, increased succinylation is associated with functionally significant reduced activity of respiratory chain complex I and widescale alterations in chromatin landscape and gene expression. Integrative analysis of the transcriptomic data also reveals perturbations in regulatory networks of neuronal transcription in the KO forebrain. Together, these findings provide evidence that protein succinylation plays a significant role in the pathogenesis of SCS deficiency.
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Affiliation(s)
- Makayla S Lancaster
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Byungwook Kim
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Emma H Doud
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mason D Tate
- Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ahmad D Sharify
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Duojiao Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ed Simpson
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Patrick Gillespie
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Xiaona Chu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Marcus J Miller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yue Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Amber L Mosley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jungsu Kim
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Stark Neuroscience Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Medical Neuroscience Graduate Program, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Brett H Graham
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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13
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Dani R, Pawloski W, Chaurasiya DK, Srilatha NS, Agarwal S, Fushman D, Naganathan AN. Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins. Biochemistry 2023; 62:2982-2996. [PMID: 37788430 PMCID: PMC10774088 DOI: 10.1021/acs.biochem.3c00449] [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: 10/05/2023]
Abstract
Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we dissect the underlying mechanism of promiscuous binding versus partial subfunctionalization in paralogues by studying structurally identical acyl-CoA binding proteins (ACBPs) from Plasmodium falciparum that serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR, and simulations on two of the paralogues, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding pocket volume compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in the holo form, which is particularly apparent in A749. The paralogues exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogues.
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Affiliation(s)
- Rahul Dani
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Westley Pawloski
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Dhruv Kumar Chaurasiya
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Sonal Agarwal
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - David Fushman
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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14
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Tokarska-Schlattner M, Zeaiter N, Cunin V, Attia S, Meunier C, Kay L, Achouri A, Hiriart-Bryant E, Couturier K, Tellier C, El Harras A, Elena-Herrmann B, Khochbin S, Le Gouellec A, Schlattner U. Multi-Method Quantification of Acetyl-Coenzyme A and Further Acyl-Coenzyme A Species in Normal and Ischemic Rat Liver. Int J Mol Sci 2023; 24:14957. [PMID: 37834405 PMCID: PMC10573920 DOI: 10.3390/ijms241914957] [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: 09/06/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Thioesters of coenzyme A (CoA) carrying different acyl chains (acyl-CoAs) are central intermediates of many metabolic pathways and donor molecules for protein lysine acylation. Acyl-CoA species largely differ in terms of cellular concentrations and physico-chemical properties, rendering their analysis challenging. Here, we compare several approaches to quantify cellular acyl-CoA concentrations in normal and ischemic rat liver, using HPLC and LC-MS/MS for multi-acyl-CoA analysis, as well as NMR, fluorimetric and spectrophotometric techniques for the quantification of acetyl-CoAs. In particular, we describe a simple LC-MS/MS protocol that is suitable for the relative quantification of short and medium-chain acyl-CoA species. We show that ischemia induces specific changes in the short-chain acyl-CoA relative concentrations, while mild ischemia (1-2 min), although reducing succinyl-CoA, has little effects on acetyl-CoA, and even increases some acyl-CoA species upstream of the tricarboxylic acid cycle. In contrast, advanced ischemia (5-6 min) also reduces acetyl-CoA levels. Our approach provides the keys to accessing the acyl-CoA metabolome for a more in-depth analysis of metabolism, protein acylation and epigenetics.
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Affiliation(s)
- Malgorzata Tokarska-Schlattner
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Nour Zeaiter
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Valérie Cunin
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Stéphane Attia
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Cécile Meunier
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Laurence Kay
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Amel Achouri
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Edwige Hiriart-Bryant
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Karine Couturier
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Cindy Tellier
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
| | - Abderrafek El Harras
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Bénédicte Elena-Herrmann
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Saadi Khochbin
- University Grenoble Alpes, Inserm U1209 and CNRS UMR5309, Institute for Advanced Biosciences (IAB), 38058 Grenoble, France; (A.E.H.); (B.E.-H.); (S.K.)
| | - Audrey Le Gouellec
- University Grenoble Alpes, CNRS UMR 5525, Laboratory TIMC—Translational Microbiology, Evolution, Engineering (TREE), Service de Biochimie, Biologie Moléculaire et Toxicologie Environnementale, CHU Grenoble-Alpes, 38058 Grenoble, France; (V.C.); (C.M.); (A.L.G.)
| | - Uwe Schlattner
- University Grenoble Alpes, Inserm U1055, Laboratory of Fundamental and Applied Bioenergetics (LBFA), 38058 Grenoble, France; (N.Z.); (S.A.); (L.K.); (A.A.); (E.H.-B.); (K.C.); (C.T.)
- Institut Universitaire de France (IUF), 75231 Paris, France
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15
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Szrok-Jurga S, Czumaj A, Turyn J, Hebanowska A, Swierczynski J, Sledzinski T, Stelmanska E. The Physiological and Pathological Role of Acyl-CoA Oxidation. Int J Mol Sci 2023; 24:14857. [PMID: 37834305 PMCID: PMC10573383 DOI: 10.3390/ijms241914857] [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: 08/25/2023] [Revised: 09/27/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Fatty acid metabolism, including β-oxidation (βOX), plays an important role in human physiology and pathology. βOX is an essential process in the energy metabolism of most human cells. Moreover, βOX is also the source of acetyl-CoA, the substrate for (a) ketone bodies synthesis, (b) cholesterol synthesis, (c) phase II detoxication, (d) protein acetylation, and (d) the synthesis of many other compounds, including N-acetylglutamate-an important regulator of urea synthesis. This review describes the current knowledge on the importance of the mitochondrial and peroxisomal βOX in various organs, including the liver, heart, kidney, lung, gastrointestinal tract, peripheral white blood cells, and other cells. In addition, the diseases associated with a disturbance of fatty acid oxidation (FAO) in the liver, heart, kidney, lung, alimentary tract, and other organs or cells are presented. Special attention was paid to abnormalities of FAO in cancer cells and the diseases caused by mutations in gene-encoding enzymes involved in FAO. Finally, issues related to α- and ω- fatty acid oxidation are discussed.
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Affiliation(s)
- Sylwia Szrok-Jurga
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Aleksandra Czumaj
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Jacek Turyn
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Areta Hebanowska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
| | - Julian Swierczynski
- Institue of Nursing and Medical Rescue, State University of Applied Sciences in Koszalin, 75-582 Koszalin, Poland;
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland;
| | - Ewa Stelmanska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (S.S.-J.); (J.T.); (A.H.)
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16
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Shibazaki C, Mashino T, Ohe T. Development of a fluorescent-labeled trapping reagent to evaluate the risk posed by acyl-CoA conjugates. Drug Metab Pharmacokinet 2023; 52:100509. [PMID: 37515836 DOI: 10.1016/j.dmpk.2023.100509] [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: 11/13/2022] [Revised: 03/13/2023] [Accepted: 04/04/2023] [Indexed: 07/31/2023]
Abstract
Although acyl-CoA conjugates are known to have higher reactivity than acyl glucuronides, few studies have been conducted to evaluate the risk of the conjugates. In the present study, we aimed to develop a trapping assay for acyl-CoA conjugates using trapping reagents we have developed previously. It was revealed that Cys-Dan, which has both a thiol and an amino group, was the most effective in forming stable adducts containing an amide bond after intramolecular acyl migration. Additionally, we also developed a hepatocyte-based trapping assay in the present study to overcome the shortcomings of liver microsomes. Although liver microsomes are commonly used as enzyme sources in trapping assays, they lack some of the enzymes required for drug metabolism and detoxification systems. In human hepatocytes, our three trapping reagents, CysGlu-Dan, Dap-Dan and Cys-Dan, captured CYP-dependent reactive metabolites, reactive acyl glucuronides, and reactive acyl-CoA conjugates, respectively. The work suggests that the trapping assay with the reagents in hepatocytes is useful to evaluate the risk of reactive metabolites in drug discovery.
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Affiliation(s)
- Chikako Shibazaki
- Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo, Japan
| | - Tadahiko Mashino
- Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo, Japan
| | - Tomoyuki Ohe
- Faculty of Pharmacy, Keio University, 1-5-30, Shibakoen, Minato-ku, Tokyo, Japan.
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17
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Dalwani S, Wierenga RK. Enzymes of the crotonase superfamily: Diverse assembly and diverse function. Curr Opin Struct Biol 2023; 82:102671. [PMID: 37542911 DOI: 10.1016/j.sbi.2023.102671] [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: 03/20/2023] [Revised: 06/08/2023] [Accepted: 07/10/2023] [Indexed: 08/07/2023]
Abstract
The crotonase fold is generated by a framework of four repeats of a ββα-unit, extended by two helical regions. The active site of crotonase superfamily (CS) enzymes is located at the N-terminal end of the helix of the third repeat, typically being covered by a C-terminal helix. A major subset of CS-enzymes catalyzes acyl-CoA-dependent reactions, allowing for a diverse range of acyl-tail modifications. Most of these enzymes occur as trimers or hexamers (dimers of trimers), but monomeric forms are also observed. A common feature of the active sites of CS-enzymes is an oxyanion hole, formed by two peptide-NH hydrogen bond donors, which stabilises the negatively charged thioester oxygen atom of the reaction intermediate. Structural properties and possible use of these enzymes for biotechnological applications are discussed.
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Affiliation(s)
- Subhadra Dalwani
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland
| | - Rik K Wierenga
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, P.O. Box 5400, FI-90014, Finland.
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18
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Szrok-Jurga S, Turyn J, Hebanowska A, Swierczynski J, Czumaj A, Sledzinski T, Stelmanska E. The Role of Acyl-CoA β-Oxidation in Brain Metabolism and Neurodegenerative Diseases. Int J Mol Sci 2023; 24:13977. [PMID: 37762279 PMCID: PMC10531288 DOI: 10.3390/ijms241813977] [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: 08/01/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
This review highlights the complex role of fatty acid β-oxidation in brain metabolism. It demonstrates the fundamental importance of fatty acid degradation as a fuel in energy balance and as an essential component in lipid homeostasis, brain aging, and neurodegenerative disorders.
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Affiliation(s)
- Sylwia Szrok-Jurga
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (J.T.); (A.H.)
| | - Jacek Turyn
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (J.T.); (A.H.)
| | - Areta Hebanowska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (J.T.); (A.H.)
| | - Julian Swierczynski
- Institute of Nursing and Medical Rescue, State University of Applied Sciences in Koszalin, 75-582 Koszalin, Poland;
| | - Aleksandra Czumaj
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland; (A.C.); (T.S.)
| | - Tomasz Sledzinski
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Medical University of Gdansk, 80-211 Gdansk, Poland; (A.C.); (T.S.)
| | - Ewa Stelmanska
- Department of Biochemistry, Faculty of Medicine, Medical University of Gdansk, 80-211 Gdansk, Poland; (J.T.); (A.H.)
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19
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Montégut L, Abdellatif M, Motiño O, Madeo F, Martins I, Quesada V, López‐Otín C, Kroemer G. Acyl coenzyme A binding protein (ACBP): An aging- and disease-relevant "autophagy checkpoint". Aging Cell 2023; 22:e13910. [PMID: 37357988 PMCID: PMC10497816 DOI: 10.1111/acel.13910] [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: 04/17/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/27/2023] Open
Abstract
Acyl coenzyme A binding protein (ACBP), also known as diazepam-binding inhibitor (DBI), is a phylogenetically ancient protein present in some eubacteria and the entire eukaryotic radiation. In several eukaryotic phyla, ACBP/DBI transcends its intracellular function in fatty acid metabolism because it can be released into the extracellular space. This ACBP/DBI secretion usually occurs in response to nutrient scarcity through an autophagy-dependent pathway. ACBP/DBI and its peptide fragments then act on a range of distinct receptors that diverge among phyla, namely metabotropic G protein-coupled receptor in yeast (and likely in the mammalian central nervous system), a histidine receptor kinase in slime molds, and ionotropic gamma-aminobutyric acid (GABA)A receptors in mammals. Genetic or antibody-mediated inhibition of ACBP/DBI orthologs interferes with nutrient stress-induced adaptations such as sporulation or increased food intake in multiple species, as it enhances lifespan or healthspan in yeast, plant leaves, nematodes, and multiple mouse models. These lifespan and healthspan-extending effects of ACBP/DBI suppression are coupled to the induction of autophagy. Altogether, it appears that neutralization of extracellular ACBP/DBI results in "autophagy checkpoint inhibition" to unleash the anti-aging potential of autophagy. Of note, in humans, ACBP/DBI levels increase in various tissues, as well as in the plasma, in the context of aging, obesity, uncontrolled infection or cardiovascular, inflammatory, neurodegenerative, and malignant diseases.
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Affiliation(s)
- Léa Montégut
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Inserm U1138Université Paris Cité, Sorbonne UniversitéParisFrance
- Metabolomics and Cell Biology PlatformsGustave Roussy InstitutVillejuifFrance
- Faculté de MédecineUniversité de Paris SaclayParisFrance
| | - Mahmoud Abdellatif
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Inserm U1138Université Paris Cité, Sorbonne UniversitéParisFrance
- Metabolomics and Cell Biology PlatformsGustave Roussy InstitutVillejuifFrance
- Department of CardiologyMedical University of GrazGrazAustria
- BioTechMed‐GrazGrazAustria
| | - Omar Motiño
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Inserm U1138Université Paris Cité, Sorbonne UniversitéParisFrance
- Metabolomics and Cell Biology PlatformsGustave Roussy InstitutVillejuifFrance
| | - Frank Madeo
- BioTechMed‐GrazGrazAustria
- Institute of Molecular Biosciences, NAWI GrazUniversity of GrazGrazAustria
- Field of Excellence BioHealthUniversity of GrazGrazAustria
| | - Isabelle Martins
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Inserm U1138Université Paris Cité, Sorbonne UniversitéParisFrance
- Metabolomics and Cell Biology PlatformsGustave Roussy InstitutVillejuifFrance
| | - Victor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA)Universidad de OviedoOviedoSpain
| | - Carlos López‐Otín
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Inserm U1138Université Paris Cité, Sorbonne UniversitéParisFrance
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias (IUOPA)Universidad de OviedoOviedoSpain
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue Contre le Cancer, Inserm U1138Université Paris Cité, Sorbonne UniversitéParisFrance
- Metabolomics and Cell Biology PlatformsGustave Roussy InstitutVillejuifFrance
- Institut du Cancer Paris CARPEM, Department of BiologyHôpital Européen Georges Pompidou, AP‐HPParisFrance
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20
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Mori K, Naganuma T, Kihara A. Role of 2-hydroxy acyl-CoA lyase HACL2 in odd-chain fatty acid production via α-oxidation in vivo. Mol Biol Cell 2023; 34:ar85. [PMID: 37285239 PMCID: PMC10398889 DOI: 10.1091/mbc.e23-02-0042] [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: 02/10/2023] [Revised: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
Although most fatty acids (FAs) are even chain, certain tissues, including brain, contain relatively large quantities of odd-chain FAs in their sphingolipids. One of the pathways producing odd-chain FAs is the α-oxidation of 2-hydroxy (2-OH) FAs, where 2-OH acyl-CoA lyases (HACL1 and HACL2) catalyze the key cleavage reaction. However, the contribution of each HACL to odd-chain FA production in vivo remains unknown. Here, we found that HACL2 and HACL1 play major roles in the α-oxidation of 2-OH FAs (especially very-long-chain types) and 3-methyl FAs (other α-oxidation substrates), respectively, using ectopic expression systems of human HACL2 and HACL1 in yeast and analyzing Hacl1 and/or Hacl2 knockout (KO) CHO-K1 cells. We then generated Hacl2 KO mice and measured the quantities of odd-chain and 2-OH lipids (free FAs and sphingolipids [ceramides, sphingomyelins, and monohexosylceramides]) in 17 tissues. We observed fewer odd-chain lipids and more 2-OH lipids in many tissues of Hacl2 KO mice than in wild-type mice, and of these differences the reductions were most prominent for odd-chain monohexosylceramides in the brain and ceramides in the stomach. These results indicate that HACL2-involved α-oxidation of 2-OH FAs is mainly responsible for odd-chain FA production in the brain and stomach.
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Affiliation(s)
- Keisuke Mori
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Tatsuro Naganuma
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
| | - Akio Kihara
- Laboratory of Biochemistry, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan
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21
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Mottillo EP, Mladenovic-Lucas L, Zhang H, Zhou L, Kelly CV, Ortiz PA, Granneman JG. A FRET sensor for the real-time detection of long chain acyl-CoAs and synthetic ABHD5 ligands. Cell Rep Methods 2023; 3:100394. [PMID: 36936069 PMCID: PMC10014278 DOI: 10.1016/j.crmeth.2023.100394] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 12/19/2022] [Accepted: 01/05/2023] [Indexed: 01/26/2023]
Abstract
Intracellular long-chain acyl-coenzyme As (LC-acyl-CoAs) are thought to be under tight spatial and temporal controls, yet the ability to image LC-acyl-CoAs in live cells is lacking. Here, we developed a fluorescence resonance energy transfer (FRET) sensor for LC-acyl-CoAs based on the allosterically regulated interaction between α/β hydrolase domain-containing 5 (ABHD5) and Perilipin 5. The genetically encoded sensor rapidly detects intracellular LC-acyl-CoAs generated from exogenous and endogenous fatty acids (FAs), as well as synthetic ABHD5 ligands. Stimulation of lipolysis in brown adipocytes elevated intracellular LC-acyl-CoAs in a cyclic fashion, which was eliminated by inhibiting PNPLA2 (ATGL), the major triglyceride lipase. Interestingly, inhibition of LC-acyl-CoA transport into mitochondria elevated intracellular LC-acyl-CoAs and dampened their cycling. Together, these observations reveal an intimate feedback control between LC-acyl-CoA generation from lipolysis and utilization in mitochondria. We anticipate that this sensor will be an important tool to dissect intracellular LC-acyl-CoA dynamics as well to discover novel synthetic ABHD5 ligands.
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Affiliation(s)
- Emilio P. Mottillo
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital, 6135 Woodward Avenue, Detroit, MI 48202, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Ljiljana Mladenovic-Lucas
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Huamei Zhang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Li Zhou
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Christopher V. Kelly
- Department of Physics and Astronomy, Wayne State University, Detroit, MI 48202, USA
| | - Pablo A. Ortiz
- Hypertension and Vascular Research Division, Department of Internal Medicine, Henry Ford Hospital, 6135 Woodward Avenue, Detroit, MI 48202, USA
| | - James G. Granneman
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48202, USA
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22
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He W, Berthiaume JM, Previs S, Kasumov T, Zhang GF. Ischemia promotes acyl-CoAs dephosphorylation and propionyl-CoA accumulation. Metabolomics 2023; 19:12. [PMID: 36750484 DOI: 10.1007/s11306-023-01975-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023]
Abstract
INTRODUCTION Our untargeted metabolic data unveiled that Acyl-CoAs undergo dephosphorylation, however little is known about these novel metabolites and their physiology/pathology relevance. OBJECTIVES To understand the relationship between acyl-CoAs dephosphorylation and energy status as implied in our previous work, we seek to investigate how ischemia (energy depletion) triggers metabolic changes, specifically acyl-CoAs dephosphorylation in this work. METHODS Rat hearts were isolated and perfused in Langendorff mode for 15 min followed by 0, 5, 15, and 30 minutes of global ischemia. The heart tissues were harvested for metabolic analysis. RESULTS As expected, ATP and phosphocreatine were significantly decreased during ischemia. Most short- and medium-chain acyl-CoAs progressively increased with ischemic time from 0 to 15 min, whereas a 30-minute ischemia did not lead to further change. Unlike other acyl-CoAs, propionyl-CoA accumulated progressively in the hearts that underwent ischemia from 0 to 30 min. Progressive dephosphorylation occurred to all assayed acyl-CoAs and free CoA regardless their level changes during the ischemia. CONCLUSION The present work further confirms that dephosphorylation of acyl-CoAs is an energy-dependent process and how this dephosphorylation is mediated warrants further investigations. It is plausible that dephosphorylation of acyl-CoAs and limited anaplerosis are involved in ischemic injuries to heart. Further investigations are warranted to examine the mechanisms of acyl-CoA dephosphorylation and how the dephosphorylation is possibly involved in ischemic injuries.
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Affiliation(s)
- Wentao He
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University, Durham, NC, 27701, USA
| | - Jessica M Berthiaume
- Department of Physiology & Biophysics, Case Western Reserve University, Cleveland, OH, 44104, USA
- Inotiv Westminster, 7581 W 103rd Ave, Westminster, CO, 80021, USA
| | - Stephen Previs
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Takhar Kasumov
- Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Guo-Fang Zhang
- Sarah W. Stedman Nutrition and Metabolism Center & Duke Molecular Physiology Institute, Duke University, Durham, NC, 27701, USA.
- Department of Medicine, Division of Endocrinology, Metabolism Nutrition, Duke University Medical Center, Durham, NC, 27701, USA.
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23
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Hu JJ, Lee JKJ, Liu YT, Yu C, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH. Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase. Structure 2023; 31:100-110.e4. [PMID: 36543169 PMCID: PMC9825669 DOI: 10.1016/j.str.2022.11.015] [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: 08/30/2022] [Revised: 10/17/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. α6β6 LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking α6β6 LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.
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Affiliation(s)
- Jason J Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Mathematics, UCLA, Los Angeles, CA 90095, USA
| | - Jane K J Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Psychology, UCLA, Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA; Department of Biochemistry, BUMC, Boston, MA 02118, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA.
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24
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Puthenveetil R, Gómez-Navarro N, Banerjee A. Access and utilization of long chain fatty acyl-CoA by zDHHC protein acyltransferases. Curr Opin Struct Biol 2022; 77:102463. [PMID: 36183446 PMCID: PMC9772126 DOI: 10.1016/j.sbi.2022.102463] [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: 06/01/2022] [Revised: 08/09/2022] [Accepted: 08/13/2022] [Indexed: 12/24/2022]
Abstract
S-acylation is a reversible posttranslational modification, where a long-chain fatty acid is attached to a protein through a thioester linkage. Being the most abundant form of lipidation in humans, a family of twenty-three human zDHHC integral membrane enzymes catalyze this reaction. Previous structures of the apo and lipid bound zDHHCs shed light into the molecular details of the active site and binding pocket. Here, we delve further into the details of fatty acyl-CoA recognition by zDHHC acyltransferases using insights from the recent structure. We additionally review indirect evidence that suggests acyl-CoAs do not diffuse freely in the cytosol, but are channeled into specific pathways, and comment on the suggested mechanisms for fatty acyl-CoA compartmentalization and intracellular transport, to finally speculate about the potential mechanisms that underlie fatty acyl-CoA delivery to zDHHC enzymes.
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Affiliation(s)
- Robbins Puthenveetil
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA. https://twitter.com/RoVeetil
| | - Natalia Gómez-Navarro
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA. https://twitter.com/NataliaGmez10
| | - Anirban Banerjee
- Section on Structural and Chemical Biology of Membrane Proteins, Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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25
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Panina IS, Krylov NA, Chugunov AO, Efremov RG, Kordyukova LV. The Mechanism of Selective Recognition of Lipid Substrate by hDHHC20 Enzyme. Int J Mol Sci 2022; 23:ijms232314791. [PMID: 36499114 PMCID: PMC9739150 DOI: 10.3390/ijms232314791] [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: 10/20/2022] [Revised: 11/18/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
S-acylation is a post-translational linkage of long chain fatty acids to cysteines, playing a key role in normal physiology and disease. In human cells, the reaction is catalyzed by a family of 23 membrane DHHC-acyltransferases (carrying an Asp-His-His-Cys catalytic motif) in two stages: (1) acyl-CoA-mediated autoacylation of the enzyme; and (2) further transfer of the acyl chain to a protein substrate. Despite the availability of a 3D-structure of human acyltransferase (hDHHC20), the molecular aspects of lipid selectivity of DHHC-acyltransferases remain unclear. In this paper, using molecular dynamics (MD) simulations, we studied membrane-bound hDHHC20 right before the acylation by C12-, C14-, C16-, C18-, and C20-CoA substrates. We found that: (1) regardless of the chain length, its terminal methyl group always reaches the "ceiling" of the enzyme's cavity; (2) only for C16, an optimal "reactivity" (assessed by a simple geometric criterion) permits the autoacylation; (3) in MD, some key interactions between an acyl-CoA and a protein differ from those in the reference crystal structure of the C16-CoA-hDHHS20 mutant complex (probably, because this structure corresponds to a non-native dimer). These features of specific recognition of full-size acyl-CoA substrates support our previous hypothesis of "geometric and physicochemical selectivity" derived for simplified acyl-CoA analogues.
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Affiliation(s)
- Irina S. Panina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- International Laboratory for Supercomputer Atomistic Modelling and Multi-Scale Analysis, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Nikolay A. Krylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- International Laboratory for Supercomputer Atomistic Modelling and Multi-Scale Analysis, National Research University Higher School of Economics, 101000 Moscow, Russia
| | - Anton O. Chugunov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- International Laboratory for Supercomputer Atomistic Modelling and Multi-Scale Analysis, National Research University Higher School of Economics, 101000 Moscow, Russia
- Moscow Institute of Physics and Technology, State University, Dolgoprudny, 141701 Moscow, Russia
| | - Roman G. Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- International Laboratory for Supercomputer Atomistic Modelling and Multi-Scale Analysis, National Research University Higher School of Economics, 101000 Moscow, Russia
- Moscow Institute of Physics and Technology, State University, Dolgoprudny, 141701 Moscow, Russia
- Correspondence:
| | - Larisa V. Kordyukova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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26
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Vickers SD, Shumar SA, Saporito DC, Kunovac A, Hathaway QA, Mintmier B, King JA, King RD, Rajendran VM, Infante AM, Hollander JM, Leonardi R. NUDT7 regulates total hepatic CoA levels and the composition of the intestinal bile acid pool in male mice fed a Western diet. J Biol Chem 2022; 299:102745. [PMID: 36436558 PMCID: PMC9792899 DOI: 10.1016/j.jbc.2022.102745] [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: 08/04/2022] [Revised: 10/25/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
Nudix hydrolase 7 (NUDT7) is an enzyme that hydrolyzes CoA species, is highly expressed in the liver, and resides in the peroxisomes. Peroxisomes are organelles where the preferential oxidation of dicarboxylic fatty acids occurs and where the hepatic synthesis of the primary bile acids cholic acid and chenodeoxycholic acid is completed. We previously showed that liver-specific overexpression of NUDT7 affects peroxisomal lipid metabolism but does not prevent the increase in total liver CoA levels that occurs during fasting. We generated Nudt7-/- mice to further characterize the role that peroxisomal (acyl-)CoA degradation plays in the modulation of the size and composition of the acyl-CoA pool and in the regulation of hepatic lipid metabolism. Here, we show that deletion of Nudt7 alters the composition of the hepatic acyl-CoA pool in mice fed a low-fat diet, but only in males fed a Western diet does the lack of NUDT7 activity increase total liver CoA levels. This effect is driven by the male-specific accumulation of medium-chain dicarboxylic acyl-CoAs, which are produced from the β-oxidation of dicarboxylic fatty acids. We also show that, under conditions of elevated synthesis of chenodeoxycholic acid derivatives, Nudt7 deletion promotes the production of tauromuricholic acid, decreasing the hydrophobicity index of the intestinal bile acid pool and increasing fecal cholesterol excretion in male mice. These findings reveal that NUDT7-mediated hydrolysis of acyl-CoA pathway intermediates in liver peroxisomes contributes to the regulation of dicarboxylic fatty acid metabolism and the composition of the bile acid pool.
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Affiliation(s)
- Schuyler D Vickers
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Stephanie A Shumar
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Dominique C Saporito
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Amina Kunovac
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Quincy A Hathaway
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Breeanna Mintmier
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Judy A King
- Department of Pathology and Translational Pathobiology, LSU Health Shreveport, Shreveport, Louisiana, USA
| | - Rachel D King
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Vazhaikkurichi M Rajendran
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA
| | - Aniello M Infante
- Genomics Core Facility, West Virginia University, Morgantown, West Virginia, USA
| | - John M Hollander
- Division of Exercise Physiology, West Virginia University, Morgantown, West Virginia, USA
| | - Roberta Leonardi
- Department of Biochemistry and Molecular Medicine, West Virginia University, Morgantown, West Virginia, USA.
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27
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Yang H, Wang Y, Tang MC, Waters P, Wang S, Allard P, Ryan RO, Nuyt AM, Paradis P, Schiffrin EL, Furtos A, Mitchell GA. Cardiac-specific deficiency of 3-hydroxy-3-methylglutaryl coenzyme A lyase in mice causes cardiomyopathy and a distinct pattern of acyl-coenzyme A-related biomarkers. Mol Genet Metab 2022; 137:257-264. [PMID: 36228350 DOI: 10.1016/j.ymgme.2022.09.008] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 10/31/2022]
Abstract
Deficiency of 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) lyase (HL) is an autosomal recessive inborn error of acyl-CoA metabolism affecting the last step of leucine degradation. Patients with HL deficiency (HLD) can develop a potentially fatal cardiomyopathy. We created mice with cardiomyocyte-specific HLD (HLHKO mice), inducing Cre recombinase-mediated deletion of exon 2 at two months of age. HLHKO mice survive, but develop left ventricular hypertrophy by 9 months. Also, within minutes after intraperitoneal injection of the leucine metabolite 2-ketoisocaproate (KIC), they show transient left ventricular hypocontractility and dilation. Leucine-related acyl-CoAs were elevated in HLHKO heart (e.g., HMG-CoA, 34.0 ± 4.4 nmol/g versus 0.211 ± 0.041 in controls, p < 0.001; 3-methylcrotonyl-CoA, 5.84 ± 0.69 nmol/g versus 0.282 ± 0.043, p < 0.001; isovaleryl-CoA, 1.86 ± 0.30 nmol/g versus 0.024 ± 0.014, p < 0.01), a similar pattern to that in liver of mice with hepatic HL deficiency. After KIC loading, HMG-CoA levels in HLHKO heart were higher than under basal conditions, as were the ratios of HMG-CoA/acetyl-CoA and of HMG-CoA/succinyl-CoA. In contrast to the high levels of multiple leucine-related acyl-CoAs, biomarkers in urine and plasma of HLHKO mice show isolated hyper-3-methylglutaconic aciduria (700.8 ± 48.4 mmol/mol creatinine versus 37.6 ± 2.4 in controls, p < 0.001), and elevated C5-hydroxyacylcarnitine in plasma (0.248 ± 0.014 μmol/L versus 0.048 ± 0.005 in controls, p < 0.001). Mice with liver-specific HLD were compared, and showed normal echocardiographic findings and normal acyl-CoA profiles in heart. This study of nonhepatic tissue-specific HLD outside of liver reveals organ-specific origins of diagnostic biomarkers for HLD in blood and urine and shows that mouse cardiac HL is essential for myocardial function in a cell-autonomous, organ-autonomous fashion.
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Affiliation(s)
- Hao Yang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Youlin Wang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | | | - Paula Waters
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Québec, Canada
| | - Shupei Wang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Pierre Allard
- Biochemical Genetics Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada
| | - Robert O Ryan
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, United States
| | - Anne-Monique Nuyt
- Sainte-Justine University Hospital and Research Center, University of Montreal, Montreal, Québec, Canada
| | - Pierre Paradis
- Hypertension and Vascular Research Unit, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Ernesto L Schiffrin
- Hypertension and Vascular Research Unit, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Alexandra Furtos
- Département de Chimie, Université de Montréal, Montreal, Québec, Canada
| | - Grant A Mitchell
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada.
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28
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Li JJ, Zhang CL, Zhang YL, Gao HN, Wang HB, Jiang H, Li YY. An apple long-chain acyl-CoA synthase, MdLACS1, enhances biotic and abiotic stress resistance in plants. Plant Physiol Biochem 2022; 189:115-125. [PMID: 36084527 DOI: 10.1016/j.plaphy.2022.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/06/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Epidermal waxes are part of the outermost hydrophobic structures of apples and play a significant role in enhancing apple resistance and improving fruit quality. The biosynthetic precursors of epidermal waxes are very long-chain fatty acids (VLCFAs), which are made into different wax components through various wax synthesis pathways. In Arabidopsis thaliana, the AtLACS1 protein can activate the alkane synthesis pathway to produce very long-chain acyl CoAs (VLC-acyl-CoAs), which provide substrates for wax synthesis, from VLCFAs. The apple protein MdLACS1, encoded by the MdLACS1 gene, belongs to the AMP-binding superfamily and has long-chain acyl coenzyme A synthase activity, but its function in apple remains unclear. Here, we identified MdLACS1 in apple (Malus × domestica) and analyzed its function. Our results suggest that MdLACS1 promotes wax synthesis and improves biotic and abiotic stress tolerance, which were directly or indirectly dependent on wax. Our study further refines the molecular mechanism of wax biosynthesis in apples and elucidates the physiological function of wax in resistance to external stresses. These findings provide candidate genes for the synergistic enhancement of apple fruit quality and stress tolerance.
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Affiliation(s)
- Jiao-Jiao Li
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation, Center of Fruit & Vegetable Quality and Efficient Production, National Research, Center for Apple Engineering and Technology, College of Horticulture Science, and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Chun-Ling Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation, Center of Fruit & Vegetable Quality and Efficient Production, National Research, Center for Apple Engineering and Technology, College of Horticulture Science, and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Ya-Li Zhang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation, Center of Fruit & Vegetable Quality and Efficient Production, National Research, Center for Apple Engineering and Technology, College of Horticulture Science, and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Huai-Na Gao
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation, Center of Fruit & Vegetable Quality and Efficient Production, National Research, Center for Apple Engineering and Technology, College of Horticulture Science, and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - He-Bing Wang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation, Center of Fruit & Vegetable Quality and Efficient Production, National Research, Center for Apple Engineering and Technology, College of Horticulture Science, and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Han Jiang
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation, Center of Fruit & Vegetable Quality and Efficient Production, National Research, Center for Apple Engineering and Technology, College of Horticulture Science, and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, Shandong Collaborative Innovation, Center of Fruit & Vegetable Quality and Efficient Production, National Research, Center for Apple Engineering and Technology, College of Horticulture Science, and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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Zavileyskiy LG, Aleshin VA, Kaehne T, Karlina IS, Artiukhov AV, Maslova MV, Graf AV, Bunik VI. The Brain Protein Acylation System Responds to Seizures in the Rat Model of PTZ-Induced Epilepsy. Int J Mol Sci 2022; 23:ijms232012302. [PMID: 36293175 PMCID: PMC9603846 DOI: 10.3390/ijms232012302] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Abnormal energy expenditure during seizures and metabolic regulation through post-translational protein acylation suggest acylation as a therapeutic target in epilepsy. Our goal is to characterize an interplay between the brain acylation system components and their changes after seizures. In a rat model of pentylenetetrazole (PTZ)-induced epilepsy, we quantify 43 acylations in 29 cerebral cortex proteins; levels of NAD+; expression of NAD+-dependent deacylases (SIRT2, SIRT3, SIRT5); activities of the acyl-CoA-producing/NAD+-utilizing complexes of 2-oxoacid dehydrogenases. Compared to the control group, acylations of 14 sites in 11 proteins are found to differ significantly after seizures, with six of the proteins involved in glycolysis and energy metabolism. Comparing the single and chronic seizures does not reveal significant differences in the acylations, pyruvate dehydrogenase activity, SIRT2 expression or NAD+. On the contrary, expression of SIRT3, SIRT5 and activity of 2-oxoglutarate dehydrogenase (OGDH) decrease in chronic seizures vs. a single seizure. Negative correlations between the protein succinylation/glutarylation and SIRT5 expression, and positive correlations between the protein acetylation and SIRT2 expression are shown. Our findings unravel involvement of SIRT5 and OGDH in metabolic adaptation to seizures through protein acylation, consistent with the known neuroprotective role of SIRT5 and contribution of OGDH to the Glu/GABA balance perturbed in epilepsy.
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Affiliation(s)
- Lev G. Zavileyskiy
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vasily A. Aleshin
- Department of Biokinetics, A.N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Thilo Kaehne
- Institute of Experimental Internal Medicine, Otto von Guericke University, 39106 Magdeburg, Germany
| | - Irina S. Karlina
- N.V. Sklifosovsky Institute of Clinical Medicine, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Artem V. Artiukhov
- Department of Biokinetics, A.N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
| | - Maria V. Maslova
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Anastasia V. Graf
- Department of Biokinetics, A.N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Victoria I. Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biokinetics, A.N. Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Sechenov University, 119048 Moscow, Russia
- Correspondence: ; Tel.: +7-(495)-939-4484
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Yang T, Juntila DJ, Fujihara N, Inada T, Yoneda K, Suzuki I. Enhancement of Squalene Production by Constitutive Expression of the 3-Hydroxy-3-Methylglutaryl-CoA Reductase in Aurantiochytrium sp. 18W-13a. Mar Biotechnol (NY) 2022; 24:733-743. [PMID: 35841466 DOI: 10.1007/s10126-022-10139-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Squalene has a wide range of applications in the industry sectors of dietary supplements, cosmetics, immunization, and pharmaceuticals. Yet, suitable organisms as the source of squalene are limited. It is reported that the thraustochytrid Aurantiochytrium sp. strain 18W-13a can accumulate high content of squalene. However, squalene production in this organism is fluctuated under various conditions and is not yet optimized for commercialization. In this organism, the mevalonate pathway supplies isopentenyl pyrophosphate, the initial substrate for squalene production. In this pathway, 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) is the rate-limiting enzyme. We found that the HMGR activity had a strong positive correlation with the squalene contents in the strain. We constitutively expressed the HMGR in this organism and found that the transformant showed increased and stable production of squalene as well as carotenoids and biomass. These results clearly indicated that the HMGR expression is the bottleneck of squalene synthesis in Aurantiochytrium sp.
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Affiliation(s)
- Tianjing Yang
- Graduate School of Science and Technology, University of Tsukuba, Ibaraki, 305-8572, Japan
| | - Darryl Joy Juntila
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Algal Bio Co. Ltd, Kashiwa, Chiba, 277-0882, Japan
| | - Naomichi Fujihara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Takashi Inada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Chitose Laboratory Corporation, Kawasaki, Kanagawa, 216-0041, Japan
| | - Kohei Yoneda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Iwane Suzuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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Wei H, Movahedi A, Zhang Y, Aghaei-Dargiri S, Liu G, Zhu S, Yu C, Chen Y, Zhong F, Zhang J. Long-Chain Acyl-CoA Synthetases Promote Poplar Resistance to Abiotic Stress by Regulating Long-Chain Fatty Acid Biosynthesis. Int J Mol Sci 2022; 23:ijms23158401. [PMID: 35955540 PMCID: PMC9369374 DOI: 10.3390/ijms23158401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 02/04/2023] Open
Abstract
Long-chain acyl-CoA synthetases (LACSs) catalyze fatty acids (FAs) to form fatty acyl-CoA thioesters, which play essential roles in FA and lipid metabolisms and cuticle wax biosynthesis. Although LACSs from Arabidopsis have been intensively studied, the characterization and function of LACSs from poplar are unexplored. Here, 10 poplar PtLACS genes were identified from the poplar genome and distributed to eight chromosomes. A phylogenetic tree indicated that PtLACSs are sorted into six clades. Collinearity analysis and duplication events demonstrated that PtLACSs expand through segmental replication events and experience purifying selective pressure during the evolutionary process. Expression patterns revealed that PtLACSs have divergent expression changes in response to abiotic stress. Interaction proteins and GO analysis could enhance the understanding of putative interactions among protein and gene regulatory networks related to FA and lipid metabolisms. Cluster networks and long-chain FA (LCFA) and very long-chain FA (VLCFA) content analysis revealed the possible regulatory mechanism in response to drought and salt stresses in poplar. The present study provides valuable information for the functional identification of PtLACSs in response to abiotic stress metabolism in poplar.
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Affiliation(s)
- Hui Wei
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Ali Movahedi
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (S.Z.)
- College of Arts and Sciences, Arlington International University, Wilmington, DE 19804, USA
- Correspondence: (A.M.); (J.Z.)
| | - Yanyan Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (S.Z.)
| | - Soheila Aghaei-Dargiri
- Department of Horticulture, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas 47916193145, Iran;
| | - Guoyuan Liu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Sheng Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (Y.Z.); (S.Z.)
| | - Chunmei Yu
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Yanhong Chen
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Fei Zhong
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
| | - Jian Zhang
- Key Laboratory of Landscape Plant Genetics and Breeding, School of Life Sciences, Nantong University, Nantong 226019, China; (H.W.); (G.L.); (C.Y.); (Y.C.); (F.Z.)
- Correspondence: (A.M.); (J.Z.)
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Kim J, Pewzner-Jung Y, Joseph T, Ben-Dor S, Futerman AH. Generation of a ceramide synthase 6 mouse lacking the DDRSDIE C-terminal motif. PLoS One 2022; 17:e0271675. [PMID: 35849604 PMCID: PMC9292091 DOI: 10.1371/journal.pone.0271675] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
The important membrane lipid, ceramide, is generated by a family of homologous enzymes, the ceramide synthases (CerSs), multi-spanning membrane proteins located in the endoplasmic reticulum. Six CerS isoforms exist in mammals with each using a subset of acyl-CoAs for (dihydro)ceramide synthesis. A number of mice have been generated in which one or other CerS has been genetically manipulated, including complete knock-outs, with each displaying phenotypes concomitant with the expression levels of the CerS in question and the presumed biological function of the ceramide species that it generates. We recently described a short C-terminal motif in the CerS which is involved in CerS dimer formation; deleting this motif had no effect on the ability of the CerS to synthesize ceramide in vitro. In the current study, we generated a CerS6 mouse using CRISPR-Cas9, in which the DDRSDIE motif was replaced by ADAAAIA. While levels of CerS6ADAAAIA expression were unaffected in the CerS6ADAAAIA mouse, and CerS6ADAAAIA was able to generate C16-ceramide in vitro, ceramide levels were significantly reduced in the CerS6ADAAAIA mouse, suggesting that replacing this motif affects an as-yet unknown mechanism of regulation of ceramide synthesis via the DDRSDIE motif in vivo. Crossing CerS6ADAAAIA mice with CerS5 null mice led to generation of viable mice in which C16-ceramide levels were reduced by up to 90%, suggesting that depletion of C16-ceramide levels is compensated for by other ceramide species with different acyl chain lengths.
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Affiliation(s)
- Jiyoon Kim
- Department Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Yael Pewzner-Jung
- Department Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tammar Joseph
- Department Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Anthony H. Futerman
- Department Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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33
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Bengtsson JD, Wallis JG, Browse J. Expression of Physaria longchain acyl-CoA synthetases and hydroxy fatty acid accumulation in transgenic Arabidopsis. J Plant Physiol 2022; 274:153717. [PMID: 35584570 PMCID: PMC9494924 DOI: 10.1016/j.jplph.2022.153717] [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: 04/07/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Hydroxy fatty acids (HFA) are industrially useful chemical feedstocks that accumulate in seed-storage triacylglycerols (TAG) of several plant species, including castor (Ricinus communis) and Physaria (Physaria fendleri). For researchers, HFA also offer a unique opportunity to trace fatty acid metabolism and modification. Past work producing HFA in Arabidopsis (Arabidopsis thaliana) has demonstrated the importance of isozymes of TAG synthesis from plants that evolved to store HFA and as a result have a high degree of specificity towards HFA substrates. Castor phospholipase A2α (RcPLA2) has specificity for HFA-containing phosphatidylcholine. However, expression of RcPLA2 in HFA-accumulating Arabidopsis line CL37-PLA2 reduced HFA content of TAG. This loss was interpreted as being due to poor ability of Arabidopsis longchain acyl-CoA synthetases (LACSs) to utilize HFAs substrates. LACS enzymes are essential to activate HFA to HFA-CoA for TAG synthesis. Physaria is a close relative of Arabidopsis in the Brassicaceae family. To test the hypothesis that this close relatedness would allow Physaria LACSs to interface successfully with Arabidopsis enzymes of seed lipid metabolism and thereby restore HFA accumulation, we transformed PfLACS4 and PfLACS8 constructs into the CL37-PLA2 line. However, HFA content was not recovered, and biochemical characterization of recombinant PfLACS4 and PfLACS8 indicated that these isozymes have substrate specificities and selectivities that are similar to their Arabidopsis orthologues. These and other results pose an important question about how HFA synthesized on phosphatidylcholine can be transferred into the acyl-CoA pool for TAG synthesis.
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Affiliation(s)
- Jesse D Bengtsson
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - James G Wallis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA
| | - John Browse
- Institute of Biological Chemistry, Washington State University, Pullman, WA, USA.
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34
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Hamdan MF, Lung SC, Guo ZH, Chye ML. Roles of acyl-CoA-binding proteins in plant reproduction. J Exp Bot 2022; 73:2918-2936. [PMID: 35560189 DOI: 10.1093/jxb/erab499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/22/2021] [Accepted: 11/11/2021] [Indexed: 06/15/2023]
Abstract
Acyl-CoA-binding proteins (ACBPs) constitute a well-conserved family of proteins in eukaryotes that are important in stress responses and development. Past studies have shown that ACBPs are involved in maintaining, transporting and protecting acyl-CoA esters during lipid biosynthesis in plants, mammals, and yeast. ACBPs show differential expression and various binding affinities for acyl-CoA esters. Hence, ACBPs can play a crucial part in maintaining lipid homeostasis. This review summarizes the functions of ACBPs during the stages of reproduction in plants and other organisms. A comprehensive understanding on the roles of ACBPs during plant reproduction may lead to opportunities in crop improvement in agriculture.
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Affiliation(s)
- Mohd Fadhli Hamdan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Ze-Hua Guo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
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Hatanaka T, Tomita Y, Matsuoka D, Sasayama D, Fukayama H, Azuma T, Soltani Gishini MF, Hildebrand D. Different acyl-CoA:diacylglycerol acyltransferases vary widely in function, and a targeted amino acid substitution enhances oil accumulation. J Exp Bot 2022; 73:3030-3043. [PMID: 35560190 DOI: 10.1093/jxb/erac084] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/02/2022] [Indexed: 06/15/2023]
Abstract
Triacylglycerols (TAGs) are the major component of plant storage lipids such as oils. Acyl-CoA:diacylglycerol acyltransferase (DGAT) catalyzes the final step of the Kennedy pathway, and is mainly responsible for plant oil accumulation. We previously found that the activity of Vernonia DGAT1 was distinctively higher than that of Arabidopsis and soybean DGAT1 in a yeast microsome assay. In this study, the DGAT1 cDNAs of Arabidopsis, Vernonia, soybean, and castor bean were introduced into Arabidopsis. All Vernonia DGAT1-expressing lines showed a significantly higher oil content (49% mean increase compared with the wild-type) followed by soybean and castor bean. Most Arabidopsis DGAT1-overexpressing lines did not show a significant increase. In addition to these four DGAT1 genes, sunflower, Jatropha, and sesame DGAT1 genes were introduced into a TAG biosynthesis-defective yeast mutant. In the yeast expression culture, DGAT1s from Arabidopsis, castor bean, and soybean only slightly increased the TAG content; however, DGAT1s from Vernonia, sunflower, Jatropha, and sesame increased TAG content >10-fold more than the former three DGAT1s. Three amino acid residues were characteristically common in the latter four DGAT1s. Using soybean DGAT1, these amino acid substitutions were created by site-directed mutagenesis and substantially increased the TAG content.
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Affiliation(s)
- Tomoko Hatanaka
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Yoshiki Tomita
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Daisuke Matsuoka
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Daisuke Sasayama
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Hiroshi Fukayama
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Tetsushi Azuma
- Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, Japan
| | - Mohammad Fazel Soltani Gishini
- Department of Production Engineering and Plant Genetics, Faculty of Sciences and Agricultural Engineering, Campus of Agriculture and Natural Resources, Razi University, Kermanshah, Iran
| | - David Hildebrand
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
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36
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Doan MT, Neinast MD, Varner EL, Bedi KC, Bartee D, Jiang H, Trefely S, Xu P, Singh JP, Jang C, Rame JE, Brady DC, Meier JL, Marguiles KB, Arany Z, Snyder NW. Direct anabolic metabolism of three carbon propionate to a six carbon metabolite occurs in vivo across tissues and species. J Lipid Res 2022; 63:100224. [PMID: 35568254 PMCID: PMC9189226 DOI: 10.1016/j.jlr.2022.100224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/20/2022] [Accepted: 05/07/2022] [Indexed: 12/12/2022] Open
Abstract
Anabolic metabolism of carbon in mammals is mediated via the one- and two-carbon carriers S-adenosyl methionine and acetyl-coenzyme A. In contrast, anabolic metabolism of three-carbon units via propionate has not been shown to extensively occur. Mammals are primarily thought to oxidize the three-carbon short chain fatty acid propionate by shunting propionyl-CoA to succinyl-CoA for entry into the TCA cycle. Here, we found that this may not be absolute as, in mammals, one nonoxidative fate of propionyl-CoA is to condense to two three-carbon units into a six-carbon trans-2-methyl-2-pentenoyl-CoA (2M2PE-CoA). We confirmed this reaction pathway using purified protein extracts provided limited substrates and verified the product via LC-MS using a synthetic standard. In whole-body in vivo stable isotope tracing following infusion of 13C-labeled valine at steady state, 2M2PE-CoA was found to form via propionyl-CoA in multiple murine tissues, including heart, kidney, and to a lesser degree, in brown adipose tissue, liver, and tibialis anterior muscle. Using ex vivo isotope tracing, we found that 2M2PE-CoA also formed in human myocardial tissue incubated with propionate to a limited extent. While the complete enzymology of this pathway remains to be elucidated, these results confirm the in vivo existence of at least one anabolic three- to six-carbon reaction conserved in humans and mice that utilizes propionate.
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Affiliation(s)
- Mary T Doan
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Michael D Neinast
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erika L Varner
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Kenneth C Bedi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Bartee
- Chemical Biology Laboratory, National Cancer Institute, Frederick MD, USA
| | - Helen Jiang
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Sophie Trefely
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA; Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Peining Xu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jay P Singh
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA
| | - Cholsoon Jang
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - J Eduardo Rame
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Donita C Brady
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick MD, USA
| | - Kenneth B Marguiles
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zoltan Arany
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Department of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA, USA.
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37
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Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S. Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. Cell 2022; 185:513-529.e21. [PMID: 35120663 PMCID: PMC8896310 DOI: 10.1016/j.cell.2022.01.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 07/23/2020] [Revised: 10/07/2021] [Accepted: 01/05/2022] [Indexed: 02/05/2023]
Abstract
The human gut microbiota resides within a diverse chemical environment challenging our ability to understand the forces shaping this ecosystem. Here, we reveal that fitness of the Bacteroidales, the dominant order of bacteria in the human gut, is an emergent property of glycans and one specific metabolite, butyrate. Distinct sugars serve as strain-variable fitness switches activating context-dependent inhibitory functions of butyrate. Differential fitness effects of butyrate within the Bacteroides are mediated by species-level variation in Acyl-CoA thioesterase activity and nucleotide polymorphisms regulating an Acyl-CoA transferase. Using in vivo multi-omic profiles, we demonstrate Bacteroides fitness in the human gut is associated together, but not independently, with Acyl-CoA transferase expression and butyrate. Our data reveal that each strain of the Bacteroides exists within a unique fitness landscape based on the interaction of chemical components unpredictable by the effect of each part alone mediated by flexibility in the core genome.
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Affiliation(s)
- Sun-Yang Park
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Chitong Rao
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Katharine Z Coyte
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Gavin A Kuziel
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wentao Huang
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Seth Rakoff-Nahoum
- Division of Infectious Diseases and Division of Gastroenterology, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA; Department of Microbiology, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Wang Y, Ye X, Takano T, Liu S, Bu Y. Biotinylated subunit of 3-methylcrotonyl-CoA carboxylase encoding gene (AtMCCA) participating in Arabidopsis resistance to carbonate Stress by transcriptome analysis. Plant Sci 2022; 315:111130. [PMID: 35067300 DOI: 10.1016/j.plantsci.2021.111130] [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] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/09/2021] [Accepted: 11/21/2021] [Indexed: 06/14/2023]
Abstract
Soil salinization is a major factor impacting modern agricultural production, and alkaline soils contain large amounts of NaHCO3. Therefore, understanding plant tolerance to high levels of NaHCO3 is essential. In this study, a transcriptome analysis of shoot and root tissues of wild-type Arabidopsis thaliana was conducted at 0, 4, 12, 24 and 48 h after exposure to a 3 mM NaHCO3 stress. We focused on differentially expressed genes (DEGs) in roots identified in the early stages (4 h and 12 h) of the NaHCO3 stress response that were enriched in GO term, carboxylic acid metabolic process, and utilize HCO3-. Six genes were identified that exhibited similar expression patterns in both the RNA-seq and qRT-PCR data. We also characterized the phenotypic response of AtMCCA-overexpressing plants to carbonate stress, and found that the ability of AtMCCA-overexpressing plants to tolerate carbonate stress was enhanced by the addition of biotin to the growth medium.
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Affiliation(s)
- Yao Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xiaoxue Ye
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Tetsuo Takano
- Asian Natural Environmental Science Center (ANESC), University of Tokyo, Nishitokyo, Tokyo, 188-0002, Japan
| | - Shenkui Liu
- Department of Silviculture, State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Lin'an, Zhejiang, 311300, China.
| | - Yuanyuan Bu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin, 150040, China; College of Life Science, Northeast Forestry University, Harbin, 150040, China.
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Trefely S, Huber K, Liu J, Noji M, Stransky S, Singh J, Doan MT, Lovell CD, von Krusenstiern E, Jiang H, Bostwick A, Pepper HL, Izzo L, Zhao S, Xu JP, Bedi KC, Rame JE, Bogner-Strauss JG, Mesaros C, Sidoli S, Wellen KE, Snyder NW. Quantitative subcellular acyl-CoA analysis reveals distinct nuclear metabolism and isoleucine-dependent histone propionylation. Mol Cell 2022; 82:447-462.e6. [PMID: 34856123 PMCID: PMC8950487 DOI: 10.1016/j.molcel.2021.11.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [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: 07/09/2021] [Revised: 09/24/2021] [Accepted: 11/03/2021] [Indexed: 01/22/2023]
Abstract
Quantitative subcellular metabolomic measurements can explain the roles of metabolites in cellular processes but are subject to multiple confounding factors. We developed stable isotope labeling of essential nutrients in cell culture-subcellular fractionation (SILEC-SF), which uses isotope-labeled internal standard controls that are present throughout fractionation and processing to quantify acyl-coenzyme A (acyl-CoA) thioesters in subcellular compartments by liquid chromatography-mass spectrometry. We tested SILEC-SF in a range of sample types and examined the compartmentalized responses to oxygen tension, cellular differentiation, and nutrient availability. Application of SILEC-SF to the challenging analysis of the nuclear compartment revealed a nuclear acyl-CoA profile distinct from that of the cytosol, with notable nuclear enrichment of propionyl-CoA. Using isotope tracing, we identified the branched chain amino acid isoleucine as a major metabolic source of nuclear propionyl-CoA and histone propionylation, thus revealing a new mechanism of crosstalk between metabolism and the epigenome.
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Affiliation(s)
- Sophie Trefely
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA; Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katharina Huber
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute of Biochemistry, Graz University of Technology, Graz 8010, Austria
| | - Joyce Liu
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Noji
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jay Singh
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Mary T Doan
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Claudia D Lovell
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eliana von Krusenstiern
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Helen Jiang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Anna Bostwick
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Hannah L Pepper
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Luke Izzo
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Steven Zhao
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jimmy P Xu
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kenneth C Bedi
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - J Eduardo Rame
- Penn Medicine Heart Failure Mechanical Assist and Cardiac Transplant Center, Hospital of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Clementina Mesaros
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA; Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Nathaniel W Snyder
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
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Błachnio-Zabielska AU, Roszczyc-Owsiejczuk K, Imierska M, Pogodzińska K, Rogalski P, Daniluk J, Zabielski P. CerS1 but Not CerS5 Gene Silencing, Improves Insulin Sensitivity and Glucose Uptake in Skeletal Muscle. Cells 2022; 11:206. [PMID: 35053322 PMCID: PMC8773817 DOI: 10.3390/cells11020206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/11/2022] Open
Abstract
Skeletal muscle is perceived as a major tissue in glucose and lipid metabolism. High fat diet (HFD) lead to the accumulation of intramuscular lipids, including: long chain acyl-CoA, diacylglycerols, and ceramides. Ceramides are considered to be one of the most important lipid groups in the generation of skeletal muscle insulin resistance. So far, it has not been clearly established whether all ceramides adversely affect the functioning of the insulin pathway, or whether there are certain ceramide species that play a pivotal role in the induction of insulin resistance. Therefore, we designed a study in which the expression of CerS1 and CerS5 genes responsible for the synthesis of C18:0-Cer and C16:0-Cer, respectively, was locally silenced in the gastrocnemius muscle of HFD-fed mice through in vivo electroporation-mediated shRNA plasmids. Our study indicates that HFD feeding induced both, the systemic and skeletal muscle insulin resistance, which was accompanied by an increase in the intramuscular lipid levels, decreased activation of the insulin pathway and, consequently, a decrease in the skeletal muscle glucose uptake. CerS1 silencing leads to a reduction in C18:0-Cer content, with a subsequent increase in the activity of the insulin pathway, and an improvement in skeletal muscle glucose uptake. Such effects were not visible in case of CerS5 silencing, which indicates that the accumulation of C18:0-Cer plays a decisive role in the induction of skeletal muscle insulin resistance.
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Affiliation(s)
- Agnieszka U. Błachnio-Zabielska
- Department of Hygiene, Epidemiology and Metabolic Disorders, Medical University of Bialystok, Mickiewicza 2c, 15-089 Bialystok, Poland; (K.R.-O.); (M.I.); (K.P.)
| | - Kamila Roszczyc-Owsiejczuk
- Department of Hygiene, Epidemiology and Metabolic Disorders, Medical University of Bialystok, Mickiewicza 2c, 15-089 Bialystok, Poland; (K.R.-O.); (M.I.); (K.P.)
| | - Monika Imierska
- Department of Hygiene, Epidemiology and Metabolic Disorders, Medical University of Bialystok, Mickiewicza 2c, 15-089 Bialystok, Poland; (K.R.-O.); (M.I.); (K.P.)
| | - Karolina Pogodzińska
- Department of Hygiene, Epidemiology and Metabolic Disorders, Medical University of Bialystok, Mickiewicza 2c, 15-089 Bialystok, Poland; (K.R.-O.); (M.I.); (K.P.)
| | - Paweł Rogalski
- Department of Gastroenterology and Internal Medicine, Medical University of Bialystok, 15-089 Bialystok, Poland; (P.R.); (J.D.)
| | - Jarosław Daniluk
- Department of Gastroenterology and Internal Medicine, Medical University of Bialystok, 15-089 Bialystok, Poland; (P.R.); (J.D.)
| | - Piotr Zabielski
- Department of Medical Biology, Medical University of Bialystok, 15-089 Bialystok, Poland
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Andrade-Pavón D, Fernández-Muñoz V, González-Ibarra W, Hernández-Rodríguez C, Ibarra JA, Villa-Tanaca L. Point mutations in Candida glabrata 3-hydroxy-3-methylglutaryl-coenzyme A reductase (CgHMGR) decrease enzymatic activity and substrate/inhibitor affinity. Sci Rep 2021; 11:20842. [PMID: 34675283 PMCID: PMC8531335 DOI: 10.1038/s41598-021-00356-w] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022] Open
Abstract
3-Hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) is a crucial enzyme in the ergosterol biosynthesis pathway. The aim of this study was to obtain, purify, characterize, and overexpress five point mutations in highly conserved regions of the catalytic domain of Candida glabrata HMGR (CgHMGR) to explore the function of key amino acid residues in enzymatic activity. Glutamic acid (Glu) was substituted by glutamine in the E680Q mutant (at the dimerization site), Glu by glutamine in E711Q (at the substrate binding site), aspartic acid by alanine in D805A, and methionine by arginine in M807R (the latter two at the cofactor binding site). A double mutation, E680Q-M807R, was included. Regarding recombinant and wild-type CgHMGR, in vitro enzymatic activity was significantly lower for the former, as was the in silico binding energy of simvastatin, alpha-asarone and the HMG-CoA substrate. E711Q displayed the lowest enzymatic activity and binding energy, suggesting the importance of Glu711 (in the substrate binding site). The double mutant CgHMGR E680Q-M807R exhibited the second lowest enzymatic activity. Based on the values of the kinetic parameters KM and Vmax, the mutated amino acids appear to participate in binding. The current findings provide insights into the role of residues in the catalytic site of CgHMGR.
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Affiliation(s)
- Dulce Andrade-Pavón
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CDMX, Prol. de Carpio y Plan de Ayala. Col. Sto. Tomás, CP 11340, Mexico City, Mexico
| | - Vanessa Fernández-Muñoz
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CDMX, Prol. de Carpio y Plan de Ayala. Col. Sto. Tomás, CP 11340, Mexico City, Mexico
| | - Wendy González-Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CDMX, Mexico City, Mexico
| | - César Hernández-Rodríguez
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CDMX, Prol. de Carpio y Plan de Ayala. Col. Sto. Tomás, CP 11340, Mexico City, Mexico
| | - J Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CDMX, Mexico City, Mexico
| | - Lourdes Villa-Tanaca
- Laboratorio de Biología Molecular de Bacterias y Levaduras, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, CDMX, Prol. de Carpio y Plan de Ayala. Col. Sto. Tomás, CP 11340, Mexico City, Mexico.
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Sunstrum FG, Liu HL, Jancsik S, Madilao LL, Bohlmann J, Irmisch S. 4-Coumaroyl-CoA ligases in the biosynthesis of the anti-diabetic metabolite montbretin A. PLoS One 2021; 16:e0257478. [PMID: 34618820 PMCID: PMC8496819 DOI: 10.1371/journal.pone.0257478] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/01/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Montbretins are rare specialized metabolites found in montbretia (Crocosmia x crocosmiiflora) corms. Montbretin A (MbA) is of particular interest as a novel therapeutic for type-2 diabetes and obesity. There is no scalable production system for this complex acylated flavonol glycoside. MbA biosynthesis has been reconstructed in Nicotiana benthamiana using montbretia genes for the assembly of MbA from its various different building blocks. However, in addition to smaller amounts of MbA, the therapeutically inactive montbretin B (MbB) was the major product of this metabolic engineering effort. MbA and MbB differ in a single hydroxyl group of their acyl side chains, which are derived from caffeoyl-CoA and coumaroyl-CoA, respectively. Biosynthesis of both MbA and MbB also require coumaroyl-CoA for the formation of the myricetin core. Caffeoyl-CoA and coumaroyl-CoA are formed in the central phenylpropanoid pathway by acyl activating enzymes (AAEs) known as 4-coumaroyl-CoA ligases (4CLs). Here we investigated a small family of montbretia AAEs and 4CLs, and their possible contribution to montbretin biosynthesis. RESULTS Transcriptome analysis for gene expression patterns related to montbretin biosynthesis identified eight different montbretia AAEs belonging to four different clades. Enzyme characterization identified 4CL activity for two clade IV members, Cc4CL1 and Cc4CL2, converting different hydroxycinnamic acids into the corresponding CoA thioesters. Both enzymes preferred coumaric acid over caffeic acid as a substrate in vitro. While expression of montbretia AAEs did not enhance MbA biosynthesis in N. benthamiana, we demonstrated that both Cc4CLs can be used to activate coumaric and caffeic acid towards flavanone biosynthesis in yeast (Saccharomyces cerevisiae). CONCLUSIONS Montbretia expresses two functional 4CLs, but neither of them is specific for the formation of caffeoyl-CoA. Based on differential expression analysis and phylogeny Cc4CL1 is most likely involved in MbA biosynthesis, while Cc4CL2 may contribute to lignin biosynthesis. Both Cc4CLs can be used for flavanone production to support metabolic engineering of MbA in yeast.
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Affiliation(s)
- Frederick G. Sunstrum
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hannah L. Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sharon Jancsik
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lufiani L. Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sandra Irmisch
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
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Li M, Ma Y, Zhang X, Zhang L, Chen X, Ye JW, Chen GQ. Tailor-Made Polyhydroxyalkanoates by Reconstructing Pseudomonas Entomophila. Adv Mater 2021; 33:e2102766. [PMID: 34322928 DOI: 10.1002/adma.202102766] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/29/2021] [Indexed: 06/13/2023]
Abstract
Microbial polyhydroxyalkanoates (PHA) containing short- and medium/long-chain-length monomers, abbreviated as SCL-co-MCL/LCL PHAs, generate suitable thermal and mechanical properties. However, SCL-co-MCL/LCL PHAs with carbon chain longer than nine are difficult to synthesize due to the low specificity of PHA synthase PhaC and the lack of either SCL- or MCL/LCL monomer precursor fluxes. This study succeeds in reprogramming a β-oxidation weakened Pseudomonas entomophila containing synthesis pathways of SCL 3-hydroxybutyryl-CoA (3HB) from glucose and MCL/LCL 3-hydroxyalkanoyl-CoA from fatty acids with carbon chain lengths from 9 to 18, respectively, that are polymerized under a low specificity PhaC61-3 to form P(3HB-co-MCL/LCL 3HA) copolymers. Through rational flux-tuning approaches, the optimized recombinant P. entomophila accumulates 55 wt% poly-3-hydroxybutyrate in 8.4 g L-1 cell dry weight. Combined with weakened β-oxidation, a series of novel P(3HB-co-MCL/LCL 3HA) copolymers with over 60 wt% PHA in 9 g L-1 cell dry weight have been synthesized for the first time. P. entomophila has become a high-performing platform to generate tailor-made new SCL-co-MCL/LCL PHAs.
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Affiliation(s)
- Mengyi Li
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yueyuan Ma
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xinyu Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center of Life Sciences, Tsinghua University, Beijing, 100084, China
- MOE Key Lab of Industrial Biocatalysts, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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Metibemu DS, Akinloye OA, Akamo AJ, Okoye JO, Omotuyi IO. In-silico HMG-CoA reductase-inhibitory and in-vivo anti-lipidaemic/anticancer effects of carotenoids from Spondias mombin. J Pharm Pharmacol 2021; 73:1377-1386. [PMID: 34343336 DOI: 10.1093/jpp/rgab103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/27/2020] [Accepted: 06/24/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Inhibition of HMG-CoA (3-hydroxy-3-methylglutaryl coenzyme A) reductase, the rate rate-determining enzyme for the biogenesis of cholesterol is known to show antineoplastic effects. Therefore, this study investigates the in-silico HMG-CoA reductase (HMGCR)-inhibitory and in-vivo anti-lipidaemic/anticancer effects of carotenoids from Spondias mombin. METHODS Carotenoids from S. mombin leaves were characterized with the aid of liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS). The characterized phytochemicals were obtained from PubChem. They were docked into the orthosteric site of human HMGCR (Protein Data Bank code 1HW8) using AutoDock 4.0 suites. DMBA (7,12-dimethylbenz[a]anthracene) model of breast cancer was treated with the carotenoids extract from S. mombin (100 mg/kg and 200 mg/kg doses) to assess its anti-lipidaemic cum anticancer effects. KEY FINDINGS Carotenoids from S. mombin; beta-carotene-15,15'-epoxide, astaxanthin and 7,7',8,8'-tetrahydro-β-β-carotene demonstrate HMGCR inhibition. They form hydrophobic interactions with key residues within the catalytic domain of HMGCR. The carotenoids extract exhibits anti-lipidaemic/anticancer effects, lowering serum triglyceride, LDL and cholesterol concentration. It increases HDL concentration and downregulates the expression of HMGR, AFP, CEACAM-3, BRCA-1 and HIF-1 mRNAs. CONCLUSION Carotenoids from S. mombin demonstrate HMG-CoA reductase (HMGCR) inhibition, anti-lipidaemic, and anticancer effects. The inhibition of HMGCR by the carotenoids extract further poses it as a potential anti-hypercholesterolaemia compounds.
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Affiliation(s)
- Damilohun Samuel Metibemu
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
- Department of Biochemistry, Federal University of Agriculture, Abeokuta, Nigeria
| | | | - Adio Jamiu Akamo
- Department of Biochemistry, Federal University of Agriculture, Abeokuta, Nigeria
| | - Jude Ogechukwu Okoye
- Department of Medical Laboratory Science, Faculty of Health Sciences and Technology, College of Medicine, Nnamdi Azikiwe University, Nnewi Campus, Nnewi, Anambra State, Nigeria
| | - Idowu Olaposi Omotuyi
- Department of Biochemistry, Adekunle Ajasin University, Akungba-Akoko, Ondo State, Nigeria
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Klińska S, Kędzierska S, Jasieniecka-Gazarkiewicz K, Banaś A. In Vitro Growth Conditions Boost Plant Lipid Remodelling and Influence Their Composition. Cells 2021; 10:2326. [PMID: 34571973 PMCID: PMC8472737 DOI: 10.3390/cells10092326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Acyl-lipids are vital components for all life functions of plants. They are widely studied using often in vitro conditions to determine inter alia the impact of genetic modifications and the description of biochemical and physiological functions of enzymes responsible for acyl-lipid metabolism. What is currently lacking is knowledge of if these results also hold in real environments-in in vivo conditions. Our study focused on the comparative analysis of both in vitro and in vivo growth conditions and their impact on the acyl-lipid metabolism of Camelina sativa leaves. The results indicate that in vitro conditions significantly decreased the lipid contents and influenced their composition. In in vitro conditions, galactolipid and trienoic acid (16:3 and 18:3) contents significantly declined, indicating the impairment of the prokaryotic pathway. Discrepancies also exist in the case of acyl-CoA:lysophospholipid acyltransferases (LPLATs). Their activity increased about 2-7 times in in vitro conditions compared to in vivo. In vitro conditions also substantially changed LPLATs' preferences towards acyl-CoA. Additionally, the acyl editing process was three times more efficient in in vitro leaves. The provided evidence suggests that the results of acyl-lipid research from in vitro conditions may not completely reflect and be directly applicable in real growth environments.
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Affiliation(s)
- Sylwia Klińska
- Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, 80-307 Gdansk, Poland; (S.K.); (K.J.-G.); (A.B.)
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Dewulf JP, Paquay S, Marbaix E, Achouri Y, Van Schaftingen E, Bommer GT. ECHDC1 knockout mice accumulate ethyl-branched lipids and excrete abnormal intermediates of branched-chain fatty acid metabolism. J Biol Chem 2021; 297:101083. [PMID: 34419447 PMCID: PMC8473548 DOI: 10.1016/j.jbc.2021.101083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/15/2022] Open
Abstract
The cytosolic enzyme ethylmalonyl-CoA decarboxylase (ECHDC1) decarboxylates ethyl- or methyl-malonyl-CoA, two side products of acetyl-CoA carboxylase. These CoA derivatives can be used to synthesize a subset of branched-chain fatty acids (FAs). We previously found that ECHDC1 limits the synthesis of these abnormal FAs in cell lines, but its effects in vivo are unknown. To further evaluate the effects of ECHDC1 deficiency, we generated knockout mice. These mice were viable, fertile, showed normal postnatal growth, and lacked obvious macroscopic and histologic changes. Surprisingly, tissues from wild-type mice already contained methyl-branched FAs due to methylmalonyl-CoA incorporation, but these FAs were only increased in the intraorbital glands of ECHDC1 knockout mice. In contrast, ECHDC1 knockout mice accumulated 16–20-carbon FAs carrying ethyl-branches in all tissues, which were undetectable in wild-type mice. Ethyl-branched FAs were incorporated into different lipids, including acylcarnitines, phosphatidylcholines, plasmanylcholines, and triglycerides. Interestingly, we found a variety of unusual glycine-conjugates in the urine of knockout mice, which included adducts of ethyl-branched compounds in different stages of oxidation. This suggests that the excretion of potentially toxic intermediates of branched-chain FA metabolism might prevent a more dramatic phenotype in these mice. Curiously, ECHDC1 knockout mice also accumulated 2,2-dimethylmalonyl-CoA. This indicates that the broad specificity of ECHDC1 might help eliminate a variety of potentially dangerous branched-chain dicarboxylyl-CoAs. We conclude that ECHDC1 prevents the formation of ethyl-branched FAs and that urinary excretion of glycine-conjugates allows mice to eliminate potentially deleterious intermediates of branched-chain FA metabolism.
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Affiliation(s)
- Joseph P Dewulf
- Department of Biochemistry, de Duve Institute, UCLouvain, Brussels, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium; Department of Laboratory Medicine, University Hospital St Luc, UCLouvain, Bruxelles, Belgium.
| | - Stéphanie Paquay
- Department of Biochemistry, de Duve Institute, UCLouvain, Brussels, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium; Department of Neuropediatrics, University Hospital St Luc, UCLouvain, Bruxelles, Belgium
| | - Etienne Marbaix
- Department of Anatomical Pathology, University Hospital St Luc, UCLouvain, Bruxelles, Belgium; Department of Cell Biology, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Younès Achouri
- Transgenesis Platform, de Duve Institute, UCLouvain, Bruxelles, Belgium
| | - Emile Van Schaftingen
- Department of Biochemistry, de Duve Institute, UCLouvain, Brussels, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium.
| | - Guido T Bommer
- Department of Biochemistry, de Duve Institute, UCLouvain, Brussels, Belgium; Walloon Excellence in Lifesciences and Biotechnology (WELBIO), Brussels, Belgium.
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Lackus ND, Schmidt A, Gershenzon J, Köllner TG. A peroxisomal β-oxidative pathway contributes to the formation of C6-C1 aromatic volatiles in poplar. Plant Physiol 2021; 186:891-909. [PMID: 33723573 PMCID: PMC8195509 DOI: 10.1093/plphys/kiab111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/19/2021] [Indexed: 05/06/2023]
Abstract
Benzenoids (C6-C1 aromatic compounds) play important roles in plant defense and are often produced upon herbivory. Black cottonwood (Populus trichocarpa) produces a variety of volatile and nonvolatile benzenoids involved in various defense responses. However, their biosynthesis in poplar is mainly unresolved. We showed feeding of the poplar leaf beetle (Chrysomela populi) on P. trichocarpa leaves led to increased emission of the benzenoid volatiles benzaldehyde, benzylalcohol, and benzyl benzoate. The accumulation of salicinoids, a group of nonvolatile phenolic defense glycosides composed in part of benzenoid units, was hardly affected by beetle herbivory. In planta labeling experiments revealed that volatile and nonvolatile poplar benzenoids are produced from cinnamic acid (C6-C3). The biosynthesis of C6-C1 aromatic compounds from cinnamic acid has been described in petunia (Petunia hybrida) flowers where the pathway includes a peroxisomal-localized chain shortening sequence, involving cinnamate-CoA ligase (CNL), cinnamoyl-CoA hydratase/dehydrogenase (CHD), and 3-ketoacyl-CoA thiolase (KAT). Sequence and phylogenetic analysis enabled the identification of small CNL, CHD, and KAT gene families in P. trichocarpa. Heterologous expression of the candidate genes in Escherichia coli and characterization of purified proteins in vitro revealed enzymatic activities similar to those described in petunia flowers. RNA interference-mediated knockdown of the CNL subfamily in gray poplar (Populus x canescens) resulted in decreased emission of C6-C1 aromatic volatiles upon herbivory, while constitutively accumulating salicinoids were not affected. This indicates the peroxisomal β-oxidative pathway participates in the formation of volatile benzenoids. The chain shortening steps for salicinoids, however, likely employ an alternative pathway.
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Affiliation(s)
- Nathalie D Lackus
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Axel Schmidt
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Tobias G Köllner
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
- Author for communication:
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Abdullah HM, Rodriguez J, Salacup JM, Castañeda IS, Schnell DJ, Pareek A, Dhankher OP. Increased Cuticle Waxes by Overexpression of WSD1 Improves Osmotic Stress Tolerance in Arabidopsis thaliana and Camelina sativa. Int J Mol Sci 2021; 22:ijms22105173. [PMID: 34068347 PMCID: PMC8153268 DOI: 10.3390/ijms22105173] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/22/2022] Open
Abstract
To ensure global food security under the changing climate, there is a strong need for developing ‘climate resilient crops’ that can thrive and produce better yields under extreme environmental conditions such as drought, salinity, and high temperature. To enhance plant productivity under the adverse conditions, we constitutively overexpressed a bifunctional wax synthase/acyl-CoA:diacylglycerol acyltransferase (WSD1) gene, which plays a critical role in wax ester synthesis in Arabidopsis stem and leaf tissues. The qRT-PCR analysis showed a strong upregulation of WSD1 transcripts by mannitol, NaCl, and abscisic acid (ABA) treatments, particularly in Arabidopsis thaliana shoots. Gas chromatography and electron microscopy analyses of Arabidopsis seedlings overexpressing WSD1 showed higher deposition of epicuticular wax crystals and increased leaf and stem wax loading in WSD1 transgenics compared to wildtype (WT) plants. WSD1 transgenics exhibited enhanced tolerance to ABA, mannitol, drought and salinity, which suggested new physiological roles for WSD1 in stress response aside from its wax synthase activity. Transgenic plants were able to recover from drought and salinity better than the WT plants. Furthermore, transgenics showed reduced cuticular transpirational rates and cuticle permeability, as well as less chlorophyll leaching than the WT. The knowledge from Arabidopsis was translated to the oilseed crop Camelina sativa (L.) Crantz. Similar to Arabidopsis, transgenic Camelina lines overexpressing WSD1 also showed enhanced tolerance to drought stress. Our results clearly show that the manipulation of cuticular waxes will be advantageous for enhancing plant productivity under a changing climate.
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Affiliation(s)
- Hesham M. Abdullah
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MA 01003, USA; (H.M.A.); (J.R.)
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA;
| | - Jessica Rodriguez
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MA 01003, USA; (H.M.A.); (J.R.)
| | - Jeffrey M. Salacup
- Department of Geosciences, University of Massachusetts Amherst, Amherst, MA 01003, USA; (J.M.S.); (I.S.C.)
| | - Isla S. Castañeda
- Department of Geosciences, University of Massachusetts Amherst, Amherst, MA 01003, USA; (J.M.S.); (I.S.C.)
| | - Danny J. Schnell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA;
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 100067, India;
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, MA 01003, USA; (H.M.A.); (J.R.)
- Correspondence: ; Tel.: +1-413-545-0062
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Armstrong AJ, Collado MS, Henke BR, Olson MW, Hoang SA, Hamilton CA, Pourtaheri TD, Chapman KA, Summar MM, Johns BA, Wamhoff BR, Reardon JE, Figler RA. A novel small molecule approach for the treatment of propionic and methylmalonic acidemias. Mol Genet Metab 2021; 133:71-82. [PMID: 33741272 PMCID: PMC9109253 DOI: 10.1016/j.ymgme.2021.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/12/2021] [Accepted: 03/02/2021] [Indexed: 12/16/2022]
Abstract
Propionic Acidemia (PA) and Methylmalonic Acidemia (MMA) are inborn errors of metabolism affecting the catabolism of valine, isoleucine, methionine, threonine and odd-chain fatty acids. These are multi-organ disorders caused by the enzymatic deficiency of propionyl-CoA carboxylase (PCC) or methylmalonyl-CoA mutase (MUT), resulting in the accumulation of propionyl-coenzyme A (P-CoA) and methylmalonyl-CoA (M-CoA in MMA only). Primary metabolites of these CoA esters include 2-methylcitric acid (MCA), propionyl-carnitine (C3), and 3-hydroxypropionic acid, which are detectable in both PA and MMA, and methylmalonic acid, which is detectable in MMA patients only (Chapman et al., 2012). We deployed liver cell-based models that utilized PA and MMA patient-derived primary hepatocytes to validate a small molecule therapy for PA and MMA patients. The small molecule, HST5040, resulted in a dose-dependent reduction in the levels of P-CoA, M-CoA (in MMA) and the disease-relevant biomarkers C3, MCA, and methylmalonic acid (in MMA). A putative working model of how HST5040 reduces the P-CoA and its derived metabolites involves the conversion of HST5040 to HST5040-CoA driving the redistribution of free and conjugated CoA pools, resulting in the differential reduction of the aberrantly high P-CoA and M-CoA. The reduction of P-CoA and M-CoA, either by slowing production (due to increased demands on the free CoA (CoASH) pool) or enhancing clearance (to replenish the CoASH pool), results in a net decrease in the CoA-derived metabolites (C3, MCA and MMA (MMA only)). A Phase 2 study in PA and MMA patients will be initiated in the United States.
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Affiliation(s)
| | | | - Brad R Henke
- HemoShear Therapeutics, Inc., Charlottesville, VA, USA
| | | | | | | | | | | | | | - Brian A Johns
- HemoShear Therapeutics, Inc., Charlottesville, VA, USA
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Lagerwaard B, van der Hoek MD, Hoeks J, Grevendonk L, Nieuwenhuizen AG, Keijer J, de Boer VCJ. Propionate hampers differentiation and modifies histone propionylation and acetylation in skeletal muscle cells. Mech Ageing Dev 2021; 196:111495. [PMID: 33932454 DOI: 10.1016/j.mad.2021.111495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 11/27/2020] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/19/2022]
Abstract
Protein acylation via metabolic acyl-CoA intermediates provides a link between cellular metabolism and protein functionality. A process in which acetyl-CoA and acetylation are fine-tuned is during myogenic differentiation. However, the roles of other protein acylations remain unknown. Protein propionylation could be functionally relevant because propionyl-CoA can be derived from the catabolism of amino acids and fatty acids and was shown to decrease during muscle differentiation. We aimed to explore the potential role of protein propionylation in muscle differentiation, by mimicking a pathophysiological situation with high extracellular propionate which increases propionyl-CoA and protein propionylation, rendering it a model to study increased protein propionylation. Exposure to extracellular propionate, but not acetate, impaired myogenic differentiation in C2C12 cells and propionate exposure impaired myogenic differentiation in primary human muscle cells. Impaired differentiation was accompanied by an increase in histone propionylation as well as histone acetylation. Furthermore, chromatin immunoprecipitation showed increased histone propionylation at specific regulatory myogenic differentiation sites of the Myod gene. Intramuscular propionylcarnitine levels are higher in old compared to young males and females, possibly indicating increased propionyl-CoA levels with age. The findings suggest a role for propionylation and propionyl-CoA in regulation of muscle cell differentiation and ageing, possibly via alterations in histone acylation.
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Affiliation(s)
- Bart Lagerwaard
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands; TI Food and Nutrition, P.O. Box 557, 6700 AN, Wageningen, the Netherlands
| | - Marjanne D van der Hoek
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands; Applied Research Centre Food and Dairy, Van Hall Larenstein University of Applied Sciences, Leeuwarden, the Netherlands; MCL Academy, Medical Centre Leeuwarden, Leeuwarden, the Netherlands
| | - Joris Hoeks
- Department of Nutrition and Movement Sciences, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, 6200 MD, Maastricht, the Netherlands
| | - Lotte Grevendonk
- TI Food and Nutrition, P.O. Box 557, 6700 AN, Wageningen, the Netherlands; Department of Nutrition and Movement Sciences, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, 6200 MD, Maastricht, the Netherlands
| | - Arie G Nieuwenhuizen
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands
| | - Vincent C J de Boer
- Human and Animal Physiology, Wageningen University and Research, PO Box 338, 6700 AH, Wageningen, the Netherlands.
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