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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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2
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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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3
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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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4
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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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5
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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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Park J, Kim YJ, Lee D, Kim KJ. Structural basis for nucleotide-independent regulation of acyl-CoA thioesterase from Bacillus cereus ATCC 14579. Int J Biol Macromol 2020; 170:390-396. [PMID: 33383082 DOI: 10.1016/j.ijbiomac.2020.12.174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
Acyl-CoA thioesterase is an enzyme that catalyzes the cleavage of thioester bonds and regulates the cellular concentrations of CoASH, fatty acids, and acyl-CoA. In this study, we report the crystal structure of acyl-CoA thioesterase from Bacillus cereus ATCC 14579 (BcACT1) complexed with the CoA product. BcACT1 possesses a monomeric structure of a hotdog-fold and forms a hexamer via the trimerization of three dimers. We identified the active site of BcACT1 and revealed that residues Asn23 and Asp38 are crucial for enzyme catalysis, indicating that BcACT1 belongs to the TE6 family. We also propose that BcACT1 might undergo an open-closed conformational change on the acyl-CoA binding pocket upon binding of the acyl-CoA substrate. Interestingly, the BcACT1 variants with dramatically increased activities were obtained during the site-directed mutagenesis experiments to confirm the residues involved in CoA binding. Finally, we found that BcACT1 is not nucleotide-regulated and suggest that the length and shape of the additional α2-helix are crucial in determining a regulation mode by nucleotides.
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Affiliation(s)
- Jiyoung Park
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeo-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Donghoon Lee
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.
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7
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Varner EL, Trefely S, Bartee D, von Krusenstiern E, Izzo L, Bekeova C, O'Connor RS, Seifert EL, Wellen KE, Meier JL, Snyder NW. Quantification of lactoyl-CoA (lactyl-CoA) by liquid chromatography mass spectrometry in mammalian cells and tissues. Open Biol 2020; 10:200187. [PMID: 32961073 PMCID: PMC7536085 DOI: 10.1098/rsob.200187] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 06/26/2020] [Accepted: 08/25/2020] [Indexed: 12/15/2022] Open
Abstract
Lysine lactoylation is a recently described protein post-translational modification (PTM). However, the biochemical pathways responsible for this acylation remain unclear. Two metabolite-dependent mechanisms have been proposed: enzymatic histone lysine lactoylation derived from lactoyl-coenzyme A (lactoyl-CoA, also termed lactyl-CoA), and non-enzymatic lysine lactoylation resulting from acyl-transfer via lactoyl-glutathione. While the former has precedent in the form of enzyme-catalysed lysine acylation, the lactoyl-CoA metabolite has not been previously quantified in mammalian systems. Here, we use liquid chromatography-high-resolution mass spectrometry (LC-HRMS) together with a synthetic standard to detect and validate the presence of lactoyl-CoA in cell and tissue samples. Conducting a retrospective analysis of data from previously analysed samples revealed the presence of lactoyl-CoA in diverse cell and tissue contexts. In addition, we describe a biosynthetic route to generate 13C315N1-isotopically labelled lactoyl-CoA, providing a co-eluting internal standard for analysis of this metabolite. We estimate lactoyl-CoA concentrations of 1.14 × 10-8 pmol per cell in cell culture and 0.0172 pmol mg-1 tissue wet weight in mouse heart. These levels are similar to crotonyl-CoA, but between 20 and 350 times lower than predominant acyl-CoAs such as acetyl-, propionyl- and succinyl-CoA. Overall our studies provide the first quantitative measurements of lactoyl-CoA in metazoans, and provide a methodological foundation for the interrogation of this novel metabolite in biology and disease.
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Affiliation(s)
- Erika L. Varner
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Sophie Trefely
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David Bartee
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Eliana von Krusenstiern
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Luke Izzo
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Carmen Bekeova
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Roddy S. O'Connor
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Center for Cellular Immunotherapies, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erin L. Seifert
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Kathryn E. Wellen
- Department of Cancer Biology and Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jordan L. Meier
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Nathaniel W. Snyder
- Center for Metabolic Disease Research, Department of Microbiology and Immunology, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
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Bailey HJ, Bezerra GA, Marcero JR, Padhi S, Foster WR, Rembeza E, Roy A, Bishop DF, Desnick RJ, Bulusu G, Dailey HA, Yue WW. Human aminolevulinate synthase structure reveals a eukaryotic-specific autoinhibitory loop regulating substrate binding and product release. Nat Commun 2020; 11:2813. [PMID: 32499479 PMCID: PMC7272653 DOI: 10.1038/s41467-020-16586-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 07/06/2019] [Accepted: 05/11/2020] [Indexed: 12/12/2022] Open
Abstract
5'-aminolevulinate synthase (ALAS) catalyzes the first step in heme biosynthesis, generating 5'-aminolevulinate from glycine and succinyl-CoA. Inherited frameshift indel mutations of human erythroid-specific isozyme ALAS2, within a C-terminal (Ct) extension of its catalytic core that is only present in higher eukaryotes, lead to gain-of-function X-linked protoporphyria (XLP). Here, we report the human ALAS2 crystal structure, revealing that its Ct-extension folds onto the catalytic core, sits atop the active site, and precludes binding of substrate succinyl-CoA. The Ct-extension is therefore an autoinhibitory element that must re-orient during catalysis, as supported by molecular dynamics simulations. Our data explain how Ct deletions in XLP alleviate autoinhibition and increase enzyme activity. Crystallography-based fragment screening reveals a binding hotspot around the Ct-extension, where fragments interfere with the Ct conformational dynamics and inhibit ALAS2 activity. These fragments represent a starting point to develop ALAS2 inhibitors as substrate reduction therapy for porphyria disorders that accumulate toxic heme intermediates.
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Affiliation(s)
- Henry J Bailey
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Gustavo A Bezerra
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Jason R Marcero
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Siladitya Padhi
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Ltd, Hyderabad, 500081, India
| | - William R Foster
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Elzbieta Rembeza
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Arijit Roy
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Ltd, Hyderabad, 500081, India
| | - David F Bishop
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Robert J Desnick
- Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gopalakrishnan Bulusu
- TCS Innovation Labs-Hyderabad (Life Sciences Division), Tata Consultancy Services Ltd, Hyderabad, 500081, India
| | - Harry A Dailey
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
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9
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Adhikari K, Lo IW, Chen CL, Wang YL, Lin KH, Zadeh SM, Rattinam R, Li YS, Wu CJ, Li TL. Chemoenzymatic Synthesis and Biological Evaluation for Bioactive Molecules Derived from Bacterial Benzoyl Coenzyme A Ligase and Plant Type III Polyketide Synthase. Biomolecules 2020; 10:biom10050738. [PMID: 32397467 PMCID: PMC7277991 DOI: 10.3390/biom10050738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 03/21/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022] Open
Abstract
Plant type III polyketide synthases produce diverse bioactive molecules with a great medicinal significance to human diseases. Here, we demonstrated versatility of a stilbene synthase (STS) from Pinus Sylvestris, which can accept various non-physiological substrates to form unnatural polyketide products. Three enzymes (4-coumarate CoA ligase, malonyl-CoA synthetase and engineered benzoate CoA ligase) along with synthetic chemistry was practiced to synthesize starter and extender substrates for STS. Of these, the crystal structures of benzoate CoA ligase (BadA) from Rhodopseudomonas palustris in an apo form or in complex with a 2-chloro-1,3-thiazole-5-carboxyl-AMP or 2-methylthiazole-5-carboxyl-AMP intermediate were determined at resolutions of 1.57 Å, 1.7 Å, and 2.13 Å, respectively, which reinforces its capacity in production of unusual CoA starters. STS exhibits broad substrate promiscuity effectively affording structurally diverse polyketide products. Seven novel products showed desired cytotoxicity against a panel of cancer cell lines (A549, HCT116, Cal27). With the treatment of two selected compounds, the cancer cells underwent cell apoptosis in a dose-dependent manner. The precursor-directed biosynthesis alongside structure-guided enzyme engineering greatly expands the pharmaceutical repertoire of lead compounds with promising/enhanced biological activities.
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Affiliation(s)
- Kamal Adhikari
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - I-Wen Lo
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Chun-Liang Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Saeid Malek Zadeh
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Taipei 11529, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Rajesh Rattinam
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Taipei 11529, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yi-Shan Li
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
| | - Chang-Jer Wu
- Department of Food Science, National Taiwan Ocean University, Keelung 20224, Taiwan;
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; (K.A.); (I-W.L.); (C.-L.C.); (Y.-L.W.); (K.-H.L.); (S.M.Z.); (R.R.); (Y.-S.L.)
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei 11529, Taiwan
- Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Taipei 11529, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Correspondence: ; Tel.: +886-22787-1235
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10
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Sanderson JM. Far from Inert: Membrane Lipids Possess Intrinsic Reactivity That Has Consequences for Cell Biology. Bioessays 2020; 42:e1900147. [PMID: 31995246 DOI: 10.1002/bies.201900147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/06/2019] [Indexed: 12/19/2022]
Abstract
In this article, it is hypothesized that a fundamental chemical reactivity exists between some non-lipid constituents of cellular membranes and ester-based lipids, the significance of which is not generally recognized. Many peptides and smaller organic molecules have now been shown to undergo lipidation reactions in model membranes in circumstances where direct reaction with the lipid is the only viable route for acyl transfer. Crucially, drugs like propranolol are lipidated in vivo with product profiles that are comparable to those produced in vitro. Some compounds have also been found to promote lipid hydrolysis. Drugs with high lytic activity in vivo tend to have higher toxicity in vitro. Deacylases and lipases are proposed as key enzymes that protect cells against the effects of intrinsic lipidation. The toxic effects of intrinsic lipidation are hypothesized to include a route by which nucleation can occur during the formation of amyloid fibrils.
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11
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Wan J, Li J, Bandyopadhyay S, Kelly SL, Xiang Y, Zhang J, Merrill AH, Duan J. Analysis of 1-Deoxysphingoid Bases and Their N-Acyl Metabolites and Exploration of Their Occurrence in Some Food Materials. J Agric Food Chem 2019; 67:12953-12961. [PMID: 31638789 DOI: 10.1021/acs.jafc.9b05708] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Most common sphingolipids are comprised of "typical" sphingoid bases (sphinganine, sphingosine, and structurally related compounds) and are produced via the condensation of l-serine with a fatty acyl-CoA by serine palmitoyltransferase. Some organisms, including mammals, also produce "atypical" sphingoid bases that lack a 1-hydroxyl group as a result of the utilization of l-alanine or glycine instead of l-serine, resulting in the formation of 1-deoxy- or 1-desoxymethylsphingoid bases, respectively. Elevated production of "atypical" sphingolipids has been associated with human disease, but 1-deoxysphingoid bases have also been found to have potential as anticancer compounds, hence, the importance of knowing more about the occurrence of these compounds in food. Most of the "typical" and "atypical" sphingoid bases are found as the N-acyl metabolites (e.g., ceramides and 1-deoxyceramides) in mammals, but this has not been uniformly assessed in previous studies nor determined in consumed food. Therefore, we developed a method for the quantitative analysis of "typical" and "atypical" sphingoid bases and their N-acyl derivatives by reverse-phase liquid chromatography coupled to electrospray ionization tandem mass spectrometry. On the basis of these analyses, there was considerable variability in the amounts and molecular subspecies of atypical sphingoid bases and their N-acyl metabolites found in different edible sources. These findings demonstrate that a broader assessment of the types of sphingolipids in foods is needed because some diets might contain sufficient amounts of atypical as well as typical sphingolipids that could have beneficial or possibly deleterious effects on human health.
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Affiliation(s)
| | - Jian Li
- College of Pharmaceutical Sciences , Ganan Medical University , Ganzhou , Jiangxi 341000 , People's Republic of China
| | - Sibali Bandyopadhyay
- Schools of Biological Sciences and the Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Samuel L Kelly
- Schools of Biological Sciences and the Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | | | | | - Alfred H Merrill
- Schools of Biological Sciences and the Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Jingjing Duan
- Schools of Biological Sciences and the Parker H. Petit Institute for Bioengineering and Bioscience , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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12
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Hou J, Zheng H, Tzou WS, Cooper DR, Chruszcz M, Chordia MD, Kwon K, Grabowski M, Minor W. Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels. FEBS J 2018; 285:2900-2921. [PMID: 29917313 PMCID: PMC6105497 DOI: 10.1111/febs.14588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 04/05/2018] [Revised: 05/31/2018] [Accepted: 06/15/2018] [Indexed: 01/14/2023]
Abstract
Vibrio cholerae, the causative pathogen of the life-threatening infection cholera, encodes two copies of β-ketoacyl-acyl carrier protein synthase III (vcFabH1 and vcFabH2). vcFabH1 and vcFabH2 are pathogenic proteins associated with fatty acid synthesis, lipid metabolism, and potential applications in biofuel production. Our biochemical assays characterize vcFabH1 as exhibiting specificity for acetyl-CoA and CoA thioesters with short acyl chains, similar to that observed for FabH homologs found in most gram-negative bacteria. vcFabH2 prefers medium chain-length acyl-CoA thioesters, particularly octanoyl-CoA, which is a pattern of specificity rarely seen in bacteria. Structural characterization of one vcFabH1 and six vcFabH2 structures determined in either apo form or in complex with acetyl-CoA/octanoyl-CoA indicate that the substrate-binding pockets of vcFabH1 and vcFabH2 are of different sizes, accounting for variations in substrate chain-length specificity. An unusual and unique feature of vcFabH2 is its C-terminal fragment that interacts with both the substrate-entrance loop and the dimer interface of the enzyme. Our discovery of the pattern of substrate specificity of both vcFabH1 and vcFabH2 can potentially aid the development of novel antibacterial agents against V. cholerae. Additionally, the distinctive substrate preference of FabH2 in V. cholerae and related facultative anaerobes conceivably make it an attractive component of genetically engineered bacteria used for commercial biofuel production.
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Affiliation(s)
- Jing Hou
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Heping Zheng
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Wen-Shyong Tzou
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Taiwan
| | - David R. Cooper
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA
| | - Mahendra D. Chordia
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Keehwan Kwon
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
- Infectious Diseases, J. Craig Venter Institute, Rockville, MD 20850, USA
| | - Marek Grabowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908-0736, USA
- Center for Structural Genomics of Infectious Diseases (CSGID) Consortium, USA
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13
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Abrankó L, Williamson G, Gardner S, Kerimi A. Comprehensive quantitative analysis of fatty-acyl-Coenzyme A species in biological samples by ultra-high performance liquid chromatography-tandem mass spectrometry harmonizing hydrophilic interaction and reversed phase chromatography. J Chromatogr A 2017; 1534:111-122. [PMID: 29290399 DOI: 10.1016/j.chroma.2017.12.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 02/07/2023]
Abstract
Fatty acyl-Coenzyme A species (acyl-CoAs) are key biomarkers in studies focusing on cellular energy metabolism. Existing analytical approaches are unable to simultaneously detect the full range of short-, medium-, and long-chain acyl-CoAs, while chromatographic limitations encountered in the analysis of limited amounts of biological samples are an often overlooked problem. We report the systematic development of a UHPLC-ESI-MS/MS method which incorporates reversed phase (RP) and hydrophilic interaction liquid chromatography (HILIC) separations in series, in an automated mode. The protocol outlined encompasses quantification of acyl-CoAs of varying hydrophobicity from C2 to C20 with recoveries in the range of 90-111 % and limit of detection (LOD) 1-5 fmol, which is substantially lower than previously published methods. We demonstrate that the poor chromatographic performance and signal losses in MS detection, typically observed for phosphorylated organic molecules, can be avoided by the incorporation of a 0.1% phosphoric acid wash step between injections. The methodological approach presented here permits a highly reliable, sensitive and precise analysis of small amounts of tissues and cell samples as demonstrated in mouse liver, human hepatic (HepG2) and skeletal muscle (LHCNM2) cells. The considerable improvements discussed pave the way for acyl-CoAs to be incorporated in routine targeted lipid biomarker profile studies.
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Affiliation(s)
- László Abrankó
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK
| | - Gary Williamson
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK
| | - Samantha Gardner
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK
| | - Asimina Kerimi
- University of Leeds, School of Food Science and Nutrition, Leeds, LS2 9JT, UK.
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14
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Stewart C, Woods K, Macias G, Allan AC, Hellens RP, Noel JP. Molecular architectures of benzoic acid-specific type III polyketide synthases. Acta Crystallogr D Struct Biol 2017; 73:1007-1019. [PMID: 29199980 PMCID: PMC5713876 DOI: 10.1107/s2059798317016618] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 07/11/2017] [Accepted: 11/17/2017] [Indexed: 11/23/2022] Open
Abstract
Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure-function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with the structure of an archetypal type III PKS: chalcone synthase from Malus × domestica. Both biphenyl synthase and benzophenone synthase contain mutations that reshape their active-site cavities to prevent the binding of 4-coumaroyl-CoA and to favor the binding of small hydrophobic substrates. The active-site cavities of biphenyl synthase and benzophenone synthase also contain a novel pocket associated with their chain-elongation and cyclization reactions. Collectively, these results illuminate structural determinants of benzoic acid-specific type III PKSs and expand the understanding of the evolution of specialized metabolic pathways in plants.
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Affiliation(s)
- Charles Stewart
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
- Macromolecular X-ray Crystallography Facility, Office of Biotechnology, Iowa State University, 0202 Molecular Biology Building, 2437 Pammel Drive, Ames, IA 50011, USA
| | - Kate Woods
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Greg Macias
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Andrew C. Allan
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Roger P. Hellens
- The New Zealand Institute for Plant and Food Research Limited (PFR), Auckland, New Zealand
- Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Joseph P. Noel
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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15
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Meng X, Song Q, Ye J, Wang L, Xu F. Characterization, Function, and Transcriptional Profiling Analysis of 3-Hydroxy-3-methylglutaryl-CoA Synthase Gene (GbHMGS1) towards Stresses and Exogenous Hormone Treatments in Ginkgo biloba. Molecules 2017; 22:molecules22101706. [PMID: 29023415 PMCID: PMC6151752 DOI: 10.3390/molecules22101706] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 08/26/2017] [Accepted: 10/08/2017] [Indexed: 12/11/2022] Open
Abstract
3-Hydroxy-3-methylglutaryl-CoA synthase (HMGS) is one of the rate-limiting enzymes in the mevalonate pathway as it catalyzes the condensation of acetoacetyl-CoA to form 3-hydroxy-3-methylglutaryl-CoA. In this study, A HMGS gene (designated as GbHMGS1) was cloned from Ginkgo biloba for the first time. GbHMGS1 contained a 1422-bp open-reading frame encoding 474 amino acids. Comparative and bioinformatics analysis revealed that GbHMGS1 was extensively homologous to HMGSs from other plant species. Phylogenetic analysis indicated that the GbHMGS1 belonged to the plant HMGS superfamily, sharing a common evolutionary ancestor with other HMGSs, and had a further relationship with other gymnosperm species. The yeast complement assay of GbHMGS1 in HMGS-deficient Saccharomyces cerevisiae strain YSC6274 demonstrated that GbHMGS1 gene encodes a functional HMGS enzyme. The recombinant protein of GbHMGS1 was successfully expressed in E. coli. The in vitro enzyme activity assay showed that the kcat and Km values of GbHMGS1 were 195.4 min−1 and 689 μM, respectively. GbHMGS1 was constitutively expressed in all tested tissues, including the roots, stems, leaves, female flowers, male flowers and fruits. The transcript accumulation for GbHMGS1 was highest in the leaves. Expression profiling analyses revealed that GbHMGS1 expression was induced by abiotic stresses (ultraviolet B and cold) and hormone treatments (salicylic acid, methyl jasmonate, and ethephon) in G. biloba, indicating that GbHMGS1 gene was involved in the response to environmental stresses and plant hormones.
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Affiliation(s)
- Xiangxiang Meng
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Qiling Song
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Lanlan Wang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
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16
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Kumar P, Ghosh Sachan S, Poddar R. Mutational analysis of microbial hydroxycinnamoyl-CoA hydratase-lyase (HCHL) towards enhancement of binding affinity: A computational approach. J Mol Graph Model 2017; 77:94-105. [PMID: 28850897 DOI: 10.1016/j.jmgm.2017.08.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/12/2017] [Accepted: 08/14/2017] [Indexed: 02/07/2023]
Abstract
Improving the industrial enzyme for better yield of the product is important and a challenging task. One of such important industrial enzymes is microbial Hydroxycinnamoyl-CoA hydratase-lyase (HCHL). It converts feruloyl-CoA to vanillin. We place our efforts towards the improvement of its catalytic activity with comprehensive computational investigation. Catalytic core of the HCHL was explored with molecular modeling and docking approaches. Site-directed mutations were introduced in the catalytic site of HCHL in a sequential manner to generate different mutants of HCHL. Basis of mutation is to increase the interaction between HCHL and substrate feruloyl-CoA through interatomic forces and hydrogen bond formation. A rigorous molecular dynamics (MD) simulation was performed to check the stability of mutant's structure. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), dynamic cross correlation (DCCM) and principal component analysis (PCA) were also performed to analyze flexibility and stability of structures. Docking studies were carried out between different mutants of HCHL and feruloyl-CoA. Investigation of the different binding sites and the interactions with mutant HCHLs and substrate allowed us to highlight the improved performance of mutants than wild type HCHL. This was further validated with MD simulation of complex consisting of different mutants and substrate. It further confirms all the structures are stable. However, mutant-2 showed better affinity towards substrate by forming hydrogen bond between active site and feruloyl-CoA. We propose that increase in hydrogen bond formation might facilitate in dissociation of vanillin from feruloyl-CoA. The current work may be useful for the future development of 'tailor-made' enzymes for better yield of vanillin.
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Affiliation(s)
- Pravin Kumar
- Department of Bio-Engineering, Birla Institute of Technology-Mesra, Ranchi, JH, 835 215, India
| | - Shashwati Ghosh Sachan
- Department of Bio-Engineering, Birla Institute of Technology-Mesra, Ranchi, JH, 835 215, India
| | - Raju Poddar
- Department of Bio-Engineering, Birla Institute of Technology-Mesra, Ranchi, JH, 835 215, India.
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17
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Kulkarni RA, Worth AJ, Zengeya TT, Shrimp JH, Garlick JM, Roberts AM, Montgomery DC, Sourbier C, Gibbs BK, Mesaros C, Tsai YC, Das S, Chan KC, Zhou M, Andresson T, Weissman AM, Linehan WM, Blair IA, Snyder NW, Meier JL. Discovering Targets of Non-enzymatic Acylation by Thioester Reactivity Profiling. Cell Chem Biol 2017; 24:231-242. [PMID: 28163016 DOI: 10.1016/j.chembiol.2017.01.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 10/14/2016] [Accepted: 01/10/2017] [Indexed: 01/15/2023]
Abstract
Non-enzymatic protein modification driven by thioester reactivity is thought to play a major role in the establishment of cellular lysine acylation. However, the specific protein targets of this process are largely unknown. Here we report an experimental strategy to investigate non-enzymatic acylation in cells. Specifically, we develop a chemoproteomic method that separates thioester reactivity from enzymatic utilization, allowing selective enrichment of non-enzymatic acylation targets. Applying this method to cancer cell lines identifies numerous candidate targets of non-enzymatic acylation, including several enzymes in lower glycolysis. Functional studies highlight malonyl-CoA as a reactive thioester metabolite that can modify and inhibit glycolytic enzyme activity. Finally, we show that synthetic thioesters can be used as novel reagents to probe non-enzymatic acylation in living cells. Our studies provide new insights into the targets and drivers of non-enzymatic acylation, and demonstrate the utility of reactivity-based methods to experimentally investigate this phenomenon in biology and disease.
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Affiliation(s)
- Rhushikesh A Kulkarni
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Andrew J Worth
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Thomas T Zengeya
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jonathan H Shrimp
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Julie M Garlick
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Allison M Roberts
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - David C Montgomery
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Carole Sourbier
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Benjamin K Gibbs
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Clementina Mesaros
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - King C Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Ming Zhou
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702, USA
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20817, USA
| | - Ian A Blair
- Penn SRP Center, Center for Excellence in Environmental Toxicology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nathaniel W Snyder
- Drexel University, A.J. Drexel Autism Institute, 3020 Market Street, Philadelphia, PA 19104, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA.
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18
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González JM, Marti-Arbona R, Chen JCH, Unkefer CJ. Structure of Methylobacterium extorquens malyl-CoA lyase: CoA-substrate binding correlates with domain shift. Acta Crystallogr F Struct Biol Commun 2017; 73:79-85. [PMID: 28177317 PMCID: PMC5297927 DOI: 10.1107/s2053230x17001029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 12/14/2016] [Accepted: 01/19/2017] [Indexed: 11/10/2022] Open
Abstract
Malyl-CoA lyase (MCL) is an Mg2+-dependent enzyme that catalyzes the reversible cleavage of (2S)-4-malyl-CoA to yield acetyl-CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. Here, the 1.56 Å resolution X-ray crystal structure of MCL from Methylobacterium extorquens AM1 with bound Mg2+ is presented. Structural alignment with the closely related Rhodobacter sphaeroides malyl-CoA lyase complexed with Mg2+, oxalate and CoA allows a detailed analysis of the domain motion of the enzyme caused by substrate binding. Alignment of the structures shows that a simple hinge motion centered on the conserved residues Phe268 and Thr269 moves the C-terminal domain by about 30° relative to the rest of the molecule. This domain motion positions a conserved aspartate residue located in the C-terminal domain in the active site of the adjacent monomer, which may serve as a general acid/base in the catalytic mechanism.
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Affiliation(s)
- Javier M. González
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Julian C.-H. Chen
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Clifford J. Unkefer
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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19
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Yang X, Ma Y, Li N, Cai H, Bartlett MG. Development of a Method for the Determination of Acyl-CoA Compounds by Liquid Chromatography Mass Spectrometry to Probe the Metabolism of Fatty Acids. Anal Chem 2017; 89:813-821. [PMID: 27990799 PMCID: PMC5679003 DOI: 10.1021/acs.analchem.6b03623] [Citation(s) in RCA: 28] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acyl-Coenzyme As (acyl-CoAs) are a group of activated fatty acid molecules participating in multiple cellular processes including lipid synthesis, oxidative metabolism of fatty acids to produce ATP, transcriptional regulation, and protein post-translational modification. Quantification of cellular acyl-CoAs is challenging due to their instability in aqueous solutions and lack of blank matrices. Here we demonstrate an LC-MS/MS analytical method which allows for absolute quantitation with broad coverage of cellular acyl-CoAs. This assay was applied to profile endogenous acyl-CoAs under the challenge of a variety of dietary fatty acids in prostate and hepatic cells. Additionally, this approach allowed for detection of multiple fatty acid metabolic processes including the biogenesis of acyl-CoAs, and their elongation, degradation, and desaturation. Hierarchical clustering in the remodeling of acyl-CoA profiles revealed a fatty-acid-specific pattern across all tested cell lines, which provides a valuable reference for making predictions in other cell models. Individual acyl-CoAs were identified which were altered differentially by exogenous fatty acids in divergent tumorigenicity states of cells. These findings demonstrate the power of acyl-CoA profiling toward understanding the mechanisms for the progression of tumors or other diseases in response to fatty acids.
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Affiliation(s)
- Xiangkun Yang
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 W. Green Street, Athens, Georgia, 30602, United States
| | - Yongjie Ma
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 W. Green Street, Athens, Georgia, 30602, United States
| | - Ning Li
- Department of Analytical Chemistry, School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, China
| | - Houjian Cai
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 W. Green Street, Athens, Georgia, 30602, United States
| | - Michael G. Bartlett
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, 250 W. Green Street, Athens, Georgia, 30602, United States
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20
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Schwander T, Schada von Borzyskowski L, Burgener S, Cortina NS, Erb TJ. A synthetic pathway for the fixation of carbon dioxide in vitro. Science 2016; 354:900-904. [PMID: 27856910 PMCID: PMC5892708 DOI: 10.1126/science.aah5237] [Citation(s) in RCA: 335] [Impact Index Per Article: 41.9] [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: 07/08/2016] [Accepted: 10/05/2016] [Indexed: 01/20/2023]
Abstract
Carbon dioxide (CO2) is an important carbon feedstock for a future green economy. This requires the development of efficient strategies for its conversion into multicarbon compounds. We describe a synthetic cycle for the continuous fixation of CO2 in vitro. The crotonyl-coenzyme A (CoA)/ethylmalonyl-CoA/hydroxybutyryl-CoA (CETCH) cycle is a reaction network of 17 enzymes that converts CO2 into organic molecules at a rate of 5 nanomoles of CO2 per minute per milligram of protein. The CETCH cycle was drafted by metabolic retrosynthesis, established with enzymes originating from nine different organisms of all three domains of life, and optimized in several rounds by enzyme engineering and metabolic proofreading. The CETCH cycle adds a seventh, synthetic alternative to the six naturally evolved CO2 fixation pathways, thereby opening the way for in vitro and in vivo applications.
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Affiliation(s)
- Thomas Schwander
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
| | - Lennart Schada von Borzyskowski
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Simon Burgener
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Niña Socorro Cortina
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany
| | - Tobias J Erb
- Biochemistry and Synthetic Biology of Microbial Metabolism Group, Max Planck Institute for Terrestrial Microbiology Marburg, D-35043 Marburg, Germany.
- Institute for Microbiology, ETH Zürich, CH-8093 Zürich, Switzerland
- LOEWE Center for Synthetic Microbiology, Universität Marburg, D-35037 Marburg, Germany
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21
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Maloney FP, Gerwick L, Gerwick WH, Sherman DH, Smith JL. Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate. Proc Natl Acad Sci U S A 2016; 113:10316-21. [PMID: 27573844 PMCID: PMC5027445 DOI: 10.1073/pnas.1607210113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [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: 12/11/2022] Open
Abstract
Alkyl branching at the β position of a polyketide intermediate is an important variation on canonical polyketide natural product biosynthesis. The branching enzyme, 3-hydroxy-3-methylglutaryl synthase (HMGS), catalyzes the aldol addition of an acyl donor to a β-keto-polyketide intermediate acceptor. HMGS is highly selective for two specialized acyl carrier proteins (ACPs) that deliver the donor and acceptor substrates. The HMGS from the curacin A biosynthetic pathway (CurD) was examined to establish the basis for ACP selectivity. The donor ACP (CurB) had high affinity for the enzyme (Kd = 0.5 μM) and could not be substituted by the acceptor ACP. High-resolution crystal structures of HMGS alone and in complex with its donor ACP reveal a tight interaction that depends on exquisite surface shape and charge complementarity between the proteins. Selectivity is explained by HMGS binding to an unusual surface cleft on the donor ACP, in a manner that would exclude the acceptor ACP. Within the active site, HMGS discriminates between pre- and postreaction states of the donor ACP. The free phosphopantetheine (Ppant) cofactor of ACP occupies a conserved pocket that excludes the acetyl-Ppant substrate. In comparison with HMG-CoA (CoA) synthase, the homologous enzyme from primary metabolism, HMGS has several differences at the active site entrance, including a flexible-loop insertion, which may account for the specificity of one enzyme for substrates delivered by ACP and the other by CoA.
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Affiliation(s)
- Finn P Maloney
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, MI 48109
| | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109; Department of Chemistry, University of Michigan, Ann Arbor, MI 48109; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Janet L Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109
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Doan TTP, Carlsson AS, Stymne S, Hofvander P. Biochemical characteristics of AtFAR2, a fatty acid reductase from Arabidopsis thaliana that reduces fatty acyl-CoA and -ACP substrates into fatty alcohols. Acta Biochim Pol 2016; 63:565-70. [PMID: 27274541 DOI: 10.18388/abp.2016_1245] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 02/04/2016] [Accepted: 02/16/2016] [Indexed: 11/10/2022]
Abstract
Fatty alcohols and derivatives are important for proper deposition of a functional pollen wall. Mutations in specific genes encoding fatty acid reductases (FAR) responsible for fatty alcohol production cause abnormal development of pollen. A disrupted AtFAR2 (MS2) gene in Arabidopsis thaliana results in pollen developing an abnormal exine layer and a reduced fertility phenotype. AtFAR2 has been shown to be targeted to chloroplasts and in a purified form to be specific for acyl-ACP substrates. Here, we present data on the in vitro and in planta characterizations of AtFAR2 from A. thaliana and show that this enzyme has the ability to use both, C16:0-ACP and C16:0-CoA, as substrates to produce C16:0-alcohol. Our results further show that AtFAR2 is highly similar in properties and substrate specificity to AtFAR6 for which in vitro data has been published, and which is also a chloroplast localized enzyme. This suggests that although AtFAR2 is the major enzyme responsible for exine layer functionality, AtFAR6 might provide functional redundancy to AtFAR2.
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Affiliation(s)
- Thuy T P Doan
- Department of Biology, Faculty of Science, Nong Lam University, Ho Chi Minh City, Vietnam
| | - Anders S Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden
| | - Sten Stymne
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden
| | - Per Hofvander
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, 230 53 Alnarp, Sweden
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23
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Aznar-Moreno JA, Venegas-Calerón M, Du ZY, Garcés R, Tanner JA, Chye ML, Martínez-Force E, Salas JJ. Characterization of a small acyl-CoA-binding protein (ACBP) from Helianthus annuus L. and its binding affinities. Plant Physiol Biochem 2016; 102:141-50. [PMID: 26938582 DOI: 10.1016/j.plaphy.2016.02.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [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: 12/17/2015] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 05/18/2023]
Abstract
Acyl-CoA-binding proteins (ACBPs) bind to acyl-CoA esters and promote their interaction with other proteins, lipids and cell structures. Small class I ACBPs have been identified in different plants, such as Arabidopsis thaliana (AtACBP6), Brassica napus (BnACBP) and Oryza sativa (OsACBP1, OsACBP2, OsACBP3), and they are capable of binding to different acyl-CoA esters and phospholipids. Here we characterize HaACBP6, a class I ACBP expressed in sunflower (Helianthus annuus) tissues, studying the specificity of its corresponding recombinant HaACBP6 protein towards various acyl-CoA esters and phospholipids in vitro, particularly using isothermal titration calorimetry and protein phospholipid binding assays. This protein binds with high affinity to de novo synthetized derivatives palmitoly-CoA, stearoyl-CoA and oleoyl-CoA (Kd 0.29, 0.14 and 0.15 μM respectively). On the contrary, it showed lower affinity towards linoleoyl-CoA (Kd 5.6 μM). Moreover, rHaACBP6 binds to different phosphatidylcholine species (dipalmitoyl-PC, dioleoyl-PC and dilinoleoyl-PC), yet it displays no affinity towards other phospholipids like lyso-PC, phosphatidic acid and lysophosphatidic acid derivatives. In the light of these results, the possible involvement of this protein in sunflower oil synthesis is considered.
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Affiliation(s)
- Jose A Aznar-Moreno
- Department of Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506
| | - Mónica Venegas-Calerón
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013 Seville, Spain
| | - Zhi-Yan Du
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Rafael Garcés
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013 Seville, Spain
| | - Julian A Tanner
- Department of Biochemistry, The University of Hong Kong, Pokfulam, Hong Kong
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Enrique Martínez-Force
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013 Seville, Spain
| | - Joaquín J Salas
- Instituto de la Grasa (CSIC), Campus Universitario Pablo de Olavide, Ctra. de Utrera Km 1, 41013 Seville, Spain.
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24
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Santos MM, Ruivo R, Lopes-Marques M, Torres T, de los Santos CB, Castro LFC, Neuparth T. Statins: An undesirable class of aquatic contaminants? Aquat Toxicol 2016; 174:1-9. [PMID: 26896816 DOI: 10.1016/j.aquatox.2016.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 11/15/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 06/05/2023]
Abstract
Emerging pollutants, such as pharmaceuticals, may pose a considerable environment risk. Hypocholesterolaemic drugs such as statins are among the most prescribed human pharmaceuticals in western European countries. In vertebrates, this therapeutic class disrupts the cholesterol synthesis by inhibiting the enzyme 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGR), responsible for the limiting step in the mevalonate pathway. Recently, functional studies have shown that statins competitively inhibit HMGR in vertebrates and arthropods, two taxa that have diverged over 450 million years ago. Importantly, chronic simvastatin exposure disrupts crustacean reproduction and development at environmentally relevant concentrations. Hence, a fundamental question emerges: what is the taxonomic scope of statins-induced HMGR inhibition across metazoans? Here, we address this central question in a large sampling of metazoans using comparative genomics, homology modelling and molecular docking. Sequence alignment of metazoan HMGRs allowed the annotation of highly conserved catalytic, co-factor and substrate binding sites, including residues highjacked for statin binding. Furthermore, molecular docking shows that the catalytic domains of metazoan HMGRs are highly conserved regarding interactions, not only with HMG-CoA, but also with both simvastatin and atorvastatin, the top prescribed statins in Europe and USA. Hence, the data indicates that both statins are expected to competitively inhibit metazoan's HMGRs, and therefore all metazoan taxa might be at risk. The environmental relevance of these findings are discussed and research priorities established. We believe that the conceptual framework used in this study can be applied to other emerging pollutants and assist in the design of toxicity testing and risk assessment.
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Affiliation(s)
- Miguel M Santos
- CIMAR/CIIMAR, LA-Interdisciplinary Centre of Marine and Environmental Research, Groups of Endocrine Disruptors and Emerging Contaminants and Animal Genetics and Evolution, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal; FCUP-Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - Raquel Ruivo
- CIMAR/CIIMAR, LA-Interdisciplinary Centre of Marine and Environmental Research, Groups of Endocrine Disruptors and Emerging Contaminants and Animal Genetics and Evolution, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal
| | - Mónica Lopes-Marques
- CIMAR/CIIMAR, LA-Interdisciplinary Centre of Marine and Environmental Research, Groups of Endocrine Disruptors and Emerging Contaminants and Animal Genetics and Evolution, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal; ICBAS, Abel Salazar Biomedical Sciences Institute, University of Porto, Porto, Portugal
| | - Tiago Torres
- CIMAR/CIIMAR, LA-Interdisciplinary Centre of Marine and Environmental Research, Groups of Endocrine Disruptors and Emerging Contaminants and Animal Genetics and Evolution, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal
| | - Carmen B de los Santos
- CIMAR/CIIMAR, LA-Interdisciplinary Centre of Marine and Environmental Research, Groups of Endocrine Disruptors and Emerging Contaminants and Animal Genetics and Evolution, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal
| | - L Filipe C Castro
- CIMAR/CIIMAR, LA-Interdisciplinary Centre of Marine and Environmental Research, Groups of Endocrine Disruptors and Emerging Contaminants and Animal Genetics and Evolution, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal; FCUP-Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Teresa Neuparth
- CIMAR/CIIMAR, LA-Interdisciplinary Centre of Marine and Environmental Research, Groups of Endocrine Disruptors and Emerging Contaminants and Animal Genetics and Evolution, University of Porto, Rua dos Bragas 177, 4050-123 Porto, Portugal
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25
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Peter DM, Vögeli B, Cortina NS, Erb TJ. A Chemo-Enzymatic Road Map to the Synthesis of CoA Esters. Molecules 2016; 21:517. [PMID: 27104508 PMCID: PMC6273144 DOI: 10.3390/molecules21040517] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [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: 03/20/2016] [Revised: 04/11/2016] [Accepted: 04/15/2016] [Indexed: 11/24/2022] Open
Abstract
Coenzyme A (CoA) is a ubiquitous cofactor present in every known organism. The thioesters of CoA are core intermediates in many metabolic processes, such as the citric acid cycle, fatty acid biosynthesis and secondary metabolism, including polyketide biosynthesis. Synthesis of CoA-thioesters is vital for the study of CoA-dependent enzymes and pathways, but also as standards for metabolomics studies. In this work we systematically tested five chemo-enzymatic methods for the synthesis of the three most abundant acyl-CoA thioester classes in biology; saturated acyl-CoAs, α,β-unsaturated acyl-CoAs (i.e., enoyl-CoA derivatives), and α-carboxylated acyl-CoAs (i.e., malonyl-CoA derivatives). Additionally we report on the substrate promiscuity of three newly described acyl-CoA dehydrogenases that allow the simple conversion of acyl-CoAs into enoyl-CoAs. With these five methods, we synthesized 26 different CoA-thioesters with a yield of 40% or higher. The CoA esters produced range from short- to long-chain, include branched and α,β-unsaturated representatives as well as other functional groups. Based on our results we provide a general guideline to the optimal synthesis method of a given CoA-thioester in respect to its functional group(s) and the commercial availability of the precursor molecule. The proposed synthetic routes can be performed in small scale and do not require special chemical equipment, making them convenient also for biological laboratories.
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Affiliation(s)
- Dominik M Peter
- Institute for Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Vladimir-Prelog-Weg 4, CH-8093 Zürich, Switzerland.
- Biochemistry & Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
| | - Bastian Vögeli
- Biochemistry & Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
| | - Niña Socorro Cortina
- Biochemistry & Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
| | - Tobias J Erb
- Biochemistry & Synthetic Biology of Microbial Metabolism Group, Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, D-35043 Marburg, Germany.
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26
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Navarro-Retamal C, Gaete-Eastman C, Herrera R, Caballero J, Alzate-Morales JH. Structural and Affinity Determinants in the Interaction between Alcohol Acyltransferase from F. x ananassa and Several Alcohol Substrates: A Computational Study. PLoS One 2016; 11:e0153057. [PMID: 27078149 PMCID: PMC4831670 DOI: 10.1371/journal.pone.0153057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/23/2016] [Indexed: 11/26/2022] Open
Abstract
Aroma and flavor are important factors of fruit quality and consumer preference. The specific pattern of aroma is generated during ripening by the accumulation of volatiles compounds, which are mainly esters. Alcohol acyltransferase (AAT) (EC 2.3.1.84) catalyzes the esterification reaction of aliphatic and aromatic alcohols and acyl-CoA into esters in fruits and flowers. In Fragaria x ananassa, there are different volatiles compounds that are obtained from different alcohol precursors, where octanol and hexanol are the most abundant during fruit ripening. At present, there is not structural evidence about the mechanism used by the AAT to synthesize esters. Experimental data attribute the kinetic role of this enzyme to 2 amino acidic residues in a highly conserved motif (HXXXD) that is located in the middle of the protein. With the aim to understand the molecular and energetic aspects of volatiles compound production from F. x ananassa, we first studied the binding modes of a series of alcohols, and also different acyl-CoA substrates, in a molecular model of alcohol acyltransferase from Fragaria x ananassa (SAAT) using molecular docking. Afterwards, the dynamical behavior of both substrates, docked within the SAAT binding site, was studied using routine molecular dynamics (MD) simulations. In addition, in order to correlate the experimental and theoretical data obtained in our laboratories, binding free energy calculations were performed; which previous results suggested that octanol, followed by hexanol, presented the best affinity for SAAT. Finally, and concerning the SAAT molecular reaction mechanism, it is suggested from molecular dynamics simulations that the reaction mechanism may proceed through the formation of a ternary complex, in where the Histidine residue at the HXXXD motif deprotonates the alcohol substrates. Then, a nucleophilic attack occurs from alcohol charged oxygen atom to the carbon atom at carbonyl group of the acyl CoA. This mechanism is in agreement with previous results, obtained in our group, in alcohol acyltransferase from Vasconcellea pubescens (VpAAT1).
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Affiliation(s)
- Carlos Navarro-Retamal
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Carlos Gaete-Eastman
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Casilla 747, Talca, Chile
| | - Raúl Herrera
- Laboratorio de Fisiología Vegetal y Genética Molecular, Instituto de Ciencias Biológicas, Universidad de Talca, Casilla 747, Talca, Chile
- * E-mail: (JAM); (RH)
| | - Julio Caballero
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
| | - Jans H. Alzate-Morales
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, 2 Norte 685, Casilla 721, Talca, Chile
- * E-mail: (JAM); (RH)
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27
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Khazneh E, Hřibová P, Hošek J, Suchý P, Kollár P, Pražanová G, Muselík J, Hanaková Z, Václavík J, Miłek M, Legáth J, Šmejkal K. The Chemical Composition of Achillea wilhelmsii C. Koch and Its Desirable Effects on Hyperglycemia, Inflammatory Mediators and Hypercholesterolemia as Risk Factors for Cardiometabolic Disease. Molecules 2016; 21:404. [PMID: 27023504 PMCID: PMC6273470 DOI: 10.3390/molecules21040404] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 02/16/2016] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 02/04/2023] Open
Abstract
This study was done to identify the content compounds of Achillea wilhelmsii (A. wilhelmsii) and to evaluate its hypoglycemic and anti-hypercholesterolemic activity and effect on inflammatory mediators. The extracts and fractions of A. wilhelmsii were thoroughly analyzed using high performance liquid chromatography (HPLC), and the total content of phenols and flavonoids was determined. The hypoglycemic activity was evaluated in vivo using alloxan-induced diabetic mice. The effect upon inflammatory mediators was evaluated in vitro using the human monocytic leukemia cell line (THP-1). The anti-hypercholesterolemic activity was evaluated in vitro using the 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase assay kit. The water extract (WE)-treated group showed the highest reduction in the fasting blood glucose levels (FBGL). The chloroform fraction (CF) and ethyl acetate fraction (EAF) both showed a significant ability to reduce the secretion of tumor necrosis factor alpha (TNF-α). The EAF, however, also attenuated the levels of matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9). The CF showed the most significant 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) inhibition activity. The five main compounds in the CF were isolated and identified. Out of the five compounds in the CF, 1β,10β-epoxydesacetoxymatricarin (CP1) and leucodin (CP2) showed the highest anti-hypercholesterolemic potential. A molecular docking study provided corresponding results.
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Affiliation(s)
- Elian Khazneh
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
| | - Petra Hřibová
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
| | - Jan Hošek
- Department of Molecular Biology and Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
| | - Pavel Suchý
- Department of Human Pharmacology and Toxicology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
| | - Peter Kollár
- Department of Human Pharmacology and Toxicology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
| | - Gabriela Pražanová
- Department of Human Pharmacology and Toxicology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
| | - Jan Muselík
- Department of Pharmaceutics, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého 1-3, Brno 61242, Czech Republic.
| | - Zuzana Hanaková
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
| | - Jiří Václavík
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
| | - Michał Miłek
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, Powstańców Warszawy 6, Rzeszów 35-959, Poland.
| | - Jaroslav Legáth
- Department of Biotechnology and Bioinformatics, Faculty of Chemistry, Rzeszów University of Technology, Powstańców Warszawy 6, Rzeszów 35-959, Poland.
- Department of Pharmacology and Toxicology, The University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, Košice 04181, Slovakia.
| | - Karel Šmejkal
- Department of Natural Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
- Department of Molecular Biology and Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého tř. 1, Brno 61242, Czech Republic.
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Yevglevskis M, Lee GL, Sun J, Zhou S, Sun X, Kociok-Köhn G, James TD, Woodman TJ, Lloyd MD. A study on the AMACR catalysed elimination reaction and its application to inhibitor testing. Org Biomol Chem 2016; 14:612-622. [PMID: 26537174 PMCID: PMC4718014 DOI: 10.1039/c5ob01541c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/27/2015] [Indexed: 12/15/2022]
Abstract
α-Methylacyl-CoA racemase (AMACR; P504S) catalyses a key step in the degradation of branched-chain fatty acids and is important for the pharmacological activation of Ibuprofen and related drugs. Levels of AMACR are increased in prostate and other cancers, and it is a drug target. Development of AMACR as a drug target is hampered by lack of a convenient assay. AMACR irreversibly catalyses the elimination of HF from 3-fluoro-2-methylacyl-CoA substrates, and this reaction was investigated for use as an assay. Several known inhibitors and alternative substrates reduced conversion of 3-fluoro-2-methyldecanoyl-CoA by AMACR, as determined by (1)H NMR. The greatest reduction of activity was observed with known potent inhibitors. A series of novel acyl-CoA esters with aromatic side chains were synthesised for testing as chromophoric substrates. These acyl-CoA esters were converted to unsaturated products by AMACR, but their use was limited by non-enzymatic elimination. Fluoride sensors were also investigated as a method of quantifying released fluoride and thus AMACR activity. These sensors generally suffered from high background signal and lacked reproducibility under the assay conditions. In summary, the elimination reaction can be used to characterise inhibitors, but it was not possible to develop a convenient colorimetric or fluorescent assay using 3-fluoro-2-methylacyl-CoA substrates.
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Affiliation(s)
- Maksims Yevglevskis
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Guat L. Lee
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Jenny Sun
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
- Department of Pharmacy , Shandong University , People's Republic of China
| | - Shiyi Zhou
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
- Department of Pharmacy , Shandong University , People's Republic of China
| | - Xiaolong Sun
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Gabriele Kociok-Köhn
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Tony D. James
- Department of Chemistry , University of Bath , Claverton Down , Bath BA2 7AY , UK
| | - Timothy J. Woodman
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
| | - Matthew D. Lloyd
- Medicinal Chemistry , Department of Pharmacy & Pharmacology , University of Bath , Claverton Down , Bath BA2 7AY , UK . ; Fax: +44 (0)1225 386114
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29
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Pan C, Hu YL, Jiang XN, Gai Y. Cloning, expression, crystallization and crystallographic analysis of CouR from Rhodopseudomonas palustris. Acta Crystallogr F Struct Biol Commun 2015; 71:1416-20. [PMID: 26527270 PMCID: PMC4631592 DOI: 10.1107/s2053230x15018968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 08/23/2015] [Accepted: 10/08/2015] [Indexed: 11/10/2022] Open
Abstract
CouR from Rhodopseudomonas palustris is a member of the MarR transcriptional regulator family. It regulates the expression of CouA and CouB, enzymes that are involved in the degradation of p-coumarate. In vivo, CouR binds to a DNA fragment containing the couAB promoter and suppresses the expression of CouA and CouB, while binding of p-coumaroyl-CoA attenuates its affinity towards DNA and activates the expression of CouA and CouB. Here, the crystallization and X-ray diffraction analyses of CouR alone and in complex with p-coumaroyl-CoA are reported. Apo and ligand-complexed CouR crystals diffracted to 2.5 and 3.3 Å resolution, respectively. The crystals of apo CouR belonged to space group P22121, with unit-cell parameters a = 62.78, b = 76.15, c = 87.38 Å, whereas the crystals of the CouR-ligand complex belonged to space group P212121, with unit-cell parameters a = 61.37, b = 69.82, c = 70.32 Å. The crystals were predicted to contain two CouR molecules or CouR-ligand complexes per asymmetric unit.
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Affiliation(s)
- Chen Pan
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People’s Republic of China
| | - Yong-lin Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People’s Republic of China
| | - Xiang-ning Jiang
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing 100083, People’s Republic of China
| | - Ying Gai
- College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, People’s Republic of China
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Han L, Shi P, Dong Y, Wang T, Li X, Hao J, Zhang Y, Wang T. New Rare Sinapoyl Acylated Flavonoid Glycosides Obtained from the Seeds of Lepidium apetalum Willd. Molecules 2015; 20:13982-96. [PMID: 26247923 PMCID: PMC6332256 DOI: 10.3390/molecules200813982] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 06/17/2015] [Accepted: 07/29/2015] [Indexed: 02/08/2023] Open
Abstract
Seven new rare sinapoyl acylated flavonoid glycosides, apetalumosides A1 (1), B8 (2), B9 (3), B10 (4), B11 (5), B12 (6), and C1 (7) were isolated from the seeds of Lepidium apetalum Willd. Their structures were elucidated by chemical and spectroscopic methods.
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Affiliation(s)
- Lifeng Han
- Tianjin Key Laboratory of TCM Chemistry and Analysis, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Road, Nankai District, Tianjin 300193, China; E-Mails: (L.H.); (T.W.)
| | - Pingping Shi
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshanxi Road, Nankai District, Tianjin 300193, China; E-Mails: (P.S.); (Y.D.); (X.L.); (J.H.)
| | - Yongzhe Dong
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshanxi Road, Nankai District, Tianjin 300193, China; E-Mails: (P.S.); (Y.D.); (X.L.); (J.H.)
| | - Tingting Wang
- Tianjin Key Laboratory of TCM Chemistry and Analysis, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Road, Nankai District, Tianjin 300193, China; E-Mails: (L.H.); (T.W.)
| | - Xiaoxia Li
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshanxi Road, Nankai District, Tianjin 300193, China; E-Mails: (P.S.); (Y.D.); (X.L.); (J.H.)
| | - Jia Hao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshanxi Road, Nankai District, Tianjin 300193, China; E-Mails: (P.S.); (Y.D.); (X.L.); (J.H.)
| | - Yi Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshanxi Road, Nankai District, Tianjin 300193, China; E-Mails: (P.S.); (Y.D.); (X.L.); (J.H.)
- Authors to whom correspondence should be addressed; E-Mails: (Y.Z.); (T.W.); Tel./Fax: +86-225-959-6163 (Y.Z./T.W.)
| | - Tao Wang
- Tianjin Key Laboratory of TCM Chemistry and Analysis, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Road, Nankai District, Tianjin 300193, China; E-Mails: (L.H.); (T.W.)
- Authors to whom correspondence should be addressed; E-Mails: (Y.Z.); (T.W.); Tel./Fax: +86-225-959-6163 (Y.Z./T.W.)
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31
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Huang J, Malhi M, Deneke J, Fraser ME. Structure of GTP-specific succinyl-CoA synthetase in complex with CoA. Acta Crystallogr F Struct Biol Commun 2015; 71:1067-71. [PMID: 26249701 PMCID: PMC4528943 DOI: 10.1107/s2053230x15011188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 06/09/2015] [Indexed: 11/10/2022] Open
Abstract
Pig GTP-specific succinyl-CoA synthetase is an αβ-heterodimer. The crystal structure of the complex with the substrate CoA was determined at 2.1 Å resolution. The structure shows CoA bound to the amino-terminal domain of the α-subunit, with the free thiol extending from the adenine portion into the site where the catalytic histidine residue resides.
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Affiliation(s)
- Ji Huang
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Manpreet Malhi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Jan Deneke
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
| | - Marie Elizabeth Fraser
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB T2N 1N4, Canada
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Abstract
BACKGROUND Vitamin B12 (cobalamin) is a necessary cofactor in methionine and succinyl-CoA metabolism. Studies estimate the deficiency prevalence as high as 30% in the elderly population. Ten to thirty percent of circulating cobalamin is bound to transcobalamin (holotranscobalamin, holoTC) which can readily enter cells and is therefore considered the bioactive form. The objective of our study was to evaluate the analytical performance of a high-throughput, automated holoTC assay (ARCHITECT i2000(SR) Active-B12 (Holotranscobalamin)) and compare it to other available methods. METHODS Manufacturer-specified limits of blank (LoB), detection (LoD), and quantitation (LoQ), imprecision, interference, and linearity were evaluated for the ARCHITECT HoloTC assay. Residual de-identified serum samples were used to compare the ARCHITECT HoloTC assay with the automated AxSYM Active-B12 (Holotranscobalamin) assay (Abbott Diagnostics) and the manual Active-B12 (Holotranscobalamin) Enzyme Immunoassay (EIA) (Axis-Shield Diagnostics, Dundee, Scotland, UK). RESULTS Manufacturer's claims of LoB, LoD, LoQ, imprecision, interference, and linearity to the highest point tested (113.4 pmol/L) were verified for the ARCHITECT HoloTC assay. Method comparison of the ARCHITECT HoloTC to the AxSYM HoloTC produced the following Deming regression statistics: (ARCHITECT(HoloTc)) = 0.941 (AxSYM(HoloTC)) + 1.2 pmol/L, S(y/x) = 6.4, r = 0.947 (n = 98). Comparison to the Active-B12 EIA produced: (ARCHITECT(HoloTC)) = 1.105 (EIA(Active-B12)) - 6.8 pmol/L, S(y/x) = 11.0, r = 0.950 (n = 221). CONCLUSIONS This assay performed acceptably for LoB, LoD, LoQ, imprecision, interference, linearity and method comparison to the predicate device (AxSYM). An additional comparison to a manual Active-B12 EIA method performed similarly, with minor exceptions. This study determined that the ARCHITECT HoloTC assay is suitable for routine clinical use, which provides a high-throughput alternative for automated testing of this emerging marker of cobalamin deficiency.
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Shao Z, Wei Z, Wang Y, Ding X, Wang J, Jiang W, Zhao G. ["Nitrate stimulating effect" in Amycolatopsis mediterranei--from discovery to mechanistic studies]. Sheng Wu Gong Cheng Xue Bao 2015; 31:845-856. [PMID: 26672361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nitrate not only remarkably stimulates the rifamycinbiosynthesis in Amycolatopsis mediterranei, but also influences the primary metabolisms, including the inhibition of fatty acids biosynthesis in the bacterial. This phenomenon has been designated as "Nitrate Stimulating Effect" by the late Prof. J.S. Chiaosince its discovery in the 1970's, and has been found in many other antibiotics-producing actinomycetes subsequently. Based on the research in his laboratory, we have revealed that the nitrate stimulation effect mainly manifests in two aspects over the last two decades. First, nitrate promotes the supply of rifamycin precursors, e.g., UDP-glucose, AHBA, malonyl-CoA and methylmalonyl-CoA. Specifically, the biosynthesis of fatty acids is inhibited by nitrate consequently the acetyl-CoA is shunted into malonyl-CoA. Second, nitrate facilitates the expression of genes in the rifclulsterthat encodes rifamycin biosynthetic enzymes. Following our current understanding, the future research will focus on the signals, the signal transduction pathway and the molecular mechanisms that dictate nitrate-mediated transcriptional and post-translational regulations.
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Chedgy RJ, Köllner TG, Constabel CP. Functional characterization of two acyltransferases from Populus trichocarpa capable of synthesizing benzyl benzoate and salicyl benzoate, potential intermediates in salicinoid phenolic glycoside biosynthesis. Phytochemistry 2015; 113:149-59. [PMID: 25561400 DOI: 10.1016/j.phytochem.2014.10.018] [Citation(s) in RCA: 18] [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: 06/30/2014] [Revised: 10/07/2014] [Accepted: 10/16/2014] [Indexed: 05/19/2023]
Abstract
Salicinoids are phenolic glycosides (PGs) characteristic of the Salicaceae and are known defenses against insect herbivory. Common examples are salicin, salicortin, tremuloidin, and tremulacin, which accumulate to high concentrations in the leaves and bark of willows and poplars. Although their biosynthetic pathway is not known, recent work has suggested that benzyl benzoate may be a potential biosynthetic intermediate. Two candidate genes, named PtACT47 and PtACT49, encoding BAHD-type acyl transferases were identified and are predicted to produce such benzylated secondary metabolites. Herein described are the cDNA cloning, heterologous expression and in vitro functional characterization of these two BAHD acyltransferases. Recombinant PtACT47 exhibited low substrate selectivity and could utilize acetyl-CoA, benzoyl-CoA, and cinnamoyl-CoA as acyl donors with a variety of alcohols as acyl acceptors. This enzyme showed the greatest Km/Kcat ratio (45.8 nM(-1) s(-1)) and lowest Km values (45.1 μM) with benzoyl-CoA and salicyl alcohol, and was named benzoyl-CoA: salicyl alcohol O-benzoyltransferase (PtSABT). Recombinant PtACT49 utilized a narrower range of substrates, including benzoyl-CoA and acetyl-CoA and a limited number of alcohols. Its highest Km/Kcat (31.8 nM(-1) s(-1)) and lowest Km (55.3 μM) were observed for benzoyl-CoA and benzyl alcohol, and it was named benzoyl-CoA: benzyl alcohol O-benzoyltransferase (PtBEBT). Both enzymes were also capable of synthesizing plant volatile alcohol esters, such as hexenyl benzoate, at trace levels. Although the activities demonstrated are consistent with roles in salicinoid biosynthesis, direct tests of this hypothesis using transgenic poplar must still be performed.
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Affiliation(s)
- Russell J Chedgy
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020, STN CSC, Victoria, BC V8W 3N5, Canada
| | - Tobias G Köllner
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - C Peter Constabel
- Centre for Forest Biology, Department of Biology, University of Victoria, P.O. Box 3020, STN CSC, Victoria, BC V8W 3N5, Canada.
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Saravanan RR, Seshadri S, Gunasekaran S, Mendoza-Meroño R, Garcia-Granda S. Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide. Spectrochim Acta A Mol Biomol Spectrosc 2015; 139:321-328. [PMID: 25574651 DOI: 10.1016/j.saa.2014.12.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 07/23/2014] [Revised: 11/22/2014] [Accepted: 12/10/2014] [Indexed: 06/04/2023]
Abstract
Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT-B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values.
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Affiliation(s)
- R R Saravanan
- Department of Physics, Misrimal Navajee Munoth Jain Engineering College, Thoraipakkam, Chennai 600 097, India.
| | - S Seshadri
- Department of Physics, L.N. Govt. Arts College, Ponneri, Thiruvallur 601 001, India
| | - S Gunasekaran
- Research & Development, St. Peter's University, Avadi, Chennai 600 054, India
| | - R Mendoza-Meroño
- Faculty of Chemistry, Department of Physical and Analytical Chemistry, University Oviedo, C/ Julian Claveria, 8, 33006 Oviedo, Asturias, Spain
| | - S Garcia-Granda
- Faculty of Chemistry, Department of Physical and Analytical Chemistry, University Oviedo, C/ Julian Claveria, 8, 33006 Oviedo, Asturias, Spain
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Caldo KMP, Greer MS, Chen G, Lemieux MJ, Weselake RJ. Purification and properties of recombinant Brassica napus diacylglycerol acyltransferase 1. FEBS Lett 2015; 589:773-8. [PMID: 25687632 DOI: 10.1016/j.febslet.2015.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/02/2015] [Accepted: 02/03/2015] [Indexed: 11/17/2022]
Abstract
Diacylglycerol acyltransferase 1 (DGAT1) catalyzes the final step in the acyl-CoA-dependent triacylglycerol biosynthesis. Although the first DGAT1 gene was identified many years ago and the encoded enzyme catalyzes a key step in lipid biosynthesis, no detailed structure-function information is available on the enzyme due to difficulties associated with its purification. This study describes the purification of recombinant Brassica napus DGAT1 (BnaC.DGAT1.a) in active form through solubilization in n-dodecyl-β-D-maltopyranoside, cobalt affinity chromatography, and size-exclusion chromatography. Different BnaC.DGAT1.a oligomers in detergent micelles were resolved during the size-exclusion process. BnaC.DGAT1.a was purified 126-fold over the solubilized fraction and exhibited a specific activity of 26 nmol TAG/min/mg protein. The purified enzyme exhibited substrate preference for α-linolenoyl-CoA>oleoyl-CoA=palmitoyl-CoA>linoleoyl-CoA>stearoyl-CoA.
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Affiliation(s)
- Kristian Mark P Caldo
- Alberta Innovates Phytola Centre, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Michael S Greer
- Alberta Innovates Phytola Centre, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Guanqun Chen
- Alberta Innovates Phytola Centre, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - M Joanne Lemieux
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Randall J Weselake
- Alberta Innovates Phytola Centre, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
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Snyder NW, Basu SS, Zhou Z, Worth AJ, Blair IA. Stable isotope dilution liquid chromatography/mass spectrometry analysis of cellular and tissue medium- and long-chain acyl-coenzyme A thioesters. Rapid Commun Mass Spectrom 2014; 28:1840-1848. [PMID: 25559454 PMCID: PMC4286313 DOI: 10.1002/rcm.6958] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 05/28/2014] [Accepted: 06/02/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE Acyl-Coenzyme A (CoA) thioesters are the principal form of activated carboxylates in cells and tissues. They are employed as acyl carriers that facilitate the transfer of acyl groups to lipids and proteins. Quantification of medium- and long-chain acyl-CoAs represents a significant bioanalytical challenge because of their instability. METHODS Stable isotope dilution liquid chromatography/selected reaction monitoring-mass spectrometry (LC/SRM-MS) provides the most specific and sensitive method for the analysis of CoA species. However, relevant heavy isotope standards are not available and they are challenging to prepare by chemical synthesis. Stable isotope labeling by essential nutrients in cell culture (SILEC), developed originally for the preparation of stable isotope labeled short-chain acyl-CoA thioester standards, has now been extended to medium-chain and long-chain acyl-CoAs and used for LC/SRM-MS analyses. RESULTS Customized SILEC standards with >98% isotopic purity were prepared using mouse Hepa 1c1c7 cells cultured in pantothenic-free media fortified with [(13) C3 (15) N1 ]-pantothenic acid and selected fatty acids. A SILEC standard in combination with LC/SRM-MS was employed to quantify cellular concentrations of arachidonoyl-CoA (a representative long-chain acyl-CoA) in two human colon cancer cell lines. A panel of SILEC standards was also employed in combination LC/SRM-MS to quantify medium- and long-chain acyl-CoAs in mouse liver. CONCLUSIONS This new SILEC-based method in combination with LC/SRM-MS will make it possible to rigorously quantify medium- and long-chain acyl-CoAs in cells and tissues. The method will facilitate studies of medium- and long-chain acyl-CoA dehydrogenase deficiencies as well as studies on the role of medium- and long-chain acyl-CoAs in cellular metabolism.
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Affiliation(s)
| | | | | | | | - Ian A. Blair
- Correspondence to Ian A. Blair, PhD, Center for Cancer Pharmacology, 854 BRB II/III, 421 Curie Blvd, University of Pennsylvania, Philadelphia PA 19104-6160, USA. Phone: 215-573-9880, Fax: 215-573-9889,
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Greer MS, Zhou T, Weselake RJ. A novel assay of DGAT activity based on high temperature GC/MS of triacylglycerol. Lipids 2014; 49:831-8. [PMID: 24934589 DOI: 10.1007/s11745-014-3921-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/23/2014] [Indexed: 11/25/2022]
Abstract
Diacylglycerol acyltransferase (DGAT) catalyzes the final step in the acyl-CoA-dependent biosynthesis of triacylglycerol (TAG), a high-energy compound composed of three fatty acids esterified to a glycerol backbone. In vitro DGAT assays, which are usually conducted with radiolabeled substrate using microsomal fractions, have been useful in identifying compounds and genetic modifications that affect DGAT activity. Here, we describe a high-temperature gas chromatography (GC)/mass spectrometry (MS)-based method for monitoring molecular species of TAG produced by the catalytic action of microsomal DGAT. This method circumvents the need for radiolabeled or modified substrates, and only requires a simple lipid extraction prior to GC. The utility of the method is demonstrated using a recombinant type-1 Brassica napus DGAT produced in a strain of Saccharomyces cerevisae that is deficient in TAG synthesis. The GC/MS-based assay of DGAT activity was strongly correlated with the typical in vitro assay of the enzyme using [1-(14)C] acyl-CoA as an acyl donor. In addition to determining DGAT activity, the method is also useful for determining substrate specificity and selectivity properties of the enzyme.
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Affiliation(s)
- Michael S Greer
- Department of Agricultural, Food and Nutritional Science, Alberta Innovates Phytola Centre, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, AB, T6G 2P5, Canada
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Abstract
B₁₂-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB₁₂-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch. When the switch is "off", the 5'-deoxyadenosyl radical moiety is stabilized by releasing the internal strain of an enzyme-imposed conformation. Turning the switch "on," the enzyme environment becomes the driving force to impose a distinct conformation of the 5'-deoxyadenosyl radical to avoid deleterious radical transfer. This mechanochemical switch illustrates the elaborate way in which enzymes attain selectivity of extremely chemically challenging reactions.
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Affiliation(s)
- Elizabeth Brunk
- Laboratory
of Computational Chemistry and Biochemistry, EPFL, Lausanne, Switzerland 1015
| | - Whitney
F. Kellett
- Indiana
University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Nigel G. J. Richards
- Indiana
University-Purdue University, Indianapolis, Indiana 46202, United States
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, EPFL, Lausanne, Switzerland 1015
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Raasch K, Bocola M, Labahn J, Leitner A, Eggeling L, Bott M. Interaction of 2-oxoglutarate dehydrogenase OdhA with its inhibitor OdhI in Corynebacterium glutamicum: Mutants and a model. J Biotechnol 2014; 191:99-105. [PMID: 24905147 DOI: 10.1016/j.jbiotec.2014.05.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 05/15/2014] [Accepted: 05/19/2014] [Indexed: 01/25/2023]
Abstract
Pyruvate dehydrogenase and oxoglutarate dehydrogenase catalyze key reactions in central metabolism. In Corynebacterium glutamicum and related bacteria like Mycobacterium tuberculosis both activities reside in a novel protein supercomplex with the fusion protein OdhA catalyzing the conversion of oxoglutarate to succinyl-coenzyme A. This activity is inhibited by the forkhead-associated (FHA) domain of the small autoinhibitory protein OdhI. Here we used a biological screen which enabled us to isolate suppressor mutants that are influenced in OdhA-OdhI interaction. Five mutants carrying an OdhI mutation were isolated and one with an OdhA mutation. The OdhA mutein OdhA-C704E and three additional C704 variants were constructed. They exhibited unaltered or even slightly enhanced OdhA activity but showed reduced inhibition and interaction with OdhI. The FHA domain of OdhI was crystallized and its structure found in full agreement with previously determined NMR structures. Based on further structural studies, OdhA-OdhI crosslinking experiments, and modeling we discuss the experimental data generated on OdhA-OdhI interaction, with the latter protein representing a rare example of an FHA domain also recognizing a non-phosphorylated interaction partner.
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Affiliation(s)
- Katharina Raasch
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Marco Bocola
- Institute of Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Jörg Labahn
- Institute of Complex Systems, ICS-6: Structural Biochemistry, Forschungszentrum Jülich, Jülich, Germany; Center for Structural Systems Biology, c/o DESY, Hamburg, Germany
| | - Alexander Leitner
- Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
| | - Lothar Eggeling
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany.
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Abstract
TRPV1 channels are an important class of membrane proteins that play an integral role in the regulation of intracellular cations such as calcium in many different tissue types. The anionic phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) is a known positive modulator of TRPV1 channels and the negatively charged phosphate groups interact with several basic amino acid residues in the proximal C-terminal TRP domain of the TRPV1 channel. We and other groups have shown that physiological sub-micromolar levels of long-chain acyl CoAs (LC-CoAs), another ubiquitous anionic lipid, can also act as positive modulators of ion channels and exchangers. Therefore, we investigated whether TRPV1 channel activity is similarly regulated by LC-CoAs. Our results show that LC-CoAs are potent activators of the TRPV1 channel and interact with the same PIP2-binding residues in TRPV1. In contrast to PIP2, LC-CoA modulation of TRPV1 is independent of Ca2+i, acting in an acyl side-chain saturation and chain-length dependent manner. Elevation of LC-CoAs in intact Jurkat T-cells leads to significant increases in agonist-induced Ca2+i levels. Our novel findings indicate that LC-CoAs represent a new fundamental mechanism for regulation of TRPV1 channel activity that may play a role in diverse cell types under physiological and pathophysiological conditions that alter fatty acid transport and metabolism such as obesity and diabetes.
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Affiliation(s)
- Yi Yu
- Department of Pharmacology, Alberta Diabetes Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Chris R. J. Carter
- Department of Pharmacology, Alberta Diabetes Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nermeen Youssef
- Department of Pharmacology, Alberta Diabetes Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Jason R. B. Dyck
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Peter E. Light
- Department of Pharmacology, Alberta Diabetes Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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Kim J, Chang JH, Kim KJ. Crystal structure and biochemical properties of the (S)-3-hydroxybutyryl-CoA dehydrogenase PaaH1 from Ralstonia eutropha. Biochem Biophys Res Commun 2014; 448:163-8. [PMID: 24792376 DOI: 10.1016/j.bbrc.2014.04.101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/16/2014] [Indexed: 01/14/2023]
Abstract
3-Hydroxybutyryl-CoA dehydrogenase is an enzyme involved in the synthesis of the biofuel n-butanol by converting acetoacetyl-CoA to 3-hydroxybutyryl-CoA. To investigate the molecular mechanism of n-butanol biosynthesis, we determined crystal structures of the Ralstonia eutropha-derived 3-hydroxybutyryl-CoA dehydrogenase (RePaaH1) in complex with either its cofactor NAD(+) or its substrate acetoacetyl-CoA. While the biologically active structure is dimeric, the monomer of RePaaH1 comprises two separated domains with an N-terminal Rossmann fold and a C-terminal helical bundle for dimerization. In this study, we show that the cofactor-binding site is located on the Rossmann fold and is surrounded by five loops and one helix. The binding mode of the acetoacetyl-CoA substrate was found to be that the adenosine diphosphate moiety is not highly stabilized compared with the remainder of the molecule. Residues involved in catalysis and substrate binding were further confirmed by site-directed mutagenesis experiments, and kinetic properties of RePaaH1were examined as well. Our findings contribute to the understanding of 3-hydroxybutyryl-CoA dehydrogenase catalysis, and will be useful in enhancing the efficiency of n-butanol biosynthesis by structure based protein engineering.
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Affiliation(s)
- Jieun Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Jeong Ho Chang
- Department of Biology, Teachers College, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Program), Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu 702-701, Republic of Korea.
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Wang H, Zhang K, Zhu J, Song W, Zhao L, Zhang X. Structure reveals regulatory mechanisms of a MaoC-like hydratase from Phytophthora capsici involved in biosynthesis of polyhydroxyalkanoates (PHAs). PLoS One 2013; 8:e80024. [PMID: 24244597 PMCID: PMC3823801 DOI: 10.1371/journal.pone.0080024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 09/27/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Polyhydroxyalkanoates (PHAs) have attracted increasing attention as "green plastic" due to their biodegradable, biocompatible, thermoplastic, and mechanical properties, and considerable research has been undertaken to develop low cost/high efficiency processes for the production of PHAs. MaoC-like hydratase (MaoC), which belongs to (R)-hydratase involved in linking the β-oxidation and the PHA biosynthetic pathways, has been identified recently. Understanding the regulatory mechanisms of (R)-hydratase catalysis is critical for efficient production of PHAs that promise synthesis an environment-friendly plastic. METHODOLOGY/PRINCIPAL FINDINGS We have determined the crystal structure of a new MaoC recognized from Phytophthora capsici. The crystal structure of the enzyme was solved at 2.00 Å resolution. The structure shows that MaoC has a canonical (R)-hydratase fold with an N-domain and a C-domain. Supporting its dimerization observed in structure, MaoC forms a stable homodimer in solution. Mutations that disrupt the dimeric MaoC result in a complete loss of activity toward crotonyl-CoA, indicating that dimerization is required for the enzymatic activity of MaoC. Importantly, structure comparison reveals that a loop unique to MaoC interacts with an α-helix that harbors the catalytic residues of MaoC. Deletion of the loop enhances the enzymatic activity of MaoC, suggesting its inhibitory role in regulating the activity of MaoC. CONCLUSIONS/SIGNIFICANCE The data in our study reveal the regulatory mechanism of an (R)-hydratase, providing information on enzyme engineering to produce low cost PHAs.
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Affiliation(s)
- Huizheng Wang
- Department of Plant Pathology, Shandong Agricultural University, Tai’an, Shandong, China
| | - Kai Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jie Zhu
- Department of Plant Pathology, Shandong Agricultural University, Tai’an, Shandong, China
| | - Weiwei Song
- Department of Plant Pathology, Shandong Agricultural University, Tai’an, Shandong, China
| | - Li Zhao
- Department of Plant Pathology, Shandong Agricultural University, Tai’an, Shandong, China
| | - Xiuguo Zhang
- Department of Plant Pathology, Shandong Agricultural University, Tai’an, Shandong, China
- * E-mail:
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Walker AM, Hayes RP, Youn B, Vermerris W, Sattler SE, Kang C. Elucidation of the structure and reaction mechanism of sorghum hydroxycinnamoyltransferase and its structural relationship to other coenzyme a-dependent transferases and synthases. Plant Physiol 2013; 162:640-51. [PMID: 23624856 PMCID: PMC3668059 DOI: 10.1104/pp.113.217836] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 04/26/2013] [Indexed: 05/18/2023]
Abstract
Hydroxycinnamoyltransferase (HCT) from sorghum (Sorghum bicolor) participates in an early step of the phenylpropanoid pathway, exchanging coenzyme A (CoA) esterified to p-coumaric acid with shikimic or quinic acid as intermediates in the biosynthesis of the monolignols coniferyl alcohol and sinapyl alcohol. In order to elucidate the mode of action of this enzyme, we have determined the crystal structures of SbHCT in its apo-form and ternary complex with shikimate and p-coumaroyl-CoA, which was converted to its product during crystal soaking. The structure revealed the roles of threonine-36, serine-38, tyrosine-40, histidine-162, arginine-371, and threonine-384 in catalysis and specificity. Based on the exact chemistry of p-coumaroyl-CoA and shikimic acid in the active site and an analysis of kinetic and thermodynamic data of the wild type and mutants, we propose a role for histidine-162 and threonine-36 in the catalytic mechanism of HCT. Considering the calorimetric data, substrate binding of SbHCT should occur sequentially, with p-coumaroyl-CoA binding prior to the acyl acceptor molecule. While some HCTs can use both shikimate and quinate as an acyl acceptor, SbHCT displays low activity toward quinate. Comparison of the structure of sorghum HCT with the HCT involved in chlorogenic acid synthesis in coffee (Coffea canephora) revealed many shared features. Taken together, these observations explain how CoA-dependent transferases with similar structural features can participate in different biochemical pathways across species.
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Renna L, Stefano G, Majeran W, Micalella C, Meinnel T, Giglione C, Brandizzi F. Golgi traffic and integrity depend on N-myristoyl transferase-1 in Arabidopsis. Plant Cell 2013; 25:1756-73. [PMID: 23673980 PMCID: PMC3694704 DOI: 10.1105/tpc.113.111393] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
N-myristoylation is a crucial irreversible eukaryotic lipid modification allowing a key subset of proteins to be targeted at the periphery of specific membrane compartments. Eukaryotes have conserved N-myristoylation enzymes, involving one or two N-myristoyltransferases (NMT1 and NMT2), among which NMT1 is the major enzyme. In the postembryonic developmental stages, defects in NMT1 lead to aberrant cell polarity, flower differentiation, fruit maturation, and innate immunity; however, no specific NMT1 target responsible for such deficiencies has hitherto been identified. Using a confocal microscopy forward genetics screen for the identification of Arabidopsis thaliana secretory mutants, we isolated STINGY, a recessive mutant with defective Golgi traffic and integrity. We mapped STINGY to a substitution at position 160 of Arabidopsis NMT1 (NMT1A160T). In vitro kinetic studies with purified NMT1A160T enzyme revealed a significant reduction in its activity due to a remarkable decrease in affinity for both myristoyl-CoA and peptide substrates. We show here that this recessive mutation is responsible for the alteration of Golgi traffic and integrity by predominantly affecting the Golgi membrane/cytosol partitioning of ADP-ribosylation factor proteins. Our results provide important functional insight into N-myristoylation in plants by ascribing postembryonic functions of Arabidopsis NMT1 that involve regulation of the functional and morphological integrity of the plant endomembranes.
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Affiliation(s)
- Luciana Renna
- Michigan State University–Department of Energy Plant Research Lab, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Giovanni Stefano
- Michigan State University–Department of Energy Plant Research Lab, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Wojciech Majeran
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Chiara Micalella
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Thierry Meinnel
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Carmela Giglione
- Centre National de la Recherche Scientifique, Campus de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
| | - Federica Brandizzi
- Michigan State University–Department of Energy Plant Research Lab, Michigan State University, East Lansing, Michigan 48824
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
- Address correspondence to
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Violante S, Ijlst L, Ruiter J, Koster J, van Lenthe H, Duran M, de Almeida IT, Wanders RJA, Houten SM, Ventura FV. Substrate specificity of human carnitine acetyltransferase: Implications for fatty acid and branched-chain amino acid metabolism. Biochim Biophys Acta Mol Basis Dis 2013; 1832:773-9. [PMID: 23485643 DOI: 10.1016/j.bbadis.2013.02.012] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [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: 10/17/2012] [Revised: 02/07/2013] [Accepted: 02/15/2013] [Indexed: 01/18/2023]
Abstract
Carnitine acyltransferases catalyze the reversible conversion of acyl-CoAs into acylcarnitine esters. This family includes the mitochondrial enzymes carnitine palmitoyltransferase 2 (CPT2) and carnitine acetyltransferase (CrAT). CPT2 is part of the carnitine shuttle that is necessary to import fatty acids into mitochondria and catalyzes the conversion of acylcarnitines into acyl-CoAs. In addition, when mitochondrial fatty acid β-oxidation is impaired, CPT2 is able to catalyze the reverse reaction and converts accumulating long- and medium-chain acyl-CoAs into acylcarnitines for export from the matrix to the cytosol. However, CPT2 is inactive with short-chain acyl-CoAs and intermediates of the branched-chain amino acid oxidation pathway (BCAAO). In order to explore the origin of short-chain and branched-chain acylcarnitines that may accumulate in various organic acidemias, we performed substrate specificity studies using purified recombinant human CrAT. Various saturated, unsaturated and branched-chain acyl-CoA esters were tested and the synthesized acylcarnitines were quantified by ESI-MS/MS. We show that CrAT converts short- and medium-chain acyl-CoAs (C2 to C10-CoA), whereas no activity was observed with long-chain species. Trans-2-enoyl-CoA intermediates were found to be poor substrates for this enzyme. Furthermore, CrAT turned out to be active towards some but not all the BCAAO intermediates tested and no activity was found with dicarboxylic acyl-CoA esters. This suggests the existence of another enzyme able to handle the acyl-CoAs that are not substrates for CrAT and CPT2, but for which the corresponding acylcarnitines are well recognized as diagnostic markers in inborn errors of metabolism.
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Affiliation(s)
- Sara Violante
- Metabolism and Genetics Group, Research Institute for Medicines and Pharmaceutical Sciences, iMed.UL, Faculty of Pharmacy, University of Lisbon, Portugal
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Sirakova TD, Deb C, Daniel J, Singh HD, Maamar H, Dubey VS, Kolattukudy PE. Wax ester synthesis is required for Mycobacterium tuberculosis to enter in vitro dormancy. PLoS One 2012; 7:e51641. [PMID: 23272127 PMCID: PMC3522743 DOI: 10.1371/journal.pone.0051641] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [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: 08/08/2012] [Accepted: 11/02/2012] [Indexed: 01/25/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is known to produce wax esters (WE) when subjected to stress. However, nothing is known about the enzymes involved in biosynthesis of WE and their role in mycobacterial dormancy. We report that two putative Mtb fatty acyl-CoA reductase genes (fcr) expressed in E. coli display catalytic reduction of fatty acyl-CoA to fatty aldehyde and fatty alcohol. Both enzymes (FCR1/Rv3391) and FCR2/Rv1543) showed a requirement for NADPH as the reductant, a preference for oleoyl-CoA over saturated fatty acyl-CoA and were inhibited by thiol-directed reagents. We generated Mtb gene-knockout mutants for each reductase. Metabolic incorporation of( 14)C-oleate into fatty alcohols and WE was severely diminished in the mutants under dormancy-inducing stress conditions that are thought to be encountered by the pathogen in the host. The fatty acyl-CoA reductase activity in cell lysates of the mutants under nitric oxide stress was significantly reduced when compared with the wild type. Complementation restored the lost activity completely in the Δfcr1 mutant and partially in the Δfcr2 mutant. WE synthesis was inhibited in both Δfcr mutants. The Δfcr mutants exhibited faster growth rates, an increased uptake of (14)C-glycerol suggesting increased permeability of the cell wall, increased metabolic activity levels and impaired phenotypic antibiotic tolerance under dormancy-inducing combined multiple stress conditions. Complementation of the mutants did not restore the development of antibiotic tolerance to wild-type levels. Transcript analysis of Δfcr mutants showed upregulation of genes involved in energy generation and transcription, indicating the inability of the mutants to become dormant. Our results indicate that the fcr1 and fcr2 gene products are involved in WE synthesis under in vitro dormancy-inducing conditions and that WE play a critical role in reaching a dormant state. Drugs targeted against the Mtb reductases may inhibit its ability to go into dormancy and therefore increase susceptibility of Mtb to currently used antibiotics thereby enhancing clearance of the pathogen from patients.
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Affiliation(s)
- Tatiana D. Sirakova
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Chirajyoti Deb
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Jaiyanth Daniel
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Harminder D. Singh
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Hedia Maamar
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Vinod S. Dubey
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
| | - Pappachan E. Kolattukudy
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, United States of America
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Palladino AA, Chen J, Kallish S, Stanley CA, Bennett MJ. Measurement of tissue acyl-CoAs using flow-injection tandem mass spectrometry: acyl-CoA profiles in short-chain fatty acid oxidation defects. Mol Genet Metab 2012; 107:679-83. [PMID: 23117082 PMCID: PMC3600647 DOI: 10.1016/j.ymgme.2012.10.007] [Citation(s) in RCA: 24] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 10/10/2012] [Accepted: 10/10/2012] [Indexed: 12/30/2022]
Abstract
The primary accumulating metabolites in fatty acid oxidation defects are intramitochondrial acyl-CoAs. Typically, secondary metabolites such as acylcarnitines, acylglycines and dicarboxylic acids are measured to study these disorders. Methods have not been adapted for tissue acyl-CoA measurement in defects with primarily acyl-CoA accumulation. Our objective was to develop a method to measure fatty acyl-CoA species that are present in tissues of mice with fatty acid oxidation defects using flow-injection tandem mass spectrometry. Following the addition of internal standards of [(13)C(2)] acetyl-CoA, [(13)C(8)] octanoyl-CoA, and [C(17)] heptadecanoic CoA, acyl-CoA's are extracted from tissue samples and are injected directly into the mass spectrometer. Data is acquired using a 506.9 neutral loss scan and multiple reaction-monitoring (MRM). This method can identify all long, medium and short-chain acyl-CoA species in wild type mouse liver including predicted 3-hydroxyacyl-CoA species. We validated the method using liver of the short-chain-acyl-CoA dehydrogenase (SCAD) knock-out mice. As expected, there is a significant increase in [C(4)] butyryl-CoA species in the SCAD -/- mouse liver compared to wild type. We then tested the assay in liver from the short-chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD) deficient mice to determine the profile of acyl-CoA accumulation in this less predictable model. There was more modest accumulation of medium chain species including 3-hydroxyacyl-CoA's consistent with the known chain-length specificity of the SCHAD enzyme.
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Affiliation(s)
- Andrew A. Palladino
- Division of Endocrinology, Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jie Chen
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U74SA
| | - Staci Kallish
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U74SA
| | - Charles A. Stanley
- Division of Endocrinology, Department of Pediatrics, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J. Bennett
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, U74SA
- Corresponding author at: Department of Pathology & Laboratory Medicine, 5NW58, Children’s Hospital of Philadelphia, 34th Street & Civic Center Blvd, Philadelphia, PA 19104, USA. (M.J. Bennett)
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Yang W, Simpson JP, Li-Beisson Y, Beisson F, Pollard M, Ohlrogge JB. A land-plant-specific glycerol-3-phosphate acyltransferase family in Arabidopsis: substrate specificity, sn-2 preference, and evolution. Plant Physiol 2012; 160:638-52. [PMID: 22864585 PMCID: PMC3461545 DOI: 10.1104/pp.112.201996] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/03/2012] [Indexed: 05/18/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) has eight glycerol-3-phosphate acyltransferase (GPAT) genes that are members of a plant-specific family with three distinct clades. Several of these GPATs are required for the synthesis of cutin or suberin. Unlike GPATs with sn-1 regiospecificity involved in membrane or storage lipid synthesis, GPAT4 and -6 are unique bifunctional enzymes with both sn-2 acyltransferase and phosphatase activity resulting in 2-monoacylglycerol products. We present enzymology, pathway organization, and evolutionary analysis of this GPAT family. Within the cutin-associated clade, GPAT8 is demonstrated as a bifunctional sn-2 acyltransferase/phosphatase. GPAT4, -6, and -8 strongly prefer C16:0 and C18:1 ω-oxidized acyl-coenzyme As (CoAs) over unmodified or longer acyl chain substrates. In contrast, suberin-associated GPAT5 can accommodate a broad chain length range of ω-oxidized and unsubstituted acyl-CoAs. These substrate specificities (1) strongly support polyester biosynthetic pathways in which acyl transfer to glycerol occurs after oxidation of the acyl group, (2) implicate GPAT specificities as one major determinant of cutin and suberin composition, and (3) argue against a role of sn-2-GPATs (Enzyme Commission 2.3.1.198) in membrane/storage lipid synthesis. Evidence is presented that GPAT7 is induced by wounding, produces suberin-like monomers when overexpressed, and likely functions in suberin biosynthesis. Within the third clade, we demonstrate that GPAT1 possesses sn-2 acyltransferase but not phosphatase activity and can utilize dicarboxylic acyl-CoA substrates. Thus, sn-2 acyltransferase activity extends to all subbranches of the Arabidopsis GPAT family. Phylogenetic analyses of this family indicate that GPAT4/6/8 arose early in land-plant evolution (bryophytes), whereas the phosphatase-minus GPAT1 to -3 and GPAT5/7 clades diverged later with the appearance of tracheophytes.
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Kim IA, Kim BG, Kim M, Ahn JH. Characterization of hydroxycinnamoyltransferase from rice and its application for biological synthesis of hydroxycinnamoyl glycerols. Phytochemistry 2012; 76:25-31. [PMID: 22285622 DOI: 10.1016/j.phytochem.2011.12.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2010] [Revised: 12/03/2011] [Accepted: 12/28/2011] [Indexed: 05/04/2023]
Abstract
Hydroxycinnamoyltransferases (HCTs) catalyze the transfer of the cinnamoyl moiety from hydroxycinnamoyl-CoA to various acceptors such as shikimic acid, quinic acid, hydroxylated acid, and glycerol. Four rice HCT homologues (OsHCT1-4) to tobacco HST were cloned, and OsHCT4 was expressed in Escherichia coli as a glutathione S-transferase fusion protein. Using the purified recombinant protein and biotransformation techniques, whether OsHCT4 shows hydroxycinnamoyltransferase activity with a variety of acyl group acceptors was investigated. The results of high performance liquid chromatography (HPLC) and mass spectrometry (MS) established that OsHCT4 mediated the trans-esterification of glycerol as well as shikimic acid in the presence of hydroxycinnamoyl-CoA. The structure of the reaction product was determined using nuclear magnetic resonance spectroscopy (NMR). E. coli cells co-expressing 4CL (4-coumarate:coenzyme A ligase) and OsHCT4 converted p-coumaric acid, ferulic acid, and caffeic acid into the corresponding glycerides. While this conversion is very efficient in vitro, the physiological significant in rice is currently unknown.
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Affiliation(s)
- In A Kim
- Department of Bioscience and Biotechnology, Bio/Molecular Informatics Center, Konkuk University, Seoul, Republic of Korea
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