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Li XL, Tei R, Uematsu M, Baskin JM. Ultralow Background Membrane Editors for Spatiotemporal Control of Phosphatidic Acid Metabolism and Signaling. ACS CENTRAL SCIENCE 2024; 10:543-554. [PMID: 38559292 PMCID: PMC10979500 DOI: 10.1021/acscentsci.3c01105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 04/04/2024]
Abstract
Phosphatidic acid (PA) is a multifunctional lipid with important metabolic and signaling functions, and efforts to dissect its pleiotropy demand strategies for perturbing its levels with spatiotemporal precision. Previous membrane editing approaches for generating local PA pools used light-mediated induced proximity to recruit a PA-synthesizing enzyme, phospholipase D (PLD), from the cytosol to the target organelle membrane. Whereas these optogenetic PLDs exhibited high activity, their residual activity in the dark led to undesired chronic lipid production. Here, we report ultralow background membrane editors for PA wherein light directly controls PLD catalytic activity, as opposed to localization and access to substrates, exploiting a light-oxygen-voltage (LOV) domain-based conformational photoswitch inserted into the PLD sequence and enabling their stable and nonperturbative targeting to multiple organelle membranes. By coupling organelle-targeted LOVPLD activation to lipidomics analysis, we discovered different rates of metabolism for PA and its downstream products depending on the subcellular location of PA production. We also elucidated signaling roles for PA pools on different membranes in conferring local activation of AMP-activated protein kinase signaling. This work illustrates how membrane editors featuring acute, optogenetic conformational switches can provide new insights into organelle-selective lipid metabolic and signaling pathways.
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Affiliation(s)
- Xiang-Ling Li
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Reika Tei
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Masaaki Uematsu
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Jeremy M. Baskin
- Weill
Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, United States
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
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2
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Li XL, Tei R, Uematsu M, Baskin JM. Ultralow background membrane editors for spatiotemporal control of lipid metabolism and signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555787. [PMID: 37693485 PMCID: PMC10491157 DOI: 10.1101/2023.08.31.555787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Phosphatidic acid (PA) is a multifunctional lipid with important metabolic and signaling functions, and efforts to dissect its pleiotropy demand strategies for perturbing its levels with spatiotemporal precision. Previous membrane editing approaches for generating local PA pools used light-mediated induced proximity to recruit a PA-synthesizing enzyme, phospholipase D (PLD), from the cytosol to the target organelle membrane. Whereas these optogenetic PLDs exhibited high activity, their residual activity in the dark led to undesired chronic lipid production. Here, we report ultralow background membrane editors for PA wherein light directly controls PLD catalytic activity, as opposed to localization and access to substrates, exploiting a LOV domain-based conformational photoswitch inserted into the PLD sequence and enabling their stable and non-perturbative targeting to multiple organelle membranes. By coupling organelle-targeted LOVPLD activation to lipidomics analysis, we discovered different rates of metabolism for PA and its downstream products depending on the subcellular location of PA production. We also elucidated signaling roles for PA pools on different membranes in conferring local activation of AMP-activated protein kinase signaling. This work illustrates how membrane editors featuring acute, optogenetic conformational switches can provide new insights into organelle-selective lipid metabolic and signaling pathways.
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Affiliation(s)
- Xiang-Ling Li
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Reika Tei
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Masaaki Uematsu
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy M. Baskin
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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3
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Tei R, Bagde SR, Fromme JC, Baskin JM. Activity-based directed evolution of a membrane editor in mammalian cells. Nat Chem 2023; 15:1030-1039. [PMID: 37217787 PMCID: PMC10525039 DOI: 10.1038/s41557-023-01214-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Cellular membranes contain numerous lipid species, and efforts to understand the biological functions of individual lipids have been stymied by a lack of approaches for controlled modulation of membrane composition in situ. Here we present a strategy for editing phospholipids, the most abundant lipids in biological membranes. Our membrane editor is based on a bacterial phospholipase D (PLD), which exchanges phospholipid head groups through hydrolysis or transphosphatidylation of phosphatidylcholine with water or exogenous alcohols. Exploiting activity-dependent directed enzyme evolution in mammalian cells, we have developed and structurally characterized a family of 'superPLDs' with up to a 100-fold enhancement in intracellular activity. We demonstrate the utility of superPLDs for both optogenetics-enabled editing of phospholipids within specific organelle membranes in live cells and biocatalytic synthesis of natural and unnatural designer phospholipids in vitro. Beyond the superPLDs, activity-based directed enzyme evolution in mammalian cells is a generalizable approach to engineer additional chemoenzymatic biomolecule editors.
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Affiliation(s)
- Reika Tei
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Saket R Bagde
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - J Christopher Fromme
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
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4
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Li C, Xia Y, Li M, Zhang T. ARTP mutagenesis of phospholipase D-producing strain Streptomyces hiroshimensis SK43.001, and its enzymatic properties. Heliyon 2022; 8:e12587. [PMID: 36619468 PMCID: PMC9816975 DOI: 10.1016/j.heliyon.2022.e12587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/16/2022] [Accepted: 12/14/2022] [Indexed: 12/26/2022] Open
Abstract
Phospholipase D (PLD) is a group of enzymes that act on phospholipid molecules, which is widely used in the fields of food and medicine. PLD is extracted from animals and plants with low transesterification activity and high price. Therefore, it is benefit to screen an efficient PLD producing strain from microorganisms. A highly productive strain of PLD with transphosphatidylation activity, named Streptomyces hiroshimensis SK43.001, was screened from soil in our laboratory and mutated using atmospheric room temperature plasma (ARTP). A mutant strain SK43.001-11 with the highest enzyme activity and superior genetic stability was obtained, and its fermentation enzyme activity was 5.3 U/mL, which was 82% increased comparing to wild strain. The purification of PLD showed that the specific enzyme activity increased to 49.48 U/mg, which was 54.37-fold higher than that of the crude enzyme, with a recovery of 32.31%. In addition, enzymatic properties of PLD have revealed that the optimal pH and temperature were 7.0 and 60 °C, respectively. Metal ion Mg2+ and surfactant Triton X-100 made the enzymatic activity increased by 16% and 100%, respectively. The reaction kinetic parameters showed that the mutant PLD had higher affinity for the substrate of egg PC and better catalytic efficiency with K m, V max and K cat of 30.20 mmol/L, 99.70 μmol/min and 76.33 s-1, respectively. This study may provide important inspiration for obtaining high enzyme activity strains with PLD.
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Affiliation(s)
- Chenchen Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yu Xia
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, 214122, China,Corresponding author.
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5
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Qi N, Liu J, Song W, Liu J, Gao C, Chen X, Guo L, Liu L, Wu J. Rational Design of Phospholipase D to Improve the Transphosphatidylation Activity for Phosphatidylserine Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6709-6718. [PMID: 35616637 DOI: 10.1021/acs.jafc.2c02212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Phosphatidylserine (PS) has been widely used in the fields of food and medicine, among others, owing to its unique chemical structure and health benefits. However, the phospholipase D (PLD)-mediated enzymatic production of PS remains a challenge due to the low transphosphatidylation activity of PLD. Therefore, in the present study, we designed a maltose-binding protein (MBP) tag and a PLD co-expression method to achieve the expression of soluble PLD in Escherichia coli. A "reconstruct substrate pocket" strategy was then proposed based on the catalytic mechanism and molecular dynamics simulation, expanding the substrate pocket and manipulating the coordination of l-Ser within the active site. The best mutant (SrMBPPLDMu6) exhibited a 2.04-fold higher transphosphatidylation/hydrolysis ratio than the wild-type Furthermore, under optimal conditions, Mu6 produced 58.6 g/L PS with 77.2% conversion, within 12 h on a 3 L scale, which demonstrates the potential of the proposed method for industrial application.
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Affiliation(s)
- Na Qi
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianmin Liu
- Shandong Huishilai Biotechnology Co., Ltd., Jinan, Shandong 250098, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
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A Novel High-Throughput Assay Reveals That the Temperature Induced Increases in Transphosphatidylation of Phospholipase D Are Dependent on the Alcohol Acceptor Concentration. Biomolecules 2022; 12:biom12050632. [PMID: 35625563 PMCID: PMC9138380 DOI: 10.3390/biom12050632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/05/2022] [Accepted: 04/09/2022] [Indexed: 12/10/2022] Open
Abstract
Phospholipase D reacts with alcohols or water, transphosphatidylating or hydrolysing lipids such as phosphatidylcholine, generating phosphatidylalcohols or phosphatidic acid, respectively. The enzyme has been employed in many applications making use of the transphosphatidylation reaction and the enzyme’s tolerance for organic solvents in order to synthesize natural and artificial phospholipids. Yet, its catalytic properties with respect to the transphosphatidylation reaction are not well understood. Here, we introduce a novel high-throughput assay, making use of 96-well plates, that employs Fluorescamine for the detection of transphosphatidylated amino alcohols. This assay allowed to monitor the KM and VMax at different temperatures, revealing that the former will be elevated by the temperature, while the latter is increased by a combination of both temperature and alcohol acceptor concentration being elevated, suggesting that increase in temperature may open up a new binding site for the alcohol acceptor.
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7
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Bose AL, Bhattacharjee D, Goswami D. Mixed micelles and bicontinuous microemulsions: Promising media for enzymatic reactions. Colloids Surf B Biointerfaces 2021; 209:112193. [PMID: 34768101 DOI: 10.1016/j.colsurfb.2021.112193] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/19/2021] [Accepted: 10/28/2021] [Indexed: 02/08/2023]
Abstract
Enzymes, the natural catalysts, replace catalysts of chemical origin in a wide spectrum of reactions and generally work under environment friendly conditions. Various strategies are adopted to modify catalytic activities of enzymes further, of which one is application of novel reaction medium. This work reviews applicability of novel media like mixed micelles and bicontinuous microemulsions in enzymatic reactions and points out their capability to play bigger roles in enzyme catalysis. Ionic reverse micelles reduced catalytic activities of enzymes through denaturation. Addition of nonionic surfactant to these reverse micelles led to corresponding mixed micelles and thus restored or sometimes enhanced catalytic abilities of enzymes. Mixed micelles comprising of two nonionic surfactants, bicontinuous microemulsion containing two anionic surfactants also acted as efficient reaction media for enzymes. Even a cationic/anionic/nonionic mixed micelle was found to increase activity of enzyme. Mixed micelles and bicontinuous microemulsions comprising of anionic and zwitterionic surfactants augmented enzyme catalysis. Mixed micelles and bicontinuous microemulsions containing ionic liquid and surfactant also had critical impact on enzyme catalysis. Catalytic abilities of enzymes altered significantly in substrate/surfactant and bile salt/surfactant mixed micelles. Concentrations of individual surfactant, molar ratio of surfactants, and molar ratio of water to total surfactants had notable impacts on enzyme catalysis in those media.
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Affiliation(s)
- Abir Lal Bose
- Department of Chemical Engineering, University College of Science and Technology, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, India.
| | - Debapriya Bhattacharjee
- Department of Chemical Engineering, University College of Science and Technology, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, India.
| | - Debajyoti Goswami
- Department of Chemical Engineering, University College of Science and Technology, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, India.
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8
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Roberts MF, Cai J, V Natarajan S, Khan HM, Reuter N, Gershenson A, Redfield AG. Phospholipids in Motion: High-Resolution 31P NMR Field Cycling Studies. J Phys Chem B 2021; 125:8827-8838. [PMID: 34320805 DOI: 10.1021/acs.jpcb.1c02105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Diverse phospholipid motions are key to membrane function but can be quite difficult to untangle and quantify. High-resolution field cycling 31P NMR spin-lattice relaxometry, where the sample is excited at high field, shuttled in the magnet bore for low-field relaxation, then shuttled back to high field for readout of the residual magnetization, provides data on phospholipid dynamics and structure. This information is encoded in the field dependence of the 31P spin-lattice relaxation rate (R1). In the field range from 11.74 down to 0.003 T, three dipolar nuclear magnetic relaxation dispersions (NMRDs) and one due to 31P chemical shift anisotropy contribute to R1 of phospholipids. Extraction of correlation times and maximum relaxation amplitudes for these NMRDs provides (1) lateral diffusion constants for different phospholipids in the same bilayer, (2) estimates of how additives alter the motion of the phospholipid about its long axis, and (3) an average 31P-1H angle with respect to the bilayer normal, which reveals that polar headgroup motion is not restricted on a microsecond timescale. Relative motions within a phospholipid are also provided by comparing 31P NMRD profiles for specifically deuterated molecules as well as 13C and 1H field dependence profiles to that of 31P. Although this work has dealt exclusively with phospholipids in small unilamellar vesicles, these same NMRDs can be measured for phospholipids in micelles and nanodisks, making this technique useful for monitoring lipid behavior in a variety of structures and assessing how additives alter specific lipid motions.
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Affiliation(s)
- Mary F Roberts
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Jingfei Cai
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Sivanandam V Natarajan
- Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, Waltham, Massachusetts 02454, United States
| | - Hanif M Khan
- Department of Molecular Biology and Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
| | - Nathalie Reuter
- Department of Molecular Biology and Computational Biology Unit, Department of Informatics, University of Bergen, 5020 Bergen, Norway
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, United States
| | - Alfred G Redfield
- Department of Biochemistry and the Rosenstiel Basic Medical Sciences Research Institute, Brandeis University, Waltham, Massachusetts 02454, United States
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9
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Vasilopoulos G, Moser R, Petersen J, Aktas M, Narberhaus F. Promiscuous phospholipid biosynthesis enzymes in the plant pathogen Pseudomonas syringae. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158926. [PMID: 33766680 DOI: 10.1016/j.bbalip.2021.158926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/09/2021] [Accepted: 03/18/2021] [Indexed: 11/22/2022]
Abstract
Bacterial membranes are primarily composed of phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and cardiolipin (CL). In the canonical PE biosynthesis pathway, phosphatidylserine (PS) is decarboxylated by the Psd enzyme. CL formation typically depends on CL synthases (Cls) using two PG molecules as substrates. Only few bacteria produce phosphatidylcholine (PC), the hallmark of eukaryotic membranes. Most of these bacteria use phospholipid N-methyltransferases to successively methylate PE to PC and/or a PC synthase (Pcs) to catalyze the condensation of choline and CDP-diacylglycerol (CDP-DAG) to PC. In this study, we show that membranes of Pseudomonas species able to interact with eukaryotes contain PE, PG, CL and PC. More specifically, we report on PC formation and a poorly characterized CL biosynthetic pathway in the plant pathogen P. syringae pv. tomato. It encodes a Pcs enzyme responsible for choline-dependent PC biosynthesis. CL formation is catalyzed by a promiscuous phospholipase D (PLD)-type enzyme (PSPTO_0095) that we characterized in vivo and in vitro. Like typical bacterial CL biosynthesis enzymes, it uses PE and PG for CL production. This enzyme is also able to convert PE and glycerol to PG, which is then combined with another PE molecule to synthesize CL. In addition, the enzyme is capable of converting ethanolamine or methylated derivatives into the corresponding phospholipids such as PE both in P. syringae and in E. coli. It can also hydrolyze CDP-DAG to yield phosphatidic acid (PA). Our study adds an example of a promiscuous Cls enzyme able to synthesize a suite of products according to the available substrates.
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Affiliation(s)
| | - Roman Moser
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Jonas Petersen
- Microbial Biology, Ruhr University Bochum, Bochum, Germany
| | - Meriyem Aktas
- Microbial Biology, Ruhr University Bochum, Bochum, Germany.
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10
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Mao S, Zhang Z, Ma X, Tian H, Lu F, Liu Y. Efficient secretion expression of phospholipase D in Bacillus subtilis and its application in synthesis of phosphatidylserine by enzyme immobilization. Int J Biol Macromol 2020; 169:282-289. [PMID: 33333097 DOI: 10.1016/j.ijbiomac.2020.12.103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/05/2020] [Accepted: 12/13/2020] [Indexed: 11/29/2022]
Abstract
Transphosphatidylation catalyzed by phospholipase D has gained increasing attention for producing phosphatidylserine (PS), which can be used in functional food and medicine. In this study, we investigated the effects of six signal peptides on the secretion of PLD (PLDsa) from Streptomyces antibioticus TCCC 21059 in the food-grade GRAS bacterium Bacillus subtilis. It indicated that the optimal signal peptide DacB with an Ala-X-Ala sequence motif at the C-terminus showed the highest secretory expression ability, resulting in increased production of 2.84 U/mL PLDsa. Then PLDsa was immobilized on the epoxy-based carriers, and one of these carriers allowed PLDsa loading of up to 2.7 mg/g. The immobilized PLDsa was more stable over a wide range of pH value (4.5-7.5) and temperature (16 °C-60 °C) than free PLDsa. Subsequently, the synthesis of PS from soybean phosphatidylcholine (PC) was carried out in purely aqueous solution using immobilized PLDsa, leading to a high yield of 65%. The immobilized PLDsa catalyst maintained a relative PS production of 60% after 5 recycles. Notably, the use of toxic solvent was completely eliminated in the whole process, which would be more profitable for the application of PS.
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Affiliation(s)
- Shuhong Mao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, State Key Laboratory of Food Nutrition and Safety, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zhaohui Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, State Key Laboratory of Food Nutrition and Safety, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xiaoyu Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, State Key Laboratory of Food Nutrition and Safety, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Huan Tian
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, State Key Laboratory of Food Nutrition and Safety, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, State Key Laboratory of Food Nutrition and Safety, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, State Key Laboratory of Food Nutrition and Safety, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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11
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Yamamoto Y, Suzuri K, Kunii T, Kurihara H, Miyashita K, Hosokawa M. Preparation of Phosphatidyl-panthenol by phospholipase D-mediated transphosphatidylation and its anti-inflammatory activity on macrophage-like RAW264.7 cells. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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12
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Hasi RY, Miyagi M, Morito K, Ishikawa T, Kawai-Yamada M, Imai H, Fukuta T, Kogure K, Kanemaru K, Hayashi J, Kawakami R, Tanaka T. Glycosylinositol phosphoceramide-specific phospholipase D activity catalyzes transphosphatidylation. J Biochem 2019; 166:441-448. [DOI: 10.1093/jb/mvz056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/12/2019] [Indexed: 12/31/2022] Open
Abstract
AbstractGlycosylinositol phosphoceramide (GIPC) is the most abundant sphingolipid in plants and fungi. Recently, we detected GIPC-specific phospholipase D (GIPC-PLD) activity in plants. Here, we found that GIPC-PLD activity in young cabbage leaves catalyzes transphosphatidylation. The available alcohol for this reaction is a primary alcohol with a chain length below C4. Neither secondary alcohol, tertiary alcohol, choline, serine nor glycerol serves as an acceptor for transphosphatidylation of GIPC-PLD. We also found that cabbage GIPC-PLD prefers GIPC containing two sugars. Neither inositol phosphoceramide, mannosylinositol phosphoceramide nor GIPC with three sugar chains served as substrate. GIPC-PLD will become a useful catalyst for modification of polar head group of sphingophospholipid.
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Affiliation(s)
- Rumana Yesmin Hasi
- Department of Pharmaceutical Health Chemistry, Graduate School of Biomedical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, Japan
| | - Makoto Miyagi
- Department of Pharmaceutical Health Chemistry, Graduate School of Biomedical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, Japan
| | - Katsuya Morito
- Department of Pharmaceutical Health Chemistry, Graduate School of Biomedical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, Japan
| | - Toshiki Ishikawa
- Department of Environmental Science and Technology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Japan
| | - Maki Kawai-Yamada
- Department of Environmental Science and Technology, Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, Japan
| | - Hiroyuki Imai
- Department of Biology, Graduate School of Natural Science, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe, Japan
| | - Tatsuya Fukuta
- Department of Pharmaceutical Health Chemistry, Graduate School of Biomedical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, Japan
| | - Kentaro Kogure
- Department of Pharmaceutical Health Chemistry, Graduate School of Biomedical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, Japan
| | - Kaori Kanemaru
- Department of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, Japan
| | - Junji Hayashi
- Department of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, Japan
| | - Ryushi Kawakami
- Department of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, Japan
| | - Tamotsu Tanaka
- Department of Pharmaceutical Health Chemistry, Graduate School of Biomedical Sciences, Tokushima University, 1-78-1 Shomachi, Tokushima, Japan
- Department of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijosanjima-cho, Tokushima, Japan
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Takaoka R, Kurosaki H, Nakao H, Ikeda K, Nakano M. Formation of asymmetric vesicles via phospholipase D-mediated transphosphatidylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:245-249. [DOI: 10.1016/j.bbamem.2017.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 10/03/2017] [Accepted: 10/09/2017] [Indexed: 10/18/2022]
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Matsumoto Y, Kashiwabara N, Oyama T, Murayama K, Matsumoto H, Sakasegawa SI, Sugimori D. Molecular cloning, heterologous expression, and enzymatic characterization of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. FEBS Open Bio 2016; 6:1113-1130. [PMID: 27833852 PMCID: PMC5095149 DOI: 10.1002/2211-5463.12131] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/09/2016] [Accepted: 09/19/2016] [Indexed: 11/28/2022] Open
Abstract
Lysoplasmalogen (LyPls)‐specific phospholipase D (LyPls‐PLD) is an enzyme that catalyses the hydrolytic cleavage of the phosphoester bond of LyPls, releasing ethanolamine or choline, and 1‐(1‐alkenyl)‐sn‐glycero‐3‐phosphate (lysoplasmenic acid). Little is known about LyPls‐PLD and metabolic pathways of plasmalogen (Pls). Reportedly, Pls levels in human serum/plasma correlate with several diseases such as Alzheimer's disease and arteriosclerosis as well as a variety of biological processes including apoptosis and cell signaling. We identified a LyPls‐PLD from Thermocrispum sp. strain RD004668, and the enzyme was purified, characterized, cloned, and expressed using pET24a(+)/Escherichia coli with a His tag. The enzyme's preferred substrate was choline LyPls (LyPlsCho), with only modest activity toward ethanolamine LyPls. Under optimum conditions (pH 8.0 and 50 °C), steady‐state kinetic analysis for LyPlsCho yielded Km and kcat values of 13.2 μm and 70.6 s−1, respectively. The ORF of LyPls‐PLD gene consisted of 1005 bp coding a 334‐amino‐acid (aa) protein. The deduced aa sequence of LyPls‐PLD showed high similarity to those of glycerophosphodiester phosphodiesterases (GDPDs); however, the substrate specificity differed completely from those of GDPDs and general phospholipase Ds (PLDs). Structural homology modeling showed that two putative catalytic residues (His46, His88) of LyPls‐PLD were highly conserved to GDPDs. Mutational and kinetic analyses suggested that Ala55, Asn56, and Phe211 in the active site of LyPls‐PLD may participate in the substrate recognition. These findings will help to elucidate differences among LyPls‐PLD, PLD, and GDPD with regard to function, substrate recognition mechanism, and biochemical roles. Data Accessibility Thermocrispum sp. strain RD004668 and its 16S rDNA sequence were deposited in the NITE Patent Microorganisms Depositary (NPMD; Chiba, Japan) as NITE BP‐01628 and in the DDBJ database under the accession number AB873024. The nucleotide sequences of the 16S rDNA of strain RD004668 and the LyPls‐PLD gene were deposited in the DDBJ database under the accession numbers AB873024 and AB874601, respectively. Enzyme EC number EC 3.1.4.4
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Affiliation(s)
- Yusaku Matsumoto
- Department of Symbiotic Systems Science and Technology Graduate School of Symbiotic Systems Science and Technology Fukushima University Japan
| | - Nana Kashiwabara
- Department of Symbiotic Systems Science and Technology Graduate School of Symbiotic Systems Science and Technology Fukushima University Japan
| | - Takayuki Oyama
- Department of Symbiotic Systems Science and Technology Graduate School of Symbiotic Systems Science and Technology Fukushima University Japan
| | - Kazutaka Murayama
- Division of Biomedical Measurements and Diagnostics Graduate School of Biomedical Engineering Tohoku University Sendai Japan
| | | | | | - Daisuke Sugimori
- Department of Symbiotic Systems Science and Technology Graduate School of Symbiotic Systems Science and Technology Fukushima University Japan
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Esnault C, Leiber D, Toffano-Nioche C, Tanfin Z, Virolle MJ. Another example of enzymatic promiscuity: the polyphosphate kinase of Streptomyces lividans is endowed with phospholipase D activity. Appl Microbiol Biotechnol 2016; 101:139-145. [DOI: 10.1007/s00253-016-7743-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 10/21/2022]
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16
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Kimura T, Kuwata H, Miyauchi K, Katayama Y, Kayahara N, Sugiuchi H, Matsushima K, Kondo Y, Ishitsuka Y, Irikura M, Irie T. An enzyme combination assay for serum sphingomyelin: Improved specificity through avoiding the interference with lysophosphatidylcholine. Anal Biochem 2016; 498:29-36. [DOI: 10.1016/j.ab.2016.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/31/2015] [Accepted: 01/01/2016] [Indexed: 12/31/2022]
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17
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Djakpa H, Kulkarni A, Barrows-Murphy S, Miller G, Zhou W, Cho H, Török B, Stieglitz K. Identifying New Drug Targets for Potent Phospholipase D Inhibitors: Combining Sequence Alignment, Molecular Docking, and Enzyme Activity/Binding Assays. Chem Biol Drug Des 2016; 87:714-29. [DOI: 10.1111/cbdd.12705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/20/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Helene Djakpa
- STEM Biotechnology Division; Roxbury Community College; Roxbury MA USA
| | - Aditya Kulkarni
- Department of Chemistry; University of Massachusetts Boston; 100 Morrissey Blvd Boston MA 02125 USA
| | | | - Greg Miller
- STEM Biotechnology Division; Roxbury Community College; Roxbury MA USA
| | - Weihong Zhou
- Department of Chemistry; University of Massachusetts Boston; 100 Morrissey Blvd Boston MA 02125 USA
| | - Hyejin Cho
- Department of Chemistry; University of Massachusetts Boston; 100 Morrissey Blvd Boston MA 02125 USA
| | - Béla Török
- Department of Chemistry; University of Massachusetts Boston; 100 Morrissey Blvd Boston MA 02125 USA
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18
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Kulkarni A, Quang P, Curry V, Keyes R, Zhou W, Cho H, Baffoe J, Török B, Stieglitz K. 1,3‐Disubstituted‐4‐Aminopyrazolo [3, 4‐d] Pyrimidines, a New Class of Potent Inhibitors for Phospholipase
D. Chem Biol Drug Des 2014; 84:270-81. [DOI: 10.1111/cbdd.12319] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 12/19/2013] [Accepted: 03/04/2014] [Indexed: 01/05/2023]
Affiliation(s)
- Aditya Kulkarni
- Department of Chemistry University of Massachusetts Boston 100 Morrissey Blvd Boston MA 02125 USA
| | - Phong Quang
- STEM Biotechnology Division Roxbury Community College Roxbury MA 02120 USA
| | - Victoriana Curry
- STEM Biotechnology Division Roxbury Community College Roxbury MA 02120 USA
| | - Renee Keyes
- STEM Biotechnology Division Roxbury Community College Roxbury MA 02120 USA
| | - Weihong Zhou
- Department of Chemistry University of Massachusetts Boston 100 Morrissey Blvd Boston MA 02125 USA
| | - Hyejin Cho
- Department of Chemistry University of Massachusetts Boston 100 Morrissey Blvd Boston MA 02125 USA
| | - Jonathan Baffoe
- Department of Chemistry University of Massachusetts Boston 100 Morrissey Blvd Boston MA 02125 USA
| | - Béla Török
- Department of Chemistry University of Massachusetts Boston 100 Morrissey Blvd Boston MA 02125 USA
| | - Kimberly Stieglitz
- STEM Biotechnology Division Roxbury Community College Roxbury MA 02120 USA
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19
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Pinsolle A, Roy P, Cansell M. Modulation of enzymatic PS synthesis by liposome membrane composition. Colloids Surf B Biointerfaces 2014; 115:157-63. [DOI: 10.1016/j.colsurfb.2013.11.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/29/2013] [Accepted: 11/18/2013] [Indexed: 11/30/2022]
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20
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Maturu P, Vaddi DR, Pannuru P, Nallanchakravarthula V. Modification of Erythrocyte Membrane Proteins, Enzymes and Transport Mechanisms in Chronic Alcoholics: An In vivo and In vitro Study. Alcohol Alcohol 2013; 48:679-86. [DOI: 10.1093/alcalc/agt071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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21
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Zhu X, Fryd M, Wayland BB. Kinetic-mechanistic studies of lipase-polymer micelle binding and catalytic degradation: Enzyme interfacial activation. Polym Degrad Stab 2013. [DOI: 10.1016/j.polymdegradstab.2013.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Phospholipase D as a catalyst: application in phospholipid synthesis, molecular structure and protein engineering. J Biosci Bioeng 2013; 116:271-80. [PMID: 23639419 DOI: 10.1016/j.jbiosc.2013.03.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/12/2013] [Accepted: 03/13/2013] [Indexed: 12/21/2022]
Abstract
Phospholipase D (PLD) is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids (PLs). Many reports exist on PLD-mediated synthesis of natural and tailor-made PLs with functional head groups, from easily available lecithin or phosphatidylcholine. Early studies on PLD-mediated synthesis mainly employed enzymes of plant origin, which were later supplanted by ones from microorganisms, especially actinomycetes. Many PLDs are members of the PLD superfamily, having one or two copies of a signature sequence, HxKxxxxD or HKD motif, in the primary structures. PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism. The catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base. PLD is being engineered to improve its activity and stability, alter head group specificity and further identify catalytically important residues. Since the knowledge on PLD enzymology is constantly expanding, this review focuses on recent advances in the field, regarding PLD-catalyzed synthesis of bioactive PLs, deeper understanding of substrate recognition and binding mechanism, altering substrate specificity, and improving thermostability. We introduced some of our recent results in combination with existing facts to further deepen the story on the nature of this useful enzyme.
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Continuous monitoring of phospholipid vesicle hydrolysis by phospholipase D (PLD) reveals differences in hydrolysis by PLDs from 2 Streptomyces species. Colloids Surf B Biointerfaces 2012; 94:1-6. [DOI: 10.1016/j.colsurfb.2011.11.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 11/21/2011] [Indexed: 11/23/2022]
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24
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Brothers MC, Ho M, Maharjan R, Clemons NC, Bannai Y, Waites MA, Faulkner MJ, Kuhlenschmidt TB, Kuhlenschmidt MS, Blanke SR, Rienstra CM, Wilson BA. Membrane interaction of Pasteurella multocida toxin involves sphingomyelin. FEBS J 2011; 278:4633-48. [PMID: 21951695 PMCID: PMC3220749 DOI: 10.1111/j.1742-4658.2011.08365.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pasteurella multocida toxin (PMT) is an AB toxin that causes pleiotropic effects in targeted host cells. The N-terminus of PMT (PMT-N) is considered to harbor the membrane receptor binding and translocation domains responsible for mediating cellular entry and delivery of the C-terminal catalytic domain into the host cytosol. Previous studies have implicated gangliosides as the host receptors for PMT binding. To gain further insight into the binding interactions involved in PMT binding to cell membranes, we explored the role of various membrane components in PMT binding, utilizing four different approaches: (a) TLC-overlay binding experiments with (125) I-labeled PMT, PMT-N or the C-terminus of PMT; (b) pull-down experiments using reconstituted membrane liposomes with full-length PMT; (c) surface plasmon resonance analysis of PMT-N binding to reconstituted membrane liposomes; (d) and surface plasmon resonance analysis of PMT-N binding to HEK-293T cell membranes without or with sphingomyelinase, phospholipase D or trypsin treatment. The results obtained revealed that, in our experimental system, full-length PMT and PMT-N did not bind to gangliosides, including monoasialogangliosides GM(1) , GM(2) or GM(3) , but instead bound to membrane phospholipids, primarily the abundant sphingophospholipid sphingomyelin or phosphatidylcholine with other lipid components. Collectively, these studies demonstrate the importance of sphingomyelin for PMT binding to membranes and suggest the involvement of a protein co-receptor.
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Affiliation(s)
| | - Mengfei Ho
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Ram Maharjan
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - Nathan C. Clemons
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - Yuka Bannai
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | - Mark A. Waites
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
| | | | | | | | - Steven R. Blanke
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
| | - Chad M. Rienstra
- Department of Chemistry, University of Illinois, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA
| | - Brenda A. Wilson
- Department of Microbiology, University of Illinois, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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25
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Selvy PE, Lavieri RR, Lindsley CW, Brown HA. Phospholipase D: enzymology, functionality, and chemical modulation. Chem Rev 2011; 111:6064-119. [PMID: 21936578 PMCID: PMC3233269 DOI: 10.1021/cr200296t] [Citation(s) in RCA: 267] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Paige E Selvy
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37064, USA
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26
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Mansfeld J, Ulbrich-Hofmann R. Modulation of phospholipase D activity in vitro. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:913-26. [DOI: 10.1016/j.bbalip.2009.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Revised: 03/03/2009] [Accepted: 03/04/2009] [Indexed: 11/30/2022]
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27
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Uesugi Y, Hatanaka T. Phospholipase D mechanism using Streptomyces PLD. Biochim Biophys Acta Mol Cell Biol Lipids 2009; 1791:962-9. [PMID: 19416643 DOI: 10.1016/j.bbalip.2009.01.020] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 01/19/2009] [Accepted: 01/28/2009] [Indexed: 11/17/2022]
Abstract
Phospholipase D (PLD) plays various roles in important biological processes and physiological functions, including cell signaling. Streptomyces PLDs show significant sequence similarity and belong to the PLD superfamily containing two catalytic HKD motifs. These PLDs have conserved catalytic regions and are among the smallest PLD enzymes. Therefore, Streptomyces PLDs are thought to be suitable models for studying the reaction mechanism among PLDs from other sources. Furthermore, Streptomyces PLDs present advantages related to their broad substrate specificity and ease of enzyme preparation. Moreover, the tertiary structure of PLD has been elucidated only for PLD from Streptomyces sp. PMF. This article presents a review of recently reported studies of the mechanism of the catalytic reaction, substrate recognition, substrate specificity and stability of Streptomyces PLD using various protein engineering methods and surface plasmon resonance analysis.
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Affiliation(s)
- Yoshiko Uesugi
- Research Institute for Biological Sciences (RIBS), Kaga-gun, Okayama, Japan
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28
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Design of isoform-selective phospholipase D inhibitors that modulate cancer cell invasiveness. Nat Chem Biol 2009; 5:108-17. [PMID: 19136975 DOI: 10.1038/nchembio.140] [Citation(s) in RCA: 237] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2008] [Accepted: 12/15/2008] [Indexed: 12/29/2022]
Abstract
Phospholipase D (PLD) is an essential enzyme responsible for the production of the lipid second messenger phosphatidic acid. Phosphatidic acid participates in both G protein-coupled receptor and receptor tyrosine kinase signal transduction networks. The lack of potent and isoform-selective inhibitors has limited progress in defining the cellular roles of PLD. We used a diversity-oriented synthetic approach and developed a library of PLD inhibitors with considerable pharmacological characterization. Here we report the rigorous evaluation of that library, which contains highly potent inhibitors, including the first isoform-selective PLD inhibitors. Specific members of this series inhibit isoforms with >100-fold selectivity both in vitro and in cells. A subset of inhibitors was shown to block invasiveness in metastatic breast cancer models. These findings demonstrate the power of diversity-oriented synthesis combined with biochemical assays and mass spectrometric lipid profiling of cellular responses to develop the first isoform-selective PLD inhibitors--a new class of antimetastatic agents.
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29
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Wagner K, Brezesinski G. Phospholipase D activity is regulated by product segregation and the structure formation of phosphatidic acid within model membranes. Biophys J 2007; 93:2373-83. [PMID: 17557794 PMCID: PMC1965428 DOI: 10.1529/biophysj.107.108787] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phospholipase D from Streptomyces chromofuscus (scPLD) hydrolyzes phosphatidylcholines (PC) to produce choline and phosphatidic acid (PA), a lipid messenger molecule within biological membranes. To scrutinize the influence of membrane structure on scPLD activity, three different substrate-containing monolayers are used as model systems: pure dipalmitoylphosphatidylcholine (DPPC) as well as equimolar mixtures of DPPC/n-hexadecanol (C(16)OH) and DPPC/dipalmitoylglycerol (DPG). The activity of scPLD toward these monolayers is tested by infrared reflection-absorption spectroscopy and exhibits different dependencies on surface pressure. For pure DPPC, the catalytic turnover drastically drops above 20 mN/m. On addition of C(16)OH, this strong decrease starts at 5 mN/m. For the DPPC/DPG system, the reaction yield linearly decreases between 5 and 25 mN/m. The difference in scPLD activity is correlated to the phase state of the monolayers as examined by x-ray diffraction, Brewster angle microscopy, and atomic force microscopy. Because the additives C(16)OH and DPG mediate the miscibility of PC and PA, only a basal activity of scPLD is observed toward the mixed systems at higher surface pressures. At pure DPPC monolayers, scPLD is activated after the segregation of initially formed PA. Furthermore, scPLD is inhibited when the lipids in the PA-rich domains adopt an upright orientation. This phenomenon offers a self-regulating mechanism for the concentration of the second messenger PA within biological membranes.
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Affiliation(s)
- Kerstin Wagner
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.
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30
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Brown HA, Henage LG, Preininger AM, Xiang Y, Exton JH. Biochemical Analysis of Phospholipase D. Methods Enzymol 2007; 434:49-87. [DOI: 10.1016/s0076-6879(07)34004-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Uesugi Y, Arima J, Iwabuchi M, Hatanaka T. C-terminal loop of Streptomyces phospholipase D has multiple functional roles. Protein Sci 2006; 16:197-207. [PMID: 17189478 PMCID: PMC2203283 DOI: 10.1110/ps.062537907] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have recently shown that two flexible loops of Streptomyces phospholipase D (PLD) affect the catalytic reaction of the enzyme by a comparative study of chimeric PLDs. Gly188 and Asp191 of PLD from Streptomyces septatus TH-2 (TH-2PLD) were identified as the key amino acid residues involved in the recognition of phospholipids. In the present study, we further investigated the relationship between a C-terminal loop of TH-2PLD and PLD activities to elucidate the reaction mechanism and the recognition of the substrate. By analyzing chimeras and mutants in terms of hydrolytic and transphosphatidylation activities, Ala426 and Lys438 of TH-2PLD were identified as the residues associated with the activities. We found that Gly188 and Asp191 recognized substrate forms, whereas residues Ala426 and Lys438 enhanced transphosphatidylation and hydrolysis activities regardless of the substrate form. By substituting Ala426 and Lys438 with Phe and His, respectively, the mutant showed not only higher activities but also higher thermostability and tolerance against organic solvents. Furthermore, the mutant also improved the selectivity of the transphosphatidylation activity. The residues Ala426 and Lys438 were located in the C-terminal flexible loop of Streptomyces PLD separate from the highly conserved catalytic HxKxxxxD motifs. We demonstrated that this C-terminal loop, which formed the entrance of the active well, has multiple functional roles in Streptomyces PLD.
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Affiliation(s)
- Yoshiko Uesugi
- Research Institute for Biological Sciences-Okayama, 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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32
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Henage LG, Exton JH, Brown HA. Kinetic analysis of a mammalian phospholipase D: allosteric modulation by monomeric GTPases, protein kinase C, and polyphosphoinositides. J Biol Chem 2006; 281:3408-17. [PMID: 16339153 PMCID: PMC3800466 DOI: 10.1074/jbc.m508800200] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In mammalian cells, phospholipase D activity is tightly regulated by diverse cellular signals, including hormones, neurotransmitters, and growth factors. Multiple signaling pathways converge upon phospholipase D to modulate cellular actions, such as cell growth, shape, and secretion. We examined the kinetics of protein kinase C and G-protein regulation of mammalian phospholipase D1 (PLD1) in order to better understand interactions between PLD1 and its regulators. Activation by Arf-1, RhoA, Rac1, Cdc42, protein kinase Calpha, and phosphatidylinositol 4,5-bisphosphate displayed surface dilution kinetics, but these effectors modulated different kinetic parameters. PKCalpha activation of PLD1 involves N- and C-terminal PLD domains. Rho GTPases were binding activators, enhancing the catalytic efficiency of a purified PLD1 catalytic domain via effects on Km. Arf-1, a catalytic activator, stimulated PLD1 by enhancing the catalytic constant, kcat. A kinetic description of PLD1 activation by multiple modulators reveals a mechanism for apparent synergy between activators. Synergy was observed only when PLD1 was simultaneously stimulated by a binding activator and a catalytic activator. Surprisingly, synergistic activation was steeply dependent on phosphatidylinositol 4,5-bisphosphate and phosphatidylcholine. Together, these findings suggest a role for PLD1 as a signaling node, in which integration of convergent signals occurs within discrete locales of the cellular membrane.
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Affiliation(s)
- Lee G. Henage
- Department of Pharmacology, Institute for Chemical Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232-6600
| | - John H. Exton
- Department of Pharmacology, Institute for Chemical Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232-6600
| | - H. Alex Brown
- Department of Pharmacology, Institute for Chemical Biology, and Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232-6600
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Phospholipases: Occurrence and production in microorganisms, assay for high-throughput screening, and gene discovery from natural and man-made diversity. J AM OIL CHEM SOC 2005. [DOI: 10.1007/s11746-005-1131-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Uesugi Y, Mori K, Arima J, Iwabuchi M, Hatanaka T. Recognition of phospholipids in Streptomyces phospholipase D. J Biol Chem 2005; 280:26143-51. [PMID: 15899903 DOI: 10.1074/jbc.m414319200] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To investigate the contribution of amino acid residues to the enzyme reaction of Streptomyces phospholipase D (PLD), we constructed a chimeric gene library between two highly homologous plds, which indicated different activity in transphosphatidylation, using RIBS (repeat-length independent and broad spectrum) in vivo DNA shuffling. By comparing the activities of chimeras, six candidate residues related to transphosphatidylation activity were shown. Based on the above result, we constructed several mutants to identify the key residues involved in the recognition of phospholipids. By kinetic analysis, we identified that Gly188 and Asp191 of PLD from Streptomyces septatus TH-2, which are not present in the highly conserved catalytic HXKXXXXD (HKD) motifs, are key amino acid residues related to the transphosphatidylation activity. To investigate the role of two residues in the recognition of phospholipids, the effects of these residues on binding to substrates were analyzed by surface plasmon spectroscopy. The result suggests that Gly188 and Asp191 are involved in the recognition of phospholipids in correlation with the N-terminal HKD motif. Furthermore, this study also provides experimental evidence that the N-terminal HKD motif contains the catalytic nucleophile, which attacks the phosphatidyl group of the substrate.
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Affiliation(s)
- Yoshiko Uesugi
- Research Institute for Biological Sciences, Okayama, 7549-1 Kibichuo-cho, Kaga-gun, Okayama 716-1241, Japan
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35
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Zambonelli C, Roberts MF. Non-HKD Phospholipase D Enzymes: New Players in Phosphatidic Acid Signaling? ACTA ACUST UNITED AC 2005; 79:133-81. [PMID: 16096028 DOI: 10.1016/s0079-6603(04)79003-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
- Carlo Zambonelli
- Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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Yang H, Roberts MF. Expression and characterization of a heterodimer of Streptomyces chromofuscus phospholipase D. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2004; 1703:43-51. [PMID: 15588701 DOI: 10.1016/j.bbapap.2004.09.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2004] [Revised: 09/10/2004] [Accepted: 09/14/2004] [Indexed: 11/20/2022]
Abstract
Streptomyces chromofuscus phospholipase D (PLD) is secreted by the bacterium and proteolytically cleaved to a more active form (PLD(37/18)) where the two parts of the molecule are still tightly associated. Based on previous sequencing results of authentic PLD(37/18), we have constructed a vector consisting of separate ORFs for the N-terminal and C-terminal portions of S. chromofuscus PLD and overexpressed active heterodimeric PLD. Neither fragment cloned separately folded properly. The identity of each peptide was confirmed by peptide-mass fingerprinting with MALDI-TOF mass spectrometry. The recombinant complex had a specific activity about six times higher than that of the recombinant intact PLD enzyme and was no longer activated by phosphatidic acid (PA). Phosphotransferase activity, binding affinity to phospholipid vesicles, loss of product activation, pH profile and pH-related Ca(2+) activation and inhibition were comparable to authentic PLD(37/18) purified from S. chromofuscus growth medium. PLD(37) alone could also be isolated; the enzyme was active but not as stable as PLD(37/18). These experimental results strongly support the hypothesis that the C-terminal peptide is necessary for correct folding and insertion of catalytic metal ions. However, they suggest the ligands involved in Fe(3+) coordination must be altered upon cleavage of the protein. Asp389, in the C-terminal fragment, whose replacement impairs Fe(3+) binding to the protein, must be replaced by another ligand, since the N-terminal fragment, once folded, is active. In the process of cloning the two peptides, the complete signal sequence for this protein was also determined. The signal peptide of S. chromofuscus PLD enzyme contained a twin arginine motif suggesting that S. chromofuscus PLD, like Bacillus subtilis phoD, is most likely secreted by the TAT translocation pathway under the transcriptional control of the pho regulon.
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Affiliation(s)
- Hongying Yang
- Merkert Chemistry Center, Boston College, 2609 Beacon Street, Chestnut Hill, MA 02167, USA
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37
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Leiros I, McSweeney S, Hough E. The reaction mechanism of phospholipase D from Streptomyces sp. strain PMF. Snapshots along the reaction pathway reveal a pentacoordinate reaction intermediate and an unexpected final product. J Mol Biol 2004; 339:805-20. [PMID: 15165852 DOI: 10.1016/j.jmb.2004.04.003] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2003] [Revised: 03/25/2004] [Accepted: 04/06/2004] [Indexed: 11/27/2022]
Abstract
Almost all enzyme-catalysed phosphohydrolytic or phosphoryl transfer reactions proceed through a five-coordinated phosphorus transition state. This is also true for the phospholipase D superfamily of enzymes, where the active site usually is made up of two identical sequence repeats of an HKD motif, positioned around an approximate 2-fold axis, where the histidine and lysine residues are essential for catalysis. An almost complete reaction pathway has been elucidated by a series of experiments where crystals of phospholipase D from Streptomyces sp. strain PMF (PLD(PMF)) were soaked for different times with (i) a soluble poor, short-chained phospholipid substrate and (ii) with a product. The various crystal structures were determined to a resolution of 1.35-1.75 A for the different time-steps. Both substrate and product-structures were determined in order to identify the different reaction states and to examine if the reaction actually terminated on formation of phosphatidic acid (the true product of phospholipase D action) or could proceed even further. The results presented support the theory that the phospholipase D superfamily shares a common reaction mechanism, although different family members have very different substrate preferences and perform different catalytic reactions. Results also show that the reaction proceeds via a phosphohistidine intermediate and provide unambiguous identification of a catalytic water molecule, ideally positioned for apical attack on the phosphorus and consistent with an associative in-line phosphoryl transfer reaction. In one of the experiments an apparent five-coordinate phosphorus transition state is observed.
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Affiliation(s)
- Ingar Leiros
- Department of Chemistry, Faculty of Science, University of Tromsø, Tromsø, Norway.
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Raymond AC, Rideout MC, Staker B, Hjerrild K, Burgin AB. Analysis of human tyrosyl-DNA phosphodiesterase I catalytic residues. J Mol Biol 2004; 338:895-906. [PMID: 15111055 DOI: 10.1016/j.jmb.2004.03.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 02/28/2004] [Accepted: 03/02/2004] [Indexed: 10/26/2022]
Abstract
Tyrosyl-DNA phosphodiesterase I (Tdp1) is involved in the repair of DNA lesions created by topoisomerase I in vivo. Tdp1 is a member of the phospholipase D (PLD) superfamily of enzymes and hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and free tyrosine in vitro. Here, we use synthetic 3'-(4-nitro)phenyl, 3'-(4-methyl)phenyl, and 3'-tyrosine phosphate oligonucleotides to study human Tdp1. Kinetic analysis of human Tdp1 (hTdp1) shows that the enzyme has nanomolar affinity for all three substrates and the overall in vitro reaction is diffusion-limited. Analysis of active-site mutants using these modified substrates demonstrates that hTdp1 uses an acid/base catalytic mechanism. The results show that histidine 493 serves as the general acid during the initial transesterification, in agreement with hypotheses based on previous crystal structure models. The results also argue that lysine 495 and asparagine 516 participate in the general acid reaction, and the analysis of crystal structures suggests that these residues may function in a proton relay. Together with previous crystal structure data, the new functional data provide a mechanistic understanding of the conserved histidine, lysine and asparagine residues found among all PLD family members.
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Affiliation(s)
- Amy C Raymond
- Biology Department, San Diego State University, CA 98182-4614, USA
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Zhang X, Wehbi H, Roberts MF. Cross-linking phosphatidylinositol-specific phospholipase C traps two activating phosphatidylcholine molecules on the enzyme. J Biol Chem 2004; 279:20490-500. [PMID: 14996830 DOI: 10.1074/jbc.m401016200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (PI-PLC), a bacterial model for the catalytic domain of mammalian PI-PLC enzymes, was cross-linked by 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride to probe for the aggregation and/or conformational changes of PI-PLC when bound to activating phosphatidylcholine (PC) interfaces. Dimers and higher order multimers (up to 31% of the total protein when cross-linked at pH 7) were observed when the enzyme was cross-linked in the presence of PC vesicles. Aggregates were also detected with PI-PLC bound to diheptanoyl-PC (diC(7)PC) micelles, although the fraction of cross-linked multimers (19% at pH 7) was lower than when the enzyme was cross-linked in the presence of vesicles. PI-PLC cross-linked in the presence of a diC(7)PC interface exhibited an enhanced specific activity for PI cleavage. The extent of this cross-linking-enhanced activation was reduced in PI-PLC mutants lacking either tryptophan in the rim (W47A and W242A) of this (betaalpha)(8)-barrel protein. The higher activity of the native protein cross-linked in the presence of diC(7)PC correlated with an increased affinity of the protein for two diC(7)PC molecules as detected by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. In contrast to wild type protein, W47A and W242A had only a single diC(7)PC tightly associated when cross-linked in the presence of that activator molecule. These results indicate that (i) each rim tryptophan residue is involved in binding a PC molecule at interfaces, (ii) the affinity of the enzyme for an activating PC molecule is enhanced when the protein is bound to a surface, and (iii) this conformation of the enzyme with at least two PC bound that is stabilized by chemical cross-linking interacts more effectively with activating interfaces, leading to higher observed specific activities for the phosphotransferase reaction.
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Affiliation(s)
- Xin Zhang
- Merkert Chemistry Center, Boston College, Chestnut Hill, MA 02467, USA
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Zambonelli C, Casali M, Roberts MF. Mutagenesis of Putative Catalytic and Regulatory Residues of Streptomyces chromofuscus Phospholipase D Differentially Modifies Phosphatase and Phosphodiesterase Activities. J Biol Chem 2003; 278:52282-9. [PMID: 14557260 DOI: 10.1074/jbc.m310252200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phospholipase D from Streptomyces chromofuscus (sc-PLD) is a member of the diverse family of metallo-phosphodiesterase/phosphatase enzymes that also includes purple acid phosphatases, protein phosphatases, and nucleotide phosphodiesterases. Whereas iron is an essential cofactor for scPLD activity, Mn2+ is also found in the enzyme. A third metal ion, Ca2+, has been shown to enhance scPLD catalytic activity although it is not an essential cofactor. Sequence alignment of scPLD with known phosphodiesterases and phosphatases requiring metal ions suggested that His-212, Glu-213, and Asp-389 could be involved in Mn2+ binding. H212A, E213A, and D389A were prepared to test this hypothesis. These three mutant enzymes and wild type scPLD show similar metal content but considerably different catalytic properties, suggesting different roles for each residue. His-212 appears involved in binding the phosphate group of substrates, whereas Glu-213 acts as a ligand for Ca2+. D389A showed a greatly reduced phosphodiesterase activity but almost unaltered ability to hydrolyze the phosphate group in p-nitrophenyl phosphate suggesting it had a critical role in aligning groups at the active site to control phosphodiesterase versus phosphatase activities. We propose a model for substrate and cofactor binding to the catalytic site of scPLD based on these results and on sequence alignment to purple acid phosphatases of known structure.
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Affiliation(s)
- Carlo Zambonelli
- Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02467, USA
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