1
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Liu Q, Zhang Q, Xue H, Bi Y, Yang X, Zong Y, Liu Z, Dov P. Effects of TrPLDs on the pathogenicity of Trichothecium roseum infected apple fruit. Food Microbiol 2024; 121:104496. [PMID: 38637067 DOI: 10.1016/j.fm.2024.104496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/03/2024] [Accepted: 02/16/2024] [Indexed: 04/20/2024]
Abstract
Phospholipase D plays a critical regulatory role in the pathogenicity of filamentous fungi. However, the molecular mechanism of PLD regulating the pathogenicity of filamentous fungi has not been reported. In this research, the previously constructed TrPLD1 and TrPLD2 (TrPLDs) mutants were used as test strains. Firstly, the function of TrPLDs in Trichothecium roseum was studied. Then, the effects of TrPLDs on the pathogenicity of T. roseum and the quality of the inoculated apples were verified. The results suggested that the deletion of TrPLD1 delayed the spore germination of ΔTrPLD1 and inhibited germ tube elongation by down-regulating the expressions of TrbrlA, TrabaA and TrwetA. By down-regulating the extracellular enzyme-coding gene expressions, ΔTrPLD1 inhibited the degradation of apple fruit cell wall and the change of fatty acid content during infection, reduced the cell membrane permeability and malondialdehyde (MDA) content of apple fruit, thereby maintaining the integrity of fruit cell membrane, and reduced the pathogenicity of ΔTrPLD1 to apple and kept the quality of apple. However, ΔTrPLD2 did not have a significant effect on the infection process of apple fruit by the pathogen.
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Affiliation(s)
- Qili Liu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Qianqian Zhang
- College of Science, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Huali Xue
- College of Science, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Yang Bi
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, PR China.
| | - Xi Yang
- College of Science, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Yuanyuan Zong
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Zhiguang Liu
- College of Science, Gansu Agricultural University, Lanzhou 730070, PR China
| | - Prusky Dov
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou 730070, PR China; Department of Postharvest Science of Fresh Produce, Agricultural Research Organization, Rishon LeZion, 7505101, Israel
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2
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Wang Y, Wakelam MJO, Bankaitis VA, McDermott MI. The wide world of non-mammalian phospholipase D enzymes. Adv Biol Regul 2024; 91:101000. [PMID: 38081756 DOI: 10.1016/j.jbior.2023.101000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 02/25/2024]
Abstract
Phospholipase D (PLD) hydrolyses phosphatidylcholine (PtdCho) to produce free choline and the critically important lipid signaling molecule phosphatidic acid (PtdOH). Since the initial discovery of PLD activities in plants and bacteria, PLDs have been identified in a diverse range of organisms spanning the taxa. While widespread interest in these proteins grew following the discovery of mammalian isoforms, research into the PLDs of non-mammalian organisms has revealed a fascinating array of functions ranging from roles in microbial pathogenesis, to the stress responses of plants and the developmental patterning of flies. Furthermore, studies in non-mammalian model systems have aided our understanding of the entire PLD superfamily, with translational relevance to human biology and health. Increasingly, the promise for utilization of non-mammalian PLDs in biotechnology is also being recognized, with widespread potential applications ranging from roles in lipid synthesis, to their exploitation for agricultural and pharmaceutical applications.
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Affiliation(s)
- Y Wang
- Department of Cell Biology & Genetics, Texas A&M Health Science Center, College Station, TX, 77843, USA; Department of Microbiology, University of Washington, Seattle, WA98109, USA
| | - M J O Wakelam
- Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - V A Bankaitis
- Department of Cell Biology & Genetics, Texas A&M Health Science Center, College Station, TX, 77843, USA; Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA; Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - M I McDermott
- Department of Cell Biology & Genetics, Texas A&M Health Science Center, College Station, TX, 77843, 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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Hu R, Wu L, Cheng Q, Chen S, Shen T, Lan D, Ma Y, Wang Y. Structural variations and phospholipid binding characteristics of Streptomyces klenkii phospholipase D at the lipid-water interface. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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5
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Fan R, Zhao F, Gong Z, Chen Y, Yang B, Zhou C, Zhang J, Du Z, Wang X, Yin P, Guo L, Liu Z. Insights into the mechanism of phospholipid hydrolysis by plant non-specific phospholipase C. Nat Commun 2023; 14:194. [PMID: 36635324 PMCID: PMC9837106 DOI: 10.1038/s41467-023-35915-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
Non-specific phospholipase C (NPC) hydrolyzes major membrane phospholipids to release diacylglycerol (DAG), a potent lipid-derived messenger regulating cell functions. Despite extensive studies on NPCs reveal their fundamental roles in plant growth and development, the mechanistic understanding of phospholipid-hydrolyzing by NPCs, remains largely unknown. Here we report the crystal structure of Arabidopsis NPC4 at a resolution of 2.1 Å. NPC4 is divided into a phosphoesterase domain (PD) and a C-terminal domain (CTD), and is structurally distinct from other characterized phospholipases. The previously uncharacterized CTD is indispensable for the full activity of NPC4. Mechanistically, CTD contributes NPC4 activity mainly via CTDα1-PD interaction, which ultimately stabilizes the catalytic pocket in PD. Together with a series of structure-guided biochemical studies, our work elucidates the structural basis and provides molecular mechanism of phospholipid hydrolysis by NPC4, and adds new insights into the members of phospholipase family.
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Affiliation(s)
- Ruyi Fan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Fen Zhao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhou Gong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Yanke Chen
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Bao Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chen Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhangmeng Du
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuemin Wang
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA.,Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. .,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
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6
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Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA. Nat Commun 2022; 13:5979. [PMID: 36216841 PMCID: PMC9550806 DOI: 10.1038/s41467-022-33690-2] [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: 02/12/2022] [Accepted: 09/28/2022] [Indexed: 11/08/2022] Open
Abstract
PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids-the main component of cell membranes-and assists the invasion of the opportunistic pathogen Pseudomonas aeruginosa. As a cognate immunity protein, PA3488 can inhibit the activity of PldA to avoid self-toxicity. However, the precise inhibitory mechanism remains elusive. We determine the crystal structures of full-length and truncated PldA and the cryogenic electron microscopy structure of the PldA-PA3488 complex. Structural analysis reveals that there are different intermediates of PldA between the "open" and "closed" states of the catalytic pocket, accompanied by significant conformational changes in the "lid" region and the peripheral helical domain. Through structure-based mutational analysis, we identify the key residues responsible for the enzymatic activity of PldA. Together, these data provide an insight into the molecular mechanisms of PldA invasion and its neutralization by PA3488, aiding future design of PLD-targeted inhibitors and drugs.
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7
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Wang F, Mao X, Deng F, Cui R, Li L, Liu S, Yang B, Lan D, Wang Y. A New Phospholipase D from Moritella sp. JT01: Biochemical Characterization, Crystallization and Application in the Synthesis of Phosphatidic Acid. Int J Mol Sci 2022; 23:ijms231911633. [PMID: 36232934 PMCID: PMC9570413 DOI: 10.3390/ijms231911633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 09/11/2022] [Accepted: 09/15/2022] [Indexed: 11/07/2022] Open
Abstract
A new phospholipase D from marine Moritella sp. JT01 (MsPLD) was recombinantly expressed and biochemically characterized. The optimal reaction temperature and pH of MsPLD were determined to be 35 °C and 8.0. MsPLD was stable at a temperature lower than 35 °C, and the t1/2 at 4 °C was 41 days. The crystal structure of apo-MsPLD was resolved and the functions of a unique extra loop segment on the enzyme activity were characterized. The results indicated that a direct deletion or fastening of the extra loop segment by introducing disulfide bonds both resulted in a complete loss of its activity. The results of the maximum insertion pressure indicated that the deletion of the extra loop segment significantly decreased MsPLD’s interfacial binding properties to phospholipid monolayers. Finally, MsPLD was applied to the synthesis of phosphatidic acid by using a biphasic reaction system. Under optimal reaction conditions, the conversion rate of phosphatidic acid reached 86%. The present research provides a foundation for revealing the structural–functional relationship of this enzyme.
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Affiliation(s)
- Fanghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Xuejing Mao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Fuli Deng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Ruiguo Cui
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Lilang Li
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Siyu Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Bo Yang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Correspondence: (D.L.); (Y.W.); Tel.: +86-20-8711-3848 (D.L.); +86-20-8711-3842 (Y.W.)
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Correspondence: (D.L.); (Y.W.); Tel.: +86-20-8711-3848 (D.L.); +86-20-8711-3842 (Y.W.)
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8
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de Kok NAW, Driessen AJM. The catalytic and structural basis of archaeal glycerophospholipid biosynthesis. Extremophiles 2022; 26:29. [PMID: 35976526 PMCID: PMC9385802 DOI: 10.1007/s00792-022-01277-w] [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: 03/21/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Archaeal glycerophospholipids are the main constituents of the cytoplasmic membrane in the archaeal domain of life and fundamentally differ in chemical composition compared to bacterial phospholipids. They consist of isoprenyl chains ether-bonded to glycerol-1-phosphate. In contrast, bacterial glycerophospholipids are composed of fatty acyl chains ester-bonded to glycerol-3-phosphate. This largely domain-distinguishing feature has been termed the “lipid-divide”. The chemical composition of archaeal membranes contributes to the ability of archaea to survive and thrive in extreme environments. However, ether-bonded glycerophospholipids are not only limited to extremophiles and found also in mesophilic archaea. Resolving the structural basis of glycerophospholipid biosynthesis is a key objective to provide insights in the early evolution of membrane formation and to deepen our understanding of the molecular basis of extremophilicity. Many of the glycerophospholipid enzymes are either integral membrane proteins or membrane-associated, and hence are intrinsically difficult to study structurally. However, in recent years, the crystal structures of several key enzymes have been solved, while unresolved enzymatic steps in the archaeal glycerophospholipid biosynthetic pathway have been clarified providing further insights in the lipid-divide and the evolution of early life.
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Affiliation(s)
- Niels A W de Kok
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, Groningen, The Netherlands.
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9
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Barriga HM, Pence IJ, Holme MN, Doutch JJ, Penders J, Nele V, Thomas MR, Carroni M, Stevens MM. Coupling Lipid Nanoparticle Structure and Automated Single-Particle Composition Analysis to Design Phospholipase-Responsive Nanocarriers. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2200839. [PMID: 35358374 PMCID: PMC7615489 DOI: 10.1002/adma.202200839] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Lipid nanoparticles (LNPs) are versatile structures with tunable physicochemical properties that are ideally suited as a platform for vaccine delivery and RNA therapeutics. A key barrier to LNP rational design is the inability to relate composition and structure to intracellular processing and function. Here Single Particle Automated Raman Trapping Analysis (SPARTA) is combined with small-angle X-ray and neutron scattering (SAXS/SANS) techniques to link LNP composition with internal structure and morphology and to monitor dynamic LNP-phospholipase D (PLD) interactions. This analysis demonstrates that PLD, a key intracellular trafficking mediator, can access the entire LNP lipid membrane to generate stable, anionic LNPs. PLD activity on vesicles with matched amounts of enzyme substrate is an order of magnitude lower, indicating that the LNP lipid membrane structure can be used to control enzyme interactions. This represents an opportunity to design enzyme-responsive LNP solutions for stimuli-responsive delivery and diseases where PLD is dysregulated.
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Affiliation(s)
- Hanna M.G. Barriga
- Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - Isaac J. Pence
- Department of Materials, Department of Bioengineering,and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Margaret N. Holme
- Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm SE-171 77, Sweden
| | - James J. Doutch
- ISIS Neutron and Muon Source, STFC, Rutherford Appleton Laboratory Didcot OX11 ODE, UK
| | - Jelle Penders
- Department of Materials, Department of Bioengineering,and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Valeria Nele
- Department of Materials, Department of Bioengineering,and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Michael R. Thomas
- Department of Materials, Department of Bioengineering,and Institute of Biomedical Engineering, Imperial College London, London SW7 2AZ, UK
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory Stockholm University, Stockholm 171 65, Sweden
| | - Molly M. Stevens
- Department of Medical Biochemistry and Biophysics Karolinska Institutet, Stockholm SE-171 77, Sweden
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10
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May-Dracka TL, Gao F, Hopkins BT, Hronowski X, Chen T, Chodaparambil JV, Metrick CM, Cullivan M, Enyedy I, Kaliszczak M, Kankel MW, Marx I, Michell-Robinson MA, Murugan P, Kumar PR, Rooney M, Schuman E, Sen A, Wang T, Ye T, Peterson EA. Discovery of Phospholipase D Inhibitors with Improved Drug-like Properties and Central Nervous System Penetrance. ACS Med Chem Lett 2022; 13:665-673. [PMID: 35450377 PMCID: PMC9014516 DOI: 10.1021/acsmedchemlett.1c00682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/01/2022] [Indexed: 11/30/2022] Open
Abstract
Phospholipase D (PLD) is a phospholipase enzyme responsible for hydrolyzing phosphatidylcholine into the lipid signaling molecule, phosphatidic acid, and choline. From a therapeutic perspective, PLD has been implicated in human cancer progression as well as a target for neurodegenerative diseases, including Alzheimer's. Moreover, knockdown of PLD rescues the ALS phenotype in multiple Drosophila models of ALS (amyotrophic lateral sclerosis) and displays modest motor benefits in an SOD1 ALS mouse model. To further validate whether inhibiting PLD is beneficial for the treatment of ALS, a brain penetrant small molecule inhibitor with suitable PK properties to test in an ALS animal model is needed. Using a combination of ligand-based drug discovery and structure-based design, a dual PLD1/PLD2 inhibitor was discovered that is single digit nanomolar in the Calu-1 cell assay and has suitable PK properties for in vivo studies. To capture the in vivo measurement of PLD inhibition, a transphosphatidylation pharmacodynamic LC-MS assay was developed, in which a dual PLD1/PLD2 inhibitor was found to reduce PLD activity by 15-20-fold.
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11
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Tei R, Baskin JM. Click chemistry and optogenetic approaches to visualize and manipulate phosphatidic acid signaling. J Biol Chem 2022; 298:101810. [PMID: 35276134 PMCID: PMC9006657 DOI: 10.1016/j.jbc.2022.101810] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/12/2022] [Accepted: 02/19/2022] [Indexed: 12/28/2022] Open
Abstract
The simple structure of phosphatidic acid (PA) belies its complex biological functions as both a key phospholipid biosynthetic intermediate and a potent signaling molecule. In the latter role, PA controls processes including vesicle trafficking, actin dynamics, cell growth, and migration. However, experimental methods to decode the pleiotropy of PA are sorely lacking. Because PA metabolism and trafficking are rapid, approaches to accurately visualize and manipulate its levels require high spatiotemporal precision. Here, we describe recent efforts to create a suite of chemical tools that enable imaging and perturbation of PA signaling. First, we describe techniques to visualize PA production by phospholipase D (PLD) enzymes, which are major producers of PA, called Imaging Phospholipase D Activity with Clickable Alcohols via Transphosphatidylation (IMPACT). IMPACT harnesses the ability of endogenous PLD enzymes to accept bioorthogonally tagged alcohols in transphosphatidylation reactions to generate functionalized reporter lipids that are subsequently fluorescently tagged via click chemistry. Second, we describe two light-controlled approaches for precisely manipulating PA signaling. Optogenetic PLDs use light-mediated heterodimerization to recruit a bacterial PLD to desired organelle membranes, and photoswitchable PA analogs contain azobenzene photoswitches in their acyl tails, enabling molecular shape and bioactivity to be controlled by light. We highlight select applications of these tools for studying GPCR-Gq signaling, discovering regulators of PLD signaling, tracking intracellular lipid transport pathways, and elucidating new oncogenic signaling roles for PA. We envision that these chemical tools hold promise for revealing many new insights into lipid signaling pathways.
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Affiliation(s)
- Reika Tei
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, USA.
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12
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Production of a High-Phosphatidylserine Lecithin That Synergistically Inhibits Lipid Oxidation with α-Tocopherol in Oil-in-Water Emulsions. Foods 2022; 11:foods11071014. [PMID: 35407101 PMCID: PMC8997968 DOI: 10.3390/foods11071014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/07/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Phosphatidylserine (PS) was shown to work synergistically with tocopherols to extend the shelf life of oil-in-water emulsions. However, the high cost of PS prevents it from being used as a food additive. This work investigated the potential use of a high-PS enzyme-modified lecithin to be used along with α-tocopherol to extend the lag phase of oil-in-water emulsions stabilized using Tween 20. Phospholipase D from Streptomyces sp. and L-serine were used to modify lecithin to increase the PS concentration. Enzyme activity was optimized as a function of pH and temperature using high-phosphatidylcholine (PC) soybean, sunflower, or egg lecithins. Under optimal conditions, the final PS concentrations were 92.0 ± 0.01%, 88.0 ± 0.01%, and 63.0 ± 0.02% for high-PC soybean, sunflower, and egg lecithins, respectively. α-Tocopherol (3.0 µmol/kg emulsion) alone increased the lag phase of hydroperoxide and hexanal lag phases by 3 and 4 days compared to the control. Phospholipase-D-modified high-PS soy lecithin increased hydroperoxide and hexanal lag phases by 3 and 4 days, respectively. The addition of phospholipase-D-modified high-PS sunflower and egg lecithin did not have any considerable effects on lag phases compared to the control. The combination of phospholipase-D-modified high-PS lecithins (15.0 µmol/kg emulsion) and α-tocopherol (3.0 µmol/kg emulsion) increased the antioxidant activity of α-tocopherol, increasing the hydroperoxide and hexanal lag phase by 6 and 9 days for soy, 5 and 7 days for sunflower, and 4 and 6 days for egg lecithin, respectively. All phospholipase-D-modified high-PS lecithin−tocopherol combinations resulted in synergistic antioxidant activity (interaction index > 1.0), except for α-tocopherol and high-PS egg lecithin, which showed an additive effect. This research showed that the combination of enzyme-modified high-PS lecithin and α-tocopherol could be an effective and commercially viable clean label antioxidant strategy to control lipid oxidation in emulsions.
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13
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Zhang P, Gong JS, Qin J, Li H, Hou HJ, Zhang XM, Xu ZH, Shi JS. Phospholipids (PLs) know-how: exploring and exploiting phospholipase D for its industrial dissemination. Crit Rev Biotechnol 2021; 41:1257-1278. [PMID: 33985392 DOI: 10.1080/07388551.2021.1921690] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 12/26/2020] [Accepted: 02/24/2021] [Indexed: 10/21/2022]
Abstract
Owing to their numerous nutritional and bioactive functions, phospholipids (PLs), which are major components of biological membranes in all living organisms, have been widely applied as nutraceuticals, food supplements, and cosmetic ingredients. To date, PLs are extracted solely from soybean or egg yolk, despite the diverse market demands and high cost, owing to a tedious and inefficient manufacturing process. A microbial-based manufacturing process, specifically phospholipase D (PLD)-based biocatalysis and biotransformation process for PLs, has the potential to address several challenges associated with the soybean- or egg yolk-based supply chain. However, poor enzyme properties and inefficient microbial expression systems for PLD limit their wide industrial dissemination. Therefore, sourcing new enzyme variants with improved properties and developing advanced PLD expression systems are important. In the present review, we systematically summarize recent achievements and trends in the discovery, their structural properties, catalytic mechanisms, expression strategies for enhancing PLD production, and its multiple applications in the context of PLs. This review is expected to assist researchers to understand current advances in this field and provide insights for further molecular engineering efforts toward PLD-mediated bioprocessing.
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Affiliation(s)
- Peng Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Jiufu Qin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Hui Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Hai-Juan Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Xiao-Mei Zhang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, P. R. China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi, P. R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, P. R. China
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14
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Hu R, Cui R, Lan D, Wang F, Wang Y. Acyl Chain Specificity of Marine Streptomyces klenkii PhosPholipase D and Its Application in Enzymatic Preparation of Phosphatidylserine. Int J Mol Sci 2021; 22:10580. [PMID: 34638918 PMCID: PMC8508628 DOI: 10.3390/ijms221910580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 02/04/2023] Open
Abstract
Mining of phospholipase D (PLD) with altered acyl group recognition except its head group specificity is also useful in terms of specific acyl size phospholipid production and as diagnostic reagents for quantifying specific phospholipid species. Microbial PLDs from Actinomycetes, especially Streptomyces, best fit this process requirements. In the present studies, a new PLD from marine Streptomyces klenkii (SkPLD) was purified and biochemically characterized. The optimal reaction temperature and pH of SkPLD were determined to be 60 °C and 8.0, respectively. Kinetic analysis showed that SkPLD had the relatively high catalytic efficiency toward phosphatidylcholines (PCs) with medium acyl chain length, especially 12:0/12:0-PC (67.13 S-1 mM-1), but lower catalytic efficiency toward PCs with long acyl chain (>16 fatty acids). Molecular docking results indicated that the different catalytic efficiency was related to the increased steric hindrance of long acyl-chains in the substrate-binding pockets and differences in hydrogen-bond interactions between the acyl chains and substrate-binding pockets. The enzyme displayed suitable transphosphatidylation activity and the reaction process showed 26.18% yield with L-serine and soybean PC as substrates. Present study not only enriched the PLD enzyme library but also provide guidance for the further mining of PLDs with special phospholipids recognition properties.
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Affiliation(s)
| | | | | | - Fanghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; (R.H.); (R.C.); (D.L.)
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; (R.H.); (R.C.); (D.L.)
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15
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Li M, Zhou Y, Duan X, Zhou L, Zhang T. Characterization of a phospholipase D from Streptomyces cinnamoneum SK43.003 suitable for phosphatidylserine synthesis. Biotechnol Appl Biochem 2021; 69:1917-1928. [PMID: 34585426 DOI: 10.1002/bab.2257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/19/2021] [Indexed: 11/11/2022]
Abstract
A phospholipase D high producing strain with transphosphatidylation activity that is suitable for phosphatidylserine synthesis was screened by our laboratory and named as Streptomyces cinnamoneum SK43.003. The enzyme structural and biochemical properties were investigated using the molecular biology method. A 1521-bp fragment of the phospholipase D gene from Streptomyces cinnamoneum SK43.003 was amplified by PCR and encoded for 506 amino acids. The primary structure contained two conserved HKD and GG/S motifs. The pld gene was cloned and expressed in Escherichia coli. The purified enzyme exhibited the highest activity at a pH value of 6.0 andtemperature of 60°C. The enzyme was stable within a pH range of 4-7 for 24 h or at temperatures below 50°C. In addition, Triton X-100, Fe2+ , and Al3+ were beneficial to the enzyme activity, whereas Zn2+ and Cu2+ dramatically inhibited its activity. In a two-phase system, the enzyme could convert phosphatidylcholine to phosphatidylserine with a 92% transformation rate.
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Affiliation(s)
- Mengli Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Yanfeng Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoli Duan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Licheng Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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16
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Deepika D, Singh A. Plant phospholipase D: novel structure, regulatory mechanism, and multifaceted functions with biotechnological application. Crit Rev Biotechnol 2021; 42:106-124. [PMID: 34167393 DOI: 10.1080/07388551.2021.1924113] [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] [Indexed: 01/05/2023]
Abstract
Phospholipases D (PLDs) are important membrane lipid-modifying enzymes in eukaryotes. Phosphatidic acid, the product of PLD activity, is a vital signaling molecule. PLD-mediated lipid signaling has been the subject of extensive research leading to discovery of its crystal structure. PLDs are involved in the pathophysiology of several human diseases, therefore, viewed as promising targets for drug design. The availability of a eukaryotic PLD crystal structure will encourage PLD targeted drug designing. PLDs have been implicated in plants response to biotic and abiotic stresses. However, the molecular mechanism of response is not clear. Recently, several novel findings have shown that PLD mediated modulation of structural and developmental processes, such as: stomata movement, root growth and microtubule organization are crucial for plants adaptation to environmental stresses. Involvement of PLDs in regulating membrane remodeling, auxin mediated alteration of root system architecture and nutrient uptake to combat nitrogen and phosphorus deficiencies and magnesium toxicity is established. PLDs via vesicle trafficking modulate cytoskeleton and exocytosis to regulate self-incompatibility (SI) signaling in flowering plants, thereby contributes to plants hybrid vigor and diversity. In addition, the important role of PLDs has been recognized in biotechnologically important functions, including oil/TAG synthesis and maintenance of seed quality. In this review, we describe the crystal structure of a plant PLD and discuss the molecular mechanism of catalysis and activity regulation. Further, the role of PLDs in regulating plant development under biotic and abiotic stresses, nitrogen and phosphorus deficiency, magnesium ion toxicity, SI signaling and pollen tube growth and in important biotechnological applications has been discussed.
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Affiliation(s)
- Deepika Deepika
- National Institute of Plant Genome Research, New Delhi, India
| | - Amarjeet Singh
- National Institute of Plant Genome Research, New Delhi, India
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17
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Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation. Biochem J 2021; 478:1749-1767. [PMID: 33843991 PMCID: PMC8133832 DOI: 10.1042/bcj20210117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 11/17/2022]
Abstract
Phospholipase D (PLD) is an enzyme useful for the enzymatic modification of phospholipids. In the presence of primary alcohols, the enzyme catalyses transphosphatidylation of the head group of phospholipid substrates to synthesise a modified phospholipid product. However, the enzyme is specific for primary alcohols and thus the limitation of the molecular size of the acceptor compounds has restricted the type of phospholipid species that can be synthesised. An engineered variant of PLD from Streptomyces antibioticus termed TNYR SaPLD was developed capable of synthesising 1-phosphatidylinositol with positional specificity of up to 98%. To gain a better understanding of the substrate binding features of the TNYR SaPLD, crystal structures have been determined for the free enzyme and its complexes with phosphate, phosphatidic acid and 1-inositol phosphate. Comparisons of these structures with the wild-type SaPLD show a larger binding site able to accommodate a bulkier secondary alcohol substrate as well as changes to the position of a flexible surface loop proposed to be involved in substrate recognition. The complex of the active TNYR SaPLD with 1-inositol phosphate reveals a covalent intermediate adduct with the ligand bound to H442 rather than to H168, the proposed nucleophile in the wild-type enzyme. This structural feature suggests that the enzyme exhibits plasticity of the catalytic mechanism different from what has been reported to date for PLDs. These structural studies provide insights into the underlying mechanism that governs the recognition of myo-inositol by TNYR SaPLD, and an important foundation for further studies of the catalytic mechanism.
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18
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Li J, Chu Y, Yang R, Lin J, Shao L, Wang L. An alkali-tolerant phospholipase D from Sphingobacterium thalpophilum 2015: Gene cloning, overproduction and characterization. J GEN APPL MICROBIOL 2021; 67:1-8. [PMID: 32981922 DOI: 10.2323/jgam.2020.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The phospholipase pl-S.t gene of Sphingobacterium thalpophilum 2015 was cloned and the gene sequence was submitted to NCBI with Accession Number KX674735.1. The phylogenetic analysis showed that this PL-S.t was clustered to phospholipase D (PLD). As far as we know, the PL-S.t with a molecular mass of 22.5 kDa is the lowest of the currently purified bacterial PLDs, which belongs to a non-HKD PLD enzyme. This PL-S.t was resistant to a wide range of alkali pHs (7.5-9.0) after 1 h incubation, retaining more than 90% of its maximum activity. The PL-S.t activity can be enhanced by Ni2+, Co2+ and Mn2+. This PL-S.t has only one cysteine residue and fewer negatively-charged amino acids (AAs). The hydrogen bonds network was found around the cystein108, which may be beneficial to the stability and activity of PL-S.t in Ni2+ solution. This study has laid the foundation for further research on the molecular mechanism of the catalytic characteristics of low molecular weight alkalic PLD from S. thalpophilum 2015.
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Affiliation(s)
- Jing Li
- College of Environment and Ecology, Chengdu University of Technology
| | - Yiwen Chu
- Sichuan Industrial Institute of Antibiotics (SIIA)
| | - Ruilan Yang
- College of Environment and Ecology, Chengdu University of Technology
| | - Jiafu Lin
- Sichuan Industrial Institute of Antibiotics (SIIA)
| | - Lin Shao
- College of Environment and Ecology, Chengdu University of Technology
| | - Li Wang
- College of Life Science and Technology, Southwest Minzu University
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19
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Wang F, Liu S, Mao X, Cui R, Yang B, Wang Y. Crystal Structure of a Phospholipase D from the Plant-Associated Bacteria Serratia plymuthica Strain AS9 Reveals a Unique Arrangement of Catalytic Pocket. Int J Mol Sci 2021; 22:3219. [PMID: 33809980 PMCID: PMC8004604 DOI: 10.3390/ijms22063219] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Phospholipases D (PLDs) play important roles in different organisms and in vitro phospholipid modifications, which attract strong interests for investigation. However, the lack of PLD structural information has seriously hampered both the understanding of their structure-function relationships and the structure-based bioengineering of this enzyme. Herein, we presented the crystal structure of a PLD from the plant-associated bacteria Serratia plymuthica strain AS9 (SpPLD) at a resolution of 1.79 Å. Two classical HxKxxxxD (HKD) motifs were found in SpPLD and have shown high structural consistence with several PLDs in the same family. While comparing the structure of SpPLD with the previous resolved PLDs from the same family, several unique conformations on the C-terminus of the HKD motif were demonstrated to participate in the arrangement of the catalytic pocket of SpPLD. In SpPLD, an extented loop conformation between β9 and α9 (aa228-246) was found. Moreover, electrostatic surface potential showed that this loop region in SpPLD was positively charged while the corresponding loops in the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9) were neutral. The shortened loop between α10 and α11 (aa272-275) made the SpPLD unable to form the gate-like structure which existed specically in the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9) and functioned to stabilize the substrates. In contrast, the shortened loop conformation at this corresponding segment was more alike to several nucleases (Nuc, Zuc, mZuc, NucT) within the same family. Moreover, the loop composition between β11 and β12 was also different from the two Streptomyces originated PLDs (PDB ID: 1F0I, 2ZE4/2ZE9), which formed the entrance of the catalytic pocket and were closely related to substrate recognition. So far, SpPLD was the only structurally characterized PLD enzyme from Serratia. The structural information derived here not only helps for the understanding of the biological function of this enzyme in plant protection, but also helps for the understanding of the rational design of the mutant, with potential application in phospholipid modification.
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Affiliation(s)
- Fanghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; (F.W.); (S.L.); (X.M.); (R.C.)
| | - Siyu Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; (F.W.); (S.L.); (X.M.); (R.C.)
| | - Xuejing Mao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; (F.W.); (S.L.); (X.M.); (R.C.)
| | - Ruiguo Cui
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; (F.W.); (S.L.); (X.M.); (R.C.)
| | - Bo Yang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China;
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China; (F.W.); (S.L.); (X.M.); (R.C.)
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20
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Lahrouchi N, Postma AV, Salazar CM, De Laughter DM, Tjong F, Piherová L, Bowling FZ, Zimmerman D, Lodder EM, Ta-Shma A, Perles Z, Beekman L, Ilgun A, Gunst Q, Hababa M, Škorić-Milosavljević D, Stránecký V, Tomek V, de Knijff P, de Leeuw R, Robinson JY, Burn SC, Mustafa H, Ambrose M, Moss T, Jacober J, Niyazov DM, Wolf B, Kim KH, Cherny S, Rousounides A, Aristidou-Kallika A, Tanteles G, Ange-Line B, Denommé-Pichon AS, Francannet C, Ortiz D, Haak MC, Ten Harkel AD, Manten GT, Dutman AC, Bouman K, Magliozzi M, Radio FC, Santen GW, Herkert JC, Brown HA, Elpeleg O, van den Hoff MJ, Mulder B, Airola MV, Kmoch S, Barnett JV, Clur SA, Frohman MA, Bezzina CR. Biallelic loss-of-function variants in PLD1 cause congenital right-sided cardiac valve defects and neonatal cardiomyopathy. J Clin Invest 2021; 131:142148. [PMID: 33645542 DOI: 10.1172/jci142148] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/16/2020] [Indexed: 01/12/2023] Open
Abstract
Congenital heart disease is the most common type of birth defect, accounting for one-third of all congenital anomalies. Using whole-exome sequencing of 2718 patients with congenital heart disease and a search in GeneMatcher, we identified 30 patients from 21 unrelated families of different ancestries with biallelic phospholipase D1 (PLD1) variants who presented predominantly with congenital cardiac valve defects. We also associated recessive PLD1 variants with isolated neonatal cardiomyopathy. Furthermore, we established that p.I668F is a founder variant among Ashkenazi Jews (allele frequency of ~2%) and describe the phenotypic spectrum of PLD1-associated congenital heart defects. PLD1 missense variants were overrepresented in regions of the protein critical for catalytic activity, and, correspondingly, we observed a strong reduction in enzymatic activity for most of the mutant proteins in an enzymatic assay. Finally, we demonstrate that PLD1 inhibition decreased endothelial-mesenchymal transition, an established pivotal early step in valvulogenesis. In conclusion, our study provides a more detailed understanding of disease mechanisms and phenotypic expression associated with PLD1 loss of function.
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Affiliation(s)
- Najim Lahrouchi
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Alex V Postma
- Department of Clinical Genetics, and.,Department of Medical Biology, Amsterdam UMC, Amsterdam, Netherlands
| | - Christian M Salazar
- Department of Pharmacological Sciences and Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, New York, USA
| | - Daniel M De Laughter
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Fleur Tjong
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Lenka Piherová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Forrest Z Bowling
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Dominic Zimmerman
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Elisabeth M Lodder
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Asaf Ta-Shma
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Zeev Perles
- Department of Pediatric Cardiology, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | - Leander Beekman
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Aho Ilgun
- Department of Medical Biology, Amsterdam UMC, Amsterdam, Netherlands
| | - Quinn Gunst
- Department of Medical Biology, Amsterdam UMC, Amsterdam, Netherlands
| | - Mariam Hababa
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Doris Škorić-Milosavljević
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Viktor Tomek
- Children's Heart Centre, 2nd Faculty of Medicine, Charles University in Prague, Motol University Hospital, Prague, Czech Republic
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Rick de Leeuw
- Department of Human Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Jamille Y Robinson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Hiba Mustafa
- Department of Obstetrics, Gynecology and Women's Health
| | - Matthew Ambrose
- Department of Pediatrics, Division of Pediatric Cardiology, and
| | - Timothy Moss
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jennifer Jacober
- Department of Pediatrics, Ochsner Clinic, Tulane University, University of Queensland, New Orleans, Louisiana, USA
| | - Dmitriy M Niyazov
- Department of Pediatrics, Ochsner Clinic, Tulane University, University of Queensland, New Orleans, Louisiana, USA
| | - Barry Wolf
- Division of Genetics, Birth Defects and Metabolic Disorders, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Katherine H Kim
- Division of Genetics, Birth Defects and Metabolic Disorders, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Sara Cherny
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,Division of Cardiology, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | | | | | - George Tanteles
- Cyprus School of Molecular Medicine, Nicosia, Cyprus.,Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Bruel Ange-Line
- UMR 1231 INSERM, GAD, Université Bourgogne Franche-Comté, Dijon, France.,Unité Fonctionnelle d'Innovation en Diagnostique Génomique des Maladies Rares, FHU-TRANSLAD, Centre Hospitalier Universitaire Estaing (CHU), Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR 1231 INSERM, GAD, Université Bourgogne Franche-Comté, Dijon, France.,Unité Fonctionnelle d'Innovation en Diagnostique Génomique des Maladies Rares, FHU-TRANSLAD, Centre Hospitalier Universitaire Estaing (CHU), Dijon Bourgogne, Dijon, France
| | | | - Damara Ortiz
- Medical Genetics Department, UPMC Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Arend D.J. Ten Harkel
- Department of Pediatric Cardiology, Leiden University Medical Centre, Leiden, Netherlands
| | | | - Annemiek C Dutman
- Department of Pathology, Isala Women and Children's Hospital, Zwolle, Netherlands
| | - Katelijne Bouman
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Monia Magliozzi
- Genetic and Rare Disease Research Division, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | | | - Gijs We Santen
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Johanna C Herkert
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - H Alex Brown
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah, Hebrew University Medical Center, Jerusalem, Israel
| | | | - Barbara Mulder
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
| | - Michael V Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine, 1st Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Joey V Barnett
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Sally-Ann Clur
- Department of Pediatric Cardiology, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Michael A Frohman
- Department of Pharmacological Sciences and Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, New York, USA
| | - Connie R Bezzina
- Amsterdam UMC, University of Amsterdam, Heart Center, Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences
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21
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Bowling FZ, Frohman MA, Airola MV. Structure and regulation of human phospholipase D. Adv Biol Regul 2021; 79:100783. [PMID: 33495125 DOI: 10.1016/j.jbior.2020.100783] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022]
Abstract
Mammalian phospholipase D (PLD) generates phosphatidic acid, a dynamic lipid secondary messenger involved with a broad spectrum of cellular functions including but not limited to metabolism, migration, and exocytosis. As a promising pharmaceutical target, the biochemical properties of PLD have been well characterized. This has led to the recent crystal structures of human PLD1 and PLD2, the development of PLD specific pharmacological inhibitors, and the identification of cellular regulators of PLD. In this review, we discuss the PLD1 and PLD2 structures, PLD inhibition by small molecules, and the regulation of PLD activity by effector proteins and lipids.
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Affiliation(s)
- Forrest Z Bowling
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA
| | - Michael A Frohman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Michael V Airola
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY, USA.
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22
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Dyrkheeva N, Anarbaev R, Lebedeva N, Kuprushkin M, Kuznetsova A, Kuznetsov N, Rechkunova N, Lavrik O. Human Tyrosyl-DNA Phosphodiesterase 1 Possesses Transphosphooligonucleotidation Activity With Primary Alcohols. Front Cell Dev Biol 2020; 8:604732. [PMID: 33425909 PMCID: PMC7786179 DOI: 10.3389/fcell.2020.604732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/05/2020] [Indexed: 12/20/2022] Open
Abstract
Human tyrosyl-DNA phosphodiesterase 1 (TDP1) belongs to the phospholipase D superfamily, whose members contain paired catalytic histidine and lysine residues within two conserved motifs and hydrolyze phosphodiester bonds. TDP1 is a DNA repair enzyme that processes 3′ DNA end blocking lesions and a wide range of synthetic DNA adducts as a substrate. TDP1 hydrolyzes DNA-adducts via two coordinated SN2 nucleophilic attacks mediated by the action of two histidine residues and leads to the formation of the covalent intermediate. Hydrolysis of this intermediate is proposed to be carried out by a water molecule that is activated by the His493 residue acting as a general base. It was known that phospholipase D enzymes are able to catalyze not only hydrolysis but also a transphosphatidylation reaction in the presence of primary alcohols in which they transfer the substrate to the alcohol instead of water. Here, we first demonstrated that TDP1 is able to undergo a “transphosphooligonucleotidation” reaction, transferring the substrate residue to the alcohol, thus inducing the formation of covalent DNA adducts with different primary alcohol residues. Such adducts can be accumulated in the conditions of high concentration of alcohol. We demonstrated that glycerol residue was efficiently cleaved from the 3′-end by TDP1 but not by its mutant form associated with the disease spinocerebellar ataxia with axonal neuropathy. Therefore, the second reaction step can be carried out not only by a water molecule but also by the other small nucleophilic molecules, e.g., glycerol and ethanol. Thus, in some cases, TDP1 can be regarded not only as a repair enzyme but also as a source of DNA damage especially in the case of mutation. Such damages can make a negative contribution to the stability of cell vitality.
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Affiliation(s)
- Nadezhda Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Rashid Anarbaev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Natalia Lebedeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim Kuprushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexandra Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikita Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nadejda Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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23
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Huang L, Ma J, Sang J, Wang N, Wang S, Wang C, Kang H, Liu F, Lu F, Liu Y. Enhancing the thermostability of phospholipase D from Streptomyces halstedii by directed evolution and elucidating the mechanism of a key amino acid residue using molecular dynamics simulation. Int J Biol Macromol 2020; 164:3065-3074. [PMID: 32858108 DOI: 10.1016/j.ijbiomac.2020.08.160] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/19/2020] [Accepted: 08/20/2020] [Indexed: 12/28/2022]
Abstract
To enhance the thermostability of phospholipase D (PLD), error-prone polymerase chain reaction method was used to create mutants of PLD (PLDsh) from Streptomyces halstedii. One desirable mutant (S163F) with Ser to Phe substitution at position 163 was screened with high-throughput assay. S163F exhibited a 10 °C higher optimum temperature than wild-type (WT). Although WT exhibited almost no activity after incubating at 50 °C for 40 min, S163F still displayed 27% of its highest activity after incubating at 50 °C for 60 min. Furthermore, the half-life of S163F at 50 °C was 3.04-fold higher than that of WT. The analysis of molecular dynamics simulation suggested that the Ser163Phe mutation led to the formation of salt bridge between Lys300 and Glu314 and a stronger hydrophobic interaction of Phe163 with Pro341, Leu342, and Trp460, resulting in an increased structural rigidity and overall enhanced stability at high temperature. This study provides novel insights on PLD tolerance to high temperature by investigating the structure-activity relationship. In addition, it provides strong theoretical foundation and preliminary information on the engineering of PLD with improved characteristics to meet industrial demand.
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Affiliation(s)
- Lin Huang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jieying Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jingcheng Sang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Nan Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shuang Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Chen Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Hongwei Kang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Fufeng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, 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, 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, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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24
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Structural insights into phospholipase D function. Prog Lipid Res 2020; 81:101070. [PMID: 33181180 DOI: 10.1016/j.plipres.2020.101070] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023]
Abstract
Phospholipase D (PLD) and its metabolic active product phosphatidic acid (PA) engage in a wide range of physiopathologic processes in the cell. PLDs have been considered as a potential and promising drug target. Recently, the crystal structures of PLDs in mammalian and plant have been solved at atomic resolution. These achievements allow us to understand the structural differences among different species of PLDs and the functions of their key domains. In this review, we summarize the sequence and structure of different species of PLD isoforms, and discuss the structural mechanisms for PLD interactions with their binding partners and the functions of each key domain in the regulation of PLDs activation and catalytic reaction.
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25
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Kaur A, Neelam K, Kaur K, Kitazumi A, de Los Reyes BG, Singh K. Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran. Sci Rep 2020; 10:6571. [PMID: 32313086 PMCID: PMC7170842 DOI: 10.1038/s41598-020-62649-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 03/16/2020] [Indexed: 11/25/2022] Open
Abstract
Rice bran, a by-product after milling, is a rich source of phytonutrients like oryzanols, tocopherols, tocotrienols, phytosterols, and dietary fibers. Moreover, exceptional properties of the rice bran oil make it unparalleled to other vegetable oils. However, a lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) causes rancidity and ‘stale flavor’ in the oil, and thus limits the rice bran usage for human consumption. To improve the rice bran quality, sequence based allele mining at OsPLDα1 locus (3.6 Kb) was performed across 48 accessions representing 11 wild Oryza species, 8 accessions of African cultivated rice, and 7 Oryza sativa cultivars. From comparative sequence analysis, 216 SNPs and 30 InDels were detected at the OsPLDα1 locus. Phylogenetic analysis revealed 20 OsPLDα1 cDNA variants which further translated into 12 protein variants. The O. officinalis protein variant, when compared to Nipponbare, showed maximum variability comprising 22 amino acid substitutions and absence of two peptides and two β-sheets. Further, expression profiling indicated significant differences in transcript abundance within as well as between the OsPLDα1 variants. Also, a new OsPLDα1 transcript variant having third exon missing in it, Os01t0172400-06, has been revealed. An O. officinalis accession (IRGC101152) had lowest gene expression which suggests the presence of novel allele, named as OsPLDα1-1a (GenBank accession no. MF966931). The identified novel allele could be further deployed in the breeding programs to overcome rice bran rancidity in elite cultivars.
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Affiliation(s)
- Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.,School of Biology and Ecology, University of Maine, Orono, Maine, United States of America
| | - Kumari Neelam
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Karminderbir Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Ai Kitazumi
- School of Biology and Ecology, University of Maine, Orono, Maine, United States of America.,Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, United States of America
| | - Benildo G de Los Reyes
- School of Biology and Ecology, University of Maine, Orono, Maine, United States of America.,Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, United States of America
| | - Kuldeep Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India. .,ICAR- National Bureau of Plant Genetic Resources, New Delhi, India.
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26
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Affiliation(s)
- Lei Zheng
- Department of Biochemistry and Molecular Biology, and Center for Membrane Biology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Guangwei Du
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.
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27
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Crystal structure of human PLD1 provides insight into activation by PI(4,5)P 2 and RhoA. Nat Chem Biol 2020; 16:400-407. [PMID: 32198492 PMCID: PMC7117805 DOI: 10.1038/s41589-020-0499-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 02/10/2020] [Indexed: 11/08/2022]
Abstract
The signal transduction enzyme phospholipase D1 (PLD1) hydrolyzes phosphatidylcholine to generate the lipid second-messenger phosphatidic acid, which plays roles in disease processes such as thrombosis and cancer. PLD1 is directly and synergistically regulated by protein kinase C, Arf and Rho GTPases, and the membrane lipid phosphatidylinositol-4,5-bisphosphate (PIP2). Here, we present a 1.8 Å-resolution crystal structure of the human PLD1 catalytic domain, which is characterized by a globular fold with a funnel-shaped hydrophobic cavity leading to the active site. Adjacent is a PIP2-binding polybasic pocket at the membrane interface that is essential for activity. The C terminus folds into and contributes part of the catalytic pocket, which harbors a phosphohistidine that mimics an intermediate stage of the catalytic cycle. Mapping of PLD1 mutations that disrupt RhoA activation identifies the RhoA-PLD1 binding interface. This structure sheds light on PLD1 regulation by lipid and protein effectors, enabling rationale inhibitor design for this well-studied therapeutic target.
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28
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Bacterial non-specific nucleases of the phospholipase D superfamily and their biotechnological potential. Appl Microbiol Biotechnol 2020; 104:3293-3304. [PMID: 32086594 DOI: 10.1007/s00253-020-10459-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/03/2020] [Accepted: 02/10/2020] [Indexed: 12/19/2022]
Abstract
Bacterial non-specific nucleases are ubiquitously distributed and involved in numerous intra- and extracellular processes. Although all nucleases share the basic chemistry for the hydrolysis of phosphodiester bonds in nucleic acid molecules, the catalysis comprises diverse modes of action, which offers great potential for versatile biotechnological applications. A major criterium for their differentiation is substrate specificity. Specific endonucleases are widely used as restriction enzymes in molecular biology approaches, whereas the main applications of non-specific nucleases (NSNs) are the removal of nucleic acids from crude extracts in industrial downstream processing and the prevention of cell clumping in microfabricated channels. In nature, the predominant role of NSNs is the acquisition of nutrient sources such as nucleotides and phosphates. The number of extensively characterized NSNs and available structures is limited. Moreover, their applicability is mostly challenged by the presence of metal chelators that impede the hydrolysis of nucleic acids in a metal ion-dependent manner. However, a few metal ion-independent NSNs that tolerate the presence of metal chelators have been characterized in recent years with none being commercially available to date. The classification and biotechnological potential of bacterial NSNs with a special focus on metal ion-independent nucleases are presented and discussed.Key Points • Bacterial phospholipases (PLD-family) exhibit nucleolytic activity. • Bacterial nucleases of the PLD-family are metal ion-independent. • NSNs can be used in downstream processing approaches.
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29
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Joensuu M, Wallis TP, Saber SH, Meunier FA. Phospholipases in neuronal function: A role in learning and memory? J Neurochem 2020; 153:300-333. [PMID: 31745996 DOI: 10.1111/jnc.14918] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/29/2019] [Accepted: 11/15/2019] [Indexed: 12/20/2022]
Abstract
Despite the human brain being made of nearly 60% fat, the vast majority of studies on the mechanisms of neuronal communication which underpin cognition, memory and learning, primarily focus on proteins and/or (epi)genetic mechanisms. Phospholipids are the main component of all cellular membranes and function as substrates for numerous phospholipid-modifying enzymes, including phospholipases, which release free fatty acids (FFAs) and other lipid metabolites that can alter the intrinsic properties of the membranes, recruit and activate critical proteins, and act as lipid signalling molecules. Here, we will review brain specific phospholipases, their roles in membrane remodelling, neuronal function, learning and memory, as well as their disease implications. In particular, we will highlight key roles of unsaturated FFAs, particularly arachidonic acid, in neurotransmitter release, neuroinflammation and memory. In light of recent findings, we will also discuss the emerging role of phospholipase A1 and the creation of saturated FFAs in the brain.
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Affiliation(s)
- Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Tristan P Wallis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Saber H Saber
- Laboratory of Molecular Cell Biology, Department of Zoology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Qld, Australia
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30
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Zhang Z, Chen M, Xu W, Zhang W, Zhang T, Guang C, Mu W. Microbial phospholipase D: Identification, modification and application. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2019.12.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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McDermott MI, Wang Y, Wakelam MJO, Bankaitis VA. Mammalian phospholipase D: Function, and therapeutics. Prog Lipid Res 2019; 78:101018. [PMID: 31830503 DOI: 10.1016/j.plipres.2019.101018] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 01/23/2023]
Abstract
Despite being discovered over 60 years ago, the precise role of phospholipase D (PLD) is still being elucidated. PLD enzymes catalyze the hydrolysis of the phosphodiester bond of glycerophospholipids producing phosphatidic acid and the free headgroup. PLD family members are found in organisms ranging from viruses, and bacteria to plants, and mammals. They display a range of substrate specificities, are regulated by a diverse range of molecules, and have been implicated in a broad range of cellular processes including receptor signaling, cytoskeletal regulation and membrane trafficking. Recent technological advances including: the development of PLD knockout mice, isoform-specific antibodies, and specific inhibitors are finally permitting a thorough analysis of the in vivo role of mammalian PLDs. These studies are facilitating increased recognition of PLD's role in disease states including cancers and Alzheimer's disease, offering potential as a target for therapeutic intervention.
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Affiliation(s)
- M I McDermott
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America.
| | - Y Wang
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States of America
| | - M J O Wakelam
- Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, United Kingdom
| | - V A Bankaitis
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX 77843-1114, United States of America; Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128, United States of America; Department of Chemistry, Texas A&M University, College Station, Texas 77840, United States of America
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32
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Crystal structure of plant PLDα1 reveals catalytic and regulatory mechanisms of eukaryotic phospholipase D. Cell Res 2019; 30:61-69. [PMID: 31619765 DOI: 10.1038/s41422-019-0244-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Phospholipase D (PLD) hydrolyzes the phosphodiester bond of glycerophospholipids and produces phosphatidic acid (PA), which acts as a second messenger in many living organisms. A large number of PLDs have been identified in eukaryotes, and are viewed as promising targets for drug design because these enzymes are known to be tightly regulated and to function in the pathophysiology of many human diseases. However, the underlying molecular mechanisms of catalysis and regulation of eukaryotic PLD remain elusive. Here, we determined the crystal structure of full-length plant PLDα1 in the apo state and in complex with PA. The structure shows that the N-terminal C2 domain hydrophobically interacts with the C-terminal catalytic domain that features two HKD motifs. Our analysis reveals the catalytic site, substrate-binding mechanism, and a new Ca2+-binding site that is required for the activation of PLD. In addition, we tested several efficient small-molecule inhibitors against PLDα1, and suggested a possible competitive inhibition mechanism according to structure-based docking analysis. This study explains many long-standing questions about PLDs and provides structural insights into PLD-targeted inhibitor/drug design.
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33
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Wang F, Wu Z, Abousalham A, Yang B, Wang Y. Deletion the C-terminal peptides of Vibrio harveyi phospholipase D significantly improved its enzymatic properties. Int J Biol Macromol 2019; 129:1140-1147. [PMID: 30550823 DOI: 10.1016/j.ijbiomac.2018.12.097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/01/2018] [Accepted: 12/11/2018] [Indexed: 12/01/2022]
Abstract
A novel phospholipase D that originate from marine Vibrio harveyi (VhPLD) was recombinant expressed and biochemically characterized. Moreover, effects of C-terminal peptides on catalytic and interfacial binding properties of VhPLD were investigated by constructing two truncated mutants (VhPLD-Δ(472-483) and VhPLD-Δ(437-483)). Optimal reaction temperature and pH value for wild-type VhPLD (VhPLD-WT) was 45 °C and pH 8.0. However, optimal reaction temperature of VhPLD-Δ(437-483) increased to 50 °C. Meanwhile, catalytic efficiency (kcat/KM) of VhPLD-Δ(472-483) and VhPLD-Δ(437-483) to the 1,2-Dioctanoyl-sn-glycero-3-phosphatidyl-p-nitrophenol (PpNP) was 12.9 and 14.2 times higher than that of VhPLD-WT. However, when compare the catalytic efficiency between VhPLD-Δ(472-483) and VhPLD-Δ(437-483), no significant change can be found between the two mutants. These results strongly indicated that the C-terminal 12 amino acids (472-483) have important role on the activity of VhPLD. Effects of C-terminal peptides on the interfacial binding properties of VhPLD to different phospholipid monolayers were also investigated by using monolayer film technology. Results of the maximum insertion pressure (MIP) indicated that deletion the C-terminal segment of VhPLD improved its interfacial binding properties to different phospholipid monolayers.
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Affiliation(s)
- Fanghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Zongze Wu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Abdelkarim Abousalham
- Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires (ICBMS), Université Lyon 1, Univ Lyon, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM2), Bât Raulin, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne CEDEX, France
| | - Bo Yang
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China.
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34
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Schmitz S, Börner P, Nölle V, Elleuche S. Comparative analysis of two non-specific nucleases of the phospholipase D family from the plant pathogen competitor bacterium Pantoea agglomerans. Appl Microbiol Biotechnol 2019; 103:2635-2648. [PMID: 30685815 DOI: 10.1007/s00253-019-09644-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 11/28/2022]
Abstract
Bacterial non-specific nucleases of the phospholipase D family are widely distributed among the members of the Enterobacteriaceae. Each genome mainly contains a single copy of a gene encoding a phospholipase D family protein. However, two distantly related isozymes (< 40% identity at the protein level) were identified by BLAST-analyses in the plant pathogenic competitor enterobacterium Pantoea agglomerans. The two nucleases PaNuc-1 and PaNuc-2 were produced in Escherichia coli. Identical gene constructs and expression conditions resulted in the production of PaNuc-1 in soluble form, while PaNuc-2 remained insoluble in inclusion bodies. PaNuc-2 was refolded and both proteins were purified by a combination of affinity and ion exchange chromatography. Proteolytic removal of the HIS-tag allowed the characterization of pure and mature tag-less proteins. Enzymatic properties of both isozymes revealed that they are non-specific nucleases, displaying activities against RNA, single- and double-stranded genomic DNA as well as circular plasmids. However, their biochemical activity profiles were clearly different, with PaNuc-1 being optimally active at 70 °C and pH 7.0, while PaNuc-2 was most active at 45 °C and pH 7.0. The enzymes retained > 90% nuclease activity at EDTA concentrations of 4 mM (PaNuc-2) and 20 mM (PaNuc-1), respectively. Different enzymatic properties suggest that the roles of PaNuc-1 and PaNuc-2 differ in the cell and might be the result of functional diversification after an ancient gene duplication event took place. The fact that both enzymes could be easily produced in recombinant form and their tolerance against metal ion chelators in combination with a broad substrate promiscuity might pave the way to versatile biotechnological applications.
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Affiliation(s)
- Sarah Schmitz
- Miltenyi Biotec GmbH, Friedrich-Ebert-Straße 68, 51429, Bergisch Gladbach, Germany
| | - Paul Börner
- Miltenyi Biotec GmbH, Friedrich-Ebert-Straße 68, 51429, Bergisch Gladbach, Germany
| | - Volker Nölle
- Miltenyi Biotec GmbH, Friedrich-Ebert-Straße 68, 51429, Bergisch Gladbach, Germany
| | - Skander Elleuche
- Miltenyi Biotec GmbH, Friedrich-Ebert-Straße 68, 51429, Bergisch Gladbach, Germany.
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35
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Abstract
Phospholipases are lipolytic enzymes that hydrolyze phospholipid substrates at specific ester bonds. Phospholipases are widespread in nature and play very diverse roles from aggression in snake venom to signal transduction, lipid mediator production, and metabolite digestion in humans. Phospholipases vary considerably in structure, function, regulation, and mode of action. Tremendous advances in understanding the structure and function of phospholipases have occurred in the last decades. This introductory chapter is aimed at providing a general framework of the current understanding of phospholipases and a discussion of their mechanisms of action and emerging biological functions.
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36
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Arhab Y, Rahier R, Noiriel A, Cherrier MV, Abousalham A. Expression and Purification of Recombinant Vigna unguiculata Phospholipase D in Pichia pastoris for Structural Studies. Methods Mol Biol 2018; 1835:191-201. [PMID: 30109653 DOI: 10.1007/978-1-4939-8672-9_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The production of pure enzymes in high quantities is a proven strategy to study the catalytic mechanism as well as the solving of structure at the atomic scale for therapeutic or industrial purposes. Phospholipase D (PLD, EC 3.1.4.4) is found in a wide majority of living organisms and has been shown to be involved in signal transduction, vesicle trafficking, and membrane metabolism processes. Located at the membrane-cytoplasm interface, plant PLDs are soluble but also bear an evident hydrophobic aspect making challenging its expression and its purification in large quantity. So far there is no high-resolution three-dimensional structure for a eukaryotic PLD. The protocols herein describe the cloning of the eukaryotic recombinant PLDα of Vigna unguiculata (cowpea) into the yeast expression system Pichia pastoris and its two-step purification process. This allowed us to purify to homogeneity hundreds of micrograms of highly pure protein to conduct in fine structural studies.
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Affiliation(s)
- Yani Arhab
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM²), Villeurbanne Cedex, 69622, France
| | - Renaud Rahier
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM²), Villeurbanne Cedex, 69622, France
| | - Alexandre Noiriel
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM²), Villeurbanne Cedex, 69622, France
| | - Mickael V Cherrier
- UMR 5086 Molecular Microbiology and Structural Biochemistry, Université de Lyon-CNRS, Institut de Biologie et Chimie des Protéines, Lyon Cedex 07, France
- Univ. Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Abdelkarim Abousalham
- Univ Lyon, Université Lyon 1, Institut de Chimie et de Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Métabolisme, Enzymes et Mécanismes Moléculaires (MEM²), Villeurbanne Cedex, 69622, France.
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37
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Structural basis for the substrate selectivity of Helicobacter pylori NucT nuclease activity. PLoS One 2017; 12:e0189049. [PMID: 29206236 PMCID: PMC5714352 DOI: 10.1371/journal.pone.0189049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/19/2017] [Indexed: 12/20/2022] Open
Abstract
The Phospholipase D (PLD) superfamily of proteins includes a group of enzymes with nuclease activity on various nucleic acid substrates. Here, with the aim of better understanding the substrate specificity determinants in this subfamily, we have characterised the enzymatic activity and the crystal structure of NucT, a nuclease implicated in Helicobacter pylori purine salvage and natural transformation and compared them to those of its bacterial and mammalian homologues. NucT exhibits an endonuclease activity with a strong preference for single stranded nucleic acids substrates. We identified histidine124 as essential for the catalytic activity of the protein. Comparison of the NucT crystal structure at 1.58 Å resolution reported here with those of other members of the sub-family suggests that the specificity of NucT for single-stranded nucleic acids is provided by the width of a positively charged groove giving access to the catalytic site.
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38
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Han EH, Petrella DP, Blakeslee JJ. 'Bending' models of halotropism: incorporating protein phosphatase 2A, ABCB transporters, and auxin metabolism. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3071-3089. [PMID: 28899081 DOI: 10.1093/jxb/erx127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Salt stress causes worldwide reductions in agricultural yields, a problem that is exacerbated by the depletion of global freshwater reserves and the use of contaminated or recycled water (i.e. effluent water). Additionally, salt stress can occur as cultivated areas are subjected to frequent rounds of irrigation followed by periods of moderate to severe evapotranspiration, which can result in the heterogeneous aggregation of salts in agricultural soils. Our understanding of the later stages of salt stress and the mechanisms by which salt is transported out of cells and roots has greatly improved over the last decade. The precise mechanisms by which plant roots perceive salt stress and translate this perception into adaptive, directional growth away from increased salt concentrations (i.e. halotropism), however, are not well understood. Here, we provide a review of the current knowledge surrounding the early responses to salt stress and the initiation of halotropism, including lipid signaling, protein phosphorylation cascades, and changes in auxin metabolism and/or transport. Current models of halotropism have focused on the role of PIN2- and PIN1-mediated auxin efflux in initiating and controlling halotropism. Recent studies, however, suggest that additional factors such as ABCB transporters, protein phosphatase 2A activity, and auxin metabolism should be included in the model of halotropic growth.
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Affiliation(s)
- Eun Hyang Han
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, USA
| | - Dominic P Petrella
- Department of Horticulture and Crop Science, The Ohio State University/OARDC, Wooster, OH, USA
| | - Joshua J Blakeslee
- Department of Horticulture and Crop Science, OARDC Metabolite Analysis Cluster (OMAC), The Ohio State University/OARDC, Wooster, OH, USA
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39
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Identification of a novel phospholipase D with high transphosphatidylation activity and its application in synthesis of phosphatidylserine and DHA-phosphatidylserine. J Biotechnol 2017; 249:51-58. [DOI: 10.1016/j.jbiotec.2017.03.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/13/2017] [Accepted: 03/23/2017] [Indexed: 12/30/2022]
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Sharma S, Patnaik SK, Taggart RT, Baysal BE. The double-domain cytidine deaminase APOBEC3G is a cellular site-specific RNA editing enzyme. Sci Rep 2016; 6:39100. [PMID: 27974822 PMCID: PMC5156925 DOI: 10.1038/srep39100] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/16/2016] [Indexed: 11/10/2022] Open
Abstract
APOBEC3G is a cytidine deaminase with two homologous domains and restricts retroelements and HIV-1. APOBEC3G deaminates single-stranded DNAs via its C-terminal domain, whereas the N-terminal domain is considered non-catalytic. Although APOBEC3G is known to bind RNAs, APOBEC3G-mediated RNA editing has not been observed. We recently discovered RNA editing by the single-domain enzyme APOBEC3A in innate immune cells. To determine if APOBEC3G is capable of RNA editing, we transiently expressed APOBEC3G in the HEK293T cell line and performed transcriptome-wide RNA sequencing. We show that APOBEC3G causes site-specific C-to-U editing of mRNAs from over 600 genes. The edited cytidines are often flanked by inverted repeats, but are largely distinct from those deaminated by APOBEC3A. We verified protein-recoding RNA editing of selected genes including several that are known to be involved in HIV-1 infectivity. APOBEC3G co-purifies with highly edited mRNA substrates. We find that conserved catalytic residues in both cytidine deaminase domains are required for RNA editing. Our findings demonstrate the novel RNA editing function of APOBEC3G and suggest a role for the N-terminal domain in RNA editing.
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Affiliation(s)
- Shraddha Sharma
- Departments of Pathology and Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets Buffalo, NY, 14263, USA
| | - Santosh K. Patnaik
- Departments of Pathology and Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets Buffalo, NY, 14263, USA
| | - Robert T. Taggart
- Departments of Pathology and Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets Buffalo, NY, 14263, USA
| | - Bora E. Baysal
- Departments of Pathology and Thoracic Surgery, Roswell Park Cancer Institute, Elm and Carlton Streets Buffalo, NY, 14263, USA
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Abstract
Bacterial sphingomyelinases and phospholipases are a heterogeneous group of esterases which are usually surface associated or secreted by a wide variety of Gram-positive and Gram-negative bacteria. These enzymes hydrolyze sphingomyelin and glycerophospholipids, respectively, generating products identical to the ones produced by eukaryotic enzymes which play crucial roles in distinct physiological processes, including membrane dynamics, cellular signaling, migration, growth, and death. Several bacterial sphingomyelinases and phospholipases are essential for virulence of extracellular, facultative, or obligate intracellular pathogens, as these enzymes contribute to phagosomal escape or phagosomal maturation avoidance, favoring tissue colonization, infection establishment and progression, or immune response evasion. This work presents a classification proposal for bacterial sphingomyelinases and phospholipases that considers not only their enzymatic activities but also their structural aspects. An overview of the main physiopathological activities is provided for each enzyme type, as are examples in which inactivation of a sphingomyelinase- or a phospholipase-encoding gene impairs the virulence of a pathogen. The identification of sphingomyelinases and phospholipases important for bacterial pathogenesis and the development of inhibitors for these enzymes could generate candidate vaccines and therapeutic agents, which will diminish the impacts of the associated human and animal diseases.
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Matsumoto Y, Sugimori D. Substrate recognition mechanism of Streptomyces phospholipase D and enzymatic measurement of plasmalogen. J Biosci Bioeng 2015; 120:372-9. [DOI: 10.1016/j.jbiosc.2015.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 02/26/2015] [Accepted: 02/28/2015] [Indexed: 01/10/2023]
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43
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Beligni MV, Bagnato C, Prados MB, Bondino H, Laxalt AM, Munnik T, Ten Have A. The diversity of algal phospholipase D homologs revealed by biocomputational analysis. JOURNAL OF PHYCOLOGY 2015; 51:943-962. [PMID: 26986890 DOI: 10.1111/jpy.12334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/09/2015] [Indexed: 06/05/2023]
Abstract
Phospholipase D (PLD) participates in the formation of phosphatidic acid, a precursor in glycerolipid biosynthesis and a second messenger. PLDs are part of a superfamily of proteins that hydrolyze phosphodiesters and share a catalytic motif, HxKxxxxD, and hence a mechanism of action. Although HKD-PLDs have been thoroughly characterized in plants, animals and bacteria, very little is known about these enzymes in algae. To fill this gap in knowledge, we performed a biocomputational analysis by means of HMMER iterative profiling, using most eukaryotic algae genomes available. Phylogenetic analysis revealed that algae exhibit very few eukaryotic-type PLDs but possess, instead, many bacteria-like PLDs. Among algae eukaryotic-type PLDs, we identified C2-PLDs and PXPH-like PLDs. In addition, the dinoflagellate Alexandrium tamarense features several proteins phylogenetically related to oomycete PLDs. Our phylogenetic analysis also showed that algae bacteria-like PLDs (proteins with putative PLD activity) fall into five clades, three of which are novel lineages in eukaryotes, composed almost entirely of algae. Specifically, Clade II is almost exclusive to diatoms, whereas Clade I and IV are mainly represented by proteins from prasinophytes. The other two clades are composed of mitochondrial PLDs (Clade V or Mito-PLDs), previously found in mammals, and a subfamily of potentially secreted proteins (Clade III or SP-PLDs), which includes a homolog formerly characterized in rice. In addition, our phylogenetic analysis shows that algae have non-PLD members within the bacteria-like HKD superfamily with putative cardiolipin synthase and phosphatidylserine/phosphatidylglycerophosphate synthase activities. Altogether, our results show that eukaryotic algae possess a moderate number of PLDs that belong to very diverse phylogenetic groups.
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Affiliation(s)
- María Verónica Beligni
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, Mar del Plata, 7600, Argentina
| | - Carolina Bagnato
- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Río Negro, Mitre 630. S. C. de Bariloche 8400, Río Negro, Argentina
| | - María Belén Prados
- Instituto de Energía y Desarrollo Sustentable - Comisión Nacional de Energía Atómica, Centro Atómico Bariloche, Av. Bustillo 9500, S. C. de Bariloche 8400, Río Negro, Argentina
| | - Hernán Bondino
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, Mar del Plata, 7600, Argentina
| | - Ana María Laxalt
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, Mar del Plata, 7600, Argentina
| | - Teun Munnik
- Department of Plant Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, NL-1098 XH, the Netherlands
| | - Arjen Ten Have
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, Mar del Plata, 7600, Argentina
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DeYonker NJ, Webster CE. A Theoretical Study of Phosphoryl Transfers of Tyrosyl-DNA Phosphodiesterase I (Tdp1) and the Possibility of a "Dead-End" Phosphohistidine Intermediate. Biochemistry 2015; 54:4236-47. [PMID: 26121557 DOI: 10.1021/acs.biochem.5b00396] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tyrosyl-DNA phosphodiesterase I (Tdp1) is a DNA repair enzyme conserved across eukaryotes that catalyzes the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3'-phosphate of DNA. Atomic level details of the mechanism of Tdp1 are proposed and analyzed using a fully quantum mechanical, geometrically constrained model. The structural basis for the computational model is the vanadate-inhibited crystal structure of human Tdp1 (hTdp1, Protein Data Bank entry 1RFF ). Density functional theory computations are used to acquire thermodynamic and kinetic data along the catalytic pathway, including the phosphoryl transfer and subsequent hydrolysis. Located transition states and intermediates along the reaction coordinate suggest an associative phosphoryl transfer mechanism with five-coordinate phosphorane intermediates. Similar to both theoretical and experimental results for phospholipase D, the proposed mechanism for hTdp1 also includes the thermodynamically favorable possibility of a four-coordinate phosphohistidine "dead-end" product.
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Affiliation(s)
- Nathan J DeYonker
- ‡Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152, United States
| | - Charles Edwin Webster
- †Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States.,‡Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152, United States
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Yang F, Abdelnabby H, Xiao Y. The role of a phospholipase (PLD) in virulence of Purpureocillium lilacinum (Paecilomyces lilacinum). Microb Pathog 2015; 85:11-20. [PMID: 26026833 DOI: 10.1016/j.micpath.2015.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 05/23/2015] [Accepted: 05/26/2015] [Indexed: 01/02/2023]
Abstract
Phospholipases are key enzymes in pathogenic fungi that cleave host phospholipids, resulting in membrane destabilization and host cell penetration. However, understanding the role of phospholipases on the virulence of the filamentous fungus Purpureocillium lilacinum has been still rather limited. In this study, pld gene was characterized. It encodes the protein phospholipase D (PLD) in P. lilacinum. This gene, 3303 bp open reading frame fragment (ORF), encodes a protein of 1100 amino acids with high similarity to the same gene from Penicillium oxalicum and Aspergillus fumigatus. Secondary structure prediction showed two PLD phosphodiesterase domains (437-464 bp and 885-912 bp). The pld gene was significantly regulated during infection of Meloidogyne incognita eggs by P. lilacinum. The expression of pld gene using RT-PCR was the highest at 36 and 48 h, which introduce evidence that the presence of M. incognita may induce the expression of the pld gene in P. lilacinum. In addition, maltose and l-alanine were found to increase the expression of pld gene. An acidic environment (pH 3.0-4.0) and moderate temperatures (27-29 °C) are favorable for pld expression in P. lilacinum.
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Affiliation(s)
- Fan Yang
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Hazem Abdelnabby
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Department of Plant Protection, Faculty of Agriculture, Benha University, Qaliubia 13736, Egypt
| | - Yannong Xiao
- Key Laboratory of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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46
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Nelson RK, Frohman MA. Physiological and pathophysiological roles for phospholipase D. J Lipid Res 2015; 56:2229-37. [PMID: 25926691 DOI: 10.1194/jlr.r059220] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 11/20/2022] Open
Abstract
Individual members of the mammalian phospholipase D (PLD) superfamily undertake roles that extend from generating the second messenger signaling lipid, phosphatidic acid, through hydrolysis of the membrane phospholipid, phosphatidylcholine, to functioning as an endonuclease to generate small RNAs and facilitating membrane vesicle trafficking through seemingly nonenzymatic mechanisms. With recent advances in genome-wide association studies, RNA interference screens, next-generation sequencing approaches, and phenotypic analyses of knockout mice, roles for PLD family members are being uncovered in autoimmune, infectious neurodegenerative, and cardiovascular disease, as well as in cancer. Some of these disease settings pose opportunities for small molecule inhibitory therapeutics, which are currently in development.
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Affiliation(s)
- Rochelle K Nelson
- Graduate Program in Physiology and Biophysics Stony Brook University, Stony Brook, NY
| | - Michael A Frohman
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY
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47
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Comeaux EQ, van Waardenburg RCAM. Tyrosyl-DNA phosphodiesterase I resolves both naturally and chemically induced DNA adducts and its potential as a therapeutic target. Drug Metab Rev 2014; 46:494-507. [PMID: 25327705 DOI: 10.3109/03602532.2014.971957] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA is subject to a wide range of insults, resulting from endogenous and exogenous sources that need to be metabolized/resolved to maintain genome integrity. Tyrosyl-DNA phosphodiesterase I (Tdp1) is a eukaryotic DNA repair enzyme that catalyzes the removal of covalent 3'-DNA adducts. As a phospholipase D superfamily member Tdp1 utilizes two catalytic histidines each within a His-Lys-Asn motif. Tdp1 was discovered for its ability to hydrolyze the 3'-phospho-tyrosyl that in the cell covalently links DNA Topoisomerase I (Topo1) and DNA. Tdp1's list of substrates has since grown and can be divided into two groups: protein-DNA adducts, such as camptothecin stabilized Topo1-DNA adducts, and modified nucleotides, including oxidized nucleotides and chain terminating nucleoside analogs. Since many of Tdp1's substrates are generated by clinically relevant chemotherapeutics, Tdp1 became a therapeutic target for molecularly targeted small molecules. Tdp1's unique catalytic cycle allows for two different targeting strategies: (1) the intuitive inhibition of Tdp1 catalysis to prevent Tdp1-mediated repair of chemotherapeutically induced DNA adducts, thereby enhancing their toxicity and (2) stabilization of the Tdp1-DNA covalent reaction intermediate, prevents resolution of Tdp1-DNA adduct and increases the half-life of this potentially toxic DNA adduct. This concept is best illustrated by a catalytic Tdp1 mutant that forms the molecular basis of the autosomal recessive neurodegenerative disease spinocerebellar ataxia with axonal neuropathy, and results in an increased stability of its Tdp1-DNA reaction intermediate. Here, we will discuss Tdp1 catalysis from a structure-function perspective, Tdp1 substrates and Tdp1 potential as a therapeutic target.
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Affiliation(s)
- Evan Q Comeaux
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham , Birmingham, AL , USA
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48
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Mahankali M, Alter G, Gomez-Cambronero J. Mechanism of enzymatic reaction and protein-protein interactions of PLD from a 3D structural model. Cell Signal 2014; 27:69-81. [PMID: 25308783 DOI: 10.1016/j.cellsig.2014.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 09/12/2014] [Indexed: 10/24/2022]
Abstract
The phospholipase D (PLD) superfamily catalyzes the hydrolysis of cell membrane phospholipids generating the key intracellular lipid second messenger phosphatidic acid. However, there is not yet any resolved structure either from a crystallized protein or from NMR of any mammalian PLDs. We propose here a 3D model of the PLD2 by combining homology and ab initio 3 dimensional structural modeling methods, and docking conformation. This model is in agreement with the biochemical and physiological behavior of PLD in cells. For the lipase activity, the N- and C-terminal histidines of the HKD motifs (His 442/His 756) form a catalytic pocket, which accommodates phosphatidylcholine head group (but not phosphatidylethanolamine or phosphatidyl serine). The model explains the mechanism of the reaction catalysis, with nucleophilic attacks of His 442 and water, the latter aided by His 756. Further, the secondary structure regions superimposed with bacterial PLD crystal structure, which indicated an agreement with the model. It also explains protein-protein interactions, such as PLD2-Rac2 transmodulation (with a 1:2 stoichiometry) and PLD2 GEF activity both relevant for cell migration, as well as the existence of binding sites for phosphoinositides such as PIP2. These consist of R236/W238 and R557/W563 and a novel PIP2 binding site in the PH domain of PLD2, specifically R210/R212/W233. In each of these, the polar inositol ring is oriented towards the basic amino acid Arginine. Since tumor-aggravating properties have been found in mice overexpressing PLD2 enzyme, the 3D model of PLD2 will be also useful, to a large extent, in developing pharmaceuticals to modulate its in vivo activity.
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Affiliation(s)
- Madhu Mahankali
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University School of Medicine, Dayton, OH 45435, USA
| | - Gerald Alter
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University School of Medicine, Dayton, OH 45435, USA
| | - Julian Gomez-Cambronero
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University School of Medicine, Dayton, OH 45435, USA.
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49
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Madyarov SR. Effect of detergents, trypsin, and bivalent metal ions on interfacial activation and functioning of phospholipase D. BIOCHEMISTRY (MOSCOW) 2014; 79:687-93. [DOI: 10.1134/s0006297914070104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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Lee GS, Park JW. Effect of Vesicle Curvature on Phospholipase D Reaction-Induced-Rupture. B KOREAN CHEM SOC 2013. [DOI: 10.5012/bkcs.2013.34.11.3223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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