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Innovative Hybrid-Alignment Annotation Method for Bioinformatics Identification and Functional Verification of a Novel Nitric Oxide Synthase in Trichomonas vaginalis. BIOLOGY 2022; 11:biology11081210. [PMID: 36009837 PMCID: PMC9404748 DOI: 10.3390/biology11081210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 08/06/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Both the annotation and identification of genes in pathogenic parasites remain challenging. As a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV). However, nitric oxide synthase (NOS) has not yet been annotated in the TV genome. By aligning whole coding sequences of TV against a thousand sequences of known proteins from other organisms via the Smith–Waterman and Needleman–Wunsch algorithms, we developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV. A novel NOS of TV (TV NOS) with a high witness-to-suspect ratio, which was originally annotated as a hydrogenase in the NCBI database, was successfully identified. We then performed in silico modeling of the protein structure and the molecular docking of all cofactors (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD)), cloned the gene, expressed and purified the protein, and ultimately performed mass spectrometry analysis and enzymatic activity assays. We clearly showed that although the predicted structure of TV NOS is not similar to that of NOS proteins of other species, all cofactor-binding motifs can interact with their ligands with high affinities. Most importantly, the purified protein is a functional NOS, as it has a high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes. Abstract Both the annotation and identification of genes in pathogenic parasites are still challenging. Although, as a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV), nitric oxide synthase (NOS) has not yet been annotated in the TV genome. We developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV via the Smith–Waterman and Needleman–Wunsch algorithms through in-depth and repeated alignment of whole coding sequences of TV against thousands of sequences of known proteins from other organisms. A novel NOS of TV (TV NOS), which was annotated as hydrogenase in the NCBI database, was successfully identified; this TV NOS had a high witness-to-suspect ratio and contained all the NOS cofactor-binding motifs (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD) motifs). To confirm this identification, we performed in silico modeling of the protein structure and cofactor docking, cloned the gene, expressed and purified the protein, performed mass spectrometry analysis, and ultimately performed an assay to measure enzymatic activity. Our data showed that although the predicted structure of the TV NOS protein was not similar to the structure of NOSs of other species, all cofactor-binding motifs could interact with their ligands with high affinities. We clearly showed that the purified protein had high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes in TV and highlights a novel NOS that might serve as a virulence factor of TV.
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Mittal A, Kakkar R. Nitric Oxide Synthases and Their Inhibitors: A Review. LETT DRUG DES DISCOV 2020. [DOI: 10.2174/1570180816666190222154457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nitric Oxide (NO), an important biological mediator, is involved in the regulation of the cardiovascular, nervous and immune systems in mammals. Synthesis of NO is catalyzed by its biosynthetic enzyme, Nitric Oxide Synthase (NOS). There are three main isoforms of the enzyme, neuronal NOS, endothelial NOS and inducible NOS, which have very similar structures but differ in their expression and activities. NO is produced in the active site of the enzyme in two distinct cycles from oxidation of the substrate L-arg (L-arginine) in nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reaction. NOS has gained considerable attention of biochemists due to its complexity and unique catalytic mechanism. The review focuses on NOS structure, its function and catalytic reaction mechanism. In particular, the review is concluded with a discussion on the role of all three isoforms of NOS in physiological and pathological conditions and their inhibitors with a focus on the role of computational techniques in their development.
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Affiliation(s)
- Anshika Mittal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
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Mittal A, Arora R, Kakkar R. Pharmacophore modeling, 3D-QSAR and molecular docking studies of quinazolines and aminopyridines as selective inhibitors of inducible nitric oxide synthase. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2019. [DOI: 10.1142/s0219633619500020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pharmacophore modeling and 3D-Quantitative Structure Activity Relationship (3D-QSAR) studies have been performed on a dataset of thirty-two quinazoline and aminopyridine derivatives to get an insight into the important structural features required for binding to inducible nitric oxide synthase (iNOS). A four-point CPH (Common Pharmacophore Hypothesis), AHPR.29, with a hydrogen bond acceptor, hydrophobic group, positively charged ionizable group and an aromatic ring, has been obtained as the best pharmacophore model. Satisfactory statistical parameters of correlation ([Formula: see text]) and cross-validated ([Formula: see text]) correlation coefficients, 0.9288 and 0.6353, respectively, show high robustness and good predictive ability of our selected model. The contour maps have been developed from this model and the analysis has provided an interpretable explanation of the effect that various features and substituents have on the potency and selectivity of inhibitors towards iNOS. Docking studies have also been performed in order to analyze the interactions between the enzyme and the inhibitors. Our proposed model can thus be further used for screening a large database of compounds and design new iNOS inhibitors.
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Affiliation(s)
- Anshika Mittal
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ritu Arora
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Rita Kakkar
- Computational Chemistry Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India
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Weisslocker-Schaetzel M, André F, Touazi N, Foresi N, Lembrouk M, Dorlet P, Frelet-Barrand A, Lamattina L, Santolini J. The NOS-like protein from the microalgae Ostreococcus tauri is a genuine and ultrafast NO-producing enzyme. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:100-111. [PMID: 29223331 DOI: 10.1016/j.plantsci.2017.09.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 09/21/2017] [Accepted: 09/24/2017] [Indexed: 05/03/2023]
Abstract
The exponential increase of genomes' sequencing has revealed the presence of NO-Synthases (NOS) throughout the tree of life, uncovering an extraordinary diversity of genetic structure and biological functions. Although NO has been shown to be a crucial mediator in plant physiology, NOS sequences seem present solely in green algae genomes, with a first identification in the picoplankton species Ostreococcus tauri. There is no rationale so far to account for the presence of NOS in this early-diverging branch of the green lineage and its absence in land plants. To address the biological function of algae NOS, we cloned, expressed and characterized the NOS oxygenase domain from Ostreococcus tauri (OtNOSoxy). We launched a phylogenetic and structural analysis of algae NOS, and achieved a 3D model of OtNOSoxy by homology modeling. We used a combination of various spectroscopies to characterize the structural and electronic fingerprints of some OtNOSoxy reaction intermediates. The analysis of OtNOSoxy catalytic activity and kinetic efficiency was achieved by stoichiometric stopped-flow. Our results highlight the conserved and particular features of OtNOSoxy structure that might explain its ultrafast NO-producing capacity. This integrative Structure-Catalysis-Function approach could be extended to the whole NOS superfamily and used for predicting potential biological activity for any new NOS.
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Affiliation(s)
- Marine Weisslocker-Schaetzel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - François André
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Nabila Touazi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Noelia Foresi
- Instituto de Investigaciones Biologicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600 Mar del Plata, Argentina, Argentina
| | - Mehdi Lembrouk
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Pierre Dorlet
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Annie Frelet-Barrand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biologicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, 7600 Mar del Plata, Argentina, Argentina
| | - Jérôme Santolini
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France.
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Shakoor A, Abdullah M, Yousaf B, Amina, Ma Y. Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016:10.1007/s11356-016-7823-6. [PMID: 27771880 DOI: 10.1007/s11356-016-7823-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 10/03/2016] [Indexed: 06/06/2023]
Abstract
Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.
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Affiliation(s)
- Awais Shakoor
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- State-Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Balal Yousaf
- CAS-Key Laboratory of Crust-Mantle Materials and the Environments, School of Earth and Space Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Amina
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Youhua Ma
- School of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China.
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Taguchi A, Yamashita A, Kawana K, Nagamatsu T, Furuya H, Inoue E, Osuga Y, Fujii T. Recent Progress in Therapeutics for Inflammation-Associated Preterm Birth. Reprod Sci 2016; 24:7-18. [DOI: 10.1177/1933719115618282] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ayumi Taguchi
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- These authors contributed equally to this work
| | - Aki Yamashita
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- These authors contributed equally to this work
| | - Kei Kawana
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Nagamatsu
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hitomi Furuya
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Inoue
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yutaka Osuga
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Fujii
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Schaap P, Barrantes I, Minx P, Sasaki N, Anderson RW, Bénard M, Biggar KK, Buchler NE, Bundschuh R, Chen X, Fronick C, Fulton L, Golderer G, Jahn N, Knoop V, Landweber LF, Maric C, Miller D, Noegel AA, Peace R, Pierron G, Sasaki T, Schallenberg-Rüdinger M, Schleicher M, Singh R, Spaller T, Storey KB, Suzuki T, Tomlinson C, Tyson JJ, Warren WC, Werner ER, Werner-Felmayer G, Wilson RK, Winckler T, Gott JM, Glöckner G, Marwan W. The Physarum polycephalum Genome Reveals Extensive Use of Prokaryotic Two-Component and Metazoan-Type Tyrosine Kinase Signaling. Genome Biol Evol 2015; 8:109-25. [PMID: 26615215 PMCID: PMC4758236 DOI: 10.1093/gbe/evv237] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2015] [Indexed: 12/13/2022] Open
Abstract
Physarum polycephalum is a well-studied microbial eukaryote with unique experimental attributes relative to other experimental model organisms. It has a sophisticated life cycle with several distinct stages including amoebal, flagellated, and plasmodial cells. It is unusual in switching between open and closed mitosis according to specific life-cycle stages. Here we present the analysis of the genome of this enigmatic and important model organism and compare it with closely related species. The genome is littered with simple and complex repeats and the coding regions are frequently interrupted by introns with a mean size of 100 bases. Complemented with extensive transcriptome data, we define approximately 31,000 gene loci, providing unexpected insights into early eukaryote evolution. We describe extensive use of histidine kinase-based two-component systems and tyrosine kinase signaling, the presence of bacterial and plant type photoreceptors (phytochromes, cryptochrome, and phototropin) and of plant-type pentatricopeptide repeat proteins, as well as metabolic pathways, and a cell cycle control system typically found in more complex eukaryotes. Our analysis characterizes P. polycephalum as a prototypical eukaryote with features attributed to the last common ancestor of Amorphea, that is, the Amoebozoa and Opisthokonts. Specifically, the presence of tyrosine kinases in Acanthamoeba and Physarum as representatives of two distantly related subdivisions of Amoebozoa argues against the later emergence of tyrosine kinase signaling in the opisthokont lineage and also against the acquisition by horizontal gene transfer.
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Affiliation(s)
- Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Israel Barrantes
- Magdeburg Centre for Systems Biology and Institute for Biology, University of Magdeburg, Magdeburg, Germany
| | - Pat Minx
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Narie Sasaki
- Department of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan
| | - Roger W Anderson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, United Kingdom
| | - Marianne Bénard
- UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), CNRS UMR-7622, Paris, France
| | - Kyle K Biggar
- Biochemistry Department, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Nicolas E Buchler
- Department of Biology and Center for Genomic and Computational Biology, Duke University, Durham Department of Physics, Duke University, Durham
| | - Ralf Bundschuh
- Department of Physics and Center for RNA Biology, The Ohio State University, Columbus Department of Chemistry & Biochemistry, The Ohio State University, Columbus Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus
| | - Xiao Chen
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton
| | - Catrina Fronick
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Lucinda Fulton
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Georg Golderer
- Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - Niels Jahn
- Genome Analysis, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Volker Knoop
- IZMB - Institut für Zelluläre und Molekulare Botanik, Universität Bonn, Bonn, Germany
| | - Laura F Landweber
- Department of Ecology & Evolutionary Biology, Princeton University, Princeton
| | - Chrystelle Maric
- Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot Paris7, Paris, France
| | - Dennis Miller
- The University of Texas at Dallas, Biological Sciences, Richardson
| | - Angelika A Noegel
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
| | - Rob Peace
- Carleton University, Ottawa, Ontario, Canada
| | - Gérard Pierron
- Institut Jacques Monod, CNRS UMR7592, Université Paris Diderot Paris7, Paris, France
| | - Taeko Sasaki
- Department of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan
| | | | - Michael Schleicher
- Institute for Anatomy III / Cell Biology, BioMedCenter, Ludwig-Maximilians-Universität, Planegg-Martinsried, Germany
| | - Reema Singh
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Thomas Spaller
- Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Jena, Germany
| | | | - Takamasa Suzuki
- Department of Biological Sciences, Graduate School of Science and JST ERATO Higashiyama Live-holonics Project, Nagoya University, Furocho, Chikusaku, Nagoya, Aichi, Japan
| | - Chad Tomlinson
- The Genome Institute, Washington University School of Medicine, St Louis
| | - John J Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg
| | - Wesley C Warren
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Ernst R Werner
- Biological Chemistry, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | | | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St Louis
| | - Thomas Winckler
- Institut für Pharmazie, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Jonatha M Gott
- Center for RNA Molecular Biology, Case Western Reserve University, School of Medicine, Cleveland
| | - Gernot Glöckner
- Institute for Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| | - Wolfgang Marwan
- Magdeburg Centre for Systems Biology and Institute for Biology, University of Magdeburg, Magdeburg, Germany
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Sarkar TS, Biswas P, Ghosh SK, Ghosh S. Nitric oxide production by necrotrophic pathogen Macrophomina phaseolina and the host plant in charcoal rot disease of jute: complexity of the interplay between necrotroph-host plant interactions. PLoS One 2014; 9:e107348. [PMID: 25208092 PMCID: PMC4160249 DOI: 10.1371/journal.pone.0107348] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/08/2014] [Indexed: 12/12/2022] Open
Abstract
M. phaseolina, a global devastating necrotrophic fungal pathogen causes charcoal rot disease in more than 500 host plants. With the aim of understanding the plant-necrotrophic pathogen interaction associated with charcoal rot disease of jute, biochemical approach was attempted to study cellular nitric oxide production under diseased condition. This is the first report on M. phaseolina infection in Corchorus capsularis (jute) plants which resulted in elevated nitric oxide, reactive nitrogen species and S nitrosothiols production in infected tissues. Time dependent nitric oxide production was also assessed with 4-Amino-5-Methylamino-2',7'-Difluorofluorescein Diacetate using single leaf experiment both in presence of M. phaseolina and xylanases obtained from fungal secretome. Cellular redox status and redox active enzymes were also assessed during plant fungal interaction. Interestingly, M. phaseolina was found to produce nitric oxide which was detected in vitro inside the mycelium and in the surrounding medium. Addition of mammalian nitric oxide synthase inhibitor could block the nitric oxide production in M. phaseolina. Bioinformatics analysis revealed nitric oxide synthase like sequence with conserved amino acid sequences in M. phaseolina genome sequence. In conclusion, the production of nitric oxide and reactive nitrogen species may have important physiological significance in necrotrophic host pathogen interaction.
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Affiliation(s)
| | - Pranjal Biswas
- Department of Biochemistry, University of Calcutta, Kolkata, India
| | - Subrata Kumar Ghosh
- Former head, Division of Crop Protection, Central Research Institute for Jute and Allied Fibres (CRIJAF), Kolkata, India
| | - Sanjay Ghosh
- Department of Biochemistry, University of Calcutta, Kolkata, India
- Centre for Research in Nanoscience and Nanotechnology (CRNN), University of Calcutta, Kolkata, India
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Samalova M, Johnson J, Illes M, Kelly S, Fricker M, Gurr S. Nitric oxide generated by the rice blast fungus Magnaporthe oryzae drives plant infection. THE NEW PHYTOLOGIST 2013; 197:207-222. [PMID: 23072575 DOI: 10.1111/j.1469-8137.2012.04368.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/31/2012] [Indexed: 05/10/2023]
Abstract
Plant-derived nitric oxide (NO) triggers defence, priming the onset of the hypersensitive response and restricting pathogen ingress during incompatibility. However, little is known about the role of pathogen-produced NO during pre-infection development and infection. We sought evidence for NO production by the rice blast fungus during early infection. NO production was measured using fluorescence of DAR-4M and the role of NO assessed using NO scavengers. The synthesis of NO was investigated by targeted knockout of genes potentially involved in NO synthesis, including nitric oxide synthase-like genes (NOL2 and NOL3) and nitrate (NIA1) and nitrite reductase (NII1), generating single and double Δnia1Δnii1, Δnia1Δnol3, and Δnol2Δnol3 mutants. We demonstrate that Magnaporthe oryzae generates NO during germination and in early development. Removal of NO delays germling development and reduces disease lesion numbers. NO is not generated by the candidate proteins tested, nor by other arginine-dependent NO systems, by polyamine oxidase activity or non-enzymatically by low pH. Furthermore, we show that, while NIA1 and NII1 are essential for nitrate assimilation, NIA1, NII1, NOL2 and NOL3 are all dispensable for pathogenicity. Development of M. oryzae and initiation of infection are critically dependent on fungal NO synthesis, but its mode of generation remains obscure.
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Affiliation(s)
- Marketa Samalova
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Jasper Johnson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Mary Illes
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Mark Fricker
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Sarah Gurr
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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Talwar PS, Gupta R, Maurya AK, Deswal R. Brassica juncea nitric oxide synthase like activity is stimulated by PKC activators and calcium suggesting modulation by PKC-like kinase. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 60:157-164. [PMID: 22947512 DOI: 10.1016/j.plaphy.2012.08.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/08/2012] [Indexed: 06/01/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule having varied physiological and regulatory roles in biological systems. The fact that nitric oxide synthase (NOS) is responsible for NO generation in animals, prompted major search for a similar enzyme in plants. Arginine dependent NOS like activity (BjNOSla) was detected in Brassica juncea seedlings using oxyhemoglobin and citrulline assays. BjNOSla showed 25% activation by NADPH (0.4 mM) and 40% by calcium (0.4 mM) but the activity was flavin mononucleotide (FMN), flavin dinucleotide (FAD) and calmodulin (CaM) independent. Pharmacological approach using mammalian NOS inhibitors, NBT (300 μM) and l-NAME (5 mM), showed significant inhibition (100% and 67% respectively) supporting that the BjNOSla operates via the oxidative pathway. Most of the BjNOSla activity (80%) was confined to shoot while root showed only 20% activity. Localization studies by NADPH-diaphorase and DAF-2DA staining showed the presence of BjNOSla in guard cells. Kinetic analysis showed positive cooperativity with calcium as reflected by a decreased K(m) (∼13%) and almost two fold increase in V(max). PMA (438 nM), a kinase activator, activated BjNOSla ∼1.9 fold while its inactive analog 4αPDD was ineffective. Calcium and PMA activated the enzyme to ∼3 folds. Interestingly, 1,2-DG6 (2.5 μM) and PS (1 μM) with calcium activated the enzyme activity to ∼7 fold. A significant inhibition of BjNOSla by PKC inhibitors-staurosporine (∼90%) and calphostin-C (∼40%), further supports involvement of PKC-like kinase. The activity was also enhanced by abiotic stress conditions (7-46%). All these findings suggest that BjNOSla generates NO via oxidative pathway and is probably regulated by phosphorylation.
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Affiliation(s)
- Pooja Saigal Talwar
- Molecular Plant Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, Delhi 110007, India
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Foresi N, Correa-Aragunde N, Parisi G, Caló G, Salerno G, Lamattina L. Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent. THE PLANT CELL 2010; 22:3816-3830. [PMID: 21119059 DOI: 10.1105/tpc.109.07351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The search for a nitric oxide synthase (NOS) sequence in the plant kingdom yielded two sequences from the recently published genomes of two green algae species of the Ostreococcus genus, O. tauri and O. lucimarinus. In this study, we characterized the sequence, protein structure, phylogeny, biochemistry, and expression of NOS from O. tauri. The amino acid sequence of O. tauri NOS was found to be 45% similar to that of human NOS. Folding assignment methods showed that O. tauri NOS can fold as the human endothelial NOS isoform. Phylogenetic analysis revealed that O. tauri NOS clusters together with putative NOS sequences of a Synechoccocus sp strain and Physarum polycephalum. This cluster appears as an outgroup of NOS representatives from metazoa. Purified recombinant O. tauri NOS has a K(m) for the substrate l-Arg of 12 ± 5 μM. Escherichia coli cells expressing recombinant O. tauri NOS have increased levels of NO and cell viability. O. tauri cultures in the exponential growth phase produce 3-fold more NOS-dependent NO than do those in the stationary phase. In O. tauri, NO production increases in high intensity light irradiation and upon addition of l-Arg, suggesting a link between NOS activity and microalgal physiology.
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Affiliation(s)
- Noelia Foresi
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
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Foresi N, Correa-Aragunde N, Parisi G, Caló G, Salerno G, Lamattina L. Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent. THE PLANT CELL 2010; 22:3816-30. [PMID: 21119059 PMCID: PMC3015112 DOI: 10.1105/tpc.109.073510] [Citation(s) in RCA: 193] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 09/17/2010] [Accepted: 11/09/2010] [Indexed: 05/18/2023]
Abstract
The search for a nitric oxide synthase (NOS) sequence in the plant kingdom yielded two sequences from the recently published genomes of two green algae species of the Ostreococcus genus, O. tauri and O. lucimarinus. In this study, we characterized the sequence, protein structure, phylogeny, biochemistry, and expression of NOS from O. tauri. The amino acid sequence of O. tauri NOS was found to be 45% similar to that of human NOS. Folding assignment methods showed that O. tauri NOS can fold as the human endothelial NOS isoform. Phylogenetic analysis revealed that O. tauri NOS clusters together with putative NOS sequences of a Synechoccocus sp strain and Physarum polycephalum. This cluster appears as an outgroup of NOS representatives from metazoa. Purified recombinant O. tauri NOS has a K(m) for the substrate l-Arg of 12 ± 5 μM. Escherichia coli cells expressing recombinant O. tauri NOS have increased levels of NO and cell viability. O. tauri cultures in the exponential growth phase produce 3-fold more NOS-dependent NO than do those in the stationary phase. In O. tauri, NO production increases in high intensity light irradiation and upon addition of l-Arg, suggesting a link between NOS activity and microalgal physiology.
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Affiliation(s)
- Noelia Foresi
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Natalia Correa-Aragunde
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Gustavo Parisi
- Centro de Estudios e Investigaciones, Universidad Nacional de Quilmes, Sáenz Peña 180, B1876BXD Bernal, Argentina
| | - Gonzalo Caló
- Centro de Investigaciones Biológicas and Centro de Estudios de Biodiversidad y Biotecnología de Mar del Plata, Fundación para Investigaciones Biológicas Aplicadas, 7600 Mar del Plata, Argentina
| | - Graciela Salerno
- Centro de Investigaciones Biológicas and Centro de Estudios de Biodiversidad y Biotecnología de Mar del Plata, Fundación para Investigaciones Biológicas Aplicadas, 7600 Mar del Plata, Argentina
| | - Lorenzo Lamattina
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
- Address correspondence to
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NO synthase: structures and mechanisms. Nitric Oxide 2010; 23:1-11. [PMID: 20303412 DOI: 10.1016/j.niox.2010.03.001] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 02/24/2010] [Accepted: 03/12/2010] [Indexed: 11/20/2022]
Abstract
Production of NO from arginine and molecular oxygen is a complex chemical reaction unique to biology. Our understanding of the chemical and regulation mechanisms of the NO synthases has developed over the past two decades, uncovering some extraordinary features. This article reviews recent progress and highlights current issues and controversies. The structure of the enzyme has now been determined almost in entirety, although it is as a selection of fragments, which are difficult to assemble unambiguously. NO synthesis is driven by electron transfer through FAD and FMN cofactors, which is controlled by calmodulin binding in the constitutive mammalian enzymes. Many of the unique structural features involved have been characterised, but the mechanics of calmodulin-dependent activation are largely unresolved. Ultimately, NO is produced in the active site by the reaction of arginine with activated heme-bound oxygen in two distinct cycles. The unique role of the tetrahydrobiopterin cofactor as an electron donor in this process has now been established, but the subsequent chemical events are currently a matter of intense speculation and debate.
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Kig C, Temizkan G. Nitric oxide as a signaling molecule in the fission yeast Schizosaccharomyces pombe. PROTOPLASMA 2009; 238:59-66. [PMID: 19795185 DOI: 10.1007/s00709-009-0074-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2009] [Accepted: 09/08/2009] [Indexed: 05/28/2023]
Abstract
Nitric oxide synthases (NOS) catalyze the synthesis of ubiquitous signaling molecule nitric oxide (NO) which controls numerous biological processes. Using a spectrofluorometric NOS assay, we have measured the rate of total NO production in the crude cell extracts of Schizosaccharomyces pombe. NO production was reduced in the absence of NOS cofactors calmodulin and tetrahydrobiopterin, and a competitive NOS inhibitor NG-nitro-L-arginine methyl ester (L-NAME) was able to cause a statistically significant inhibition on the rate of total NO production. These results, for the first time, provide evidence that an enzyme with a NOS-like activity may be present in the fission yeast. In order to assess the possible regulatory roles of NO as a signaling molecule in this yeast, using the differential display technique, we screened for NO-responsive genes whose expression decreased upon exposure to L-NAME and increased in response to an NO donor, sodium nitroprusside treatment. Differential expression patterns of byr1, pek1, sid1, and wis1 genes were confirmed by quantitative real-time PCR. The physiological experiments performed based on the functions and molecular interactions of these genes have pointed to the possibility that NO production might be required for sporulation in S. pombe. Taken together, these findings suggest that NO may function as a signaling molecule which can induce both transcriptional and physiological changes in the fission yeast. Hence, these data also imply that S. pombe can be used as a model system for investigating the mechanisms underlying NO-related complex signaling pathways.
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Affiliation(s)
- Cenk Kig
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134 Istanbul, Turkey.
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