1
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Amos BK, Pook V, Prates E, Stork J, Shah M, Jacobson DA, DeBolt S. Discovery and Characterization of Fluopipamine, a Putative Cellulose Synthase 1 Antagonist within Arabidopsis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:3171-3179. [PMID: 38291808 PMCID: PMC10870765 DOI: 10.1021/acs.jafc.3c05199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 02/01/2024]
Abstract
Herbicide-resistant weeds are increasingly a problem in crop fields when exposed to similar chemistry over time. To avoid future yield losses, identifying herbicidal chemistry needs to be accelerated. We screened 50,000 small molecules using a liquid-handling robot and light microscopy focusing on pre-emergent herbicides in the family of cellulose biosynthesis inhibitors. Through phenotypic, chemical, genetic, and in silico methods we uncovered 6-{[4-(2-fluorophenyl)-1-piperazinyl]methyl}-N-(2-methoxy-5-methylphenyl)-1,3,5-triazine-2,4-diamine (fluopipamine). Symptomologies support fluopipamine as a putative antagonist of cellulose synthase enzyme 1 (CESA1) from Arabidopsis (Arabidopsis thaliana). Ectopic lignification, inhibition of etiolation, phenotypes including loss of anisotropic cellular expansion, swollen roots, and live cell imaging link fluopipamine to cellulose biosynthesis inhibition. Radiolabeled glucose incorporation of cellulose decreased in short-duration experiments when seedlings were incubated in fluopipamine. To elucidate the mechanism, ethylmethanesulfonate mutagenized M2 seedlings were screened for fluopipamine resistance. Two loci of genetic resistance were linked to CESA1. In silico docking of fluopipamine, quinoxyphen, and flupoxam against various CESA1 mutations suggests that an alternative binding site at the interface between CESA proteins is necessary to preserve cellulose polymerization in compound presence. These data uncovered potential fundamental mechanisms of cellulose biosynthesis in plants along with feasible leads for herbicidal uses.
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Affiliation(s)
- B Kirtley Amos
- Electrical
and Computer Engineering, North Carolina
State University, Raleigh, North Carolina 27606, United States
- N.C.
Plant Sciences Initiative, North Carolina
State University, Raleigh, North Carolina 27606, United States
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Victoria Pook
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Erica Prates
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jozsef Stork
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
| | - Manesh Shah
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Daniel A. Jacobson
- Biosciences
Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Center
for Bioenergy Innovation, Oak Ridge National
Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Seth DeBolt
- Department
of Horticulture, University of Kentucky, Lexington, Kentucky 40546, United States
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2
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Antony N. Dodd. THE NEW PHYTOLOGIST 2024; 241:32-34. [PMID: 38058282 DOI: 10.1111/nph.19232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
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3
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El Houari I, Klíma P, Baekelandt A, Staswick PE, Uzunova V, Del Genio CI, Steenackers W, Dobrev PI, Filepová R, Novák O, Napier R, Petrášek J, Inzé D, Boerjan W, Vanholme B. Non-specific effects of the CINNAMATE-4-HYDROXYLASE inhibitor piperonylic acid. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37036146 DOI: 10.1111/tpj.16237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Chemical inhibitors are often implemented for the functional characterization of genes to overcome the limitations associated with genetic approaches. Although it is well established that the specificity of the compound is key to success of a pharmacological approach, off-target effects are often overlooked or simply neglected in a complex biological setting. Here we illustrate the cause and implications of such secondary effects by focusing on piperonylic acid (PA), an inhibitor of CINNAMATE-4-HYDROXYLASE (C4H) that is frequently used to investigate the involvement of lignin during plant growth and development. When supplied to plants, we found that PA is recognized as a substrate by GRETCHEN HAGEN 3.6 (GH3.6), an amido synthetase involved in the formation of the indole-3-acetic acid (IAA) conjugate IAA-Asp. By competing for the same enzyme, PA interferes with IAA conjugation, resulting in an increase in IAA concentrations in the plant. In line with the broad substrate specificity of the GH3 family of enzymes, treatment with PA increased not only IAA levels but also those of other GH3-conjugated phytohormones, namely jasmonic acid and salicylic acid. Finally, we found that interference with the endogenous function of GH3s potentially contributes to phenotypes previously observed upon PA treatment. We conclude that deregulation of phytohormone homeostasis by surrogate occupation of the conjugation machinery in the plant is likely a general phenomenon when using chemical inhibitors. Our results hereby provide a novel and important basis for future reference in studies using chemical inhibitors.
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Affiliation(s)
- Ilias El Houari
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Petr Klíma
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Paul E Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Veselina Uzunova
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Charo I Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, Coventry University, Prior Street, Coventry, CV1 5FB, UK
| | - Ward Steenackers
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Petre I Dobrev
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Roberta Filepová
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ondrej Novák
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jan Petrášek
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 43, Prague 2, Czech Republic
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Bartel Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
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4
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Lardon R, Trinh HK, Xu X, Vu LD, Van De Cotte B, Pernisová M, Vanneste S, De Smet I, Geelen D. Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants. FRONTIERS IN PLANT SCIENCE 2022; 13:894208. [PMID: 36684719 PMCID: PMC9847488 DOI: 10.3389/fpls.2022.894208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.
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Affiliation(s)
- Robin Lardon
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hoang Khai Trinh
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Biotechnology Research and Development Institute, Can Tho University, Can Tho, Vietnam
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Markéta Pernisová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Steffen Vanneste
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon, South Korea
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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5
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Bloch I, Haviv H, Rapoport I, Cohen E, Shushan RSB, Dotan N, Sher I, Hacham Y, Amir R, Gal M. Discovery and characterization of small molecule inhibitors of cystathionine gamma-synthase with in planta activity. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1785-1797. [PMID: 33773037 PMCID: PMC8428831 DOI: 10.1111/pbi.13591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 03/15/2021] [Accepted: 03/21/2021] [Indexed: 06/12/2023]
Abstract
The synthesis of essential amino acids in plants is pivotal for their viability and growth, and these cellular pathways are therefore targeted for the discovery of new molecules for weed control. Herein, we describe the discovery and design of small molecule inhibitors of cystathionine gamma-synthase, a key enzyme in the biosynthesis of methionine. Based on in silico screening and filtering of a large molecular database followed by the in vitro selection of molecules, we identified small molecules capable of binding the target enzyme. Molecular modelling of the interaction and direct biophysical binding enabled us to explore a focussed chemical expansion set of molecules characterized by an active phenyl-benzamide chemical group. These molecules are bio-active and efficiently inhibit the viability of BY-2 tobacco cells and seedlings growth of Arabidopsis thaliana on agar plates.
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Affiliation(s)
- Itai Bloch
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
| | - Hadar Haviv
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
| | | | - Elad Cohen
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
| | | | - Nesly Dotan
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
| | - Inbal Sher
- Department of Oral BiologyThe Goldschleger School of Dental MedicineSackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Yael Hacham
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
- Tel‐Hai CollegeUpper GalileeIsrael
| | - Rachel Amir
- Migal – Galilee Technology CenterKiryat ShmonaIsrael
- Tel‐Hai CollegeUpper GalileeIsrael
| | - Maayan Gal
- Department of Oral BiologyThe Goldschleger School of Dental MedicineSackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
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6
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Luzarowski M, Skirycz A. Emerging strategies for the identification of protein-metabolite interactions. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4605-4618. [PMID: 31087097 PMCID: PMC6760282 DOI: 10.1093/jxb/erz228] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 05/10/2019] [Indexed: 05/31/2023]
Abstract
Interactions between biological molecules enable life. The significance of a cell-wide understanding of molecular complexes is thus obvious. In comparison to protein-protein interactions, protein-metabolite interactions remain under-studied. However, this has been gradually changing due to technological progress. Here, we focus on the interactions between ligands and receptors, the triggers of signalling events. While the number of small molecules with proven or proposed signalling roles is rapidly growing, most of their protein receptors remain unknown. Conversely, there are numerous signalling proteins with predicted ligand-binding domains for which the identities of the metabolite counterparts remain elusive. Here, we discuss the current biochemical strategies for identifying protein-metabolite interactions and how they can be used to characterize known metabolite regulators and identify novel ones.
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Affiliation(s)
- Marcin Luzarowski
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
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7
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Li W, Li H, Xu P, Xie Z, Ye Y, Li L, Li D, Zhang Y, Li L, Zhao Y. Identification of Auxin Activity Like 1, a chemical with weak functions in auxin signaling pathway. PLANT MOLECULAR BIOLOGY 2018; 98:275-287. [PMID: 30311174 DOI: 10.1007/s11103-018-0779-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/17/2018] [Indexed: 05/05/2023]
Abstract
A new synthetic auxin AAL1 with new structure was identified. Different from known auxins, it has weak effects. By AAL1, we found specific amino acids could restore the effects of auxin with similar structure. Auxin, one of the most important phytohormones, plays crucial roles in plant growth, development and environmental response. Although many critical regulators have been identified in auxin signaling pathway, some factors, especially those with weak fine-tuning roles, are still yet to be discovered. Through chemical genetic screenings, we identified a small molecule, Auxin Activity Like 1 (AAL1), which can effectively inhibit dark-grown Arabidopsis thaliana seedlings. Genetic screening identified AAL1 resistant mutants are also hyposensitive to indole-3-acetic acid (IAA) and 2,4-dichlorophenoxyacetic acid (2,4-D). AAL1 resistant mutants such as shy2-3c and ecr1-2 are well characterized as mutants in auxin signaling pathway. Genetic studies showed that AAL1 functions through auxin receptor Transport Inhibitor Response1 (TIR1) and its functions depend on auxin influx and efflux carriers. Compared with known auxins, AAL1 exhibits relatively weak effects on plant growth, with 20 µM and 50 µM IC50 (half growth inhibition chemical concentration) in root and hypocotyl growth respectively. Interestingly, we found the inhibitory effects of AAL1 and IAA could be partially restored by tyrosine and tryptophan respectively, suggesting some amino acids can also affect auxin signaling pathway in a moderate manner. Taken together, our results demonstrate that AAL1 acts through auxin signaling pathway, and AAL1, as a weak auxin activity analog, provides us a tool to study weak genetic interactions in auxin pathway.
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Affiliation(s)
- Wenbo Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Haimin Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Peng Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhi Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yajin Ye
- University of Chinese Academy of Sciences, Shanghai, 200032, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lingting Li
- University of Chinese Academy of Sciences, Shanghai, 200032, China
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Deqiang Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yijing Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yang Zhao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 68 Wenchang Road, Yunnan, 650000, China.
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8
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Joglekar S, Suliman M, Bartsch M, Halder V, Maintz J, Bautor J, Zeier J, Parker JE, Kombrink E. Chemical Activation of EDS1/PAD4 Signaling Leading to Pathogen Resistance in Arabidopsis. PLANT & CELL PHYSIOLOGY 2018; 59:1592-1607. [PMID: 29931201 DOI: 10.1093/pcp/pcy106] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Indexed: 05/20/2023]
Abstract
In a chemical screen we identified thaxtomin A (TXA), a phytotoxin from plant pathogenic Streptomyces scabies, as a selective and potent activator of FLAVIN-DEPENDENT MONOOXYGENASE1 (FMO1) expression in Arabidopsis (Arabidopsis thaliana). TXA induction of FMO1 was unrelated to the production of reactive oxygen species (ROS), plant cell death or its known inhibition of cellulose synthesis. TXA-stimulated FMO1 expression was strictly dependent on ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) but independent of salicylic acid (SA) synthesis via ISOCHORISMATE SYNTHASE1 (ICS1). TXA induced the expression of several EDS1/PAD4-regulated genes, including EDS1, PAD4, SENESCENCE ASSOCIATED GENE101 (SAG101), ICS1, AGD2-LIKE DEFENSE RESPONSE PROTEIN1 (ALD1) and PATHOGENESIS-RELATED PROTEIN1 (PR1), and accumulation of SA. Notably, enhanced ALD1 expression did not result in accumulation of the product pipecolic acid (PIP), which promotes FMO1 expression during biologically induced systemic acquired resistance. TXA treatment preferentially stimulated expression of PAD4 compared with EDS1, which was mirrored by PAD4 protein accumulation, suggesting that TXA leads to increased PAD4 availability to form EDS1-PAD4 signaling complexes. Also, TXA treatment of Arabidopsis plants led to enhanced disease resistance to bacterial and oomycete infection, which was dependent on EDS1 and PAD4, as well as on FMO1 and ICS1. Collectively, the data identify TXA as a potentially useful chemical tool to conditionally activate and interrogate EDS1- and PAD4-controlled pathways in plant immunity.
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Affiliation(s)
- Shachi Joglekar
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Mohamed Suliman
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Michael Bartsch
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Vivek Halder
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jens Maintz
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jaqueline Bautor
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jürgen Zeier
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Jane E Parker
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Erich Kombrink
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
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9
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Wase N, Black P, DiRusso C. Innovations in improving lipid production: Algal chemical genetics. Prog Lipid Res 2018; 71:101-123. [DOI: 10.1016/j.plipres.2018.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/25/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
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10
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Amos BK, Pook VG, Debolt S. Optimizing the Use of a Liquid Handling Robot to Conduct a High Throughput Forward Chemical Genetics Screen of Arabidopsis thaliana. J Vis Exp 2018:57393. [PMID: 29757282 PMCID: PMC6101032 DOI: 10.3791/57393] [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: 12/14/2022] Open
Abstract
Chemical genetics is increasingly being employed to decode traits in plants that may be recalcitrant to traditional genetics due to gene redundancy or lethality. However, the probability of a synthetic small molecule being bioactive is low; therefore, thousands of molecules must be tested in order to find those of interest. Liquid handling robotics systems are designed to handle large numbers of samples, increasing the speed with which a chemical library can be screened in addition to minimizing/standardizing error. To achieve a high-throughput forward chemical genetics screen of a library of 50,000 small molecules on Arabidopsis thaliana (Arabidopsis), protocols using a bench-top multichannel liquid handling robot were developed that require minimal technician involvement. With these protocols, 3,271 small molecules were discovered that caused visible phenotypic alterations. 1,563 compounds induced short roots, 1,148 compounds altered coloration, 383 compounds caused root hair and other, non-categorized, alterations, and 177 compounds inhibited germination.
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Affiliation(s)
- B K Amos
- Department of Horticulture, University of Kentucky
| | | | - Seth Debolt
- Department of Horticulture, University of Kentucky;
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11
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Fozard S, Forde BG. Novel Micro-Phenotyping Approach to Chemical Genetic Screening for Increased Plant Tolerance to Abiotic Stress. Methods Mol Biol 2018; 1795:9-25. [PMID: 29846915 DOI: 10.1007/978-1-4939-7874-8_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Studying the effects of small molecules on root system development in the context of a large-scale chemical genetic screen has previously been a technical challenge. The recent development of novel seedling growth devices ("Phytostrips"), used in combination with standard 96-well microtiter plates, has made it possible to perform detailed studies of changes in root morphology and root system architecture following the application of a library of chemical compounds. Phytostrips were originally designed to allow automated robotic capture of images of roots and shoots of the model species Arabidopsis thaliana, but can also be used for manual screens that are more laborious but do not require the investment in expensive robotics.Here we describe a protocol for the use of Phytostrips to perform chemical genetic screens that rely on clearly observable changes in root morphology or root system architecture. As an example, we describe the use of polyethylene glycol to impose an abiotic stress related to reduced water potential and the application of a chemical screen for small molecules that are able to rescue Arabidopsis root development from the disruptive effect of the polyethylene glycol treatment. The protocol we describe provides a template for the application of a multiplicity of other screens for compounds that can antagonize the effects of a range of abiotic stresses on root development.
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Affiliation(s)
- Susan Fozard
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Brian G Forde
- Lancaster Environment Centre, Lancaster University, Lancaster, UK.
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12
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Abstract
Sequence-specific nucleases (SSNs) are nowadays fundamental tools to generate mutants that impaired in genes of interest. The bioactive molecules screened in the chemical genomics studies affect specific physiological process by disrupting the function of its target protein(s). Mutation analysis of the gene(s) of target protein(s) of the screened chemical is necessary to resolve how the chemical works in plants. Clustered regularly interspersed short palindromic repeats (CRISPR) from Prevotella and Francisella 1 (Cpf1) are newly characterized RNA-directed endonuclease. Several papers have shown clearly that Cpf1 could be a versatile SSN in plant genome engineering. Cfp1 from Francisella novicida (FnCpf1) recognizes TTN as its protospacer adjacent motif (PAM). FnCpf1 utilizes a shorter PAM compared to other known Cpf1s such as AsCpf1 or LbCpf1, which use TTTN as PAM. Since PAM length can be a limiting factor in target selection, this feature of FnCpf1 is practical for targeted mutagenesis experiments. The application of FnCpf1-mediated targeted mutagenesis to the chemical genomics could accelerate to figure out the mechanism of action of screened chemicals. Here, we describe procedures for targeted mutagenesis in rice and tobacco using FnCpf1.
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Affiliation(s)
- Akira Endo
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Seiichi Toki
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan.
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High-Throughput Screening of Chemical Compound Libraries for Modulators of Salicylic Acid Signaling by In Situ Monitoring of Glucuronidase-Based Reporter Gene Expression. Methods Mol Biol 2018; 1795:49-63. [PMID: 29846918 DOI: 10.1007/978-1-4939-7874-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Salicylic acid (SA) is a vital phytohormone that is intimately involved in coordination of the complex plant defense response to pathogen attack. Many aspects of SA signaling have been unraveled by classical genetic and biochemical methods using the model plant Arabidopsis thaliana, but many details remain unknown, owing to the inherent limitations of these methods. In recent years, chemical genetics has emerged as an alternative scientific strategy to complement classical genetics by virtue of identifying bioactive chemicals or probes that act selectively on their protein targets causing either activation or inhibition. Such selective tools have the potential to create conditional and reversible chemical mutant phenotypes that may be combined with genetic mutants. Here, we describe a facile chemical screening methodology for intact Arabidopsis seedlings harboring the β-glucuronidase (GUS) reporter by directly quantifying GUS activity in situ with 4-methylumbelliferyl-β-D-glucuronide (4-MUG) as substrate. The quantitative nature of this screening assay has an obvious advantage over the also convenient histochemical GUS staining method, as it allows application of statistical procedures and unbiased hit selection based on threshold values as well as distinction between compounds with strong or weak bioactivity. We show pilot screens for chemical activators or inhibitors of salicylic acid-mediated defense signaling using the Arabidopsis line expressing the SA-inducible PR1p::GUS reporter gene. Importantly, the screening methodology provided here can be adopted for any inducible GUS reporter line.
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Identification of Chemical Inducers of the Phosphate-Starvation Signaling Pathway in A. thaliana Using Chemical Genetics. Methods Mol Biol 2018; 1795:65-84. [PMID: 29846919 DOI: 10.1007/978-1-4939-7874-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In spite of its importance for agriculture and 30 years of genetic studies, the phosphate-starvation signaling pathway, that allows plants to detect, respond, and adapt to changes in the phosphate concentration of the rhizosphere, remains poorly known. Chemical genetics has been increasingly and successfully used as a complementary approach to genetics for the dissection of signaling pathways in diverse organisms. Screens can be designed to identify chemicals interfering specifically with a pathway of interest. We designed a screen that led to the discovery of the first chemical capable to induce specifically the phosphate-starvation signaling pathway in Arabidopsis thaliana. This procedure, described here, can be adapted for the discovery of inducers or repressors of other pathways.
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15
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Ling Y, Alshareef S, Butt H, Lozano-Juste J, Li L, Galal AA, Moustafa A, Momin AA, Tashkandi M, Richardson DN, Fujii H, Arold S, Rodriguez PL, Duque P, Mahfouz MM. Pre-mRNA splicing repression triggers abiotic stress signaling in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:291-309. [PMID: 27664942 DOI: 10.1111/tpj.13383] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 05/24/2023]
Abstract
Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work has shown that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various inhibitors of AS. Here, we show that the macrolide pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA sequencing (RNA-seq) data revealed that PB mimics abiotic stress signals including salt, drought and abscisic acid (ABA). PB activates the abiotic stress- and ABA-responsive reporters RD29A::LUC and MAPKKK18::uidA in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2C phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling and post-transcriptional regulation in plants.
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Affiliation(s)
- Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Sahar Alshareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Jorge Lozano-Juste
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Lixin Li
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Aya A Galal
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Afaque A Momin
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Dale N Richardson
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Hiroaki Fujii
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Stefan Arold
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Pedro L Rodriguez
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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Fiers M, Hoogenboom J, Brunazzi A, Wennekes T, Angenent GC, Immink RGH. A plant-based chemical genomics screen for the identification of flowering inducers. PLANT METHODS 2017; 13:78. [PMID: 29026434 PMCID: PMC5627458 DOI: 10.1186/s13007-017-0230-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 09/25/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Floral timing is a carefully regulated process, in which the plant determines the optimal moment to switch from the vegetative to reproductive phase. While there are numerous genes known that control flowering time, little information is available on chemical compounds that are able to influence this process. We aimed to discover novel compounds that are able to induce flowering in the model plant Arabidopsis. For this purpose we developed a plant-based screening platform that can be used in a chemical genomics study. RESULTS Here we describe the set-up of the screening platform and various issues and pitfalls that need to be addressed in order to perform a chemical genomics screening on Arabidopsis plantlets. We describe the choice for a molecular marker, in combination with a sensitive reporter that's active in plants and is sufficiently sensitive for detection. In this particular screen, the firefly Luciferase marker was used, fused to the regulatory sequences of the floral meristem identity gene APETALA1 (AP1), which is an early marker for flowering. Using this screening platform almost 9000 compounds were screened, in triplicate, in 96-well plates at a concentration of 25 µM. One of the identified potential flowering inducing compounds was studied in more detail and named Flowering1 (F1). F1 turned out to be an analogue of the plant hormone Salicylic acid (SA) and appeared to be more potent than SA in the induction of flowering. The effect could be confirmed by watering Arabidopsis plants with SA or F1, in which F1 gave a significant reduction in time to flowering in comparison to SA treatment or the control. CONCLUSIONS In this study a chemical genomics screening platform was developed to discover compounds that can induce flowering in Arabidopsis. This platform was used successfully, to identify a compound that can speed-up flowering in Arabidopsis.
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Affiliation(s)
- Martijn Fiers
- Bioscience, Wageningen University and Research, 6700 AP Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Jorin Hoogenboom
- Laboratory of Organic Chemistry, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
| | - Alice Brunazzi
- Bioscience, Wageningen University and Research, 6700 AP Wageningen, The Netherlands
| | - Tom Wennekes
- Laboratory of Organic Chemistry, Wageningen University and Research, 6708 WE Wageningen, The Netherlands
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Gerco C. Angenent
- Bioscience, Wageningen University and Research, 6700 AP Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Richard G. H. Immink
- Bioscience, Wageningen University and Research, 6700 AP Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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17
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Ong WD, Okubo-Kurihara E, Kurihara Y, Shimada S, Makita Y, Kawashima M, Honda K, Kondoh Y, Watanabe N, Osada H, Cutler SR, Sudesh K, Matsui M. Chemical-Induced Inhibition of Blue Light-Mediated Seedling Development Caused by Disruption of Upstream Signal Transduction Involving Cryptochromes in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2017; 58:95-105. [PMID: 28011868 DOI: 10.1093/pcp/pcw181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Plants have a remarkable ability to perceive and respond to various wavelengths of light and initiate regulation of different cascades of light signaling and molecular components. While the perception of red light and the mechanisms of its signaling involving phytochromes are largely known, knowledge of the mechanisms of blue light signaling is still limited. Chemical genetics involves the use of diverse small active or synthetic molecules to evaluate biological processes. By combining chemicals and analyzing the effects they have on plant morphology, we identified a chemical, 3-bromo-7-nitroindazole (3B7N), that promotes hypocotyl elongation of wild-type Arabidopsis only under continuous blue light. Further evaluation with loss-of-function mutants confirmed that 3B7N inhibits photomorphogenesis through cryptochrome-mediated light signaling. Microarray analysis demonstrated that the effect of 3B7N treatment on gene expression in cry1cry2 is considerably smaller than that in the wild type, indicating that 3B7N specifically interrupts cryptochrome function in the control of seedling development in a light-dependent manner. We demonstrated that 3B7N directly binds to CRY1 protein using an in vitro binding assay. These results suggest that 3B7N is a novel chemical that directly inhibits plant cryptochrome function by physical binding. The application of 3B7N can be used on other plants to study further the blue light mechanism and the genetic control of cryptochromes in the growth and development of plant species.
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Affiliation(s)
- Wen-Dee Ong
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Emiko Okubo-Kurihara
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Yukio Kurihara
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Setsuko Shimada
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Yuko Makita
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Mika Kawashima
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Kaori Honda
- Bio-Active Compounds Discovery Research Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Nobumoto Watanabe
- Bio-Active Compounds Discovery Research Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Sean R Cutler
- Department of Botany and Plant Sciences, Center for Plant Cell Biology and Institute for Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Kumar Sudesh
- Ecobiomaterial Research Laboratory, School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Minami Matsui
- Synthetic Genomics Research Group, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
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Mark C, Zór K, Heiskanen A, Dufva M, Emnéus J, Finnie C. Monitoring intra- and extracellular redox capacity of intact barley aleurone layers responding to phytohormones. Anal Biochem 2016; 515:1-8. [PMID: 27641112 DOI: 10.1016/j.ab.2016.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 11/29/2022]
Abstract
Redox regulation is important for numerous processes in plant cells including abiotic stress, pathogen defence, tissue development, seed germination and programmed cell death. However, there are few methods allowing redox homeostasis to be addressed in whole plant cells, providing insight into the intact in vivo environment. An electrochemical redox assay that applies the menadione-ferricyanide double mediator is used to assess changes in the intracellular and extracellular redox environment in living aleurone layers of barley (Hordeum vulgare cv. Himalaya) grains, which respond to the phytohormones gibberellic acid and abscisic acid. Gibberellic acid is shown to elicit a mobilisation of electrons as detected by an increase in the reducing capacity of the aleurone layers. By taking advantage of the membrane-permeable menadione/menadiol redox pair to probe the membrane-impermeable ferricyanide/ferrocyanide redox pair, the mobilisation of electrons was dissected into an intracellular and an extracellular, plasma membrane-associated component. The intracellular and extracellular increases in reducing capacity were both suppressed when the aleurone layers were incubated with abscisic acid. By probing redox levels in intact plant tissue, the method provides a complementary approach to assays of reactive oxygen species and redox-related enzyme activities in tissue extracts.
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Affiliation(s)
- Christina Mark
- Agricultural and Environmental Proteomics, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs.Lyngby, Denmark
| | - Kinga Zór
- Bioanalytics, Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs.Lyngby, Denmark
| | - Arto Heiskanen
- Bioanalytics, Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs.Lyngby, Denmark
| | - Martin Dufva
- Fluidic Array Systems and Technology, Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs.Lyngby, Denmark
| | - Jenny Emnéus
- Bioanalytics, Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs.Lyngby, Denmark
| | - Christine Finnie
- Agricultural and Environmental Proteomics, Department of Systems Biology, Technical University of Denmark, DK-2800 Kgs.Lyngby, Denmark; Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark.
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19
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Hou X, Rivers J, León P, McQuinn RP, Pogson BJ. Synthesis and Function of Apocarotenoid Signals in Plants. TRENDS IN PLANT SCIENCE 2016; 21:792-803. [PMID: 27344539 DOI: 10.1016/j.tplants.2016.06.001] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 05/20/2016] [Accepted: 06/02/2016] [Indexed: 05/17/2023]
Abstract
In plants, carotenoids are essential for photosynthesis and photoprotection. However, carotenoids are not the end products of the pathway; apocarotenoids are produced by carotenoid cleavage dioxygenases (CCDs) or non-enzymatic processes. Apocarotenoids are more soluble or volatile than carotenoids but they are not simply breakdown products, as there can be modifications post-cleavage and their functions include hormones, volatiles, and signals. Evidence is emerging for a class of apocarotenoids, here referred to as apocarotenoid signals (ACSs), that have regulatory roles throughout plant development beyond those ascribed to abscisic acid (ABA) and strigolactone (SL). In this context we review studies of carotenoid feedback regulation, chloroplast biogenesis, stress signaling, and leaf and root development providing evidence that apocarotenoids may fine-tune plant development and responses to environmental stimuli.
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Affiliation(s)
- Xin Hou
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - John Rivers
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Patricia León
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62210, Mexico
| | - Ryan P McQuinn
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra ACT 2601, Australia.
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20
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Engqvist MKM. Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes. FRONTIERS IN PLANT SCIENCE 2016; 7:1127. [PMID: 27516767 PMCID: PMC4963410 DOI: 10.3389/fpls.2016.01127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/14/2016] [Indexed: 05/15/2023]
Abstract
The biology of living organisms is determined by the action and interaction of a large number of individual gene products, each with specific functions. Discovering and annotating the function of gene products is key to our understanding of these organisms. Controlled experiments and bioinformatic predictions both contribute to functional gene annotation. For most species it is difficult to gain an overview of what portion of gene annotations are based on experiments and what portion represent predictions. Here, I survey the current state of experimental knowledge of enzymes and metabolism in Arabidopsis thaliana as well as eleven economically important crops and forestry trees - with a particular focus on reactions involving organic acids in central metabolism. I illustrate the limited availability of experimental data for functional annotation of enzymes in most of these species. Many enzymes involved in metabolism of citrate, malate, fumarate, lactate, and glycolate in crops and forestry trees have not been characterized. Furthermore, enzymes involved in key biosynthetic pathways which shape important traits in crops and forestry trees have not been characterized. I argue for the development of novel high-throughput platforms with which limited functional characterization of gene products can be performed quickly and relatively cheaply. I refer to this approach as systems-level experimental characterization. The data collected from such platforms would form a layer intermediate between bioinformatic gene function predictions and in-depth experimental studies of these functions. Such a data layer would greatly aid in the pursuit of understanding a multiplicity of biological processes in living organisms.
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21
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Bonnot C, Pinson B, Clément M, Bernillon S, Chiarenza S, Kanno S, Kobayashi N, Delannoy E, Nakanishi TM, Nussaume L, Desnos T. A chemical genetic strategy identify the PHOSTIN, a synthetic molecule that triggers phosphate starvation responses in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2016; 209:161-76. [PMID: 26243630 PMCID: PMC4737292 DOI: 10.1111/nph.13591] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 07/01/2015] [Indexed: 05/18/2023]
Abstract
Plants display numerous strategies to cope with phosphate (Pi)-deficiency. Despite multiple genetic studies, the molecular mechanisms of low-Pi-signalling remain unknown. To validate the interest of chemical genetics to investigate this pathway we discovered and analysed the effects of PHOSTIN (PSN), a drug mimicking Pi-starvation in Arabidopsis. We assessed the effects of PSN and structural analogues on the induction of Pi-deficiency responses in mutants and wild-type and followed their accumulation in plants organs by high pressure liquid chromotography (HPLC) or mass-spectrophotometry. We show that PSN is cleaved in the growth medium, releasing its active motif (PSN11), which accumulates in plants roots. Despite the overaccumulation of Pi in the roots of treated plants, PSN11 elicits both local and systemic Pi-starvation effects. Nevertheless, albeit that the transcriptional activation of low-Pi genes by PSN11 is lost in the phr1;phl1 double mutant, neither PHO1 nor PHO2 are required for PSN11 effects. The range of local and systemic responses to Pi-starvation elicited, and their dependence on the PHR1/PHL1 function suggests that PSN11 affects an important and early step of Pi-starvation signalling. Its independence from PHO1 and PHO2 suggest the existence of unknown pathway(s), showing the usefulness of PSN and chemical genetics to bring new elements to this field.
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Affiliation(s)
- Clémence Bonnot
- CEAInstitut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des PlantesSaint‐Paul‐lez‐DuranceF‐13108France
- CNRSUnité Mixte de Recherche 7265 Biologie Végétale & Microbiologie EnvironnementaleSaint‐Paul‐lez‐DuranceF‐13108France
- Aix‐Marseille UniversitéSaint‐Paul‐lez‐DuranceF‐13108France
| | - Benoît Pinson
- CNRSUnité Mixte de Recherche 5095 Institut de Biochimie et Génétique CellulairesBordeauxF‐33077 CedexFrance
- Université Bordeaux 2 Victor SegalenBordeauxF‐33000France
| | - Mathilde Clément
- CEAInstitut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des PlantesSaint‐Paul‐lez‐DuranceF‐13108France
- CNRSUnité Mixte de Recherche 7265 Biologie Végétale & Microbiologie EnvironnementaleSaint‐Paul‐lez‐DuranceF‐13108France
- Aix‐Marseille UniversitéSaint‐Paul‐lez‐DuranceF‐13108France
| | - Stéphane Bernillon
- INRAUnité Mixte de Recherche 1332 Biologie du Fruit et PathologieCentre INRA de BordeauxVillenave d'OrnonF‐33140France
- Metabolome Facility of Bordeaux Functional Genomics CentreIBVMCentre INRA de BordeauxVillenave d'OrnonF‐33140France
| | - Serge Chiarenza
- CEAInstitut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des PlantesSaint‐Paul‐lez‐DuranceF‐13108France
- CNRSUnité Mixte de Recherche 7265 Biologie Végétale & Microbiologie EnvironnementaleSaint‐Paul‐lez‐DuranceF‐13108France
- Aix‐Marseille UniversitéSaint‐Paul‐lez‐DuranceF‐13108France
| | - Satomi Kanno
- Graduate School of Agricultural and Life Sciencesthe University of Tokyo1‐1‐1, YayoiBunkyo‐kuTokyo113‐8657Japan
| | - Natsuko Kobayashi
- Graduate School of Agricultural and Life Sciencesthe University of Tokyo1‐1‐1, YayoiBunkyo‐kuTokyo113‐8657Japan
| | - Etienne Delannoy
- CEAInstitut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des PlantesSaint‐Paul‐lez‐DuranceF‐13108France
- CNRSUnité Mixte de Recherche 7265 Biologie Végétale & Microbiologie EnvironnementaleSaint‐Paul‐lez‐DuranceF‐13108France
- Aix‐Marseille UniversitéSaint‐Paul‐lez‐DuranceF‐13108France
| | - Tomoko M. Nakanishi
- Graduate School of Agricultural and Life Sciencesthe University of Tokyo1‐1‐1, YayoiBunkyo‐kuTokyo113‐8657Japan
| | - Laurent Nussaume
- CEAInstitut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des PlantesSaint‐Paul‐lez‐DuranceF‐13108France
- CNRSUnité Mixte de Recherche 7265 Biologie Végétale & Microbiologie EnvironnementaleSaint‐Paul‐lez‐DuranceF‐13108France
- Aix‐Marseille UniversitéSaint‐Paul‐lez‐DuranceF‐13108France
| | - Thierry Desnos
- CEAInstitut de Biologie Environnementale et de Biotechnologie, Laboratoire de Biologie du Développement des PlantesSaint‐Paul‐lez‐DuranceF‐13108France
- CNRSUnité Mixte de Recherche 7265 Biologie Végétale & Microbiologie EnvironnementaleSaint‐Paul‐lez‐DuranceF‐13108France
- Aix‐Marseille UniversitéSaint‐Paul‐lez‐DuranceF‐13108France
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González N, Inzé D. Molecular systems governing leaf growth: from genes to networks. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1045-54. [PMID: 25601785 DOI: 10.1093/jxb/eru541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Arabidopsis leaf growth consists of a complex sequence of interconnected events involving cell division and cell expansion, and requiring multiple levels of genetic regulation. With classical genetics, numerous leaf growth regulators have been identified, but the picture is far from complete. With the recent advances made in quantitative phenotyping, the study of the quantitative, dynamic, and multifactorial features of leaf growth is now facilitated. The use of high-throughput phenotyping technologies to study large numbers of natural accessions or mutants, or to screen for the effects of large sets of chemicals will allow for further identification of the additional players that constitute the leaf growth regulatory networks. Only a tight co-ordination between these numerous molecular players can support the formation of a functional organ. The connections between the components of the network and their dynamics can be further disentangled through gene-stacking approaches and ultimately through mathematical modelling. In this review, we describe these different approaches that should help to obtain a holistic image of the molecular regulation of organ growth which is of high interest in view of the increasing needs for plant-derived products.
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Affiliation(s)
- Nathalie González
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
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23
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Maintz J, Cavdar M, Tamborski J, Kwaaitaal M, Huisman R, Meesters C, Kombrink E, Panstruga R. Comparative Analysis of MAMP-induced Calcium Influx in Arabidopsis Seedlings and Protoplasts. ACTA ACUST UNITED AC 2014; 55:1813-25. [DOI: 10.1093/pcp/pcu112] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Meesters C, Mönig T, Oeljeklaus J, Krahn D, Westfall CS, Hause B, Jez JM, Kaiser M, Kombrink E. A chemical inhibitor of jasmonate signaling targets JAR1 in Arabidopsis thaliana. Nat Chem Biol 2014; 10:830-6. [PMID: 25129030 DOI: 10.1038/nchembio.1591] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 06/12/2014] [Indexed: 12/11/2022]
Abstract
Jasmonates are lipid-derived plant hormones that regulate plant defenses and numerous developmental processes. Although the biosynthesis and molecular function of the most active form of the hormone, (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile), have been unraveled, it remains poorly understood how the diversity of bioactive jasmonates regulates such a multitude of plant responses. Bioactive analogs have been used as chemical tools to interrogate the diverse and dynamic processes of jasmonate action. By contrast, small molecules impairing jasmonate functions are currently unknown. Here, we report on jarin-1 as what is to our knowledge the first small-molecule inhibitor of jasmonate responses that was identified in a chemical screen using Arabidopsis thaliana. Jarin-1 impairs the activity of JA-Ile synthetase, thereby preventing the synthesis of the active hormone, JA-Ile, whereas closely related enzymes are not affected. Thus, jarin-1 may serve as a useful chemical tool in search for missing regulatory components and further dissection of the complex jasmonate signaling networks.
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Affiliation(s)
- Christian Meesters
- 1] Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany. [2] Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Timon Mönig
- Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Julian Oeljeklaus
- Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Daniel Krahn
- Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Corey S Westfall
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Joseph M Jez
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Markus Kaiser
- Center for Medical Biotechnology, Department of Chemical Biology, Faculty of Biology, University Duisburg-Essen, Essen, Germany
| | - Erich Kombrink
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Köln, Germany
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25
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Kissoudis C, van de Wiel C, Visser RGF, van der Linden G. Enhancing crop resilience to combined abiotic and biotic stress through the dissection of physiological and molecular crosstalk. FRONTIERS IN PLANT SCIENCE 2014; 5:207. [PMID: 24904607 PMCID: PMC4032886 DOI: 10.3389/fpls.2014.00207] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/28/2014] [Indexed: 05/18/2023]
Abstract
Plants growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic. Research has so far been limited to responses to individual stresses, and understanding of adaptation to combinatorial stress is limited, but indicative of non-additive interactions. Omics data analysis and functional characterization of individual genes has revealed a convergence of signaling pathways for abiotic and biotic stress adaptation. Taking into account that most data originate from imposition of individual stress factors, this review summarizes these findings in a physiological context, following the pathogenesis timeline and highlighting potential differential interactions occurring between abiotic and biotic stress signaling across the different cellular compartments and at the whole plant level. Potential effects of abiotic stress on resistance components such as extracellular receptor proteins, R-genes and systemic acquired resistance will be elaborated, as well as crosstalk at the levels of hormone, reactive oxygen species, and redox signaling. Breeding targets and strategies are proposed focusing on either manipulation and deployment of individual common regulators such as transcription factors or pyramiding of non- (negatively) interacting components such as R-genes with abiotic stress resistance genes. We propose that dissection of broad spectrum stress tolerance conferred by priming chemicals may provide an insight on stress cross regulation and additional candidate genes for improving crop performance under combined stress. Validation of the proposed strategies in lab and field experiments is a first step toward the goal of achieving tolerance to combinatorial stress in crops.
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26
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Meesters C, Kombrink E. Screening for bioactive small molecules by in vivo monitoring of luciferase-based reporter gene expression in Arabidopsis thaliana. Methods Mol Biol 2014; 1056:19-31. [PMID: 24306859 DOI: 10.1007/978-1-62703-592-7_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chemical genetics is a scientific strategy that utilizes bioactive small molecules as experimental tools to dissect biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that potentially can be used as activators or inhibitors of biochemical pathways, transport processes, regulatory networks, or developmental programs. Screening methods to identify bioactive small molecules can vary greatly, ranging from visual evaluation of phenotypic alterations to quantifying biometric traits such as enzyme activities. Here, we describe a general methodology that permits identification of compounds modulating the expression of reporter genes in Arabidopsis thaliana seedlings. The selection of luciferase-based reporter systems has the advantage that it allows in vivo imaging of reporter gene activity in a semiquantitative manner without affecting plant viability. We chose an Arabidopsis line harboring the luciferase reporter under the control of the jasmonate-inducible LOX2 promoter to screen for either activators or inhibitors of gene expression. The outlined assay conditions can readily be applied to Arabidopsis lines containing other reporter genes. Thereby screening for small molecules affecting different signaling pathways and/or phenotypic responses is possible.
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Affiliation(s)
- Christian Meesters
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Köln, Germany
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27
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Lin LC, Chueh CM, Wang LC. Investigating the phytohormone ethylene response pathway by chemical genetics. Methods Mol Biol 2014; 1056:63-77. [PMID: 24306863 DOI: 10.1007/978-1-62703-592-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Conventional mutant screening in forward genetics research is indispensible to understand the biological operation behind any given phenotype. However, several issues, such as functional redundancy and lethality or sterility resulting from null mutations, frequently impede the functional characterization of genetic mutants. As an alternative approach, chemical screening with natural products or synthetic small molecules that act as conditional mutagens allows for identifying bioactive compounds as bioprobes to overcome the above-mentioned issues. Ethylene is the simplest olefin and is one of the major phytohormones playing crucial roles in plant physiology. Most of the current information on how ethylene works in plants came primarily from genetic studies of ethylene mutants identified by conventional genetic screening two decades ago. However, we lack a complete picture of functional interaction among components in the ethylene pathway and cross talk of ethylene with other phytohormones. Here, we describe our methodology for using chemical genetics to identify small molecules that interfere with the ethylene response. We set up a phenotype-based screening platform and a reporter gene-based system for verification of the hit compounds identified by chemical screening. We have successfully identified small molecules affecting the ethylene phenotype in etiolated seedlings and showed that a group of structurally similar compounds are novel inhibitors of ACC synthase, a rate-limiting enzyme in the ethylene biosynthesis pathway.
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Affiliation(s)
- Lee-Chung Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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28
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Fonseca S, Rosado A, Vaughan-Hirsch J, Bishopp A, Chini A. Molecular locks and keys: the role of small molecules in phytohormone research. FRONTIERS IN PLANT SCIENCE 2014; 5:709. [PMID: 25566283 PMCID: PMC4269113 DOI: 10.3389/fpls.2014.00709] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 11/26/2014] [Indexed: 05/03/2023]
Abstract
Plant adaptation, growth and development rely on the integration of many environmental and endogenous signals that collectively determine the overall plant phenotypic plasticity. Plant signaling molecules, also known as phytohormones, are fundamental to this process. These molecules act at low concentrations and regulate multiple aspects of plant fitness and development via complex signaling networks. By its nature, phytohormone research lies at the interface between chemistry and biology. Classically, the scientific community has always used synthetic phytohormones and analogs to study hormone functions and responses. However, recent advances in synthetic and combinational chemistry, have allowed a new field, plant chemical biology, to emerge and this has provided a powerful tool with which to study phytohormone function. Plant chemical biology is helping to address some of the most enduring questions in phytohormone research such as: Are there still undiscovered plant hormones? How can we identify novel signaling molecules? How can plants activate specific hormone responses in a tissue-specific manner? How can we modulate hormone responses in one developmental context without inducing detrimental effects on other processes? The chemical genomics approaches rely on the identification of small molecules modulating different biological processes and have recently identified active forms of plant hormones and molecules regulating many aspects of hormone synthesis, transport and response. We envision that the field of chemical genomics will continue to provide novel molecules able to elucidate specific aspects of hormone-mediated mechanisms. In addition, compounds blocking specific responses could uncover how complex biological responses are regulated. As we gain information about such compounds we can design small alterations to the chemical structure to further alter specificity, enhance affinity or modulate the activity of these compounds.
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Affiliation(s)
- Sandra Fonseca
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología- Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Abel Rosado
- The Botany Department, University of British ColumbiaVancouver, BC, Canada
| | - John Vaughan-Hirsch
- Centre for Plant Integrative Biology, University of NottinghamNottingham, UK
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, University of NottinghamNottingham, UK
| | - Andrea Chini
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología- Consejo Superior de Investigaciones CientíficasMadrid, Spain
- *Correspondence: Andrea Chini, Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología- Consejo Superior de Investigaciones Científicas, Campus Universidad Autónoma, C/ Darwin 3, 28049 Madrid, Spain e-mail:
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29
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Genetic variation in plant CYP51s confers resistance against voriconazole, a novel inhibitor of brassinosteroid-dependent sterol biosynthesis. PLoS One 2013; 8:e53650. [PMID: 23335967 PMCID: PMC3546049 DOI: 10.1371/journal.pone.0053650] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 12/04/2012] [Indexed: 01/19/2023] Open
Abstract
Brassinosteroids (BRs) are plant steroid hormones with structural similarity to mammalian sex steroids and ecdysteroids from insects. The BRs are synthesized from sterols and are essential regulators of cell division, cell elongation and cell differentiation. In this work we show that voriconazole, an antifungal therapeutic drug used in human and veterinary medicine, severely impairs plant growth by inhibiting sterol-14α-demethylation and thereby interfering with BR production. The plant growth regulatory properties of voriconazole and related triazoles were identified in a screen for compounds with the ability to alter BR homeostasis. Voriconazole suppressed growth of the model plant Arabidopsis thaliana and of a wide range of both monocotyledonous and dicotyledonous plants. We uncover that voriconazole toxicity in plants is a result of a deficiency in BRs that stems from an inhibition of the cytochrome P450 CYP51, which catalyzes a step of BR-dependent sterol biosynthesis. Interestingly, we found that the woodland strawberry Fragaria vesca, a member of the Rosaceae, is naturally voriconazole resistant and that this resistance is conferred by the specific CYP51 variant of F. vesca. The potential of voriconazole as a novel tool for plant research is discussed.
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30
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Alfred SE, Surendra A, Le C, Lin K, Mok A, Wallace IM, Proctor M, Urbanus ML, Giaever G, Nislow C. A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis. Genome Biol 2012; 13:R105. [PMID: 23158586 PMCID: PMC3580497 DOI: 10.1186/gb-2012-13-11-r105] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/18/2012] [Indexed: 12/12/2022] Open
Abstract
Chemical biology, the interfacial discipline of using small molecules as probes to investigate biology, is a powerful approach of developing specific, rapidly acting tools that can be applied across organisms. The single-celled alga Chlamydomonas reinhardtii is an excellent model system because of its photosynthetic ability, cilia-related motility and simple genetics. We report the results of an automated fitness screen of 5,445 small molecules and subsequent assays on motility/phototaxis and photosynthesis. Cheminformatic analysis revealed active core structures and was used to construct a naïve Bayes model that successfully predicts algal bioactive compounds.
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31
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Kombrink E. Chemical and genetic exploration of jasmonate biosynthesis and signaling paths. PLANTA 2012; 236:1351-66. [PMID: 23011567 DOI: 10.1007/s00425-012-1705-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 06/27/2012] [Indexed: 05/03/2023]
Abstract
Jasmonates are lipid-derived compounds that act as signals in plant stress responses and developmental processes. Enzymes participating in biosynthesis of jasmonic acid (JA) and components of JA signaling have been extensively characterized by biochemical and molecular-genetic tools. Mutants have helped to define the pathway for synthesis of jasmonoyl-L-isoleucine (JA-Ile), the bioactive form of JA, and to identify the F-box protein COI1 as central regulatory unit. Details on the molecular mechanism of JA signaling were recently unraveled by the discovery of JAZ proteins that together with the adaptor protein NINJA and the general co-repressor TOPLESS form a transcriptional repressor complex. The current model of JA perception and signaling implies the SCF(COI1) complex operating as E3 ubiquitin ligase that upon binding of JA-Ile targets JAZ proteins for degradation by the 26S proteasome pathway, thereby allowing MYC2 and other transcription factors to activate gene expression. Chemical strategies, as integral part of jasmonate research, have helped the establishment of structure-activity relationships and the discovery of (+)-7-iso-JA-L-Ile as the major bioactive form of the hormone. The transient nature of its accumulation highlights the need to understand catabolism and inactivation of JA-Ile and recent studies indicate that oxidation of JA-Ile by cytochrome P450 monooxygenase is the major mechanism for turning JA signaling off. Plants contain numerous JA metabolites, which may have pronounced and differential bioactivity. A major challenge in the field of plant lipid signaling is to identify the cognate receptors and modes of action of these bioactive jasmonates/oxylipins.
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Affiliation(s)
- Erich Kombrink
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Köln, Germany.
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32
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Schulz P, Neukermans J, Van Der Kelen K, Mühlenbock P, Van Breusegem F, Noctor G, Teige M, Metzlaff M, Hannah MA. Chemical PARP inhibition enhances growth of Arabidopsis and reduces anthocyanin accumulation and the activation of stress protective mechanisms. PLoS One 2012; 7:e37287. [PMID: 22662141 PMCID: PMC3360695 DOI: 10.1371/journal.pone.0037287] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 04/17/2012] [Indexed: 12/29/2022] Open
Abstract
Poly-ADP-ribose polymerase (PARP) post-translationally modifies proteins through the addition of ADP-ribose polymers, yet its role in modulating plant development and stress responses is only poorly understood. The experiments presented here address some of the gaps in our understanding of its role in stress tolerance and thereby provide new insights into tolerance mechanisms and growth. Using a combination of chemical and genetic approaches, this study characterized phenotypes associated with PARP inhibition at the physiological level. Molecular analyses including gene expression analysis, measurement of primary metabolites and redox metabolites were used to understand the underlying processes. The analysis revealed that PARP inhibition represses anthocyanin and ascorbate accumulation under stress conditions. The reduction in defense is correlated with enhanced biomass production. Even in unstressed conditions protective genes and molecules are repressed by PARP inhibition. The reduced anthocyanin production was shown to be based on the repression of transcription of key regulatory and biosynthesis genes. PARP is a key factor for understanding growth and stress responses of plants. PARP inhibition allows plants to reduce protection such as anthocyanin, ascorbate or Non-Photochemical-Quenching whilst maintaining high energy levels likely enabling the observed enhancement of biomass production under stress, opening interesting perspectives for increasing crop productivity.
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Affiliation(s)
- Philipp Schulz
- Bayer CropScience NV, Gent, Belgium
- Department of Biochemistry and Cell Biology, MFPL, University of Vienna, Vienna, Austria
| | - Jenny Neukermans
- Institut de Biologie des Plantes, Université de Paris Sud XI, Orsay, France
| | - Katrien Van Der Kelen
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Per Mühlenbock
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Frank Van Breusegem
- VIB Department of Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Graham Noctor
- Institut de Biologie des Plantes, Université de Paris Sud XI, Orsay, France
| | - Markus Teige
- Department of Biochemistry and Cell Biology, MFPL, University of Vienna, Vienna, Austria
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33
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Cottier S, Mönig T, Wang Z, Svoboda J, Boland W, Kaiser M, Kombrink E. The yeast three-hybrid system as an experimental platform to identify proteins interacting with small signaling molecules in plant cells: potential and limitations. FRONTIERS IN PLANT SCIENCE 2011; 2:101. [PMID: 22639623 PMCID: PMC3355722 DOI: 10.3389/fpls.2011.00101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 12/07/2011] [Indexed: 05/18/2023]
Abstract
Chemical genetics is a powerful scientific strategy that utilizes small bioactive molecules as experimental tools to unravel biological processes. Bioactive compounds occurring in nature represent an enormous diversity of structures that can be used to dissect functions of biological systems. Once the bioactivity of a natural or synthetic compound has been critically evaluated the challenge remains to identify its molecular target and mode of action, which usually is a time-consuming and labor-intensive process. To facilitate this task, we decided to implement the yeast three-hybrid (Y3H) technology as a general experimental platform to scan the whole Arabidopsis proteome for targets of small signaling molecules. The Y3H technology is based on the yeast two-hybrid system and allows direct cloning of proteins that interact in vivo with a synthetic hybrid ligand, which comprises the biologically active molecule of interest covalently linked to methotrexate (Mtx). In yeast nucleus the hybrid ligand connects two fusion proteins: the Mtx part binding to dihydrofolate reductase fused to a DNA-binding domain (encoded in the yeast strain), and the bioactive molecule part binding to its potential protein target fused to a DNA-activating domain (encoded on a cDNA expression vector). During cDNA library screening, the formation of this ternary, transcriptional activator complex leads to reporter gene activation in yeast cells, and thereby allows selection of the putative targets of small bioactive molecules of interest. Here we present the strategy and experimental details for construction and application of a Y3H platform, including chemical synthesis of different hybrid ligands, construction of suitable cDNA libraries, the choice of yeast strains, and appropriate screening conditions. Based on the results obtained and the current literature we discuss the perspectives and limitations of the Y3H approach for identifying targets of small bioactive molecules.
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Affiliation(s)
- Stéphanie Cottier
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding ResearchKöln, Germany
| | - Timon Mönig
- Center for Medical Biotechnology, University of Duisburg–EssenEssen, Germany
| | - Zheming Wang
- Center for Medical Biotechnology, University of Duisburg–EssenEssen, Germany
| | - Jiří Svoboda
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical EcologyJena, Germany
| | - Markus Kaiser
- Center for Medical Biotechnology, University of Duisburg–EssenEssen, Germany
| | - Erich Kombrink
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding ResearchKöln, Germany
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Kepka M, Benson CL, Gonugunta VK, Nelson KM, Christmann A, Grill E, Abrams SR. Action of natural abscisic acid precursors and catabolites on abscisic acid receptor complexes. PLANT PHYSIOLOGY 2011; 157:2108-19. [PMID: 21976481 PMCID: PMC3327214 DOI: 10.1104/pp.111.182584] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The phytohormone abscisic acid (ABA) regulates stress responses and controls numerous aspects of plant growth and development. Biosynthetic precursors and catabolites of ABA have been shown to trigger ABA responses in physiological assays, but it is not clear whether these are intrinsically active or whether they are converted into ABA in planta. In this study, we analyzed the effect of ABA precursors, conjugates, and catabolites on hormone signaling in Arabidopsis (Arabidopsis thaliana). The compounds were also tested in vitro for their ability to regulate the phosphatase moiety of ABA receptor complexes consisting of the protein phosphatase 2C ABI2 and the coreceptors RCAR1/PYL9, RCAR3/PYL8, and RCAR11/PYR1. Using mutants defective in ABA biosynthesis, we show that the physiological activity associated with ABA precursors derives predominantly from their bioconversion to ABA. The ABA glucose ester conjugate, which is the most widespread storage form of ABA, showed weak ABA-like activity in germination assays and in triggering ABA signaling in protoplasts. The ABA conjugate and precursors showed negligible activity as a regulatory ligand of the ABI2/RCAR receptor complexes. The majority of ABA catabolites were inactive in our assays. To analyze the chemically unstable 8'- and 9'-hydroxylated ABA catabolites, we used stable tetralone derivatives of these compounds, which did trigger selective ABA responses. ABA synthetic analogs exhibited differential activity as regulatory ligands of different ABA receptor complexes in vitro. The data show that ABA precursors, catabolites, and conjugates have limited intrinsic bioactivity and that both natural and synthetic ABA-related compounds can be used to probe the structural requirements of ABA ligand-receptor interactions.
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Bolle C, Schneider A, Leister D. Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends. Curr Genomics 2011; 12:1-14. [PMID: 21886450 PMCID: PMC3129038 DOI: 10.2174/138920211794520187] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 10/28/2010] [Accepted: 11/23/2010] [Indexed: 11/22/2022] Open
Abstract
Since the sequencing of the nuclear genome of Arabidopsis thaliana ten years ago, various large-scale analyses of gene function have been performed in this model species. In particular, the availability of collections of lines harbouring random T-DNA or transposon insertions, which include mutants for almost all of the ~27,000 A. thaliana genes, has been crucial for the success of forward and reverse genetic approaches. In the foreseeable future, genome-wide phenotypic data from mutant analyses will become available for Arabidopsis, and will stimulate a flood of novel in-depth gene-function analyses. In this review, we consider the present status of resources and concepts for systematic studies of gene function in A. thaliana. Current perspectives on the utility of loss-of-function and gain-of-function mutants will be discussed in light of the genetic and functional redundancy of many A. thaliana genes.
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Affiliation(s)
- C Bolle
- Lehrstuhl für Molekularbiologie der Pflanzen (Botanik), Department Biologie I, Ludwig-Maximilians-Universität München, Großhaderner Str. 2, D-82152 Planegg-Martinsried, Germany
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36
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Affiliation(s)
- Eiji Nambara
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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37
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Miyashita M, Oda M, Ono Y, Komoda E, Miyagawa H. Discovery of a small peptide from combinatorial libraries that can activate the plant immune system by a jasmonic acid signaling pathway. Chembiochem 2011; 12:1323-9. [PMID: 21567702 DOI: 10.1002/cbic.201000694] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Indexed: 11/11/2022]
Abstract
Plants defend themselves by using an innate immune system that is activated in response to a variety of molecules derived from pathogens. These molecules have provided profound insights into the mechanisms of pathogen recognition and subsequent signaling pathways in plants. In the present study, we screened a combinatorial random hexapeptide library for peptides that activate the plant immune system, by using a cell-based high-throughput screening system in which H(2)O(2) generation was monitored. We discovered a novel small peptide (YGIHTH-amide, PIP-1) that triggered H(2)O(2) production in tobacco and tomato cells, but not in Arabidopsis cells. PIP-1 induced significant levels of phytoalexin biosynthesis and defense-related gene expression in tobacco cells; this is likely to be activated by a jasmonic acid pathway.
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Affiliation(s)
- Masahiro Miyashita
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
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