1
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Gong X, Haywood J, Yang WC. Chemical genetics approaches for pesticide target mining. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00148-1. [PMID: 38987060 DOI: 10.1016/j.tplants.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024]
Affiliation(s)
- Xueyan Gong
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, PR China
| | - Joel Haywood
- Center for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
| | - Wen-Chao Yang
- State Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang 550025, PR China.
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2
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Yan B, Zhang F, Wang M, Zhang Y, Fu S. Flexible wearable sensors for crop monitoring: a review. FRONTIERS IN PLANT SCIENCE 2024; 15:1406074. [PMID: 38867881 PMCID: PMC11167128 DOI: 10.3389/fpls.2024.1406074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Crops were the main source of human food, which have met the increasingly diversified demand of consumers. Sensors were used to monitor crop phenotypes and environmental information in real time, which will provide a theoretical reference for optimizing crop growth environment, resisting biotic and abiotic stresses, and improve crop yield. Compared with non-contact monitoring methods such as optical imaging and remote sensing, wearable sensing technology had higher time and spatial resolution. However, the existing crop sensors were mainly rigid mechanical structures, which were easy to cause damage to crop organs, and there were still challenges in terms of accuracy and biosafety. Emerging flexible sensors had attracted wide attention in the field of crop phenotype monitoring due to their excellent mechanical properties and biocompatibility. The article introduced the key technologies involved in the preparation of flexible wearable sensors from the aspects of flexible preparation materials and advanced preparation processes. The monitoring function of flexible sensors in crop growth was highlighted, including the monitoring of crop nutrient, physiological, ecological and growth environment information. The monitoring principle, performance together with pros and cons of each sensor were analyzed. Furthermore, the future opportunities and challenges of flexible wearable devices in crop monitoring were discussed in detail from the aspects of new sensing theory, sensing materials, sensing structures, wireless power supply technology and agricultural sensor network, which will provide reference for smart agricultural management system based on crop flexible sensors, and realize efficient management of agricultural production and resources.
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Affiliation(s)
- Baoping Yan
- College of Agricultural Equipment Engineering, Henan University of Science and Technology, Luoyang, China
| | - Fu Zhang
- College of Agricultural Equipment Engineering, Henan University of Science and Technology, Luoyang, China
| | - Mengyao Wang
- College of Agricultural Equipment Engineering, Henan University of Science and Technology, Luoyang, China
| | - Yakun Zhang
- College of Agricultural Equipment Engineering, Henan University of Science and Technology, Luoyang, China
| | - Sanling Fu
- College of Physical Engineering, Henan University of Science and Technology, Luoyang, China
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3
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Andres J, Schmunk LJ, Grau-Enguix F, Braguy J, Samodelov SL, Blomeier T, Ochoa-Fernandez R, Weber W, Al-Babili S, Alabadí D, Blázquez MA, Zurbriggen MD. Ratiometric gibberellin biosensors for the analysis of signaling dynamics and metabolism in plant protoplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:927-939. [PMID: 38525669 DOI: 10.1111/tpj.16725] [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: 07/26/2021] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Gibberellins (GAs) are major regulators of developmental and growth processes in plants. Using the degradation-based signaling mechanism of GAs, we have built transcriptional regulator (DELLA)-based, genetically encoded ratiometric biosensors as proxies for hormone quantification at high temporal resolution and sensitivity that allow dynamic, rapid and simple analysis in a plant cell system, i.e. Arabidopsis protoplasts. These ratiometric biosensors incorporate a DELLA protein as a degradation target fused to a firefly luciferase connected via a 2A peptide to a renilla luciferase as a co-expressed normalization element. We have implemented these biosensors for all five Arabidopsis DELLA proteins, GA-INSENSITIVE, GAI; REPRESSOR-of-ga1-3, RGA; RGA-like1, RGL1; RGL2 and RGL3, by applying a modular design. The sensors are highly sensitive (in the low pm range), specific and dynamic. As a proof of concept, we have tested the applicability in three domains: the study of substrate specificity and activity of putative GA-oxidases, the characterization of GA transporters, and the use as a discrimination platform coupled to a GA agonists' chemical screening. This work demonstrates the development of a genetically encoded quantitative biosensor complementary to existing tools that allow the visualization of GA in planta.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Lisa J Schmunk
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Federico Grau-Enguix
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Justine Braguy
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- The BioActives Lab, Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sophia L Samodelov
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Rocio Ochoa-Fernandez
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Salim Al-Babili
- The BioActives Lab, Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
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4
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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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5
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Kim S, Cho M, Kim TH. Novel Compounds Derived from DFPM Induce Root Growth Arrest through the Specific VICTR Alleles of Arabidopsis Accessions. Life (Basel) 2023; 13:1797. [PMID: 37763201 PMCID: PMC10532556 DOI: 10.3390/life13091797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
The small compound [5-(3,4-dichlorophenyl) furan-2-yl]-piperidine-1-ylmethanethione (DFPM) inhibits ABA responses by activating effector-triggered immune signal transduction in Arabidopsis. In addition to the known function of DFPM as an antagonist of ABA signaling, DFPM causes accession-specific root growth arrest in Arabidopsis Columbia-0 via the TIR-NLR protein VICTR (VARIATION IN COMPOUND TRIGGERED ROOT growth response) in an EDS1/PAD4/RAR1/SGT1B-dependent manner. Although DFPM could control the specific steps of various cellular responses, the functional residues for the activity of DFPM or the existence of a stronger version of DFPM modification have not been characterized thoroughly. This study analyzed twenty-two DFPM derivatives during root growth arrest, inhibition of ABA signaling, and induction of biotic signal transduction to determine critical residues that confer the specific activity of DFPM. Furthermore, this study identified two more Arabidopsis accessions that generate significant root growth arrest in response to DFPM derivatives dependent on multiple amino acid polymorphisms in the coding region of VICTR. The isolation of novel compounds, such as DFPM-5, and specific amino acid polymorphisms critical for the compound-induced responses will help determine the detailed regulatory mechanism for how DFPM regulates abiotic and biotic stress signaling interactions.
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Affiliation(s)
- Seojung Kim
- Department of Bio-Health Convergence, Duksung Women’s University, Seoul 01369, Republic of Korea
| | - Miri Cho
- Department of Bio-Health Convergence, Duksung Women’s University, Seoul 01369, Republic of Korea
| | - Tae-Houn Kim
- Department of Bio-Health Convergence, Duksung Women’s University, Seoul 01369, Republic of Korea
- Department of Biotechnology, Duksung Women’s University, Seoul 01369, Republic of Korea
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6
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Ninck S, Halder V, Krahn JH, Beisser D, Resch S, Dodds I, Scholtysik R, Bormann J, Sewald L, Gupta MD, Heilmann G, Bhandari DD, Morimoto K, Buscaill P, Hause B, van der Hoorn RAL, Kaschani F, Kaiser M. Chemoproteomics Reveals the Pan-HER Kinase Inhibitor Neratinib To Target an Arabidopsis Epoxide Hydrolase Related to Phytohormone Signaling. ACS Chem Biol 2023; 18:1076-1088. [PMID: 37115018 DOI: 10.1021/acschembio.2c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Plant phytohormone pathways are regulated by an intricate network of signaling components and modulators, many of which still remain unknown. Here, we report a forward chemical genetics approach for the identification of functional SA agonists in Arabidopsis thaliana that revealed Neratinib (Ner), a covalent pan-HER kinase inhibitor drug in humans, as a modulator of SA signaling. Instead of a protein kinase, chemoproteomics unveiled that Ner covalently modifies a surface-exposed cysteine residue of Arabidopsis epoxide hydrolase isoform 7 (AtEH7), thereby triggering its allosteric inhibition. Physiologically, the Ner application induces jasmonate metabolism in an AtEH7-dependent manner as an early response. In addition, it modulates PATHOGENESIS RELATED 1 (PR1) expression as a hallmark of SA signaling activation as a later effect. AtEH7, however, is not the exclusive target for this physiological readout induced by Ner. Although the underlying molecular mechanisms of AtEH7-dependent modulation of jasmonate signaling and Ner-induced PR1-dependent activation of SA signaling and thus defense response regulation remain unknown, our present work illustrates the powerful combination of forward chemical genetics and chemical proteomics for identifying novel phytohormone signaling modulatory factors. It also suggests that marginally explored metabolic enzymes such as epoxide hydrolases may have further physiological roles in modulating signaling.
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Affiliation(s)
- Sabrina Ninck
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Vivek Halder
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
- Chemical Biology Laboratory, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Jan H Krahn
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Daniela Beisser
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45117 Essen, Germany
| | - Sarah Resch
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Isobel Dodds
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - René Scholtysik
- Genomics and Transcriptomics Facility, Institute for Cell Biology (Tumour Research), University of Duisburg-Essen, Virchowstr. 173, 45122 Essen, Germany
| | - Jenny Bormann
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Leonard Sewald
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Mainak D Gupta
- Department of Molecular Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Geronimo Heilmann
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Deepak D Bhandari
- Department of Plant-Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, Cologne 50829, Germany
| | - Kyoko Morimoto
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Pierre Buscaill
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Bettina Hause
- Department of Metabolic and Cell Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120 Halle, Germany
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Farnusch Kaschani
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
| | - Markus Kaiser
- Department of Chemical Biology, ZMB, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
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7
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Lepri A, Longo C, Messore A, Kazmi H, Madia VN, Di Santo R, Costi R, Vittorioso P. Plants and Small Molecules: An Up-and-Coming Synergy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1729. [PMID: 37111951 PMCID: PMC10145415 DOI: 10.3390/plants12081729] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
The emergence of Arabidopsis thaliana as a model system has led to a rapid and wide improvement in molecular genetics techniques for studying gene function and regulation. However, there are still several drawbacks that cannot be easily solved with molecular genetic approaches, such as the study of unfriendly species, which are of increasing agronomic interest but are not easily transformed, thus are not prone to many molecular techniques. Chemical genetics represents a methodology able to fill this gap. Chemical genetics lies between chemistry and biology and relies on small molecules to phenocopy genetic mutations addressing specific targets. Advances in recent decades have greatly improved both target specificity and activity, expanding the application of this approach to any biological process. As for classical genetics, chemical genetics also proceeds with a forward or reverse approach depending on the nature of the study. In this review, we addressed this topic in the study of plant photomorphogenesis, stress responses and epigenetic processes. We have dealt with some cases of repurposing compounds whose activity has been previously proven in human cells and, conversely, studies where plants have been a tool for the characterization of small molecules. In addition, we delved into the chemical synthesis and improvement of some of the compounds described.
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Affiliation(s)
- A. Lepri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - C. Longo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - A. Messore
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - H. Kazmi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - V. N. Madia
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Di Santo
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Costi
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - P. Vittorioso
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
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8
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Oliveira-Garcia E, Tamang TM, Park J, Dalby M, Martin-Urdiroz M, Rodriguez Herrero C, Vu AH, Park S, Talbot NJ, Valent B. Clathrin-mediated endocytosis facilitates the internalization of Magnaporthe oryzae effectors into rice cells. THE PLANT CELL 2023:koad094. [PMID: 36976907 DOI: 10.1093/plcell/koad094] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
Fungi and oomycetes deliver effectors into living plant cells to suppress defenses and control plant processes needed for infection. Little is known about the mechanism by which these pathogens translocate effector proteins across the plasma membrane into the plant cytoplasm. The blast fungus Magnaporthe oryzae secretes cytoplasmic effectors into a specialized biotrophic interfacial complex (BIC) before translocation. Here we show that cytoplasmic effectors within BICs are packaged into punctate membranous effector compartments that are occasionally observed in the host cytoplasm. Live cell imaging with fluorescently labeled proteins in rice (Oryza sativa) showed that these effector puncta colocalize with the plant plasma membrane and with CLATHRIN LIGHT CHAIN 1, a component of clathrin-mediated endocytosis (CME). Inhibiting CME using virus-induced gene silencing and chemical treatments resulted in cytoplasmic effectors in swollen BICs lacking effector puncta. By contrast, fluorescent marker co-localization, gene silencing and chemical inhibitor studies failed to support a major role for clathrin-independent endocytosis in effector translocation. Effector localization patterns indicated that cytoplasmic effector translocation occurs underneath appressoria before invasive hyphal growth. Taken together, this study provides evidence that cytoplasmic effector translocation is mediated by clathrin-mediated endocytosis in BICs and suggests a role for M. oryzae effectors in co-opting plant endocytosis.
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Affiliation(s)
- Ely Oliveira-Garcia
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Tej Man Tamang
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS 66506, USA
| | - Jungeun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS 66506, USA
| | - Melinda Dalby
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | | | - Clara Rodriguez Herrero
- School of Biosciences, University of Exeter, Exeter, EX4 4QD, UK
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - An Hong Vu
- Department of Plant Pathology and Crop Physiology, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
| | - Sunghun Park
- Department of Horticulture and Natural Resources, Kansas State University, Manhattan, KS 66506, USA
| | - Nicholas J Talbot
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
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9
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Hayashi K, Kato N, Bashir K, Nomoto H, Nakayama M, Chini A, Takahashi S, Saito H, Watanabe R, Takaoka Y, Tanaka M, Nagano AJ, Seki M, Solano R, Ueda M. Subtype-selective agonists of plant hormone co-receptor COI1-JAZs identified from the stereoisomers of coronatine. Commun Biol 2023; 6:320. [PMID: 36966228 PMCID: PMC10039919 DOI: 10.1038/s42003-023-04709-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/14/2023] [Indexed: 03/27/2023] Open
Abstract
Severe genetic redundancy is particularly clear in gene families encoding plant hormone receptors, each subtype sharing redundant and specific functions. Genetic redundancy of receptor family members represents a major challenge for the functional dissection of each receptor subtype. A paradigmatic example is the perception of the hormone (+)-7-iso-jasmonoyl-L-isoleucine, perceived by several COI1-JAZ complexes; the specific role of each receptor subtype still remains elusive. Subtype-selective agonists of the receptor are valuable tools for analyzing the responses regulated by individual receptor subtypes. We constructed a stereoisomer library consisting of all stereochemical isomers of coronatine (COR), a mimic of the plant hormone (+)-7-iso-jasmonoyl-L-isoleucine, to identify subtype-selective agonists for COI1-JAZ co-receptors in Arabidopsis thaliana and Solanum lycopersicum. An agonist selective for the Arabidopsis COI1-JAZ9 co-receptor efficiently revealed that JAZ9 is not involved in most of the gene downregulation caused by COR, and the degradation of JAZ9-induced defense without inhibiting growth.
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Affiliation(s)
- Kengo Hayashi
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Nobuki Kato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Department of Life Sciences, SBA School of Science and Engineering, Lahore University of Management Sciences, 54792, Lahore, Pakistan
| | - Haruna Nomoto
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Misuzu Nakayama
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Andrea Chini
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Cientificas (CSIC), Campus University Autonoma, 28049, Madrid, Spain
| | - Satoshi Takahashi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Hiroaki Saito
- Faculty of Pharmaceutical Sciences, Hokuriku University, Kanazawa, 920-1181, Japan
| | - Raku Watanabe
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Yousuke Takaoka
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0017, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Roberto Solano
- Plant Molecular Genetics Department, National Centre for Biotechnology (CNB), Consejo Superior de Investigaciones Cientificas (CSIC), Campus University Autonoma, 28049, Madrid, Spain
| | - Minoru Ueda
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8578, Japan.
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10
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Jiang K, Guo H, Zhai J. Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:381-398. [PMID: 36223083 DOI: 10.1111/jipb.13384] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.
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Affiliation(s)
- Kai Jiang
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
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11
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Lu Q, Russinova E. Cellular Thermal Shift Assay for the Detection of Small Molecule-Target Interactions in Arabidopsis Cells. Methods Mol Biol 2023; 2554:21-34. [PMID: 36178618 DOI: 10.1007/978-1-0716-2624-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chemical genetics takes advantage of small molecule-protein interactions to explore various biological processes. Although an attractive alternative to classical genetics in plants, the identification of small-molecule targets remains a challenge and limits the broad use of the compounds. The cellular thermal shift assay (CETSA), based on the principle that binding of small molecules could affect the thermal stability of proteins, has been applied for target validation in plant cells. Combined with high-resolution mass spectrometry, CETSA can detect small-molecule targets by monitoring the changes in the protein thermal stability caused by the interactions with small molecules at the proteome level. Here we describe the small-molecule target validation as well as the target identification with mass spectrometry by means of CETSA.
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Affiliation(s)
- Qing Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
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12
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Hsiao AS, Huang JY. Bioimaging tools move plant physiology studies forward. FRONTIERS IN PLANT SCIENCE 2022; 13:976627. [PMID: 36204075 PMCID: PMC9530904 DOI: 10.3389/fpls.2022.976627] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Affiliation(s)
- An-Shan Hsiao
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Ji-Ying Huang
- Cell Biology Core Lab, Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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13
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Nakamichi N, Yamaguchi J, Sato A, Fujimoto KJ, Ota E. Chemical biology to dissect molecular mechanisms underlying plant circadian clocks. THE NEW PHYTOLOGIST 2022; 235:1336-1343. [PMID: 35661165 DOI: 10.1111/nph.18298] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
Circadian clocks regulate the diel rhythmic physiological activities of plants, enabling them to anticipate and adapt to day-night and seasonal changes. Genetic and biochemical approaches have suggested that transcription-translation feedback loops (TTFL) are crucial for Arabidopsis clock function. Recently, the study of chemical chronobiology has emerged as a discipline within the circadian clock field, with important and complementary discoveries from both plant and animal research. In this review, we introduce recent advances in chemical biology using small molecules to perturb plant circadian clock function through TTFL components. Studies using small molecule clock modulators have been instrumental for revealing the role of post-translational modification in the clock, or the metabolite-dependent clock input pathway, as well as for controlling clock-dependent flowering time.
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Affiliation(s)
- Norihito Nakamichi
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Junichiro Yamaguchi
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 169-8555, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Eisuke Ota
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 169-8555, Japan
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14
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Ma Q, Chang M, Drakakaki G, Russinova E. Selective chemical probes can untangle the complexity of the plant cell endomembrane system. CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102223. [PMID: 35567926 DOI: 10.1016/j.pbi.2022.102223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/18/2022] [Indexed: 06/15/2023]
Abstract
The endomembrane system is critical for plant growth and development and understanding its function and regulation is of great interest for plant biology research. Small-molecule targeting distinctive endomembrane components have proven powerful tools to dissect membrane trafficking in plant cells. However, unambiguous elucidation of the complex and dynamic trafficking processes requires chemical probes with enhanced precision. Determination of the mechanism of action of a compound, which is facilitated by various chemoproteomic approaches, opens new avenues for the improvement of its specificity. Moreover, rational molecule design and reverse chemical genetics with the aid of virtual screening and artificial intelligence will enable us to discover highly precise chemical probes more efficiently. The next decade will witness the emergence of more such accurate tools, which together with advanced live quantitative imaging techniques of subcellular phenotypes, will deepen our insights into the plant endomembrane system.
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Affiliation(s)
- Qian Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Mingqin Chang
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA.
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
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15
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Synergistic Role of Plant Extracts and Essential Oils against Multidrug Resistance and Gram-Negative Bacterial Strains Producing Extended-Spectrum β-Lactamases. Antibiotics (Basel) 2022; 11:antibiotics11070855. [PMID: 35884109 PMCID: PMC9312036 DOI: 10.3390/antibiotics11070855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 02/06/2023] Open
Abstract
Plants, being the significant and natural source of medication for humankind against several ailments with characteristic substances hidden on them, have been recognized for many centuries. Accessibility of various methodologies for the revelation of therapeutically characteristic items has opened new avenues to redefine plants as the best reservoirs of new structural types. The role of plant metabolites to hinder the development and movement of pathogenic microbes is cherished. Production of extended-spectrum β-lactamases is an amazing tolerance mechanism that hinders the antibacterial treatment of infections caused by Gram-negative bacteria and is a serious problem for the current antimicrobial compounds. The exploration of the invention from sources of plant metabolites gives sustenance against the concern of the development of resistant pathogens. Essential oils are volatile, natural, complex compounds described by a solid odor and are framed by aromatic plants as secondary metabolites. The bioactive properties of essential oils are commonly controlled by the characteristic compounds present in them. They have been commonly utilized for bactericidal, virucidal, fungicidal, antiparasitic, insecticidal, medicinal, and antioxidant applications. Alkaloids are plant secondary metabolites that have appeared to have strong pharmacological properties. The impact of alkaloids from Callistemon citrinus and Vernonia adoensis leaves on bacterial development and efflux pump activity was assessed on Pseudomonas aeruginosa. Plant-derived chemicals may have direct antibacterial activity and/or indirect antibacterial activity as antibiotic resistance modifying agents, increasing the efficiency of antibiotics when used in combination. The thorough screening of plant-derived bioactive chemicals as resistance-modifying agents, including those that can act synergistically with antibiotics, is a viable method to overcome bacterial resistance. The synergistic assessment studies with the plant extract/essential oil and the antibiotic compounds is essential with a target for achieving a redesigned model with sustainable effects which are appreciably noticeable in specific sites of the plants compared to the entirety of their individual parts.
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16
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Prieto Kullmer CN, Kautzky JA, Krska SW, Nowak T, Dreher SD, MacMillan DWC. Accelerating reaction generality and mechanistic insight through additive mapping. Science 2022; 376:532-539. [PMID: 35482871 DOI: 10.1126/science.abn1885] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Reaction generality is crucial in determining the overall impact and usefulness of synthetic methods. Typical generalization protocols require a priori mechanistic understanding and suffer when applied to complex, less understood systems. We developed an additive mapping approach that rapidly expands the utility of synthetic methods while generating concurrent mechanistic insight. Validation of this approach on the metallaphotoredox decarboxylative arylation resulted in the discovery of a phthalimide ligand additive that overcomes many lingering limitations of this reaction and has important mechanistic implications for nickel-catalyzed cross-couplings.
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Affiliation(s)
| | - Jacob A Kautzky
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
| | - Shane W Krska
- Department of Process and Analytical Chemistry, MRL, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Timothy Nowak
- Department of Discovery Chemistry, MRL, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Spencer D Dreher
- Department of Process and Analytical Chemistry, MRL, Merck & Co., Inc., Rahway, NJ 07065, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
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17
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Valuchova S, Mikulkova P, Pecinkova J, Riha K. Application of Chemical Inhibitors in Live Cell Imaging of Plant Meiosis Using Light Sheet Fluorescence Microscopy. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2484:93-105. [PMID: 35461447 DOI: 10.1007/978-1-0716-2253-7_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Live imaging combined with the application of chemical inhibitors is a powerful research tool that enables researchers to precisely time the inhibition of cellular processes and study the consequences of these perturbations. This approach is usually applied to in vitro cultivated cells that are easily accessible to chemical treatments and microscopic observations. Here we describe a method for live cell imaging of Arabidopsis meiocytes embedded within floral organs combined with the application of a chemical drug at desired timepoints during meiosis. We describe a customized solution for the Zeiss Z.1 light sheet microscope, including sample preparation and data processing, and demonstrate its utility for the analysis of meiotic progression upon spindle inhibition.
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Affiliation(s)
- Sona Valuchova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Pavlina Mikulkova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jana Pecinkova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Karel Riha
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.
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18
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Pa V, Vijayaraghavareddy P, Uttarkar A, Dawane A, D S, V A, Kc B, Niranjan V, Ms S, Cv A, Makarla U, Vemanna RS. Novel small molecules targeting bZIP23 TF improve stomatal conductance and photosynthesis under mild drought stress by regulating ABA. FEBS J 2022; 289:6058-6077. [PMID: 35445538 DOI: 10.1111/febs.16461] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022]
Abstract
Drought-induced abscisic acid (ABA) accumulation plays a key role in plant water relations by regulating stomatal movements. Although ABA helps in the survival of the plants, reduced carbon gain affects plant productivity. To improve crop productivity under mild drought stress conditions, it is necessary to manipulate ABA responses. Other research groups have used forward chemical genomics for the identification of ABA agonists and antagonists aiming to manipulate ABA biosynthesis and signalling. In the present study, we identified indolyl-ethyl amine and serotonin small molecules using a reverse chemical genomics approach, with these acting as potent inhibitors of ABA biosynthesis through transient regulation of bZIP23 transcription factor activity. In rice, wheat and soybean, each of the small molecules enhanced the germination of seeds, even in the presence of ABA. These molecules nullified the effect of ABA on intact and detached leaves, resulting in higher photosynthesis. Furthermore, these small molecules effectively reduced the transcription levels of bZIP23 targeting NCED4, PP2C49 and CO3 genes. Rice plants treated with the small molecules were found to have improved stomatal conductance, spikelet fertility and yield compared to untreated plants under mild drought stress conditions. Our results suggest that indolyl-ethyl amine and serotonin small molecules could be utilized to improve yield under mild drought conditions.
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Affiliation(s)
- Vanitha Pa
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, India.,Department of Biochemistry & Biotechnology, Annamalai University, Chidambaram, Tamil Nadu, India
| | | | - Akshay Uttarkar
- Department of Biotechnology, R.V. College of Engineering, Bengaluru, India
| | - Akashata Dawane
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sujitha D
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, India
| | - Ashwin V
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, India
| | - Babitha Kc
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Vidya Niranjan
- Department of Biotechnology, R.V. College of Engineering, Bengaluru, India
| | - Sheshshayee Ms
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, India
| | - Anuradha Cv
- Department of Biochemistry & Biotechnology, Annamalai University, Chidambaram, Tamil Nadu, India
| | - Udayakumar Makarla
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bengaluru, India
| | - Ramu S Vemanna
- Laboratory of Plant Functional Genomics, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
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19
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Uehara TN, Nonoyama T, Taki K, Kuwata K, Sato A, Fujimoto KJ, Hirota T, Matsuo H, Maeda AE, Ono A, Takahara TT, Tsutsui H, Suzuki T, Yanai T, Kay SA, Itami K, Kinoshita T, Yamaguchi J, Nakamichi N. Phosphorylation of RNA Polymerase II by CDKC;2 Maintains the Arabidopsis Circadian Clock Period. PLANT & CELL PHYSIOLOGY 2022; 63:450-462. [PMID: 35086143 PMCID: PMC9016870 DOI: 10.1093/pcp/pcac011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock is an internal timekeeping system that governs about 24 h biological rhythms of a broad range of developmental and metabolic activities. The clocks in eukaryotes are thought to rely on lineage-specific transcriptional-translational feedback loops. However, the mechanisms underlying the basic transcriptional regulation events for clock function have not yet been fully explored. Here, through a combination of chemical biology and genetic approaches, we demonstrate that phosphorylation of RNA polymerase II by CYCLIN DEPENDENT KINASE C; 2 (CDKC;2) is required for maintaining the circadian period in Arabidopsis. Chemical screening identified BML-259, the inhibitor of mammalian CDK2/CDK5, as a compound lengthening the circadian period of Arabidopsis. Short-term BML-259 treatment resulted in decreased expression of most clock-associated genes. Development of a chemical probe followed by affinity proteomics revealed that BML-259 binds to CDKC;2. Loss-of-function mutations of cdkc;2 caused a long period phenotype. In vitro experiments demonstrated that the CDKC;2 immunocomplex phosphorylates the C-terminal domain of RNA polymerase II, and BML-259 inhibits this phosphorylation. Collectively, this study suggests that transcriptional activity maintained by CDKC;2 is required for proper period length, which is an essential feature of the circadian clock in Arabidopsis.
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Affiliation(s)
| | | | | | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Kazuhiro J Fujimoto
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Hiromi Matsuo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Akari E Maeda
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Azusa Ono
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Tomoaki T Takahara
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 162-0041 Japan
| | - Hiroki Tsutsui
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, 487-8501 Japan
| | - Takeshi Yanai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, 1975 Zonal Avenue, Los Angeles, CA 90033, USA
| | - Kenichiro Itami
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
- JST ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Junichiro Yamaguchi
- *Corresponding authors: Norihito Nakamichi, E-mail, ; Junichiro Yamaguchi, E-mail,
| | - Norihito Nakamichi
- *Corresponding authors: Norihito Nakamichi, E-mail, ; Junichiro Yamaguchi, E-mail,
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20
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Proteome-wide cellular thermal shift assay reveals unexpected cross-talk between brassinosteroid and auxin signaling. Proc Natl Acad Sci U S A 2022; 119:e2118220119. [PMID: 35254915 PMCID: PMC8931322 DOI: 10.1073/pnas.2118220119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chemical genetics, which investigates biological processes using small molecules, is gaining interest in plant research. However, a major challenge is to uncover the mode of action of the small molecules. Here, we applied the cellular thermal shift assay coupled with mass spectrometry (CETSA MS) to intact Arabidopsis cells and showed that bikinin, the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, changed the thermal stability of some of its direct targets and putative GSK3-interacting proteins. In combination with phosphoproteomics, we also revealed that GSK3s phosphorylated the auxin carrier PIN-FORMED1 and regulated its polarity that is required for the vascular patterning in the leaf. Despite the growing interest in using chemical genetics in plant research, small molecule target identification remains a major challenge. The cellular thermal shift assay coupled with high-resolution mass spectrometry (CETSA MS) that monitors changes in the thermal stability of proteins caused by their interactions with small molecules, other proteins, or posttranslational modifications, allows the discovery of drug targets or the study of protein–metabolite and protein–protein interactions mainly in mammalian cells. To showcase the applicability of this method in plants, we applied CETSA MS to intact Arabidopsis thaliana cells and identified the thermal proteome of the plant-specific glycogen synthase kinase 3 (GSK3) inhibitor, bikinin. A comparison between the thermal and the phosphoproteomes of bikinin revealed the auxin efflux carrier PIN-FORMED1 (PIN1) as a substrate of the Arabidopsis GSK3s that negatively regulate the brassinosteroid signaling. We established that PIN1 phosphorylation by the GSK3s is essential for maintaining its intracellular polarity that is required for auxin-mediated regulation of vascular patterning in the leaf, thus revealing cross-talk between brassinosteroid and auxin signaling.
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21
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Lei B, Song M, Li X, Dang X, Qin R, Zhu S, An X, Liu Q, Yao X, Nie Y, Ma C. SMART v1.0: A Database for Small Molecules with Functional Implications in Plants. Interdiscip Sci 2022; 14:279-283. [PMID: 34648133 DOI: 10.1007/s12539-021-00480-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
We developed SMART v1.0 ( http://smart.omicstudio.cloud ), the first database for small molecules with functional implications in plants. The SMART database is devoted to providing and managing small molecules and their associated structural data, chemoinformatic data, protein targets, pathways and induced phenotype/function information. Currently, SMART v1.0 encompasses 1218 unique small molecules which are involved in multiple biological pathways. SMART v1.0 is featured with user-friendly interfaces, through which pathway-centered visualization of small molecules can be efficiently performed, and multiple types of searches (i.e., text search, structure similarity search and sequence similarity search) can be conveniently conducted. SMART v1.0 is also specifically designed to be a small molecule-sharing database, allowing users to release their newly discovered small molecules to public via the Contribute webpage. The SMART database will facilitate the comprehensive understanding of small molecules in complex biological processes in plants.
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Affiliation(s)
- Beilei Lei
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Minggui Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiyang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoxue Dang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Runwen Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuai Zhu
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyan An
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Qinchang Liu
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry, Department of Chemistry, Lanzhou University, Lanzhou, Gansu, China
| | - Yanming Nie
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China.
| | - Chuang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Center of Bioinformatics, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.
- Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, China.
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22
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Identification of stomatal-regulating molecules from de novo arylamine collection through aromatic C-H amination. Sci Rep 2022; 12:949. [PMID: 35042960 PMCID: PMC8766585 DOI: 10.1038/s41598-022-04947-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 01/04/2022] [Indexed: 11/08/2022] Open
Abstract
Stomata—small pores generally found on the leaves of plants—control gas exchange between plant and the atmosphere. Elucidating the mechanism that underlies such control through the regulation of stomatal opening/closing is important to understand how plants regulate photosynthesis and tolerate against drought. However, up-to-date, molecular components and their function involved in stomatal regulation are not fully understood. We challenged such problem through a chemical genetic approach by isolating and characterizing synthetic molecules that influence stomatal movement. Here, we describe that a small chemical collection, prepared during the development of C–H amination reactions, lead to the discovery of a Stomata Influencing Molecule (SIM); namely, a sulfonimidated oxazole that inhibits stomatal opening. The starting molecule SIM1 was initially isolated from screening of compounds that inhibit light induced opening of dayflower stomata. A range of SIM molecules were rapidly accessed using our state-of-the-art C–H amination technologies. This enabled an efficient structure–activity relationship (SAR) study, culminating in the discovery of a sulfonamidated oxazole derivative (SIM*) having higher activity and enhanced specificity against stomatal regulation. Biological assay results have shed some light on the mode of action of SIM molecules within the cell, which may ultimately lead to drought tolerance-conferring agrochemicals through the control of stomatal movement.
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Balcerowicz M, Shetty KN, Jones AM. Fluorescent biosensors illuminating plant hormone research. PLANT PHYSIOLOGY 2021; 187:590-602. [PMID: 35237816 PMCID: PMC8491072 DOI: 10.1093/plphys/kiab278] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/22/2021] [Indexed: 05/20/2023]
Abstract
Phytohormones act as key regulators of plant growth that coordinate developmental and physiological processes across cells, tissues and organs. As such, their levels and distribution are highly dynamic owing to changes in their biosynthesis, transport, modification and degradation that occur over space and time. Fluorescent biosensors represent ideal tools to track these dynamics with high spatiotemporal resolution in a minimally invasive manner. Substantial progress has been made in generating a diverse set of hormone sensors with recent FRET biosensors for visualising hormone concentrations complementing information provided by transcriptional, translational and degron-based reporters. In this review, we provide an update on fluorescent biosensor designs, examine the key properties that constitute an ideal hormone biosensor, discuss the use of these sensors in conjunction with in vivo hormone perturbations and highlight the latest discoveries made using these tools.
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Affiliation(s)
| | | | - Alexander M. Jones
- Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, UK
- Author for communication:
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24
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Wang T, Ye W, Wang Y, Zhang M, Aihara Y, Kinoshita T. Protease Inhibitor-Dependent Inhibition of Light-Induced Stomatal Opening. FRONTIERS IN PLANT SCIENCE 2021; 12:735328. [PMID: 34567048 PMCID: PMC8462734 DOI: 10.3389/fpls.2021.735328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Stomata in the epidermis of plants play essential roles in the regulation of photosynthesis and transpiration. Stomata open in response to blue light (BL) by phosphorylation-dependent activation of the plasma membrane (PM) H+-ATPase in guard cells. Under water stress, the plant hormone abscisic acid (ABA) promotes stomatal closure via the ABA-signaling pathway to reduce water loss. We established a chemical screening method to identify compounds that affect stomatal movements in Commelina benghalensis. We performed chemical screening using a protease inhibitor (PI) library of 130 inhibitors to identify inhibitors of stomatal movement. We discovered 17 PIs that inhibited light-induced stomatal opening by more than 50%. Further analysis of the top three inhibitors (PI1, PI2, and PI3; inhibitors of ubiquitin-specific protease 1, membrane type-1 matrix metalloproteinase, and matrix metalloproteinase-2, respectively) revealed that these inhibitors suppressed BL-induced phosphorylation of the PM H+-ATPase but had no effect on the activity of phototropins or ABA-dependent responses. The results suggest that these PIs suppress BL-induced stomatal opening at least in part by inhibiting PM H+-ATPase activity but not the ABA-signaling pathway. The targets of PI1, PI2, and PI3 were predicted by bioinformatics analyses, which provided insight into factors involved in BL-induced stomatal opening.
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Affiliation(s)
- Tenghua Wang
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Wenxiu Ye
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yin Wang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of Ministry of Education, Institute of Ecology, Peking University, Beijing, China
| | - Maoxing Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
- Department of Horticulture, International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Yusuke Aihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
| | - Toshinori Kinoshita
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
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25
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van der Woude L, Piotrowski M, Klaasse G, Paulus JK, Krahn D, Ninck S, Kaschani F, Kaiser M, Novák O, Ljung K, Bulder S, van Verk M, Snoek BL, Fiers M, Martin NI, van der Hoorn RAL, Robert S, Smeekens S, van Zanten M. The chemical compound 'Heatin' stimulates hypocotyl elongation and interferes with the Arabidopsis NIT1-subfamily of nitrilases. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1523-1540. [PMID: 33768644 PMCID: PMC8360157 DOI: 10.1111/tpj.15250] [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: 01/06/2021] [Accepted: 03/22/2021] [Indexed: 05/17/2023]
Abstract
Temperature passively affects biological processes involved in plant growth. Therefore, it is challenging to study the dedicated temperature signalling pathways that orchestrate thermomorphogenesis, a suite of elongation growth-based adaptations that enhance leaf-cooling capacity. We screened a chemical library for compounds that restored hypocotyl elongation in the pif4-2-deficient mutant background at warm temperature conditions in Arabidopsis thaliana to identify modulators of thermomorphogenesis. The small aromatic compound 'Heatin', containing 1-iminomethyl-2-naphthol as a pharmacophore, was selected as an enhancer of elongation growth. We show that ARABIDOPSIS ALDEHYDE OXIDASES redundantly contribute to Heatin-mediated hypocotyl elongation. Following a chemical proteomics approach, the members of the NITRILASE1-subfamily of auxin biosynthesis enzymes were identified among the molecular targets of Heatin. Our data reveal that nitrilases are involved in promotion of hypocotyl elongation in response to high temperature and Heatin-mediated hypocotyl elongation requires the NITRILASE1-subfamily members, NIT1 and NIT2. Heatin inhibits NIT1-subfamily enzymatic activity in vitro and the application of Heatin accordingly results in the accumulation of NIT1-subfamily substrate indole-3-acetonitrile in vivo. However, levels of the NIT1-subfamily product, bioactive auxin (indole-3-acetic acid), were also significantly increased. It is likely that the stimulation of hypocotyl elongation by Heatin might be independent of its observed interaction with NITRILASE1-subfamily members. However, nitrilases may contribute to the Heatin response by stimulating indole-3-acetic acid biosynthesis in an indirect way. Heatin and its functional analogues present novel chemical entities for studying auxin biology.
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Affiliation(s)
- Lennard van der Woude
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Markus Piotrowski
- Department of Molecular Genetics and Physiology of PlantsFaculty of Biology and BiotechnologyUniversitätsstraße 150Bochum44801Germany
| | - Gruson Klaasse
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
| | - Judith K. Paulus
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Daniel Krahn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Sabrina Ninck
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Farnusch Kaschani
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Markus Kaiser
- Chemische BiologieZentrum für Medizinische BiotechnologieFakultät für BiologieUniversität Duisburg‐EssenUniversitätsstr. 2Essen45117Germany
| | - Ondřej Novák
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
- Laboratory of Growth RegulatorsThe Czech Academy of Sciences & Faculty of ScienceInstitute of Experimental BotanyPalacký UniversityŠlechtitelů 27Olomouc78371Czech Republic
| | - Karin Ljung
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Suzanne Bulder
- Bejo Zaden B.V.Trambaan 1Warmenhuizen1749 CZthe Netherlands
| | - Marcel van Verk
- Plant‐Microbe InteractionsInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
- KeygeneAgro Business Park 90Wageningen6708 PWthe Netherlands
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Basten L. Snoek
- Theoretical Biology and BioinformaticsInstitute of Biodynamics and BiocomplexityUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn Fiers
- BioscienceWageningen University and ResearchDroevendaalsesteeg 1Wageningen6708 PBthe Netherlands
| | - Nathaniel I. Martin
- Department of Chemical Biology & Drug DiscoveryUtrecht Institute for Pharmaceutical SciencesUniversity UtrechtUniversiteitsweg 99Utrecht3584 CGthe Netherlands
- Biological Chemistry GroupSylvius LaboratoriesInstitute of Biology LeidenLeiden UniversitySylviusweg 72Leiden2333 BEthe Netherlands
| | - Renier A. L. van der Hoorn
- Plant Chemetics LaboratoryDepartment of Plant SciencesUniversity of OxfordSouth Parks RoadOxfordOX1 3RBUK
| | - Stéphanie Robert
- Umeå Plant Science CentreDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSE‐901 83Sweden
| | - Sjef Smeekens
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
| | - Martijn van Zanten
- Molecular Plant PhysiologyInstitute of Environmental BiologyUtrecht UniversityPadualaan 8Utrecht3584 CHthe Netherlands
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Abstract
Molecular genetic and structural studies have revealed the mechanisms of fundamental components of key auxin regulatory pathways consisting of auxin biosynthesis, transport, and signaling. Chemical biology methods applied in auxin research have been greatly expanded through the understanding of auxin regulatory pathways. Many small-molecule modulators of auxin metabolism, transport, and signaling have been generated on the basis of the outcomes of genetic and structural studies on auxin regulatory pathways. These chemical modulators are now widely used as essential tools for dissecting auxin biology in diverse plants. This review covers the structures, primary targets, modes of action, and applications of chemical tools in auxin biosynthesis, transport, and signaling.
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Affiliation(s)
- Ken-Ichiro Hayashi
- Department of Biochemistry, Okayama University of Science, Okayama City 700-0005, Japan
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Kinoshita T, Toh S, Torii KU. Chemical control of stomatal function and development. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:102010. [PMID: 33667824 DOI: 10.1016/j.pbi.2021.102010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/22/2021] [Accepted: 01/31/2021] [Indexed: 05/28/2023]
Abstract
Stomata control trade-offs for plants: carbon dioxide uptake for photosynthetic growth and water loss via transpiration. While agrochemical control of transpiration is an old concept, recent discoveries of the core signaling components controlling stomatal function and numbers opened the door to develop chemical compounds with high potency and specificity. ABA agonists with potent anti-transpiration activity have been developed via in silico virtual screens and structure guided design and synthesis. Library-based chemical screens identified new compounds that influence stomatal movement in ABA-independent manners as well as those affecting stomatal numbers and division polarity. Subsequent hit compound derivatization can be employed to separate adverse side effects. Ultimately, such chemicals might help in optimizing plant productivity and water use in agriculture and florist industries.
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Affiliation(s)
- Toshinori Kinoshita
- Institute of Transformative Biomolecules (WPI-ITbM) and Faculty of Science, Nagoya University, Aichi 464-8601, Japan.
| | - Shigeo Toh
- Department of Environmental Bioscience, Meijo University, Aichi 468-8502, Japan
| | - Keiko U Torii
- Institute of Transformative Biomolecules (WPI-ITbM) and Faculty of Science, Nagoya University, Aichi 464-8601, Japan; Howard Hughes Medical Institute and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.
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28
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Fabrissin I, Sano N, Seo M, North HM. Ageing beautifully: can the benefits of seed priming be separated from a reduced lifespan trade-off? JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2312-2333. [PMID: 33512455 DOI: 10.1093/jxb/erab004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 01/12/2021] [Indexed: 05/15/2023]
Abstract
Germination performance is affected following seed exposure to a combination of temperature fluctuations and cycles of hydration and dehydration. This has long been exploited in a seed technology termed priming, which increases germination speed and seedling vigour, but these benefits have often been associated with effects on seed lifespan, or longevity, with conflicting evidence for positive and negative effects. Seed longevity is a key seed trait influencing not only the storage of commercial stocks but also in situ and ex situ seed conservation. In the context of increasingly variable environmental conditions faced by both crops and wild species, this has led to renewed interest in understanding the molecular factors that underlie priming. Here, we provide an overview of the literature relating to the effect of priming on seed lifespan, and catalogue the different parameters used for priming treatments and their consequences on longevity for a range of species. Our current limited understanding of the molecular basis for priming effects is also outlined, with an emphasis on recent advances and promising approaches that should lead towards the application and monitoring of the priming process in a less empirical manner.
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Affiliation(s)
- Isabelle Fabrissin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Naoto Sano
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Helen M North
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
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29
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García-Maquilón I, Rodriguez PL, Vaidya AS, Lozano-Juste J. A Luciferase Reporter Assay to Identify Chemical Activators of ABA Signaling. Methods Mol Biol 2021; 2213:113-121. [PMID: 33270197 DOI: 10.1007/978-1-0716-0954-5_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Plant stress tolerance relies on intricate signaling networks that are not fully understood. Several plant hormones are involved in the adaptation to different environmental conditions. Abscisic acid (ABA) has an essential role in stress tolerance, especially in the adaptation to drought. During the last years, chemical genomics has gained attention as an alternative approach to decipher complex traits. Additionally, chemical-based strategies have been very useful to untangle genetic redundancy, which is hard to address by other approaches such as classical genetics. Here, we describe the use of an ABA-inducible luciferase (LUC) reporter line for the high-throughput identification of chemical activators of the ABA signaling pathway. In this assay, seven-day-old pMAPKKK18-LUC+ seedlings are grown on 96-well plates and treated with test compounds. Next, the activity of the LUC reporter is quantified semiautomatically by image analysis. Candidate compounds able to activate the reporter are thus identified and subjected to a secondary screen by analyzing their effect on ABA-related phenotypes (e.g., inhibition of seed germination). This assay is fast, high-throughput, nondestructive, semiquantitative and can be applied to any other luciferase reporter lines, making it ideal for forward chemical genetic screenings.
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Affiliation(s)
- Irene García-Maquilón
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain
| | - Aditya S Vaidya
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (IBMCP-CSIC-UPV), Valencia, Spain.
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30
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Dallery JF, Zimmer M, Halder V, Suliman M, Pigné S, Le Goff G, Gianniou DD, Trougakos IP, Ouazzani J, Gasperini D, O’Connell RJ. Inhibition of jasmonate-mediated plant defences by the fungal metabolite higginsianin B. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2910-2921. [PMID: 32006004 PMCID: PMC7260715 DOI: 10.1093/jxb/eraa061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/29/2020] [Indexed: 05/22/2023]
Abstract
Infection of Arabidopsis thaliana by the ascomycete fungus Colletotrichum higginsianum is characterized by an early symptomless biotrophic phase followed by a destructive necrotrophic phase. The fungal genome contains 77 secondary metabolism-related biosynthetic gene clusters, whose expression during the infection process is tightly regulated. Deleting CclA, a chromatin regulator involved in the repression of some biosynthetic gene clusters through H3K4 trimethylation, allowed overproduction of three families of terpenoids and isolation of 12 different molecules. These natural products were tested in combination with methyl jasmonate, an elicitor of jasmonate responses, for their capacity to alter defence gene induction in Arabidopsis. Higginsianin B inhibited methyl jasmonate-triggered expression of the defence reporter VSP1p:GUS, suggesting it may block bioactive jasmonoyl isoleucine (JA-Ile) synthesis or signalling in planta. Using the JA-Ile sensor Jas9-VENUS, we found that higginsianin B, but not three other structurally related molecules, suppressed JA-Ile signalling by preventing the degradation of JAZ proteins, the repressors of jasmonate responses. Higginsianin B likely blocks the 26S proteasome-dependent degradation of JAZ proteins because it inhibited chymotrypsin- and caspase-like protease activities. The inhibition of target degradation by higginsianin B also extended to auxin signalling, as higginsianin B treatment reduced auxin-dependent expression of DR5p:GUS. Overall, our data indicate that specific fungal secondary metabolites can act similarly to protein effectors to subvert plant immune and developmental responses.
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Affiliation(s)
- Jean-Félix Dallery
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Thiverval-Grignon, France
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, Gif-sur-Yvette, France
| | - Marlene Zimmer
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Vivek Halder
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Current address: Rijk Zwaan, De Lier, 2678 ZG, Netherlands
| | - Mohamed Suliman
- Chemical Biology Laboratory, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Current address: Desert Research Center, Cairo, Egypt
| | - Sandrine Pigné
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Thiverval-Grignon, France
| | - Géraldine Le Goff
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, Gif-sur-Yvette, France
| | - Despoina D Gianniou
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Jamal Ouazzani
- Centre National de la Recherche Scientifique, Institut de Chimie des Substances Naturelles ICSN, Gif-sur-Yvette, France
| | - Debora Gasperini
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
- Correspondence: or
| | - Richard J O’Connell
- Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, Thiverval-Grignon, France
- Correspondence: or
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31
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Recent Advances in Plant Chemical Biology of Jasmonates. Int J Mol Sci 2020; 21:ijms21031124. [PMID: 32046227 PMCID: PMC7036767 DOI: 10.3390/ijms21031124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Accepted: 02/06/2020] [Indexed: 11/29/2022] Open
Abstract
Lipid-derived plant hormone jasmonates are implicated in plant growth, reproductive performance, senescence, secondary metabolite productions, and defense against both necrotrophic pathogens and feeding insects. A major jasmonate is (+)-7-iso-jasmonoyl-l-isoleucine (JA-Ile), which is perceived by the unique COI1-JAZ coreceptor system. Recent advances in plant chemical biology have greatly informed the bioscience of jasmonate, including the development of chemical tools such as the antagonist COR-MO; the agonist NOPh; and newly developed jasmonates, including JA-Ile-macrolactone and 12-OH-JA-Ile. This review article summarizes the current status of plant chemical biology as it pertains to jasmonates, and offers some perspectives for the future.
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Two marine natural products, penicillide and verrucarin J, are identified from a chemical genetic screen for neutral lipid accumulation effectors in Phaeodactylum tricornutum. Appl Microbiol Biotechnol 2020; 104:2731-2743. [PMID: 32002603 DOI: 10.1007/s00253-020-10411-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/03/2020] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
Abstract
There are a large number of valuable substances in diatoms, such as neutral lipid and pigments. However, due to the lack of clear metabolic pathways, their applications are still limited. Recently, chemical modulators are found to be powerful tools to investigate the metabolic pathways of neutral lipids. Thus, in this study, to identify new neutral lipid accumulation effectors, we screened the natural products that we separated before in the model diatom Phaeodactylum tricornutum (P. tricornutum) by using Nile-red staining method. Two compounds, penicillide and verrucarin J which were isolated from two marine fungal strains, were identified to promote neutral lipid accumulation. However, penicillide and verrucarin J were also found to significantly inhibit the growth of P. tricornutum through specifically inhibiting the photosynthesis of P. tricornutum. Quantitative analysis results showed that penicillide and verrucarin J significantly increased total lipid and triacylglycerol (TAG) contents, which are consistent with previous Nile-red staining results. The expression of key genes such as DGAT2D, GPAT2, LPAT2, and PAP involved in TAG synthesis and unsaturated fatty acids also increased after penicillide and verrucarin J treatments. Besides, many TAG-rich plastoglobuli formed in plastids shown by increased lipid droplets in the cytosol. Finally, penicillide and verrucarin J were found to reduce the expression of synthetic genes of fucoxanthin, and consequently reduced the content of fucoxanthin, indicating that there might be crosstalk between lipid metabolism and fucoxanthin metabolism. Thus, our work exhibits two useful compounds that could be used to further study the metabolic pathways of neutral lipid and fucoxanthin, which will fulfill the promise of diatoms as low cost, high value, sustainable feedstock for high-value products such as neutral lipid and pigments.
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Takaoka Y, Hayashi K, Suzuki K, Azizah IN, Ueda M. A Fluorescence Anisotropy-Based Comprehensive Method for the In Vitro Screening of COI1-JAZs Agonists and Antagonists. Methods Mol Biol 2020; 2085:145-160. [PMID: 31734923 DOI: 10.1007/978-1-0716-0142-6_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The phytohormone (+)-7-iso-jasmonoyl-L-isoleucine (JA-Ile) causes protein-protein interactions (PPI) between F-box Protein CORONATINE INSENSITIVE 1 (COI1) and JASMONATE ZIM DOMAIN (JAZ) transcriptional repressor. A total of 13 JAZ subtypes are encoded in the genome of Arabidopsis thaliana; however, their genetic redundancy obfuscates the individual function of each JAZ. One approach to decipher this redundant signaling network is chemical genetics, using small molecules specific to individual JAZ subtype, for which a reliable and high-throughput screening system of the ligands for all combinations of COI1-JAZs would be indispensable. In this chapter, we describe a fluorescence anisotropy-based quantitative screening system for the ligands of COI1-JAZ co-receptors. Our method is applicable to agonists and antagonists of the COI1-JAZs.
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Affiliation(s)
- Yousuke Takaoka
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
- Precursory Research for Embryonic Science and Technology (PREST), Japan Science and Technology Agency, Tokyo, Japan
| | - Kengo Hayashi
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Kaho Suzuki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Ika Nurul Azizah
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan
| | - Minoru Ueda
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan.
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34
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Huang L, Li X, Zhang C. Progress in using chemical biology as a tool to uncover novel regulators of plant endomembrane trafficking. CURRENT OPINION IN PLANT BIOLOGY 2019; 52:106-113. [PMID: 31546132 DOI: 10.1016/j.pbi.2019.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/12/2019] [Accepted: 07/09/2019] [Indexed: 05/20/2023]
Abstract
The regulated dynamic transport of materials among organelles through endomembrane trafficking pathways is essential for plant growth, development, and environmental adaptation, and thus is a major topic of plant biology research. Large-scale chemical library screens have identified small molecules that could potentially inhibit different plant endomembrane trafficking steps. Further characterization of these molecules has provided valuable tools for understanding plant endomembrane trafficking and uncovered novel regulators of trafficking processes.
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Affiliation(s)
- Lei Huang
- Department of Botany and Plant Pathology, Purdue University, 915 W. State St., West Lafayette, IN, 47907, United States; Center for Plant Biology, Purdue University, 610 Purdue Mall, West Lafayette, IN, 47907, United States
| | - Xiaohui Li
- Department of Botany and Plant Pathology, Purdue University, 915 W. State St., West Lafayette, IN, 47907, United States; Center for Plant Biology, Purdue University, 610 Purdue Mall, West Lafayette, IN, 47907, United States
| | - Chunhua Zhang
- Department of Botany and Plant Pathology, Purdue University, 915 W. State St., West Lafayette, IN, 47907, United States; Center for Plant Biology, Purdue University, 610 Purdue Mall, West Lafayette, IN, 47907, United States.
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Zhu Y, Li HJ, Su Q, Wen J, Wang Y, Song W, Xie Y, He W, Yang Z, Jiang K, Guo H. A phenotype-directed chemical screen identifies ponalrestat as an inhibitor of the plant flavin monooxygenase YUCCA in auxin biosynthesis. J Biol Chem 2019; 294:19923-19933. [PMID: 31732559 DOI: 10.1074/jbc.ra119.010480] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/11/2019] [Indexed: 11/06/2022] Open
Abstract
Plant development is regulated by both synergistic and antagonistic interactions of different phytohormones, including a complex crosstalk between ethylene and auxin. For instance, auxin and ethylene synergistically control primary root elongation and root hair formation. However, a lack of chemical agents that specifically modulate ethylene or auxin production has precluded precise delineation of the contribution of each hormone to root development. Here, we performed a chemical genetic screen based on the recovery of root growth in ethylene-related Arabidopsis mutants with constitutive "short root" phenotypes (eto1-2 and ctr1-1). We found that ponalrestat exposure recovers root elongation in these mutants in an ethylene signal-independent manner. Genetic and pharmacological investigations revealed that ponalrestat inhibits the enzymatic activity of the flavin-containing monooxygenase YUCCA, which catalyzes the rate-limiting step of the indole-3-pyruvic acid branch of the auxin biosynthesis pathway. In summary, our findings have identified a YUCCA inhibitor that may be useful as a chemical tool to dissect the distinct steps in auxin biosynthesis and in the regulation of root development.
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Affiliation(s)
- Ying Zhu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Hong-Jiang Li
- State Key Laboratory of Protein and Plant Gene Research, College of Life Science, Peking University, Beijing 100871, China
| | - Qi Su
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jing Wen
- Max-Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Yuefan Wang
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wen Song
- Max-Planck Institute for Plant Breeding Research, Cologne 50829, Germany
| | - Yinpeng Xie
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Wenrong He
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037
| | - Zhen Yang
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kai Jiang
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China .,SUSTech Academy for Advanced and Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong 518055, China
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Zhu D, Zhang M, Gao C, Shen J. Protein trafficking in plant cells: Tools and markers. SCIENCE CHINA-LIFE SCIENCES 2019; 63:343-363. [DOI: 10.1007/s11427-019-9598-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/22/2019] [Indexed: 12/26/2022]
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Izumi M. How To Identify Autophagy Modulators. PLANT PHYSIOLOGY 2019; 181:853-854. [PMID: 31685689 PMCID: PMC6836852 DOI: 10.1104/pp.19.01146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Masanori Izumi
- RIKEN Center for Sustainable Resource Science, Wako 351-0198, Japan
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Ono A, Sato A, Fujimoto KJ, Matsuo H, Yanai T, Kinoshita T, Nakamichi N. 3,4-Dibromo-7-Azaindole Modulates Arabidopsis Circadian Clock by Inhibiting Casein Kinase 1 Activity. PLANT & CELL PHYSIOLOGY 2019; 60:2360-2368. [PMID: 31529098 PMCID: PMC6839374 DOI: 10.1093/pcp/pcz183] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/10/2019] [Indexed: 05/05/2023]
Abstract
The circadian clock is a timekeeping system for regulation of numerous biological daily rhythms. One characteristic of the circadian clock is that period length remains relatively constant in spite of environmental fluctuations, such as temperature change. Here, using the curated collection of in-house small molecule chemical library (ITbM chemical library), we show that small molecule 3,4-dibromo-7-azaindole (B-AZ) lengthened the circadian period of Arabidopsis thaliana (Arabidopsis). B-AZ has not previously been reported to have any biological and biochemical activities. Target identification can elucidate the mode of action of small molecules, but we were unable to make a molecular probe of B-AZ for target identification. Instead, we performed other analysis, gene expression profiling that potentially reveals mode of action of molecules. Short-term treatment of B-AZ decreased the expression of four dawn- and morning-phased clock-associated genes, CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), LATE ELONGATED HYPOCOTYL (LHY), PSEUDO-RESPONSE REGULATOR 9 (PRR9) and PRR7. Consistently, amounts of PRR5 and TIMING OF CAB EXPRESSION 1 (TOC1) proteins, transcriptional repressors of CCA1, LHY, PRR9 and PRR7 were increased upon B-AZ treatment. B-AZ inhibited Casein Kinase 1 family (CK1) that phosphorylates PRR5 and TOC1 for targeted degradation. A docking study and molecular dynamics simulation suggested that B-AZ interacts with the ATP-binding pocket of human CK1 delta, whose amino acid sequences are highly similar to those of Arabidopsis CK1. B-AZ-induced period-lengthening effect was attenuated in prr5 toc1 mutants. Collectively, this study provides a novel and simple structure CK1 inhibitor that modulates circadian clock via accumulation of PRR5 and TOC1.
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Affiliation(s)
- Azusa Ono
- Division of Biological Science, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Hiromi Matsuo
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Takeshi Yanai
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
| | - Norihito Nakamichi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa, Nagoya, Japan
- * Corresponding author: E-mail, ; Fax, +81-789-4778
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Halder V, Suliman MNS, Kaschani F, Kaiser M. Plant chemical genetics reveals colistin sulphate as a SA and NPR1-independent PR1 inducer functioning via a p38-like kinase pathway. Sci Rep 2019; 9:11196. [PMID: 31371749 PMCID: PMC6671972 DOI: 10.1038/s41598-019-47526-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 07/18/2019] [Indexed: 01/07/2023] Open
Abstract
In plants, low-dose of exogenous bacterial cyclic lipopeptides (CLPs) trigger transient membrane changes leading to activation of early and late defence responses. Here, a forward chemical genetics approach identifies colistin sulphate (CS) CLP as a novel plant defence inducer. CS uniquely triggers activation of the PATHOGENESIS-RELATED 1 (PR1) gene and resistance against Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) in Arabidopsis thaliana (Arabidopsis) independently of the PR1 classical inducer, salicylic acid (SA) and the key SA-signalling protein, NON-EXPRESSOR OF PR1 (NPR1). Low bioactive concentration of CS does not trigger activation of early defence markers such as reactive oxygen species (ROS) and mitogen activated protein kinase (MAPK). However, it strongly suppresses primary root length elongation. Structure activity relationship (SAR) assays and mode-of-action (MoA) studies show the acyl chain and activation of a ∼46 kDa p38-like kinase pathway to be crucial for CS' bioactivity. Selective pharmacological inhibition of the active p38-like kinase pathway by SB203580 reverses CS' effects on PR1 activation and root length suppression. Our results with CS as a chemical probe highlight the existence of a novel SA- and NPR1-independent branch of PR1 activation functioning via a membrane-sensitive p38-like kinase pathway.
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Affiliation(s)
- Vivek Halder
- Chemical Biology Laboratory, Max Planck Institute of Plant Breeding Research, Carl-von-Linnè-Weg 10, 50829, Köln, Germany. .,Chemical Biology, Centre of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45141, Essen, Germany. .,Rijk Zwaan, De Lier, 2678 ZG, The Netherlands.
| | - Mohamed N S Suliman
- Chemical Biology Laboratory, Max Planck Institute of Plant Breeding Research, Carl-von-Linnè-Weg 10, 50829, Köln, Germany.,Desert Research Centre, 11753 El matareya, Cairo, Egypt
| | - Farnusch Kaschani
- Chemical Biology, Centre of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45141, Essen, Germany
| | - Markus Kaiser
- Chemical Biology, Centre of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, 45141, Essen, Germany.
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Abstract
The mechanisms of eukaryotic circadian clocks rely on transcriptional-translational feedback loops (TTFLs), but components of TTFLs from different phylogenetic lineages are thought to be evolutionarily diverse. Posttranslational modification is also required for clock function, but those within the plant clock are less studied, likely due to genetic redundancy. Here, we identified a small synthetic molecule that lengthened the Arabidopsis circadian period. Using an affinity probe, we found that the molecule inhibited multiple members of the casein kinase I (CK1) family, which is also essential in animal, fungal, and algal clocks. The CK1 family modulated plant-specific clock-associated transcriptional repressors. With other studies, our results established the prominent role of CK1 family to control circadian clocks among vastly divergent phylogenetic lineages. The circadian clock provides organisms with the ability to adapt to daily and seasonal cycles. Eukaryotic clocks mostly rely on lineage-specific transcriptional-translational feedback loops (TTFLs). Posttranslational modifications are also crucial for clock functions in fungi and animals, but the posttranslational modifications that affect the plant clock are less understood. Here, using chemical biology strategies, we show that the Arabidopsis CASEIN KINASE 1 LIKE (CKL) family is involved in posttranslational modification in the plant clock. Chemical screening demonstrated that an animal CDC7/CDK9 inhibitor, PHA767491, lengthens the Arabidopsis circadian period. Affinity proteomics using a chemical probe revealed that PHA767491 binds to and inhibits multiple CKL proteins, rather than CDC7/CDK9 homologs. Simultaneous knockdown of Arabidopsis CKL-encoding genes lengthened the circadian period. CKL4 phosphorylated transcriptional repressors PSEUDO-RESPONSE REGULATOR 5 (PRR5) and TIMING OF CAB EXPRESSION 1 (TOC1) in the TTFL. PHA767491 treatment resulted in accumulation of PRR5 and TOC1, accompanied by decreasing expression of PRR5- and TOC1-target genes. A prr5 toc1 double mutant was hyposensitive to PHA767491-induced period lengthening. Together, our results reveal posttranslational modification of transcriptional repressors in plant clock TTFL by CK1 family proteins, which also modulate nonplant circadian clocks.
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Gu SY, Wang LC, Cheuh CM, Lo WS. CHITINASE LIKE1 Regulates Root Development of Dark-Grown Seedlings by Modulating Ethylene Biosynthesis in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:600. [PMID: 31156671 PMCID: PMC6530356 DOI: 10.3389/fpls.2019.00600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 04/24/2019] [Indexed: 05/07/2023]
Abstract
The plant hormone ethylene plays a regulatory role in development in light- and dark-grown seedlings. We previously isolated a group of small-molecule compounds with a quinazolinone backbone, which were named acsinones (for ACC synthase inhibitor quinazolinones), that act as uncompetitive inhibitors of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS). Thus, the triple response phenotype, which consists of shortened hypocotyls and roots, radial swelling of hypocotyls and exaggerated curvature of apical hooks, was suppressed by acsinones in dark-grown (etiolated) ethylene overproducer (eto) seedlings. Here, we describe our isolation and characterization of an Arabidopsis revert to eto1 9 (ret9) mutant, which showed reduced sensitivity to acsinones in etiolated eto1 seedlings. Map-based cloning of RET9 revealed an amino acid substitution in CHITINASE LIKE1 (CTL1), which is required for cell wall biogenesis and stress resistance in Arabidopsis. Etiolated seedlings of ctl1ret9 showed short hypocotyls and roots, which were augmented in combination with eto1-4. Consistently, ctl1ret9 seedlings showed enhanced sensitivity to exogenous ACC to suppress primary root elongation as compared with the wild type. After introducing ctl1ret9 to mutants completely insensitive to ethylene, genetic analysis indicated that an intact ethylene response pathway is essential for the alterations in root and apical hook but not hypocotyl in etiolated ctl1ret9 seedlings. Furthermore, a mild yet significantly increased ethylene level in ctl1 mutants was related to elevated mRNA level and activity of ACC oxidase (ACO). Moreover, genes associated with ethylene biosynthesis (ACO1 and ACO2) and response (ERF1 and EDF1) were upregulated in etiolated ctl1ret9 seedlings. By characterizing a new recessive allele of CTL1, we reveal that CTL1 negatively regulates ACO activity and the ethylene response, which thus contributes to understanding a role for ethylene in root elongation in response to perturbed cell wall integrity.
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Affiliation(s)
- Shin-Yuan Gu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Life Sciences, National Central University, Taoyuan City, Taiwan
| | - Long-Chi Wang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chiao-Mei Cheuh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Sheng Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
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Sano N, Seo M. Cell cycle inhibitors improve seed storability after priming treatments. JOURNAL OF PLANT RESEARCH 2019; 132:263-271. [PMID: 30637553 PMCID: PMC7205848 DOI: 10.1007/s10265-018-01084-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/14/2018] [Indexed: 05/05/2023]
Abstract
Seed priming is a treatment that controls seed water content to partially activate germination processes such as metabolism but prevents full germination of the seeds. The treatment is well known to enhance seed performance, including germination, but sometimes reduces seed storability or longevity as a side effect. Toward developing a novel priming technique that can maintain seed longevity for a longer time period, chemicals that suppress the seed deterioration under a controlled condition were screened from 80 known biologically active compounds contained in the RIKEN NPDepo authentic library using Arabidopsis thaliana seeds. Seeds primed with mimosine, a cell cycle inhibitor, retained higher survival rate after a controlled deterioration treatment compared to seeds primed without the chemical. In addition, other cell cycle inhibitors such as aphidicolin, hydroxyurea and oryzalin had similar effects on the seed storability after priming. Our results suggest that progression of the cell cycle during priming is an important checkpoint that determines the storability of seeds after the treatment.
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Affiliation(s)
- Naoto Sano
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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Soleilhac E, Brillet-Guéguen L, Roussel V, Prudent R, Touquet B, Dass S, Aci-Sèche S, Kasam V, Barette C, Imberty A, Breton V, Vantard M, Horvath D, Botté C, Tardieux I, Roy S, Maréchal E, Lafanechère L. Specific Targeting of Plant and Apicomplexa Parasite Tubulin through Differential Screening Using In Silico and Assay-Based Approaches. Int J Mol Sci 2018; 19:ijms19103085. [PMID: 30304836 PMCID: PMC6213459 DOI: 10.3390/ijms19103085] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 02/08/2023] Open
Abstract
Dinitroanilines are chemical compounds with high selectivity for plant cell α-tubulin in which they promote microtubule depolymerization. They target α-tubulin regions that have diverged over evolution and show no effect on non-photosynthetic eukaryotes. Hence, they have been used as herbicides over decades. Interestingly, dinitroanilines proved active on microtubules of eukaryotes deriving from photosynthetic ancestors such as Toxoplasma gondii and Plasmodium falciparum, which are responsible for toxoplasmosis and malaria, respectively. By combining differential in silico screening of virtual chemical libraries on Arabidopsis thaliana and mammal tubulin structural models together with cell-based screening of chemical libraries, we have identified dinitroaniline related and non-related compounds. They inhibit plant, but not mammalian tubulin assembly in vitro, and accordingly arrest A. thaliana development. In addition, these compounds exhibit a moderate cytotoxic activity towards T. gondii and P. falciparum. These results highlight the potential of novel herbicidal scaffolds in the design of urgently needed anti-parasitic drugs.
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Affiliation(s)
- Emmanuelle Soleilhac
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, INSERM, BGE U1038, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
| | - Loraine Brillet-Guéguen
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, INSERM, BGE U1038, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.
| | - Véronique Roussel
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, INSERM, BGE U1038, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherches 5168 CNRS, CEA, INRA, Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
| | - Renaud Prudent
- Institute for Advanced Biosciences (IAB), Team Regulation and Pharmacology of the Cytoskeleton, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38000 Grenoble, France.
| | - Bastien Touquet
- Institute for Advanced Biosciences (IAB), Team Membrane and Cell Dynamics of Host Parasite Interactions, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38000 Grenoble, France.
| | - Sheena Dass
- Institute for Advanced Biosciences (IAB), Team ApicoLipid, CNRS UMR5309, Université Grenoble Alpes, INSERM U1209, 38000 Grenoble, France.
| | - Samia Aci-Sèche
- Institut de Chimie Organique et Analytique (ICOA), UMR7311 CNRS-Université d'Orléans, Université d'Orléans, 45067 Orléans CEDEX 2, France.
| | - Vinod Kasam
- Laboratoire de Physique de Clermont, Université Clermont Auvergne, CNRS/IN2P3, UMR6533, 4 Avenue Blaise Pascal TSA 60026, CS 60026 63178 Aubière CEDEX, France.
| | - Caroline Barette
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, INSERM, BGE U1038, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
| | - Anne Imberty
- Centre de Recherche sur les Macromolécules Végétales, Université Grenoble Alpes, CNRS, 38000 Grenoble, France.
| | - Vincent Breton
- Laboratoire de Physique de Clermont, Université Clermont Auvergne, CNRS/IN2P3, UMR6533, 4 Avenue Blaise Pascal TSA 60026, CS 60026 63178 Aubière CEDEX, France.
| | - Marylin Vantard
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherches 5168 CNRS, CEA, INRA, Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
- Grenoble Institut des Neurosciences; Inserm U1216; Université Grenoble Alpes, 38000 Grenoble, France.
| | - Dragos Horvath
- Laboratoire de Chemoinformatique, UMR7140 CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France.
| | - Cyrille Botté
- Institute for Advanced Biosciences (IAB), Team ApicoLipid, CNRS UMR5309, Université Grenoble Alpes, INSERM U1209, 38000 Grenoble, France.
| | - Isabelle Tardieux
- Institute for Advanced Biosciences (IAB), Team Membrane and Cell Dynamics of Host Parasite Interactions, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38000 Grenoble, France.
| | - Sylvaine Roy
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA, INSERM, BGE U1038, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherches 5168 CNRS, CEA, INRA, Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire Végétale, Unité Mixte de Recherches 5168 CNRS, CEA, INRA, Institut de Biosciences et Biotechnologies de Grenoble (BIG), Université Grenoble Alpes, CEA-Grenoble, 17 rue des Martyrs, 38000 Grenoble, France.
| | - Laurence Lafanechère
- Institute for Advanced Biosciences (IAB), Team Regulation and Pharmacology of the Cytoskeleton, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38000 Grenoble, France.
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Jiang K, Asami T. Chemical regulators of plant hormones and their applications in basic research and agriculture*. Biosci Biotechnol Biochem 2018; 82:1265-1300. [DOI: 10.1080/09168451.2018.1462693] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
ABSTRACT
Plant hormones are small molecules that play versatile roles in regulating plant growth, development, and responses to the environment. Classic methodologies, including genetics, analytic chemistry, biochemistry, and molecular biology, have contributed to the progress in plant hormone studies. In addition, chemical regulators of plant hormone functions have been important in such studies. Today, synthetic chemicals, including plant growth regulators, are used to study and manipulate biological systems, collectively referred to as chemical biology. Here, we summarize the available chemical regulators and their contributions to plant hormone studies. We also pose questions that remain to be addressed in plant hormone studies and that might be solved with the help of chemical regulators.
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Affiliation(s)
- Kai Jiang
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tadao Asami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Toh S, Inoue S, Toda Y, Yuki T, Suzuki K, Hamamoto S, Fukatsu K, Aoki S, Uchida M, Asai E, Uozumi N, Sato A, Kinoshita T. Identification and Characterization of Compounds that Affect Stomatal Movements. PLANT & CELL PHYSIOLOGY 2018; 59:1568-1580. [PMID: 29635388 DOI: 10.1093/pcp/pcy061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 03/13/2018] [Indexed: 05/09/2023]
Abstract
Regulation of stomatal aperture is essential for plant growth and survival in response to environmental stimuli. Opening of stomata induces uptake of CO2 for photosynthesis and transpiration, which enhances uptake of nutrients from roots. Light is the most important stimulus for stomatal opening. Under drought stress, the plant hormone ABA induces stomatal closure to prevent water loss. However, the molecular mechanisms of stomatal movements are not fully understood. In this study, we screened chemical libraries to identify compounds that affect stomatal movements in Commelina benghalensis and characterize the underlying molecular mechanisms. We identified nine stomatal closing compounds (SCL1-SCL9) that suppress light-induced stomatal opening by >50%, and two compounds (temsirolimus and CP-100356) that induce stomatal opening in the dark. Further investigations revealed that SCL1 and SCL2 had no effect on autophosphorylation of phototropin or the activity of the inward-rectifying plasma membrane (PM) K+ channel, KAT1, but suppressed blue light-induced phosphorylation of the penultimate residue, threonine, in PM H+-ATPase, which is a key enzyme for stomatal opening. SCL1 and SCL2 had no effect on ABA-dependent responses, including seed germination and expression of ABA-induced genes. These results suggest that SCL1 and SCL2 suppress light-induced stomatal opening at least in part by inhibiting blue light-induced activation of PM H+-ATPase, but not by the ABA signaling pathway. Interestingly, spraying leaves onto dicot and monocot plants with SCL1 suppressed wilting of leaves, indicating that inhibition of stomatal opening by these compounds confers tolerance to drought stress in plants.
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Affiliation(s)
- Shigeo Toh
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Shinpei Inoue
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Yosuke Toda
- JST PRESTO, 7 Gobancho, Chiyoda, Tokyo, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Takahiro Yuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Kyota Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai, Japan
| | - Shin Hamamoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai, Japan
| | - Kohei Fukatsu
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Saya Aoki
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Mami Uchida
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Eri Asai
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai, Japan
| | - Ayato Sato
- JST PRESTO, 7 Gobancho, Chiyoda, Tokyo, Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- JST PRESTO, 7 Gobancho, Chiyoda, Tokyo, Japan
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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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Enantiodifferential Approach for the Target Protein Detection of the Jasmonate Glucoside That Controls the Leaf Closure of Samanea saman. Methods Mol Biol 2018. [PMID: 29846926 DOI: 10.1007/978-1-4939-7874-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The synthetic photoaffinity probe designed to mimic bioactive molecules is one of the powerful tools for the identification of the target protein in living organisms. However, nonspecific interaction between the probe and nontargets would cause a misleading result in many cases of the photoaffinity labeling. In this chapter, we describe an enantiodifferential approach as a reliable method for the detection of the specific target protein of the bioactive natural product, jasmonate glucoside, a chemical factor that controls the nyctinastic leaf movement of the leguminous plants.
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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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50
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Ma Q, Grones P, Robert S. Auxin signaling: a big question to be addressed by small molecules. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:313-328. [PMID: 29237069 PMCID: PMC5853230 DOI: 10.1093/jxb/erx375] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/16/2017] [Indexed: 05/20/2023]
Abstract
Providing a mechanistic understanding of the crucial roles of the phytohormone auxin has been an important and coherent aspect of plant biology research. Since its discovery more than a century ago, prominent advances have been made in the understanding of auxin action, ranging from metabolism and transport to cellular and transcriptional responses. However, there is a long road ahead before a thorough understanding of its complex effects is achieved, because a lot of key information is still missing. The availability of an increasing number of technically advanced scientific tools has boosted the basic discoveries in auxin biology. A plethora of bioactive small molecules, consisting of the synthetic auxin-like herbicides and the more specific auxin-related compounds, developed as a result of the exploration of chemical space by chemical biology, have made the tool box for auxin research more comprehensive. This review mainly focuses on the compounds targeting the auxin co-receptor complex, demonstrates the various ways to use them, and shows clear examples of important basic knowledge obtained by their usage. Application of these precise chemical tools, together with an increasing amount of structural information for the major components in auxin action, will certainly aid in strengthening our insights into the complexity and diversity of auxin response.
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Affiliation(s)
- Qian Ma
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
| | - Peter Grones
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Sweden
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