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Qi W, Zhang Y, Li M, Zhang P, Xing J, Chen Y, Zhang L. Endocytic recycling in plants: pathways and regulation. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4712-4728. [PMID: 38655916 DOI: 10.1093/jxb/erae188] [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: 02/05/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Endocytic recycling is an intracellular trafficking pathway that returns endocytosed molecules to the plasma membrane via the recycling endosome. This pathway plays a crucial role in remodelling plasma membrane composition and is thus essential for cellular homeostasis. In plants, endocytic recycling regulates the localization and abundance of receptors, transporters, and channels at the plasma membrane that are involved in many aspects of plant growth and development. Despite its importance, the recycling endosome and the underlying sorting mechanisms for cargo recycling in plants remain understudied in comparison to the endocytic recycling pathways in animals. In this review, we focus on the cumulative evidence suggesting the existence of endosomes decorated by regulators that contribute to recycling in plant cells. We summarize the chemical inhibitors used for analysing cargo recycling and discuss recent advances in our understanding of how endocytic recycling participates in various plant cellular and physiological events.
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Affiliation(s)
- Wencai Qi
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Yu Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Mengting Li
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Peipei Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Jingjing Xing
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Yanmei Chen
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Liang Zhang
- College of Life Science, Henan Normal University, Xinxiang 453007, China
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2
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Kraus M, Pleskot R, Van Damme D. Structural and Evolutionary Aspects of Plant Endocytosis. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:521-550. [PMID: 38237062 DOI: 10.1146/annurev-arplant-070122-023455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Endocytosis is an essential eukaryotic process that maintains the homeostasis of the plasma membrane proteome by vesicle-mediated internalization. Its predominant mode of operation utilizes the polymerization of the scaffold protein clathrin forming a coat around the vesicle; therefore, it is termed clathrin-mediated endocytosis (CME). Throughout evolution, the machinery that mediates CME is marked by losses, multiplications, and innovations. CME employs a limited number of conserved structural domains and folds, whose assembly and connections are species dependent. In plants, many of the domains are grouped into an ancient multimeric complex, the TPLATE complex, which occupies a central position as an interaction hub for the endocytic machinery. In this review, we provide an overview of the current knowledge regarding the structural aspects of plant CME, and we draw comparisons to other model systems. To do so, we have taken advantage of recent developments with respect to artificial intelligence-based protein structure prediction.
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Affiliation(s)
- Michael Kraus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; ,
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Roman Pleskot
- Institute of Experimental Botany, Czech Academy of Sciences, Prague, Czech Republic;
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; ,
- VIB Center for Plant Systems Biology, Ghent, Belgium
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3
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Li X, Wang D, Yin X, Dai M, Staiger CJ, Zhang C. A chemical genetic screen with the EXO70 inhibitor Endosidin2 uncovers potential modulators of exocytosis in Arabidopsis. PLANT DIRECT 2024; 8:e592. [PMID: 38881683 PMCID: PMC11176578 DOI: 10.1002/pld3.592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/09/2024] [Accepted: 04/26/2024] [Indexed: 06/18/2024]
Abstract
Exocytosis plays an essential role in delivering proteins, lipids, and cell wall polysaccharides to the plasma membrane and extracellular spaces. Accurate secretion through exocytosis is key to normal plant development as well as responses to biotic and abiotic stresses. During exocytosis, an octameric protein complex named the exocyst facilitates the tethering of secretory vesicles to the plasma membrane. Despite some understanding of molecular and cellular aspects of exocyst function obtained through reverse genetics and direct interaction assays, knowledge about upstream modulators and genetic interactors remains limited. Traditional genetic screens encounter practical issues in exocyst subunit mutant backgrounds, such as lethality of certain knockout mutants and/or potential redundancy of EXO70 homologs. To address these challenges, this study leverages the tunable and reversible nature of chemical genetics, employing Endosidin2 (ES2)-a synthetic inhibitor of EXO70-for a large-scale chemical genetic mutant screen in Arabidopsis. This approach led to the identification of 70 ES2-hypersensitive mutants, named es2s. Through a whole-genome sequencing-based mapping strategy, 14 nonallelic es2s mutants were mapped and the candidate mutations reported here. In addition, T-DNA insertion lines were tested as alternative alleles to identify causal mutations. We found that T-DNA insertion alleles for DCP5, VAS1/ISS1, ArgJ, and MEF11 were hypersensitive to ES2 for root growth inhibition. This research not only offers new genetic resources for systematically identifying molecular players interacting with the exocyst in Arabidopsis but also enhances understanding of the regulation of exocytosis.
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Affiliation(s)
- Xiaohui Li
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana USA
- Center for Plant Biology Purdue University West Lafayette Indiana USA
| | - Diwen Wang
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana USA
- Center for Plant Biology Purdue University West Lafayette Indiana USA
| | - Xianglin Yin
- Department of Chemistry Purdue University West Lafayette Indiana USA
| | - Mingji Dai
- Department of Chemistry Purdue University West Lafayette Indiana USA
- Present address: Department of Chemistry Emory University Atlanta Georgia USA
- Present address: Department of Chemistry Emory University Atlanta Georgia USA
| | - Christopher J Staiger
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana USA
- Center for Plant Biology Purdue University West Lafayette Indiana USA
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
| | - Chunhua Zhang
- Department of Botany and Plant Pathology Purdue University West Lafayette Indiana USA
- Center for Plant Biology Purdue University West Lafayette Indiana USA
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4
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Sinclair R, Wang M, Jawaid MZ, Longkumer T, Aaron J, Rossetti B, Wait E, McDonald K, Cox D, Heddleston J, Wilkop T, Drakakaki G. Four-dimensional quantitative analysis of cell plate development in Arabidopsis using lattice light sheet microscopy identifies robust transition points between growth phases. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2829-2847. [PMID: 38436428 PMCID: PMC11282576 DOI: 10.1093/jxb/erae091] [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: 09/20/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Cell plate formation during cytokinesis entails multiple stages occurring concurrently and requiring orchestrated vesicle delivery, membrane remodelling, and timely deposition of polysaccharides, such as callose. Understanding such a dynamic process requires dissection in time and space; this has been a major hurdle in studying cytokinesis. Using lattice light sheet microscopy (LLSM), we studied cell plate development in four dimensions, through the behavior of yellow fluorescent protein (YFP)-tagged cytokinesis-specific GTPase RABA2a vesicles. We monitored the entire duration of cell plate development, from its first emergence, with the aid of YFP-RABA2a, in both the presence and absence of cytokinetic callose. By developing a robust cytokinetic vesicle volume analysis pipeline, we identified distinct behavioral patterns, allowing the identification of three easily trackable cell plate developmental phases. Notably, the phase transition between phase I and phase II is striking, indicating a switch from membrane accumulation to the recycling of excess membrane material. We interrogated the role of callose using pharmacological inhibition with LLSM and electron microscopy. Loss of callose inhibited the phase transitions, establishing the critical role and timing of the polysaccharide deposition in cell plate expansion and maturation. This study exemplifies the power of combining LLSM with quantitative analysis to decode and untangle such a complex process.
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Affiliation(s)
- Rosalie Sinclair
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Minmin Wang
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Muhammad Zaki Jawaid
- Department of Physics and Astronomy, University of California Davis, Davis, CA, USA
| | | | | | | | - Eric Wait
- Janelia Research Campus, Ashburn, VA, USA
| | - Kent McDonald
- Electron Microscope Laboratory, University of California, Berkeley, CA, USA
| | - Daniel Cox
- Department of Physics and Astronomy, University of California Davis, Davis, CA, USA
| | | | - Thomas Wilkop
- Department of Molecular and Cellular Biology, Light Microscopy Imaging Facility, University of California Davis, Davis, CA, USA
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
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5
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Shin J, Douglas CJ, Zhang S, Seath CP, Bao H. Targeting Recycling Endosomes to Potentiate mRNA Lipid Nanoparticles. NANO LETTERS 2024; 24:5104-5109. [PMID: 38640421 PMCID: PMC11066955 DOI: 10.1021/acs.nanolett.3c04415] [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: 11/14/2023] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/21/2024]
Abstract
mRNA lipid nanoparticles (LNPs) have emerged as powerful modalities for gene therapies to control cancer and infectious and immune diseases. Despite the escalating interest in mRNA-LNPs over the past few decades, endosomal entrapment of delivered mRNAs vastly impedes therapeutic developments. In addition, the molecular mechanism of LNP-mediated mRNA delivery is poorly understood to guide further improvement through rational design. To tackle these challenges, we characterized LNP-mediated mRNA delivery using a library of small molecules targeting endosomal trafficking. We found that the expression of delivered mRNAs is greatly enhanced via inhibition of endocytic recycling in cells and in live mice. One of the most potent small molecules, endosidine 5 (ES5), interferes with recycling endosomes through Annexin A6, thereby promoting the release and expression of mRNA into the cytoplasm. Together, these findings suggest that targeting endosomal trafficking with small molecules is a viable strategy to potentiate the efficacy of mRNA-LNPs.
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Affiliation(s)
- Jeehae Shin
- Department
of Molecular Physiology and Biological Physics, University of Virginia, 480 Ray C. Hunt Drive, Charlottesville, 22903 Virginia, United States
- Department
of Molecular Medicine, UF Scripps Biomedical
Research, 130 Scripps
Way, Jupiter, 33458 Florida, United States
| | - Cameron J. Douglas
- Department
of Chemistry, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, 33458 Florida, United States
- Skaggs
Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, 33458 Florida, United States
| | - Shanwen Zhang
- Department
of Molecular Medicine, UF Scripps Biomedical
Research, 130 Scripps
Way, Jupiter, 33458 Florida, United States
| | - Ciaran P. Seath
- Department
of Chemistry, UF Scripps Biomedical Research, 130 Scripps Way, Jupiter, 33458 Florida, United States
| | - Huan Bao
- Department
of Molecular Physiology and Biological Physics, University of Virginia, 480 Ray C. Hunt Drive, Charlottesville, 22903 Virginia, United States
- Department
of Molecular Medicine, UF Scripps Biomedical
Research, 130 Scripps
Way, Jupiter, 33458 Florida, United States
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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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Larson ER, Armstrong EM, Harper H, Knapp S, Edwards KJ, Grierson D, Poppy G, Chase MW, Jones JDG, Bastow R, Jellis G, Barnes S, Temple P, Clarke M, Oldroyd G, Grierson CS. One hundred important questions for plant science - reflecting on a decade of plant research. THE NEW PHYTOLOGIST 2023; 238:464-469. [PMID: 36924326 DOI: 10.1111/nph.18663] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 06/18/2023]
Affiliation(s)
- Emily R Larson
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Emily May Armstrong
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Helen Harper
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Sandra Knapp
- Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Keith J Edwards
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Don Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, nr Loughborough, LE12 5RD, UK
| | - Guy Poppy
- Biological Sciences, University of Southampton, University Road, Southampton, SO17 1BJ, UK
| | - Mark W Chase
- Department of Environment and Agriculture, Curtin University, Perth, WA, 6845, Australia
- Royal Botanic Gardens Kew, Richmond, London, TW9 3AE, UK
| | | | - Ruth Bastow
- Crop Health and Protection Ltd, York Biotech Campus, Sand Hutton, York, YO41 1LZ, UK
| | - Graham Jellis
- Agrifood Charities Partnership, The Bullock Building, University Way, Cranfield, Bedford, MK43 OGH, UK
| | | | - Paul Temple
- Wold Farm, Driffield, East Yorkshire, YO25 3BB, UK
| | - Matthew Clarke
- Bayer - Crop Science, Monsanto UK Ltd, 230 Science Park, Cambridge, CB4 0WB, UK
| | - Giles Oldroyd
- Crop Science Centre, Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Claire S Grierson
- School of Biological Sciences, Bristol University, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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8
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Bormann E, Xu R, Nargi C, Wu M, Vidali L. Inhibition of the Exocyst Complex with Endosidin 2 Reduces Polarized Growth in Physcomitrium patens.. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000655. [PMID: 36411798 PMCID: PMC9674970 DOI: 10.17912/micropub.biology.000655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/08/2022] [Accepted: 10/18/2022] [Indexed: 05/30/2023]
Abstract
Endosidin 2 (ES2) is a cell-permeable drug that binds to the Exo70 subunit of the exocyst complex, disrupting the final stages of exocytosis. This allows for a dose-dependent control over the process of exocytosis and greater ease in studying exocytic-dependent processes such as polarized cell growth. ES2 was utilized in studying polarized cell growth in the moss Physcomitrium patens , in which plants were exposed to increasing concentrations of ES2 with an IC50 between 8.8 and 12.3 µM. At 50 µM, tip-growing cells ruptured close to their tips, an indication that ES2 inhibits the deposition of new cell wall material via exocytosis. This data serves to further support the use of ES2 as a tool to interfere with exocytosis with lethality only seen at high levels of ES2.
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Affiliation(s)
- Eric Bormann
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Rholee Xu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Clare Nargi
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Min Wu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
- Department of Mathematical Sciences, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA, USA
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9
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Ercoli MF, Ramos PZ, Jain R, Pilotte J, Dong OX, Thompson T, Wells CI, Elkins JM, Edwards AM, Couñago RM, Drewry DH, Ronald PC. An open source plant kinase chemogenomics set. PLANT DIRECT 2022; 6:e460. [PMID: 36447653 PMCID: PMC9694430 DOI: 10.1002/pld3.460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for expression in Escherichia coli. Forty of these rice kinases were purified and screened using differential scanning fluorimetry (DSF) against 627 diverse kinase inhibitors, with a range of structures and activities targeting diverse human kinases. Thirty-seven active compounds were then tested for their ability to modify primary root development in Arabidopsis. Of these, 14 compounds caused a significant reduction of primary root length compared with control plants. Two of these inhibitory compounds bind to the predicted orthologue of Arabidopsis PSKR1, one of two receptors for PSK, a small sulfated peptide that positively controls root development. The reduced root length phenotype could not be rescued by the exogenous addition of the PSK peptide, suggesting that chemical treatment may inhibit both PSKR1 and its closely related receptor PSKR2. Six of the compounds acting as root growth inhibitors in Arabidopsis conferred the same effect in rice. Compound RAF265 (CHIR-265), previously shown to bind the human kinase BRAF (B-Raf proto-oncogene, serine/threonine kinase), also binds to nine highly conserved rice kinases tested. The binding of human and rice kinases to the same compound suggests that human kinase inhibitor sets will be useful for dissecting the function of plant kinases.
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Affiliation(s)
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - Rashmi Jain
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Joseph Pilotte
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Oliver Xiaoou Dong
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Ty Thompson
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
| | - Carrow I. Wells
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Jonathan M. Elkins
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
- Centre for Medicines DiscoveryUniversity of OxfordOxfordUK
| | - Aled M. Edwards
- Structural Genomics ConsortiumUniversity of TorontoTorontoCanada
| | - Rafael M. Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG)Universidade Estadual de Campinas (UNICAMP)CampinasSPBrazil
| | - David H. Drewry
- Structural Genomics Consortium (SGC)UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC‐CH)Chapel HillNCUSA
- Division of Chemical Biology and Medicinal ChemistryUNC Eshelman School of Pharmacy, UNC‐CHChapel HillNCUSA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome CenterUniversity of CaliforniaDavisCAUSA
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10
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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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11
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Dünser K, Schöller M, Rößling AK, Löfke C, Xiao N, Pařízková B, Melnik S, Rodriguez-Franco M, Stöger E, Novák O, Kleine-Vehn J. Endocytic trafficking promotes vacuolar enlargements for fast cell expansion rates in plants. eLife 2022; 11:75945. [PMID: 35686734 PMCID: PMC9187339 DOI: 10.7554/elife.75945] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
The vacuole has a space-filling function, allowing a particularly rapid plant cell expansion with very little increase in cytosolic content (Löfke et al., 2015; Scheuring et al., 2016; Dünser et al., 2019). Despite its importance for cell size determination in plants, very little is known about the mechanisms that define vacuolar size. Here, we show that the cellular and vacuolar size expansions are coordinated. By developing a pharmacological tool, we enabled the investigation of membrane delivery to the vacuole during cellular expansion. Our data reveal that endocytic membrane sorting from the plasma membrane to the vacuole is enhanced in the course of rapid root cell expansion. While this ‘compromise’ mechanism may theoretically at first decelerate cell surface enlargements, it fuels vacuolar expansion and, thereby, ensures the coordinated augmentation of vacuolar occupancy in dynamically expanding plant cells.
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Affiliation(s)
- Kai Dünser
- Molecular Plant Physiology (MoPP), Faculty of Biology, University of Freiburg, Freiburg, Germany.,Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.,Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Maria Schöller
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ann-Kathrin Rößling
- Molecular Plant Physiology (MoPP), Faculty of Biology, University of Freiburg, Freiburg, Germany.,Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
| | - Christian Löfke
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nannan Xiao
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Barbora Pařízková
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Stanislav Melnik
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Eva Stöger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ondřej Novák
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Jürgen Kleine-Vehn
- Molecular Plant Physiology (MoPP), Faculty of Biology, University of Freiburg, Freiburg, Germany.,Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.,Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
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12
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Gu Y, Rasmussen CG. Cell biology of primary cell wall synthesis in plants. THE PLANT CELL 2022; 34:103-128. [PMID: 34613413 PMCID: PMC8774047 DOI: 10.1093/plcell/koab249] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 10/01/2021] [Indexed: 05/07/2023]
Abstract
Building a complex structure such as the cell wall, with many individual parts that need to be assembled correctly from distinct sources within the cell, is a well-orchestrated process. Additional complexity is required to mediate dynamic responses to environmental and developmental cues. Enzymes, sugars, and other cell wall components are constantly and actively transported to and from the plasma membrane during diffuse growth. Cell wall components are transported in vesicles on cytoskeletal tracks composed of microtubules and actin filaments. Many of these components, and additional proteins, vesicles, and lipids are trafficked to and from the cell plate during cytokinesis. In this review, we first discuss how the cytoskeleton is initially organized to add new cell wall material or to build a new cell wall, focusing on similarities during these processes. Next, we discuss how polysaccharides and enzymes that build the cell wall are trafficked to the correct location by motor proteins and through other interactions with the cytoskeleton. Finally, we discuss some of the special features of newly formed cell walls generated during cytokinesis.
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Affiliation(s)
- Ying Gu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Carolyn G Rasmussen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
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13
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Larson RT, McFarlane HE. Small but Mighty: An Update on Small Molecule Plant Cellulose Biosynthesis Inhibitors. PLANT & CELL PHYSIOLOGY 2021; 62:1828-1838. [PMID: 34245306 DOI: 10.1093/pcp/pcab108] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 06/14/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Cellulose is one of the most abundant biopolymers on Earth. It provides mechanical support to growing plant cells and important raw materials for paper, textiles and biofuel feedstocks. Cellulose biosynthesis inhibitors (CBIs) are invaluable tools for studying cellulose biosynthesis and can be important herbicides for controlling weed growth. Here, we review CBIs with particular focus on the most widely used CBIs and recently discovered CBIs. We discuss the effects of these CBIs on plant growth and development and plant cell biology and summarize what is known about the mode of action of these different CBIs.
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Affiliation(s)
- Raegan T Larson
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
| | - Heather E McFarlane
- Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON M5S 3G5, Canada
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14
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A target fishing study to spot possible biological targets of fusaric acid: Inhibition of protein kinase-A and insights on the underpinning mechanisms. Food Chem Toxicol 2021; 159:112663. [PMID: 34748883 DOI: 10.1016/j.fct.2021.112663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 12/23/2022]
Abstract
Fusaric acid is a secondary metabolite produced by various Fusarium fungi, present with relatively high incidence in Fusarium-contaminated foods. It was already described as phytotoxic and cytotoxic. However, the understanding of its molecular mechanisms is still fragmentary and further data are needed to ensure an informed assessment of the risk related to its presence in food. This work applied an integrated in silico/in vitro approach to reveal novel potential biological activities of fusaric acid and to investigate the underpinning mechanisms. An in silico reverse screening was used to identify novel biological targets for fusaric acid. Computational results indicated as target protein kinase-A, which was confirmed with biochemical cell-free assays providing evidence of its actual inhibitory potential. Cell-based experiments on intestinal cells (HCEC-1CT cells) identified the mitochondrial network and cell membranes as potentially affected organelles, possibly resulting from PKA inhibition. The integration of 3D molecular modeling supported the plausibility of fusaric acid-dependent inhibition. From the hazard identification perspective, considering the Low Observed Adverse Effect Level described here (0.1 mM) and the possible level of contamination in food, fusaric acid might raise concern from a food safety standpoint and the gastrointestinal tract was described as a meaningful system to investigate with priority.
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15
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Chini A, Monte I, Fernández-Barbero G, Boter M, Hicks G, Raikhel N, Solano R. A small molecule antagonizes jasmonic acid perception and auxin responses in vascular and nonvascular plants. PLANT PHYSIOLOGY 2021; 187:1399-1413. [PMID: 34618088 PMCID: PMC8566257 DOI: 10.1093/plphys/kiab369] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/03/2021] [Indexed: 05/12/2023]
Abstract
The phytohormone jasmonoyl-L-isoleucine (JA-Ile) regulates many stress responses and developmental processes in plants. A co-receptor complex formed by the F-box protein Coronatine Insensitive 1 (COI1) and a Jasmonate (JA) ZIM-domain (JAZ) repressor perceives the hormone. JA-Ile antagonists are invaluable tools for exploring the role of JA-Ile in specific tissues and developmental stages, and for identifying regulatory processes of the signaling pathway. Using two complementary chemical screens, we identified three compounds that exhibit a robust inhibitory effect on both the hormone-mediated COI-JAZ interaction and degradation of JAZ1 and JAZ9 in vivo. One molecule, J4, also restrains specific JA-induced physiological responses in different angiosperm plants, including JA-mediated gene expression, growth inhibition, chlorophyll degradation, and anthocyanin accumulation. Interaction experiments with purified proteins indicate that J4 directly interferes with the formation of the Arabidopsis (Arabidopsis thaliana) COI1-JAZ complex otherwise induced by JA. The antagonistic effect of J4 on COI1-JAZ also occurs in the liverwort Marchantia polymorpha, suggesting the mode of action is conserved in land plants. Besides JA signaling, J4 works as an antagonist of the closely related auxin signaling pathway, preventing Transport Inhibitor Response1/Aux-indole-3-acetic acid interaction and auxin responses in planta, including hormone-mediated degradation of an auxin repressor, gene expression, and gravitropic response. However, J4 does not affect other hormonal pathways. Altogether, our results show that this dual antagonist competes with JA-Ile and auxin, preventing the formation of phylogenetically related receptor complexes. J4 may be a useful tool to dissect both the JA-Ile and auxin pathways in particular tissues and developmental stages since it reversibly inhibits these pathways. One-sentence summary: A chemical screen identified a molecule that antagonizes jasmonate perception by directly interfering with receptor complex formation in phylogenetically distant vascular and nonvascular plants.
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Affiliation(s)
- Andrea Chini
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
- Author for correspondence:
| | - Isabel Monte
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
- Present address: Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, Zurich, 8008, Switzerland
| | - Gemma Fernández-Barbero
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
| | - Marta Boter
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
- Present address: Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Glenn Hicks
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, 92521, USA
| | - Natasha Raikhel
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California, 92521, USA
| | - Roberto Solano
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Campus Universidad Autónoma, Madrid, 28049, Spain
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16
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Daras G, Templalexis D, Avgeri F, Tsitsekian D, Karamanou K, Rigas S. Updating Insights into the Catalytic Domain Properties of Plant Cellulose synthase ( CesA) and Cellulose synthase-like ( Csl) Proteins. Molecules 2021; 26:molecules26144335. [PMID: 34299608 PMCID: PMC8306620 DOI: 10.3390/molecules26144335] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 11/24/2022] Open
Abstract
The wall is the last frontier of a plant cell involved in modulating growth, development and defense against biotic stresses. Cellulose and additional polysaccharides of plant cell walls are the most abundant biopolymers on earth, having increased in economic value and thereby attracted significant interest in biotechnology. Cellulose biosynthesis constitutes a highly complicated process relying on the formation of cellulose synthase complexes. Cellulose synthase (CesA) and Cellulose synthase-like (Csl) genes encode enzymes that synthesize cellulose and most hemicellulosic polysaccharides. Arabidopsis and rice are invaluable genetic models and reliable representatives of land plants to comprehend cell wall synthesis. During the past two decades, enormous research progress has been made to understand the mechanisms of cellulose synthesis and construction of the plant cell wall. A plethora of cesa and csl mutants have been characterized, providing functional insights into individual protein isoforms. Recent structural studies have uncovered the mode of CesA assembly and the dynamics of cellulose production. Genetics and structural biology have generated new knowledge and have accelerated the pace of discovery in this field, ultimately opening perspectives towards cellulose synthesis manipulation. This review provides an overview of the major breakthroughs gathering previous and recent genetic and structural advancements, focusing on the function of CesA and Csl catalytic domain in plants.
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17
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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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18
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Eldridge BM, Larson ER, Weldon L, Smyth KM, Sellin AN, Chenchiah IV, Liverpool TB, Grierson CS. A Centrifuge-Based Method for Identifying Novel Genetic Traits That Affect Root-Substrate Adhesion in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2021; 12:602486. [PMID: 33732271 PMCID: PMC7959780 DOI: 10.3389/fpls.2021.602486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
The physical presence of roots and the compounds they release affect the cohesion between roots and their environment. However, the plant traits that are important for these interactions are unknown and most methods that quantify the contributions of these traits are time-intensive and require specialist equipment and complex substrates. Our lab developed an inexpensive, high-throughput phenotyping assay that quantifies root-substrate adhesion in Arabidopsis thaliana. We now report that this method has high sensitivity and versatility for identifying different types of traits affecting root-substrate adhesion including root hair morphology, vesicle trafficking pathways, and root exudate composition. We describe a practical protocol for conducting this assay and introduce its use in a forward genetic screen to identify novel genes affecting root-substrate interactions. This assay is a powerful tool for identifying and quantifying genetic contributions to cohesion between roots and their environment.
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Affiliation(s)
- Bethany M. Eldridge
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Emily R. Larson
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Laura Weldon
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Kevin M. Smyth
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Annabelle N. Sellin
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | | | - Claire S. Grierson
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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19
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Chemical Genetics to Uncover Mechanisms Underlying Lipid-Mediated Signaling Events in Plants. Methods Mol Biol 2021; 2213:3-16. [PMID: 33270188 DOI: 10.1007/978-1-0716-0954-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Like animals, plants use various lipids as signaling molecules to guide their growth and development. The focus of our work is on the N-acylethanolamine (NAE) group of lipid mediators, which have been shown to play important physiological roles in plants. However, mechanisms by which NAEs modulate plant function remain elusive. Chemical genetics has emerged as a potent tool to elucidate signaling pathways in plants, particularly those orchestrated by plant hormones. Like plant hormones, exogenous application of NAEs elicits distinct plant growth phenotypes that can serve as biological readouts for chemical genetic screens. For example, N-lauroylethanolamide (NAE 12:0) inhibits seedling development in the model plant Arabidopsis thaliana. Thus, a library of small synthetic chemical compounds can be rapidly screened for their ability to reverse the inhibitory effect of NAE 12:0 on seedling development. Chemicals identified through such screens could be potential agonists/antagonists of NAE receptors or signaling pathways and therefore serve as additional tools for understanding NAE function in plants. In this chapter, we describe general protocols for NAE 12:0-based chemical genetic screens in Arabidopsis. Although such screens were designed primarily for NAE 12:0, they could potentially be applied for similar work with other NAE species or plant lipid mediators.
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20
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NMR spectroscopy analysis reveals differential metabolic responses in arabidopsis roots and leaves treated with a cytokinesis inhibitor. PLoS One 2020; 15:e0241627. [PMID: 33156865 PMCID: PMC7647083 DOI: 10.1371/journal.pone.0241627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/16/2020] [Indexed: 12/26/2022] Open
Abstract
In plant cytokinesis, de novo formation of a cell plate evolving into the new cell wall partitions the cytoplasm of the dividing cell. In our earlier chemical genomics studies, we identified and characterized the small molecule endosidin-7, that specifically inhibits callose deposition at the cell plate, arresting late-stage cytokinesis in arabidopsis. Endosidin-7 has emerged as a very valuable tool for dissecting this essential plant process. To gain insights regarding its mode of action and the effects of cytokinesis inhibition on the overall plant response, we investigated the effect of endosidin-7 through a nuclear magnetic resonance spectroscopy (NMR) metabolomics approach. In this case study, metabolomics profiles of arabidopsis leaf and root tissues were analyzed at different growth stages and endosidin-7 exposure levels. The results show leaf and root-specific metabolic profile changes and the effects of endosidin-7 treatment on these metabolomes. Statistical analyses indicated that the effect of endosidin-7 treatment was more significant than the developmental impact. The endosidin-7 induced metabolic profiles suggest compensations for cytokinesis inhibition in central metabolism pathways. This study further shows that long-term treatment of endosidin-7 profoundly changes, likely via alteration of hormonal regulation, the primary metabolism of arabidopsis seedlings. Hormonal pathway-changes are likely reflecting the plant’s responses, compensating for the arrested cell division, which in turn are leading to global metabolite modulation. The presented NMR spectral data are made available through the Metabolomics Workbench, providing a reference resource for the scientific community.
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21
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Davis DJ, Wang M, Sørensen I, Rose JKC, Domozych DS, Drakakaki G. Callose deposition is essential for the completion of cytokinesis in the unicellular alga Penium margaritaceum. J Cell Sci 2020; 133:jcs249599. [PMID: 32895244 DOI: 10.1242/jcs.249599] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/27/2020] [Indexed: 11/20/2022] Open
Abstract
Cytokinesis in land plants involves the formation of a cell plate that develops into the new cell wall. Callose, a β-1,3 glucan, accumulates at later stages of cell plate development, presumably to stabilize this delicate membrane network during expansion. Cytokinetic callose is considered specific to multicellular plant species, because it has not been detected in unicellular algae. Here we present callose at the cytokinesis junction of the unicellular charophyte, Penium margaritaceum Callose deposition at the division plane of P. margaritaceum showed distinct, spatiotemporal patterns likely representing distinct roles of this polymer in cytokinesis. Pharmacological inhibition of callose deposition by endosidin 7 resulted in cytokinesis defects, consistent with the essential role for this polymer in P. margaritaceum cell division. Cell wall deposition at the isthmus zone was also affected by the absence of callose, demonstrating the dynamic nature of new wall assembly in P. margaritaceum The identification of candidate callose synthase genes provides molecular evidence for callose biosynthesis in P. margaritaceum The evolutionary implications of cytokinetic callose in this unicellular zygnematopycean alga is discussed in the context of the conquest of land by plants.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Destiny J Davis
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Minmin Wang
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Iben Sørensen
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - David S Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, NY 12866, USA
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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22
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Endosidin 2 accelerates PIN2 endocytosis and disturbs intracellular trafficking of PIN2, PIN3, and PIN4 but not of SYT1. PLoS One 2020; 15:e0237448. [PMID: 32790800 PMCID: PMC7425933 DOI: 10.1371/journal.pone.0237448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 07/27/2020] [Indexed: 11/29/2022] Open
Abstract
We established that Endosidin2 (ES2) affected the trafficking routes of both newly synthesized and endocytic pools of PIN-FORMED2 (PIN2) in Arabidopsis root epidermal cells. PIN2 populations accumulated in separated patches, which gradually merged into large and compact ES2 aggregates (ES2As). FM4-64 endocytic tracer labeled ES2As as well. Both PIN2 pools also appeared in vacuoles. Accelerated endocytosis of PIN2, its aggregation in the cytoplasm, and redirection of PIN2 flows to vacuoles led to a substantial reduction of the abundance of this protein in the plasma membrane. Whereas PIN-FORMED3 and PIN-FORMED4 also aggregated in the cytoplasm, SYT1 was not sensitive to ES2 treatment and did not appear either in the cytoplasmic aggregates or vacuoles. Ultrastructural analysis revealed that ES2 affects the Golgi apparatus so that stacks acquired cup-shape and even circular shape surrounded by several vesicles. Abnormally shaped Golgi stacks, stack remnants, multi-lamellar structures, separated Golgi cisterna rings, tubular structures, and vesicles formed discrete clusters.
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23
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Gibson CL, Isley JW, Falbel TG, Mattox CT, Lewis DR, Metcalf KE, Muday GK. A Conditional Mutation in SCD1 Reveals Linkage Between PIN Protein Trafficking, Auxin Transport, Gravitropism, and Lateral Root Initiation. FRONTIERS IN PLANT SCIENCE 2020; 11:910. [PMID: 32733502 PMCID: PMC7358545 DOI: 10.3389/fpls.2020.00910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 06/03/2020] [Indexed: 05/13/2023]
Abstract
Auxin is transported in plants with distinct polarity, defined by transport proteins of the PIN-formed (PIN) family. Components of the complex trafficking machinery responsible for polar PIN protein localization have been identified by genetic approaches, but severe developmental phenotypes of trafficking mutants complicate dissection of this pathway. We utilized a temperature sensitive allele of Arabidopsis thaliana SCD1 (stomatal cytokinesis defective1) that encodes a RAB-guanine nucleotide exchange factor. Auxin transport, lateral root initiation, asymmetric auxin-induced gene expression after gravitropic reorientation, and differential gravitropic growth were reduced in the roots of the scd1-1 mutant relative to wild type at the restrictive temperature of 25°C, but not at the permissive temperature of 18°C. In scd1-1 at 25°C, PIN1- and PIN2-GFP accumulated in endomembrane bodies. Transition of seedlings from 18 to 25°C for as little as 20 min resulted in the accumulation of PIN2-GFP in endomembranes, while gravitropism and root developmental defects were not detected until hours after transition to the non-permissive temperature. The endomembrane compartments that accumulated PIN2-GFP in scd1-1 exhibited FM4-64 signal colocalized with ARA7 and ARA6 fluorescent marker proteins, consistent with PIN2 accumulation in the late or multivesicular endosome. These experiments illustrate the power of using a temperature sensitive mutation in the gene encoding SCD1 to study the trafficking of PIN2 between the endosome and the plasma membrane. Using the conditional feature of this mutation, we show that altered trafficking of PIN2 precedes altered auxin transport and defects in gravitropism and lateral root development in this mutant upon transition to the restrictive temperature.
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Affiliation(s)
- Carole L. Gibson
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, United States
| | - Jonathan W. Isley
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Tanya G. Falbel
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Cassie T. Mattox
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, United States
| | - Daniel R. Lewis
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, United States
| | - Kasee E. Metcalf
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, United States
| | - Gloria K. Muday
- Department of Biology, Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, United States
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Huang L, Li X, Zhang W, Ung N, Liu N, Yin X, Li Y, Mcewan RE, Dilkes B, Dai M, Hicks GR, Raikhel NV, Staiger CJ, Zhang C. Endosidin20 Targets the Cellulose Synthase Catalytic Domain to Inhibit Cellulose Biosynthesis. THE PLANT CELL 2020; 32:2141-2157. [PMID: 32327535 PMCID: PMC7346566 DOI: 10.1105/tpc.20.00202] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/13/2020] [Accepted: 04/20/2020] [Indexed: 05/02/2023]
Abstract
Plant cellulose is synthesized by rosette-structured cellulose synthase (CESA) complexes (CSCs). Each CSC is composed of multiple subunits of CESAs representing three different isoforms. Individual CESA proteins contain conserved catalytic domains for catalyzing cellulose synthesis, other domains such as plant-conserved sequences, and class-specific regions that are thought to facilitate complex assembly and CSC trafficking. Because of the current lack of atomic-resolution structures for plant CSCs or CESAs, the molecular mechanism through which CESA catalyzes cellulose synthesis and whether its catalytic activity influences efficient CSC transport at the subcellular level remain unknown. Here, by performing chemical genetic analyses, biochemical assays, structural modeling, and molecular docking, we demonstrate that Endosidin20 (ES20) targets the catalytic site of CESA6 in Arabidopsis (Arabidopsis thaliana). Chemical genetic analysis revealed important amino acids that potentially participate in the catalytic activity of plant CESA6, in addition to previously identified conserved motifs across kingdoms. Using high spatiotemporal resolution live cell imaging, we found that inhibiting the catalytic activity of CESA6 by ES20 treatment reduced the efficiency of CSC transport to the plasma membrane. Our results demonstrate that ES20 is a chemical inhibitor of CESA activity and trafficking that represents a powerful tool for studying cellulose synthesis in plants.
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Affiliation(s)
- Lei Huang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Xiaohui Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Weiwei Zhang
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Nolan Ung
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Nana Liu
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Xianglin Yin
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
- Center for Cancer Research, Purdue University, West Lafayette, Indiana 47906
| | - Yong Li
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
- Center for Cancer Research, Purdue University, West Lafayette, Indiana 47906
| | - Robert E Mcewan
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Brian Dilkes
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
| | - Mingji Dai
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907
- Center for Cancer Research, Purdue University, West Lafayette, Indiana 47906
| | - Glenn R Hicks
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
- Uppsala Bio Center, Swedish University of Agricultural Sciences, Uppsala SE-75007, 19 Sweden
| | - Natasha V Raikhel
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Christopher J Staiger
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Chunhua Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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25
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Renna L, Brandizzi F. The mysterious life of the plant trans-Golgi network: advances and tools to understand it better. J Microsc 2020; 278:154-163. [PMID: 32115699 DOI: 10.1111/jmi.12881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/04/2020] [Accepted: 02/27/2020] [Indexed: 12/29/2022]
Abstract
By being at the interface of the exocytic and endocytic pathways, the plant trans-Golgi network (TGN) is a multitasking and highly diversified organelle. Despite governing vital cellular processes, the TGN remains one of the most uncharacterized organelle of plant cells. In this review, we highlight recent studies that have contributed new insights and to the generation of markers needed to answer several important questions on the plant TGN. Several drugs specifically affecting proteins critical for the TGN functions have been extremely useful for the identification of mutants of the TGN in the pursuit to understand how the morphology and the function of this organelle are controlled. In addition to these chemical tools, we review emerging microscopy techniques that help visualize the TGN at an unpreceded resolution and appreciate the heterogeneity and dynamics of this organelle in plant cells.
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Affiliation(s)
- L Renna
- MSU-DOE Plant Research Lab, Michigan State University, East Lansing, Michigan, U.S.A
| | - F Brandizzi
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, U.S.A
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26
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De Caroli M, Manno E, Perrotta C, De Lorenzo G, Di Sansebastiano GP, Piro G. CesA6 and PGIP2 Endocytosis Involves Different Subpopulations of TGN-Related Endosomes. FRONTIERS IN PLANT SCIENCE 2020; 11:350. [PMID: 32292410 PMCID: PMC7118220 DOI: 10.3389/fpls.2020.00350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/10/2020] [Indexed: 05/04/2023]
Abstract
Endocytosis is an essential process for the internalization of plasma membrane proteins, lipids and extracellular molecules into the cells. The mechanisms underlying endocytosis in plant cells involve several endosomal organelles whose origins and specific role needs still to be clarified. In this study we compare the internalization events of a GFP-tagged polygalacturonase-inhibiting protein of Phaseolus vulgaris (PGIP2-GFP) to that of a GFP-tagged subunit of cellulose synthase complex of Arabidopsis thaliana (secGFP-CesA6). Through the use of endocytic traffic chemical inhibitors (tyrphostin A23, salicylic acid, wortmannin, concanamycin A, Sortin 2, Endosidin 5 and BFA) it was evidenced that the two protein fusions were endocytosed through distinct endosomes with different mechanisms. PGIP2-GFP endocytosis is specifically sensitive to tyrphostin A23, salicylic acid and Sortin 2; furthermore, SYP51, a tSNARE with interfering effect on late steps of vacuolar traffic, affects its arrival in the central vacuole. SecGFP-CesA6, specifically sensitive to Endosidin 5, likely reaches the plasma membrane passing through the trans Golgi network (TGN), since the BFA treatment leads to the formation of BFA bodies, compatible with the aggregation of TGNs. BFA treatments determine the accumulation and tethering of the intracellular compartments labeled by both proteins, but PGIP2-GFP aggregated compartments overlap with those labeled by the endocytic dye FM4-64 while secGFP-CesA6 fills different compartments. Furthermore, secGFP-CesA6 co-localization with RFP-NIP1.1, marker of the direct ER-to-Vacuole traffic, in small compartments separated from ER suggests that secGFP-CesA6 is sorted through TGNs in which the direct contribution from the ER plays an important role. All together the data indicate the existence of a heterogeneous population of Golgi-independent TGNs.
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Affiliation(s)
- Monica De Caroli
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Elisa Manno
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Carla Perrotta
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
| | - Giulia De Lorenzo
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, Rome, Italy
| | - Gian-Pietro Di Sansebastiano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
- *Correspondence: Gian-Pietro Di Sansebastiano,
| | - Gabriella Piro
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
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27
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Kerchev P, van der Meer T, Sujeeth N, Verlee A, Stevens CV, Van Breusegem F, Gechev T. Molecular priming as an approach to induce tolerance against abiotic and oxidative stresses in crop plants. Biotechnol Adv 2019; 40:107503. [PMID: 31901371 DOI: 10.1016/j.biotechadv.2019.107503] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 11/20/2019] [Accepted: 12/30/2019] [Indexed: 12/31/2022]
Abstract
Abiotic stresses, including drought, salinity, extreme temperature, and pollutants, are the main cause of crop losses worldwide. Novel climate-adapted crops and stress tolerance-enhancing compounds are increasingly needed to counteract the negative effects of unfavorable stressful environments. A number of natural products and synthetic chemicals can protect model and crop plants against abiotic stresses through induction of molecular and physiological defense mechanisms, a process known as molecular priming. In addition to their stress-protective effect, some of these compounds can also stimulate plant growth. Here, we provide an overview of the known physiological and molecular mechanisms that induce molecular priming, together with a survey of the approaches aimed to discover and functionally study new stress-alleviating chemicals.
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Affiliation(s)
- Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic; Phytophthora Research Centre, Faculty of AgriSciences, Mendel University in Brno, 613 00 Brno, Czech Republic
| | - Tom van der Meer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Centre for Plant Systems Biology,VIB, 9052 Ghent, Belgium
| | | | - Arno Verlee
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Christian V Stevens
- Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Centre for Plant Systems Biology,VIB, 9052 Ghent, Belgium
| | - Tsanko Gechev
- Department of Molecular Stress Physiology, Center of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria; Department of Plant Physiology and Molecular Biology, University of Plovdiv, Plovdiv 4000, Bulgaria.
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28
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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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29
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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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30
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Dauphinee AN, Cardoso C, Dalman K, Ohlsson JA, Fick SB, Robert S, Hicks GR, Bozhkov PV, Minina EA. Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators. PLANT PHYSIOLOGY 2019; 181:855-866. [PMID: 31488572 PMCID: PMC6836817 DOI: 10.1104/pp.19.00647] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 05/18/2023]
Abstract
Autophagy is a major catabolic process in eukaryotes with a key role in homeostasis, programmed cell death, and aging. In plants, autophagy is also known to regulate agronomically important traits such as stress resistance, longevity, vegetative biomass, and seed yield. Despite its significance, there is still a shortage of reliable tools modulating plant autophagy. Here, we describe the first robust pipeline for identification of specific plant autophagy-modulating compounds. Our screening protocol comprises four phases: (1) high-throughput screening of chemical compounds in cell cultures of tobacco (Nicotiana tabacum); (2) confirmation of the identified hits in planta using Arabidopsis (Arabidopsis thaliana); (3) further characterization of the effect using conventional molecular biology methods; and (4) verification of chemical specificity on autophagy in planta. The methods detailed here streamline the identification of specific plant autophagy modulators and aid in unraveling the molecular mechanisms of plant autophagy.
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Affiliation(s)
- Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Catarina Cardoso
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
- Plant Genetics, School of Life Science Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Kerstin Dalman
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Jonas A Ohlsson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | | | - Stéphanie Robert
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden
| | - Glenn R Hicks
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California, 92521
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-750 07, Sweden
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
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Rodriguez-Furlan C, Domozych D, Qian W, Enquist PA, Li X, Zhang C, Schenk R, Winbigler HS, Jackson W, Raikhel NV, Hicks GR. Interaction between VPS35 and RABG3f is necessary as a checkpoint to control fusion of late compartments with the vacuole. Proc Natl Acad Sci U S A 2019; 116:21291-21301. [PMID: 31570580 PMCID: PMC6800349 DOI: 10.1073/pnas.1905321116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Vacuoles are essential organelles in plants, playing crucial roles, such as cellular material degradation, ion and metabolite storage, and turgor maintenance. Vacuoles receive material via the endocytic, secretory, and autophagic pathways. Membrane fusion is the last step during which prevacuolar compartments (PVCs) and autophagosomes fuse with the vacuole membrane (tonoplast) to deliver cargoes. Protein components of the canonical intracellular fusion machinery that are conserved across organisms, including Arabidopsis thaliana, include complexes, such as soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), that catalyze membrane fusion, and homotypic fusion and vacuole protein sorting (HOPS), that serve as adaptors which tether cargo vesicles to target membranes for fusion under the regulation of RAB-GTPases. The mechanisms regulating the recruitment and assembly of tethering complexes are not well-understood, especially the role of RABs in this dynamic regulation. Here, we report the identification of the small synthetic molecule Endosidin17 (ES17), which interferes with synthetic, endocytic, and autophagic traffic by impairing the fusion of late endosome compartments with the tonoplast. Multiple independent target identification techniques revealed that ES17 targets the VPS35 subunit of the retromer tethering complex, preventing its normal interaction with the Arabidopsis RAB7 homolog RABG3f. ES17 interference with VPS35-RABG3f interaction prevents the retromer complex to endosome anchoring, resulting in retention of RABG3f. Using multiple approaches, we show that VPS35-RABG3f-GTP interaction is necessary to trigger downstream events like HOPS complex assembly and fusion of late compartments with the tonoplast. Overall, our results support a role for the interaction of RABG3f-VPS35 as a checkpoint in the control of traffic toward the vacuole.
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Affiliation(s)
- Cecilia Rodriguez-Furlan
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92506
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92506
| | - David Domozych
- Biology Department, Skidmore College, Saratoga Springs, NY 12866
| | - Weixing Qian
- Department of Chemistry, Umea University, SE-901 87 Umea, Sweden
- Department of Chemistry, Chemical Biology Consortium Sweden, SE-901 87 Umea, Sweden
| | - Per-Anders Enquist
- Department of Chemistry, Umea University, SE-901 87 Umea, Sweden
- Department of Chemistry, Chemical Biology Consortium Sweden, SE-901 87 Umea, Sweden
| | - Xiaohui Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47906
- Center for Plant Biology, Purdue University, West Lafayette, IN 47906
| | - Chunhua Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47906
- Center for Plant Biology, Purdue University, West Lafayette, IN 47906
| | - Rolf Schenk
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92506
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92506
| | - Holly Saulsbery Winbigler
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 20201
| | - William Jackson
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 20201
| | - Natasha V Raikhel
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92506
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92506
| | - Glenn R Hicks
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92506;
- Institute of Integrative Genome Biology, University of California, Riverside, CA 92506
- Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
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Rifaioglu AS, Atas H, Martin MJ, Cetin-Atalay R, Atalay V, Doğan T. Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases. Brief Bioinform 2019; 20:1878-1912. [PMID: 30084866 PMCID: PMC6917215 DOI: 10.1093/bib/bby061] [Citation(s) in RCA: 237] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 05/25/2018] [Indexed: 01/16/2023] Open
Abstract
The identification of interactions between drugs/compounds and their targets is crucial for the development of new drugs. In vitro screening experiments (i.e. bioassays) are frequently used for this purpose; however, experimental approaches are insufficient to explore novel drug-target interactions, mainly because of feasibility problems, as they are labour intensive, costly and time consuming. A computational field known as 'virtual screening' (VS) has emerged in the past decades to aid experimental drug discovery studies by statistically estimating unknown bio-interactions between compounds and biological targets. These methods use the physico-chemical and structural properties of compounds and/or target proteins along with the experimentally verified bio-interaction information to generate predictive models. Lately, sophisticated machine learning techniques are applied in VS to elevate the predictive performance. The objective of this study is to examine and discuss the recent applications of machine learning techniques in VS, including deep learning, which became highly popular after giving rise to epochal developments in the fields of computer vision and natural language processing. The past 3 years have witnessed an unprecedented amount of research studies considering the application of deep learning in biomedicine, including computational drug discovery. In this review, we first describe the main instruments of VS methods, including compound and protein features (i.e. representations and descriptors), frequently used libraries and toolkits for VS, bioactivity databases and gold-standard data sets for system training and benchmarking. We subsequently review recent VS studies with a strong emphasis on deep learning applications. Finally, we discuss the present state of the field, including the current challenges and suggest future directions. We believe that this survey will provide insight to the researchers working in the field of computational drug discovery in terms of comprehending and developing novel bio-prediction methods.
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Affiliation(s)
- Ahmet Sureyya Rifaioglu
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
- Department of Computer Engineering, İskenderun Technical University, Hatay, Turkey
| | - Heval Atas
- Cancer System Biology Laboratory (CanSyL), Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Maria Jesus Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Cambridge, Hinxton, UK
| | - Rengul Cetin-Atalay
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
| | - Volkan Atalay
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
| | - Tunca Doğan
- Cancer System Biology Laboratory (CanSyL), Graduate School of Informatics, Middle East Technical University, Ankara, Turkey and European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL–EBI), Cambridge, Hinxton, UK
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34
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Braking plant endocytosis. Nat Chem Biol 2019; 15:553-555. [PMID: 31011213 DOI: 10.1038/s41589-019-0273-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle E, De Rycke R, Vasileva M, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN, Winne J, Russinova E. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nat Chem Biol 2019; 15:641-649. [DOI: 10.1038/s41589-019-0262-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 03/04/2019] [Indexed: 11/09/2022]
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36
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Mishev K, Lu Q, Denoo B, Peurois F, Dejonghe W, Hullaert J, De Rycke R, Boeren S, Bretou M, De Munck S, Sharma I, Goodman K, Kalinowska K, Storme V, Nguyen LSL, Drozdzecki A, Martins S, Nerinckx W, Audenaert D, Vert G, Madder A, Otegui MS, Isono E, Savvides SN, Annaert W, De Vries S, Cherfils J, Winne J, Russinova E. Nonselective Chemical Inhibition of Sec7 Domain-Containing ARF GTPase Exchange Factors. THE PLANT CELL 2018; 30:2573-2593. [PMID: 30018157 PMCID: PMC6241273 DOI: 10.1105/tpc.18.00145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 06/25/2018] [Accepted: 07/17/2018] [Indexed: 05/12/2023]
Abstract
Small GTP-binding proteins from the ADP-ribosylation factor (ARF) family are important regulators of vesicle formation and cellular trafficking in all eukaryotes. ARF activation is accomplished by a protein family of guanine nucleotide exchange factors (GEFs) that contain a conserved catalytic Sec7 domain. Here, we identified and characterized Secdin, a small-molecule inhibitor of Arabidopsis thaliana ARF-GEFs. Secdin application caused aberrant retention of plasma membrane (PM) proteins in late endosomal compartments, enhanced vacuolar degradation, impaired protein recycling, and delayed secretion and endocytosis. Combined treatments with Secdin and the known ARF-GEF inhibitor Brefeldin A (BFA) prevented the BFA-induced PM stabilization of the ARF-GEF GNOM, impaired its translocation from the Golgi to the trans-Golgi network/early endosomes, and led to the formation of hybrid endomembrane compartments reminiscent of those in ARF-GEF-deficient mutants. Drug affinity-responsive target stability assays revealed that Secdin, unlike BFA, targeted all examined Arabidopsis ARF-GEFs, but that the interaction was probably not mediated by the Sec7 domain because Secdin did not interfere with the Sec7 domain-mediated ARF activation. These results show that Secdin and BFA affect their protein targets through distinct mechanisms, in turn showing the usefulness of Secdin in studies in which ARF-GEF-dependent endomembrane transport cannot be manipulated with BFA.
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Affiliation(s)
- Kiril Mishev
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Qing Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Bram Denoo
- Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Ghent, Belgium
| | - François Peurois
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique, Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France
| | - Wim Dejonghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jan Hullaert
- Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Ghent, Belgium
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- VIB BioImaging Core, 9052 Ghent, Belgium
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University, 6708 Wageningen, The Netherlands
| | - Marine Bretou
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, KU Leuven, Department of Neurosciences, 3000 Leuven, Belgium
| | - Steven De Munck
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
- Center for Inflammation Research, VIB, 9052 Ghent, Belgium
| | - Isha Sharma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Kaija Goodman
- Laboratory of Cell and Molecular Biology and Departments of Botany and Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Kamila Kalinowska
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Le Son Long Nguyen
- VIB Screening Core, 9052 Ghent, Belgium
- Expertise Centre for Bioassay Development and Screening (C-BIOS), Ghent University, 9052 Ghent, Belgium
| | - Andrzej Drozdzecki
- VIB Screening Core, 9052 Ghent, Belgium
- Expertise Centre for Bioassay Development and Screening (C-BIOS), Ghent University, 9052 Ghent, Belgium
| | - Sara Martins
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Wim Nerinckx
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
- Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Dominique Audenaert
- VIB Screening Core, 9052 Ghent, Belgium
- Expertise Centre for Bioassay Development and Screening (C-BIOS), Ghent University, 9052 Ghent, Belgium
| | - Grégory Vert
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Université Paris Sud, Université Paris-Saclay, Gif-sur-Yvette 91198, France
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Ghent, Belgium
| | - Marisa S Otegui
- Laboratory of Cell and Molecular Biology and Departments of Botany and Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Erika Isono
- School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Savvas N Savvides
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
- Center for Inflammation Research, VIB, 9052 Ghent, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB Center for Brain and Disease Research, KU Leuven, Department of Neurosciences, 3000 Leuven, Belgium
| | - Sacco De Vries
- Laboratory of Biochemistry, Wageningen University, 6708 Wageningen, The Netherlands
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique, Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France
| | - Johan Winne
- Department of Organic and Macromolecular Chemistry, Ghent University, 9000 Ghent, Belgium
| | - 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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Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De Rycke R, Grones P, Robert S, Russinova E, Friml J. The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Subcellular Trafficking in Eukaryotes. THE PLANT CELL 2018; 30:2553-2572. [PMID: 30018156 PMCID: PMC6241256 DOI: 10.1105/tpc.18.00127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/29/2018] [Accepted: 07/17/2018] [Indexed: 05/10/2023]
Abstract
The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Saccharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development.
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Affiliation(s)
- Urszula Kania
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
- Department of Plant Biotechnology and Bioinformatics, Ghent University and Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Tomasz Nodzyński
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, CZ-625 00 Brno, Czech Republic
| | - Qing Lu
- Department of Plant Biotechnology and Bioinformatics, Ghent University and Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Glenn R Hicks
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Wim Nerinckx
- VIB-UGent Center for Medical Biotechnology, 9052 Ghent-Zwijnaarde, Belgium
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Kiril Mishev
- Department of Plant Biotechnology and Bioinformatics, Ghent University and Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - François Peurois
- Laboratoire de Biologie et Pharmacologie Appliquée CNRS, Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée CNRS, Ecole Normale Supérieure Paris-Saclay, 94235 Cachan, France
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University and Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- VIB BioImaging Core, 9052Ghent, Belgium
| | - Peter Grones
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Stéphanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University and Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Jiří Friml
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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38
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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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39
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Chemical Genomics Translatability from Unicellular to Multicellular Models. Methods Mol Biol 2018; 1795:189-201. [PMID: 29846929 DOI: 10.1007/978-1-4939-7874-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Chemical genomics has proven to be a useful and successful approach to study complex systems where conventional genetics fails to render feasible results. High-throughput phenotype screenings in model organisms have identified a large collection of powerful and selective bioactive chemicals. Nevertheless, applying chemical high-throughput screening to crops still represents a big challenge for researchers. Fortunately, a circumvent approach could be taken by means of translational research. In this case, searching bioactive chemicals in a much handy model organism would be the starting point for discovering compounds with activity in relevant plants for improving a desirable trait. In this chapter, we describe strategies that have been proven to successfully translate chemical biology and genetics from unicellular yeast to Arabidopsis thaliana and finally to crops.
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40
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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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41
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Profile of Natasha V. Raikhel. Proc Natl Acad Sci U S A 2018; 115:1672-1674. [DOI: 10.1073/pnas.1721892115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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42
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Reynolds GD, Wang C, Pan J, Bednarek SY. Inroads into Internalization: Five Years of Endocytic Exploration. PLANT PHYSIOLOGY 2018; 176:208-218. [PMID: 29074601 PMCID: PMC5761813 DOI: 10.1104/pp.17.01117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/23/2017] [Indexed: 05/21/2023]
Abstract
Advances over recent years underlines a growing interest in investigating endocytosis in plants.
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Affiliation(s)
- Gregory D Reynolds
- Department of Biochemistry University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Chao Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jianwei Pan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, College of Life Sciences, Lanzhou University, Lanzhou 730000, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Zhejiang 321004, China
| | - Sebastian Y Bednarek
- Department of Biochemistry University of Wisconsin-Madison, Madison, Wisconsin 53706
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43
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Rodriguez-Furlan C, Raikhel NV, Hicks GR. Merging roads: chemical tools and cell biology to study unconventional protein secretion. JOURNAL OF EXPERIMENTAL BOTANY 2017; 69:39-46. [PMID: 28992077 DOI: 10.1093/jxb/erx261] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The endomembrane trafficking network is highly complex and dynamic, with both conventional and so-called unconventional routes which are in essence recently discovered pathways that are poorly understood in plants. One approach to dissecting endomembrane pathways that we have pioneered is the use of chemical biology. Classical genetic manipulations often deal with indirect pleiotropic phenotypes resulting from the perturbation of key players of the trafficking routes. Many of these difficulties can be circumvented using small molecules to modify or disrupt the function or localization of key proteins regulating these pathways. In this review, we summarize how small molecules have been used as probes to define these pathways, and how they could be used to increase current knowledge of unconventional protein secretion pathways.
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Affiliation(s)
- Cecilia Rodriguez-Furlan
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, USA
| | - Natasha V Raikhel
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, USA
| | - Glenn R Hicks
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, USA
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44
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Wang X, Chung KP, Lin W, Jiang L. Protein secretion in plants: conventional and unconventional pathways and new techniques. JOURNAL OF EXPERIMENTAL BOTANY 2017; 69:21-37. [PMID: 28992209 DOI: 10.1093/jxb/erx262] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein secretion is an essential process in all eukaryotic cells and its mechanisms have been extensively studied. Proteins with an N-terminal leading sequence or transmembrane domain are delivered through the conventional protein secretion (CPS) pathway from the endoplasmic reticulum (ER) to the Golgi apparatus. This feature is conserved in yeast, animals, and plants. In contrast, the transport of leaderless secretory proteins (LSPs) from the cytosol to the cell exterior is accomplished via the unconventional protein secretion (UPS) pathway. So far, the CPS pathway has been well characterized in plants, with several recent studies providing new information about the regulatory mechanisms involved. On the other hand, studies on UPS pathways in plants remain descriptive, although a connection between UPS and the plant defense response is becoming more and more apparent. In this review, we present an update on CPS and UPS. With the emergence of new techniques, a more comprehensive understanding of protein secretion in plants can be expected in the future.
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Affiliation(s)
- Xiangfeng Wang
- State Key Laboratory of Agrobiotechnology, Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Kin Pan Chung
- State Key Laboratory of Agrobiotechnology, Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Weili Lin
- State Key Laboratory of Agrobiotechnology, Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Liwen Jiang
- State Key Laboratory of Agrobiotechnology, Centre for Cell and Developmental Biology, School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
- CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, China
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45
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Rodriguez-Furlan C, Zhang C, Raikhel N, Hicks GR. Drug Affinity Responsive Target Stability (DARTS) to Resolve Protein-Small Molecule Interaction in Arabidopsis. ACTA ACUST UNITED AC 2017; 2:370-378. [PMID: 33383985 DOI: 10.1002/cppb.20062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Target identification remains a challenging step in plant chemical genomics approaches. Drug affinity responsive target stability (DARTS) represents a straightforward technique to identify small molecules' protein targets and assist in the characterization of interactions between small molecules and putative targets identified by other methods. When a small molecule interacts with a protein, it has the potential to stabilize the protein's structure, resulting in a reduced susceptibility to protease action. During the DARTS procedure, protein extracts are treated with proteolytic enzymes, and only proteins that bind to the small molecule are protected from proteolysis. DARTS represents a protocol independent of the molecule's mechanism of action or chemical structure. Another advantage of DARTS is that it does not require additional modifications or tagging of the small molecule. The protocols outlined in this article describe in detail the DARTS technique applied to plant proteins and propose several detection procedures according to protein abundance. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Cecilia Rodriguez-Furlan
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, California
| | - Chunhua Zhang
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana.,Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana
| | - Natasha Raikhel
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, California
| | - Glenn R Hicks
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, and Department of Botany and Plant Sciences, University of California, Riverside, California
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Childress ES, Alexopoulos SJ, Hoehn KL, Santos WL. Small Molecule Mitochondrial Uncouplers and Their Therapeutic Potential. J Med Chem 2017; 61:4641-4655. [DOI: 10.1021/acs.jmedchem.7b01182] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth S. Childress
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Stephanie J. Alexopoulos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2033, Australia
| | - Kyle L. Hoehn
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2033, Australia
- Departments of Pharmacology and Medicine, Cardiovascular Research Center, and Emily Couric Clinical Cancer Center, University of Virginia, Charlottesville, Virginia 22908, United States
| | - Webster L. Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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47
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Kitakura S, Adamowski M, Matsuura Y, Santuari L, Kouno H, Arima K, Hardtke CS, Friml J, Kakimoto T, Tanaka H. BEN3/BIG2 ARF GEF is Involved in Brefeldin A-Sensitive Trafficking at the trans-Golgi Network/Early Endosome in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2017; 58:1801-1811. [PMID: 29016942 DOI: 10.1093/pcp/pcx118] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/11/2017] [Indexed: 06/07/2023]
Abstract
Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to the fungal toxin brefeldin A (BFA), which is known to inhibit guanine nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been fully revealed. In a previous study, we identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. BEN3/BIG2 tagged with fluorescent proteins co-localized with markers for the TGN/early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA sensitive, and established BEN3/BIG2 as a crucial component of this BFA action at the level of the TGN/EE. Furthermore, ben3 mutation alleviated BFA-induced agglomeration of another TGN-localized ARF GEF, BEN1/MIN7. Taken together, our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.
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Affiliation(s)
- Saeko Kitakura
- Department of Biological Science, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan
| | - Maciek Adamowski
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Yuki Matsuura
- Department of Biological Science, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan
- Interdisciplinary Program for Biomedical Sciences (IPBS), Institute for Academic Initiatives, Osaka University, Suita, Japan
| | - Luca Santuari
- Plant Developmental Biology, Wageningen University and Research Centre, 6708PB Wageningen, The Netherlands
| | - Hirotaka Kouno
- Department of Biological Science, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan
| | - Kohei Arima
- Department of Biological Science, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan
| | - Christian S Hardtke
- Plant Developmental Biology, Wageningen University and Research Centre, 6708PB Wageningen, The Netherlands
| | - Jirí Friml
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University (MU), Kamenice 5, Brno, CZ-625 00 Czech Republic
| | - Tatsuo Kakimoto
- Department of Biological Science, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan
| | - Hirokazu Tanaka
- Department of Biological Science, Graduate School of Science, Osaka University, Osaka, 560-0043 Japan
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48
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Thioether-stapled macrocyclic inhibitors of the EH domain of EHD1. Bioorg Med Chem 2017; 26:1206-1211. [PMID: 28951093 DOI: 10.1016/j.bmc.2017.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/31/2017] [Accepted: 09/06/2017] [Indexed: 11/24/2022]
Abstract
Recycling of receptors from the endosomal recycling compartment to the plasma membrane is a critical cellular process, and recycling is particularly important for maintaining invasiveness in solid tumors. In this work, we continue our efforts to inhibit EHD1, a critical adaptor protein involved in receptor recycling. We applied a diversity-oriented macrocyclization approach to produce cyclic peptides with varied conformations, but that each contain a motif that binds to the EH domain of EHD1. Screening these uncovered several new inhibitors for EHD1's EH domain, the most potent of which bound with a Kd of 3.1μM. Several of the most potent inhibitors were tested in a cellular assay that measures extent of vesicle recycling. Inhibiting EHD1 could potentially slow cancer invasiveness and metastasis, and these cyclic peptides represent the most potent inhibitors of EHD1 to date.
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49
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Faulkner C, Zhou J, Evrard A, Bourdais G, MacLean D, Häweker H, Eckes P, Robatzek S. An automated quantitative image analysis tool for the identification of microtubule patterns in plants. Traffic 2017; 18:683-693. [PMID: 28746801 DOI: 10.1111/tra.12505] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 07/23/2017] [Accepted: 07/23/2017] [Indexed: 12/20/2022]
Abstract
High throughput confocal imaging poses challenges in the computational image analysis of complex subcellular structures such as the microtubule cytoskeleton. Here, we developed CellArchitect, an automated image analysis tool that quantifies changes to subcellular patterns illustrated by microtubule markers in plants. We screened microtubule-targeted herbicides and demonstrate that high throughput confocal imaging with integrated image analysis by CellArchitect can distinguish effects induced by the known herbicides indaziflam and trifluralin. The same platform was used to examine 6 other compounds with herbicidal activity, and at least 3 different effects induced by these compounds were profiled. We further show that CellArchitect can detect subcellular patterns tagged by actin and endoplasmic reticulum markers. Thus, the platform developed here can be used to automate image analysis of complex subcellular patterns for purposes such as herbicide discovery and mode of action characterisation. The capacity to use this tool to quantitatively characterize cellular responses lends itself to application across many areas of biology.
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Affiliation(s)
| | - Ji Zhou
- Norwich Research Park, The Sainsbury Laboratory, Norwich, UK
| | | | - Gildas Bourdais
- Norwich Research Park, The Sainsbury Laboratory, Norwich, UK
| | - Dan MacLean
- Norwich Research Park, The Sainsbury Laboratory, Norwich, UK
| | - Heidrun Häweker
- Norwich Research Park, The Sainsbury Laboratory, Norwich, UK
| | - Peter Eckes
- Bayer AG, Crop Science Division, Industrial Park Hoechst, Frankfurt, Germany
| | - Silke Robatzek
- Norwich Research Park, The Sainsbury Laboratory, Norwich, UK
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50
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Dejonghe W, Russinova E. Plant Chemical Genetics: From Phenotype-Based Screens to Synthetic Biology. PLANT PHYSIOLOGY 2017; 174:5-20. [PMID: 28275150 PMCID: PMC5411137 DOI: 10.1104/pp.16.01805] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/20/2017] [Indexed: 05/21/2023]
Abstract
The treatment of a biological system with small molecules to specifically perturb cellular functions is commonly referred to as chemical biology. Small molecules are used commercially as drugs, herbicides, and fungicides in different systems, but in recent years they are increasingly exploited as tools for basic research. For instance, chemical genetics involves the discovery of small-molecule effectors of various cellular functions through screens of compound libraries. Whereas the drug discovery field has largely been driven by target-based screening approaches followed by drug optimization, chemical genetics in plant systems tends to be fueled by more general phenotype-based screens, opening the possibility to identify a wide range of small molecules that are not necessarily directly linked to the process of interest. Here, we provide an overview of the current progress in chemical genetics in plants, with a focus on the discoveries regarding small molecules identified in screens designed with a basic biology perspective. We reflect on the possibilities that lie ahead and discuss some of the potential pitfalls that might be encountered upon adopting a given chemical genetics approach.
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Affiliation(s)
- Wim Dejonghe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (W.D., E.R); and
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium (W.D., E.R.)
| | - Eugenia Russinova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium (W.D., E.R); and
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium (W.D., E.R.)
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