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Yang X, Wang J, Li F, Zhou C, Wu M, Zheng C, Yang L, Li Z, Li Y, Guo S, Song C. RotatedStomataNet: a deep rotated object detection network for directional stomata phenotype analysis. PLANT CELL REPORTS 2024; 43:126. [PMID: 38652181 DOI: 10.1007/s00299-024-03149-3] [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: 11/28/2023] [Accepted: 01/02/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE Innovatively, we consider stomatal detection as rotated object detection and provide an end-to-end, batch, rotated, real-time stomatal density and aperture size intelligent detection and identification system, RotatedeStomataNet. Stomata acts as a pathway for air and water vapor in the course of respiration, transpiration, and other gas metabolism, so the stomata phenotype is important for plant growth and development. Intelligent detection of high-throughput stoma is a key issue. Nevertheless, currently available methods usually suffer from detection errors or cumbersome operations when facing densely and unevenly arranged stomata. The proposed RotatedStomataNet innovatively regards stomata detection as rotated object detection, enabling an end-to-end, real-time, and intelligent phenotype analysis of stomata and apertures. The system is constructed based on the Arabidopsis and maize stomatal data sets acquired destructively, and the maize stomatal data set acquired in a non-destructive way, enabling the one-stop automatic collection of phenotypic, such as the location, density, length, and width of stomata and apertures without step-by-step operations. The accuracy of this system to acquire stomata and apertures has been well demonstrated in monocotyledon and dicotyledon, such as Arabidopsis, soybean, wheat, and maize. The experimental results that the prediction results of the method are consistent with those of manual labeling. The test sets, the system code, and their usage are also given ( https://github.com/AITAhenu/RotatedStomataNet ).
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Affiliation(s)
- Xiaohui Yang
- Henan Engineering Research Center for Artificial Intelligence Theory and Algorithms, School of Mathematics and Statistics, Henan University, Kaifeng, 475004, Henan, China.
| | - Jiahui Wang
- Henan Engineering Research Center for Artificial Intelligence Theory and Algorithms, School of Mathematics and Statistics, Henan University, Kaifeng, 475004, Henan, China
| | - Fan Li
- School of Automation, Central South University, Changsha, 410000, Hunan, China
| | - Chenglong Zhou
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Wuxi, 214400, Jiangsu, China
| | - Minghui Wu
- Henan Engineering Research Center for Artificial Intelligence Theory and Algorithms, School of Mathematics and Statistics, Henan University, Kaifeng, 475004, Henan, China
| | - Chen Zheng
- Henan Engineering Research Center for Artificial Intelligence Theory and Algorithms, School of Mathematics and Statistics, Henan University, Kaifeng, 475004, Henan, China
| | - Lijun Yang
- Henan Engineering Research Center for Artificial Intelligence Theory and Algorithms, School of Mathematics and Statistics, Henan University, Kaifeng, 475004, Henan, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, Henan, China
| | - Yong Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, Henan, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, Henan, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, 475004, Henan, China
| | - Chunpeng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, 475004, Henan, China
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2
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Petre B, Contreras MP, Bozkurt TO, Schattat MH, Sklenar J, Schornack S, Abd-El-Haliem A, Castells-Graells R, Lozano-Durán R, Dagdas YF, Menke FLH, Jones AME, Vossen JH, Robatzek S, Kamoun S, Win J. Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process. THE PLANT CELL 2021. [PMID: 33677602 DOI: 10.1101/2020.09.24.308585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry. This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and colocalize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. This interactome dataset will serve as a useful resource for functional studies of P. infestans effectors and of effector-targeted host processes.
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Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tolga O Bozkurt
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Martin H Schattat
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Plant Physiology, Institute for Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Schornack
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Roger Castells-Graells
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Rosa Lozano-Durán
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yasin F Dagdas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Alexandra M E Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Silke Robatzek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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3
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Petre B, Contreras MP, Bozkurt TO, Schattat MH, Sklenar J, Schornack S, Abd-El-Haliem A, Castells-Graells R, Lozano-Durán R, Dagdas YF, Menke FLH, Jones AME, Vossen JH, Robatzek S, Kamoun S, Win J. Host-interactor screens of Phytophthora infestans RXLR proteins reveal vesicle trafficking as a major effector-targeted process. THE PLANT CELL 2021; 33:1447-1471. [PMID: 33677602 PMCID: PMC8254500 DOI: 10.1093/plcell/koab069] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/19/2021] [Indexed: 05/20/2023]
Abstract
Pathogens modulate plant cell structure and function by secreting effectors into host tissues. Effectors typically function by associating with host molecules and modulating their activities. This study aimed to identify the host processes targeted by the RXLR class of host-translocated effectors of the potato blight pathogen Phytophthora infestans. To this end, we performed an in planta protein-protein interaction screen by transiently expressing P. infestans RXLR effectors in Nicotiana benthamiana leaves followed by coimmunoprecipitation and liquid chromatography-tandem mass spectrometry. This screen generated an effector-host protein interactome matrix of 59 P. infestans RXLR effectors x 586 N. benthamiana proteins. Classification of the host interactors into putative functional categories revealed over 35 biological processes possibly targeted by P. infestans. We further characterized the PexRD12/31 family of RXLR-WY effectors, which associate and colocalize with components of the vesicle trafficking machinery. One member of this family, PexRD31, increased the number of FYVE positive vesicles in N. benthamiana cells. FYVE positive vesicles also accumulated in leaf cells near P. infestans hyphae, indicating that the pathogen may enhance endosomal trafficking during infection. This interactome dataset will serve as a useful resource for functional studies of P. infestans effectors and of effector-targeted host processes.
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Affiliation(s)
- Benjamin Petre
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Université de Lorraine, INRAE, IAM, Nancy, France
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tolga O Bozkurt
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Martin H Schattat
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Department of Plant Physiology, Institute for Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sebastian Schornack
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | | | - Roger Castells-Graells
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, USA
| | - Rosa Lozano-Durán
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yasin F Dagdas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Frank L H Menke
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Alexandra M E Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Jack H Vossen
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Silke Robatzek
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
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4
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Bourdais G, McLachlan DH, Rickett LM, Zhou J, Siwoszek A, Häweker H, Hartley M, Kuhn H, Morris RJ, MacLean D, Robatzek S. The use of quantitative imaging to investigate regulators of membrane trafficking in Arabidopsis stomatal closure. Traffic 2019; 20:168-180. [PMID: 30447039 DOI: 10.1111/tra.12625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 12/26/2022]
Abstract
Expansion of gene families facilitates robustness and evolvability of biological processes but impedes functional genetic dissection of signalling pathways. To address this, quantitative analysis of single cell responses can help characterize the redundancy within gene families. We developed high-throughput quantitative imaging of stomatal closure, a response of plant guard cells, and performed a reverse genetic screen in a group of Arabidopsis mutants to five stimuli. Focussing on the intersection between guard cell signalling and the endomembrane system, we identified eight clusters based on the mutant stomatal responses. Mutants generally affected in stomatal closure were mostly in genes encoding SNARE and SCAMP membrane regulators. By contrast, mutants in RAB5 GTPase genes played specific roles in stomatal closure to microbial but not drought stress. Together with timed quantitative imaging of endosomes revealing sequential patterns in FLS2 trafficking, our imaging pipeline can resolve non-redundant functions of the RAB5 GTPase gene family. Finally, we provide a valuable image-based tool to dissect guard cell responses and outline a genetic framework of stomatal closure.
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Affiliation(s)
- Gildas Bourdais
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Deirdre H McLachlan
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Lydia M Rickett
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Ji Zhou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,The Earlham Institute, Norwich Research Park, Norwich, UK
| | | | - Heidrun Häweker
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | | | - Hannah Kuhn
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,Unit of Plant Molecular Cell Biology, Institute for Biology I, RWTH Aachen University, Aachen, Germany
| | | | - Dan MacLean
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
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5
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A simple microfluidic device for live cell imaging of Arabidopsis cotyledons, leaves, and seedlings. Biotechniques 2018; 64:255-261. [PMID: 29939090 PMCID: PMC8592504 DOI: 10.2144/btn-2018-0044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
One of the challenges of performing live-cell imaging in plants is establishing a system for securing the sample during imaging that allows for the rapid addition of treatments. Here we report how a commercially available device called a HybriWell™ can be repurposed to create an imaging chamber suitable for Arabidopsis seedlings, cotyledons and leaves. Liquid in the imaging chamber can be rapidly exchanged to introduce chemical treatments via microfluidic passive pumping. When used in conjunction with fluorescent biosensors, this system can facilitate live-cell imaging studies of signal transduction pathways triggered by different treatments. As a demonstration, we show how the HybriWell can be used to monitor flg22-induced calcium transients using the R-GECO1 calcium indicator in detached Arabidopsis leaves.
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6
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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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7
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Higaki T. Quantitative evaluation of cytoskeletal organizations by microscopic image analysis. ACTA ACUST UNITED AC 2017. [DOI: 10.5685/plmorphol.29.15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Takumi Higaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
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8
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Bayle V, Platre MP, Jaillais Y. Automatic Quantification of the Number of Intracellular Compartments in Arabidopsis thaliana Root Cells. Bio Protoc 2017; 7:e2145. [PMID: 28255574 DOI: 10.21769/bioprotoc.2145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
In the era of quantitative biology, it is increasingly required to quantify confocal microscopy images. If possible, quantification should be performed in an automatic way, in order to avoid bias from the experimenter, to allow the quantification of a large number of samples, and to increase reproducibility between laboratories. In this protocol, we describe procedures for automatic counting of the number of intracellular compartments in Arabidopsis root cells, which can be used for example to study endocytosis or secretory trafficking pathways and to compare membrane organization between different genotypes or treatments. While developed for Arabidopsis roots, this method can be used on other tissues, cell types and plant species.
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Affiliation(s)
- Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Matthieu Pierre Platre
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, Lyon, France
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9
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Haus MJ, Kelsch RD, Jacobs TW. Application of Optical Topometry to Analysis of the Plant Epidermis. PLANT PHYSIOLOGY 2015; 169:946-59. [PMID: 26290539 PMCID: PMC4587452 DOI: 10.1104/pp.15.00613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/17/2015] [Indexed: 05/20/2023]
Abstract
The plant epidermis regulates key physiological functions contributing to photosynthetic rate, plant productivity, and ecosystem stability. Yet, quantitative characterization of this interface between a plant and its aerial environment is laborious and destructive with current techniques, making large-scale characterization of epidermal cell parameters impractical. Here, we present our exploration of optical topometry (OT) for the analysis of plant organ surfaces. OT is a mature, confocal microscopy-based implementation of surface metrology that generates nanometer-scale digital characterizations of any surface. We report epidermal analyses in Arabidopsis (Arabidopsis thaliana) and other species as well as dried herbarium specimens and fossilized plants. We evaluate the technology's analytical potential for identifying an array of epidermal characters, including cell type distributions, variation in cell morphology and stomatal depth, differentiation of herbarium specimens, and real-time deformations in living tissue following detachment. As applied to plant material, OT is very fast and nondestructive, yielding richly mineable data sets describing living tissues and rendering a variety of their characteristics accessible for statistical, quantitative genetic, and structural analysis.
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Affiliation(s)
- Miranda J Haus
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801
| | - Ryan D Kelsch
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801
| | - Thomas W Jacobs
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801
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10
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Zwiewka M, Nodzyński T, Robert S, Vanneste S, Friml J. Osmotic Stress Modulates the Balance between Exocytosis and Clathrin-Mediated Endocytosis in Arabidopsis thaliana. MOLECULAR PLANT 2015; 8:1175-87. [PMID: 25795554 DOI: 10.1016/j.molp.2015.03.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 03/04/2015] [Accepted: 03/05/2015] [Indexed: 05/18/2023]
Abstract
The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.
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Affiliation(s)
- Marta Zwiewka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Tomasz Nodzyński
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Stéphanie Robert
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Jiří Friml
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic; Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Gent, Belgium; Institute of Science and Technology (IST) Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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11
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McLachlan DH, Kopischke M, Robatzek S. Gate control: guard cell regulation by microbial stress. THE NEW PHYTOLOGIST 2014; 203:1049-1063. [PMID: 25040778 DOI: 10.1111/nph.12916] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/26/2014] [Indexed: 05/07/2023]
Abstract
Terrestrial plants rely on stomata, small pores in the leaf surface, for photosynthetic gas exchange and transpiration of water. The stomata, formed by a pair of guard cells, dynamically increase and decrease their volume to control the pore size in response to environmental cues. Stresses can trigger similar or opposing movements: for example, drought induces closure of stomata, whereas many pathogens exploit stomata and cause them to open to facilitate entry into plant tissues. The latter is an active process as stomatal closure is part of the plant's immune response. Stomatal research has contributed much to clarify the signalling pathways of abiotic stress, but guard cell signalling in response to microbes is a relatively new area of research. In this article, we discuss present knowledge of stomatal regulation in response to microbes and highlight common points of convergence, and differences, compared to stomatal regulation by abiotic stresses. We also expand on the mechanisms by which pathogens manipulate these processes to promote disease, for example by delivering effectors to inhibit closure or trigger opening of stomata. The study of pathogen effectors in stomatal manipulation will aid our understanding of guard cell signalling.
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Affiliation(s)
| | | | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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12
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Lozano-Durán R, Bourdais G, He SY, Robatzek S. The bacterial effector HopM1 suppresses PAMP-triggered oxidative burst and stomatal immunity. THE NEW PHYTOLOGIST 2014; 202:259-269. [PMID: 24372399 DOI: 10.1111/nph.12651] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 11/08/2013] [Indexed: 05/19/2023]
Abstract
Successful pathogens counter immunity at multiple levels, mostly through the action of effectors. Pseudomonas syringae secretes c. 30 effectors, some of which have been shown to inhibit plant immunity triggered upon perception of conserved pathogen-associated molecular patterns (PAMPs). One of these is HopM1, which impairs late immune responses through targeting the vesicle trafficking-related AtMIN7 for degradation. Here, we report that in planta expressed HopM1 suppresses two early PAMP-triggered responses, the oxidative burst and stomatal immunity, both of which seem to require proteasomal function but are independent of AtMIN7. Notably, a 14-3-3 protein, GRF8/AtMIN10, was found previously to be a target of HopM1 in vivo, and expression of HopM1 mimics the effect of chemically and genetically disrupting 14-3-3 function. Our data further show that the function of 14-3-3 proteins is required for PAMP-triggered oxidative burst and stomatal immunity, and chemical-mediated disruption of the 14-3-3 interactions with their client proteins restores virulence of a HopM1-deficient P. syringae mutant, providing a link between HopM1 and the involvement of 14-3-3 proteins in plant immunity. Taken together, these results unveil the impact of HopM1 on the PAMP-triggered oxidative burst and stomatal immunity in an AtMIN7-independent manner, most likely acting at the function of (a) 14-3-3 protein(s).
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Affiliation(s)
- Rosa Lozano-Durán
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Gildas Bourdais
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sheng Yang He
- Department of Energy Plant Research Laboratory, Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Michigan State University, East Lansing, MI, 48824, USA
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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13
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Abstract
Fluorescence confocal microscopy has emerged in the past decade as an important method for studying the cellular changes associated with plant-microbe interactions. One such change is the internalization into endosomes of the cell surface receptor FLAGELLIN SENSING 2 (FLS2) upon activation by its ligand, bacterial flagellin (flg22). Quantification of endosomes containing FLS2 can thus be used as a direct readout of immune response activation at the cellular level. High-throughput imaging of cellular events is routinely applied in chemical screening for pharmaceutical drug discovery, and we have adapted this system for quantification of plant leaf cellular parameters. In this chapter we describe the instrument setup for high-throughput imaging of leaves, protocols for flg22-induced endocytosis, image acquisition for fluorescent-tagged FLS2 receptors and subcellular markers, automated image analysis of cellular parameters, and data outputs of FLS2 endocytosis.
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Affiliation(s)
- Martina Beck
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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14
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Hicks GR, Raikhel NV. Plant chemical biology: are we meeting the promise? FRONTIERS IN PLANT SCIENCE 2014; 5:455. [PMID: 25250041 PMCID: PMC4157539 DOI: 10.3389/fpls.2014.00455] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/22/2014] [Indexed: 05/04/2023]
Abstract
As an early adopter of plant chemical genetics to the study of endomembrane trafficking, we have observed the growth of small molecule approaches. Within the field, we often describe the strengths of the approach in a broad, generic manner, such as the ability to address redundancy and lethality. But, we are now in a much better position to evaluate the demonstrated value of the approach based on examples. In this perspective, we offer an assessment of chemical genetics in plants and where its applications may be of particular utility from the perspective of the cell biologist. Beyond this, we suggest areas to be addressed to provide broader access and enhance the effectiveness of small molecule approaches in plant biology.
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Affiliation(s)
- Glenn R. Hicks
- *Correspondence: Glenn R. Hicks, Center for Plant Cell Biology, Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California, Riverside,CA 92521, USA e-mail:
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15
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Worden N, Girke T, Drakakaki G. Endomembrane dissection using chemically induced bioactive clusters. Methods Mol Biol 2014; 1056:159-168. [PMID: 24306872 DOI: 10.1007/978-1-62703-592-7_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Chemical genomics is a novel approach that allows for the rapid functional analysis of plant proteins, complexes, pathways, and networks. Systematic screens for bioactive small molecules causing specific subcellular phenotypes have been successfully performed in mammalian cells, but thus far, are limited in plants. This protocol describes a systematic chemical screen of plasma membrane recycling markers in plants, using confocal microscopy and the subsequent clustering of subcellular phenotypes, to identify chemicals with desired effects. The method provides an approach to identify novel chemicals for pathway dissection, making chemical genomics more accessible to the scientific community. The matrix of novel chemicals described in this protocol can be expanded and analyzed continuously as more data is collected, increasing our knowledge of the endomembrane system, and accumulating compartment-specific markers and chemical probes that perturb specific aspects of endomembrane trafficking.
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Affiliation(s)
- Natasha Worden
- Department of Plant Sciences, University of California, Davis, CA, USA
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16
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Spallek T, Beck M, Ben Khaled S, Salomon S, Bourdais G, Schellmann S, Robatzek S. ESCRT-I mediates FLS2 endosomal sorting and plant immunity. PLoS Genet 2013; 9:e1004035. [PMID: 24385929 PMCID: PMC3873229 DOI: 10.1371/journal.pgen.1004035] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 11/01/2013] [Indexed: 11/19/2022] Open
Abstract
The plant immune receptor FLAGELLIN SENSING 2 (FLS2) is present at the plasma membrane and is internalized following activation of its ligand flagellin (flg22). We show that ENDOSOMAL SORTING COMPLEX REQUIRED FOR TRANSPORT (ESCRT)-I subunits play roles in FLS2 endocytosis in Arabidopsis. VPS37-1 co-localizes with FLS2 at endosomes and immunoprecipitates with the receptor upon flg22 elicitation. Vps37-1 mutants are reduced in flg22-induced FLS2 endosomes but not in endosomes labeled by Rab5 GTPases suggesting a defect in FLS2 trafficking rather than formation of endosomes. FLS2 localizes to the lumen of multivesicular bodies, but this is altered in vps37-1 mutants indicating compromised endosomal sorting of FLS2 by ESCRT-I loss-of-function. VPS37-1 and VPS28-2 are critical for immunity against bacterial infection through a role in stomatal closure. Our findings identify that VPS37-1, and likewise VPS28-2, regulate late FLS2 endosomal sorting and reveals that ESCRT-I is critical for flg22-activated stomatal defenses involved in plant immunity. Plants deploy plasma membrane immune receptors to survey their environment for potential threats. One of these receptors, FLAGELIN SENSING 2 (FLS2) recognizes bacterial flagellin (flg22) and thereby triggers a multitude of defense responses, enhancing immunity against infectious pathogens. Regulation of the subcellular localization of FLS2 is therefore an important aspect in plant disease resistance. FLS2 is known to shuttle between the plasma membrane and endosomal compartments but enters the late endosomal trafficking pathway upon ligand-dependent activation. A key question is the regulation of activated FLS2 in late endosomal trafficking. Here, we show that FLS2 is internalized into the lumen of multivesicular bodies and discovered by genetic inhibition that this step is regulated by components of the ENDOSOMAL SORTING COMPLEXES REQUIRED FOR TRANSPORT-I (ESCRT-I). Furthermore, we reveal that these ESCRT-I components play crucial roles in plant immunity impacting the flg22-triggered closure of stomata, prominent entry points of pathogenic bacteria, which occurred downstream of the known flg22 responses. These findings highlight the roles of endosomal trafficking in regulating FLS2 subcellular localization and plant immunity.
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Affiliation(s)
- Thomas Spallek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Martina Beck
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Sara Ben Khaled
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Susanne Salomon
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Gildas Bourdais
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | | | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- * E-mail:
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17
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Endocytosis: At the Crossroads of Pattern Recognition Immune Receptors and Pathogen Effectors. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/978-3-642-41787-0_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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18
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Dhondt S, Wuyts N, Inzé D. Cell to whole-plant phenotyping: the best is yet to come. TRENDS IN PLANT SCIENCE 2013; 18:428-39. [PMID: 23706697 DOI: 10.1016/j.tplants.2013.04.008] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/18/2013] [Accepted: 04/22/2013] [Indexed: 05/18/2023]
Abstract
Imaging and image processing have revolutionized plant phenotyping and are now a major tool for phenotypic trait measurement. Here we review plant phenotyping systems by examining three important characteristics: throughput, dimensionality, and resolution. First, whole-plant phenotyping systems are highlighted together with advances in automation that enable significant throughput increases. Organ and cellular level phenotyping and its tools, often operating at a lower throughput, are then discussed as a means to obtain high-dimensional phenotypic data at elevated spatial and temporal resolution. The significance of recent developments in sensor technologies that give access to plant morphology and physiology-related traits is shown. Overall, attention is focused on spatial and temporal resolution because these are crucial aspects of imaging procedures in plant phenotyping systems.
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Affiliation(s)
- Stijn Dhondt
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium
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19
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Ung N, Brown MQ, Hicks GR, Raikhel NV. An approach to quantify endomembrane dynamics in pollen utilizing bioactive chemicals. MOLECULAR PLANT 2013; 6:1202-13. [PMID: 23118478 PMCID: PMC7105205 DOI: 10.1093/mp/sss092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/05/2012] [Indexed: 05/03/2023]
Abstract
Tip growth of pollen tubes and root hairs occurs via rapid polar growth. These rapidly elongating cells require tip-focused endomembrane trafficking for the deposition and recycling of proteins, membranes, and cell wall materials. Most of the image-based data published to date are subjective and non-quantified. Quantitative and comparative descriptors of these highly dynamic processes have been a major challenge, but are highly desirable for genetic and chemical genomics approaches to dissect this biological network. To address this problem, we screened for small molecules that perturbed the localization of a marker for the Golgi Ras-like monomeric G-protein RAB2:GFP expressed in transgenic tobacco pollen. Semi-automated high-throughput imaging and image analysis resulted in the identification of novel compounds that altered pollen tube development and endomembrane trafficking. Six compounds that caused mislocalization and varying degrees of altered movement of RAB2:GFP-labeled endomembrane bodies were used to generate a training set of image data from which to quantify vesicle dynamics. The area, velocity, straightness, and intensity of each body were quantified using semi-automated image analysis tools revealing quantitative differences in the phenotype caused by each compound. A score was then given to each compound enabling quantitative comparisons between compounds. Our results demonstrate that image analysis can be used to quantitatively evaluate dynamic subcellular endomembrane phenotypes induced by bioactive chemicals, mutations, or other perturbing agents as part of a strategy to quantitatively dissect the endomembrane network.
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Affiliation(s)
- Nolan Ung
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
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20
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Fitzgibbon J, Beck M, Zhou J, Faulkner C, Robatzek S, Oparka K. A developmental framework for complex plasmodesmata formation revealed by large-scale imaging of the Arabidopsis leaf epidermis. THE PLANT CELL 2013; 25:57-70. [PMID: 23371949 PMCID: PMC3584549 DOI: 10.1105/tpc.112.105890] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 12/03/2012] [Accepted: 01/07/2013] [Indexed: 05/18/2023]
Abstract
Plasmodesmata (PD) form tubular connections that function as intercellular communication channels. They are essential for transporting nutrients and for coordinating development. During cytokinesis, simple PDs are inserted into the developing cell plate, while during wall extension, more complex (branched) forms of PD are laid down. We show that complex PDs are derived from existing simple PDs in a pattern that is accelerated when leaves undergo the sink-source transition. Complex PDs are inserted initially at the three-way junctions between epidermal cells but develop most rapidly in the anisocytic complexes around stomata. For a quantitative analysis of complex PD formation, we established a high-throughput imaging platform and constructed PDQUANT, a custom algorithm that detected cell boundaries and PD numbers in different wall faces. For anticlinal walls, the number of complex PDs increased with increasing cell size, while for periclinal walls, the number of PDs decreased. Complex PD insertion was accelerated by up to threefold in response to salicylic acid treatment and challenges with mannitol. In a single 30-min run, we could derive data for up to 11k PDs from 3k epidermal cells. This facile approach opens the door to a large-scale analysis of the endogenous and exogenous factors that influence PD formation.
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Affiliation(s)
- Jessica Fitzgibbon
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Martina Beck
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - Ji Zhou
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - Christine Faulkner
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich NR4 7UH, United Kingdom
| | - Karl Oparka
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
- Address correspondence to
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21
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Zhou J, Spallek T, Faulkner C, Robatzek S. CalloseMeasurer: a novel software solution to measure callose deposition and recognise spreading callose patterns. PLANT METHODS 2012; 8:49. [PMID: 23244621 PMCID: PMC3571893 DOI: 10.1186/1746-4811-8-49] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 12/13/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND Quantification of callose deposits is a useful measure for the activities of plant immunity and pathogen growth by fluorescence imaging. For robust scoring of differences, this normally requires many technical and biological replicates and manual or automated quantification of the callose deposits. However, previously available software tools for quantifying callose deposits from bioimages were limited, making batch processing of callose image data problematic. In particular, it is challenging to perform large-scale analysis on images with high background noise and fused callose deposition signals. RESULTS We developed CalloseMeasurer, an easy-to-use application that quantifies callose deposition, a plant immune response triggered by potentially pathogenic microbes. Additionally, by tracking identified callose deposits between multiple images, the software can recognise patterns of how a given filamentous pathogen grows in plant leaves. The software has been evaluated with typical noisy experimental images and can be automatically executed without the need for user intervention. The automated analysis is achieved by using standard image analysis functions such as image enhancement, adaptive thresholding, and object segmentation, supplemented by several novel methods which filter background noise, split fused signals, perform edge-based detection, and construct networks and skeletons for extracting pathogen growth patterns. To efficiently batch process callose images, we implemented the algorithm in C/C++ within the Acapella™ framework. Using the tool we can robustly score significant differences between different plant genotypes when activating the immune response. We also provide examples for measuring the in planta hyphal growth of filamentous pathogens. CONCLUSIONS CalloseMeasurer is a new software solution for batch-processing large image data sets to quantify callose deposition in plants. We demonstrate its high accuracy and usefulness for two applications: 1) the quantification of callose deposition in different genotypes as a measure for the activity of plant immunity; and 2) the quantification and detection of spreading networks of callose deposition triggered by filamentous pathogens as a measure for growing pathogen hyphae. The software is an easy-to-use protocol which is executed within the Acapella software system without requiring any additional libraries. The source code of the software is freely available at https://sourceforge.net/projects/bioimage/files/Callose.
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Affiliation(s)
- Ji Zhou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Thomas Spallek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- Present address: RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Christine Faulkner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
- Present address: Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
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22
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Beck M, Zhou J, Faulkner C, MacLean D, Robatzek S. Spatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting. THE PLANT CELL 2012; 24:4205-19. [PMID: 23085733 PMCID: PMC3516521 DOI: 10.1105/tpc.112.100263] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 08/17/2012] [Accepted: 09/25/2012] [Indexed: 05/18/2023]
Abstract
The activity of surface receptors is location specific, dependent upon the dynamic membrane trafficking network and receptor-mediated endocytosis (RME). Therefore, the spatio-temporal dynamics of RME are critical to receptor function. The plasma membrane receptor flagellin sensing2 (FLS2) confers immunity against bacterial infection through perception of flagellin (flg22). Following elicitation, FLS2 is internalized into vesicles. To resolve FLS2 trafficking, we exploited quantitative confocal imaging for colocalization studies and chemical interference. FLS2 localizes to bona fide endosomes via two distinct endocytic trafficking routes depending on its activation status. FLS2 receptors constitutively recycle in a Brefeldin A (BFA)-sensitive manner, while flg22-activated receptors traffic via ARA7/Rab F2b- and ARA6/Rab F1-positive endosomes insensitive to BFA. FLS2 endocytosis required a functional Rab5 GTPase pathway as revealed by dominant-negative ARA7/Rab F2b. Flg22-induced FLS2 endosomal numbers were increased by Concanamycin A treatment but reduced by Wortmannin, indicating that activated FLS2 receptors are targeted to late endosomes. RME inhibitors Tyrphostin A23 and Endosidin 1 altered but did not block induced FLS2 endocytosis. Additional inhibitor studies imply the involvement of the actin-myosin system in FLS2 internalization and trafficking. Altogether, we report a dynamic pattern of subcellular trafficking for FLS2 and reveal a defined framework for ligand-dependent endocytosis of this receptor.
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23
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Segonzac C, Nimchuk ZL, Beck M, Tarr PT, Robatzek S, Meyerowitz EM, Zipfel C. The shoot apical meristem regulatory peptide CLV3 does not activate innate immunity. THE PLANT CELL 2012; 24:3186-92. [PMID: 22923673 PMCID: PMC3462624 DOI: 10.1105/tpc.111.091264] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 01/24/2012] [Accepted: 08/01/2012] [Indexed: 05/20/2023]
Abstract
The Arabidopsis thaliana leucine-rich repeat receptor kinase FLAGELLIN SENSING2 (FLS2) is required for the recognition of bacterial flagellin in innate immunity. Recently, FLS2 was proposed to act as a multispecific receptor recognizing unrelated exogenous and endogenous peptide ligands, including CLAVATA3 (CLV3), a key regulator of shoot meristem stem cell production. Here, we report experimental evidence demonstrating that FLS2 does not recognize CLV3 and that the shoot apical meristem is immune to bacteria independently of CLV3 perception.
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Affiliation(s)
- Cécile Segonzac
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Zachary L. Nimchuk
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Martina Beck
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Paul T. Tarr
- Division of Biology, California Institute of Technology, Pasadena, California 91125
| | - Silke Robatzek
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Elliot M. Meyerowitz
- Division of Biology, California Institute of Technology, Pasadena, California 91125
- The Sainsbury Laboratory–University of Cambridge, Cambridge CB2 1LR, United Kingdom
| | - Cyril Zipfel
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
- Address correspondence to
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24
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Zwiewka M, Friml J. Fluorescence imaging-based forward genetic screens to identify trafficking regulators in plants. FRONTIERS IN PLANT SCIENCE 2012; 3:97. [PMID: 22654887 PMCID: PMC3359526 DOI: 10.3389/fpls.2012.00097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2012] [Accepted: 04/25/2012] [Indexed: 05/25/2023]
Abstract
Coordinated, subcellular trafficking of proteins is one of the fundamental properties of the multicellular eukaryotic organisms. Trafficking involves a large diversity of compartments, pathways, cargo molecules, and vesicle-sorting events. It is also crucial in regulating the localization and, thus, the activity of various proteins, but the process is still poorly genetically defined in plants. In the past, forward genetics screens had been used to determine the function of genes by searching for a specific morphological phenotype in the organism population in which mutations had been induced chemically or by irradiation. Unfortunately, these straightforward genetic screens turned out to be limited in identifying new regulators of intracellular protein transport, because mutations affecting essential trafficking pathways often lead to lethality. In addition, the use of these approaches has been restricted by functional redundancy among trafficking regulators. Screens for mutants that rely on the observation of changes in the cellular localization or dynamics of fluorescent subcellular markers enable, at least partially, to circumvent these issues. Hence, such image-based screens provide the possibility to identify either alleles with weak effects or components of the subcellular trafficking machinery that have no strong impact on the plant growth.
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Affiliation(s)
- Marta Zwiewka
- Department of Plant Systems Biology, VIB Life Sciences Research InstituteGent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent UniversityGent, Belgium
| | - Jiří Friml
- Department of Plant Systems Biology, VIB Life Sciences Research InstituteGent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent UniversityGent, Belgium
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25
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Sparkes I, Brandizzi F. Fluorescent protein-based technologies: shedding new light on the plant endomembrane system. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:96-107. [PMID: 22449045 DOI: 10.1111/j.1365-313x.2011.04884.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Without doubt, GFP and spectral derivatives have revolutionized the way biologists approach their journey toward the discovery of how plant cells function. It is fascinating that in its early days GFP was used merely for localization studies, but as time progressed researchers successfully explored new avenues to push the power of GFP technology to reach new and exciting research frontiers. This has had a profound impact on the way we can now study complex and dynamic systems such as plant endomembranes. Here we briefly describe some of the approaches where GFP has revolutionized in vivo studies of protein distribution and dynamics and focus on two emerging approaches for the application of GFP technology in plant endomembranes, namely optical tweezers and forward genetics approaches, which are based either on the light or on genetic manipulation of secretory organelles to gain insights on the factors that control their activities and integrity.
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Affiliation(s)
- Imogen Sparkes
- Biosciences,College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Stocker Road, Exeter, UK
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26
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Hicks GR, Raikhel NV. Small molecules present large opportunities in plant biology. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:261-82. [PMID: 22404475 DOI: 10.1146/annurev-arplant-042811-105456] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Since the introduction of chemical genomics to plant biology as a tool for basic research, the field has advanced significantly. There are now examples of important basic discoveries that demonstrate the power and untapped potential of this approach. Given the combination of protein and small-molecule complexity, new phenotypes can be described through the perturbation of cellular functions that can be linked to growth and developmental phenotypes. There are now clear examples of overcoming functional redundancy in plants to dissect molecular mechanisms or critical pathways such as hormone signaling and dynamic intracellular processes. Owing to ongoing advances, including more sophisticated high-content screening and rapid approaches for target identification, the field is beginning to move forward. However, there are also challenges to improve automation, imaging, and analysis and provide chemical biology resources to the broader plant biology community.
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Affiliation(s)
- Glenn R Hicks
- Center for Plant Cell Biology, Institute for Integrative Genome Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
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27
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Hückelhoven R, Panstruga R. Cell biology of the plant-powdery mildew interaction. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:738-46. [PMID: 21924669 DOI: 10.1016/j.pbi.2011.08.002] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Revised: 08/09/2011] [Accepted: 08/17/2011] [Indexed: 05/08/2023]
Abstract
Powdery mildew fungi represent a paradigm for obligate biotrophic parasites, which only propagate in long-lasting intimate interactions with living host cells. These highly specialized phytopathogens induce re-organization of host cell architecture and physiology for their own demands. This probably includes the corruption of basal host cellular functions for successful fungal pathogenesis. Recent studies revealed secretory processes by both interaction partners as key incidents of the combat at the plant-fungus interface. The analysis of cellular events during plant-powdery mildew interactions may not only lead to a better understanding of plant pathological features, but may also foster novel discoveries in the area of plant cell biology.
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Affiliation(s)
- Ralph Hückelhoven
- Lehrstuhl für Phytopathologie, Technische Universität München, Emil-Ramann-Straße 2, 85350 Freising-Weihenstephan, Germany
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28
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Drakakaki G, Robert S, Szatmari AM, Brown MQ, Nagawa S, Van Damme D, Leonard M, Yang Z, Girke T, Schmid SL, Russinova E, Friml J, Raikhel NV, Hicks GR. Clusters of bioactive compounds target dynamic endomembrane networks in vivo. Proc Natl Acad Sci U S A 2011; 108:17850-5. [PMID: 22006339 PMCID: PMC3203817 DOI: 10.1073/pnas.1108581108] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery.
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Affiliation(s)
- Georgia Drakakaki
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Stéphanie Robert
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Anna-Maria Szatmari
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Michelle Q. Brown
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Shingo Nagawa
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Daniel Van Damme
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Marilyn Leonard
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Zhenbiao Yang
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Thomas Girke
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Sandra L. Schmid
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Eugenia Russinova
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Jiří Friml
- Department of Plant Systems Biology, University of Ghent, Flanders Institute for Biotechnology (VIB), 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, University of Ghent, 9052 Ghent, Belgium; and
| | - Natasha V. Raikhel
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
| | - Glenn R. Hicks
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521
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