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Shi B, Felipo-Benavent A, Cerutti G, Galvan-Ampudia C, Jilli L, Brunoud G, Mutterer J, Vallet E, Sakvarelidze-Achard L, Davière JM, Navarro-Galiano A, Walia A, Lazary S, Legrand J, Weinstain R, Jones AM, Prat S, Achard P, Vernoux T. A quantitative gibberellin signaling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem. Nat Commun 2024; 15:3895. [PMID: 38719832 PMCID: PMC11079023 DOI: 10.1038/s41467-024-48116-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
Growth at the shoot apical meristem (SAM) is essential for shoot architecture construction. The phytohormones gibberellins (GA) play a pivotal role in coordinating plant growth, but their role in the SAM remains mostly unknown. Here, we developed a ratiometric GA signaling biosensor by engineering one of the DELLA proteins, to suppress its master regulatory function in GA transcriptional responses while preserving its degradation upon GA sensing. We demonstrate that this degradation-based biosensor accurately reports on cellular changes in GA levels and perception during development. We used this biosensor to map GA signaling activity in the SAM. We show that high GA signaling is found primarily in cells located between organ primordia that are the precursors of internodes. By gain- and loss-of-function approaches, we further demonstrate that GAs regulate cell division plane orientation to establish the typical cellular organization of internodes, thus contributing to internode specification in the SAM.
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Affiliation(s)
- Bihai Shi
- College of Agriculture, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, 510642, Guangzhou, China
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Amelia Felipo-Benavent
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Guillaume Cerutti
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Carlos Galvan-Ampudia
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Lucas Jilli
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Geraldine Brunoud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Jérome Mutterer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Elody Vallet
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Lali Sakvarelidze-Achard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Jean-Michel Davière
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | | | - Ankit Walia
- Sainsbury Laboratory, Cambridge University, Cambridge, CB2 1LR, UK
| | - Shani Lazary
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jonathan Legrand
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Roy Weinstain
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, 69978, Israel
| | | | - Salomé Prat
- Centre for Research in Agricultural Genomics, 08193 Cerdanyola, Barcelona, Spain
| | - Patrick Achard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France.
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France.
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2
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Andres J, Schmunk LJ, Grau-Enguix F, Braguy J, Samodelov SL, Blomeier T, Ochoa-Fernandez R, Weber W, Al-Babili S, Alabadí D, Blázquez MA, Zurbriggen MD. Ratiometric gibberellin biosensors for the analysis of signaling dynamics and metabolism in plant protoplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:927-939. [PMID: 38525669 DOI: 10.1111/tpj.16725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Gibberellins (GAs) are major regulators of developmental and growth processes in plants. Using the degradation-based signaling mechanism of GAs, we have built transcriptional regulator (DELLA)-based, genetically encoded ratiometric biosensors as proxies for hormone quantification at high temporal resolution and sensitivity that allow dynamic, rapid and simple analysis in a plant cell system, i.e. Arabidopsis protoplasts. These ratiometric biosensors incorporate a DELLA protein as a degradation target fused to a firefly luciferase connected via a 2A peptide to a renilla luciferase as a co-expressed normalization element. We have implemented these biosensors for all five Arabidopsis DELLA proteins, GA-INSENSITIVE, GAI; REPRESSOR-of-ga1-3, RGA; RGA-like1, RGL1; RGL2 and RGL3, by applying a modular design. The sensors are highly sensitive (in the low pm range), specific and dynamic. As a proof of concept, we have tested the applicability in three domains: the study of substrate specificity and activity of putative GA-oxidases, the characterization of GA transporters, and the use as a discrimination platform coupled to a GA agonists' chemical screening. This work demonstrates the development of a genetically encoded quantitative biosensor complementary to existing tools that allow the visualization of GA in planta.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Lisa J Schmunk
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Federico Grau-Enguix
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Justine Braguy
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- The BioActives Lab, Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sophia L Samodelov
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Rocio Ochoa-Fernandez
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Wilfried Weber
- Signalling Research Centres BIOSS and CIBSS and Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Salim Al-Babili
- The BioActives Lab, Division of Biological and Environmental Science and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), Valencia, Spain
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
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3
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Bull T, Khakhar A. Design principles for synthetic control systems to engineer plants. PLANT CELL REPORTS 2023; 42:1875-1889. [PMID: 37789180 DOI: 10.1007/s00299-023-03072-z] [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: 02/21/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023]
Abstract
KEY MESSAGE Synthetic control systems have led to significant advancement in the study and engineering of unicellular organisms, but it has been challenging to apply these tools to multicellular organisms like plants. The ability to predictably engineer plants will enable the development of novel traits capable of alleviating global problems, such as climate change and food insecurity. Engineering predictable multicellular phenotypes will require the development of synthetic control systems that can precisely regulate how the information encoded in genomes is translated into phenotypes. Many efficient control systems have been developed for unicellular organisms. However, it remains challenging to use such tools to study or engineer multicellular organisms. Plants are a good chassis within which to develop strategies to overcome these challenges, thanks to their capacity to withstand large-scale reprogramming without lethality. Additionally, engineered plants have great potential for solving major societal problems. Here we briefly review the progress of control system development in unicellular organisms, and how that information can be leveraged to characterize control systems in plants. Further, we discuss strategies for developing control systems designed to regulate the expression of transgenes or endogenous loci and generate dosage-dependent or discrete traits. Finally, we discuss the utility that mathematical models of biological processes have for control system deployment.
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Affiliation(s)
- Tawni Bull
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Arjun Khakhar
- Department of Biology, Colorado State University, Fort Collins, CO, USA.
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4
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Molinari PE, Krapp AR, Weiner A, Beyer HM, Kondadi AK, Blomeier T, López M, Bustos-Sanmamed P, Tevere E, Weber W, Reichert AS, Calcaterra NB, Beller M, Carrillo N, Zurbriggen MD. NERNST: a genetically-encoded ratiometric non-destructive sensing tool to estimate NADP(H) redox status in bacterial, plant and animal systems. Nat Commun 2023; 14:3277. [PMID: 37280202 DOI: 10.1038/s41467-023-38739-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/12/2023] [Indexed: 06/08/2023] Open
Abstract
NADP(H) is a central metabolic hub providing reducing equivalents to multiple biosynthetic, regulatory and antioxidative pathways in all living organisms. While biosensors are available to determine NADP+ or NADPH levels in vivo, no probe exists to estimate the NADP(H) redox status, a determinant of the cell energy availability. We describe herein the design and characterization of a genetically-encoded ratiometric biosensor, termed NERNST, able to interact with NADP(H) and estimate ENADP(H). NERNST consists of a redox-sensitive green fluorescent protein (roGFP2) fused to an NADPH-thioredoxin reductase C module which selectively monitors NADP(H) redox states via oxido-reduction of the roGFP2 moiety. NERNST is functional in bacterial, plant and animal cells, and organelles such as chloroplasts and mitochondria. Using NERNST, we monitor NADP(H) dynamics during bacterial growth, environmental stresses in plants, metabolic challenges to mammalian cells, and wounding in zebrafish. NERNST estimates the NADP(H) redox poise in living organisms, with various potential applications in biochemical, biotechnological and biomedical research.
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Affiliation(s)
- Pamela E Molinari
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Adriana R Krapp
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Andrea Weiner
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Hannes M Beyer
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany
| | - Arun Kumar Kondadi
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany
| | - Melina López
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Pilar Bustos-Sanmamed
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Evelyn Tevere
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Wilfried Weber
- Faculty of Biology and Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- INM - Leibniz Institute for New Materials and Department of Materials Sciences and Engineering, Saarland University, Saarbrücken, Germany
| | - Andreas S Reichert
- Institute of Biochemistry and Molecular Biology I, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Nora B Calcaterra
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina
| | - Mathias Beller
- Institute of Mathematical Modeling of Biological Systems, University of Düsseldorf, Düsseldorf, Germany
| | - Nestor Carrillo
- Instituto de Biología Molecular y Celular de Rosario (IBR-UNR/CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR), 2000, Rosario, Argentina.
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf, Germany.
- CEPLAS - Cluster of Excellence on Plant Sciences, Düsseldorf, Germany.
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5
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Konrad KR, Gao S, Zurbriggen MD, Nagel G. Optogenetic Methods in Plant Biology. ANNUAL REVIEW OF PLANT BIOLOGY 2023; 74:313-339. [PMID: 37216203 DOI: 10.1146/annurev-arplant-071122-094840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Optogenetics is a technique employing natural or genetically engineered photoreceptors in transgene organisms to manipulate biological activities with light. Light can be turned on or off, and adjusting its intensity and duration allows optogenetic fine-tuning of cellular processes in a noninvasive and spatiotemporally resolved manner. Since the introduction of Channelrhodopsin-2 and phytochrome-based switches nearly 20 years ago, optogenetic tools have been applied in a variety of model organisms with enormous success, but rarely in plants. For a long time, the dependence of plant growth on light and the absence of retinal, the rhodopsin chromophore, prevented the establishment of plant optogenetics until recent progress overcame these difficulties. We summarize the recent results of work in the field to control plant growth and cellular motion via green light-gated ion channels and present successful applications to light-control gene expression with single or combined photoswitches in plants. Furthermore, we highlight the technical requirements and options for future plant optogenetic research.
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Affiliation(s)
- Kai R Konrad
- Molecular Plant Physiology and Biophysics, Julius-von-Sachs Institute for Biosciences, Biocenter, University of Würzburg, Würzburg, Germany;
| | - Shiqiang Gao
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany;
| | - Georg Nagel
- Department of Neurophysiology, Institute of Physiology, Biocenter, University of Würzburg, Würzburg, Germany; ,
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6
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Heucken N, Tang K, Hüsemann L, Heßler N, Müntjes K, Feldbrügge M, Göhre V, Zurbriggen MD. Engineering and Implementation of Synthetic Molecular Tools in the Basidiomycete Fungus Ustilago maydis. J Fungi (Basel) 2023; 9:jof9040480. [PMID: 37108934 PMCID: PMC10140897 DOI: 10.3390/jof9040480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/30/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The basidiomycete Ustilago maydis is a well-characterized model organism for studying pathogen-host interactions and of great interest for a broad spectrum of biotechnological applications. To facilitate research and enable applications, in this study, three luminescence-based and one enzymatic quantitative reporter were implemented and characterized. Several dual-reporter constructs were generated for ratiometric normalization that can be used as a fast-screening platform for reporter gene expression, applicable to in vitro and in vivo detection. Furthermore, synthetic bidirectional promoters that enable bicisitronic expression for gene expression studies and engineering strategies were constructed and implemented. These noninvasive, quantitative reporters and expression tools will significantly widen the application range of biotechnology in U. maydis and enable the in planta detection of fungal infection.
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Affiliation(s)
- Nicole Heucken
- Institute of Synthetic Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Kun Tang
- Institute of Synthetic Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Lisa Hüsemann
- Institute of Synthetic Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Natascha Heßler
- Institute of Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Kira Müntjes
- Institute of Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Michael Feldbrügge
- Institute of Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Vera Göhre
- Institute of Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, 40225 Düsseldorf, Germany
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7
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Jedličková V, Ebrahimi Naghani S, Robert HS. On the trail of auxin: Reporters and sensors. THE PLANT CELL 2022; 34:3200-3213. [PMID: 35708654 PMCID: PMC9421466 DOI: 10.1093/plcell/koac179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/07/2022] [Indexed: 05/22/2023]
Abstract
The phytohormone auxin is a master regulator of plant growth and development in response to many endogenous and environmental signals. The underlying coordination of growth is mediated by the formation of auxin maxima and concentration gradients. The visualization of auxin dynamics and distribution can therefore provide essential information to increase our understanding of the mechanisms by which auxin orchestrates these growth and developmental processes. Several auxin reporters have been developed to better perceive the auxin distribution and signaling machinery in vivo. This review focuses on different types of auxin reporters and biosensors used to monitor auxin distribution and its dynamics, as well as auxin signaling, at the cellular and tissue levels in different plant species. We provide a brief history of each reporter and biosensor group and explain their principles and utilities.
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8
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Perico C, Tan S, Langdale JA. Developmental regulation of leaf venation patterns: monocot versus eudicots and the role of auxin. THE NEW PHYTOLOGIST 2022; 234:783-803. [PMID: 35020214 PMCID: PMC9994446 DOI: 10.1111/nph.17955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Organisation and patterning of the vascular network in land plants varies in different taxonomic, developmental and environmental contexts. In leaves, the degree of vascular strand connectivity influences both light and CO2 harvesting capabilities as well as hydraulic capacity. As such, developmental mechanisms that regulate leaf venation patterning have a direct impact on physiological performance. Development of the leaf venation network requires the specification of procambial cells within the ground meristem of the primordium and subsequent proliferation and differentiation of the procambial lineage to form vascular strands. An understanding of how diverse venation patterns are manifest therefore requires mechanistic insight into how procambium is dynamically specified in a growing leaf. A role for auxin in this process was identified many years ago, but questions remain. In this review we first provide an overview of the diverse venation patterns that exist in land plants, providing an evolutionary perspective. We then focus on the developmental regulation of leaf venation patterns in angiosperms, comparing patterning in eudicots and monocots, and the role of auxin in each case. Although common themes emerge, we conclude that the developmental mechanisms elucidated in eudicots are unlikely to fully explain how parallel venation patterns in monocot leaves are elaborated.
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Affiliation(s)
- Chiara Perico
- Department of Plant SciencesUniversity of OxfordSouth Parks RdOxfordOX1 3RBUK
| | - Sovanna Tan
- Department of Plant SciencesUniversity of OxfordSouth Parks RdOxfordOX1 3RBUK
| | - Jane A. Langdale
- Department of Plant SciencesUniversity of OxfordSouth Parks RdOxfordOX1 3RBUK
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9
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Iacopino S, Licausi F, Giuntoli B. Exploiting the Gal4/UAS System as Plant Orthogonal Molecular Toolbox to Control Reporter Expression in Arabidopsis Protoplasts. Methods Mol Biol 2022; 2379:99-111. [PMID: 35188658 DOI: 10.1007/978-1-0716-1791-5_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The ability of protein domains to fold independently from the rest of the polypeptide is the principle governing the generation of fusion proteins with customized functions. A clear example is the split transcription factor system based on the yeast GAL4 protein and its cognate UAS enhancer. The rare occurrence of the UAS element in the transcriptionally sensitive regions of the Arabidopsis genome makes this transcription factor an ideal orthogonal platform to control reporter induction. Moreover, heterodimeric transcriptional complexes can be generated by exploiting posttranslational modifications hampering or promoting the interaction between GAL4-fused transcriptional partners, whenever this leads to the reconstitution of a fully functional GAL4 factor.The assembly of multiple engineered proteins into a synthetic transcriptional complex requires preliminary testing, before its components can be stably introduced into the plant genome. Mesophyll protoplast transformation represents a fast and reliable technique to test and optimize synthetic regulatory modules. Remarkable properties are the possibility to transform different combinations of plasmids (co-transformation) and the physiological resemblance of these isolated cells with the original tissue.Here we describe an extensive protocol to produce and exploit Arabidopsis mesophyll protoplasts to investigate the transcriptional output of GAL4/UAS-based complexes that are sensitive to posttranslational protein modifications.
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Affiliation(s)
| | - Francesco Licausi
- University of Pisa, Pisa, Italy
- Sant'Anna School of Advanced Studies, Pisa, Italy
| | - Beatrice Giuntoli
- University of Pisa, Pisa, Italy.
- Sant'Anna School of Advanced Studies, Pisa, Italy.
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10
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Andres J, Zurbriggen MD. Genetically Encoded Biosensors for the Quantitative Analysis of Auxin Dynamics in Plant Cells. Methods Mol Biol 2022; 2379:183-195. [PMID: 35188663 DOI: 10.1007/978-1-0716-1791-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plants, as sessile organisms, possess complex and intertwined signaling networks to react and adapt their behavior toward different internal and external stimuli. Due to this high level of complexity, the implementation of quantitative molecular tools in planta remains challenging. Synthetic biology as an ever-growing interdisciplinary field applies basic engineering principles in life sciences. A plethora of synthetic switches, circuits, and even higher order networks has been implemented in different organisms, such as bacteria and mammalian cells, and facilitates the study of signaling and metabolic pathways. However, the application of such tools in plants lags behind, and thus only a few genetically encoded biosensors and switches have been engineered toward the quantitative investigation of plant signaling. Here, we present a protocol for the quantitative analysis of auxin signaling in Arabidopsis thaliana protoplasts. We implemented genetically encoded, ratiometric, degradation-based luminescent biosensors and applied them for studying auxin perception dynamics. For this, we utilized three different Aux/IAAs as sensor modules and analyzed their degradation behavior in response to auxin. Our experimental approach requires simple hardware and experimental reagents and can thus be implemented in every plant-related or cell culture laboratory. The system allows for the analysis of auxin perception and signaling aspects on various levels and can be easily expanded to other hormones, as for example strigolactones. In addition, the modular sensor design enables the implementation of sensor modules in a straightforward and time-saving approach.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany.
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11
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Balcerowicz M, Shetty KN, Jones AM. Fluorescent biosensors illuminating plant hormone research. PLANT PHYSIOLOGY 2021; 187:590-602. [PMID: 35237816 PMCID: PMC8491072 DOI: 10.1093/plphys/kiab278] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/22/2021] [Indexed: 05/20/2023]
Abstract
Phytohormones act as key regulators of plant growth that coordinate developmental and physiological processes across cells, tissues and organs. As such, their levels and distribution are highly dynamic owing to changes in their biosynthesis, transport, modification and degradation that occur over space and time. Fluorescent biosensors represent ideal tools to track these dynamics with high spatiotemporal resolution in a minimally invasive manner. Substantial progress has been made in generating a diverse set of hormone sensors with recent FRET biosensors for visualising hormone concentrations complementing information provided by transcriptional, translational and degron-based reporters. In this review, we provide an update on fluorescent biosensor designs, examine the key properties that constitute an ideal hormone biosensor, discuss the use of these sensors in conjunction with in vivo hormone perturbations and highlight the latest discoveries made using these tools.
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Affiliation(s)
| | | | - Alexander M. Jones
- Sainsbury Laboratory, Cambridge University, Cambridge CB2 1LR, UK
- Author for communication:
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12
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Guiziou S, Chu JC, Nemhauser JL. Decoding and recoding plant development. PLANT PHYSIOLOGY 2021; 187:515-526. [PMID: 35237818 PMCID: PMC8491033 DOI: 10.1093/plphys/kiab336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/26/2021] [Indexed: 05/04/2023]
Abstract
The development of multicellular organisms has been studied for centuries, yet many critical events and mechanisms of regulation remain challenging to observe directly. Early research focused on detailed observational and comparative studies. Molecular biology has generated insights into regulatory mechanisms, but only for a limited number of species. Now, synthetic biology is bringing these two approaches together, and by adding the possibility of sculpting novel morphologies, opening another path to understanding biology. Here, we review a variety of recently invented techniques that use CRISPR/Cas9 and phage integrases to trace the differentiation of cells over various timescales, as well as to decode the molecular states of cells in high spatiotemporal resolution. Most of these tools have been implemented in animals. The time is ripe for plant biologists to adopt and expand these approaches. Here, we describe how these tools could be used to monitor development in diverse plant species, as well as how they could guide efforts to recode programs of interest.
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Affiliation(s)
- Sarah Guiziou
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - Jonah C. Chu
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
| | - Jennifer L. Nemhauser
- Department of Biology, University of Washington, Seattle, Washington 98195, USA
- Author for communication:
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13
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A Protoplast-Based Bioassay to Quantify Strigolactone Activity in Arabidopsis Using StrigoQuant. Methods Mol Biol 2021; 2309:201-218. [PMID: 34028689 DOI: 10.1007/978-1-0716-1429-7_16] [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] [Indexed: 01/31/2023]
Abstract
Understanding the biological background of strigolactone (SL) structural diversity and the SL signaling pathway at molecular level requires quantitative and sensitive tools that precisely determine SL dynamics. Such biosensors may be also very helpful in screening for SL analogs and mimics with defined biological functions.Recently, the genetically encoded, ratiometric sensor StrigoQuant was developed and allowed the quantification of the activity of a wide concentration range of SLs. StrigoQuant can be used for studies on the biosynthesis, function and signal transduction of this hormone class.Here, we provide a comprehensive protocol for establishing the use of StrigoQuant in Arabidopsis protoplasts. We first describe the generation and transformation of the protoplasts with StrigoQuant and detail the application of the synthetic SL analogue GR24. We then show the recording of the luminescence signal and how the obtained data are processed and used to assess/determine SL perception.
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14
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Zhao C, Yaschenko A, Alonso JM, Stepanova AN. Leveraging synthetic biology approaches in plant hormone research. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:101998. [PMID: 33476945 DOI: 10.1016/j.pbi.2020.101998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/20/2020] [Accepted: 12/25/2020] [Indexed: 05/18/2023]
Abstract
The study of plant hormones is critical to understanding development, physiology and interactions of plants with their environment. Synthetic biology holds promise to provide a new perspective and shed fresh light on the molecular mechanisms of plant hormone action and propel the design of novel biotechnologies. With the recent adoption of synthetic biology in plant sciences, exciting first examples of successful tool development and their applications in the area of plant hormone research are emerging, paving the way for new cadres to enter this promising field of science.
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Affiliation(s)
- Chengsong Zhao
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna Yaschenko
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Jose M Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Anna N Stepanova
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.
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15
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Teale WD, Pasternak T, Dal Bosco C, Dovzhenko A, Kratzat K, Bildl W, Schwörer M, Falk T, Ruperti B, V Schaefer J, Shahriari M, Pilgermayer L, Li X, Lübben F, Plückthun A, Schulte U, Palme K. Flavonol-mediated stabilization of PIN efflux complexes regulates polar auxin transport. EMBO J 2021; 40:e104416. [PMID: 33185277 PMCID: PMC7780147 DOI: 10.15252/embj.2020104416] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 09/04/2020] [Accepted: 10/06/2020] [Indexed: 01/08/2023] Open
Abstract
The transport of auxin controls the rate, direction and localization of plant growth and development. The course of auxin transport is defined by the polar subcellular localization of the PIN proteins, a family of auxin efflux transporters. However, little is known about the composition and regulation of the PIN protein complex. Here, using blue-native PAGE and quantitative mass spectrometry, we identify native PIN core transport units as homo- and heteromers assembled from PIN1, PIN2, PIN3, PIN4 and PIN7 subunits only. Furthermore, we show that endogenous flavonols stabilize PIN dimers to regulate auxin efflux in the same way as does the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). This inhibitory mechanism is counteracted both by the natural auxin indole-3-acetic acid and by phosphomimetic amino acids introduced into the PIN1 cytoplasmic domain. Our results lend mechanistic insights into an endogenous control mechanism which regulates PIN function and opens the way for a deeper understanding of the protein environment and regulation of the polar auxin transport complex.
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Affiliation(s)
- William D Teale
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
| | - Taras Pasternak
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
| | | | | | | | - Wolfgang Bildl
- Institute of Physiology IIFaculty of MedicineUniversity of FreiburgFreiburgGermany
| | - Manuel Schwörer
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
| | - Thorsten Falk
- Institute for Computer ScienceUniversity of FreiburgFreiburgGermany
| | - Benadetto Ruperti
- Department of Agronomy, Food, Natural resources, Animals and Environment—DAFNAEUniversity of PadovaPadovaItaly
| | - Jonas V Schaefer
- High‐Throughput Binder Selection FacilityDepartment of BiochemistryUniversity of ZurichZurichSwitzerland
| | | | | | - Xugang Li
- Sino German Joint Research Center for Agricultural Biology, and State Key Laboratory of Crop BiologyCollege of Life Sciences, Shandong Agricultural UniversityTai'anChina
| | - Florian Lübben
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
| | - Andreas Plückthun
- High‐Throughput Binder Selection FacilityDepartment of BiochemistryUniversity of ZurichZurichSwitzerland
| | - Uwe Schulte
- Institute of Physiology IIFaculty of MedicineUniversity of FreiburgFreiburgGermany
- Logopharm GmbHFreiburgGermany
- Signalling Research Centres BIOSS and CIBSSFreiburgGermany
| | - Klaus Palme
- Institute of Biology IIUniversity of FreiburgFreiburgGermany
- Signalling Research Centres BIOSS and CIBSSFreiburgGermany
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16
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Isoda R, Yoshinari A, Ishikawa Y, Sadoine M, Simon R, Frommer WB, Nakamura M. Sensors for the quantification, localization and analysis of the dynamics of plant hormones. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:542-557. [PMID: 33231903 PMCID: PMC7898640 DOI: 10.1111/tpj.15096] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/19/2020] [Indexed: 05/13/2023]
Abstract
Plant hormones play important roles in plant growth and development and physiology, and in acclimation to environmental changes. The hormone signaling networks are highly complex and interconnected. It is thus important to not only know where the hormones are produced, how they are transported and how and where they are perceived, but also to monitor their distribution quantitatively, ideally in a non-invasive manner. Here we summarize the diverse set of tools available for quantifying and visualizing hormone distribution and dynamics. We provide an overview over the tools that are currently available, including transcriptional reporters, degradation sensors, and luciferase and fluorescent sensors, and compare the tools and their suitability for different purposes.
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Affiliation(s)
- Reika Isoda
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| | - Akira Yoshinari
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
| | - Yuuma Ishikawa
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Mayuri Sadoine
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Rüdiger Simon
- Developmental GeneticsHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Wolf B. Frommer
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
- Molecular PhysiologyHeinrich‐Heine‐UniversityDüsseldorfGermany
| | - Masayoshi Nakamura
- Institute of Transformative Bio‐Molecules (WPI‐ITbM)Nagoya UniversityChikusaNagoya464‐8601Japan
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17
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Waadt R. Phytohormone signaling mechanisms and genetic methods for their modulation and detection. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:31-40. [PMID: 32622326 DOI: 10.1016/j.pbi.2020.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/24/2020] [Accepted: 05/29/2020] [Indexed: 06/11/2023]
Abstract
Phytohormones enable plants to regulate their development, growth and physiology according to the environmental requirements. Knowledge about the underlying signaling mechanisms, combined with the ability to pharmacologically or genetically manipulate phytohormone responses is steadily being incorporated into modern plant biology research and agriculture. This knowledge also enabled the development of genetically encoded phytohormone indicators that allow the tracking of spatiotemporal phytohormone dynamics and signaling processes in vivo. This review aims to provide an overview about core phytohormone signaling mechanisms, and about genetic tools for the manipulation and in vivo tracking of phytohormone actions.
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18
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Novel markers for high-throughput protoplast-based analyses of phytohormone signaling. PLoS One 2020; 15:e0234154. [PMID: 32497144 PMCID: PMC7272087 DOI: 10.1371/journal.pone.0234154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/19/2020] [Indexed: 02/03/2023] Open
Abstract
Phytohormones mediate most diverse processes in plants, ranging from organ development to immune responses. Receptor protein complexes perceive changes in intracellular phytohormone levels and trigger a signaling cascade to effectuate downstream responses. The in planta analysis of elements involved in phytohormone signaling can be achieved through transient expression in mesophyll protoplasts, which are a fast and versatile alternative to generating plant lines that stably express a transgene. While promoter-reporter constructs have been used successfully to identify internal or external factors that change phytohormone signaling, the range of available marker constructs does not meet the potential of the protoplast technique for large scale approaches. The aim of our study was to provide novel markers for phytohormone signaling in the Arabidopsis mesophyll protoplast system. We validated 18 promoter::luciferase constructs towards their phytohormone responsiveness and specificity and suggest an experimental setup for high-throughput analyses. We recommend novel markers for the analysis of auxin, abscisic acid, cytokinin, salicylic acid and jasmonic acid responses that will facilitate future screens for biological elements and environmental stimuli affecting phytohormone signaling.
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19
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Khosla A, Rodriguez‐Furlan C, Kapoor S, Van Norman JM, Nelson DC. A series of dual-reporter vectors for ratiometric analysis of protein abundance in plants. PLANT DIRECT 2020; 4:e00231. [PMID: 32582876 PMCID: PMC7306620 DOI: 10.1002/pld3.231] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/10/2020] [Accepted: 05/13/2020] [Indexed: 05/06/2023]
Abstract
Ratiometric reporter systems enable comparisons of the abundance of a protein of interest, or "target," relative to a reference protein. Both proteins are encoded on a single transcript but are separated during translation. This arrangement bypasses the potential for discordant expression that can arise when the target and reference proteins are encoded by separate genes. We generated a set of 18 Gateway-compatible vectors termed pRATIO that combine a variety of promoters, fluorescent, and bioluminescent reporters, and 2A "self-cleaving" peptides. These constructs are easily modified to produce additional combinations or introduce new reporter proteins. We found that mScarlet-I provides the best signal-to-noise ratio among several fluorescent reporter proteins during transient expression experiments in Nicotiana benthamiana. Firefly and Gaussia luciferase also produce high signal-to-noise in N. benthamiana. As proof of concept, we used this system to investigate whether degradation of the receptor KAI2 after karrikin treatment is influenced by its subcellular localization. KAI2 is normally found in the cytoplasm and the nucleus of plant cells. In N. benthamiana, karrikin-induced degradation of KAI2 was only observed when it was retained in the nucleus. These vectors are tools to easily monitor in vivo the abundance of a protein that is transiently expressed in plants, and will be particularly useful for investigating protein turnover in response to different stimuli.
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Affiliation(s)
- Aashima Khosla
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCAUSA
| | | | - Suraj Kapoor
- Department of GeneticsUniversity of GeorgiaAthensGAUSA
| | | | - David C. Nelson
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCAUSA
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20
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Galvan-Ampudia CS, Cerutti G, Legrand J, Brunoud G, Martin-Arevalillo R, Azais R, Bayle V, Moussu S, Wenzl C, Jaillais Y, Lohmann JU, Godin C, Vernoux T. Temporal integration of auxin information for the regulation of patterning. eLife 2020; 9:55832. [PMID: 32379043 PMCID: PMC7205470 DOI: 10.7554/elife.55832] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/29/2020] [Indexed: 12/27/2022] Open
Abstract
Positional information is essential for coordinating the development of multicellular organisms. In plants, positional information provided by the hormone auxin regulates rhythmic organ production at the shoot apex, but the spatio-temporal dynamics of auxin gradients is unknown. We used quantitative imaging to demonstrate that auxin carries high-definition graded information not only in space but also in time. We show that, during organogenesis, temporal patterns of auxin arise from rhythmic centrifugal waves of high auxin travelling through the tissue faster than growth. We further demonstrate that temporal integration of auxin concentration is required to trigger the auxin-dependent transcription associated with organogenesis. This provides a mechanism to temporally differentiate sites of organ initiation and exemplifies how spatio-temporal positional information can be used to create rhythmicity. Plants, like animals and many other multicellular organisms, control their body architecture by creating organized patterns of cells. These patterns are generally defined by signal molecules whose levels differ across the tissue and change over time. This tells the cells where they are located in the tissue and therefore helps them know what tasks to perform. A plant hormone called auxin is one such signal molecule and it controls when and where plants produce new leaves and flowers. Over time, this process gives rise to the dashing arrangements of spiraling organs exhibited by many plant species. The leaves and flowers form from a relatively small group of cells at the tip of a growing stem known as the shoot apical meristem. Auxin accumulates at precise locations within the shoot apical meristem before cells activate the genes required to make a new leaf or flower. However, the precise role of auxin in forming these new organs remained unclear because the tools to observe the process in enough detail were lacking. Galvan-Ampudia, Cerutti et al. have now developed new microscopy and computational approaches to observe auxin in a small plant known as Arabidopsis thaliana. This showed that dozens of shoot apical meristems exhibited very similar patterns of auxin. Images taken over a period of several hours showed that the locations where auxin accumulated were not fixed on a group of cells but instead shifted away from the center of the shoot apical meristems faster than the tissue grew. This suggested the cells experience rapidly changing levels of auxin. Further experiments revealed that the cells needed to be exposed to a high level of auxin over time to activate genes required to form an organ. This mechanism sheds a new light on how auxin regulates when and where plants make new leaves and flowers. The tools developed by Galvan-Ampudia, Cerutti et al. could be used to study the role of auxin in other plant tissues, and to investigate how plants regulate the response to other plant hormones.
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Affiliation(s)
- Carlos S Galvan-Ampudia
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Guillaume Cerutti
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Jonathan Legrand
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Géraldine Brunoud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Raquel Martin-Arevalillo
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Romain Azais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Steven Moussu
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Christian Wenzl
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Christophe Godin
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
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21
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Khakhar A, Starker CG, Chamness JC, Lee N, Stokke S, Wang C, Swanson R, Rizvi F, Imaizumi T, Voytas DF. Building customizable auto-luminescent luciferase-based reporters in plants. eLife 2020; 9:52786. [PMID: 32209230 PMCID: PMC7164954 DOI: 10.7554/elife.52786] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/24/2020] [Indexed: 01/09/2023] Open
Abstract
Bioluminescence is a powerful biological signal that scientists have repurposed as a reporter for gene expression in plants and animals. However, there are downsides associated with the need to provide a substrate to these reporters, including its high cost and non-uniform tissue penetration. In this work we reconstitute a fungal bioluminescence pathway (FBP) in planta using a composable toolbox of parts. We demonstrate that the FBP can create luminescence across various tissues in a broad range of plants without external substrate addition. We also show how our toolbox can be used to deploy the FBP in planta to build auto-luminescent reporters for the study of gene-expression and hormone fluxes. A low-cost imaging platform for gene expression profiling is also described. These experiments lay the groundwork for future construction of programmable auto-luminescent plant traits, such as light driven plant-pollinator interactions or light emitting plant-based sensors.
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Affiliation(s)
- Arjun Khakhar
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Colby G Starker
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - James C Chamness
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Nayoung Lee
- Department of Biology, University of Washington, Seattle, United States
| | - Sydney Stokke
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Cecily Wang
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Ryan Swanson
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Furva Rizvi
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
| | - Takato Imaizumi
- Department of Biology, University of Washington, Seattle, United States
| | - Daniel F Voytas
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis, United States.,Center for Precision Plant Genomics, University of Minnesota, St. Paul, United States
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22
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Martin-Arevalillo R, Vernoux T. Shining light on plant hormones with genetically encoded biosensors. Biol Chem 2019; 400:477-486. [PMID: 30511920 DOI: 10.1515/hsz-2018-0310] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/05/2018] [Indexed: 12/30/2022]
Abstract
Signalling molecules are produced, degraded, modified and transported throughout the development of higher organisms. Understanding their mode of action implies understanding these dynamics in vivo and in real time. Genetically encoded biosensors are being more and more used as tools to 'follow' signalling molecules and their responses inside an organism. This is the case for plants, where important progresses have been made in the development of such biosensors. Here, we summarize the main genetically encoded biosensors built for plant hormones, constructed using diverse components and steps of their signalling pathways.
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Affiliation(s)
- Raquel Martin-Arevalillo
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342 Lyon, France
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23
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Recent developments in biosensors to combat agricultural challenges and their future prospects. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.03.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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24
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Argueso CT, Assmann SM, Birnbaum KD, Chen S, Dinneny JR, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall‐Colón A, Mason GA, O'Lexy R, Peck SC, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM. Directions for research and training in plant omics: Big Questions and Big Data. PLANT DIRECT 2019; 3:e00133. [PMID: 31245771 PMCID: PMC6589541 DOI: 10.1002/pld3.133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 03/21/2019] [Indexed: 05/04/2023]
Abstract
A key remit of the NSF-funded "Arabidopsis Research and Training for the 21st Century" (ART-21) Research Coordination Network has been to convene a series of workshops with community members to explore issues concerning research and training in plant biology, including the role that research using Arabidopsis thaliana can play in addressing those issues. A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al., Plant Physiology, 175, 2017, 1499). In this white paper, we provide a summary of the discussions and insights arising from the second ART-21 workshop. The second workshop focused on experimental aspects of omics data acquisition and analysis and involved a broad spectrum of participants from academics and industry, ranging from graduate students through post-doctorates, early career and established investigators. Our hope is that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.
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Affiliation(s)
- Cristiana T. Argueso
- Department of Bioagricultural Sciences and Pest ManagementColorado State UniversityFort CollinsColorado
| | - Sarah M. Assmann
- Biology DepartmentPenn State UniversityUniversity ParkPennsylvania
| | - Kenneth D. Birnbaum
- Department of BiologyCenter for Genomics and Systems BiologyNew York UniversityNew YorkNew York
| | - Sixue Chen
- Department of BiologyGenetics InstitutePlant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFlorida
- Proteomics and Mass SpectrometryInterdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFlorida
| | | | - Colleen J. Doherty
- Department of Molecular and Structural BiochemistryNorth Carolina State UniversityRaleighNorth Carolina
| | | | | | - Vanessa R. Greenlee
- International ProgramsCollege of Agriculture and Life SciencesCornell UniversityIthacaNew York
| | - Julie A. Law
- Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCalifornia
- Division of Biological SciencesUniversity of California, San DiegoLa JollaCalifornia
| | - Amy Marshall‐Colón
- Department of Plant BiologyUniversity of Illinois Urbana‐ChampaignUrbanaIllinois
| | - Grace Alex Mason
- Department of Plant Biology and Genome CenterUC DavisDavisCalifornia
| | - Ruby O'Lexy
- Coriell Institute for Medical ResearchCamdenNew Jersey
| | - Scott C. Peck
- Division of BiochemistryChristopher S. Bond Life Sciences CenterInterdisciplinary Plant GroupUniversity of MissouriColumbiaMissouri
| | | | - Liang Song
- Department of BotanyThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | | | | | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIowa
| | - Cranos M. Williams
- Department of Electrical and Computer EngineeringNorth Carolina State UniversityRaleighNorth Carolina
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25
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Wright RC, Nemhauser J. Plant Synthetic Biology: Quantifying the "Known Unknowns" and Discovering the "Unknown Unknowns". PLANT PHYSIOLOGY 2019; 179:885-893. [PMID: 30630870 PMCID: PMC6393784 DOI: 10.1104/pp.18.01222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/14/2018] [Indexed: 05/03/2023]
Abstract
Biosensors, advanced microscopy, and single- cell transcriptomics are advancing plant synthetic biology.
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Affiliation(s)
- R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, Virginia
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26
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Andres J, Blomeier T, Zurbriggen MD. Synthetic Switches and Regulatory Circuits in Plants. PLANT PHYSIOLOGY 2019; 179:862-884. [PMID: 30692218 PMCID: PMC6393786 DOI: 10.1104/pp.18.01362] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/18/2019] [Indexed: 05/20/2023]
Abstract
Synthetic biology is an established but ever-growing interdisciplinary field of research currently revolutionizing biomedicine studies and the biotech industry. The engineering of synthetic circuitry in bacterial, yeast, and animal systems prompted considerable advances for the understanding and manipulation of genetic and metabolic networks; however, their implementation in the plant field lags behind. Here, we review theoretical-experimental approaches to the engineering of synthetic chemical- and light-regulated (optogenetic) switches for the targeted interrogation and control of cellular processes, including existing applications in the plant field. We highlight the strategies for the modular assembly of genetic parts into synthetic circuits of different complexity, ranging from Boolean logic gates and oscillatory devices up to semi- and fully synthetic open- and closed-loop molecular and cellular circuits. Finally, we explore potential applications of these approaches for the engineering of novel functionalities in plants, including understanding complex signaling networks, improving crop productivity, and the production of biopharmaceuticals.
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Affiliation(s)
- Jennifer Andres
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
| | - Tim Blomeier
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, 40225 Duesseldorf, Germany
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27
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Geisler M. Seeing is better than believing: visualization of membrane transport in plants. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:104-112. [PMID: 30253307 DOI: 10.1016/j.pbi.2018.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 05/27/2023]
Abstract
Recently, the plant transport field has shifted their research focus toward a more integrative investigation of transport networks thought to provide the basis for long-range transport routes. Substantial progress was provided by of a series of elegant techniques that allow for a visualization or prediction of substrate movements in plant tissues in contrast to established quantitative methods offering low spatial resolution. These methods are critically evaluated in respect to their spatio-temporal resolution, invasiveness, dynamics and overall quality. Current limitations of transport route predictions-based on transporter locations and transport modeling are addressed. Finally, the potential of new tools that have not yet been fully implemented into plant research is indicated.
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Affiliation(s)
- Markus Geisler
- University of Fribourg, Department of Biology, Chemin du Musée 10, CH-1700 Fribourg, Switzerland.
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28
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Kassaw TK, Donayre-Torres AJ, Antunes MS, Morey KJ, Medford JI. Engineering synthetic regulatory circuits in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:13-22. [PMID: 29907304 DOI: 10.1016/j.plantsci.2018.04.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Revised: 04/05/2018] [Accepted: 04/07/2018] [Indexed: 05/21/2023]
Abstract
Plant synthetic biology is a rapidly emerging field that aims to engineer genetic circuits to function in plants with the same reliability and precision as electronic circuits. These circuits can be used to program predictable plant behavior, producing novel traits to improve crop plant productivity, enable biosensors, and serve as platforms to synthesize chemicals and complex biomolecules. Herein we introduce the importance of developing orthogonal plant parts and the need for quantitative part characterization for mathematical modeling of complex circuits. In particular, transfer functions are important when designing electronic-like genetic controls such as toggle switches, positive/negative feedback loops, and Boolean logic gates. We then discuss potential constraints and challenges in synthetic regulatory circuit design and integration when using plants. Finally, we highlight current and potential plant synthetic regulatory circuit applications.
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Affiliation(s)
- Tessema K Kassaw
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Alberto J Donayre-Torres
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Mauricio S Antunes
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - Kevin J Morey
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA
| | - June I Medford
- Department of Biology, 1878 Campus Delivery, Colorado State University, Fort Collins, CO 80523-1878, USA.
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29
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Goold HD, Wright P, Hailstones D. Emerging Opportunities for Synthetic Biology in Agriculture. Genes (Basel) 2018; 9:E341. [PMID: 29986428 PMCID: PMC6071285 DOI: 10.3390/genes9070341] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/27/2018] [Accepted: 07/03/2018] [Indexed: 12/11/2022] Open
Abstract
Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and forestry, face significant and global challenges; addressing them will be assisted by the sector’s strong history of early adoption of transformative innovation, such as the genetic technologies that underlie synthetic biology. The implementation of synthetic biology within agriculture may, however, be hampered given the industry is dominated by higher plants and mammals, where large and often polyploid genomes and the lack of adequate tools challenge the ability to deliver outcomes in the short term. However, synthetic biology is a rapidly growing field, new techniques in genome design and synthesis, and more efficient molecular tools such as CRISPR/Cas9 may harbor opportunities more broadly than the development of new cultivars and breeds. In particular, the ability to use synthetic biology to engineer biosensors, synthetic speciation, microbial metabolic engineering, mammalian multiplexed CRISPR, novel anti microbials, and projects such as Yeast 2.0 all have significant potential to deliver transformative changes to agriculture in the short, medium and longer term. Specifically, synthetic biology promises to deliver benefits that increase productivity and sustainability across primary industries, underpinning the industry’s prosperity in the face of global challenges.
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Affiliation(s)
- Hugh Douglas Goold
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia.
| | - Philip Wright
- New South Wales Department of Primary Industries, Locked Bag 21, 161 Kite St, Orange, NSW 2800, Australia.
| | - Deborah Hailstones
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia.
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30
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Abstract
Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.
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31
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Chatelle C, Ochoa-Fernandez R, Engesser R, Schneider N, Beyer HM, Jones AR, Timmer J, Zurbriggen MD, Weber W. A Green-Light-Responsive System for the Control of Transgene Expression in Mammalian and Plant Cells. ACS Synth Biol 2018; 7:1349-1358. [PMID: 29634242 DOI: 10.1021/acssynbio.7b00450] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The ever-increasing complexity of synthetic gene networks and applications of synthetic biology requires precise and orthogonal gene expression systems. Of particular interest are systems responsive to light as they enable the control of gene expression dynamics with unprecedented resolution in space and time. While broadly used in mammalian backgrounds, however, optogenetic approaches in plant cells are still limited due to interference of the activating light with endogenous photoreceptors. Here, we describe the development of the first synthetic light-responsive system for the targeted control of gene expression in mammalian and plant cells that responds to the green range of the light spectrum in which plant photoreceptors have minimal activity. We first engineered a system based on the light-sensitive bacterial transcription factor CarH and its cognate DNA operator sequence CarO from Thermus thermophilus to control gene expression in mammalian cells. The system was functional in various mammalian cell lines, showing high induction (up to 350-fold) along with low leakiness, as well as high reversibility. We quantitatively described the systems characteristics by the development and experimental validation of a mathematical model. Finally, we transferred the system into A. thaliana protoplasts and demonstrated gene repression in response to green light. We expect that this system will provide new opportunities in applications based on synthetic gene networks and will open up perspectives for optogenetic studies in mammalian and plant cells.
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Affiliation(s)
| | | | | | | | | | - Alex R. Jones
- National Physical Laboratory, Teddington, Middlesex TW11 0LW, U.K
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32
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Middleton AM, Dal Bosco C, Chlap P, Bensch R, Harz H, Ren F, Bergmann S, Wend S, Weber W, Hayashi KI, Zurbriggen MD, Uhl R, Ronneberger O, Palme K, Fleck C, Dovzhenko A. Data-Driven Modeling of Intracellular Auxin Fluxes Indicates a Dominant Role of the ER in Controlling Nuclear Auxin Uptake. Cell Rep 2018. [DOI: 10.1016/j.celrep.2018.02.074] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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33
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Pařízková B, Pernisová M, Novák O. What Has Been Seen Cannot Be Unseen-Detecting Auxin In Vivo. Int J Mol Sci 2017; 18:ijms18122736. [PMID: 29258197 PMCID: PMC5751337 DOI: 10.3390/ijms18122736] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022] Open
Abstract
Auxins mediate various processes that are involved in plant growth and development in response to specific environmental conditions. Its proper spatio-temporal distribution that is driven by polar auxin transport machinery plays a crucial role in the wide range of auxins physiological effects. Numbers of approaches have been developed to either directly or indirectly monitor auxin distribution in vivo in order to elucidate the basis of its precise regulation. Herein, we provide an updated list of valuable techniques used for monitoring auxins in plants, with their utilities and limitations. Because the spatial and temporal resolutions of the presented approaches are different, their combination may provide a comprehensive outcome of auxin distribution in diverse developmental processes.
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Affiliation(s)
- Barbora Pařízková
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
| | - Markéta Pernisová
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
- Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
| | - Ondřej Novák
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic.
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34
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Shigenaga AM, Berens ML, Tsuda K, Argueso CT. Towards engineering of hormonal crosstalk in plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2017. [PMID: 28624670 DOI: 10.1016/j.pbi.2017.04.021] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant hormones regulate physiological responses in plants, including responses to pathogens and beneficial microbes. The last decades have provided a vast amount of evidence about the contribution of different plant hormones to plant immunity, and also of how they cooperate to orchestrate immunity activation, in a process known as hormone crosstalk. In this review we highlight the complexity of hormonal crosstalk in immunity and approaches currently being used to further understand this process, as well as perspectives to engineer hormone crosstalk for enhanced pathogen resistance and overall plant fitness.
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Affiliation(s)
- Alexandra M Shigenaga
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA
| | - Matthias L Berens
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Kenichi Tsuda
- Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.
| | - Cristiana T Argueso
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.
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35
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Samodelov SL, Zurbriggen MD. Quantitatively Understanding Plant Signaling: Novel Theoretical-Experimental Approaches. TRENDS IN PLANT SCIENCE 2017; 22:685-704. [PMID: 28668509 DOI: 10.1016/j.tplants.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
With the need to respond to and integrate a multitude of external and internal stimuli, plant signaling is highly complex, exhibiting signaling component redundancy and high interconnectedness between individual pathways. We review here novel theoretical-experimental approaches in manipulating plant signaling towards the goal of a comprehensive understanding and targeted quantitative control of plant processes. We highlight approaches taken in the field of synthetic biology used in other systems and discuss their applicability in plants. Finally, we introduce existing tools for the quantitative analysis and monitoring of plant signaling and the integration of experimentally obtained quantitative data into mathematical models. Incorporating principles of synthetic biology into plant sciences more widely will lead this field forward in both fundamental and applied research.
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Affiliation(s)
- Sophia L Samodelov
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany.
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36
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De Col V, Fuchs P, Nietzel T, Elsässer M, Voon CP, Candeo A, Seeliger I, Fricker MD, Grefen C, Møller IM, Bassi A, Lim BL, Zancani M, Meyer AJ, Costa A, Wagner S, Schwarzländer M. ATP sensing in living plant cells reveals tissue gradients and stress dynamics of energy physiology. eLife 2017; 6. [PMID: 28716182 PMCID: PMC5515573 DOI: 10.7554/elife.26770] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/28/2017] [Indexed: 12/13/2022] Open
Abstract
Growth and development of plants is ultimately driven by light energy captured through photosynthesis. ATP acts as universal cellular energy cofactor fuelling all life processes, including gene expression, metabolism, and transport. Despite a mechanistic understanding of ATP biochemistry, ATP dynamics in the living plant have been largely elusive. Here, we establish MgATP2- measurement in living plants using the fluorescent protein biosensor ATeam1.03-nD/nA. We generate Arabidopsis sensor lines and investigate the sensor in vitro under conditions appropriate for the plant cytosol. We establish an assay for ATP fluxes in isolated mitochondria, and demonstrate that the sensor responds rapidly and reliably to MgATP2- changes in planta. A MgATP2- map of the Arabidopsis seedling highlights different MgATP2- concentrations between tissues and within individual cell types, such as root hairs. Progression of hypoxia reveals substantial plasticity of ATP homeostasis in seedlings, demonstrating that ATP dynamics can be monitored in the living plant.
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Affiliation(s)
- Valentina De Col
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany.,Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Philippe Fuchs
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Thomas Nietzel
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Marlene Elsässer
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Chia Pao Voon
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Alessia Candeo
- Dipartimento di Fisica, Politecnico di Milano, Milano, Italy
| | - Ingo Seeliger
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Mark D Fricker
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Christopher Grefen
- Centre for Plant Molecular Biology, Developmental Genetics, University of Tübingen, Tübingen, Germany
| | - Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Andrea Bassi
- Dipartimento di Fisica, Politecnico di Milano, Milano, Italy
| | - Boon Leong Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China.,State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong, China
| | - Marco Zancani
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Andreas J Meyer
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany.,Bioeconomy Science Center, Forschungszentrum Jülich, Jülich, Germany
| | - Alex Costa
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Stephan Wagner
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany
| | - Markus Schwarzländer
- Institute of Crop Science and Resource Conservation, University of Bonn, Bonn, Germany.,Bioeconomy Science Center, Forschungszentrum Jülich, Jülich, Germany
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37
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Abstract
Plants are attractive platforms for synthetic biology and metabolic engineering. Plants' modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. However, efforts in this area have been constrained by slow growth, long life cycles, the requirement for specialized facilities, a paucity of efficient tools for genetic manipulation, and the complexity of multicellularity. There is a need for better experimental and theoretical frameworks to understand the way genetic networks, cellular populations, and tissue-wide physical processes interact at different scales. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits.
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Affiliation(s)
- Christian R Boehm
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Bernardo Pollak
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | | | | | - Jim Haseloff
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
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38
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Winkler M, Niemeyer M, Hellmuth A, Janitza P, Christ G, Samodelov SL, Wilde V, Majovsky P, Trujillo M, Zurbriggen MD, Hoehenwarter W, Quint M, Calderón Villalobos LIA. Variation in auxin sensing guides AUX/IAA transcriptional repressor ubiquitylation and destruction. Nat Commun 2017; 8:15706. [PMID: 28589936 PMCID: PMC5467235 DOI: 10.1038/ncomms15706] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 04/21/2017] [Indexed: 12/24/2022] Open
Abstract
Auxin is a small molecule morphogen that bridges SCFTIR1/AFB-AUX/IAA co-receptor interactions leading to ubiquitylation and proteasome-dependent degradation of AUX/IAA transcriptional repressors. Here, we systematically dissect auxin sensing by SCFTIR1-IAA6 and SCFTIR1-IAA19 co-receptor complexes, and assess IAA6/IAA19 ubiquitylation in vitro and IAA6/IAA19 degradation in vivo. We show that TIR1-IAA19 and TIR1-IAA6 have distinct auxin affinities that correlate with ubiquitylation and turnover dynamics of the AUX/IAA. We establish a system to track AUX/IAA ubiquitylation in IAA6 and IAA19 in vitro and show that it occurs in flexible hotspots in degron-flanking regions adorned with specific Lys residues. We propose that this signature is exploited during auxin-mediated SCFTIR1-AUX/IAA interactions. We present evidence for an evolving AUX/IAA repertoire, typified by the IAA6/IAA19 ohnologues, that discriminates the range of auxin concentrations found in plants. We postulate that the intrinsic flexibility of AUX/IAAs might bias their ubiquitylation and destruction kinetics enabling specific auxin responses.
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Affiliation(s)
- Martin Winkler
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) D-06120, Germany
| | - Michael Niemeyer
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) D-06120, Germany
| | - Antje Hellmuth
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) D-06120, Germany
| | - Philipp Janitza
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) D-06120, Germany
| | - Gideon Christ
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) D-06120, Germany
| | - Sophia L. Samodelov
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf D-40225, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg D-79104, Germany
| | - Verona Wilde
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) D-06120, Germany
| | - Petra Majovsky
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) D-06120, Germany
| | - Marco Trujillo
- Independent Junior Research Group Ubiquitination in Immunity, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) D-06120, Germany
| | - Matias D. Zurbriggen
- Institute of Synthetic Biology, University of Düsseldorf, Düsseldorf D-40225, Germany
- Cluster of Excellence on Plant Science (CEPLAS), University of Düsseldorf, Düsseldorf D-40225, Germany
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale) D-06120, Germany
| | - Marcel Quint
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale) D-06120, Germany
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39
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Novák O, Napier R, Ljung K. Zooming In on Plant Hormone Analysis: Tissue- and Cell-Specific Approaches. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:323-348. [PMID: 28226234 DOI: 10.1146/annurev-arplant-042916-040812] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plant hormones are a group of naturally occurring, low-abundance organic compounds that influence physiological processes in plants. Our knowledge of the distribution profiles of phytohormones in plant organs, tissues, and cells is still incomplete, but advances in mass spectrometry have enabled significant progress in tissue- and cell-type-specific analyses of phytohormones over the last decade. Mass spectrometry is able to simultaneously identify and quantify hormones and their related substances. Biosensors, on the other hand, offer continuous monitoring; can visualize local distributions and real-time quantification; and, in the case of genetically encoded biosensors, are noninvasive. Thus, biosensors offer additional, complementary technologies for determining temporal and spatial changes in phytohormone concentrations. In this review, we focus on recent advances in mass spectrometry-based quantification, describe monitoring systems based on biosensors, and discuss validations of the various methods before looking ahead at future developments for both approaches.
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Affiliation(s)
- Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden; ,
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS and Faculty of Science of Palacký University, CZ-78371 Olomouc, Czech Republic;
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom;
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden; ,
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40
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Hu Y, Vandenbussche F, Van Der Straeten D. Regulation of seedling growth by ethylene and the ethylene-auxin crosstalk. PLANTA 2017; 245:467-489. [PMID: 28188422 DOI: 10.1007/s00425-017-2651-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/08/2017] [Indexed: 05/06/2023]
Abstract
This review highlights that the auxin gradient, established by local auxin biosynthesis and transport, can be controlled by ethylene, and steers seedling growth. A better understanding of the mechanisms in Arabidopsis will increase potential applications in crop species. In dark-grown Arabidopsis seedlings, exogenous ethylene treatment triggers an exaggeration of the apical hook, the inhibition of both hypocotyl and root elongation, and radial swelling of the hypocotyl. These features are predominantly based on the differential cell elongation in different cells/tissues mediated by an auxin gradient. Interestingly, the physiological responses regulated by ethylene and auxin crosstalk can be either additive or synergistic, as in primary root and root hair elongation, or antagonistic, as in hypocotyl elongation. This review focuses on the crosstalk of these two hormones at the seedling stage. Before illustrating the crosstalk, ethylene and auxin biosynthesis, metabolism, transport and signaling are briefly discussed.
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Affiliation(s)
- Yuming Hu
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Filip Vandenbussche
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium
| | - Dominique Van Der Straeten
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, 9000, Ghent, Belgium.
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41
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Waadt R, Hsu PK, Schroeder JI. Abscisic acid and other plant hormones: Methods to visualize distribution and signaling. Bioessays 2016; 37:1338-49. [PMID: 26577078 DOI: 10.1002/bies.201500115] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The exploration of plant behavior on a cellular scale in a minimal invasive manner is key to understanding plant adaptations to their environment. Plant hormones regulate multiple aspects of growth and development and mediate environmental responses to ensure a successful life cycle. To monitor the dynamics of plant hormone actions in intact tissue, we need qualitative and quantitative tools with high temporal and spatial resolution. Here, we describe a set of biological instruments (reporters) for the analysis of the distribution and signaling of various plant hormones. Furthermore, we provide examples of their utility for gaining novel insights into plant hormone action with a deeper focus on the drought hormone abscisic acid.
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Affiliation(s)
- Rainer Waadt
- Centre for Organismal Studies, Plant Developmental Biology, Ruprecht-Karls-University of Heidelberg, Heidelberg, Germany.,Division of Biological Sciences, Cell and Developmental Biology Section and Centre for Food and Fuel for the 21st Century, University of California San Diego, La Jolla, CA, USA
| | - Po-Kai Hsu
- Division of Biological Sciences, Cell and Developmental Biology Section and Centre for Food and Fuel for the 21st Century, University of California San Diego, La Jolla, CA, USA
| | - Julian I Schroeder
- Division of Biological Sciences, Cell and Developmental Biology Section and Centre for Food and Fuel for the 21st Century, University of California San Diego, La Jolla, CA, USA
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42
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Samodelov SL, Beyer HM, Guo X, Augustin M, Jia KP, Baz L, Ebenhöh O, Beyer P, Weber W, Al-Babili S, Zurbriggen MD. StrigoQuant: A genetically encoded biosensor for quantifying strigolactone activity and specificity. SCIENCE ADVANCES 2016; 2:e1601266. [PMID: 27847871 PMCID: PMC5099991 DOI: 10.1126/sciadv.1601266] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 09/29/2016] [Indexed: 05/20/2023]
Abstract
Strigolactones are key regulators of plant development and interaction with symbiotic fungi; however, quantitative tools for strigolactone signaling analysis are lacking. We introduce a genetically encoded hormone biosensor used to analyze strigolactone-mediated processes, including the study of the components involved in the hormone perception/signaling complex and the structural specificity and sensitivity of natural and synthetic strigolactones in Arabidopsis, providing quantitative insights into the stereoselectivity of strigolactone perception. Given the high specificity, sensitivity, dynamic range of activity, modular construction, ease of implementation, and wide applicability, the biosensor StrigoQuant will be useful in unraveling multiple levels of strigolactone metabolic and signaling networks.
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Affiliation(s)
- Sophia L. Samodelov
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Hannes M. Beyer
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Xiujie Guo
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, 23955-6900 Thuwal, Saudi Arabia
| | | | - Kun-Peng Jia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, 23955-6900 Thuwal, Saudi Arabia
| | - Lina Baz
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, 23955-6900 Thuwal, Saudi Arabia
| | - Oliver Ebenhöh
- Institute of Quantitative and Theoretical Biology and CEPLAS, University of Düsseldorf, Düsseldorf, Germany
| | - Peter Beyer
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wilfried Weber
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Salim Al-Babili
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, 23955-6900 Thuwal, Saudi Arabia
- Corresponding author. (M.D.Z.); (S.A.-B.)
| | - Matias D. Zurbriggen
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany
- Corresponding author. (M.D.Z.); (S.A.-B.)
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43
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Khosla A, Nelson DC. Strigolactones, super hormones in the fight against Striga. CURRENT OPINION IN PLANT BIOLOGY 2016; 33:57-63. [PMID: 27318656 DOI: 10.1016/j.pbi.2016.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/27/2016] [Accepted: 06/01/2016] [Indexed: 05/18/2023]
Abstract
Strigolactones are plant hormones that control diverse aspects of plant growth, but are also exuded into soil as recruitment signals for arbuscular mycorrhizal fungi interactions. Highly damaging parasitic weeds in the Orobanchaceae family have coopted strigolactones as germination cues that indicate the presence of a host. Recent studies have established how strigolactones are actively transported within and out of plants. Key components of the strigolactone signaling system have been identified, including strigolactone receptors in angiosperms and parasites, as well as downstream targets that are polyubiquitinated and proteolyzed following strigolactone perception. The basis for protein-protein interactions among these signaling components has also been explored. We propose several strategies to translate current knowledge of strigolactone transport and signaling into parasite control methods.
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Affiliation(s)
- Aashima Khosla
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - David C Nelson
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
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44
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Braguy J, Zurbriggen MD. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:118-38. [PMID: 27227549 DOI: 10.1111/tpj.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 05/15/2023]
Abstract
Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.
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Affiliation(s)
- Justine Braguy
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
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45
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Sanchez Carranza AP, Singh A, Steinberger K, Panigrahi K, Palme K, Dovzhenko A, Dal Bosco C. Hydrolases of the ILR1-like family of Arabidopsis thaliana modulate auxin response by regulating auxin homeostasis in the endoplasmic reticulum. Sci Rep 2016; 6:24212. [PMID: 27063913 PMCID: PMC4827090 DOI: 10.1038/srep24212] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/22/2016] [Indexed: 12/21/2022] Open
Abstract
Amide-linked conjugates of indole-3-acetic acid (IAA) have been identified in most plant species. They function in storage, inactivation or inhibition of the growth regulator auxin. We investigated how the major known endogenous amide-linked IAA conjugates with auxin-like activity act in auxin signaling and what role ILR1-like proteins play in this process in Arabidopsis. We used a genetically encoded auxin sensor to show that IAA-Leu, IAA-Ala and IAA-Phe act through the TIR1-dependent signaling pathway. Furthermore, by using the sensor as a free IAA reporter, we followed conjugate hydrolysis mediated by ILR1, ILL2 and IAR3 in plant cells and correlated the activity of the hydrolases with a modulation of auxin response. The conjugate preferences that we observed are in agreement with available in vitro data for ILR1. Moreover, we identified IAA-Leu as an additional substrate for IAR3 and showed that ILL2 has a more moderate kinetic performance than observed in vitro. Finally, we proved that IAR3, ILL2 and ILR1 reside in the endoplasmic reticulum, indicating that in this compartment the hydrolases regulate the rates of amido-IAA hydrolysis which results in activation of auxin signaling.
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Affiliation(s)
- Ana Paula Sanchez Carranza
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Aparajita Singh
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Karoline Steinberger
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Kishore Panigrahi
- National Institute of Science Education and Research, Institute of Physics Campus, Bhubaneswar, Odisha 751005, India
| | - Klaus Palme
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.,Freiburg Institute for Advanced Sciences (FRIAS), University of Freiburg, 79104 Freiburg, Germany.,Centre for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany
| | - Alexander Dovzhenko
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
| | - Cristina Dal Bosco
- Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Germany
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46
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Ochoa-Fernandez R, Samodelov SL, Brandl SM, Wehinger E, Müller K, Weber W, Zurbriggen MD. Optogenetics in Plants: Red/Far-Red Light Control of Gene Expression. Methods Mol Biol 2016; 1408:125-39. [PMID: 26965120 DOI: 10.1007/978-1-4939-3512-3_9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Optogenetic tools to control gene expression have many advantages over the classical chemically inducible systems, overcoming intrinsic limitations of chemical inducers such as solubility, diffusion, and cell toxicity. They offer an unmatched spatiotemporal resolution and permit quantitative and noninvasive control of the gene expression. Here we describe a protocol of a synthetic light-inducible system for the targeted control of gene expression in plants based on the plant photoreceptor phytochrome B and one of its interacting factors (PIF6). The synthetic toggle switch system is in the ON state when plant protoplasts are illuminated with red light (660 nm) and can be returned to the OFF state by subsequent illumination with far-red light (760 nm). In this protocol, the implementation of a red light-inducible expression system in plants using Light-Emitting Diode (LED) illumination boxes is described, including the isolation and transient transformation of plant protoplasts from Arabidopsis thaliana and Nicotiana tabacum.
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Affiliation(s)
- Rocio Ochoa-Fernandez
- Institute of Synthetic Biology, University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
- iGRAD Plant International Graduate Program for Plant Science, University of Düsseldorf, Düsseldorf, Germany
| | - Sophia L Samodelov
- Institute of Synthetic Biology, University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Alberstrasse 19a, 79104, Freiburg, Germany
| | - Simon M Brandl
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Elke Wehinger
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
| | - Konrad Müller
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- Novartis Pharma AG, Biologics Process R&D, 4002, Basel, Switzerland
| | - Wilfried Weber
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Alberstrasse 19a, 79104, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany
- BIOSS - Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, University of Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany.
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.
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47
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Beyer HM, Gonschorek P, Samodelov SL, Meier M, Weber W, Zurbriggen MD. AQUA Cloning: A Versatile and Simple Enzyme-Free Cloning Approach. PLoS One 2015; 10:e0137652. [PMID: 26360249 PMCID: PMC4567319 DOI: 10.1371/journal.pone.0137652] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/20/2015] [Indexed: 11/23/2022] Open
Abstract
Assembly cloning is increasingly replacing conventional restriction enzyme and DNA-ligase-dependent cloning methods for reasons of efficiency and performance. Here, we describe AQUA (advanced quick assembly), a simple and versatile seamless assembly cloning approach. We demonstrate the applicability and versatility of AQUA Cloning in selected proof-of-principle applications including targeted insertion-, deletion- and site-directed point-mutagenesis, and combinatorial cloning. Furthermore, we show the one pot de novo assembly of multiple DNA fragments into a single circular plasmid encoding a complex light- and chemically-regulated Boolean A NIMPLY B logic operation. AQUA Cloning harnesses intrinsic in vivo processing of linear DNA fragments with short regions of homology of 16 to 32 bp mediated by Escherichia coli. It does not require any kits, enzymes or preparations of reagents and is the simplest assembly cloning protocol to date.
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Affiliation(s)
- Hannes M. Beyer
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | | | - Sophia L. Samodelov
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Matthias Meier
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- IMTEK, Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Matias D. Zurbriggen
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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48
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Affiliation(s)
- Rainer Waadt
- University of Heidelberg, Centre for Organismal Studies, Plant Developmental Biology, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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49
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Reporters for sensitive and quantitative measurement of auxin response. Nat Methods 2015; 12:207-10, 2 p following 210. [PMID: 25643149 PMCID: PMC4344836 DOI: 10.1038/nmeth.3279] [Citation(s) in RCA: 268] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 12/23/2014] [Indexed: 01/25/2023]
Abstract
Visualization of hormonal signaling input and output is of key importance for understanding regulation of multicellular development. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack sensitivity or precision to visualize these. We developed a set of novel fluorescent reporters that allow sensitive and semi-quantitative readout of auxin responses at cellular resolution in Arabidopsis. These generic tools are suitable for any transformable plant species.
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50
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Larrieu A, Champion A, Legrand J, Lavenus J, Mast D, Brunoud G, Oh J, Guyomarc'h S, Pizot M, Farmer EE, Turnbull C, Vernoux T, Bennett MJ, Laplaze L. A fluorescent hormone biosensor reveals the dynamics of jasmonate signalling in plants. Nat Commun 2015; 6:6043. [PMID: 25592181 PMCID: PMC4338584 DOI: 10.1038/ncomms7043] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 12/05/2014] [Indexed: 01/26/2023] Open
Abstract
Activated forms of jasmonic acid (JA) are central signals coordinating plant responses to stresses, yet tools to analyse their spatial and temporal distribution are lacking. Here we describe a JA perception biosensor termed Jas9-VENUS that allows the quantification of dynamic changes in JA distribution in response to stress with high spatiotemporal sensitivity. We show that Jas9-VENUS abundance is dependent on bioactive JA isoforms, the COI1 co-receptor, a functional Jas motif and proteasome activity. We demonstrate the utility of Jas9-VENUS to analyse responses to JA in planta at a cellular scale, both quantitatively and dynamically. This included using Jas9-VENUS to determine the cotyledon-to-root JA signal velocities on wounding, revealing two distinct phases of JA activity in the root. Our results demonstrate the value of developing quantitative sensors such as Jas9-VENUS to provide high-resolution spatiotemporal data about hormone distribution in response to plant abiotic and biotic stresses. Jasmonate regulates multiple aspects of plant growth, development and stress responses. Here, Larrieu et al. develop a fluorescent biosensor that allows jasmonate perception to be monitored at previously unobtainable levels of spatiotemporal resolution in Arabidopsis.
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Affiliation(s)
- Antoine Larrieu
- 1] Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 69364 Lyon, France [2] Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Antony Champion
- 1] Institut de Recherche pour le Développement, Unité Mixte de Recherche Diversité Adaptation et Développement des plantes, 911 Avenue Agropolis, 34394 Montpellier, France [2] Laboratoire mixte international Adaptation des Plantes et microorganismes associés aux Stress Environnementaux, CP 18534 Dakar, Senegal
| | - Jonathan Legrand
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 69364 Lyon, France
| | - Julien Lavenus
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Diversité Adaptation et Développement des plantes, 911 Avenue Agropolis, 34394 Montpellier, France
| | - David Mast
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 69364 Lyon, France
| | - Géraldine Brunoud
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 69364 Lyon, France
| | - Jaesung Oh
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Soazig Guyomarc'h
- Université Montpellier 2, Unité Mixte de Recherche Diversité Adaptation et Développement des plantes, 34394 Montpellier, France
| | - Maxime Pizot
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Diversité Adaptation et Développement des plantes, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Edward E Farmer
- Department of Plant Molecular Biology, Université de Lausanne, 1015 Lausanne, Switzerland
| | - Colin Turnbull
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 69364 Lyon, France
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Laurent Laplaze
- 1] Institut de Recherche pour le Développement, Unité Mixte de Recherche Diversité Adaptation et Développement des plantes, 911 Avenue Agropolis, 34394 Montpellier, France [2] Laboratoire mixte international Adaptation des Plantes et microorganismes associés aux Stress Environnementaux, CP 18534 Dakar, Senegal
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