1
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Ragland CJ, Shih KY, Dinneny JR. Choreographing root architecture and rhizosphere interactions through synthetic biology. Nat Commun 2024; 15:1370. [PMID: 38355570 PMCID: PMC10866969 DOI: 10.1038/s41467-024-45272-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/18/2024] [Indexed: 02/16/2024] Open
Abstract
Climate change is driving extreme changes to the environment, posing substantial threats to global food security and bioenergy. Given the direct role of plant roots in mediating plant-environment interactions, engineering the form and function of root systems and their associated microbiota may mitigate these effects. Synthetic genetic circuits have enabled sophisticated control of gene expression in microbial systems for years and a surge of advances has heralded the extension of this approach to multicellular plant species. Targeting these tools to affect root structure, exudation, and microbe activity on root surfaces provide multiple strategies for the advancement of climate-ready crops.
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Affiliation(s)
- Carin J Ragland
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Y Shih
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
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2
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Verslues PE, Bailey-Serres J, Brodersen C, Buckley TN, Conti L, Christmann A, Dinneny JR, Grill E, Hayes S, Heckman RW, Hsu PK, Juenger TE, Mas P, Munnik T, Nelissen H, Sack L, Schroeder JI, Testerink C, Tyerman SD, Umezawa T, Wigge PA. Burning questions for a warming and changing world: 15 unknowns in plant abiotic stress. Plant Cell 2023; 35:67-108. [PMID: 36018271 PMCID: PMC9806664 DOI: 10.1093/plcell/koac263] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/21/2022] [Indexed: 05/08/2023]
Abstract
We present unresolved questions in plant abiotic stress biology as posed by 15 research groups with expertise spanning eco-physiology to cell and molecular biology. Common themes of these questions include the need to better understand how plants detect water availability, temperature, salinity, and rising carbon dioxide (CO2) levels; how environmental signals interface with endogenous signaling and development (e.g. circadian clock and flowering time); and how this integrated signaling controls downstream responses (e.g. stomatal regulation, proline metabolism, and growth versus defense balance). The plasma membrane comes up frequently as a site of key signaling and transport events (e.g. mechanosensing and lipid-derived signaling, aquaporins). Adaptation to water extremes and rising CO2 affects hydraulic architecture and transpiration, as well as root and shoot growth and morphology, in ways not fully understood. Environmental adaptation involves tradeoffs that limit ecological distribution and crop resilience in the face of changing and increasingly unpredictable environments. Exploration of plant diversity within and among species can help us know which of these tradeoffs represent fundamental limits and which ones can be circumvented by bringing new trait combinations together. Better defining what constitutes beneficial stress resistance in different contexts and making connections between genes and phenotypes, and between laboratory and field observations, are overarching challenges.
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Affiliation(s)
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA
| | - Craig Brodersen
- School of the Environment, Yale University, New Haven, Connecticut 06511, USA
| | - Thomas N Buckley
- Department of Plant Sciences, University of California, Davis, California 95616, USA
| | - Lucio Conti
- Department of Biosciences, University of Milan, Milan 20133, Italy
| | - Alexander Christmann
- School of Life Sciences, Technical University Munich, Freising-Weihenstephan 85354, Germany
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Erwin Grill
- School of Life Sciences, Technical University Munich, Freising-Weihenstephan 85354, Germany
| | - Scott Hayes
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Robert W Heckman
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Po-Kai Hsu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712, USA
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona 08193, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona 08028, Spain
| | - Teun Munnik
- Department of Plant Cell Biology, Green Life Sciences Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam NL-1098XH, The Netherlands
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, Ghent 9052, Belgium
| | - Lawren Sack
- Department of Ecology and Evolutionary Biology, Institute of the Environment and Sustainability, University of California, Los Angeles, California 90095, USA
| | - Julian I Schroeder
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Christa Testerink
- Laboratory of Plant Physiology, Plant Sciences Group, Wageningen University and Research, Wageningen 6708 PB, The Netherlands
| | - Stephen D Tyerman
- ARC Center Excellence, Plant Energy Biology, School of Agriculture Food and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
| | - Taishi Umezawa
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo 6708 PB, Japan
| | - Philip A Wigge
- Leibniz-Institut für Gemüse- und Zierpflanzenbau, Großbeeren 14979, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam 14476, Germany
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3
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LaRue T, Lindner H, Srinivas A, Exposito-Alonso M, Lobet G, Dinneny JR. Uncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platform. eLife 2022; 11:76968. [PMID: 36047575 PMCID: PMC9499532 DOI: 10.7554/elife.76968] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022] Open
Abstract
The plant kingdom contains a stunning array of complex morphologies easily observed above-ground, but more challenging to visualize below-ground. Understanding the magnitude of diversity in root distribution within the soil, termed root system architecture (RSA), is fundamental in determining how this trait contributes to species adaptation in local environments. Roots are the interface between the soil environment and the shoot system and therefore play a key role in anchorage, resource uptake, and stress resilience. Previously, we presented the GLO-Roots (Growth and Luminescence Observatory for Roots) system to study the RSA of soil-grown Arabidopsis thaliana plants from germination to maturity (Rellán-Álvarez et al., 2015). In this study, we present the automation of GLO-Roots using robotics and the development of image analysis pipelines in order to examine the temporal dynamic regulation of RSA and the broader natural variation of RSA in Arabidopsis, over time. These datasets describe the developmental dynamics of two independent panels of accessions and reveal highly complex and polygenic RSA traits that show significant correlation with climate variables of the accessions’ respective origins.
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Affiliation(s)
- Therese LaRue
- Department of Biology, Stanford University, Stanford, United States
| | - Heike Lindner
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Ankit Srinivas
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | | | - Guillaume Lobet
- Agrosphere Institute, Forschungszentrum Jülich, Jülich, Germany
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, United States
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4
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Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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5
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Brophy JAN, Magallon KJ, Duan L, Zhong V, Ramachandran P, Kniazev K, Dinneny JR. Synthetic genetic circuits as a means of reprogramming plant roots. Science 2022; 377:747-751. [PMID: 35951698 DOI: 10.1126/science.abo4326] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The shape of a plant's root system influences its ability to reach essential nutrients in the soil and to acquire water during drought. Progress in engineering plant roots to optimize water and nutrient acquisition has been limited by our capacity to design and build genetic programs that alter root growth in a predictable manner. We developed a collection of synthetic transcriptional regulators for plants that can be compiled to create genetic circuits. These circuits control gene expression by performing Boolean logic operations and can be used to predictably alter root structure. This work demonstrates the potential of synthetic genetic circuits to control gene expression across tissues and reprogram plant growth.
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Affiliation(s)
- Jennifer A N Brophy
- Department of Biology, Stanford University, Stanford, CA, USA.,Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Lina Duan
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Vivian Zhong
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Kiril Kniazev
- Department of Biology, Stanford University, Stanford, CA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA
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6
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Sun Y, Oh DH, Duan L, Ramachandran P, Ramirez A, Bartlett A, Tran KN, Wang G, Dassanayake M, Dinneny JR. Divergence in the ABA gene regulatory network underlies differential growth control. Nat Plants 2022; 8:549-560. [PMID: 35501452 DOI: 10.1038/s41477-022-01139-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The phytohormone abscisic acid (ABA) is a central regulator of acclimation to environmental stress; however, its contribution to differences in stress tolerance between species is unclear. To establish a comparative framework for understanding how stress hormone signalling pathways diverge across species, we studied the growth response of four Brassicaceae species to ABA treatment and generated transcriptomic and DNA affinity purification and sequencing datasets to construct a cross-species gene regulatory network (GRN) for ABA. Comparison of genes bound directly by ABA-responsive element binding factors suggests that cis-factors are most important for determining the target loci represented in the ABA GRN of a particular species. Using this GRN, we reveal how rewiring of growth hormone subnetworks contributes to stark differences in the response to ABA in the extremophyte Schrenkiella parvula. Our study provides a model for understanding how divergence in gene regulation can lead to species-specific physiological outcomes in response to hormonal cues.
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Affiliation(s)
- Ying Sun
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Dong-Ha Oh
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Lina Duan
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Andrea Ramirez
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Anna Bartlett
- Genomic Analysis Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Kieu-Nga Tran
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Guannan Wang
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA.
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7
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G. Viana W, Scharwies JD, Dinneny JR. Deconstructing the root system of grasses through an exploration of development, anatomy and function. Plant Cell Environ 2022; 45:602-619. [PMID: 35092025 PMCID: PMC9303260 DOI: 10.1111/pce.14270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 05/16/2023]
Abstract
Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.
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Affiliation(s)
| | | | - José R. Dinneny
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
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8
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Dickinson AJ, Zhang J, Luciano M, Wachsman G, Sandoval E, Schnermann M, Dinneny JR, Benfey PN. A plant lipocalin promotes retinal-mediated oscillatory lateral root initiation. Science 2021; 373:1532-1536. [PMID: 34446443 DOI: 10.1126/science.abf7461] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Alexandra J Dickinson
- Department of Biology, Duke University, Durham, NC, USA.,Department of Plant Biology, Carnegie Institute of Science, Stanford, CA, USA.,Department of Biology, Stanford University, Palo Alto, CA, USA.,Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC, USA.,Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | | | - Michael Luciano
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Guy Wachsman
- Department of Biology, Duke University, Durham, NC, USA.,Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC, USA
| | - Evan Sandoval
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Martin Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institute of Science, Stanford, CA, USA.,Department of Biology, Stanford University, Palo Alto, CA, USA
| | - Philip N Benfey
- Department of Biology, Duke University, Durham, NC, USA.,Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC, USA
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9
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Cuevas-Velazquez CL, Vellosillo T, Guadalupe K, Schmidt HB, Yu F, Moses D, Brophy JAN, Cosio-Acosta D, Das A, Wang L, Jones AM, Covarrubias AA, Sukenik S, Dinneny JR. Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells. Nat Commun 2021; 12:5438. [PMID: 34521831 DOI: 10.1101/2021.02.17.431712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/27/2021] [Indexed: 05/17/2023] Open
Abstract
Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.
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Affiliation(s)
- Cesar L Cuevas-Velazquez
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| | - Tamara Vellosillo
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Karina Guadalupe
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA
| | - Hermann Broder Schmidt
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Feng Yu
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA
| | - David Moses
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA
| | - Jennifer A N Brophy
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Dante Cosio-Acosta
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Alakananda Das
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Lingxin Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | | | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
| | - Shahar Sukenik
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA.
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
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10
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Cuevas-Velazquez CL, Vellosillo T, Guadalupe K, Schmidt HB, Yu F, Moses D, Brophy JAN, Cosio-Acosta D, Das A, Wang L, Jones AM, Covarrubias AA, Sukenik S, Dinneny JR. Intrinsically disordered protein biosensor tracks the physical-chemical effects of osmotic stress on cells. Nat Commun 2021; 12:5438. [PMID: 34521831 PMCID: PMC8440526 DOI: 10.1038/s41467-021-25736-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/27/2021] [Indexed: 12/15/2022] Open
Abstract
Cell homeostasis is perturbed when dramatic shifts in the external environment cause the physical-chemical properties inside the cell to change. Experimental approaches for dynamically monitoring these intracellular effects are currently lacking. Here, we leverage the environmental sensitivity and structural plasticity of intrinsically disordered protein regions (IDRs) to develop a FRET biosensor capable of monitoring rapid intracellular changes caused by osmotic stress. The biosensor, named SED1, utilizes the Arabidopsis intrinsically disordered AtLEA4-5 protein expressed in plants under water deficit. Computational modeling and in vitro studies reveal that SED1 is highly sensitive to macromolecular crowding. SED1 exhibits large and near-linear osmolarity-dependent changes in FRET inside living bacteria, yeast, plant, and human cells, demonstrating the broad utility of this tool for studying water-associated stress. This study demonstrates the remarkable ability of IDRs to sense the cellular environment across the tree of life and provides a blueprint for their use as environmentally-responsive molecular tools.
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Affiliation(s)
- Cesar L Cuevas-Velazquez
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
| | - Tamara Vellosillo
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Karina Guadalupe
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA
| | - Hermann Broder Schmidt
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Feng Yu
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA
| | - David Moses
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA
| | - Jennifer A N Brophy
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Dante Cosio-Acosta
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico
| | - Alakananda Das
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Lingxin Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | | | - Alejandra A Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, 62210, Mexico.
| | - Shahar Sukenik
- Center for Cellular and Biomolecular Machines (CCBM), University of California, Merced, CA, 95343, USA.
- Chemistry and Chemical Biology Program, University of California, Merced, CA, 95343, USA.
- Quantitative Systems Biology Program, University of California, Merced, CA, 95343, USA.
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA.
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11
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Friesner J, Colón‐Carmona A, Schnoes AM, Stepanova A, Mason GA, Macintosh GC, Ullah H, Baxter I, Callis J, Sierra‐Cajas K, Elliott K, Haswell ES, Zavala ME, Wildermuth M, Williams M, Ayalew M, Henkhaus N, Prunet N, Lemaux PG, Yadegari R, Amasino R, Hangarter R, Innes R, Brady S, Long T, Woodford‐Thomas T, May V, Sun Y, Dinneny JR. Broadening the impact of plant science through innovative, integrative, and inclusive outreach. Plant Direct 2021; 5:e00316. [PMID: 33870032 PMCID: PMC8045900 DOI: 10.1002/pld3.316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/26/2021] [Accepted: 02/28/2021] [Indexed: 05/04/2023]
Abstract
Population growth and climate change will impact food security and potentially exacerbate the environmental toll that agriculture has taken on our planet. These existential concerns demand that a passionate, interdisciplinary, and diverse community of plant science professionals is trained during the 21st century. Furthermore, societal trends that question the importance of science and expert knowledge highlight the need to better communicate the value of rigorous fundamental scientific exploration. Engaging students and the general public in the wonder of plants, and science in general, requires renewed efforts that take advantage of advances in technology and new models of funding and knowledge dissemination. In November 2018, funded by the National Science Foundation through the Arabidopsis Research and Training for the 21st century (ART 21) research coordination network, a symposium and workshop were held that included a diverse panel of students, scientists, educators, and administrators from across the US. The purpose of the workshop was to re-envision how outreach programs are funded, evaluated, acknowledged, and shared within the plant science community. One key objective was to generate a roadmap for future efforts. We hope that this document will serve as such, by providing a comprehensive resource for students and young faculty interested in developing effective outreach programs. We also anticipate that this document will guide the formation of community partnerships to scale up currently successful outreach programs, and lead to the design of future programs that effectively engage with a more diverse student body and citizenry.
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Affiliation(s)
- Joanna Friesner
- UC Davis & North American Arabidopsis Steering CommitteeAtlantaGAUSA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mary Williams
- American Society of Plant BiologistsGlasgowUnited Kingdom
| | | | | | | | | | | | | | | | | | | | - Terri Long
- North Carolina State UniversityDavisCAUSA
| | | | - Victoria May
- University of Washington in St LouisSt LouisMOUSA
| | - Ying Sun
- Stanford UniversityLas VegasNVUSA
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12
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Duan L, Pérez-Ruiz JM, Cejudo FJ, Dinneny JR. Characterization of CYCLOPHILLIN38 shows that a photosynthesis-derived systemic signal controls lateral root emergence. Plant Physiol 2021; 185:503-518. [PMID: 33721893 PMCID: PMC8133581 DOI: 10.1093/plphys/kiaa032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/29/2020] [Indexed: 05/10/2023]
Abstract
Photosynthesis in leaves generates fixed-carbon resources and essential metabolites that support sink tissues, such as roots. Two of these metabolites, sucrose and auxin, promote growth in root systems, but the explicit connection between photosynthetic activity and control of root architecture has not been explored. Through a mutant screen to identify pathways regulating root system architecture, we identified a mutation in the Arabidopsis thaliana CYCLOPHILIN 38 (CYP38) gene, which causes accumulation of pre-emergent stage lateral roots. CYP38 was previously reported to stabilize photosystem II (PSII) in chloroplasts. CYP38 expression is enriched in shoots, and grafting experiments show that the gene acts non-cell-autonomously to promote lateral root emergence. Growth of wild-type plants under low-light conditions phenocopies the cyp38 lateral root emergence defect, as does the inhibition of PSII-dependent electron transport or Nicotinamide adenine dinucleotide phosphate (NADPH) production. Importantly, these perturbations to photosynthetic activity rapidly suppress lateral root emergence, which is separate from their effects on shoot size. Supplementary exogenous sucrose largely rescued primary root (PR) growth in cyp38, but not lateral root growth. Auxin (indole-3-acetic acid (IAA)) biosynthesis from tryptophan is dependent on reductant generated during photosynthesis. Consistently, we found that wild-type seedlings grown under low light and cyp38 mutants have highly diminished levels of IAA in root tissues. IAA treatment rescued the cyp38 lateral root defect, revealing that photosynthesis promotes lateral root emergence partly through IAA biosynthesis. These data directly confirm the importance of CYP38-dependent photosynthetic activity in supporting root growth, and define the specific contributions of two metabolites in refining root architecture under light-limited conditions.
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Affiliation(s)
- Lina Duan
- Biology Department, Stanford University, Stanford, CA 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Juan Manuel Pérez-Ruiz
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Avda Américo Vespucio 49, 41092 Sevilla, Spain
| | - Francisco Javier Cejudo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and Consejo Superior de Investigaciones Científicas, Avda Américo Vespucio 49, 41092 Sevilla, Spain
| | - José R Dinneny
- Biology Department, Stanford University, Stanford, CA 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
- Author for communication:
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13
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Rui Y, Dinneny JR. A wall with integrity: surveillance and maintenance of the plant cell wall under stress. New Phytol 2020; 225:1428-1439. [PMID: 31486535 DOI: 10.1111/nph.16166] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 08/16/2019] [Indexed: 05/21/2023]
Abstract
The structural and functional integrity of the cell wall needs to be constantly monitored and fine-tuned to allow for growth while preventing mechanical failure. Many studies have advanced our understanding of the pathways that contribute to cell wall biosynthesis and how these pathways are regulated by external and internal cues. Recent evidence also supports a model in which certain aspects of the wall itself may act as growth-regulating signals. Molecular components of the signaling pathways that sense and maintain cell wall integrity have begun to be revealed, including signals arising in the wall, sensors that detect changes at the cell surface, and downstream signal transduction modules. Abiotic and biotic stress conditions provide new contexts for the study of cell wall integrity, but the nature and consequences of wall disruptions due to various stressors require further investigation. A deeper understanding of cell wall signaling will provide insights into the growth regulatory mechanisms that allow plants to survive in changing environments.
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Affiliation(s)
- Yue Rui
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
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14
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Abstract
Roots provide the primary mechanism that plants use to absorb water and nutrients from their environment. These functions are dependent on developmental mechanisms that direct root growth and branching into regions of soil where these resources are relatively abundant. Water is the most limiting factor for plant growth, and its availability is determined by the weather, soil structure, and salinity. In this review, we define the developmental pathways that regulate the direction of growth and branching pattern of the root system, which together determine the expanse of soil from which a plant can access water. The ability of plants to regulate development in response to the spatial distribution of water is a focus of many recent studies and provides a model for understanding how biological systems utilize positional cues to affect signaling and morphogenesis. A better understanding of these processes will inform approaches to improve crop water use efficiency to more sustainably feed a growing population.
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Affiliation(s)
- José R. Dinneny
- Department of Biology, Stanford University, Stanford, California 94305, USA
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15
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Waidmann S, Ruiz Rosquete M, Schöller M, Sarkel E, Lindner H, LaRue T, Petřík I, Dünser K, Martopawiro S, Sasidharan R, Novak O, Wabnik K, Dinneny JR, Kleine-Vehn J. Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots. Nat Commun 2019; 10:3540. [PMID: 31387989 PMCID: PMC6684572 DOI: 10.1038/s41467-019-11483-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/16/2019] [Indexed: 11/09/2022] Open
Abstract
Directional organ growth allows the plant root system to strategically cover its surroundings. Intercellular auxin transport is aligned with the gravity vector in the primary root tips, facilitating downward organ bending at the lower root flank. Here we show that cytokinin signaling functions as a lateral root specific anti-gravitropic component, promoting the radial distribution of the root system. We performed a genome-wide association study and reveal that signal peptide processing of Cytokinin Oxidase 2 (CKX2) affects its enzymatic activity and, thereby, determines the degradation of cytokinins in natural Arabidopsis thaliana accessions. Cytokinin signaling interferes with growth at the upper lateral root flank and thereby prevents downward bending. Our interdisciplinary approach proposes that two phytohormonal cues at opposite organ flanks counterbalance each other's negative impact on growth, suppressing organ growth towards gravity and allow for radial expansion of the root system.
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Affiliation(s)
- Sascha Waidmann
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Michel Ruiz Rosquete
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Maria Schöller
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Elizabeth Sarkel
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Heike Lindner
- Department of Biology, Stanford University, 260 Panama Street, Stanford, CA, 94305, USA
| | - Therese LaRue
- Department of Biology, Stanford University, 260 Panama Street, Stanford, CA, 94305, USA.,Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
| | - Ivan Petřík
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Kai Dünser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria
| | - Shanice Martopawiro
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Rashmi Sasidharan
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Ondrej Novak
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science of Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Autopista M-40, Km 38-Pozuelo de Alarcón, 28223, Madrid, Spain
| | - José R Dinneny
- Department of Biology, Stanford University, 260 Panama Street, Stanford, CA, 94305, USA.,Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
| | - Jürgen Kleine-Vehn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Vienna, Austria.
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16
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Zengler K, Hofmockel K, Baliga NS, Behie SW, Bernstein HC, Brown JB, Dinneny JR, Floge SA, Forry SP, Hess M, Jackson SA, Jansson C, Lindemann SR, Pett-Ridge J, Maranas C, Venturelli OS, Wallenstein MD, Shank EA, Northen TR. EcoFABs: advancing microbiome science through standardized fabricated ecosystems. Nat Methods 2019; 16:567-571. [PMID: 31227812 PMCID: PMC6733021 DOI: 10.1038/s41592-019-0465-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microbiomes play critical roles in ecosystems and human health, yet in most cases scientists lack standardized and reproducible model microbial communities. The development of fabricated microbial ecosystems, which we term EcoFABs, will provide such model systems for microbiome studies.
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Affiliation(s)
- Karsten Zengler
- Department of Pediatrics, University of California, San Diego, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Kirsten Hofmockel
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA, USA
- Departments of Microbiology and Biology, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Scott W Behie
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Hans C Bernstein
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- The Norwegian College of Fishery Science and Arctic Centre for Sustainable Energy, UiT-The Arctic University of Norway, Tromsø, Norway
| | - James B Brown
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Centre for Computational Biology, School of Biosciences, University of Birmingham, Birmingham, UK
- Statistics Department, University of California, Berkeley, Berkeley, CA, USA
- Preminon, LLC, Antioch, CA, USA
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Sheri A Floge
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | - Samuel P Forry
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Matthias Hess
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Scott A Jackson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Christer Jansson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN, USA
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Costas Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | | | - Matthew D Wallenstein
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Elizabeth A Shank
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- DOE Joint Genome Institute, Walnut Creek, CA, USA.
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17
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Abstract
New research reveals how low levels of salinity in soil inhibit a plant's ability to respond to shade through a signaling mechanism involving the plant stress hormone abscisic acid.
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Affiliation(s)
- Katie J Magallon
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA; Stanford University, Department of Biology, Stanford, CA 94305, USA.
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18
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Abstract
Sufficient water availability in the environment is critical for plant survival. Perception of water by plants is necessary to balance water uptake and water loss and to control plant growth. Plant physiology and soil science research have contributed greatly to our understanding of how water moves through soil, is taken up by roots, and moves to leaves where it is lost to the atmosphere by transpiration. Water uptake from the soil is affected by soil texture itself and soil water content. Hydraulic resistances for water flow through soil can be a major limitation for plant water uptake. Changes in water supply and water loss affect water potential gradients inside plants. Likewise, growth creates water potential gradients. It is known that plants respond to changes in these gradients. Water flow and loss are controlled through stomata and regulation of hydraulic conductance via aquaporins. When water availability declines, water loss is limited through stomatal closure and by adjusting hydraulic conductance to maintain cell turgor. Plants also adapt to changes in water supply by growing their roots towards water and through refinements to their root system architecture. Mechanosensitive ion channels, aquaporins, proteins that sense the cell wall and cell membrane environment, and proteins that change conformation in response to osmotic or turgor changes could serve as putative sensors. Future research is required to better understand processes in the rhizosphere during soil drying and how plants respond to spatial differences in water availability. It remains to be investigated how changes in water availability and water loss affect different tissues and cells in plants and how these biophysical signals are translated into chemical signals that feed into signaling pathways like abscisic acid response or organ development.
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Affiliation(s)
- Johannes Daniel Scharwies
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA, 94305, USA.
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA.
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19
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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20
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Orosa-Puente B, Leftley N, von Wangenheim D, Banda J, Srivastava AK, Hill K, Truskina J, Bhosale R, Morris E, Srivastava M, Kümpers B, Goh T, Fukaki H, Vermeer JEM, Vernoux T, Dinneny JR, French AP, Bishopp A, Sadanandom A, Bennett MJ. Root branching toward water involves posttranslational modification of transcription factor ARF7. Science 2018; 362:1407-1410. [PMID: 30573626 DOI: 10.1126/science.aau3956] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/06/2018] [Indexed: 01/01/2023]
Abstract
Plants adapt to heterogeneous soil conditions by altering their root architecture. For example, roots branch when in contact with water by using the hydropatterning response. We report that hydropatterning is dependent on auxin response factor ARF7. This transcription factor induces asymmetric expression of its target gene LBD16 in lateral root founder cells. This differential expression pattern is regulated by posttranslational modification of ARF7 with the small ubiquitin-like modifier (SUMO) protein. SUMOylation negatively regulates ARF7 DNA binding activity. ARF7 SUMOylation is required to recruit the Aux/IAA (indole-3-acetic acid) repressor protein IAA3. Blocking ARF7 SUMOylation disrupts IAA3 recruitment and hydropatterning. We conclude that SUMO-dependent regulation of auxin response controls root branching pattern in response to water availability.
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Affiliation(s)
| | - Nicola Leftley
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Daniel von Wangenheim
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Jason Banda
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | | | - Kristine Hill
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Jekaterina Truskina
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, F-69342, Lyon, France
| | - Rahul Bhosale
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Emily Morris
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | | | - Britta Kümpers
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Tatsuaki Goh
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Joop E M Vermeer
- Department of Plant and Microbial Biology, University of Zurich, CH-8008 Zurich, Switzerland
- Developmental Biology, Wageningen University and Research, Wageningen, Netherlands
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, F-69342, Lyon, France
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Andrew P French
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
- School of Computer Science, Jubilee Campus, University of Nottingham, Nottingham NG8 1BB, UK
| | - Anthony Bishopp
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK
| | - Ari Sadanandom
- Department of Biosciences, University of Durham, Durham DH1 3LE, UK.
| | - Malcolm J Bennett
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, UK.
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21
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Sechet J, Htwe S, Urbanowicz B, Agyeman A, Feng W, Ishikawa T, Colomes M, Kumar KS, Kawai‐Yamada M, Dinneny JR, O'Neill MA, Mortimer JC. Suppression of Arabidopsis GGLT1 affects growth by reducing the L-galactose content and borate cross-linking of rhamnogalacturonan-II. Plant J 2018; 96:1036-1050. [PMID: 30203879 PMCID: PMC6263843 DOI: 10.1111/tpj.14088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/14/2018] [Accepted: 08/20/2018] [Indexed: 05/16/2023]
Abstract
Boron is a micronutrient that is required for the normal growth and development of vascular plants, but its precise functions remain a subject of debate. One established role for boron is in the cell wall where it forms a diester cross-link between two monomers of the low-abundance pectic polysaccharide rhamnogalacturonan-II (RG-II). The inability of RG-II to properly assemble into a dimer results in the formation of cell walls with abnormal biochemical and biomechanical properties and has a severe impact on plant productivity. Here we describe the effects on RG-II structure and cross-linking and on the growth of plants in which the expression of a GDP-sugar transporter (GONST3/GGLT1) has been reduced. In the GGLT1-silenced plants the amount of L-galactose in side-chain A of RG-II is reduced by up to 50%. This leads to a reduction in the extent of RG-II cross-linking in the cell walls as well as a reduction in the stability of the dimer in the presence of calcium chelators. The silenced plants have a dwarf phenotype, which is rescued by growth in the presence of increased amounts of boric acid. Similar to the mur1 mutant, which also disrupts RG-II cross-linking, GGLT1-silenced plants display a loss of cell wall integrity under salt stress. We conclude that GGLT1 is probably the primary Golgi GDP-L-galactose transporter, and provides GDP-L-galactose for RG-II biosynthesis. We propose that the L-galactose residue is critical for RG-II dimerization and for the stability of the borate cross-link.
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Affiliation(s)
- Julien Sechet
- Joint BioEnergy InstituteEmeryvilleCA94608USA
- Biosciences AreaLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Present address:
INRAVersailles78000France
| | - Soe Htwe
- Joint BioEnergy InstituteEmeryvilleCA94608USA
- Biosciences AreaLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Breeanna Urbanowicz
- Complex Carbohydrate Research CenterThe University of GeorgiaAthensGA30602USA
| | - Abigail Agyeman
- Complex Carbohydrate Research CenterThe University of GeorgiaAthensGA30602USA
- Present address:
School of PharmacySouth UniversitySavannahGA31406USA
| | - Wei Feng
- Department of Plant BiologyCarnegie Institute for ScienceStanfordCA94305USA
| | - Toshiki Ishikawa
- Graduate School of Science and EngineeringSaitama UniversitySaitama338‐8570Japan
| | - Marianne Colomes
- Joint BioEnergy InstituteEmeryvilleCA94608USA
- Biosciences AreaLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Present address:
NutribioParis75440France
| | - Kavitha Satish Kumar
- Joint BioEnergy InstituteEmeryvilleCA94608USA
- Biosciences AreaLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Maki Kawai‐Yamada
- Graduate School of Science and EngineeringSaitama UniversitySaitama338‐8570Japan
| | - José R. Dinneny
- Department of Plant BiologyCarnegie Institute for ScienceStanfordCA94305USA
- Department of BiologyStanford UniversityStanfordCA94305USA
| | - Malcolm A. O'Neill
- Complex Carbohydrate Research CenterThe University of GeorgiaAthensGA30602USA
| | - Jenny C. Mortimer
- Joint BioEnergy InstituteEmeryvilleCA94608USA
- Biosciences AreaLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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22
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Cuevas-Velazquez CL, Dinneny JR. Organization out of disorder: liquid-liquid phase separation in plants. Curr Opin Plant Biol 2018; 45:68-74. [PMID: 29859470 DOI: 10.1016/j.pbi.2018.05.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/17/2018] [Accepted: 05/09/2018] [Indexed: 05/06/2023]
Abstract
Membraneless compartments are formed from the dynamic physical association of proteins and RNAs through liquid-liquid phase separation, and have recently emerged as an exciting new mechanism to explain the dynamic organization of biochemical processes in the cell. In this review, we provide an overview of the current knowledge of the process of phase separation in plants and other eukaryotes. We discuss specific examples of liquid-like membraneless compartments found in green plants, their composition, and the intriguing prevalence of proteins with intrinsically disordered domains. Finally, we speculate on the function of disordered proteins in regulating the formation of membraneless compartments and how their conformational flexibility may be important for molecular memory and for sensing perturbations in the physicochemical environment of the cell, particularly important processes in sessile organisms.
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Affiliation(s)
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
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23
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Wu R, Duan L, Pruneda-Paz JL, Oh DH, Pound M, Kay S, Dinneny JR. The 6xABRE Synthetic Promoter Enables the Spatiotemporal Analysis of ABA-Mediated Transcriptional Regulation. Plant Physiol 2018; 177:1650-1665. [PMID: 29884679 PMCID: PMC6084650 DOI: 10.1104/pp.18.00401] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 05/16/2018] [Indexed: 05/17/2023]
Abstract
The water stress-associated hormone abscisic acid (ABA) acts through a well-defined signal transduction cascade to mediate downstream transcriptional events important for acclimation to stress. Although ABA signaling is known to function in specific tissues to regulate root growth, little is understood regarding the spatial pattern of ABA-mediated transcriptional regulation. Here, we describe the construction and evaluation of an ABSCISIC ACID RESPONSIVE ELEMENT (ABRE)-based synthetic promoter reporter that reveals the transcriptional response of tissues to different levels of exogenous ABA and stresses. Genome-scale yeast one-hybrid screens complemented these approaches and revealed how promoter sequence and architecture affect the recruitment of diverse transcription factors (TFs) to the ABRE. Our analysis also revealed ABA-independent activity of the ABRE-reporter under nonstress conditions, with expression being enriched at the quiescent center and stem cell niche. We show that the WUSCHEL RELATED HOMEOBOX5 and NAC DOMAIN PROTEIN13 TFs regulate QC/SCN expression of the ABRE reporter, which highlights the convergence of developmental and DNA-damage signaling pathways onto this cis-element in the absence of water stress. This work establishes a tool to study the spatial pattern of ABA-mediated transcriptional regulation and a repertoire of TF-ABRE interactions that contribute to the developmental and environmental control of gene expression in roots.
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Affiliation(s)
- Rui Wu
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
- Temasek Lifesciences Laboratory, 117604, Singapore, Singapore
- National University of Singapore, Department of Biological Sciences, 117543, Singapore, Singapore
| | - Lina Duan
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - José L Pruneda-Paz
- University of California San Diego, Section of Cell and Developmental Biology, La Jolla, California 92093
| | - Dong-Ha Oh
- Louisiana State University, Department of Biological Sciences, Baton Rouge, Louisiana 70803
| | - Michael Pound
- University of Nottingham, School of Computer Science, Jubilee Campus, Nottingham, NG8 1BB, United Kingdom
| | - Steve Kay
- University of Southern California, The Keck School of Medicine, Los Angeles, California 90089
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
- Temasek Lifesciences Laboratory, 117604, Singapore, Singapore
- National University of Singapore, Department of Biological Sciences, 117543, Singapore, Singapore
- Stanford University, Department of Biology, Stanford, California 94305
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24
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Affiliation(s)
- José R. Dinneny
- The reviewer is at the Department of Biology, Stanford University, Stanford, CA 94305, USA
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25
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Abstract
A gene regulatory network (GRN) describes the hierarchical relationship between transcription factors, associated proteins, and their target genes. Studying GRNs allows us to understand how a plant's genotype and environment are integrated to regulate downstream physiological responses. Current efforts in plants have focused on defining the GRNs that regulate functions such as development and stress response and have been performed primarily in genetically tractable model plant species such as Arabidopsis thaliana. Future studies will likely focus on how GRNs function in non-model plants and change over evolutionary time to allow for adaptation to extreme environments. This broader understanding will inform efforts to engineer GRNs to create tailored crop traits.
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Affiliation(s)
- Ying Sun
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA
| | - José R Dinneny
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA, 94305, USA. .,Department of Plant Biology, Carnegie Institution for Science, 260 Panama St, Stanford, CA, 94305, USA.
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26
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Feng W, Kita D, Peaucelle A, Cartwright HN, Doan V, Duan Q, Liu MC, Maman J, Steinhorst L, Schmitz-Thom I, Yvon R, Kudla J, Wu HM, Cheung AY, Dinneny JR. The FERONIA Receptor Kinase Maintains Cell-Wall Integrity during Salt Stress through Ca 2+ Signaling. Curr Biol 2018; 28:666-675.e5. [PMID: 29456142 PMCID: PMC5894116 DOI: 10.1016/j.cub.2018.01.023] [Citation(s) in RCA: 370] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/06/2017] [Accepted: 01/10/2018] [Indexed: 01/09/2023]
Abstract
Cells maintain integrity despite changes in their mechanical properties elicited during growth and environmental stress. How cells sense their physical state and compensate for cell-wall damage is poorly understood, particularly in plants. Here we report that FERONIA (FER), a plasma-membrane-localized receptor kinase from Arabidopsis, is necessary for the recovery of root growth after exposure to high salinity, a widespread soil stress. The extracellular domain of FER displays tandem regions of homology with malectin, an animal protein known to bind diglucose in vitro and important for protein quality control in the endoplasmic reticulum. The presence of malectin-like domains in FER and related receptor kinases has led to widespread speculation that they interact with cell-wall polysaccharides and can potentially serve a wall-sensing function. Results reported here show that salinity causes softening of the cell wall and that FER is necessary to sense these defects. When this function is disrupted in the fer mutant, root cells explode dramatically during growth recovery. Similar defects are observed in the mur1 mutant, which disrupts pectin cross-linking. Furthermore, fer cell-wall integrity defects can be rescued by treatment with calcium and borate, which also facilitate pectin cross-linking. Sensing of these salinity-induced wall defects might therefore be a direct consequence of physical interaction between the extracellular domain of FER and pectin. FER-dependent signaling elicits cell-specific calcium transients that maintain cell-wall integrity during salt stress. These results reveal a novel extracellular toxicity of salinity, and identify FER as a sensor of damage to the pectin-associated wall.
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Affiliation(s)
- Wei Feng
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - Daniel Kita
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Lederle Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Alexis Peaucelle
- Institut Jean-Pierre Bourgin, UMR1318, Institut National pour la Recherche Agronomique-AgroParisTech, Saclay Plant Science, Route de St-Cyr, Versailles 78026, France; Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge CB2 1LR, UK
| | - Heather N Cartwright
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA
| | - Vinh Doan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Lederle Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Qiaohong Duan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Lederle Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Ming-Che Liu
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Lederle Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Jacob Maman
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Lederle Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Leonie Steinhorst
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster 48149, Germany
| | - Ina Schmitz-Thom
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster 48149, Germany
| | - Robert Yvon
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Lederle Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Jörg Kudla
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster, Schlossplatz 7, Münster 48149, Germany
| | - Hen-Ming Wu
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Lederle Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003, USA
| | - Alice Y Cheung
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Lederle Graduate Research Tower, 710 North Pleasant Street, Amherst, MA 01003, USA.
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA; Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA.
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27
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Abstract
A plant's form is an important determinant of its fitness and economic value. Here, we review strategies for producing plants with altered forms. Historically, the process of changing a plant's form has been slow in agriculture, requiring iterative rounds of growth and selection. We discuss modern techniques for identifying genes involved in the development of plant form and tools that will be needed to effectively design and engineer plants with altered forms. Synthetic genetic circuits are highlighted for their potential to generate novel plant forms. We emphasize understanding development as a prerequisite to engineering and discuss the potential role of computer models in translating knowledge about single genes or pathways into a more comprehensive understanding of development.
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Affiliation(s)
- Jennifer A N Brophy
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA
| | - Therese LaRue
- Stanford University, Department of Biology, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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28
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Pruitt RN, Joe A, Zhang W, Feng W, Stewart V, Schwessinger B, Dinneny JR, Ronald PC. A microbially derived tyrosine-sulfated peptide mimics a plant peptide hormone. New Phytol 2017; 215:725-736. [PMID: 28556915 PMCID: PMC5901733 DOI: 10.1111/nph.14609] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/18/2017] [Indexed: 05/13/2023]
Abstract
The biotrophic pathogen Xanthomonas oryzae pv. oryzae (Xoo) produces a sulfated peptide named RaxX, which shares similarity to peptides in the PSY (plant peptide containing sulfated tyrosine) family. We hypothesize that RaxX mimics the growth-stimulating activity of PSY peptides. Root length was measured in Arabidopsis and rice treated with synthetic RaxX peptides. We also used comparative genomic analyses and reactive oxygen species burst assays to evaluate the activity of RaxX and PSY peptides. Here we found that a synthetic sulfated RaxX derivative comprising 13 residues (RaxX13-sY), highly conserved between RaxX and PSY, induces root growth in Arabidopsis and rice in a manner similar to that triggered by PSY. We identified residues that are required for activation of immunity mediated by the rice XA21 receptor but that are not essential for root growth induced by PSY. Finally, we showed that a Xanthomonas strain lacking raxX is impaired in virulence. These findings suggest that RaxX serves as a molecular mimic of PSY peptides to facilitate Xoo infection and that XA21 has evolved the ability to recognize and respond specifically to the microbial form of the peptide.
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Affiliation(s)
- Rory N. Pruitt
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
- Feedstocks Division, Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Joe
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
- Feedstocks Division, Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Weiguo Zhang
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
| | - Wei Feng
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Valley Stewart
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
- Feedstocks Division, Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - José R. Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305, USA
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616, USA
- Feedstocks Division, Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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29
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Feldman MJ, Paul RE, Banan D, Barrett JF, Sebastian J, Yee MC, Jiang H, Lipka AE, Brutnell TP, Dinneny JR, Leakey ADB, Baxter I. Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria. PLoS Genet 2017. [PMID: 28644860 PMCID: PMC5507400 DOI: 10.1371/journal.pgen.1006841] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line population to assess how the genetic architecture of plant height is influenced by developmental queues, water availability and planting density. The non-destructive nature of plant height measurements has enabled us to monitor height throughout the plant life cycle in both field and controlled environments. We find that plant height is reduced under water limitation and high density planting and affected by growth environment (field vs. growth chamber). The results support a model where plant height is a heritable, polygenic trait and that the major genetic loci that influence plant height function independent of growth environment. The identity and contribution of loci that influence height changes dynamically throughout development and the reduction of growth observed in water limited environments is a consequence of delayed progression through the genetic program which establishes plant height in Setaria. In this population, alleles inherited from the weedy S. viridis parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated S. italica parent collectively act to increase plant height later in development. Growth is a dynamic process that responds to a changing environment. Most of the methods that we have for measuring are static and collecting information throughout an organisms lifecycle is labor and cost prohibitive. Advances in imaging and robotics technology have enabled novel approaches to understanding how plants adapt to the environment. Using the model grass Setaria and new methods for measuring parameters from images, we investigate the genetic architecture of plant height in response to water availability and planting density. Height is one of the most influential components of plant architecture, determining tradeoffs between competition and resource allocation and is an important trait for boosting yields. The non-destructive nature of plant height measurements has enabled us to monitor growth throughout the plant life cycle in both field and controlled environments. We identified several loci controlling height in a population derived from a wild strain of Setaria viridis and its domesticated relative Setaria italica, as well as the developmental time in which these loci act. In this population, alleles inherited from the wild parent act to increase plant height early, whereas a larger number of small effect alleles inherited from the domesticated parent collectively act to increase plant height later in development.
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Affiliation(s)
- Max J. Feldman
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Rachel E. Paul
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Darshi Banan
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jennifer F. Barrett
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Jose Sebastian
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Muh-Ching Yee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Thomas P. Brutnell
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - José R. Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Andrew D. B. Leakey
- Department of Plant Biology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- USDA-ARS, Plant Genetics Research Unit, St. Louis, Missouri, United States of America
- * E-mail:
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30
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Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM, Owen MR, Band LR, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ. Root hydrotropism is controlled via a cortex-specific growth mechanism. Nat Plants 2017; 3:17057. [PMID: 28481327 DOI: 10.1038/nplants.2017.57] [Citation(s) in RCA: 134] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 03/23/2017] [Indexed: 05/24/2023]
Abstract
Plants can acclimate by using tropisms to link the direction of growth to environmental conditions. Hydrotropism allows roots to forage for water, a process known to depend on abscisic acid (ABA) but whose molecular and cellular basis remains unclear. Here we show that hydrotropism still occurs in roots after laser ablation removed the meristem and root cap. Additionally, targeted expression studies reveal that hydrotropism depends on the ABA signalling kinase SnRK2.2 and the hydrotropism-specific MIZ1, both acting specifically in elongation zone cortical cells. Conversely, hydrotropism, but not gravitropism, is inhibited by preventing differential cell-length increases in the cortex, but not in other cell types. We conclude that root tropic responses to gravity and water are driven by distinct tissue-based mechanisms. In addition, unlike its role in root gravitropism, the elongation zone performs a dual function during a hydrotropic response, both sensing a water potential gradient and subsequently undergoing differential growth.
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Affiliation(s)
- Daniela Dietrich
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Lei Pang
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Akie Kobayashi
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - John A Fozard
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Véronique Boudolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark 927), 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052 Ghent, Belgium
| | - Rahul Bhosale
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark 927), 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052 Ghent, Belgium
| | - Regina Antoni
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Tuan Nguyen
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK
| | - Sotaro Hiratsuka
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Nobuharu Fujii
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Yutaka Miyazawa
- Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Tae-Woong Bae
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Darren M Wells
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Markus R Owen
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Centre for Mathematical Medicine &Biology, University of Nottingham, Nottingham NG7 2RD, UK
| | - Leah R Band
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Centre for Mathematical Medicine &Biology, University of Nottingham, Nottingham NG7 2RD, UK
| | - Rosemary J Dyson
- School of Mathematics, University of Birmingham, Birmingham B15 2TT, UK
| | - Oliver E Jensen
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- School of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - John R King
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Centre for Mathematical Medicine &Biology, University of Nottingham, Nottingham NG7 2RD, UK
| | - Saoirse R Tracy
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Craig J Sturrock
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Sacha J Mooney
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Jeremy A Roberts
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Rishikesh P Bhalerao
- Department of Forest Genetics and Plant Physiology, SLU, S-901 83 Umea, Sweden
- College of Science, KSU, Riyadh, Saudi Arabia
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022 Valencia, Spain
| | - Akira Nagatani
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichiroh Hosokawa
- Graduate School of Materials Science, Nara Institute of Science &Technology, Ikoma 630-0101, Japan
| | - Tobias I Baskin
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Biology Department, University of Massachusetts, Amherst, Massachusetts 01003-9297, USA
| | - Tony P Pridmore
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark 927), 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052 Ghent, Belgium
| | - Hideyuki Takahashi
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
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31
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Dietrich D, Pang L, Kobayashi A, Fozard JA, Boudolf V, Bhosale R, Antoni R, Nguyen T, Hiratsuka S, Fujii N, Miyazawa Y, Bae TW, Wells DM, Owen MR, Band LR, Dyson RJ, Jensen OE, King JR, Tracy SR, Sturrock CJ, Mooney SJ, Roberts JA, Bhalerao RP, Dinneny JR, Rodriguez PL, Nagatani A, Hosokawa Y, Baskin TI, Pridmore TP, De Veylder L, Takahashi H, Bennett MJ. Root hydrotropism is controlled via a cortex-specific growth mechanism. Nat Plants 2017; 3:965-972. [PMID: 28481327 DOI: 10.1038/s41477-017-0064-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/27/2017] [Indexed: 05/24/2023]
Abstract
Plants can acclimate by using tropisms to link the direction of growth to environmental conditions. Hydrotropism allows roots to forage for water, a process known to depend on abscisic acid (ABA) but whose molecular and cellular basis remains unclear. Here we show that hydrotropism still occurs in roots after laser ablation removed the meristem and root cap. Additionally, targeted expression studies reveal that hydrotropism depends on the ABA signalling kinase SnRK2.2 and the hydrotropism-specific MIZ1, both acting specifically in elongation zone cortical cells. Conversely, hydrotropism, but not gravitropism, is inhibited by preventing differential cell-length increases in the cortex, but not in other cell types. We conclude that root tropic responses to gravity and water are driven by distinct tissue-based mechanisms. In addition, unlike its role in root gravitropism, the elongation zone performs a dual function during a hydrotropic response, both sensing a water potential gradient and subsequently undergoing differential growth.
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Affiliation(s)
- Daniela Dietrich
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Lei Pang
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Akie Kobayashi
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - John A Fozard
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Véronique Boudolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark 927), 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052 Ghent, Belgium
| | - Rahul Bhosale
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark 927), 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052 Ghent, Belgium
| | - Regina Antoni
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
| | - Tuan Nguyen
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK
| | - Sotaro Hiratsuka
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Nobuharu Fujii
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Yutaka Miyazawa
- Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Tae-Woong Bae
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Darren M Wells
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Markus R Owen
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Centre for Mathematical Medicine &Biology, University of Nottingham, Nottingham NG7 2RD, UK
| | - Leah R Band
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Centre for Mathematical Medicine &Biology, University of Nottingham, Nottingham NG7 2RD, UK
| | - Rosemary J Dyson
- School of Mathematics, University of Birmingham, Birmingham B15 2TT, UK
| | - Oliver E Jensen
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- School of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - John R King
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Centre for Mathematical Medicine &Biology, University of Nottingham, Nottingham NG7 2RD, UK
| | - Saoirse R Tracy
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Craig J Sturrock
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Sacha J Mooney
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Agricultural and Environmental Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Jeremy A Roberts
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Rishikesh P Bhalerao
- Department of Forest Genetics and Plant Physiology, SLU, S-901 83 Umea, Sweden
- College of Science, KSU, Riyadh, Saudi Arabia
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, California 94305, USA
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022 Valencia, Spain
| | - Akira Nagatani
- Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Yoichiroh Hosokawa
- Graduate School of Materials Science, Nara Institute of Science &Technology, Ikoma 630-0101, Japan
| | - Tobias I Baskin
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Biology Department, University of Massachusetts, Amherst, Massachusetts 01003-9297, USA
| | - Tony P Pridmore
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, (Technologiepark 927), 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, (Technologiepark 927), 9052 Ghent, Belgium
| | - Hideyuki Takahashi
- Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, UK
- Plant &Crop Sciences, School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
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32
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Sebastian J, Yee MC, Goudinho Viana W, Rellán-Álvarez R, Feldman M, Priest HD, Trontin C, Lee T, Jiang H, Baxter I, Mockler TC, Hochholdinger F, Brutnell TP, Dinneny JR. Grasses suppress shoot-borne roots to conserve water during drought. Proc Natl Acad Sci U S A 2016; 113:8861-8866. [PMID: 27422554 DOI: 10.1073/pnas.160421113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C4 grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.
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Affiliation(s)
- Jose Sebastian
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305
| | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305
| | - Willian Goudinho Viana
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305; Coordination for the Improvement of Higher Education Personnel (CAPES) Foundation, Ministry of Education of Brazil, Brasilia-DF 70.040-020, Brazil
| | - Rubén Rellán-Álvarez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305; Unidad de Genómica Avanzada, Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36821 Irapuato, Mexico
| | - Max Feldman
- Donald Danforth Plant Science Center, St. Louis, MO 63162
| | - Henry D Priest
- Donald Danforth Plant Science Center, St. Louis, MO 63162
| | - Charlotte Trontin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305
| | - Tak Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, MO 63162
| | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO 63162; Plant Physiology and Genetics Research, Agricultural Research Unit, US Department of Agriculture, St. Louis, MO 63132
| | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO 63162
| | - Frank Hochholdinger
- Crop Functional Genomics, Institute of Crop Science and Resource Conservation, University of Bonn, D-53113 Bonn, Germany
| | | | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305;
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33
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Feng W, Lindner H, Robbins NE, Dinneny JR. Growing Out of Stress: The Role of Cell- and Organ-Scale Growth Control in Plant Water-Stress Responses. Plant Cell 2016; 28:1769-82. [PMID: 27503468 PMCID: PMC5006702 DOI: 10.1105/tpc.16.00182] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/20/2016] [Accepted: 08/07/2016] [Indexed: 05/20/2023]
Abstract
Water is the most limiting resource on land for plant growth, and its uptake by plants is affected by many abiotic stresses, such as salinity, cold, heat, and drought. While much research has focused on exploring the molecular mechanisms underlying the cellular signaling events governing water-stress responses, it is also important to consider the role organismal structure plays as a context for such responses. The regulation of growth in plants occurs at two spatial scales: the cell and the organ. In this review, we focus on how the regulation of growth at these different spatial scales enables plants to acclimate to water-deficit stress. The cell wall is discussed with respect to how the physical properties of this structure affect water loss and how regulatory mechanisms that affect wall extensibility maintain growth under water deficit. At a higher spatial scale, the architecture of the root system represents a highly dynamic physical network that facilitates access of the plant to a heterogeneous distribution of water in soil. We discuss the role differential growth plays in shaping the structure of this system and the physiological implications of such changes.
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Affiliation(s)
- Wei Feng
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Heike Lindner
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
| | - Neil E Robbins
- Department of Biology, Stanford University, Stanford, California 94305
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305
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34
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Abstract
The plant root system traverses one of the most complex environments on earth. Understanding how roots support plant life on land requires knowing how soil properties affect the availability of nutrients and water and how roots manipulate the soil environment to optimize acquisition of these resources. Imaging of roots in soil allows the integrated analysis and modeling of environmental interactions occurring at micro- to macroscales. Advances in phenotyping of root systems is driving innovation in cross-platform-compatible methods for data analysis. Root systems acclimate to the environment through architectural changes that act at the root-type level as well as through tissue-specific changes that affect the metabolic needs of the root and the efficiency of nutrient uptake. A molecular understanding of the signaling mechanisms that guide local and systemic signaling is providing insight into the regulatory logic of environmental responses and has identified points where crosstalk between pathways occurs.
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Affiliation(s)
- Rubén Rellán-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36821, Mexico;
| | - Guillaume Lobet
- PhytoSYSTEMS, University of Liège, 4000 Liège, Belgium;
- Institut für Bio- und Geowissenschaften: Agrosphäre, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305;
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35
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Affiliation(s)
- Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Rebecca Bart
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
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36
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Rellán-Álvarez R, Lobet G, Lindner H, Pradier PL, Sebastian J, Yee MC, Geng Y, Trontin C, LaRue T, Schrager-Lavelle A, Haney CH, Nieu R, Maloof J, Vogel JP, Dinneny JR. GLO-Roots: an imaging platform enabling multidimensional characterization of soil-grown root systems. eLife 2015; 4:e07597. [PMID: 26287479 PMCID: PMC4589753 DOI: 10.7554/elife.07597] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/18/2015] [Indexed: 12/16/2022] Open
Abstract
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction, and metabolic activity that define a dynamic physical network. Current methods for analyzing root biology balance physiological relevance with imaging capability. To bridge this divide, we developed an integrated-imaging system called Growth and Luminescence Observatory for Roots (GLO-Roots) that uses luminescence-based reporters to enable studies of root architecture and gene expression patterns in soil-grown, light-shielded roots. We have developed image analysis algorithms that allow the spatial integration of soil properties, gene expression, and root system architecture traits. We propose GLO-Roots as a system that has great utility in presenting environmental stimuli to roots in ways that evoke natural adaptive responses and in providing tools for studying the multi-dimensional nature of such processes.
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Affiliation(s)
- Rubén Rellán-Álvarez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | | | - Heike Lindner
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Pierre-Luc Pradier
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Jose Sebastian
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Muh-Ching Yee
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Yu Geng
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
- Department of Energy, Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - Charlotte Trontin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Therese LaRue
- Department of Biology, Stanford University, Stanford, United States
| | | | - Cara H Haney
- Department of Genetics, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Rita Nieu
- Western Regional Research Center, United States Department of Agriculture, Albany, United States
| | - Julin Maloof
- Department of Plant Biology, University of California, Davis, Davis, United States
| | - John P Vogel
- Department of Energy, Department of Energy Joint Genome Institute, Walnut Creek, United States
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
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37
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Abstract
Water is fundamental to plant life, but the mechanisms by which plant roots sense and respond to variations in water availability in the soil are poorly understood. Many studies of responses to water deficit have focused on large-scale effects of this stress, but have overlooked responses at the sub-organ or cellular level that give rise to emergent whole-plant phenotypes. We have recently discovered hydropatterning, an adaptive environmental response in which roots position new lateral branches according to the spatial distribution of available water across the circumferential axis. This discovery illustrates that roots are capable of sensing and responding to water availability at spatial scales far lower than those normally studied for such processes. This review will explore how roots respond to water availability with an emphasis on what is currently known at different spatial scales. Beginning at the micro-scale, there is a discussion of water physiology at the cellular level and proposed sensory mechanisms cells use to detect osmotic status. The implications of these principles are then explored in the context of cell and organ growth under non-stress and water-deficit conditions. Following this, several adaptive responses employed by roots to tailor their functionality to the local moisture environment are discussed, including patterning of lateral root development and generation of hydraulic barriers to limit water loss. We speculate that these micro-scale responses are necessary for optimal functionality of the root system in a heterogeneous moisture environment, allowing for efficient water uptake with minimal water loss during periods of drought.
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Affiliation(s)
- Neil E Robbins
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA
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38
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Abstract
Water is fundamental to plant life, but the mechanisms by which plant roots sense and respond to variations in water availability in the soil are poorly understood. Many studies of responses to water deficit have focused on large-scale effects of this stress, but have overlooked responses at the sub-organ or cellular level that give rise to emergent whole-plant phenotypes. We have recently discovered hydropatterning, an adaptive environmental response in which roots position new lateral branches according to the spatial distribution of available water across the circumferential axis. This discovery illustrates that roots are capable of sensing and responding to water availability at spatial scales far lower than those normally studied for such processes. This review will explore how roots respond to water availability with an emphasis on what is currently known at different spatial scales. Beginning at the micro-scale, there is a discussion of water physiology at the cellular level and proposed sensory mechanisms cells use to detect osmotic status. The implications of these principles are then explored in the context of cell and organ growth under non-stress and water-deficit conditions. Following this, several adaptive responses employed by roots to tailor their functionality to the local moisture environment are discussed, including patterning of lateral root development and generation of hydraulic barriers to limit water loss. We speculate that these micro-scale responses are necessary for optimal functionality of the root system in a heterogeneous moisture environment, allowing for efficient water uptake with minimal water loss during periods of drought.
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Affiliation(s)
- Neil E Robbins
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA
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39
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Dinneny JR. Traversing organizational scales in plant salt-stress responses. Curr Opin Plant Biol 2015; 23:70-5. [PMID: 25449729 DOI: 10.1016/j.pbi.2014.10.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 05/07/2023]
Abstract
Modern society has developed in large part due to our ability to reliably grow plants for food and renewable resources. Predicted increases in environmental variability will impact agricultural productivity and may have extensive secondary effects on the stability of our society. Thus, a concerted effort to understand plant response strategies to stress is needed. High salinity is an agriculturally important environmental stress and generates complex effects on the physiology of the plant. The abiotic-stress-associated hormone, abscisic acid (ABA), mediates a major component of this response. I highlight recent work studying salt-stress responses at different spatial and organizational scales from the action of ABA in specific cell types to global networks of proteins that predict critical regulatory events during acclimation.
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40
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Abstract
The root endodermis is characterized by the Casparian strip and by the suberin lamellae, two hydrophobic barriers that restrict the free diffusion of molecules between the inner cell layers of the root and the outer environment. The presence of these barriers and the position of the endodermis between the inner and outer parts of the root require that communication between these two domains acts through the endodermis. Recent work on hormone signaling, propagation of calcium waves, and plant-fungal symbiosis has provided evidence in support of the hypothesis that the endodermis acts as a signaling center. The endodermis is also a unique mechanical barrier to organogenesis, which must be overcome through chemical and mechanical cross talk between cell layers to allow for development of new lateral organs while maintaining its barrier functions. In this review, we discuss recent findings regarding these two important aspects of the endodermis.
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Affiliation(s)
- Neil E Robbins
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (N.E.R., C.T., L.D., J.R.D.); andDepartment of Biology, Stanford University, Stanford, California 94305 (N.E.R.)
| | - Charlotte Trontin
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (N.E.R., C.T., L.D., J.R.D.); andDepartment of Biology, Stanford University, Stanford, California 94305 (N.E.R.)
| | - Lina Duan
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (N.E.R., C.T., L.D., J.R.D.); andDepartment of Biology, Stanford University, Stanford, California 94305 (N.E.R.)
| | - José R Dinneny
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305 (N.E.R., C.T., L.D., J.R.D.); andDepartment of Biology, Stanford University, Stanford, California 94305 (N.E.R.)
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41
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Abstract
Setaria viridis has recently emerged as a promising genetic model system to study diverse aspects of monocot biology. While the post-germination life cycle of S. viridis is approximately 8 weeks long, the prolonged dormancy of freshly harvested seeds can more than double the total time required between successive generations. Here we describe methods that promote seed germination in S. viridis. Our results demonstrate that treating S. viridis seeds with liquid smoke or a GA3 and KNO3 solution improves germination rates to 90% or higher even in seeds that are 6 days post-harvest with similar results obtained whether seeds are planted in soil or on gel-based media. Importantly, we show that these treatments have no significant effect on the growth of the adult plant. We have tested these treatments on diverse S. viridis accessions and show variation in their response. The methods described here will help advance research using this model grass species by increasing the pace at which successive generations of plants can be analyzed.
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Affiliation(s)
- Jose Sebastian
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Mandy Ka Wong
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - Evan Tang
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
| | - José R. Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California, United States of America
- * E-mail:
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42
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Dinneny JR. A gateway with a guard: how the endodermis regulates growth through hormone signaling. Plant Sci 2014; 214:14-9. [PMID: 24268159 DOI: 10.1016/j.plantsci.2013.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 05/08/2023]
Abstract
The endodermis is a defining feature of plant roots and is most widely studied as a differentially permeable barrier limiting solute uptake from the soil into the vascular stream. Recent work has revealed that this inner cell layer is also an important signaling center for hormone-mediated control of growth. Auxin, gibberellic acid, abscisic acid and strigalactones all appear to depend on the endodermis to regulate root biology and point to this cell type as having important inter-cell layer regulatory activity, as well. In this review I discuss recent work detailing the importance of the endodermis in growth control and how this function is affected during responses to the environment.
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Affiliation(s)
- José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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43
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Geng Y, Wu R, Wee CW, Xie F, Wei X, Chan PMY, Tham C, Duan L, Dinneny JR. A spatio-temporal understanding of growth regulation during the salt stress response in Arabidopsis. Plant Cell 2013; 25:2132-54. [PMID: 23898029 PMCID: PMC3723617 DOI: 10.1105/tpc.113.112896] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 06/05/2013] [Accepted: 06/11/2013] [Indexed: 05/18/2023]
Abstract
Plant environmental responses involve dynamic changes in growth and signaling, yet little is understood as to how progress through these events is regulated. Here, we explored the phenotypic and transcriptional events involved in the acclimation of the Arabidopsis thaliana seedling root to a rapid change in salinity. Using live-imaging analysis, we show that growth is dynamically regulated with a period of quiescence followed by recovery then homeostasis. Through the use of a new high-resolution spatio-temporal transcriptional map, we identify the key hormone signaling pathways that regulate specific transcriptional programs, predict their spatial domain of action, and link the activity of these pathways to the regulation of specific phases of growth. We use tissue-specific approaches to suppress the abscisic acid (ABA) signaling pathway and demonstrate that ABA likely acts in select tissue layers to regulate spatially localized transcriptional programs and promote growth recovery. Finally, we show that salt also regulates many tissue-specific and time point-specific transcriptional responses that are expected to modify water transport, Casparian strip formation, and protein translation. Together, our data reveal a sophisticated assortment of regulatory programs acting together to coordinate spatially patterned biological changes involved in the immediate and long-term response to a stressful shift in environment.
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Affiliation(s)
- Yu Geng
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
- Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Rui Wu
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
- Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Choon Wei Wee
- Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
| | - Fei Xie
- Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
| | - Xueliang Wei
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
| | - Penny Mei Yeen Chan
- Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Cliff Tham
- Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
| | - Lina Duan
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
- Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - José R. Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
- Temasek Lifesciences Laboratory, National University of Singapore, Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
- Address correspondence to
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44
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Duan L, Dietrich D, Ng CH, Chan PMY, Bhalerao R, Bennett MJ, Dinneny JR. Endodermal ABA signaling promotes lateral root quiescence during salt stress in Arabidopsis seedlings. Plant Cell 2013; 25:324-41. [PMID: 23341337 PMCID: PMC3584545 DOI: 10.1105/tpc.112.107227] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/19/2012] [Accepted: 12/30/2012] [Indexed: 05/18/2023]
Abstract
The endodermal tissue layer is found in the roots of vascular plants and functions as a semipermeable barrier, regulating the transport of solutes from the soil into the vascular stream. As a gateway for solutes, the endodermis may also serve as an important site for sensing and responding to useful or toxic substances in the environment. Here, we show that high salinity, an environmental stress widely impacting agricultural land, regulates growth of the seedling root system through a signaling network operating primarily in the endodermis. We report that salt stress induces an extended quiescent phase in postemergence lateral roots (LRs) whereby the rate of growth is suppressed for several days before recovery begins. Quiescence is correlated with sustained abscisic acid (ABA) response in LRs and is dependent upon genes necessary for ABA biosynthesis, signaling, and transcriptional regulation. We use a tissue-specific strategy to identify the key cell layers where ABA signaling acts to regulate growth. In the endodermis, misexpression of the ABA insensitive1-1 mutant protein, which dominantly inhibits ABA signaling, leads to a substantial recovery in LR growth under salt stress conditions. Gibberellic acid signaling, which antagonizes the ABA pathway, also acts primarily in the endodermis, and we define the crosstalk between these two hormones. Our results identify the endodermis as a gateway with an ABA-dependent guard, which prevents root growth into saline environments.
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Affiliation(s)
- Lina Duan
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
- Temasek Lifesciences Laboratory, National University of Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, 117604, Singapore
| | - Daniela Dietrich
- Plant Sciences Division, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Chong Han Ng
- Temasek Lifesciences Laboratory, National University of Singapore, 117604, Singapore
| | - Penny Mei Yeen Chan
- Temasek Lifesciences Laboratory, National University of Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, 117604, Singapore
| | - Rishikesh Bhalerao
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, S-901 83 Umea, Sweden
| | - Malcolm J. Bennett
- Plant Sciences Division, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - José R. Dinneny
- Carnegie Institution for Science, Department of Plant Biology, Stanford, California 94305
- Temasek Lifesciences Laboratory, National University of Singapore, 117604, Singapore
- Department of Biological Sciences, National University of Singapore, 117604, Singapore
- Address correspondence to
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45
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Emami S, Yee MC, Dinneny JR. A robust family of Golden Gate Agrobacterium vectors for plant synthetic biology. Front Plant Sci 2013; 4:339. [PMID: 24032037 PMCID: PMC3759027 DOI: 10.3389/fpls.2013.00339] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 08/13/2013] [Indexed: 05/18/2023]
Abstract
Tools that allow for rapid, accurate and inexpensive assembly of multi-component combinatorial libraries of DNA for transformation into plants will accelerate the progress of synthetic biology research. Recent innovations in molecular cloning methods has vastly expanded the repertoire with which plant biologists can engineer a transgene. Here we describe a new set of binary vectors for use in Agrobacterium-mediated plant transformation that utilizes the Golden-Gate Cloning approach. Our optimized protocol facilitates the rapid and inexpensive generation of multi-component transgenes for later introduction into plants.
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Affiliation(s)
| | | | - José R. Dinneny
- *Correspondence: José R. Dinneny, Department of Plant Biology, Carnegie Institution for Science, 260 Panama Street, Stanford, CA 94305, USA e-mail:
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Wee CW, Dinneny JR. Tools for high-spatial and temporal-resolution analysis of environmental responses in plants. Biotechnol Lett 2010; 32:1361-71. [PMID: 20502944 DOI: 10.1007/s10529-010-0307-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 05/10/2010] [Indexed: 01/09/2023]
Abstract
Understanding how plants cope with environmental change requires a spatiotemporal perspective. In this review, we highlight recent work which has led to the development and use of novel tools for the high spatial and temporal-resolution analysis of the plant-environment interaction. FACS-based transcriptome and immunoprecipitation-based translatome data sets have provided an important foundation for the analysis of the transcriptional and translational control of environmental responses in each tissue layer of the plant. Complementary approaches, based on a proteomic toolkit, have provided insight into the biological response of Arabidopsis to NaCl and the relationship between transcript and protein levels. The development and adaptation of biosensors and ion-specific dyes provides the capacity to visualize changes in the transport and accumulation of metabolites and small molecules such as sugars, Na(+) and Ca(2+) at the cellular level. Finally, live-imaging approaches coupled with automated image-analysis algorithms are revealing new levels of dynamism and plasticity in the response to light and gravity. Together, these tools will provide a more comprehensive understanding of environmental responses in plants, which will aide in the development of new crop varieties for sustainable agriculture.
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Affiliation(s)
- Choon W Wee
- Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Republic of Singapore
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Orlando DA, Brady SM, Koch JD, Dinneny JR, Benfey PN. Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment. Methods Mol Biol 2009; 553:57-77. [PMID: 19588101 DOI: 10.1007/978-1-60327-563-7_4] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A series of large-scale Arabidopsis thaliana microarray expression experiments profiling genome-wide expression across different developmental stages, cell types, and environmental conditions have resulted in tremendous amounts of gene expression data. This gene expression is the output of complex transcriptional regulatory networks and provides a starting point for identifying the dominant transcriptional regulatory modules acting within the plant. Highly co-expressed groups of genes are likely to be regulated by similar transcription factors. Therefore, finding these co-expressed groups can reduce the dimensionality of complex expression data into a set of dominant transcriptional regulatory modules. Determining the biological significance of these patterns is an informatics challenge and has required the development of new methods. Using these new methods we can begin to understand the biological information contained within large-scale expression data sets.
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Brady SM, Orlando DA, Lee JY, Wang JY, Koch J, Dinneny JR, Mace D, Ohler U, Benfey PN. A high-resolution root spatiotemporal map reveals dominant expression patterns. Science 2007; 318:801-6. [PMID: 17975066 DOI: 10.1126/science.1146265] [Citation(s) in RCA: 779] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transcriptional programs that regulate development are exquisitely controlled in space and time. Elucidating these programs that underlie development is essential to understanding the acquisition of cell and tissue identity. We present microarray expression profiles of a high-resolution set of developmental time points within a single Arabidopsis root and a comprehensive map of nearly all root cell types. These cell type-specific transcriptional signatures often predict previously unknown cellular functions. A computational pipeline identified dominant expression patterns that demonstrate transcriptional similarity between disparate cell types. Dominant expression patterns along the root's longitudinal axis do not strictly correlate with previously defined developmental zones, and in many cases, we observed expression fluctuation along this axis. Both robust co-regulation of gene expression and potential phasing of gene expression were identified between individual roots. Methods that combine these profiles demonstrate transcriptionally rich and complex programs that define Arabidopsis root development in both space and time.
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Affiliation(s)
- Siobhan M Brady
- Department of Biology, Duke University, Durham, NC 27708, USA
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Abstract
Differential growth of tissues during lateral organ development is essential for producing variation in shape and size. Previous studies have identified JAGGED (JAG), a gene that encodes a putative C2H2 zinc-finger transcription factor, as a key regulator of shape that promotes growth in lateral organs. Although JAG expression is detected in all floral organs, loss-of-function jag alleles have their strongest effects on sepal and petal development, suggesting that JAG may act redundantly with other factors in stamens and carpels. Here, we show that NUBBIN (NUB), a gene closely related to JAG, is responsible for this redundancy. Unlike JAG, NUB is exclusively expressed in leaves, stamens and carpels, and briefly in petal primordia. Furthermore, whereas JAG expression extends into all cell layers of lateral organs, NUB is restricted to the interior adaxial side. Our analysis focuses on stamen and gynoecium development, where we find that NUB acts redundantly with JAG to promote the growth of the pollen-bearing microsporangia of the anthers and the carpel walls of the gynoecium, which enclose the ovules. JAG and NUB also act redundantly to promote the differentiation of adaxial cell types in the carpel walls, and in the establishment of the correct number of cell layers. The important role these two factors play in regulating organ growth is further demonstrated by gain-of-function experiments showing that ectopic NUB expression is sufficient to drive the proliferation of tissues and the amplification of cell-layer number.
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Affiliation(s)
- José R Dinneny
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
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Abstract
Both cellular differentiation and stem cell maintenance must occur at the root apex in order to ensure the continuous growth of plant roots. In this issue of Cell, it is revealed that a canonical retinoblastoma pathway plays a crucial role in regulating the balance between differentiation and renewal of plant root stem cells.
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Affiliation(s)
- José R Dinneny
- Department of Biology, Duke University, Durham, NC 27708, USA
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