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Griffiths J, Rizza A, Tang B, Frommer WB, Jones AM. GIBBERELLIN PERCEPTION SENSOR 2 reveals genesis and role of cellular GA dynamics in light-regulated hypocotyl growth. THE PLANT CELL 2024:koae198. [PMID: 39039020 DOI: 10.1093/plcell/koae198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 06/27/2024] [Indexed: 07/24/2024]
Abstract
The phytohormone gibberellic acid (GA) is critical for environmentally sensitive plant development including germination, skotomorphogenesis, and flowering. The Förster resonance energy transfer biosensor GIBBERELLIN PERCEPTION SENSOR1, which permits single-cell GA measurements in vivo, has been used to observe a GA gradient correlated with cell length in dark-grown, but not light-grown, hypocotyls. We sought to understand how light signaling integrates into cellular GA regulation. Here, we show how the E3 ligase CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) and transcription factor ELONGATED HYPOCOTYL 5 (HY5) play central roles in directing cellular GA distribution in skoto- and photomorphogenic hypocotyls, respectively. We demonstrate that the expression pattern of the GA biosynthetic enzyme gene GA20ox1 is the key determinant of the GA gradient in dark-grown hypocotyls and is a target of COP1 signaling. We engineered a second generation GPS2 biosensor with improved orthogonality and reversibility. GPS2 revealed a previously undetectable cellular pattern of GA depletion during the transition to growth in the light. This GA depletion partly explains the resetting of hypocotyl growth dynamics during photomorphogenesis. Achieving cell-level resolution has revealed how GA distributions link environmental conditions with morphology and morphological plasticity. The GPS2 biosensor is an ideal tool for GA studies in many conditions, organs, and plant species.
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Affiliation(s)
- Jayne Griffiths
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Annalisa Rizza
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Bijun Tang
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Wolf B Frommer
- Heinrich Heine University, Institute for Molecular Physiology, 40225 Düsseldorf, Germany
| | - Alexander M Jones
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
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2
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Voothuluru P, Wu Y, Sharp RE. Not so hidden anymore: Advances and challenges in understanding root growth under water deficits. THE PLANT CELL 2024; 36:1377-1409. [PMID: 38382086 PMCID: PMC11062450 DOI: 10.1093/plcell/koae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Limited water availability is a major environmental factor constraining plant development and crop yields. One of the prominent adaptations of plants to water deficits is the maintenance of root growth that enables sustained access to soil water. Despite early recognition of the adaptive significance of root growth maintenance under water deficits, progress in understanding has been hampered by the inherent complexity of root systems and their interactions with the soil environment. We highlight selected milestones in the understanding of root growth responses to water deficits, with emphasis on founding studies that have shaped current knowledge and set the stage for further investigation. We revisit the concept of integrated biophysical and metabolic regulation of plant growth and use this framework to review central growth-regulatory processes occurring within root growth zones under water stress at subcellular to organ scales. Key topics include the primary processes of modifications of cell wall-yielding properties and osmotic adjustment, as well as regulatory roles of abscisic acid and its interactions with other hormones. We include consideration of long-recognized responses for which detailed mechanistic understanding has been elusive until recently, for example hydrotropism, and identify gaps in knowledge, ongoing challenges, and opportunities for future research.
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Affiliation(s)
- Priya Voothuluru
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Yajun Wu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Robert E Sharp
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
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3
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Kiradjiev KB, Band LR. Multiscale Asymptotic Analysis Reveals How Cell Growth and Subcellular Compartments Affect Tissue-Scale Hormone Transport. Bull Math Biol 2023; 85:101. [PMID: 37702758 PMCID: PMC10499980 DOI: 10.1007/s11538-023-01199-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
Determining how cell-scale processes lead to tissue-scale patterns is key to understanding how hormones and morphogens are distributed within biological tissues and control developmental processes. In this article, we use multiscale asymptotic analysis to derive a continuum approximation for hormone transport in a long file of cells to determine how subcellular compartments and cell growth and division affect tissue-scale hormone transport. Focusing our study on plant tissues, we begin by presenting a discrete multicellular ODE model tracking the hormone concentration in each cell's cytoplasm, subcellular vacuole, and surrounding apoplast, represented by separate compartments in the cell-file geometry. We allow the cells to grow at a rate that can depend both on space and time, accounting for both cytoplasmic and vacuolar expansion. Multiscale asymptotic analysis enables us to systematically derive the corresponding continuum model, obtaining an effective reaction-advection-diffusion equation and revealing how the effective diffusivity, effective advective velocity, and the effective sink term depend on the parameters in the cell-scale model. The continuum approximation reveals how subcellular compartments, such as vacuoles, can act as storage vessels, that significantly alter the effective properties of hormone transport, such as the effective diffusivity and the induced effective velocity. Furthermore, we show how cell growth and spatial variance across cell lengths affect the effective diffusivity and the induced effective velocity, and how these affect the tissue-scale hormone distribution. In particular, we find that cell growth naturally induces an effective velocity in the direction of growth, whereas spatial variance across cell lengths induces effective velocity due to the presence of an extra compartment, such as the apoplast and the vacuole, and variations in the relative sizes between the compartments across the file of cells. It is revealed that hormone transport is faster across cells of decreasing lengths than cells with increasing lengths. We also investigate the effect of cell division on transport dynamics, assuming that each cell divides as soon as it doubles in size, and find that increasing the time between successive cell divisions decreases the growth rate, which enhances the effect of cell division in slowing hormone transport. Motivated by recent experimental discoveries, we discuss particular applications for transport of gibberellic acid (GA), an important growth hormone, within the Arabidopsis root. The model reveals precisely how membrane proteins that mediate facilitated GA transport affect the effective tissue-scale transport. However, the results are general enough to be relevant to other plant hormones, or other substances that are transported in a similar way in any type of cells.
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Affiliation(s)
- K B Kiradjiev
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - L R Band
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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4
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Sidhu JS, Ajmera I, Arya S, Lynch JP. RootSlice-A novel functional-structural model for root anatomical phenotypes. PLANT, CELL & ENVIRONMENT 2023; 46:1671-1690. [PMID: 36708192 DOI: 10.1111/pce.14552] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Root anatomy is an important determinant of root metabolic costs, soil exploration, and soil resource capture. Root anatomy varies substantially within and among plant species. RootSlice is a multicellular functional-structural model of root anatomy developed to facilitate the analysis and understanding of root anatomical phenotypes. RootSlice can capture phenotypically accurate root anatomy in three dimensions of different root classes and developmental zones, of both monocotyledonous and dicotyledonous species. Several case studies are presented illustrating the capabilities of the model. For maize nodal roots, the model illustrated the role of vacuole expansion in cell elongation; and confirmed the individual and synergistic role of increasing root cortical aerenchyma and reducing the number of cortical cell files in reducing root metabolic costs. Integration of RootSlice for different root zones as the temporal properties of the nodal roots in the whole-plant and soil model OpenSimRoot/maize enabled the multiscale evaluation of root anatomical phenotypes, highlighting the role of aerenchyma formation in enhancing the utility of cortical cell files for improving plant performance over varying soil nitrogen supply. Such integrative in silico approaches present avenues for exploring the fitness landscape of root anatomical phenotypes.
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Affiliation(s)
- Jagdeep Singh Sidhu
- Department of Plant Science, The Pennsylvania State University, University Park, State College, Pennsylvania, USA
| | - Ishan Ajmera
- Department of Plant Science, The Pennsylvania State University, University Park, State College, Pennsylvania, USA
| | - Sankalp Arya
- Department of Plant Science, The Pennsylvania State University, University Park, State College, Pennsylvania, USA
| | - Jonathan P Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, State College, Pennsylvania, USA
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5
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Chen W, Mou X, Meng P, Chen J, Tang X, Meng G, Xin K, Zhang Y, Wang C. Effects of arbuscular mycorrhizal fungus inoculation on the growth and nitrogen metabolism of Catalpa bungei C.A.Mey. under different nitrogen levels. FRONTIERS IN PLANT SCIENCE 2023; 14:1138184. [PMID: 36909441 PMCID: PMC9996104 DOI: 10.3389/fpls.2023.1138184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Evidence suggests that arbuscular mycorrhizal fungi (AMF) may promote the growth of woody plants. However, the effects of AMF on nitrogen (N) metabolism in plants, especially trees, and its regulatory mechanism are rarely reported. Here, the effects of AMF inoculation on the growth and N nutrition status of Catalpa bungei under different N levels were reported. Three N levels (low, medium, high) and two mycorrhizal inoculation treatments (inoculation with Rhizophagus intraradices or not) were used with factorial design. The results showed that medium N could significantly improve the physiological metabolism and growth of C. bungei seedlings. However, when N was excessive, growth was significantly inhibited whether inoculated AMF or not. Compared with non-inoculated treatments, AMF inoculation could promote the absorption of N and P, improve photosynthesis under low to medium N levels, thus promoting the growth of seedlings. AMF changed the biomass allocation in seedlings by reducing the stem mass ratio and root/shoot ratio, and increasing the leaf mass ratio. At medium N levels, compared with non-inoculated treatment, AMF inoculation could significantly promote root growth by changing root hormone levels and improving root architecture and root activity. Under N addition, AMF inoculation could improve the absorption and assimilation of N by regulating the expression of key enzyme genes of N metabolism and nitrate transporter genes (NRT2.4, NRT2.5, NRT2.7) in roots, and enhancing the activities of the key enzyme of N metabolism. This study may provide a reference for the application of AMF in the cultivation and afforestation technology of C. bungei in Northwest China.
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Chen M, Guo L, Ramakrishnan M, Fei Z, Vinod KK, Ding Y, Jiao C, Gao Z, Zha R, Wang C, Gao Z, Yu F, Ren G, Wei Q. Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors. THE PLANT CELL 2022; 34:3577-3610. [PMID: 35766883 PMCID: PMC9516176 DOI: 10.1093/plcell/koac193] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/24/2022] [Indexed: 05/09/2023]
Abstract
Moso bamboo (Phyllostachys edulis) shows remarkably rapid growth (114.5 cm/day), but the underlying biological mechanisms remain unclear. After examining more than 12,750 internodes from more than 510 culms from 17 Moso populations, we identified internode 18 as a representative internode for rapid growth. This internode includes a 2-cm cell division zone (DZ), a cell elongation zone up to 12 cm, and a secondary cell wall (SCW) thickening zone. These zones elongated 11.8 cm, produced approximately 570,000,000 cells, and deposited ∼28 mg g-1 dry weight (DW) lignin and ∼44 mg g-1 DW cellulose daily, far exceeding vegetative growth observed in other plants. We used anatomical, mathematical, physiological, and genomic data to characterize development and transcriptional networks during rapid growth in internode 18. Our results suggest that (1) gibberellin may directly trigger the rapid growth of Moso shoots, (2) decreased cytokinin and increased auxin accumulation may trigger cell DZ elongation, and (3) abscisic acid and mechanical pressure may stimulate rapid SCW thickening via MYB83L. We conclude that internode length involves a possible tradeoff mediated by mechanical pressure caused by rapid growth, possibly influenced by environmental temperature and regulated by genes related to cell division and elongation. Our results provide insight into the rapid growth of Moso bamboo.
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Affiliation(s)
- Ming Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Lin Guo
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA
| | - Kunnummal K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Yulong Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | | | - Zhipeng Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ruofei Zha
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Chunyue Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China
| | - Fen Yu
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China
| | - Guodong Ren
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
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7
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Modeling reveals posttranscriptional regulation of GA metabolism enzymes in response to drought and cold. Proc Natl Acad Sci U S A 2022; 119:e2121288119. [PMID: 35878042 PMCID: PMC9351370 DOI: 10.1073/pnas.2121288119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The hormone gibberellin (GA) controls plant growth and regulates growth responses to environmental stress. In monocotyledonous leaves, GA controls growth by regulating division-zone size. We used a systems approach to investigate the establishment of the GA distribution in the maize leaf growth zone to understand how drought and cold alter leaf growth. By developing and parameterizing a multiscale computational model that includes cell movement, growth-induced dilution, and metabolic activities, we revealed that the GA distribution is predominantly determined by variations in GA metabolism. Considering wild-type and UBI::GA20-OX-1 leaves, the model predicted the peak in GA concentration, which has been shown to determine division-zone size. Drought and cold modified enzyme transcript levels, although the model revealed that this did not explain the observed GA distributions. Instead, the model predicted that GA distributions are also mediated by posttranscriptional modifications increasing the activity of GA 20-oxidase in drought and of GA 2-oxidase in cold, which we confirmed by enzyme activity measurements. This work provides a mechanistic understanding of the role of GA metabolism in plant growth regulation.
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8
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Rutten J, van den Berg T, Tusscher KT. Modeling Auxin Signaling in Roots: Auxin Computations. Cold Spring Harb Perspect Biol 2022; 14:a040089. [PMID: 34001532 PMCID: PMC8805645 DOI: 10.1101/cshperspect.a040089] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Auxin signaling and patterning is an inherently complex process, involving polarized auxin transport, metabolism, and signaling, its effect on developmental zones, as well as growth rates, and the feedback between all these different aspects. This complexity has led to an important role for computational modeling in unraveling the multifactorial roles of auxin in plant developmental and adaptive processes. Here we discuss the basic ingredients of auxin signaling and patterning models for root development as well as a series of key modeling studies in this area. These modeling studies have helped elucidate how plants use auxin signaling to compute the size of their root meristem, the direction in which to grow, and when and where to form lateral roots. Importantly, these models highlight how auxin, through patterning of and collaborating with other factors, can fulfill all these roles simultaneously.
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Affiliation(s)
- Jaap Rutten
- Computational Developmental Biology Group, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Thea van den Berg
- Computational Developmental Biology Group, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Kirsten Ten Tusscher
- Computational Developmental Biology Group, Utrecht University, Utrecht 3584 CH, The Netherlands
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9
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Differential biosynthesis and cellular permeability explain longitudinal gibberellin gradients in growing roots. Proc Natl Acad Sci U S A 2021; 118:1921960118. [PMID: 33602804 PMCID: PMC7923382 DOI: 10.1073/pnas.1921960118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Growth hormones are mobile chemicals that exert considerable influence over how multicellular organisms like animals and plants take on their shape and form. Of particular interest is the distribution of such hormones across cells and tissues. In plants, one of these hormones, gibberellin (GA), is known to regulate cell multiplication and cell expansion to increase the rate at which roots grow. In this work, biosensor measurements were combined with theoretical models to elucidate the biochemical mechanisms that direct GA distribution and how these patterns relate to root growth. Our detailed understanding of how GA distributions are controlled in roots should prove a valuable model for understanding the makings of the many other hormone distributions that influence how plants grow. Control over cell growth by mobile regulators underlies much of eukaryotic morphogenesis. In plant roots, cell division and elongation are separated into distinct longitudinal zones and both division and elongation are influenced by the growth regulatory hormone gibberellin (GA). Previously, a multicellular mathematical model predicted a GA maximum at the border of the meristematic and elongation zones. However, GA in roots was recently measured using a genetically encoded fluorescent biosensor, nlsGPS1, and found to be low in the meristematic zone grading to a maximum at the end of the elongation zone. Furthermore, the accumulation rate of exogenous GA was also found to be higher in the elongation zone. It was still unknown which biochemical activities were responsible for these mobile small molecule gradients and whether the spatiotemporal correlation between GA levels and cell length is important for root cell division and elongation patterns. Using a mathematical modeling approach in combination with high-resolution GA measurements in vivo, we now show how differentials in several biosynthetic enzyme steps contribute to the endogenous GA gradient and how differential cellular permeability contributes to an accumulation gradient of exogenous GA. We also analyzed the effects of altered GA distribution in roots and did not find significant phenotypes resulting from increased GA levels or signaling. We did find a substantial temporal delay between complementation of GA distribution and cell division and elongation phenotypes in a GA deficient mutant. Together, our results provide models of how GA gradients are directed and in turn direct root growth.
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10
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Khakhar A, Wang C, Swanson R, Stokke S, Rizvi F, Sarup S, Hobbs J, Voytas DF. VipariNama: RNA viral vectors to rapidly elucidate the relationship between gene expression and phenotype. PLANT PHYSIOLOGY 2021; 186:2222-2238. [PMID: 34009393 PMCID: PMC8331131 DOI: 10.1093/plphys/kiab197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 04/01/2021] [Indexed: 05/05/2023]
Abstract
Synthetic transcription factors have great promise as tools to help elucidate relationships between gene expression and phenotype by allowing tunable alterations of gene expression without genomic alterations of the loci being studied. However, the years-long timescales, high cost, and technical skill associated with plant transformation have limited their use. In this work, we developed a technology called VipariNama (ViN) in which vectors based on the tobacco rattle virus are used to rapidly deploy Cas9-based synthetic transcription factors and reprogram gene expression in planta. We demonstrate that ViN vectors can implement activation or repression of multiple genes systemically and persistently over several weeks in Nicotiana benthamiana, Arabidopsis (Arabidopsis thaliana), and tomato (Solanum lycopersicum). By exploring strategies including RNA scaffolding, viral vector ensembles, and viral engineering, we describe how the flexibility and efficacy of regulation can be improved. We also show how this transcriptional reprogramming can create predictable changes to metabolic phenotypes, such as gibberellin biosynthesis in N. benthamiana and anthocyanin accumulation in Arabidopsis, as well as developmental phenotypes, such as plant size in N. benthamiana, Arabidopsis, and tomato. These results demonstrate how ViN vector-based reprogramming of different aspects of gibberellin signaling can be used to engineer plant size in a range of plant species in a matter of weeks. In summary, ViN accelerates the timeline for generating phenotypes from over a year to just a few weeks, providing an attractive alternative to transgenesis for synthetic transcription factor-enabled hypothesis testing and crop engineering.
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Affiliation(s)
- Arjun Khakhar
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Cecily Wang
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Ryan Swanson
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Sydney Stokke
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Furva Rizvi
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Surbhi Sarup
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - John Hobbs
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
| | - Daniel F Voytas
- Department Genetics, Cell Biology, & Development, University of Minnesota, Minneapolis 55108, USA
- Center for Precision Plant Genomics, University of Minnesota, St Paul, Minneapolis 55108, USA
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11
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Xiong CY, Gong QY, Pei H, Liao CJ, Yang RC, Li GK, Huang J. Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process. Int J Mol Sci 2021; 22:ijms22137029. [PMID: 34209973 PMCID: PMC8268914 DOI: 10.3390/ijms22137029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
In maize, the ear shank is a short branch that connects the ear to the stalk. The length of the ear shank mainly affects the transportation of photosynthetic products to the ear, and also influences the dehydration of the grain by adjusting the tightness of the husks. However, the molecular mechanisms of maize shank elongation have rarely been described. It has been reported that the maize ear shank length is a quantitative trait, but its genetic basis is still unclear. In this study, RNA-seq was performed to explore the transcriptional dynamics and determine the key genes involved in maize shank elongation at four different developmental stages. A total of 8145 differentially expressed genes (DEGs) were identified, including 729 transcription factors (TFs). Some important genes which participate in shank elongation were detected via function annotation and temporal expression pattern analyses, including genes related to signal transduction hormones (auxin, brassinosteroids, gibberellin, etc.), xyloglucan and xyloglucan xyloglucosyl transferase, and transcription factor families. The results provide insights into the genetic architecture of maize ear shanks and developing new varieties with ideal ear shank lengths, enabling adjustments for mechanized harvesting in the future.
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Affiliation(s)
- Cai-Yun Xiong
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (C.-Y.X.); (R.-C.Y.)
| | - Qing-You Gong
- Zhuhai Modern Agriculture Development Center, Zhuhai 519070, China;
| | - Hu Pei
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Chang-Jian Liao
- Technical Research Center of Dry Crop Variety Breeding in Fujian Province, Crop Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China;
| | - Rui-Chun Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (C.-Y.X.); (R.-C.Y.)
| | - Gao-Ke Li
- Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Crop Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Correspondence: (G.-K.L.); (J.H.)
| | - Jun Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (C.-Y.X.); (R.-C.Y.)
- Correspondence: (G.-K.L.); (J.H.)
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12
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Ding T, Zhang F, Wang J, Wang F, Liu J, Xie C, Hu Y, Shani E, Kong X, Ding Z, Tian H. Cell-type action specificity of auxin on Arabidopsis root growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:928-941. [PMID: 33609310 DOI: 10.1111/tpj.15208] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/05/2021] [Accepted: 02/15/2021] [Indexed: 05/09/2023]
Abstract
The plant hormone auxin plays a critical role in root growth and development; however, the contributions or specific roles of cell-type auxin signals in root growth and development are not well understood. Here, we mapped tissue and cell types that are important for auxin-mediated root growth and development by manipulating the local response and synthesis of auxin. Repressing auxin signaling in the epidermis, cortex, endodermis, pericycle or stele strongly inhibited root growth, with the largest effect observed in the endodermis. Enhancing auxin signaling in the epidermis, cortex, endodermis, pericycle or stele also caused reduced root growth, albeit to a lesser extent. Moreover, we established that root growth was inhibited by enhancement of auxin synthesis in specific cell types of the epidermis, cortex and endodermis, whereas increased auxin synthesis in the pericycle and stele had only minor effects on root growth. Our study thus establishes an association between cellular identity and cell type-specific auxin signaling that guides root growth and development.
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Affiliation(s)
- Tingting Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Feng Zhang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Junxia Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Fengxia Wang
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Jiajia Liu
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Chuantian Xie
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Yangjie Hu
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Xiangpei Kong
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Zhaojun Ding
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
| | - Huiyu Tian
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China
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Zluhan-Martínez E, López-Ruíz BA, García-Gómez ML, García-Ponce B, de la Paz Sánchez M, Álvarez-Buylla ER, Garay-Arroyo A. Integrative Roles of Phytohormones on Cell Proliferation, Elongation and Differentiation in the Arabidopsis thaliana Primary Root. FRONTIERS IN PLANT SCIENCE 2021; 12:659155. [PMID: 33981325 PMCID: PMC8107238 DOI: 10.3389/fpls.2021.659155] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/24/2021] [Indexed: 05/17/2023]
Abstract
The growth of multicellular organisms relies on cell proliferation, elongation and differentiation that are tightly regulated throughout development by internal and external stimuli. The plasticity of a growth response largely depends on the capacity of the organism to adjust the ratio between cell proliferation and cell differentiation. The primary root of Arabidopsis thaliana offers many advantages toward understanding growth homeostasis as root cells are continuously produced and move from cell proliferation to elongation and differentiation that are processes spatially separated and could be studied along the longitudinal axis. Hormones fine tune plant growth responses and a huge amount of information has been recently generated on the role of these compounds in Arabidopsis primary root development. In this review, we summarized the participation of nine hormones in the regulation of the different zones and domains of the Arabidopsis primary root. In some cases, we found synergism between hormones that function either positively or negatively in proliferation, elongation or differentiation. Intriguingly, there are other cases where the interaction between hormones exhibits unexpected results. Future analysis on the molecular mechanisms underlying crosstalk hormone action in specific zones and domains will unravel their coordination over PR development.
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Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Brenda Anabel López-Ruíz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mónica L. García-Gómez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- *Correspondence: Adriana Garay-Arroyo,
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14
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Rowe JH, Jones AM. Focus on biosensors: Looking through the lens of quantitative biology. QUANTITATIVE PLANT BIOLOGY 2021; 2:e12. [PMID: 37077214 PMCID: PMC10095858 DOI: 10.1017/qpb.2021.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/27/2021] [Accepted: 07/27/2021] [Indexed: 05/02/2023]
Abstract
In recent years, plant biologists interested in quantifying molecules and molecular events in vivo have started to complement reporter systems with genetically encoded fluorescent biosensors (GEFBs) that directly sense an analyte. Such biosensors can allow measurements at the level of individual cells and over time. This information is proving valuable to mathematical modellers interested in representing biological phenomena in silico, because improved measurements can guide improved model construction and model parametrisation. Advances in synthetic biology have accelerated the pace of biosensor development, and the simultaneous expression of spectrally compatible biosensors now allows quantification of multiple nodes in signalling networks. For biosensors that directly respond to stimuli, targeting to specific cellular compartments allows the observation of differential accumulation of analytes in distinct organelles, bringing insights to reactive oxygen species/calcium signalling and photosynthesis research. In conjunction with improved image analysis methods, advances in biosensor imaging can help close the loop between experimentation and mathematical modelling.
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Affiliation(s)
- James H. Rowe
- Sainsbury Laboratory, Cambridge University, Cambridge, United Kingdom
| | - Alexander M. Jones
- Sainsbury Laboratory, Cambridge University, Cambridge, United Kingdom
- Author for correspondence: Alexander M. Jones, E-mail:
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15
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López-Ruiz BA, Zluhan-Martínez E, Sánchez MDLP, Álvarez-Buylla ER, Garay-Arroyo A. Interplay between Hormones and Several Abiotic Stress Conditions on Arabidopsis thaliana Primary Root Development. Cells 2020; 9:E2576. [PMID: 33271980 PMCID: PMC7759812 DOI: 10.3390/cells9122576] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 01/17/2023] Open
Abstract
As sessile organisms, plants must adjust their growth to withstand several environmental conditions. The root is a crucial organ for plant survival as it is responsible for water and nutrient acquisition from the soil and has high phenotypic plasticity in response to a lack or excess of them. How plants sense and transduce their external conditions to achieve development, is still a matter of investigation and hormones play fundamental roles. Hormones are small molecules essential for plant growth and their function is modulated in response to stress environmental conditions and internal cues to adjust plant development. This review was motivated by the need to explore how Arabidopsis thaliana primary root differentially sense and transduce external conditions to modify its development and how hormone-mediated pathways contribute to achieve it. To accomplish this, we discuss available data of primary root growth phenotype under several hormone loss or gain of function mutants or exogenous application of compounds that affect hormone concentration in several abiotic stress conditions. This review shows how different hormones could promote or inhibit primary root development in A. thaliana depending on their growth in several environmental conditions. Interestingly, the only hormone that always acts as a promoter of primary root development is gibberellins.
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Affiliation(s)
- Brenda Anabel López-Ruiz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico; (B.A.L.-R.); (E.Z.-M.); (M.d.l.P.S.); (E.R.Á.-B.)
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de Mexico, Mexico City 04510, Mexico
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16
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Ding L, Song A, Zhang X, Li S, Su J, Xia W, Zhao K, Zhao W, Guan Y, Fang W, Chen S, Jiang J, Chen F. The core regulatory networks and hub genes regulating flower development in Chrysanthemum morifolium. PLANT MOLECULAR BIOLOGY 2020; 103:669-688. [PMID: 32472481 DOI: 10.1007/s11103-020-01017-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/24/2020] [Indexed: 05/17/2023]
Abstract
The study has facilitated important insights into the regulatory networks involved in flower development in chrysanthemum (Asteraceae), and is informative with respect to the mechanism of flower shape determination. Chrysanthemum morifolium, valued as an ornamental species given the diversity of its inflorescence form, is viewed as a model for understanding flower development in the Asteraceae. Yet, the underlying regulatory networks remain largely unexplored. Here, a transcriptomic survey of the Chrysanthemum morifolium variety 'Jinba' was undertaken to uncover the global gene expression profiles and identify the modules of co-transcribed genes associated with flower development. The weighted gene coexpression network analysis revealed important networks and hub genes including ray floret petals-specific coexpression network, disc floret petals-specific network, B and E class genes involved network and CYC2 genes network. Three ray floret petal-specific hub genes were also strongly transcribed in the ray florets of a selection of six diverse varieties and especially so in those which form ligulate ray floret petals. CmCYC2c was strongly transcribed in the distal and lateral regions of the ray floret petals, and also, along with CmCYC2d, in the tubular ray florets. Furthermore, CmOFP, belonging to the family of ovate proteins, was identified in the CYC2 genes network. CmOFP can interact with CmCYC2d that physically interact with CmCYC2c. This work provides important insights into the regulatory networks involved in flower development in chrysanthemum, and is informative with respect to the mechanistic basis of the regulation of flower shape.
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Affiliation(s)
- Lian Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Aiping Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xue Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Song Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weikang Xia
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kunkun Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunxiao Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sumei Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Landscaping, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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17
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Baskin TI, Preston S, Zelinsky E, Yang X, Elmali M, Bellos D, Wells DM, Bennett MJ. Positioning the Root Elongation Zone Is Saltatory and Receives Input from the Shoot. iScience 2020; 23:101309. [PMID: 32645582 PMCID: PMC7341455 DOI: 10.1016/j.isci.2020.101309] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/28/2020] [Accepted: 06/18/2020] [Indexed: 02/04/2023] Open
Abstract
In the root, meristem and elongation zone lengths remain stable, despite growth and division of cells. To gain insight into zone stability, we imaged individual Arabidopsis thaliana roots through a horizontal microscope and used image analysis to obtain velocity profiles. For a root, velocity profiles obtained every 5 min over 3 h coincided closely, implying that zonation is regulated tightly. However, the position of the elongation zone saltated, by on average 17 μm every 5 min. Saltation was apparently driven by material elements growing faster and then slower, while moving through the growth zone. When the shoot was excised, after about 90 min, growth zone dynamics resembled those of intact roots, except that the position of the elongation zone moved, on average, rootward, by several hundred microns in 24 h. We hypothesize that mechanisms determining elongation zone position receive input from the shoot.
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Affiliation(s)
- Tobias I Baskin
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK; Biology Department, University of Massachusetts, Amherst, MA 01003, USA.
| | - Simon Preston
- School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Ellen Zelinsky
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Xiaoli Yang
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Melissa Elmali
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Dimitrios Bellos
- School of Computer Science, University of Nottingham, Nottingham NG8 1BB, UK
| | - Darren M Wells
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK
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18
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Zhao Y, Antoniou-Kourounioti RL, Calder G, Dean C, Howard M. Temperature-dependent growth contributes to long-term cold sensing. Nature 2020; 583:825-829. [PMID: 32669706 PMCID: PMC7116785 DOI: 10.1038/s41586-020-2485-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 05/29/2020] [Indexed: 11/28/2022]
Abstract
Temperature is a key factor in the growth and development of all organisms1,2. Plants have to interpret temperature fluctuations, over hourly to monthly timescales, to align their growth and development with the seasons. Much is known about how plants respond to acute thermal stresses3,4, but the mechanisms that integrate long-term temperature exposure remain unknown. The slow, winter-long upregulation of VERNALIZATION INSENSITIVE 3 (VIN3)5-7, a PHD protein that functions with Polycomb repressive complex 2 to epigenetically silence FLOWERING LOCUS C (FLC) during vernalization, is central to plants interpreting winter progression5,6,8-11. Here, by a forward genetic screen, we identify two dominant mutations of the transcription factor NTL8 that constitutively activate VIN3 expression and alter the slow VIN3 cold induction profile. In the wild type, the NTL8 protein accumulates slowly in the cold, and directly upregulates VIN3 transcription. Through combining computational simulation and experimental validation, we show that a major contributor to this slow accumulation is reduced NTL8 dilution due to slow growth at low temperatures. Temperature-dependent growth is thus exploited through protein dilution to provide the long-term thermosensory information for VIN3 upregulation. Indirect mechanisms involving temperature-dependent growth, in addition to direct thermosensing, may be widely relevant in long-term biological sensing of naturally fluctuating temperatures.
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Affiliation(s)
- Yusheng Zhao
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Grant Calder
- John Innes Centre, Norwich Research Park, Norwich, UK
- Department of Biology, University of York, York, UK
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK.
| | - Martin Howard
- John Innes Centre, Norwich Research Park, Norwich, UK.
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19
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De Vos D, Nelissen H, AbdElgawad H, Prinsen E, Broeckhove J, Inzé D, Beemster GT. How grass keeps growing: an integrated analysis of hormonal crosstalk in the maize leaf growth zone. THE NEW PHYTOLOGIST 2020; 225:2513-2525. [PMID: 31705666 PMCID: PMC7116270 DOI: 10.1111/nph.16315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/02/2019] [Indexed: 05/07/2023]
Abstract
We studied the maize leaf to understand how long-distance signals, auxin and cytokinin, control leaf growth dynamics. We constructed a mathematical model describing the transport of these hormones along the leaf growth zone and their interaction with the local gibberellin (GA) metabolism in the control of cell division. Assuming gradually declining auxin and cytokinin supply at the leaf base, the model generated spatiotemporal hormone distribution and growth patterns that matched experimental data. At the cellular level, the model predicted a basal leaf growth as a result of cell division driven by auxin and cytokinin. Superimposed on this, GA synthesis regulated growth through the control of the size of the region of active cell division. The predicted hormone and cell length distributions closely matched experimental data. To correctly predict the leaf growth profiles and final organ size of lines with reduced or elevated GA production, the model required a signal proportional to the size of the emerged part of the leaf that inhibited the basal leaf growth driven by auxin and cytokinin. Excision and shading of the emerged part of the growing leaf allowed us to demonstrate that this signal exists and depends on the perception of light intensity.
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Affiliation(s)
- Dirk De Vos
- Laboratory for Integrated Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
- Modeling Of Systems And Internet Communication (MOSAIC), Department of Mathematics and Informatics, University of Antwerp, 2020 Antwerp, Belgium
- Corresponding Authors ,+32 3 265 34 21 , +32 3 265 34 21
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Hamada AbdElgawad
- Laboratory for Integrated Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
- Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Els Prinsen
- Laboratory for Integrated Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
| | - Jan Broeckhove
- Modeling Of Systems And Internet Communication (MOSAIC), Department of Mathematics and Informatics, University of Antwerp, 2020 Antwerp, Belgium
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Gerrit T.S. Beemster
- Laboratory for Integrated Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
- Corresponding Authors ,+32 3 265 34 21 , +32 3 265 34 21
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20
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Molecular and functional characterization of two DELLA protein-coding genes in litchi. Gene 2020; 738:144455. [PMID: 32061763 DOI: 10.1016/j.gene.2020.144455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 11/20/2022]
Abstract
DELLA proteins are members of the plant-specific GRAS family, acting as negative regulators of plant growth. In this study, we identified two DELLA protein-coding genes in litchi, denoted as LcGAI and LcRGL1. Motif analysis showed that LcGAI and LcRGL1 proteins both contain a conserved DELLA and TVHYNP motif at the N-terminus as well as LHR1, VHIID, LHR2, PFYRE, and SAW motifs at the C terminus. The fused proteins of LcGAI-GFP and LcRGL1-GFP were both localized in the nucleus. Overexpression of LcGAI and LcRGL1 in Arabidopsis substantially inhibits leaf growth. Expression analysis showed that HLH factors, PRE1 and PRE5, were restrained, whereas gibberellin (GA) receptors GID1a and LcGID1b were enhanced in LcGAI and LcRGL1 overexpression lines. Results of the yeast two-hybrid assay showed that LcGAI and LcRGL1 interact with LcGID1b/LcGID1c in a GA dose-dependent manner, whereas LcGAI and LcRGL1 had a greater binding capacity to LcGID1b than LcGID1c. These observations suggested that LcGAI and LcRGL1 proteins are nuclear growth repressors.
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21
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Ackerman-Lavert M, Savaldi-Goldstein S. Growth models from a brassinosteroid perspective. CURRENT OPINION IN PLANT BIOLOGY 2020; 53:90-97. [PMID: 31809963 DOI: 10.1016/j.pbi.2019.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 05/19/2023]
Abstract
Plant growth relies on interconnected hormonal pathways, their corresponding transcriptional networks and mechanical signals. This work reviews recent brassinosteroid (BR) studies and integrates them with current growth models derived from research in roots. The relevance of spatiotemporal BR signaling in the longitudinal and radial root axes and its multifaceted interaction with auxin, the impact of BR on final cell size determination and its interplay with microtubules and the cell wall are discussed. Also highlighted are emerging variations of canonical BR signaling that could function in developmental-specific context.
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22
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Erlich A, Jones GW, Tisseur F, Moulton DE, Goriely A. The role of topology and mechanics in uniaxially growing cell networks. Proc Math Phys Eng Sci 2020; 476:20190523. [PMID: 32082058 PMCID: PMC7016545 DOI: 10.1098/rspa.2019.0523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/10/2019] [Indexed: 01/18/2023] Open
Abstract
In biological systems, the growth of cells, tissues and organs is influenced by mechanical cues. Locally, cell growth leads to a mechanically heterogeneous environment as cells pull and push their neighbours in a cell network. Despite this local heterogeneity, at the tissue level, the cell network is remarkably robust, as it is not easily perturbed by changes in the mechanical environment or the network connectivity. Through a network model, we relate global tissue structure (i.e. the cell network topology) and local growth mechanisms (growth laws) to the overall tissue response. Within this framework, we investigate the two main mechanical growth laws that have been proposed: stress-driven or strain-driven growth. We show that in order to create a robust and stable tissue environment, networks with predominantly series connections are naturally driven by stress-driven growth, whereas networks with predominantly parallel connections are associated with strain-driven growth.
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Affiliation(s)
- Alexander Erlich
- Laboratoire Interdisciplinaire de Physique (LIPhy), Université Grenoble Alpes, CNRS, Grenoble 38000, France
| | - Gareth W. Jones
- School of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Françoise Tisseur
- School of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Derek E. Moulton
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK
| | - Alain Goriely
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK
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23
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Zhou AP, Gan PH, Zong D, Fei X, Zhong YY, Li SQ, Yu JD, He CZ. Bark tissue transcriptome analyses of inverted Populus yunnanensis cuttings reveal the crucial role of plant hormones in response to inversion. PeerJ 2019; 7:e7740. [PMID: 31592192 PMCID: PMC6777492 DOI: 10.7717/peerj.7740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/25/2019] [Indexed: 01/11/2023] Open
Abstract
Inverted cuttings of Populus yunnanensis exhibit an interesting growth response to inversion. This response is characterized by enlargement of the stem above the shoot site, while the upright stem shows obvious outward growth below the shoot site. In this study, we examined transcriptome changes in bark tissue at four positions on upright and inverted cuttings of P. yunnanensis: position B, the upper portion of the stem; position C, the lower portion of the stem; position D, the bottom of new growth; and position E, the top of new growth. The results revealed major transcriptomic changes in the stem, especially at position B, but little alteration was observed in the bark tissue of the new shoot. The differentially expressed genes (DEGs) were mainly assigned to four pathways: plant hormone signal transduction, plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway-plant, and adenosine triphosphate-binding cassette (ABC) transporters. Most of these DEGs were involved in at least two pathways. The levels of many hormones, such as auxin (IAA), cytokinin (CTK), gibberellins (GAs), ethylene (ET), and brassinosteroids (BRs), underwent large changes in the inverted cuttings. A coexpression network showed that the top 20 hub unigenes at position B in the upright and inverted cutting groups were associated mainly with the BR and ET signaling pathways, respectively. Furthermore, brassinosteroid insensitive 1-associated receptor kinase 1 (BAK1) in the BR pathway and both ethylene response (ETR) and constitutive triple response 1 (CTR1) in the ET pathway were important hubs that interfaced with multiple pathways.
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Affiliation(s)
- An-Pei Zhou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Pei-Hua Gan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Xuan Fei
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Yuan-Yuan Zhong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Si-Qi Li
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Jin-De Yu
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Cheng-Zhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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Tan H, Man C, Xie Y, Yan J, Chu J, Huang J. A Crucial Role of GA-Regulated Flavonol Biosynthesis in Root Growth of Arabidopsis. MOLECULAR PLANT 2019; 12:521-537. [PMID: 30630075 DOI: 10.1016/j.molp.2018.12.021] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 12/26/2018] [Accepted: 12/28/2018] [Indexed: 05/03/2023]
Abstract
Flavonols have been demonstrated to play many important roles in plant growth, development, and communication with other organisms. Flavonol biosynthesis is spatiotemporally regulated by the subgroup 7 R2R3-MYB (SG7 MYB) transcription factors including MYB11/MYB12/MYB111. However, whether SG7-MYB activity is subject to post-translational regulation remains unclear. Here, we show that gibberellic acid (GA) inhibits flavonol biosynthesis via DELLA proteins in Arabidopsis. Protein-protein interaction analyses revealed that DELLAs (RGA and GAI) interacted with SG7 MYBs (MYB12 and MYB111) both in vitro and in vivo, leading to enhanced affinity of MYB binding to the promoter regions of key genes for flavonol biosynthesis and thus increasing their transcriptional levels. We observed that the level of auxin in the root tip was negatively correlated with root flavonol content. Furthermore, genetic assays showed that loss-of-function mutations in MYB12, which is predominantly expressed in roots, partially rescued the short-root phenotype of the GA-deficient mutant ga1-3 by increasing root meristem size and mature cell size. Consistent with these observations, exogenous application of the flavonol quercetin restored the root meristem size of myb12 ga1-3 to that of ga1-3. Taken together, our data elucidate a molecular mechanism by which GA promotes root growth by directly reducing flavonol biosynthesis.
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Affiliation(s)
- Huijuan Tan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Cong Man
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Ye Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jijun Yan
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
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25
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Rutten JP, Ten Tusscher K. In Silico Roots: Room for Growth. TRENDS IN PLANT SCIENCE 2019; 24:250-262. [PMID: 30665820 DOI: 10.1016/j.tplants.2018.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/14/2018] [Accepted: 11/19/2018] [Indexed: 06/09/2023]
Abstract
Computational models are invaluable tools for understanding the hormonal and genetic control of root development. Thus far, models have focused on the crucial roles that auxin transport and metabolism play in determining the auxin signaling gradient that controls the root meristem. Other hormones such as cytokinins, gibberellins, and ethylene have predominantly been considered as modulators of auxin dynamics, but their underlying patterning mechanisms are currently unresolved. In addition, the effects of cell- and tissue-level growth dynamics, which induce dilution and displacement of signaling molecules, have remained unexplored. Elucidating these additional mechanisms will be essential to unravel how root growth is patterned in a robust and self-organized manner. Models incorporating growth will thus be crucial in unraveling the underlying logic of root developmental decision making.
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Affiliation(s)
- Jacob Pieter Rutten
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Kirsten Ten Tusscher
- Computational Developmental Biology Group, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
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26
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Rizza A, Jones AM. The makings of a gradient: spatiotemporal distribution of gibberellins in plant development. CURRENT OPINION IN PLANT BIOLOGY 2019; 47:9-15. [PMID: 30173065 PMCID: PMC6414749 DOI: 10.1016/j.pbi.2018.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 05/15/2023]
Abstract
The gibberellin phytohormones regulate growth and development throughout the plant lifecycle. Upstream regulation and downstream responses to gibberellins vary across cells and tissues, developmental stages, environmental conditions, and plant species. The spatiotemporal distribution of gibberellins is the result of an ensemble of biosynthetic, catabolic and transport activities, each of which can be targeted to influence gibberellin levels in space and time. Understanding gibberellin distributions has recently benefited from discovery of transport proteins capable of importing gibberellins as well as novel methods for detecting gibberellins with high spatiotemporal resolution. For example, a genetically-encoded fluorescent biosensor for gibberellins was deployed in Arabidopsis and revealed gibberellin gradients in rapidly elongating tissues. Although cellular accumulations of gibberellins are hypothesized to regulate cell growth in developing embryos, germinating seeds, elongating stems and roots, and developing floral organs, understanding the quantitative relationship between cellular gibberellin levels and cellular growth awaits further investigation. It is also unclear how spatiotemporal gibberellin distributions result from myriad endogenous and environmental factors directing an ensemble of known gibberellin enzymatic and transport steps.
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Affiliation(s)
- Annalisa Rizza
- Sainsbury Laboratory, Cambridge University, Cambridge, UK
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27
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Zhou AP, Zong D, Gan PH, Zou XL, Fei X, Zhong YY, He CZ. Physiological Analysis and Transcriptome Profiling of Inverted Cuttings of Populus yunnanensis Reveal That Cell Wall Metabolism Plays a Crucial Role in Responding to Inversion. Genes (Basel) 2018; 9:E572. [PMID: 30477186 PMCID: PMC6316517 DOI: 10.3390/genes9120572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/15/2018] [Accepted: 11/20/2018] [Indexed: 01/24/2023] Open
Abstract
Inverted cuttings of Populus yunnanensis remain alive by rooting from the original morphological apex and sprouting from the base, but the lateral branches exhibit less vigorous growth than those of the upright plant. In this study, we examined the changes in hormone contents, oxidase activities, and transcriptome profiles between upright and inverted cuttings of P. yunnanensis. The results showed that the indole-3-acetic acid (IAA) and gibberellic acid (GA₃) contents were significantly lower in inverted cuttings than in upright cuttings only in the late growth period (September and October), while the abscisic acid (ABA) level was always similar between the two direction types. The biosynthesis of these hormones was surprisingly unrelated to the inversion of P. yunnanensis during the vegetative growth stage (July and August). Increased levels of peroxidases (PODs) encoded by 13 differentially expressed genes (DEGs) served as lignification promoters that protected plants against oxidative stress. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that most DEGs (107) were related to carbohydrate metabolism. Furthermore, altered activities of uridine diphosphate (UDP)-sugar pyrophosphorylase (USP, 15 DEGs) for nucleotide sugars, pectin methylesterase (PME, 7 DEGs) for pectin, and POD (13 DEGs) for lignin were important factors in the response of the trees to inversion, and these enzymes are all involved cell wall metabolism.
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Affiliation(s)
- An-Pei Zhou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China.
| | - Dan Zong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China.
| | - Pei-Hua Gan
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China.
| | - Xin-Lian Zou
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China.
| | - Xuan Fei
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China.
| | - Yuan-Yuan Zhong
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China.
| | - Cheng-Zhong He
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China.
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China.
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28
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Band LR, Preston SP. Parameter inference to motivate asymptotic model reduction: An analysis of the gibberellin biosynthesis pathway. J Theor Biol 2018; 457:66-78. [PMID: 30040964 DOI: 10.1016/j.jtbi.2018.05.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/15/2018] [Accepted: 05/24/2018] [Indexed: 11/29/2022]
Abstract
Developing effective strategies to use models in conjunction with experimental data is essential to understand the dynamics of biological regulatory networks. In this study, we demonstrate how combining parameter estimation with asymptotic analysis can reveal the key features of a network and lead to simplified models that capture the observed network dynamics. Our approach involves fitting the model to experimental data and using the profile likelihood to identify small parameters and cases where model dynamics are insensitive to changing particular individual parameters. Such parameter diagnostics provide understanding of the dominant features of the model and motivate asymptotic model reductions to derive simpler models in terms of identifiable parameter groupings. We focus on the particular example of biosynthesis of the plant hormone gibberellin (GA), which controls plant growth and has been mutated in many current crop varieties. This pathway comprises two parallel series of enzyme-substrate reactions, which have previously been modelled using the law of mass action (Middleton et al., 2012). Considering the GA20ox-mediated steps, we analyse the identifiability of the model parameters using published experimental data; the analysis reveals the ratio between enzyme and GA levels to be small and motivates us to perform a quasi-steady state analysis to derive a reduced model. Fitting the parameters in the reduced model reveals additional features of the pathway and motivates further asymptotic analysis which produces a hierarchy of reduced models. Calculating the Akaike information criterion and parameter confidence intervals enables us to select a parsimonious model with identifiable parameters. As well as demonstrating the benefits of combining parameter estimation and asymptotic analysis, the analysis shows how GA biosynthesis is limited by the final GA20ox-mediated steps in the pathway and generates a simple mathematical description of this part of the GA biosynthesis pathway.
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Affiliation(s)
- Leah R Band
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom; School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom.
| | - Simon P Preston
- School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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29
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Youssef C, Bizet F, Bastien R, Legland D, Bogeat-Triboulot MB, Hummel I. Quantitative dissection of variations in root growth rate: a matter of cell proliferation or of cell expansion? JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5157-5168. [PMID: 30053124 PMCID: PMC6184812 DOI: 10.1093/jxb/ery272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/16/2018] [Indexed: 05/24/2023]
Abstract
Plant organ growth results from cell production and cell expansion. Deciphering the contribution of each of these processes to growth rate is an important issue in developmental biology. Here, we investigated the cellular processes governing root elongation rate, considering two sources of variation: genotype and disturbance by chemicals (NaCl, polyethylene glycol, H2O2, abscisic acid). Exploiting the adventitious rooting capacity of the Populus genus, and using time-lapse imaging under infrared-light, particle image velocimetry, histological analysis, and kinematics, we quantified the cellular processes involved in root growth variation, and analysed the covariation patterns between growth parameters. The rate of cell production by the root apical meristem and the number of dividing cells were estimated in vivo without destructive measurement. We found that the rate of cell division contributed more to the variation in cell production rate than the number of dividing cells. Regardless of the source of variation, the length of the elongation zone was the best proxy for growth rate, summarizing rates of cell production and cell elongation into a single parameter. Our results demonstrate that cell production rate is the main driver of growth rate, whereas elemental elongation rate is a key driver of short-term growth adjustments.
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Affiliation(s)
- Chvan Youssef
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, Nancy, France
| | - François Bizet
- UMR PIAF, INRA, Université Clermont Auvergne, Aubière, France
| | - Renaud Bastien
- Department of Collective Behaviour, Max Planck Institute for Ornithology, University of Konstanz, Konstanz, Germany
| | - David Legland
- UMR Biopolymers, Interactions and Assemblies, INRA, Nantes, France
| | | | - Irène Hummel
- Université de Lorraine, AgroParisTech, INRA, UMR Silva, Nancy, France
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30
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Tardieu F, Cabrera-Bosquet L, Pridmore T, Bennett M. Plant Phenomics, From Sensors to Knowledge. Curr Biol 2018; 27:R770-R783. [PMID: 28787611 DOI: 10.1016/j.cub.2017.05.055] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Major improvements in crop yield are needed to keep pace with population growth and climate change. While plant breeding efforts have greatly benefited from advances in genomics, profiling the crop phenome (i.e., the structure and function of plants) associated with allelic variants and environments remains a major technical bottleneck. Here, we review the conceptual and technical challenges facing plant phenomics. We first discuss how, given plants' high levels of morphological plasticity, crop phenomics presents distinct challenges compared with studies in animals. Next, we present strategies for multi-scale phenomics, and describe how major improvements in imaging, sensor technologies and data analysis are now making high-throughput root, shoot, whole-plant and canopy phenomic studies possible. We then suggest that research in this area is entering a new stage of development, in which phenomic pipelines can help researchers transform large numbers of images and sensor data into knowledge, necessitating novel methods of data handling and modelling. Collectively, these innovations are helping accelerate the selection of the next generation of crops more sustainable and resilient to climate change, and whose benefits promise to scale from physiology to breeding and to deliver real world impact for ongoing global food security efforts.
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Affiliation(s)
- François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F34060, Montpellier, France.
| | - Llorenç Cabrera-Bosquet
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, F34060, Montpellier, France
| | - Tony Pridmore
- School of Computer Science, University of Nottingham, NG8 1BB, UK
| | - Malcolm Bennett
- Plant & Crop Sciences, School of Biosciences, University of Nottingham, LE12 3RD, UK.
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31
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Ren G, Li L, Huang Y, Wang Y, Zhang W, Zheng R, Zhong C, Wang X. GhWIP2, a WIP zinc finger protein, suppresses cell expansion in Gerbera hybrida by mediating crosstalk between gibberellin, abscisic acid, and auxin. THE NEW PHYTOLOGIST 2018; 219:728-742. [PMID: 29681133 DOI: 10.1111/nph.15175] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/19/2018] [Indexed: 05/19/2023]
Abstract
Cell expansion is a key determinant for the final size and shape of plant organ, and is regulated by various phytohormones. Zinc finger proteins (ZFPs) consist of a superfamily involved in multiple aspects of organ morphogenesis. However, little is known about WIP-type ZFP function in phytohormone-mediated organ growth. Using reverse genetics, RNA-seq and phytohormone quantification, we elucidated the role of a new WIP-type ZFP from Gerbera hybrida, GhWIP2, in controlling organ growth via regulation of cell expansion. GhWIP2 localizes to the nucleus and acts as a transcriptional repressor. Constitutive overexpression of GhWIP2 (GhWIP2OE) in both Gerbera and Arabidopsis thaliana caused major developmental defects associated with cell expansion, including dwarfism, short petals, scapes, and petioles. Furthermore, GhWIP2OE plants were hypersensitive to GA, but not to ABA, and showed a reduction in endogenous GA and auxin, but not ABA concentrations. Consistent with these observations, RNA-seq analysis revealed that genes involved in GA and auxin signaling were down-regulated, while those involved in ABA signaling were up-regulated in GhWIP2OE plants. Our findings suggest that GhWIP2 acts as a transcriptional repressor, suppressing cell expansion during organ growth by modulating crosstalk between GA, ABA, and auxin.
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Affiliation(s)
- Guiping Ren
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Lingfei Li
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, 518004, Guangdong, China
| | - Yuhua Huang
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Yaqin Wang
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Wenbin Zhang
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Rouyan Zheng
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Chunmei Zhong
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Xiaojing Wang
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
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32
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Joshi M, Baghel RS, Fogelman E, Stern RA, Ginzberg I. Identification of candidate genes mediating apple fruit-cracking resistance following the application of gibberellic acids 4 + 7 and the cytokinin 6-benzyladenine. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 127:436-445. [PMID: 29684828 DOI: 10.1016/j.plaphy.2018.04.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 05/09/2023]
Abstract
Calyx-end cracking in 'Pink Lady' apple is treated by a solution of gibberellic acids 4 and 7 (GA4+7) and the cytokinin 6-benzyladenine (BA). Although the GA4+7 and BA mixture is applied early in apple fruit development, it mitigates cracking that becomes evident in the mature fruit, implying a long-term treatment effect. The reduced incidence of peel cracking is associated with increased epidermal cell density, which is maintained until fruit maturation. Presently, the expression of genes that have been previously reported to be associated with epidermal cell patterning and cuticle formation, or cracking resistance, was monitored in the peel during fruit development and following GA4+7 and BA treatment. For most of the genes whose expression is naturally upregulated during fruit development, the early GA4+7 and BA treatment maintained or further increased the high expression level in the mature peel. Where the expression of a gene was downregulated during development, no change was detected in the treated mature peel. Gene-networking analysis supported the interaction between gene clusters of cell-wall synthesis, cuticle formation and GA signaling. Overall, the data suggested that the GA4+7 and BA treatment did not modify developmental cues, but promoted or enhanced the innate developmental program.
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Affiliation(s)
- Mukul Joshi
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel
| | - Ravi Singh Baghel
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel
| | - Edna Fogelman
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel
| | - Raphael A Stern
- MIGAL, Galilee Technology Center, P.O. Box 831, Kiryat Shmona 11016, Israel; Department of Biotechnology, Faculty of Life Sciences, Tel-Hai College, Upper Galilee 1220800, Israel
| | - Idit Ginzberg
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel.
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33
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Binenbaum J, Weinstain R, Shani E. Gibberellin Localization and Transport in Plants. TRENDS IN PLANT SCIENCE 2018; 23:410-421. [PMID: 29530380 DOI: 10.1016/j.tplants.2018.02.005] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 05/20/2023]
Abstract
Distribution patterns and finely-tuned concentration gradients of plant hormones govern plant growth and development. Gibberellin (GA) is a plant hormone regulating key processes in plants; many of them are of significant agricultural importance, such as seed germination, root and shoot elongation, flowering, and fruit patterning. Although studies have demonstrated that GA movement is essential for multiple developmental aspects, how GAs are transported throughout the plant and where exactly they accumulate remain largely unknown. Here, we summarize recent findings from studies of GA movement and localization, and discuss the importance of GA intermediates in long- and short-distance movement. We further review recently identified Arabidopsis GA transporters and highlight their complex specialization and robust functional redundancy in GA transport activity.
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Affiliation(s)
- Jenia Binenbaum
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Roy Weinstain
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Eilon Shani
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
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34
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Pavelescu I, Vilarrasa-Blasi J, Planas-Riverola A, González-García MP, Caño-Delgado AI, Ibañes M. A Sizer model for cell differentiation in Arabidopsis thaliana root growth. Mol Syst Biol 2018; 14:e7687. [PMID: 29321184 PMCID: PMC5787709 DOI: 10.15252/msb.20177687] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Plant roots grow due to cell division in the meristem and subsequent cell elongation and differentiation, a tightly coordinated process that ensures growth and adaptation to the changing environment. How the newly formed cells decide to stop elongating becoming fully differentiated is not yet understood. To address this question, we established a novel approach that combines the quantitative phenotypic variability of wild‐type Arabidopsis roots with computational data from mathematical models. Our analyses reveal that primary root growth is consistent with a Sizer mechanism, in which cells sense their length and stop elongating when reaching a threshold value. The local expression of brassinosteroid receptors only in the meristem is sufficient to set this value. Analysis of roots insensitive to BR signaling and of roots with gibberellin biosynthesis inhibited suggests distinct roles of these hormones on cell expansion termination. Overall, our study underscores the value of using computational modeling together with quantitative data to understand root growth.
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Affiliation(s)
- Irina Pavelescu
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra (Cerdanyola del Vallès), Barcelona, Spain.,Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
| | - Josep Vilarrasa-Blasi
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Ainoa Planas-Riverola
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Mary-Paz González-García
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB Bellaterra (Cerdanyola del Vallès), Barcelona, Spain
| | - Marta Ibañes
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain .,Universitat de Barcelona Institute of Complex Systems (UBICS) Universitat de Barcelona, Barcelona, Spain
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35
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Ajmera I, Shi J, Giri J, Wu P, Stekel DJ, Lu C, Hodgman TC. Regulatory feedback response mechanisms to phosphate starvation in rice. NPJ Syst Biol Appl 2018; 4:4. [PMID: 29354282 PMCID: PMC5758793 DOI: 10.1038/s41540-017-0041-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 11/14/2017] [Accepted: 11/24/2017] [Indexed: 01/31/2023] Open
Abstract
Phosphorus is a growth-limiting nutrient for plants. The growing scarcity of phosphate stocks threatens global food security. Phosphate-uptake regulation is so complex and incompletely known that attempts to improve phosphorus use efficiency have had extremely limited success. This study improves our understanding of the molecular mechanisms underlying phosphate uptake by investigating the transcriptional dynamics of two regulators: the Ubiquitin ligase PHO2 and the long non-coding RNA IPS1. Temporal measurements of RNA levels have been integrated into mechanistic mathematical models using advanced statistical techniques. Models based solely on current knowledge could not adequately explain the temporal expression profiles. Further modeling and bioinformatics analysis have led to the prediction of three regulatory features: the PHO2 protein mediates the degradation of its own transcriptional activator to maintain constant PHO2 mRNA levels; the binding affinity of the transcriptional activator of PHO2 is impaired by a phosphate-sensitive transcriptional repressor/inhibitor; and the extremely high levels of IPS1 and its rapid disappearance upon Pi re-supply are best explained by Pi-sensitive RNA protection. This work offers both new opportunities for plant phosphate research that will be essential for informing the development of phosphate efficient crop varieties, and a foundation for the development of models integrating phosphate with other stress responses. Food security is a global priority. One aspect of this is the ability to grow crops in poorer soils with less fertilizer input, of which phosphate is both essential and resource limited. This study provides a quantitative understanding of the genetic regulation of phosphate uptake in rice upon its deficiency. The mathematical models developed in this article lead to three hypotheses for the gaps identified in current knowledge. One of these hypotheses has previously only been reported in animals while the other prompted laboratory experiments, revealing an extra level of regulation at short timescales. These models provide the basis for crop systems biologists to study other aspects of phosphate regulation, including its internal utilisation, external availability and foraging, and, more crucially, in response to other stresses.
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Affiliation(s)
- Ishan Ajmera
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, LE12 5RD UK.,2Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Jing Shi
- 3State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.,4Department of Biology, Texas A&M University, College Station, TX USA
| | - Jitender Giri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Ping Wu
- 3State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China
| | - Dov J Stekel
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, LE12 5RD UK
| | - Chungui Lu
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, LE12 5RD UK.,6School of Animal, Rural and Environmental Sciences, Nottingham Trent University, Nottingham, NG1 4FQ UK
| | - T Charlie Hodgman
- School of Biosciences, The University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough, LE12 5RD UK.,2Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD UK
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36
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Phyo P, Wang T, Kiemle SN, O'Neill H, Pingali SV, Hong M, Cosgrove DJ. Gradients in Wall Mechanics and Polysaccharides along Growing Inflorescence Stems. PLANT PHYSIOLOGY 2017; 175:1593-1607. [PMID: 29084904 PMCID: PMC5717741 DOI: 10.1104/pp.17.01270] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/29/2017] [Indexed: 05/02/2023]
Abstract
At early stages of Arabidopsis (Arabidopsis thaliana) flowering, the inflorescence stem undergoes rapid growth, with elongation occurring predominantly in the apical ∼4 cm of the stem. We measured the spatial gradients for elongation rate, osmotic pressure, cell wall thickness, and wall mechanical compliances and coupled these macroscopic measurements with molecular-level characterization of the polysaccharide composition, mobility, hydration, and intermolecular interactions of the inflorescence cell wall using solid-state nuclear magnetic resonance spectroscopy and small-angle neutron scattering. Force-extension curves revealed a gradient, from high to low, in the plastic and elastic compliances of cell walls along the elongation zone, but plots of growth rate versus wall compliances were strikingly nonlinear. Neutron-scattering curves showed only subtle changes in wall structure, including a slight increase in cellulose microfibril alignment along the growing stem. In contrast, solid-state nuclear magnetic resonance spectra showed substantial decreases in pectin amount, esterification, branching, hydration, and mobility in an apical-to-basal pattern, while the cellulose content increased modestly. These results suggest that pectin structural changes are connected with increases in pectin-cellulose interaction and reductions in wall compliances along the apical-to-basal gradient in growth rate. These pectin structural changes may lessen the ability of the cell wall to undergo stress relaxation and irreversible expansion (e.g. induced by expansins), thus contributing to the growth kinematics of the growing stem.
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Affiliation(s)
- Pyae Phyo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Sarah N Kiemle
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Sai Venkatesh Pingali
- Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Daniel J Cosgrove
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
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37
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Rizza A, Walia A, Lanquar V, Frommer WB, Jones AM. In vivo gibberellin gradients visualized in rapidly elongating tissues. NATURE PLANTS 2017; 3:803-813. [PMID: 28970478 DOI: 10.1038/s41477-017-0021-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/24/2017] [Indexed: 05/27/2023]
Abstract
The phytohormone gibberellin (GA) is a key regulator of plant growth and development. Although the upstream regulation and downstream responses to GA vary across cells and tissues, developmental stages and environmental conditions, the spatiotemporal distribution of GA in vivo remains unclear. Using a combinatorial screen in yeast, we engineered an optogenetic biosensor, GIBBERELLIN PERCEPTION SENSOR 1 (GPS1), that senses nanomolar levels of bioactive GAs. Arabidopsis thaliana plants expressing a nuclear localized GPS1 report on GAs at the cellular level. GA gradients were correlated with gradients of cell length in rapidly elongating roots and dark-grown hypocotyls. In roots, accumulation of exogenously applied GA also correlated with cell length, intimating that a root GA gradient can be established independently of GA biosynthesis. In hypocotyls, GA levels were reduced in a phytochrome interacting factor (pif) quadruple mutant in the dark and increased in a phytochrome double mutant in the light, indicating that PIFs elevate GA in the dark and that phytochrome inhibition of PIFs could lower GA in the light. As GA signalling directs hypocotyl elongation largely through promoting PIF activity, PIF promotion of GA accumulation represents a positive feedback loop within the molecular framework driving rapid hypocotyl growth.
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Affiliation(s)
- Annalisa Rizza
- Sainsbury Laboratory, Cambridge University, Cambridge, UK
| | - Ankit Walia
- Sainsbury Laboratory, Cambridge University, Cambridge, UK
| | - Viviane Lanquar
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
| | - Wolf B Frommer
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA.
- Institute for Molecular Physiology, Heinrich Heine Universität, 40225, Düsseldorf, Germany.
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany.
| | - Alexander M Jones
- Sainsbury Laboratory, Cambridge University, Cambridge, UK.
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA.
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38
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Li H, Torres-Garcia J, Latrasse D, Benhamed M, Schilderink S, Zhou W, Kulikova O, Hirt H, Bisseling T. Plant-Specific Histone Deacetylases HDT1/2 Regulate GIBBERELLIN 2-OXIDASE2 Expression to Control Arabidopsis Root Meristem Cell Number. THE PLANT CELL 2017; 29:2183-2196. [PMID: 28855334 PMCID: PMC5635991 DOI: 10.1105/tpc.17.00366] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/20/2017] [Accepted: 08/29/2017] [Indexed: 05/02/2023]
Abstract
Root growth is modulated by environmental factors and depends on cell production in the root meristem (RM). New cells in the meristem are generated by stem cells and transit-amplifying cells, which together determine RM cell number. Transcription factors and chromatin-remodeling factors have been implicated in regulating the switch from stem cells to transit-amplifying cells. Here, we show that two Arabidopsis thaliana paralogs encoding plant-specific histone deacetylases, HDT1 and HDT2, regulate a second switch from transit-amplifying cells to expanding cells. Knockdown of HDT1/2 (hdt1,2i) results in an earlier switch and causes a reduced RM cell number. Our data show that HDT1/2 negatively regulate the acetylation level of the C19-GIBBERELLIN 2-OXIDASE2 (GA2ox2) locus and repress the expression of GA2ox2 in the RM and elongation zone. Overexpression of GA2ox2 in the RM phenocopies the hdt1,2i phenotype. Conversely, knockout of GA2ox2 partially rescues the root growth defect of hdt1,2i These results suggest that by repressing the expression of GA2ox2, HDT1/2 likely fine-tune gibberellin metabolism and they are crucial for regulating the switch from cell division to expansion to determine RM cell number. We propose that HDT1/2 function as part of a mechanism that modulates root growth in response to environmental factors.
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Affiliation(s)
- Huchen Li
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Jesus Torres-Garcia
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - David Latrasse
- Unité de Recherche en Génomique Végétale, UMR INRA 1165, Université d'Evry Val d'Essonne, ERL CNRS 8196, Saclay Plant Sciences, 91057 Evry, France
- Institut de Biologie des Plantes, CNRS-Université Paris-Sud 11, UMR 8618, 91405 Orsay cedex, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, CNRS-Université Paris-Sud 11, UMR 8618, 91405 Orsay cedex, France
- King Abdullah University of Sciences and Technology, Thuwal 23955, Saudi Arabia
| | - Stefan Schilderink
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Wenkun Zhou
- Department of Plant Sciences, Plant Developmental Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Olga Kulikova
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Heribert Hirt
- Unité de Recherche en Génomique Végétale, UMR INRA 1165, Université d'Evry Val d'Essonne, ERL CNRS 8196, Saclay Plant Sciences, 91057 Evry, France
- King Abdullah University of Sciences and Technology, Thuwal 23955, Saudi Arabia
| | - Ton Bisseling
- Department of Plant Sciences, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands
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39
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The Dynamics of Root Growth: A Geometric Model. Bull Math Biol 2017; 79:1820-1845. [PMID: 28687952 DOI: 10.1007/s11538-017-0308-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 06/08/2017] [Indexed: 10/19/2022]
Abstract
A new model for macroscopic root growth based on a dynamical Riemannian geometry is presented. Assuming that the thickness of the root is much less than its length, the model is restricted to growth in one dimension (1D). We treat 1D tissues as continuous, deformable, growing geometries for sizes larger than 1 mm. The dynamics of the growing root are described by a set of coupled tensor equations for the metric of the tissue and velocity field of material transport in non-Euclidean space. These coupled equations represent a novel feedback mechanism between growth and geometry. We compare 1D numerical simulations of these tissue growth equations to two measures of root growth. First, sectional growth along the simulated root shows an elongation zone common to many species of plant roots. Second, the relative elemental growth rate calculated in silico exhibits spatio-temporal dynamics recently characterized in high-resolution root growth studies but which thus far lack a biological hypothesis to explain them. In our model, these dynamics are a direct consequence of considering growth as both a geometric reaction-diffusion process and expansion due to a distributed source of new materials.
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40
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De Vos D, Dzhurakhalov A, Stijven S, Klosiewicz P, Beemster GTS, Broeckhove J. Virtual Plant Tissue: Building Blocks for Next-Generation Plant Growth Simulation. FRONTIERS IN PLANT SCIENCE 2017; 8:686. [PMID: 28523006 PMCID: PMC5415617 DOI: 10.3389/fpls.2017.00686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 04/13/2017] [Indexed: 05/11/2023]
Abstract
Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks. Multiple levels of model integration and coordination enable combining existing and new models from different sources, with diverse options in terms of input/output. Besides the core simulator the toolset also comprises a tissue editor for manipulating tissue geometry and cell, wall, and node attributes in an interactive manner. A parameter exploration tool is available to study parameter dependence of simulation results by distributing calculations over multiple systems. Availability: Virtual Plant Tissue is available as open source (EUPL license) on Bitbucket (https://bitbucket.org/vptissue/vptissue). The project has a website https://vptissue.bitbucket.io.
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Affiliation(s)
- Dirk De Vos
- Integrated Molecular Plant Physiology Research, Department of Biology, University of AntwerpAntwerp, Belgium
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
| | - Abdiravuf Dzhurakhalov
- Integrated Molecular Plant Physiology Research, Department of Biology, University of AntwerpAntwerp, Belgium
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
| | - Sean Stijven
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
| | - Przemyslaw Klosiewicz
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
| | - Gerrit T. S. Beemster
- Integrated Molecular Plant Physiology Research, Department of Biology, University of AntwerpAntwerp, Belgium
| | - Jan Broeckhove
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
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41
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Yang X, Dong G, Palaniappan K, Mi G, Baskin TI. Temperature-compensated cell production rate and elongation zone length in the root of Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2017; 40:264-276. [PMID: 27813107 DOI: 10.1111/pce.12855] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/26/2016] [Accepted: 10/31/2016] [Indexed: 05/13/2023]
Abstract
To understand how root growth responds to temperature, we used kinematic analysis to quantify division and expansion parameters in the root of Arabidopsis thaliana. Plants were grown at temperatures from 15 to 30 °C, given continuously from germination. Over these temperatures, root length varies more than threefold in the wild type but by only twofold in a double mutant for phytochrome-interacting factor 4 and 5. For kinematics, the spatial profile of velocity was obtained with new software, Stripflow. We find that 30 °C truncates the elongation zone and curtails cell production, responses that probably reflect the elicitation of a common pathway for handling severe stresses. Curiously, rates of cell division at all temperatures are closely correlated with rates of radial expansion. Between 15 to 25 °C, root growth rate, maximal elemental elongation rate, and final cell length scale positively with temperature whereas the length of the meristem scales negatively. Non-linear temperature scaling characterizes meristem cell number, time to transit through either meristem or elongation zone, and average cell division rate. Surprisingly, the length of the elongation zone and the total rate of cell production are temperature invariant, constancies that have implications for our understanding of how the underlying cellular processes are integrated.
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Affiliation(s)
- Xiaoli Yang
- Biology Department, University of Massachusetts, Amherst, 01003, MA, USA
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
| | - Gang Dong
- Biology Department, University of Massachusetts, Amherst, 01003, MA, USA
| | - K Palaniappan
- Computer Science Department, University of Missouri, Columbia, 65211, MO, USA
| | - Guohua Mi
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, China
| | - Tobias I Baskin
- Biology Department, University of Massachusetts, Amherst, 01003, MA, USA
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42
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Fonouni-Farde C, Diet A, Frugier F. Root Development and Endosymbioses: DELLAs Lead the Orchestra. TRENDS IN PLANT SCIENCE 2016; 21:898-900. [PMID: 27666515 DOI: 10.1016/j.tplants.2016.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 08/24/2016] [Accepted: 08/25/2016] [Indexed: 05/08/2023]
Abstract
DELLA proteins, acting as integrators of gibberellin (GA) action, are emerging as key regulators of root system architecture. Recent studies have revealed how they dictate the dynamics of root growth and are required for the establishment of root endosymbioses with rhizobial bacteria and mycorrhizal fungi. Like conductors, DELLAs can thereby harmonize root development depending on soil environments.
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Affiliation(s)
- Camille Fonouni-Farde
- Institute of Plant Sciences Paris Saclay (IPS2), CNRS, Université Paris-Diderot, Université Paris-Sud, INRA, Université Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| | - Anouck Diet
- Institute of Plant Sciences Paris Saclay (IPS2), CNRS, Université Paris-Diderot, Université Paris-Sud, INRA, Université Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| | - Florian Frugier
- Institute of Plant Sciences Paris Saclay (IPS2), CNRS, Université Paris-Diderot, Université Paris-Sud, INRA, Université Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France.
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43
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Zhang N, Xie YD, Guo HJ, Zhao LS, Xiong HC, Gu JY, Li JH, Kong FQ, Sui L, Zhao ZW, Zhao SR, Liu LX. Gibberellins regulate the stem elongation rate without affecting the mature plant height of a quick development mutant of winter wheat (Triticum aestivum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 107:228-236. [PMID: 27317908 DOI: 10.1016/j.plaphy.2016.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/20/2016] [Accepted: 06/04/2016] [Indexed: 06/06/2023]
Abstract
Gibberellin (GA) is essential for determining plant height. Alteration of GA content or GA signaling results in a dwarf or slender phenotype. Here, we characterized a novel wheat mutant, quick development (qd), in which GA regulates stem elongation but does not affect mature plant height. qd and wild-type plants did not exhibit phenotypic differences at the seedling stage. From jointing to heading stage, qd plants were taller than wild-type plants due to elongated cells. However, wild-type and qd plants were the same height at heading. Unlike wild-type plants, qd plants were sensitive to exogenous GA due to mutation of Rht-B1. With continuous GA stimulation, qd seedlings and adult plants were taller than wild-type. Thus, the GA content of qd plants might differ from that of wild-type during the growth process. Analysis of GA biosynthetic gene expression verified this hypothesis and showed that TaKAO, which is involved in catalyzing the early steps of GA biosynthesis, was differentially expressed in qd plants compared with wild-type. The bioactive GA associated gene TaGA20ox was downregulated in qd plants during the late growth stages. Measurements of endogenous GA content were consistent with the gene-expression analysis results. Consistent with the GA content variation, the first three basal internodes were longer and the last two internodes were shorter in qd than in wild-type plants. The qd mutant might be useful in dissecting the mechanism by which GA regulates stem-growing process, and it may be serve as a GA responsive semi-dwarf germplasm in breeding programs.
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Affiliation(s)
- Ning Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Yong-Dun Xie
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Hui-Jun Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Lin-Shu Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Hong-Chun Xiong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Jia-Yu Gu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Jun-Hui Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Fu-Quan Kong
- China Institute of Atomic Energy, Beijing 102413, China
| | - Li Sui
- China Institute of Atomic Energy, Beijing 102413, China
| | - Zi-Wei Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Shi-Rong Zhao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China
| | - Lu-Xiang Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, National Center of Space Mutagenesis for Crop Improvement, Beijing 100081, China.
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44
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Hamant O, Moulia B. How do plants read their own shapes? THE NEW PHYTOLOGIST 2016; 212:333-7. [PMID: 27532273 DOI: 10.1111/nph.14143] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/27/2016] [Indexed: 05/26/2023]
Abstract
Contents 333 I. 333 II. 334 III. 334 IV. 336 336 References 337 SUMMARY: Although the sensing of shape and deformation was historically involved in the control of animal locomotion, it is now increasingly being incorporated in developmental biology. Proprioception, the perception of the self, is particularly key to the question of the reproducibility of shapes: the many regulators of growth may lead to a large array of geometries, but shape sensing restricts these diverse outputs to a limited number of forms. Mechanistically, and in addition to geometrical feedback onto the diffusion and transport of molecular factors, we highlight the role of shape-derived mechanical stress and strain in this process. Through examples at the cell, tissue and organism scales, it appears that such mechanical feedback adds robustness to morphogenesis. Interestingly, synergies exist between shape sensing and response to external cues, such as wind and gravity. Understanding the molecular basis of proprioception is now within reach and opens up many avenues for an integrative view of development.
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Affiliation(s)
- Olivier Hamant
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, F-69342, Lyon, France.
| | - Bruno Moulia
- UCA, INRA, UMR PIAF, 63000, Clermont-Ferrand, France
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45
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Kumar A, Pathak RK, Gupta SM, Gaur VS, Pandey D. Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 19:581-601. [PMID: 26484978 DOI: 10.1089/omi.2015.0106] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes.
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Affiliation(s)
| | - Rajesh Kumar Pathak
- 2 Department of Biotechnology, G. B. Pant Engineering College , Pauri Garhwal-246194, Uttarakhand, India
| | - Sanjay Mohan Gupta
- 3 Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research , DRDO, Haldwani, Uttarakhand, India
| | - Vikram Singh Gaur
- 4 College of Agriculture , Waraseoni, Balaghat, Madhya Pradesh, India
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46
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Rowe JH, Topping JF, Liu J, Lindsey K. Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin. THE NEW PHYTOLOGIST 2016; 211:225-39. [PMID: 26889752 PMCID: PMC4982081 DOI: 10.1111/nph.13882] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 01/06/2016] [Indexed: 05/17/2023]
Abstract
Understanding the mechanisms regulating root development under drought conditions is an important question for plant biology and world agriculture. We examine the effect of osmotic stress on abscisic acid (ABA), cytokinin and ethylene responses and how they mediate auxin transport, distribution and root growth through effects on PIN proteins. We integrate experimental data to construct hormonal crosstalk networks to formulate a systems view of root growth regulation by multiple hormones. Experimental analysis shows: that ABA-dependent and ABA-independent stress responses increase under osmotic stress, but cytokinin responses are only slightly reduced; inhibition of root growth under osmotic stress does not require ethylene signalling, but auxin can rescue root growth and meristem size; osmotic stress modulates auxin transporter levels and localization, reducing root auxin concentrations; PIN1 levels are reduced under stress in an ABA-dependent manner, overriding ethylene effects; and the interplay among ABA, ethylene, cytokinin and auxin is tissue-specific, as evidenced by differential responses of PIN1 and PIN2 to osmotic stress. Combining experimental analysis with network construction reveals that ABA regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin.
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Affiliation(s)
- James H. Rowe
- The Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Jennifer F. Topping
- The Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Junli Liu
- The Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Keith Lindsey
- The Integrative Cell Biology LaboratorySchool of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
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47
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Muraro D, Larrieu A, Lucas M, Chopard J, Byrne H, Godin C, King J. A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J Theor Biol 2016; 404:182-205. [PMID: 27157127 DOI: 10.1016/j.jtbi.2016.04.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 10/25/2015] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
Abstract
The growth of the root of Arabidopsis thaliana is sustained by the meristem, a region of cell proliferation and differentiation which is located in the root apex and generates cells which move shootwards, expanding rapidly to cause root growth. The balance between cell division and differentiation is maintained via a signalling network, primarily coordinated by the hormones auxin, cytokinin and gibberellin. Since these hormones interact at different levels of spatial organisation, we develop a multi-scale computational model which enables us to study the interplay between these signalling networks and cell-cell communication during the specification of the root meristem. We investigate the responses of our model to hormonal perturbations, validating the results of our simulations against experimental data. Our simulations suggest that one or more additional components are needed to explain the observed expression patterns of a regulator of cytokinin signalling, ARR1, in roots not producing gibberellin. By searching for novel network components, we identify two mutant lines that affect significantly both root length and meristem size, one of which also differentially expresses a central component of the interaction network (SHY2). More generally, our study demonstrates how a multi-scale investigation can provide valuable insight into the spatio-temporal dynamics of signalling networks in biological tissues.
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Affiliation(s)
- D Muraro
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK; The Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK; Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK.
| | - A Larrieu
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK
| | - M Lucas
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK; Equipe CERES, UMR DIADE, IRD, 34394 Montpellier, France
| | - J Chopard
- Virtual Plants Project-Team, UMR AGAP, INRIA/CIRAD, Montpellier, France
| | - H Byrne
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK; Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK; School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - C Godin
- Virtual Plants Project-Team, UMR AGAP, INRIA/CIRAD, Montpellier, France
| | - J King
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
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48
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Lavedrine C, Farcot E, Vernoux T. Modeling plant development: from signals to gene networks. CURRENT OPINION IN PLANT BIOLOGY 2015; 27:148-153. [PMID: 26247125 DOI: 10.1016/j.pbi.2015.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/29/2015] [Accepted: 07/07/2015] [Indexed: 06/04/2023]
Abstract
Mathematical modeling has become a common tool in plant developmental biology. Indeed, it allows for the prediction of complex and often unintuitive dynamics of the molecular networks driving plant development. This has enabled the test of their possible involvement in robust and specific developmental processes. Modeling has also been fruitful in predicting new interactions within gene networks, such as the Arabidopsis circadian clock. A new challenge is to integrate patterning issues with tissue growth and biomechanics. The development of new tools to gain resolution in data collection as well as new frameworks to confront models and data might provide even more robust predictions.
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Affiliation(s)
- Cyril Lavedrine
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Etienne Farcot
- School of Mathematical Sciences & Centre for Plant Integrative Biology, University of Nottingham, NG7 2RD, United Kingdom.
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France.
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49
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Jensen OE, Fozard JA. Multiscale models in the biomechanics of plant growth. Physiology (Bethesda) 2015; 30:159-66. [PMID: 25729061 DOI: 10.1152/physiol.00030.2014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Plant growth occurs through the coordinated expansion of tightly adherent cells, driven by regulated softening of cell walls. It is an intrinsically multiscale process, with the integrated properties of multiple cell walls shaping the whole tissue. Multiscale models encode physical relationships to bring new understanding to plant physiology and development.
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Affiliation(s)
- Oliver E Jensen
- School of Mathematics, University of Manchester, Manchester, United Kingdom; and
| | - John A Fozard
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
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50
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Montenegro-Johnson TD, Stamm P, Strauss S, Topham AT, Tsagris M, Wood ATA, Smith RS, Bassel GW. Digital Single-Cell Analysis of Plant Organ Development Using 3DCellAtlas. THE PLANT CELL 2015; 27:1018-33. [PMID: 25901089 PMCID: PMC4558707 DOI: 10.1105/tpc.15.00175] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 03/27/2015] [Indexed: 05/04/2023]
Abstract
Diverse molecular networks underlying plant growth and development are rapidly being uncovered. Integrating these data into the spatial and temporal context of dynamic organ growth remains a technical challenge. We developed 3DCellAtlas, an integrative computational pipeline that semiautomatically identifies cell types and quantifies both 3D cellular anisotropy and reporter abundance at single-cell resolution across whole plant organs. Cell identification is no less than 97.8% accurate and does not require transgenic lineage markers or reference atlases. Cell positions within organs are defined using an internal indexing system generating cellular level organ atlases where data from multiple samples can be integrated. Using this approach, we quantified the organ-wide cell-type-specific 3D cellular anisotropy driving Arabidopsis thaliana hypocotyl elongation. The impact ethylene has on hypocotyl 3D cell anisotropy identified the preferential growth of endodermis in response to this hormone. The spatiotemporal dynamics of the endogenous DELLA protein RGA, expansin gene EXPA3, and cell expansion was quantified within distinct cell types of Arabidopsis roots. A significant regulatory relationship between RGA, EXPA3, and growth was present in the epidermis and endodermis. The use of single-cell analyses of plant development enables the dynamics of diverse regulatory networks to be integrated with 3D organ growth.
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Affiliation(s)
| | - Petra Stamm
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Soeren Strauss
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Alexander T Topham
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Michail Tsagris
- University of Nottingham, Division of Statistics, School of Mathematical Sciences, Nottingham NG7 2RD, United Kingdom
| | - Andrew T A Wood
- University of Nottingham, Division of Statistics, School of Mathematical Sciences, Nottingham NG7 2RD, United Kingdom
| | - Richard S Smith
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - George W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
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