51
|
Robbins NE, Dinneny JR. The divining root: moisture-driven responses of roots at the micro- and macro-scale. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2145-54. [PMID: 25617469 PMCID: PMC4817643 DOI: 10.1093/jxb/eru496] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Water is fundamental to plant life, but the mechanisms by which plant roots sense and respond to variations in water availability in the soil are poorly understood. Many studies of responses to water deficit have focused on large-scale effects of this stress, but have overlooked responses at the sub-organ or cellular level that give rise to emergent whole-plant phenotypes. We have recently discovered hydropatterning, an adaptive environmental response in which roots position new lateral branches according to the spatial distribution of available water across the circumferential axis. This discovery illustrates that roots are capable of sensing and responding to water availability at spatial scales far lower than those normally studied for such processes. This review will explore how roots respond to water availability with an emphasis on what is currently known at different spatial scales. Beginning at the micro-scale, there is a discussion of water physiology at the cellular level and proposed sensory mechanisms cells use to detect osmotic status. The implications of these principles are then explored in the context of cell and organ growth under non-stress and water-deficit conditions. Following this, several adaptive responses employed by roots to tailor their functionality to the local moisture environment are discussed, including patterning of lateral root development and generation of hydraulic barriers to limit water loss. We speculate that these micro-scale responses are necessary for optimal functionality of the root system in a heterogeneous moisture environment, allowing for efficient water uptake with minimal water loss during periods of drought.
Collapse
Affiliation(s)
- Neil E Robbins
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA
| |
Collapse
|
52
|
Robbins NE, Dinneny JR. The divining root: moisture-driven responses of roots at the micro- and macro-scale. JOURNAL OF EXPERIMENTAL BOTANY 2015. [PMID: 25617469 DOI: 10.1093/jxb/eru49496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Water is fundamental to plant life, but the mechanisms by which plant roots sense and respond to variations in water availability in the soil are poorly understood. Many studies of responses to water deficit have focused on large-scale effects of this stress, but have overlooked responses at the sub-organ or cellular level that give rise to emergent whole-plant phenotypes. We have recently discovered hydropatterning, an adaptive environmental response in which roots position new lateral branches according to the spatial distribution of available water across the circumferential axis. This discovery illustrates that roots are capable of sensing and responding to water availability at spatial scales far lower than those normally studied for such processes. This review will explore how roots respond to water availability with an emphasis on what is currently known at different spatial scales. Beginning at the micro-scale, there is a discussion of water physiology at the cellular level and proposed sensory mechanisms cells use to detect osmotic status. The implications of these principles are then explored in the context of cell and organ growth under non-stress and water-deficit conditions. Following this, several adaptive responses employed by roots to tailor their functionality to the local moisture environment are discussed, including patterning of lateral root development and generation of hydraulic barriers to limit water loss. We speculate that these micro-scale responses are necessary for optimal functionality of the root system in a heterogeneous moisture environment, allowing for efficient water uptake with minimal water loss during periods of drought.
Collapse
Affiliation(s)
- Neil E Robbins
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA Department of Biology, Stanford University, 371 Serra Mall, Stanford, CA 94305, USA
| | - José R Dinneny
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA
| |
Collapse
|
53
|
Li G, Zhu C, Gan L, Ng D, Xia K. GA(3) enhances root responsiveness to exogenous IAA by modulating auxin transport and signalling in Arabidopsis. PLANT CELL REPORTS 2015; 34:483-94. [PMID: 25540118 DOI: 10.1007/s00299-014-1728-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/13/2014] [Accepted: 12/03/2014] [Indexed: 05/22/2023]
Abstract
We used auxin-signalling mutants, auxin transport mutants, and auxin-related marker lines to show that exogenously applied GA enhances auxin-induced root inhibition by affecting auxin signalling and transport. Variation in root elongation is valuable when studying the interactions of phytohormones. Auxins influence the biosynthesis and signalling of gibberellins (GAs), but the influence of GAs on auxins in root elongation is poorly understood. This study was conducted to investigate the effect of GA3 on Arabidopsis root elongation in the presence of auxin. Root elongation was inhibited in roots treated with both IAA and GA3, compared to IAA alone, and the effect was dose dependent. Further experiments showed that GA3 could modulate auxin signalling based on root elongation in auxin-signalling mutants and the expression of auxin-responsive reporters. The GA3-enhanced inhibition of root elongation observed in the wild type was not found in the auxin-signalling mutants tir1-1 and axr1-3. GA3 increased DR5::GUS expression in the root meristem and elongation zones, and IAA2::GUS in the columella. The DR5rev::GFP signal was enhanced in columella cells of the root caps and in the elongation zone in GA3-treated seedling roots. A reduction was observed in the stele of PAC-treated roots. We also examined the effect of GA3 on auxin transport. The enhanced responsiveness caused by GA3 was not observed in the auxin influx mutant aux1-7 or the efflux mutant eir1-1. Additional molecular data demonstrated that GA3 could promote auxin transport via AUX1 and PIN proteins. However, GA3-induced PIN gene expression did not fully explain GA-enhanced PIN protein accumulation. These results suggest that GA3 is involved in auxin-mediated primary root elongation by modulating auxin signalling and transport, and thus enhances root responsiveness to exogenous IAA.
Collapse
Affiliation(s)
- Guijun Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | | | | | | | | |
Collapse
|
54
|
González N, Inzé D. Molecular systems governing leaf growth: from genes to networks. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1045-54. [PMID: 25601785 DOI: 10.1093/jxb/eru541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Arabidopsis leaf growth consists of a complex sequence of interconnected events involving cell division and cell expansion, and requiring multiple levels of genetic regulation. With classical genetics, numerous leaf growth regulators have been identified, but the picture is far from complete. With the recent advances made in quantitative phenotyping, the study of the quantitative, dynamic, and multifactorial features of leaf growth is now facilitated. The use of high-throughput phenotyping technologies to study large numbers of natural accessions or mutants, or to screen for the effects of large sets of chemicals will allow for further identification of the additional players that constitute the leaf growth regulatory networks. Only a tight co-ordination between these numerous molecular players can support the formation of a functional organ. The connections between the components of the network and their dynamics can be further disentangled through gene-stacking approaches and ultimately through mathematical modelling. In this review, we describe these different approaches that should help to obtain a holistic image of the molecular regulation of organ growth which is of high interest in view of the increasing needs for plant-derived products.
Collapse
Affiliation(s)
- Nathalie González
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| |
Collapse
|
55
|
Hodgman T, Ajmera I. The successful application of systems approaches in plant biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 117:59-68. [DOI: 10.1016/j.pbiomolbio.2015.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/12/2015] [Indexed: 11/26/2022]
|
56
|
Cole RA, McInally SA, Fowler JE. Developmentally distinct activities of the exocyst enable rapid cell elongation and determine meristem size during primary root growth in Arabidopsis. BMC PLANT BIOLOGY 2014; 14:386. [PMID: 25551204 PMCID: PMC4302519 DOI: 10.1186/s12870-014-0386-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 12/15/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Exocytosis is integral to root growth: trafficking components of systems that control growth (e.g., PIN auxin transport proteins) to the plasma membrane, and secreting materials that expand the cell wall to the apoplast. Spatiotemporal regulation of exocytosis in eukaryotes often involves the exocyst, an octameric complex that tethers selected secretory vesicles to specific sites on the plasma membrane and facilitates their exocytosis. We evaluated Arabidopsis lines with mutations in four exocyst components (SEC5, SEC8, EXO70A1 and EXO84B) to explore exocyst function in primary root growth. RESULTS The mutants have root growth rates that are 82% to 11% of wild-type. Even in lines with the most severe defects, the organization of the quiescent center and tissue layers at the root tips appears similar to wild-type, although meristematic, transition, and elongation zones are shorter. Reduced cell production rates in the mutants are due to the shorter meristems, but not to lengthened cell cycles. Additionally, mutants demonstrate reduced anisotropic cell expansion in the elongation zone, but not the meristematic zone, resulting in shorter mature cells that are similar in shape to wild-type. As expected, hypersensitivity to brefeldin A links the mutant root growth defect to altered vesicular trafficking. Several experimental approaches (e.g., dose-response measurements, localization of signaling components) failed to identify aberrant auxin or brassinosteroid signaling as a primary driver for reduced root growth in exocyst mutants. CONCLUSIONS The exocyst participates in two spatially distinct developmental processes, apparently by mechanisms not directly linked to auxin or brassinosteroid signaling pathways, to help establish root meristem size, and to facilitate rapid cell expansion in the elongation zone.
Collapse
Affiliation(s)
- Rex A Cole
- Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, 97331 OR USA
| | - Samantha A McInally
- Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, 97331 OR USA
| | - John E Fowler
- Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, 97331 OR USA
| |
Collapse
|
57
|
Regnault T, Davière JM, Heintz D, Lange T, Achard P. The gibberellin biosynthetic genes AtKAO1 and AtKAO2 have overlapping roles throughout Arabidopsis development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:462-74. [PMID: 25146977 DOI: 10.1111/tpj.12648] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 05/10/2023]
Abstract
Ent-kaurenoic acid oxidase (KAO), a class of cytochrome P450 monooxygenases of the subfamily CYP88A, catalyzes the conversion of ent-kaurenoic acid (KA) to gibberellin (GA) GA12 , the precursor of all GAs, thereby playing an important role in determining GA concentration in plants. Past work has demonstrated the importance of KAO activity for growth in various plant species. In Arabidopsis, this enzyme is encoded by two genes designated KAO1 and KAO2. In this study, we used various approaches to determine the physiological roles of KAO1 and KAO2 throughout plant development. Analysis of gene expression pattern reveals that both genes are mainly expressed in germinating seeds and young developing organs, thus suggesting functional redundancy. Consistent with this, kao1 and kao2 single mutants are indistinguishable from wild-type plants. By contrast, the kao1 kao2 double mutant exhibits typical non-germinating GA-dwarf phenotypes, similar to those observed in the severely GA-deficient ga1-3 mutant. Phenotypic characterization and quantitative analysis of endogenous GA contents of single and double kao mutants further confirm an overlapping role of KAO1 and KAO2 throughout Arabidopsis development.
Collapse
Affiliation(s)
- Thomas Regnault
- Institut de Biologie Moléculaire des Plantes, UPR2357, conventionné avec l'Université de Strasbourg, 67084, Strasbourg, France
| | | | | | | | | |
Collapse
|
58
|
De Vos D, Vissenberg K, Broeckhove J, Beemster GTS. Putting theory to the test: which regulatory mechanisms can drive realistic growth of a root? PLoS Comput Biol 2014; 10:e1003910. [PMID: 25358093 PMCID: PMC4214622 DOI: 10.1371/journal.pcbi.1003910] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 09/15/2014] [Indexed: 01/20/2023] Open
Abstract
In recent years there has been a strong development of computational approaches to mechanistically understand organ growth regulation in plants. In this study, simulation methods were used to explore which regulatory mechanisms can lead to realistic output at the cell and whole organ scale and which other possibilities must be discarded as they result in cellular patterns and kinematic characteristics that are not consistent with experimental observations for the Arabidopsis thaliana primary root. To aid in this analysis, a ‘Uniform Longitudinal Strain Rule’ (ULSR) was formulated as a necessary condition for stable, unidirectional, symplastic growth. Our simulations indicate that symplastic structures are robust to differences in longitudinal strain rates along the growth axis only if these differences are small and short-lived. Whereas simple cell-autonomous regulatory rules based on counters and timers can produce stable growth, it was found that steady developmental zones and smooth transitions in cell lengths are not feasible. By introducing spatial cues into growth regulation, those inadequacies could be avoided and experimental data could be faithfully reproduced. Nevertheless, a root growth model based on previous polar auxin-transport mechanisms violates the proposed ULSR due to the presence of lateral gradients. Models with layer-specific regulation or layer-driven growth offer potential solutions. Alternatively, a model representing the known cross-talk between auxin, as the cell proliferation promoting factor, and cytokinin, as the cell differentiation promoting factor, predicts the effect of hormone-perturbations on meristem size. By down-regulating PIN-mediated transport through the transcription factor SHY2, cytokinin effectively flattens the lateral auxin gradient, at the basal boundary of the division zone, (thereby imposing the ULSR) to signal the exit of proliferation and start of elongation. This model exploration underlines the value of generating virtual root growth kinematics to dissect and understand the mechanisms controlling this biological system. The growth of a plant root is driven by cell division and cell expansion occurring in spatially distinct developmental zones. Although these zones are in principle stable, depending on the conditions, their size and properties can be modulated. This has been meticulously described by kinematic studies, which have led to the proposal of mechanisms underpinning those observations. At the same time, much knowledge of the identities and interactions of molecules involved in these mechanisms has accumulated, in particular from the model species Arabidopsis thaliana. Here we attempt to resolve the longstanding question whether observed growth patterns can be explained by autonomous decision-making at the level of individual cells or if the aid of some external signal is required. We then ask, building on the accumulated molecular information, which minimal models can provide for stable growth while keeping sufficient flexibility to regulate growth. Therefore, we constructed computational models for different growth mechanisms operating in a virtual two-dimensional Arabidopsis root and compared their behaviour with biological experiments. The simulations provide strong indications that spatial signals are required for realistic and flexible root growth, likely orchestrated by the plant hormones auxin and cytokinin.
Collapse
Affiliation(s)
- Dirk De Vos
- Molecular Plant Physiology and Biotechnology, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Kris Vissenberg
- Plant Growth and Development, Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Jan Broeckhove
- Computational Modelling and Programming, Department of Mathematics and Informatics, University of Antwerp, Antwerp, Belgium
| | - Gerrit T. S. Beemster
- Molecular Plant Physiology and Biotechnology, Department of Biology, University of Antwerp, Antwerp, Belgium
- * E-mail:
| |
Collapse
|
59
|
Wang L, Mu C, Du M, Chen Y, Tian X, Zhang M, Li Z. The effect of mepiquat chloride on elongation of cotton (Gossypium hirsutum L.) internode is associated with low concentration of gibberellic acid. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 225:15-23. [PMID: 25017155 DOI: 10.1016/j.plantsci.2014.05.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/05/2014] [Accepted: 05/12/2014] [Indexed: 05/03/2023]
Abstract
The growth regulator mepiquat chloride (MC) is globally used in cotton (Gossypium hirsutum L.) canopy manipulation to avoid excess growth and yield loss. However, little information is available as to whether the modification of plant architecture by MC is related to alterations in gibberellic acid (GA) metabolism and signaling. Here, the role of GA metabolism and signaling was investigated in cotton seedlings treated with MC. The MC significantly decreased endogenous GA3 and GA4 levels in the elongating internode, which inhibited cell elongation by downregulating GhEXP and GhXTH2, and then reducing plant height. Biosynthetic and metabolic genes of GA were markedly suppressed within 2-10d of MC treatment, which also downregulated the expression of DELLA-like genes. A remarkable feedback regulation was observed at the early stage of MC treatment when GA biosynthetic and metabolic genes expression was evidently upregulated. Mepiquat chloride action was controlled by temporal translocation and spatial accumulation which regulated GA biosynthesis and signal expression for maintaining GA homeostasis. The results suggested that MC application could reduce endogenous GA levels in cotton through controlled GA biosynthetic and metabolic genes expression, which might inhibit cell elongation, thereby shortening the internode and reducing plant height.
Collapse
Affiliation(s)
- Li Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China; College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, China
| | - Chun Mu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Mingwei Du
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yin Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaoli Tian
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Mingcai Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Zhaohu Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
60
|
Dyson RJ, Vizcay-Barrena G, Band LR, Fernandes AN, French AP, Fozard JA, Hodgman TC, Kenobi K, Pridmore TP, Stout M, Wells DM, Wilson MH, Bennett MJ, Jensen OE. Mechanical modelling quantifies the functional importance of outer tissue layers during root elongation and bending. THE NEW PHYTOLOGIST 2014; 202:1212-1222. [PMID: 24641449 PMCID: PMC4286105 DOI: 10.1111/nph.12764] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 02/02/2014] [Indexed: 05/18/2023]
Abstract
Root elongation and bending require the coordinated expansion of multiple cells of different types. These processes are regulated by the action of hormones that can target distinct cell layers. We use a mathematical model to characterise the influence of the biomechanical properties of individual cell walls on the properties of the whole tissue. Taking a simple constitutive model at the cell scale which characterises cell walls via yield and extensibility parameters, we derive the analogous tissue-level model to describe elongation and bending. To accurately parameterise the model, we take detailed measurements of cell turgor, cell geometries and wall thicknesses. The model demonstrates how cell properties and shapes contribute to tissue-level extensibility and yield. Exploiting the highly organised structure of the elongation zone (EZ) of the Arabidopsis root, we quantify the contributions of different cell layers, using the measured parameters. We show how distributions of material and geometric properties across the root cross-section contribute to the generation of curvature, and relate the angle of a gravitropic bend to the magnitude and duration of asymmetric wall softening. We quantify the geometric factors which lead to the predominant contribution of the outer cell files in driving root elongation and bending.
Collapse
Affiliation(s)
- Rosemary J Dyson
- School of Mathematics, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Gema Vizcay-Barrena
- Centre for Ultrastructural Imaging, King's College London, London, SE1 1UL, UK
| | - Leah R Band
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Anwesha N Fernandes
- School of Physics & Astronomy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Andrew P French
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - John A Fozard
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - T Charlie Hodgman
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Kim Kenobi
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Tony P Pridmore
- School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham, NG8 1BB, UK
| | - Michael Stout
- School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Darren M Wells
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Michael H Wilson
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Oliver E Jensen
- School of Mathematics, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| |
Collapse
|
61
|
Voß U, Bishopp A, Farcot E, Bennett MJ. Modelling hormonal response and development. TRENDS IN PLANT SCIENCE 2014; 19:311-9. [PMID: 24630843 PMCID: PMC4013931 DOI: 10.1016/j.tplants.2014.02.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 05/20/2023]
Abstract
As our knowledge of the complexity of hormone homeostasis, transport, perception, and response increases, and their outputs become less intuitive, modelling is set to become more important. Initial modelling efforts have focused on hormone transport and response pathways. However, we now need to move beyond the network scales and use multicellular and multiscale modelling approaches to predict emergent properties at different scales. Here we review some examples where such approaches have been successful, for example, auxin-cytokinin crosstalk regulating root vascular development or a study of lateral root emergence where an iterative cycle of modelling and experiments lead to the identification of an overlooked role for PIN3. Finally, we discuss some of the remaining biological and technical challenges.
Collapse
Affiliation(s)
- Ute Voß
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Etienne Farcot
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK.
| |
Collapse
|
62
|
Claeys H, De Bodt S, Inzé D. Gibberellins and DELLAs: central nodes in growth regulatory networks. TRENDS IN PLANT SCIENCE 2014; 19:231-9. [PMID: 24182663 DOI: 10.1016/j.tplants.2013.10.001] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/27/2013] [Accepted: 10/04/2013] [Indexed: 05/22/2023]
Abstract
Gibberellins (GAs) are growth-promoting phytohormones that were crucial in breeding improved semi-dwarf varieties during the green revolution. However, the molecular basis for GA-induced growth stimulation is poorly understood. In this review, we use light-regulated hypocotyl elongation as a case study, combined with a meta-analysis of available transcriptome data, to discuss the role of GAs as central nodes in networks connecting environmental inputs to growth. These networks are highly tissue-specific, with dynamic and rapid regulation that mostly occurs at the protein level, directly affecting the activity and transcription of effectors. New systems biology approaches addressing the role of GAs in growth should take these properties into account, combining tissue-specific interactomics, transcriptomics and modeling, to provide essential knowledge to fuel a second green revolution.
Collapse
Affiliation(s)
- Hannes Claeys
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Stefanie De Bodt
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
| |
Collapse
|
63
|
Sozzani R, Iyer-Pascuzzi A. Postembryonic control of root meristem growth and development. CURRENT OPINION IN PLANT BIOLOGY 2014; 17:7-12. [PMID: 24507488 DOI: 10.1016/j.pbi.2013.10.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 10/10/2013] [Indexed: 05/08/2023]
Abstract
Organ development in multicellular organisms is dependent on the proper balance between cell proliferation and differentiation. In the Arabidopsis root apical meristem, meristem growth is the result of cell divisions in the proximal meristem and cell differentiation in the elongation and differentiation zones. Hormones, transcription factors and small peptides underpin the molecular mechanisms governing these processes. Computer modeling has aided our understanding of the dynamic interactions involved in stem cell maintenance and meristem activity. Here we review recent advances in our understanding of postembryonic root stem cell maintenance and control of meristem size.
Collapse
Affiliation(s)
- Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Anjali Iyer-Pascuzzi
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States.
| |
Collapse
|
64
|
Baluška F, Mancuso S. Root apex transition zone as oscillatory zone. FRONTIERS IN PLANT SCIENCE 2013; 4:354. [PMID: 24106493 PMCID: PMC3788588 DOI: 10.3389/fpls.2013.00354] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/22/2013] [Indexed: 05/17/2023]
Abstract
Root apex of higher plants shows very high sensitivity to environmental stimuli. The root cap acts as the most prominent plant sensory organ; sensing diverse physical parameters such as gravity, light, humidity, oxygen, and critical inorganic nutrients. However, the motoric responses to these stimuli are accomplished in the elongation region. This spatial discrepancy was solved when we have discovered and characterized the transition zone which is interpolated between the apical meristem and the subapical elongation zone. Cells of this zone are very active in the cytoskeletal rearrangements, endocytosis and endocytic vesicle recycling, as well as in electric activities. Here we discuss the oscillatory nature of the transition zone which, together with several other features of this zone, suggest that it acts as some kind of command center. In accordance with the early proposal of Charles and Francis Darwin, cells of this root zone receive sensory information from the root cap and instruct the motoric responses of cells in the elongation zone.
Collapse
Affiliation(s)
- František Baluška
- Institute of Cellular and Molecular Botany, Department of Plant Cell Biology, University of BonnBonn, Germany
| | - Stefano Mancuso
- LINV – DiSPAA, Department of Agri-Food and Environmental Science, University of FlorenceSesto Fiorentino, Italy
| |
Collapse
|
65
|
Wasternack C, Hause B. Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. ANNALS OF BOTANY 2013; 111:1021-1058. [PMID: 23558912 DOI: 10.1093/aob/mct06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
BACKGROUND Jasmonates are important regulators in plant responses to biotic and abiotic stresses as well as in development. Synthesized from lipid-constituents, the initially formed jasmonic acid is converted to different metabolites including the conjugate with isoleucine. Important new components of jasmonate signalling including its receptor were identified, providing deeper insight into the role of jasmonate signalling pathways in stress responses and development. SCOPE The present review is an update of the review on jasmonates published in this journal in 2007. New data of the last five years are described with emphasis on metabolites of jasmonates, on jasmonate perception and signalling, on cross-talk to other plant hormones and on jasmonate signalling in response to herbivores and pathogens, in symbiotic interactions, in flower development, in root growth and in light perception. CONCLUSIONS The last few years have seen breakthroughs in the identification of JASMONATE ZIM DOMAIN (JAZ) proteins and their interactors such as transcription factors and co-repressors, and the crystallization of the jasmonate receptor as well as of the enzyme conjugating jasmonate to amino acids. Now, the complex nature of networks of jasmonate signalling in stress responses and development including hormone cross-talk can be addressed.
Collapse
Affiliation(s)
- C Wasternack
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg, 3, Halle (Saale), Germany.
| | | |
Collapse
|
66
|
Wasternack C, Hause B. Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany. ANNALS OF BOTANY 2013; 111:1021-58. [PMID: 23558912 PMCID: PMC3662512 DOI: 10.1093/aob/mct067] [Citation(s) in RCA: 1442] [Impact Index Per Article: 131.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 01/23/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND Jasmonates are important regulators in plant responses to biotic and abiotic stresses as well as in development. Synthesized from lipid-constituents, the initially formed jasmonic acid is converted to different metabolites including the conjugate with isoleucine. Important new components of jasmonate signalling including its receptor were identified, providing deeper insight into the role of jasmonate signalling pathways in stress responses and development. SCOPE The present review is an update of the review on jasmonates published in this journal in 2007. New data of the last five years are described with emphasis on metabolites of jasmonates, on jasmonate perception and signalling, on cross-talk to other plant hormones and on jasmonate signalling in response to herbivores and pathogens, in symbiotic interactions, in flower development, in root growth and in light perception. CONCLUSIONS The last few years have seen breakthroughs in the identification of JASMONATE ZIM DOMAIN (JAZ) proteins and their interactors such as transcription factors and co-repressors, and the crystallization of the jasmonate receptor as well as of the enzyme conjugating jasmonate to amino acids. Now, the complex nature of networks of jasmonate signalling in stress responses and development including hormone cross-talk can be addressed.
Collapse
Affiliation(s)
- C Wasternack
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg, 3, Halle (Saale), Germany.
| | | |
Collapse
|
67
|
Ivanov VB, Dubrovsky JG. Longitudinal zonation pattern in plant roots: conflicts and solutions. TRENDS IN PLANT SCIENCE 2013; 18:237-43. [PMID: 23123304 DOI: 10.1016/j.tplants.2012.10.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/27/2012] [Accepted: 10/05/2012] [Indexed: 05/21/2023]
Abstract
Despite the relative simplicity of Arabidopsis root organization, there is no general agreement regarding the terminology used to describe the longitudinal zonation pattern (LZP) of this model system. In this opinion article, we examine inconsistencies in the terminology and provide a conceptual framework for the LZP that may be applied to all angiosperms. We propose that the root apical meristem (RAM) consists of the cell-proliferation domain where cells maintain a high probability to divide and the transition domain with a low probability of cell division; in both domains cells grow at the same, relatively low, rate. Owing to stochastic termination of cell proliferation in the RAM, the border between the domains is 'fuzzy'. Molecular markers analyzed together with quantitative growth and cell analyses could help to identify developmental zones along the root and lead to a better understanding of the LZP in angiosperms.
Collapse
Affiliation(s)
- Victor B Ivanov
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya ul. 35, Moscow, 127276 Russia.
| | | |
Collapse
|
68
|
Abstract
The plant hormone gibberellin (GA) regulates major aspects of plant growth and development. The role of GA in determining plant stature had major impacts on agriculture in the 1960s, and the development of semi-dwarf varieties that show altered GA responses contributed to a huge increase in grain yields during the ‘green revolution’. The past decade has brought great progress in understanding the molecular basis of GA action, with the cloning and characterization of GA signaling components. Here, we review the molecular basis of the GA signaling pathway, from the perception of GA to the regulation of downstream genes.
Collapse
Affiliation(s)
- Jean-Michel Davière
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l’Université de Strasbourg, 67084 Strasbourg, France
| | - Patrick Achard
- Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, Unité Propre de Recherche 2357, Conventionné avec l’Université de Strasbourg, 67084 Strasbourg, France
| |
Collapse
|
69
|
Mapping the site of action of the Green Revolution hormone gibberellin. Proc Natl Acad Sci U S A 2013; 110:4443-4. [PMID: 23476062 DOI: 10.1073/pnas.1301609110] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
70
|
Gibberellins accumulate in the elongating endodermal cells of Arabidopsis root. Proc Natl Acad Sci U S A 2013; 110:4834-9. [PMID: 23382232 DOI: 10.1073/pnas.1300436110] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Plant hormones are small-molecule signaling compounds that are collectively involved in all aspects of plant growth and development. Unlike animals, plants actively regulate the spatial distribution of several of their hormones. For example, auxin transport results in the formation of auxin maxima that have a key role in developmental patterning. However, the spatial distribution of the other plant hormones, including gibberellic acid (GA), is largely unknown. To address this, we generated two bioactive fluorescent GA compounds and studied their distribution in Arabidopsis thaliana roots. The labeled GAs specifically accumulated in the endodermal cells of the root elongation zone. Pharmacological studies, along with examination of mutants affected in endodermal specification, indicate that GA accumulation is an active and highly regulated process. Our results strongly suggest the presence of an active GA transport mechanism that would represent an additional level of GA regulation.
Collapse
|
71
|
Oliva M, Farcot E, Vernoux T. Plant hormone signaling during development: insights from computational models. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:19-24. [PMID: 23219863 DOI: 10.1016/j.pbi.2012.11.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/09/2012] [Accepted: 11/13/2012] [Indexed: 05/23/2023]
Abstract
Recent years have seen an impressive increase in our knowledge of the topology of plant hormone signaling networks. The complexity of these topologies has motivated the development of models for several hormones to aid understanding of how signaling networks process hormonal inputs. Such work has generated essential insights into the mechanisms of hormone perception and of regulation of cellular responses such as transcription in response to hormones. In addition, modeling approaches have contributed significantly to exploring how spatio-temporal regulation of hormone signaling contributes to plant growth and patterning. New tools have also been developed to obtain quantitative information on hormone distribution during development and to test model predictions, opening the way for quantitative understanding of the developmental roles of hormones.
Collapse
Affiliation(s)
- Marina Oliva
- Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | | | | |
Collapse
|
72
|
Baldazzi V, Bertin N, de Jong H, Génard M. Towards multiscale plant models: integrating cellular networks. TRENDS IN PLANT SCIENCE 2012; 17:728-36. [PMID: 22818768 DOI: 10.1016/j.tplants.2012.06.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 06/22/2012] [Accepted: 06/26/2012] [Indexed: 05/22/2023]
Abstract
One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models.
Collapse
Affiliation(s)
- Valentina Baldazzi
- INRA, UR 1115 Plantes et Systèmes de Culture Horticoles, Domaine St Paul, Site Agroparc, F-84941 Avignon Cedex 9, France.
| | | | | | | |
Collapse
|
73
|
Baldazzi V, Bertin N, de Jong H, Génard M. Towards multiscale plant models: integrating cellular networks. TRENDS IN PLANT SCIENCE 2012. [PMID: 22818768 DOI: 10.1016/j.tplants.2012.06.012 [epub ahead of print]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
One of the ambitions of 'crop systems biology' is to combine information from molecular biology with a broader view of plant development and growth. In the context of modeling, this calls for a multiscale perspective that focuses on the interplay between cellular and macroscopic studies. With this in mind, in this review we aim to draw attention to a panel of approaches that were developed in the context of systems biology and are used for analyzing and describing the behavior of cellular networks. Ultimately, insights obtained from these methods can be exploited to refine the description of plant processes, leading to integrated plant-cellular models.
Collapse
Affiliation(s)
- Valentina Baldazzi
- INRA, UR 1115 Plantes et Systèmes de Culture Horticoles, Domaine St Paul, Site Agroparc, F-84941 Avignon Cedex 9, France.
| | | | | | | |
Collapse
|
74
|
Baskin TI. Patterns of root growth acclimation: constant processes, changing boundaries. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 2:65-73. [DOI: 10.1002/wdev.94] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
75
|
Band LR, Fozard JA, Godin C, Jensen OE, Pridmore T, Bennett MJ, King JR. Multiscale systems analysis of root growth and development: modeling beyond the network and cellular scales. THE PLANT CELL 2012; 24:3892-906. [PMID: 23110897 PMCID: PMC3517226 DOI: 10.1105/tpc.112.101550] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 08/31/2012] [Accepted: 10/14/2012] [Indexed: 05/21/2023]
Abstract
Over recent decades, we have gained detailed knowledge of many processes involved in root growth and development. However, with this knowledge come increasing complexity and an increasing need for mechanistic modeling to understand how those individual processes interact. One major challenge is in relating genotypes to phenotypes, requiring us to move beyond the network and cellular scales, to use multiscale modeling to predict emergent dynamics at the tissue and organ levels. In this review, we highlight recent developments in multiscale modeling, illustrating how these are generating new mechanistic insights into the regulation of root growth and development. We consider how these models are motivating new biological data analysis and explore directions for future research. This modeling progress will be crucial as we move from a qualitative to an increasingly quantitative understanding of root biology, generating predictive tools that accelerate the development of improved crop varieties.
Collapse
Affiliation(s)
- Leah R. Band
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom
| | - John A. Fozard
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom
| | - Christophe Godin
- Virtual Plants Institut National de Recherche en Informatique et en Automatique Project-Team, joint with Institut National de la Recherche Agronomique and Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes, Montpellier cedex 5, France
| | - Oliver E. Jensen
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom
- School of Mathematics, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Tony Pridmore
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom
| | - Malcolm J. Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom
| | - John R. King
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham LE12 5RD, United Kingdom
| |
Collapse
|
76
|
Middleton AM, Farcot E, Owen MR, Vernoux T. Modeling regulatory networks to understand plant development: small is beautiful. THE PLANT CELL 2012; 24:3876-91. [PMID: 23110896 PMCID: PMC3517225 DOI: 10.1105/tpc.112.101840] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We now have unprecedented capability to generate large data sets on the myriad genes and molecular players that regulate plant development. Networks of interactions between systems components can be derived from that data in various ways and can be used to develop mathematical models of various degrees of sophistication. Here, we discuss why, in many cases, it is productive to focus on small networks. We provide a brief and accessible introduction to relevant mathematical and computational approaches to model regulatory networks and discuss examples of small network models that have helped generate new insights into plant biology (where small is beautiful), such as in circadian rhythms, hormone signaling, and tissue patterning. We conclude by outlining some of the key technical and modeling challenges for the future.
Collapse
Affiliation(s)
- Alistair M. Middleton
- Center for Modeling and Simulation in the Biosciences and Interdisciplinary Center for Scientific Computing, University of Heidelberg, 69120 Heidelberg, Germany
| | - Etienne Farcot
- Virtual Plants Inria Team, Université Montpellier 2, 34095 Montpellier cedex 5, France
| | - Markus R. Owen
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
- Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des Plantes, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Ecole Normale Supérieure de Lyon, Université Lyon I, Université de Lyon, 69364 Lyon cedex 07, France
- Address correspondence to
| |
Collapse
|
77
|
Middleton AM, Úbeda-Tomás S, Griffiths J, Holman T, Hedden P, Thomas SG, Phillips AL, Holdsworth MJ, Bennett MJ, King JR, Owen MR. Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling. Proc Natl Acad Sci U S A 2012; 109:7571-6. [PMID: 22523240 PMCID: PMC3358864 DOI: 10.1073/pnas.1113666109] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The hormone gibberellin (GA) is a key regulator of plant growth. Many of the components of the gibberellin signal transduction [e.g., GIBBERELLIN INSENSITIVE DWARF 1 (GID1) and DELLA], biosynthesis [e.g., GA 20-oxidase (GA20ox) and GA3ox], and deactivation pathways have been identified. Gibberellin binds its receptor, GID1, to form a complex that mediates the degradation of DELLA proteins. In this way, gibberellin relieves DELLA-dependent growth repression. However, gibberellin regulates expression of GID1, GA20ox, and GA3ox, and there is also evidence that it regulates DELLA expression. In this paper, we use integrated mathematical modeling and experiments to understand how these feedback loops interact to control gibberellin signaling. Model simulations are in good agreement with in vitro data on the signal transduction and biosynthesis pathways and in vivo data on the expression levels of gibberellin-responsive genes. We find that GA-GID1 interactions are characterized by two timescales (because of a lid on GID1 that can open and close slowly relative to GA-GID1 binding and dissociation). Furthermore, the model accurately predicts the response to exogenous gibberellin after a number of chemical and genetic perturbations. Finally, we investigate the role of the various feedback loops in gibberellin signaling. We find that regulation of GA20ox transcription plays a significant role in both modulating the level of endogenous gibberellin and generating overshoots after the removal of exogenous gibberellin. Moreover, although the contribution of other individual feedback loops seems relatively small, GID1 and DELLA transcriptional regulation acts synergistically with GA20ox feedback.
Collapse
Affiliation(s)
- Alistair M. Middleton
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
- Zentrum für Biosystemanalyse, Albert-Ludwigs-Universität, 79104 Freiburg im Breisgau, Germany
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom; and
| | - Susana Úbeda-Tomás
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Jayne Griffiths
- Plant Science Department, Rothamsted Research, Harpenden, Herts AL5 2JQ, United Kingdom
| | - Tara Holman
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Peter Hedden
- Plant Science Department, Rothamsted Research, Harpenden, Herts AL5 2JQ, United Kingdom
| | - Stephen G. Thomas
- Plant Science Department, Rothamsted Research, Harpenden, Herts AL5 2JQ, United Kingdom
| | - Andrew L. Phillips
- Plant Science Department, Rothamsted Research, Harpenden, Herts AL5 2JQ, United Kingdom
| | - Michael J. Holdsworth
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Malcolm J. Bennett
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - John R. King
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom; and
| | - Markus R. Owen
- Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, United Kingdom; and
| |
Collapse
|