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Seifu YW, Pukyšová V, Rýdza N, Bilanovičová V, Zwiewka M, Sedláček M, Nodzyński T. Mapping the membrane orientation of auxin homeostasis regulators PIN5 and PIN8 in Arabidopsis thaliana root cells reveals their divergent topology. PLANT METHODS 2024; 20:84. [PMID: 38825682 PMCID: PMC11145782 DOI: 10.1186/s13007-024-01182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 04/10/2024] [Indexed: 06/04/2024]
Abstract
PIN proteins establish the auxin concentration gradient, which coordinates plant growth. PIN1-4 and 7 localized at the plasma membrane (PM) and facilitate polar auxin transport while the endoplasmic reticulum (ER) localized PIN5 and PIN8 maintain the intracellular auxin homeostasis. Although an antagonistic activity of PIN5 and PIN8 proteins in regulating the intracellular auxin homeostasis and other developmental events have been reported, the membrane topology of these proteins, which might be a basis for their antagonistic function, is poorly understood. In this study we optimized digitonin based PM-permeabilizing protocols coupled with immunocytochemistry labeling to map the membrane topology of PIN5 and PIN8 in Arabidopsis thaliana root cells. Our results indicate that, except for the similarities in the orientation of the N-terminus, PIN5 and PIN8 have an opposite orientation of the central hydrophilic loop and the C-terminus, as well as an unequal number of transmembrane domains (TMDs). PIN8 has ten TMDs with groups of five alpha-helices separated by the central hydrophilic loop (HL) residing in the ER lumen, and its N- and C-terminals are positioned in the cytoplasm. However, the topology of PIN5 comprises nine TMDs. Its N-terminal end and the central HL face the cytoplasm while its C-terminus resides in the ER lumen. Overall, this study shows that PIN5 and PIN8 proteins have a divergent membrane topology while introducing a toolkit of methods for studying membrane topology of integral proteins including those localized at the ER membrane.
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Affiliation(s)
- Yewubnesh Wendimu Seifu
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Vendula Pukyšová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Nikola Rýdza
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Veronika Bilanovičová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Marta Zwiewka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Marek Sedláček
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic
| | - Tomasz Nodzyński
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, CZ-625 00, Czech Republic.
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Favre P, van Schaik E, Schorderet M, Yerly F, Reinhardt D. Regulation of tissue growth in plants - A mathematical modeling study on shade avoidance response in Arabidopsis hypocotyls. FRONTIERS IN PLANT SCIENCE 2024; 15:1285655. [PMID: 38486850 PMCID: PMC10938469 DOI: 10.3389/fpls.2024.1285655] [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: 08/30/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024]
Abstract
Introduction Plant growth is a plastic phenomenon controlled both by endogenous genetic programs and by environmental cues. The embryonic stem, the hypocotyl, is an ideal model system for the quantitative study of growth due to its relatively simple geometry and cellular organization, and to its essentially unidirectional growth pattern. The hypocotyl of Arabidopsis thaliana has been studied particularly well at the molecular-genetic level and at the cellular level, and it is the model of choice for analysis of the shade avoidance syndrome (SAS), a growth reaction that allows plants to compete with neighboring plants for light. During SAS, hypocotyl growth is controlled primarily by the growth hormone auxin, which stimulates cell expansion without the involvement of cell division. Methods We assessed hypocotyl growth at cellular resolution in Arabidopsis mutants defective in auxin transport and biosynthesis and we designed a mathematical auxin transport model based on known polar and non-polar auxin transporters (ABCB1, ABCB19, and PINs) and on factors that control auxin homeostasis in the hypocotyl. In addition, we introduced into the model biophysical properties of the cell types based on precise cell wall measurements. Results and Discussion Our model can generate the observed cellular growth patterns based on auxin distribution along the hypocotyl resulting from production in the cotyledons, transport along the hypocotyl, and general turnover of auxin. These principles, which resemble the features of mathematical models of animal morphogen gradients, allow to generate robust shallow auxin gradients as they are expected to exist in tissues that exhibit quantitative auxin-driven tissue growth, as opposed to the sharp auxin maxima generated by patterning mechanisms in plant development.
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Affiliation(s)
- Patrick Favre
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Evert van Schaik
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | - Florence Yerly
- Haute école d’ingénierie et d’architecture Fribourg, Haute Ecole Spécialisée de Suisse Occidentale (HES-SO), University of Applied Sciences and Arts of Western Switzerland, Fribourg, Switzerland
| | - Didier Reinhardt
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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Bellows S, Janes G, Avitabile D, King JR, Bishopp A, Farcot E. Fluctuations in auxin levels depend upon synchronicity of cell divisions in a one-dimensional model of auxin transport. PLoS Comput Biol 2023; 19:e1011646. [PMID: 38032890 PMCID: PMC10688697 DOI: 10.1371/journal.pcbi.1011646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Auxin is a well-studied plant hormone, the spatial distribution of which remains incompletely understood. Here, we investigate the effects of cell growth and divisions on the dynamics of auxin patterning, using a combination of mathematical modelling and experimental observations. In contrast to most prior work, models are not designed or tuned with the aim to produce a specific auxin pattern. Instead, we use well-established techniques from dynamical systems theory to uncover and classify ranges of auxin patterns as exhaustively as possible as parameters are varied. Previous work using these techniques has shown how a multitude of stable auxin patterns may coexist, each attainable from a specific ensemble of initial conditions. When a key parameter spans a range of values, these steady patterns form a geometric curve with successive folds, often nicknamed a snaking diagram. As we introduce growth and cell division into a one-dimensional model of auxin distribution, we observe new behaviour which can be explained in terms of this diagram. Cell growth changes the shape of the snaking diagram, and this corresponds in turn to deformations in the patterns of auxin distribution. As divisions occur this can lead to abrupt creation or annihilation of auxin peaks. We term this phenomenon 'snake-jumping'. Under rhythmic cell divisions, we show how this can lead to stable oscillations of auxin. We also show that this requires a high level of synchronisation between cell divisions. Using 18 hour time-lapse imaging of the auxin reporter DII:Venus in roots of Arabidopsis thaliana, we show auxin fluctuates greatly, both in terms of amplitude and periodicity, consistent with the snake-jumping events observed with non-synchronised cell divisions. Periodic signals downstream of the auxin signalling pathway have previously been recorded in plant roots. The present work shows that auxin alone is unlikely to play the role of a pacemaker in this context.
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Affiliation(s)
- Simon Bellows
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - George Janes
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Daniele Avitabile
- Department of Mathematics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - John R. King
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Anthony Bishopp
- School of Biosciences, University of Nottingham, Nottingham, United Kingdom
| | - Etienne Farcot
- School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom
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Marconi M, Wabnik K. Computer models of cell polarity establishment in plants. PLANT PHYSIOLOGY 2023; 193:42-53. [PMID: 37144853 PMCID: PMC10469401 DOI: 10.1093/plphys/kiad264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/30/2023] [Accepted: 04/14/2023] [Indexed: 05/06/2023]
Abstract
Plant development is a complex task, and many processes involve changes in the asymmetric subcellular distribution of cell components that strongly depend on cell polarity. Cell polarity regulates anisotropic growth and polar localization of membrane proteins and helps to identify the cell's position relative to its neighbors within an organ. Cell polarity is critical in a variety of plant developmental processes, including embryogenesis, cell division, and response to external stimuli. The most conspicuous downstream effect of cell polarity is the polar transport of the phytohormone auxin, which is the only known hormone transported in a polar fashion in and out of cells by specialized exporters and importers. The biological processes behind the establishment of cell polarity are still unknown, and researchers have proposed several models that have been tested using computer simulations. The evolution of computer models has progressed in tandem with scientific discoveries, which have highlighted the importance of genetic, chemical, and mechanical input in determining cell polarity and regulating polarity-dependent processes such as anisotropic growth, protein subcellular localization, and the development of organ shapes. The purpose of this review is to provide a comprehensive overview of the current understanding of computer models of cell polarity establishment in plants, focusing on the molecular and cellular mechanisms, the proteins involved, and the current state of the field.
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Affiliation(s)
- Marco Marconi
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
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Zhang X, Kuang T, Dong W, Qian Z, Zhang H, Landis JB, Feng T, Li L, Sun Y, Huang J, Deng T, Wang H, Sun H. Genomic convergence underlying high-altitude adaptation in alpine plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36960823 DOI: 10.1111/jipb.13485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/21/2023] [Indexed: 06/18/2023]
Abstract
Evolutionary convergence is one of the most striking examples of adaptation driven by natural selection. However, genomic evidence for convergent adaptation to extreme environments remains scarce. Here, we assembled reference genomes of two alpine plants, Saussurea obvallata (Asteraceae) and Rheum alexandrae (Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes, we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of disease-resistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens present. We identified signatures of positive selection on a set of genes involved in reproduction and respiration (e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification, DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive "greenhouse" morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level, aiding in a deep understanding of genetic adaptation to complex environments.
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Affiliation(s)
- Xu Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Tianhui Kuang
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Wenlin Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihao Qian
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huajie Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L. H. Bailey Hortorium, Cornell University, Ithaca, New York, 14850, USA
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, New York, 14853, USA
| | - Tao Feng
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Lijuan Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanxia Sun
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Jinling Huang
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Tao Deng
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
| | - Hengchang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, The Chinese Academy of Sciences, Wuhan Botanical Garden, Wuhan, 430074, China
- Center of Conservation Biology, Core Botanical Gardens, The Chinese Academy of Sciences, Wuhan, 430074, China
| | - Hang Sun
- Yunnan International Joint Laboratory for Biodiversity of Central Asia, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming, 650201, China
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Bakker BH, Faver TE, Hupkes HJ, Merks RMH, van der Voort J. Scaling relations for auxin waves. J Math Biol 2022; 85:41. [PMID: 36163567 PMCID: PMC9512763 DOI: 10.1007/s00285-022-01793-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 07/05/2022] [Accepted: 07/17/2022] [Indexed: 11/24/2022]
Abstract
We analyze an 'up-the-gradient' model for the formation of transport channels of the phytohormone auxin, through auxin-mediated polarization of the PIN1 auxin transporter. We show that this model admits a family of travelling wave solutions that is parameterized by the height of the auxin-pulse. We uncover scaling relations for the speed and width of these waves and verify these rigorous results with numerical computations. In addition, we provide explicit expressions for the leading-order wave profiles, which allows the influence of the biological parameters in the problem to be readily identified. Our proofs are based on a generalization of the scaling principle developed by Friesecke and Pego to construct pulse solutions to the classic Fermi-Pasta-Ulam-Tsingou model, which describes a one-dimensional chain of coupled nonlinear springs.
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Affiliation(s)
- Bente Hilde Bakker
- Mathematical Institute, Universiteit Leiden, P.O. Box 9512, 2300 RA Leiden, The Netherlands
| | - Timothy E. Faver
- Department of Mathematics, Kennesaw State University, 850 Polytechnic Lane, MD #9085, Marietta, GA 30060 USA
| | - Hermen Jan Hupkes
- Mathematical Institute, Universiteit Leiden, P.O. Box 9512, 2300 RA Leiden, The Netherlands
| | - Roeland M. H. Merks
- Mathematical Institute and Institute of Biology Leiden, Universiteit Leiden, P.O. Box 9512, 2300 RA Leiden, The Netherlands
| | - Jelle van der Voort
- Mathematical Institute, Universiteit Leiden, P.O. Box 9512, 2300 RA Leiden, The Netherlands
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Kim H, Jang J, Seomun S, Yoon Y, Jang G. Division of cortical cells is regulated by auxin in Arabidopsis roots. FRONTIERS IN PLANT SCIENCE 2022; 13:953225. [PMID: 36186058 PMCID: PMC9515965 DOI: 10.3389/fpls.2022.953225] [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: 05/25/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
The root cortex transports water and nutrients absorbed by the root epidermis into the vasculature and stores substances such as starch, resins, and essential oils. The cortical cells are also deeply involved in determining epidermal cell fate. In Arabidopsis thaliana roots, the cortex is composed of a single cell layer generated by a single round of periclinal division of the cortex/endodermis initials. To further explore cortex development, we traced the development of the cortex by counting cortical cells. Unlike vascular cells, whose number increased during the development of root apical meristem (RAM), the number of cortical cells did not change, indicating that cortical cells do not divide during RAM development. However, auxin-induced cortical cell division, and this finding was confirmed by treatment with the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) and examining transgenic plants harboring CO2::ΔARF5, in which cortical expression of truncated AUXIN RESPONSE FACTOR5 (ΔARF5) induces auxin responses. NPA-induced cortical auxin accumulation and CO2::ΔARF5-mediated cortical auxin response induced anticlinal and periclinal cell divisions, thus increasing the number of cortical cells. These findings reveal a tight link between auxin and cortical cell division, suggesting that auxin is a key player in determining root cortical cell division.
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Affiliation(s)
- Huijin Kim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Jinwoo Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Subhin Seomun
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
| | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul, South Korea
| | - Geupil Jang
- School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea
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Yu Y, Meng N, Chen S, Zhang H, Liu Z, Wang Y, Jing Y, Wang Y, Chen S. Transcriptomic profiles of poplar (Populus simonii × P. nigra) cuttings during adventitious root formation. Front Genet 2022; 13:968544. [PMID: 36160010 PMCID: PMC9493132 DOI: 10.3389/fgene.2022.968544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/16/2022] [Indexed: 11/21/2022] Open
Abstract
The formation of adventitious roots (ARs) is vital for the vegetative propagation of poplars. However, the relevant mechanisms remain unclear. To reveal the underlying molecular mechanism, we used RNA-seq to investigate the transcriptional alterations of poplar cuttings soaked in water for 0, 2, 4, 6, 8, and 10 d; 3,798 genes were differentially expressed at all the time points, including 2,448 upregulated and 1,350 downregulated genes. Biological processes including “cell cycle,” “photosynthesis,” “regulation of hormone levels,” and “auxin transport” were enriched in the differentially expressed genes (DEGs). KEGG results showed that the common DEGs were most enriched in the pathway of “Carbon fixation in photosynthetic organisms” and “Starch and sucrose metabolism.” We further dissected 38 DEGs related to root and auxin, including two lateral root primordium 1 (LRP1), one root meristem growth factor (RGF9), one auxin-induced in the root (AIR12), three rooting-associated genes (AUR1 and AUR3), eight auxin transcription factors (ARFs and LBDs), 10 auxin respective genes (SAURs and GH3s), nine auxin transporters (PINs, ABCs, LAX2, and AUXs), and four auxin signal genes (IAAs and TIR1). We found that the rooting abilities of poplar cuttings with and without leaves are different. By applying different concentrations of IBA and sucrose to the top of cuttings without leaves, we found that 0.2 mg/ml IBA and 2 mg/ml sucrose had the best effect on promoting AR formation. The transcriptome results indicated photosynthesis may influence AR formation in poplar cuttings with leaves and revealed a potential regulatory mechanism of leafy cuttage from poplar cuttings. In addition, we provided a new perspective to resolve rooting difficulties in recalcitrant species.
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Affiliation(s)
- Yue Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Nan Meng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hongjiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhijie Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yiran Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yanan Jing
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yuting Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- *Correspondence: Su Chen,
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Kinoshita A, Tsukaya H. Auxin and cytokinin control fate determination of cotyledons in the one-leaf plant Monophyllaea glabra. FRONTIERS IN PLANT SCIENCE 2022; 13:980138. [PMID: 36119619 PMCID: PMC9481249 DOI: 10.3389/fpls.2022.980138] [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: 06/28/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
One-leaf plants in the Gesneriaceae family initially have two cotyledons of identical size; one cotyledon stops growing shortly after germination, whereas the other continues indeterminate growth. Factors involved in the unequal growth have been investigated, and a competitive relationship between the two cotyledons was previously proposed. However, questions regarding the fate determination of the two cotyledons remain: Why does only one cotyledon grow indeterminately while the other stops; is the fate of the cotyledons reversible; and what role does light quality play in the fate determination of the cotyledons? In this study, physiological experiments using the one-leaf plant species Monophyllaea glabra suggest that a biased auxin concentration between the two cotyledons and subsequent cytokinin levels may determine the fate of the cotyledons. In addition, observation of relatively mature individuals without hormone treatment and younger individuals with cytokinin treatment under laboratory growth conditions revealed that the fate determination of the microcotyledon is reversible. Although light quality has been suggested to be important for the determination of cotyledon fate in Streptocarpus rexii, an anisocotylous species, we conclude that light quality is not important in M. glabra.
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Karannagoda N, Spokevicius A, Hussey S, Cassan-Wang H, Grima-Pettenati J, Bossinger G. Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13) is a novel transcriptional regulator of xylogenesis. PLANT MOLECULAR BIOLOGY 2022; 109:51-65. [PMID: 35292886 PMCID: PMC9072461 DOI: 10.1007/s11103-022-01255-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Our Induced Somatic Sector Analysis and protein-protein interaction experiments demonstrate that Eucalyptus grandis IAA13 regulates xylem fibre and vessel development, potentially via EgrIAA13 modules involving ARF2, ARF5, ARF6 and ARF19. Auxin is a crucial phytohormone regulating multiple aspects of plant growth and differentiation, including regulation of vascular cambium activity, xylogenesis and its responsiveness towards gravitropic stress. Although the regulation of these biological processes greatly depends on auxin and regulators of the auxin signalling pathway, many of their specific functions remain unclear. Therefore, the present study aims to functionally characterise Eucalyptus grandis AUX/INDOLE-3-ACETIC ACID 13 (EgrIAA13), a member of the auxin signalling pathway. In Eucalyptus and Populus, EgrIAA13 and its orthologs are preferentially expressed in the xylogenic tissues and downregulated in tension wood. Therefore, to further investigate EgrIAA13 and its function during xylogenesis, we conducted subcellular localisation and Induced Somatic Sector Analysis experiments using overexpression and RNAi knockdown constructs of EgrIAA13 to create transgenic tissue sectors on growing stems of Eucalyptus and Populus. Since Aux/IAAs interact with Auxin Responsive Factors (ARFs), in silico predictions of IAA13-ARF interactions were explored and experimentally validated via yeast-2-hybrid experiments. Our results demonstrate that EgrIAA13 localises to the nucleus and that downregulation of EgrIAA13 impedes Eucalyptus xylem fibre and vessel development. We also observed that EgrIAA13 interacts with Eucalyptus ARF2, ARF5, ARF6 and ARF19A. Based on these results, we conclude that EgrIAA13 is a regulator of Eucalyptus xylogenesis and postulate that the observed phenotypes are likely to result from alterations in the auxin-responsive transcriptome via IAA13-ARF modules such as EgrIAA13-EgrARF5. Our results provide the first insights into the regulatory role of EgrIAA13 during xylogenesis.
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Affiliation(s)
- Nadeeshani Karannagoda
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia.
- Centre for AgriBioscience, Agriculture Victoria, AgriBio, Bundoora, Victoria, 3083, Australia.
| | - Antanas Spokevicius
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia
| | - Steven Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - Hua Cassan-Wang
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Jacqueline Grima-Pettenati
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, UPS, UMR 5546, 24 Chemin de Borde Rouge, 31320, Castanet-Tolosan, France
| | - Gerd Bossinger
- School of Ecosystem and Forest Sciences, The University of Melbourne, Creswick, VIC, 3363, Australia
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11
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Desnitskiy AG, Chetverikov PE. Induction of Leaf Galls by Four-Legged Mites (Eriophyoidea) as a Problem of Developmental Biology. Russ J Dev Biol 2022. [DOI: 10.1134/s1062360422010039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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12
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Cieslak M, Owens A, Prusinkiewicz P. Computational Models of Auxin-Driven Patterning in Shoots. Cold Spring Harb Perspect Biol 2022; 14:a040097. [PMID: 34001531 PMCID: PMC8886983 DOI: 10.1101/cshperspect.a040097] [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 regulates many aspects of plant development and behavior, including the initiation of new outgrowth, patterning of vascular systems, control of branching, and responses to the environment. Computational models have complemented experimental studies of these processes. We review these models from two perspectives. First, we consider cellular and tissue-level models of interaction between auxin and its transporters in shoots. These models form a coherent body of results exploring different hypotheses pertinent to the patterning of new outgrowth and vascular strands. Second, we consider models operating at the level of plant organs and entire plants. We highlight techniques used to reduce the complexity of these models, which provide a path to capturing the essence of studied phenomena while running simulations efficiently.
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Affiliation(s)
- Mikolaj Cieslak
- Department of Computer Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Andrew Owens
- Department of Computer Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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13
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Li Y, Shao J, Fu Y, Chen Y, Wang H, Xu Z, Feng H, Xun W, Liu Y, Zhang N, Shen Q, Xuan W, Zhang R. The volatile cedrene from Trichoderma guizhouense modulates Arabidopsis root development through auxin transport and signalling. PLANT, CELL & ENVIRONMENT 2022; 45:969-984. [PMID: 34800291 DOI: 10.1111/pce.14230] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 06/13/2023]
Abstract
Rhizosphere microorganisms interact with plant roots by producing chemical signals that regulate root development. However, the distinct bioactive compounds and signal transduction pathways remain to be identified. Here, we showed that sesquiterpenes are the main volatile compounds produced by plant-beneficial Trichoderma guizhouense NJAU4742. Inhibition of sesquiterpene biosynthesis eliminated the promoting effect of this strain on root growth, indicating its involvement in plant-fungus cross-kingdom signalling. Sesquiterpene component analysis identified cedrene, a highly abundant sesquiterpene in strain NJAU4742, to stimulate plant growth and root development. Genetic analysis and auxin transport inhibition showed that the TIR1 and AFB2 auxin receptors, IAA14 auxin-responsive protein, and ARF7 and ARF19 transcription factors affected the response of lateral roots to cedrene. Moreover, the AUX1 auxin influx carrier and PIN2 efflux carrier were also found to be indispensable for cedrene-induced lateral root formation. Confocal imaging showed that cedrene affected the expression of pPIN2:PIN2:GFP and pPIN3:PIN3:GFP, which might be related to the effect of cedrene on root morphology. These results suggested that a novel sesquiterpene molecule from plant-beneficial T. guizhouense regulates plant root development through the transport and signalling of auxin.
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Affiliation(s)
- Yucong Li
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yansong Fu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yu Chen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Hongzhe Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Haichao Feng
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Weibing Xun
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Wei Xuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Kuan C, Yang SL, Ho CMK. Using quantitative methods to understand leaf epidermal development. QUANTITATIVE PLANT BIOLOGY 2022; 3:e28. [PMID: 37077990 PMCID: PMC10097589 DOI: 10.1017/qpb.2022.25] [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: 05/06/2022] [Revised: 10/25/2022] [Accepted: 11/13/2022] [Indexed: 05/03/2023]
Abstract
As the interface between plants and the environment, the leaf epidermis provides the first layer of protection against drought, ultraviolet light, and pathogen attack. This cell layer comprises highly coordinated and specialised cells such as stomata, pavement cells and trichomes. While much has been learned from the genetic dissection of stomatal, trichome and pavement cell formation, emerging methods in quantitative measurements that monitor cellular or tissue dynamics will allow us to further investigate cell state transitions and fate determination in leaf epidermal development. In this review, we introduce the formation of epidermal cell types in Arabidopsis and provide examples of quantitative tools to describe phenotypes in leaf research. We further focus on cellular factors involved in triggering cell fates and their quantitative measurements in mechanistic studies and biological patterning. A comprehensive understanding of how a functional leaf epidermis develops will advance the breeding of crops with improved stress tolerance.
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Affiliation(s)
- Chi Kuan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei City, Taiwan
| | - Shao-Li Yang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei City, Taiwan
| | - Chin-Min Kimmy Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei City, Taiwan
- Author for correspondence: C.-M. K. Ho, E-mail:
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15
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Marhava P. Recent developments in the understanding of PIN polarity. THE NEW PHYTOLOGIST 2022; 233:624-630. [PMID: 34882802 DOI: 10.1111/nph.17867] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 10/05/2021] [Indexed: 05/20/2023]
Abstract
Polar localization of PIN-FORMED proteins (PINs) at the plasma membrane is essential for plant development as they direct the transport of phytohormone auxin between cells. PIN polar localization to certain sides of a given cell is dynamic, strictly regulated and provides directionality to auxin flow. Signals that act upstream to control subcellular PIN localization modulate auxin distribution, thereby regulating diverse aspects of plant development. Here I summarize the current understanding of mechanisms by which PIN polarity is established, maintained and rearranged to provide a glimpse into the complexity of PIN polarity.
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Affiliation(s)
- Petra Marhava
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), University of Agricultural Sciences (SLU), 90183, Umeå, Sweden
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16
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Farcot E, Mellor N. Gene Regulatory Network Investigation Using Ordinary Differential Equations. Methods Mol Biol 2022; 2395:33-58. [PMID: 34822148 DOI: 10.1007/978-1-0716-1816-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This chapter reviews mathematical models of gene regulation, either as "pure" gene regulatory networks, as signal transduction pathways or as combinations of these. The basic underlying methods are discussed from first principles, relying on rigorous mathematical concepts but with an aim to avoid technical details and focus on the intuitive aspects of this type of mathematical models. After reviewing the principles, some real biological examples are presented to illustrate the practice of modeling, using recent examples from the literature. The proposed examples all arise in the context of plant biology, either at the single cell scale, looking at auxin signaling, or at higher scales, looking at auxin active transport.
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Affiliation(s)
- Etienne Farcot
- School of Mathematical Sciences, University of Nottingham, Nottingham, UK.
| | - Nathan Mellor
- School of Biosciences, University of Nottingham, Nottingham, UK
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17
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Marconi M, Gallemi M, Benkova E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife 2021; 10:72132. [PMID: 34723798 PMCID: PMC8716106 DOI: 10.7554/elife.72132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/26/2021] [Indexed: 11/21/2022] Open
Abstract
Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.
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Affiliation(s)
- Marco Marconi
- CBGP Centro de Biotecnologia y Genomica de Plantas UPM-INIA, Pozuelo de Alarcón, Spain
| | - Marcal Gallemi
- Institute of Science and Technology (IST), Klosterneuburg, Austria
| | - Eva Benkova
- Institute of Science and Technology (IST), Klosterneuburg, Austria
| | - Krzysztof Wabnik
- CBGP Centro de Biotecnologia y Genomica de Plantas UPM-INIA, Pozuelo de Alarcón, Spain
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18
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Deslauriers SD, Spalding EP. Electrophysiological study of Arabidopsis ABCB4 and PIN2 auxin transporters: Evidence of auxin activation and interaction enhancing auxin selectivity. PLANT DIRECT 2021; 5:e361. [PMID: 34816076 PMCID: PMC8595762 DOI: 10.1002/pld3.361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/21/2021] [Indexed: 05/25/2023]
Abstract
Polar auxin transport through plant tissue strictly requires polarly localized PIN proteins and uniformly distributed ABCB proteins. A functional synergy between the two types of membrane protein where their localizations overlap may create the degree of asymmetric auxin efflux required to produce polar auxin transport. We investigated this possibility by expressing ABCB4 and PIN2 in human embryonic kidney cells and measuring whole-cell ionic currents with the patch-clamp technique and CsCl-based electrolytes. ABCB4 activity was 1.81-fold more selective for Cl- over Cs+ and for PIN2 the value was 2.95. We imposed auxin gradients and determined that ABCB4 and PIN2 were 12-fold more permeable to the auxin anion (IAA-) than Cl-. This measure of the intrinsic selectivity of the transport pathway was 21-fold when ABCB4 and PIN2 were co-expressed. If this increase occurs in plants, it could explain why asymmetric PIN localization is not sufficient to create polar auxin flow. Some form of co-action or synergy between ABCB4 and PIN2 that increases IAA- selectivity at the cell face where both occur may be important. We also found that auxin stimulated ABCB4 activity, which may contribute to a self-reinforcement of auxin transport known as canalization.
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Affiliation(s)
- Stephen D. Deslauriers
- Department of BotanyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Division of Science and MathUniversity of MinnesotaMorrisMNUSA
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19
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Chen J, Li Y, Li Y, Li Y, Wang Y, Jiang C, Choisy P, Xu T, Cai Y, Pei D, Jiang CZ, Gan SS, Gao J, Ma N. AUXIN RESPONSE FACTOR 18-HISTONE DEACETYLASE 6 module regulates floral organ identity in rose (Rosa hybrida). PLANT PHYSIOLOGY 2021; 186:1074-1087. [PMID: 33729501 PMCID: PMC8195501 DOI: 10.1093/plphys/kiab130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
The phytohormone auxin plays a pivotal role in floral meristem initiation and gynoecium development, but whether and how auxin controls floral organ identity remain largely unknown. Here, we found that auxin levels influence organ specification, and changes in auxin levels influence homeotic transformation between petals and stamens in rose (Rosa hybrida). The PIN-FORMED-LIKES (PILS) gene RhPILS1 governs auxin levels in floral buds during floral organogenesis. RhAUXIN RESPONSE FACTOR 18 (RhARF18), whose expression decreases with increasing auxin content, encodes a transcriptional repressor of the C-class gene RhAGAMOUS (RhAG), and controls stamen-petal organ specification in an auxin-dependent manner. Moreover, RhARF18 physically interacts with the histone deacetylase (HDA) RhHDA6. Silencing of RhHDA6 increases H3K9/K14 acetylation levels at the site adjacent to the RhARF18-binding site in the RhAG promoter and reduces petal number, indicating that RhARF18 might recruit RhHDA6 to the RhAG promoter to reinforce the repression of RhAG transcription. We propose a model for how auxin homeostasis controls floral organ identity via regulating transcription of RhAG.
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Affiliation(s)
- Jiwei Chen
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yang Li
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yonghong Li
- School of Applied Chemistry and Biotechnology, Shenzhen Polytechnic, Shenzhen, Guangdong 518055, China
| | - Yuqi Li
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Yi Wang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Chuyan Jiang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | | | - Tao Xu
- LVMH Recherche, F-45800 St Jean de Braye, France
| | - Youming Cai
- Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Cai-Zhong Jiang
- Crop Pathology and Genetic Research Unit, US Department of Agriculture, Agricultural Research Service, University of California, Davis, California, USA
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Su-Sheng Gan
- Plant Biology Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | - Junping Gao
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Nan Ma
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
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20
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ten Tusscher KH. What remains of the evidence for auxin feedback on PIN polarity patterns? PLANT PHYSIOLOGY 2021; 186:804-807. [PMID: 33760101 PMCID: PMC8195499 DOI: 10.1093/plphys/kiab118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 03/20/2021] [Indexed: 05/29/2023]
Abstract
In light of recent findings, the feedback between auxin and PIN that plays a major role in models for self-organized auxin patterning requires revisiting.
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Affiliation(s)
- Kirsten H ten Tusscher
- Department of Theoretical Biology, Faculty of Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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21
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Vernoux T, Besnard F, Godin C. What shoots can teach about theories of plant form. NATURE PLANTS 2021; 7:716-724. [PMID: 34099903 DOI: 10.1038/s41477-021-00930-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Plants generate a large variety of shoot forms with regular geometries. These forms emerge primarily from the activity of a stem cell niche at the shoot tip. Recent efforts have established a theoretical framework of form emergence at the shoot tip, which has empowered the use of modelling in conjunction with biological approaches to begin to disentangle the biochemical and physical mechanisms controlling form development at the shoot tip. Here, we discuss how these advances get us closer to identifying the construction principles of plant shoot tips. Considering the current limits of our knowledge, we propose a roadmap for developing a general theory of form development at the shoot tip.
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Affiliation(s)
- Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon, France.
| | - Fabrice Besnard
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon, France
| | - Christophe Godin
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon, France
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22
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Oosterbeek M, Lozano-Torres JL, Bakker J, Goverse A. Sedentary Plant-Parasitic Nematodes Alter Auxin Homeostasis via Multiple Strategies. FRONTIERS IN PLANT SCIENCE 2021; 12:668548. [PMID: 34122488 PMCID: PMC8193132 DOI: 10.3389/fpls.2021.668548] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Abstract
Sedentary endoparasites such as cyst and root-knot nematodes infect many important food crops and are major agro-economical pests worldwide. These plant-parasitic nematodes exploit endogenous molecular and physiological pathways in the roots of their host to establish unique feeding structures. These structures function as highly active transfer cells and metabolic sinks and are essential for the parasites' growth and reproduction. Plant hormones like indole-3-acetic acid (IAA) are a fundamental component in the formation of these feeding complexes. However, their underlying molecular and biochemical mechanisms are still elusive despite recent advances in the field. This review presents a comprehensive overview of known functions of various auxins in plant-parasitic nematode infection sites, based on a systematic analysis of current literature. We evaluate multiple aspects involved in auxin homeostasis in plants, including anabolism, catabolism, transport, and signalling. From these analyses, a picture emerges that plant-parasitic nematodes have evolved multiple strategies to manipulate auxin homeostasis to establish a successful parasitic relationship with their host. Additionally, there appears to be a potential role for auxins other than IAA in plant-parasitic nematode infections that might be of interest to be further elucidated.
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23
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Mboene Noah A, Casanova-Sáez R, Makondy Ango RE, Antoniadi I, Karady M, Novák O, Niemenak N, Ljung K. Dynamics of Auxin and Cytokinin Metabolism during Early Root and Hypocotyl Growth in Theobroma cacao. PLANTS (BASEL, SWITZERLAND) 2021; 10:967. [PMID: 34066241 PMCID: PMC8151989 DOI: 10.3390/plants10050967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022]
Abstract
The spatial location and timing of plant developmental events are largely regulated by the well balanced effects of auxin and cytokinin phytohormone interplay. Together with transport, localized metabolism regulates the concentration gradients of their bioactive forms, ultimately eliciting growth responses. In order to explore the dynamics of auxin and cytokinin metabolism during early seedling growth in Theobroma cacao (cacao), we have performed auxin and cytokinin metabolite profiling in hypocotyls and root developmental sections at different times by using ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS). Our work provides quantitative characterization of auxin and cytokinin metabolites throughout early root and hypocotyl development and identifies common and distinctive features of auxin and cytokinin metabolism during cacao seedling development.
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Affiliation(s)
- Alexandre Mboene Noah
- Department of Biochemistry, Faculty of Science, University of Douala, Douala P.O. Box 24157, Cameroon
| | - Rubén Casanova-Sáez
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183 Umeå, Sweden; (R.C.-S.); (I.A.); (M.K.); (O.N.); (K.L.)
| | - Rolande Eugenie Makondy Ango
- Laboratory of Plant Physiology and Biochemistry, Department of Biological Science, Higher Teachers’ Training College, University of Yaounde I, Yaounde P.O. Box 47, Cameroon; (R.E.M.A.); (N.N.)
| | - Ioanna Antoniadi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183 Umeå, Sweden; (R.C.-S.); (I.A.); (M.K.); (O.N.); (K.L.)
| | - Michal Karady
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183 Umeå, Sweden; (R.C.-S.); (I.A.); (M.K.); (O.N.); (K.L.)
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Ondřej Novák
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183 Umeå, Sweden; (R.C.-S.); (I.A.); (M.K.); (O.N.); (K.L.)
- Laboratory of Growth Regulators, Faculty of Science, Institute of Experimental Botany of the Czech Academy of Sciences, Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Nicolas Niemenak
- Laboratory of Plant Physiology and Biochemistry, Department of Biological Science, Higher Teachers’ Training College, University of Yaounde I, Yaounde P.O. Box 47, Cameroon; (R.E.M.A.); (N.N.)
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences (SLU), 90183 Umeå, Sweden; (R.C.-S.); (I.A.); (M.K.); (O.N.); (K.L.)
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24
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Alshammari SO, Dakshanamurthy S, Ullah H. Small compounds targeting tyrosine phosphorylation of Scaffold Protein Receptor for Activated C Kinase1A (RACK1A) regulate auxin mediated lateral root development in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2021; 16:1899488. [PMID: 33784940 PMCID: PMC8078533 DOI: 10.1080/15592324.2021.1899488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Receptor for activated C kinase 1 (RACK1) is WD-40 type scaffold protein, conserved in all eukaryote organisms. Many reports implicated RACK1 in plant hormone signal transduction pathways including in auxin and diverse stress signaling pathways; however, the precise molecular mechanism of its role is not understood. Previously, a group of small compounds targeting the Arabidopsis RACK1A functional site-Tyr248 have been developed. Here, the three different small compounds are used to elucidate the role of RACK1A in auxin mediated lateral root development. Through monitoring the auxin response in the architecture of lateral roots and auxin reporter assays, a small molecule- SD29-12 was found to stabilize the auxin induced RACK1A Tyr248 phosphorylation, thereby stimulating auxin signaling and inducing lateral roots formation. In contrast, two other compounds, SD29 and SD29-14, inhibited auxin induced RACK1A Tyr248 phosphorylation resulting in the inhibition of auxin sensitivity and alternation in the lateral roots formation. Taken together, auxin induced RACK1A Tyr248 phosphorylation is found to be the critical regulatory mechanism for auxin-mediated lateral root development. This work leads to the molecular understanding of the role RACK1A plays in the auxin induced lateral root development signaling pathways. The auxin signal stimulating compound has the potential to be used as auxin-based root inducing bio-stimulant.
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Affiliation(s)
- Shifaa O Alshammari
- Department of Biology, Howard University, Washington, USA
- Department of Biology, College of Science, University of Hafr Al Batin, Hafar Al Batin, Saudi Arabia
| | - Sivanesan Dakshanamurthy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, USA
- Department of Biochemistry and Molecular Biology, Georgetown University, Washington, USA
- CONTACT Sivanesan Dakshanamurthy Department of Biochemistry and Molecular Biology,Georgetown University, Washington, DC 20057 United States
| | - Hemayet Ullah
- Department of Biology, Howard University, Washington, USA
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Abstract
Plants encompass unparalleled multi-scale regenerative potential. Despite lacking specialized cells that are recruited to injured sites, and despite their cells being encased in rigid cell walls, plants exhibit a variety of regenerative responses ranging from the regeneration of specific cell types, tissues and organs, to the rebuilding of an entire organism. Over the years, extensive studies on embryo, shoot and root development in the model plant species Arabidopsis thaliana have provided insights into the mechanisms underlying plant regeneration. These studies highlight how Arabidopsis, with its wide array of refined molecular, genetic and cell biological tools, provides a perfect model to interrogate the cellular and molecular mechanisms of reprogramming during regeneration.
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Affiliation(s)
- Mabel Maria Mathew
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695551, India
| | - Kalika Prasad
- School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram, 695551, India
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26
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Abstract
Gravity determines shape of body tissue and affects the functions of life, both in plants and animals. The cellular response to gravity is an active process of mechanotransduction. Although plants and animals share some common mechanisms of gravity sensing in spite of their distant phylogenetic origin, each species has its own mechanism to sense and respond to gravity. In this review, we discuss current understanding regarding the mechanisms of cellular gravity sensing in plants and animals. Understanding gravisensing also contributes to life on Earth, e.g., understanding osteoporosis and muscle atrophy. Furthermore, in the current age of Mars exploration, understanding cellular responses to gravity will form the foundation of living in space.
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Ponnu J, Hoecker U. Illuminating the COP1/SPA Ubiquitin Ligase: Fresh Insights Into Its Structure and Functions During Plant Photomorphogenesis. FRONTIERS IN PLANT SCIENCE 2021; 12:662793. [PMID: 33841486 PMCID: PMC8024647 DOI: 10.3389/fpls.2021.662793] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/04/2021] [Indexed: 05/07/2023]
Abstract
CONSTITUTIVE PHOTOMORPHOGENIC 1 functions as an E3 ubiquitin ligase in plants and animals. Discovered originally in Arabidopsis thaliana, COP1 acts in a complex with SPA proteins as a central repressor of light-mediated responses in plants. By ubiquitinating and promoting the degradation of several substrates, COP1/SPA regulates many aspects of plant growth, development and metabolism. In contrast to plants, human COP1 acts as a crucial regulator of tumorigenesis. In this review, we discuss the recent important findings in COP1/SPA research including a brief comparison between COP1 activity in plants and humans.
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Dale R, Oswald S, Jalihal A, LaPorte MF, Fletcher DM, Hubbard A, Shiu SH, Nelson ADL, Bucksch A. Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling. FRONTIERS IN PLANT SCIENCE 2021; 12:687652. [PMID: 34354723 PMCID: PMC8329482 DOI: 10.3389/fpls.2021.687652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/01/2021] [Indexed: 05/10/2023]
Abstract
The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.
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Affiliation(s)
- Renee Dale
- Donald Danforth Plant Science Center, St. Louis, MO, United States
- *Correspondence: Renee Dale
| | - Scott Oswald
- Warnell School of Forestry and Natural Resources and Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Amogh Jalihal
- Department of Systems Biology, Harvard Medical School, Boston, MA, United States
| | - Mary-Francis LaPorte
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Daniel M. Fletcher
- Bioengineering Sciences Research Group, Department of Mechanical Engineering, School of Engineering, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, United Kingdom
| | - Allen Hubbard
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Shin-Han Shiu
- Department of Plant Biology and Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, MI, United States
| | | | - Alexander Bucksch
- Warnell School of Forestry and Natural Resources and Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
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Ali S, Khan N, Xie L. Molecular and Hormonal Regulation of Leaf Morphogenesis in Arabidopsis. Int J Mol Sci 2020; 21:ijms21145132. [PMID: 32698541 PMCID: PMC7404056 DOI: 10.3390/ijms21145132] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/28/2022] Open
Abstract
Shoot apical meristems (SAM) are tissues that function as a site of continuous organogenesis, which indicates that a small pool of pluripotent stem cells replenishes into lateral organs. The coordination of intercellular and intracellular networks is essential for maintaining SAM structure and size and also leads to patterning and formation of lateral organs. Leaves initiate from the flanks of SAM and then develop into a flattened structure with variable sizes and forms. This process is mainly regulated by the transcriptional regulators and mechanical properties that modulate leaf development. Leaf initiation along with proper orientation is necessary for photosynthesis and thus vital for plant survival. Leaf development is controlled by different components such as hormones, transcription factors, miRNAs, small peptides, and epigenetic marks. Moreover, the adaxial/abaxial cell fate, lamina growth, and shape of margins are determined by certain regulatory mechanisms. The over-expression and repression of various factors responsible for leaf initiation, development, and shape have been previously studied in several mutants. However, in this review, we collectively discuss how these factors modulate leaf development in the context of leaf initiation, polarity establishment, leaf flattening and shape.
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Affiliation(s)
- Shahid Ali
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Correspondence: (S.A.); (L.X.)
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - Linan Xie
- College of Life Sciences, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (S.A.); (L.X.)
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Semeradova H, Montesinos JC, Benkova E. All Roads Lead to Auxin: Post-translational Regulation of Auxin Transport by Multiple Hormonal Pathways. PLANT COMMUNICATIONS 2020; 1:100048. [PMID: 33367243 PMCID: PMC7747973 DOI: 10.1016/j.xplc.2020.100048] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/26/2020] [Accepted: 04/18/2020] [Indexed: 05/03/2023]
Abstract
Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development.
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Affiliation(s)
- Hana Semeradova
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | | | - Eva Benkova
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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31
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Galvan-Ampudia CS, Cerutti G, Legrand J, Brunoud G, Martin-Arevalillo R, Azais R, Bayle V, Moussu S, Wenzl C, Jaillais Y, Lohmann JU, Godin C, Vernoux T. Temporal integration of auxin information for the regulation of patterning. eLife 2020; 9:55832. [PMID: 32379043 PMCID: PMC7205470 DOI: 10.7554/elife.55832] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 03/29/2020] [Indexed: 12/27/2022] Open
Abstract
Positional information is essential for coordinating the development of multicellular organisms. In plants, positional information provided by the hormone auxin regulates rhythmic organ production at the shoot apex, but the spatio-temporal dynamics of auxin gradients is unknown. We used quantitative imaging to demonstrate that auxin carries high-definition graded information not only in space but also in time. We show that, during organogenesis, temporal patterns of auxin arise from rhythmic centrifugal waves of high auxin travelling through the tissue faster than growth. We further demonstrate that temporal integration of auxin concentration is required to trigger the auxin-dependent transcription associated with organogenesis. This provides a mechanism to temporally differentiate sites of organ initiation and exemplifies how spatio-temporal positional information can be used to create rhythmicity. Plants, like animals and many other multicellular organisms, control their body architecture by creating organized patterns of cells. These patterns are generally defined by signal molecules whose levels differ across the tissue and change over time. This tells the cells where they are located in the tissue and therefore helps them know what tasks to perform. A plant hormone called auxin is one such signal molecule and it controls when and where plants produce new leaves and flowers. Over time, this process gives rise to the dashing arrangements of spiraling organs exhibited by many plant species. The leaves and flowers form from a relatively small group of cells at the tip of a growing stem known as the shoot apical meristem. Auxin accumulates at precise locations within the shoot apical meristem before cells activate the genes required to make a new leaf or flower. However, the precise role of auxin in forming these new organs remained unclear because the tools to observe the process in enough detail were lacking. Galvan-Ampudia, Cerutti et al. have now developed new microscopy and computational approaches to observe auxin in a small plant known as Arabidopsis thaliana. This showed that dozens of shoot apical meristems exhibited very similar patterns of auxin. Images taken over a period of several hours showed that the locations where auxin accumulated were not fixed on a group of cells but instead shifted away from the center of the shoot apical meristems faster than the tissue grew. This suggested the cells experience rapidly changing levels of auxin. Further experiments revealed that the cells needed to be exposed to a high level of auxin over time to activate genes required to form an organ. This mechanism sheds a new light on how auxin regulates when and where plants make new leaves and flowers. The tools developed by Galvan-Ampudia, Cerutti et al. could be used to study the role of auxin in other plant tissues, and to investigate how plants regulate the response to other plant hormones.
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Affiliation(s)
- Carlos S Galvan-Ampudia
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Guillaume Cerutti
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Jonathan Legrand
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Géraldine Brunoud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Raquel Martin-Arevalillo
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Romain Azais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Vincent Bayle
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Steven Moussu
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Christian Wenzl
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yvon Jaillais
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Christophe Godin
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Inria, Lyon, France
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32
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Allen HR, Ptashnyk M. Mathematical Modelling of Auxin Transport in Plant Tissues: Flux Meets Signalling and Growth. Bull Math Biol 2020; 82:17. [PMID: 31970524 PMCID: PMC6976557 DOI: 10.1007/s11538-019-00685-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/02/2019] [Indexed: 11/25/2022]
Abstract
Plant hormone auxin has critical roles in plant growth, dependent on its heterogeneous distribution in plant tissues. Exactly how auxin transport and developmental processes such as growth coordinate to achieve the precise patterns of auxin observed experimentally is not well understood. Here we use mathematical modelling to examine the interplay between auxin dynamics and growth and their contribution to formation of patterns in auxin distribution in plant tissues. Mathematical models describing the auxin-related signalling pathway, PIN and AUX1 dynamics, auxin transport, and cell growth in plant tissues are derived. A key assumption of our models is the regulation of PIN proteins by the auxin-responsive ARF-Aux/IAA signalling pathway, with upregulation of PIN biosynthesis by ARFs. Models are analysed and solved numerically to examine the long-time behaviour and auxin distribution. Changes in auxin-related signalling processes are shown to be able to trigger transition between passage- and spot-type patterns in auxin distribution. The model was also shown to be able to generate isolated cells with oscillatory dynamics in levels of components of the auxin signalling pathway which could explain oscillations in levels of ARF targets that have been observed experimentally. Cell growth was shown to have influence on PIN polarisation and determination of auxin distribution patterns. Numerical simulation results indicate that auxin-related signalling processes can explain the different patterns in auxin distributions observed in plant tissues, whereas the interplay between auxin transport and growth can explain the ‘reverse-fountain’ pattern in auxin distribution observed at plant root tips.
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Affiliation(s)
- Henry R Allen
- Department of Mathematics, Fulton Building, University of Dundee, Dundee, DD1 4HN, UK
| | - Mariya Ptashnyk
- Department of Mathematics, Colin Maclaurin Building, Heriot-Watt University, Edinburgh, EH14 4AS, UK.
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33
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Abstract
The root meristem-one of the plant's centers of continuous growth-is a conveyer belt in which cells of different identities are pushed through gradients along the root's longitudinal axis. An auxin gradient has long been implicated in controlling the progression of cell states in the root meristem. Recent work has shown that a PLETHORA (PLT) protein transcription factor gradient, which is under a delayed auxin response, has a dose-dependent effect on the differentiation state of cells. The direct effect of auxin concentration on differential transcriptional outputs remains unclear. Genomic and other analyses of regulatory sequences show that auxin responses are likely controlled by combinatorial inputs from transcription factors outside the core auxin signaling pathway. The passage through the meristem exposes cells to varying positional signals that could help them interpret auxin inputs independent of gradient effects. One open question is whether cells process information from the changes in the gradient over time as they move through the auxin gradient.
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Affiliation(s)
- Bruno Guillotin
- New York University, The Department of Biology, The Center for Genomics and Systems Biology, New York, NY, United States
| | - Kenneth D Birnbaum
- New York University, The Department of Biology, The Center for Genomics and Systems Biology, New York, NY, United States.
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34
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Ronellenfitsch H, Katifori E. Phenotypes of Vascular Flow Networks. PHYSICAL REVIEW LETTERS 2019; 123:248101. [PMID: 31922876 DOI: 10.1103/physrevlett.123.248101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Indexed: 06/10/2023]
Abstract
Complex distribution networks are pervasive in biology. Examples include nutrient transport in the slime mold Physarum polycephalum as well as mammalian and plant venation. Adaptive rules are believed to guide development of these networks and lead to a reticulate, hierarchically nested topology that is both efficient and resilient against perturbations. However, as of yet, no mechanism is known that can generate such networks on all scales. We show how hierarchically organized reticulation can be constructed and maintained through spatially correlated load fluctuations on a particular length scale. We demonstrate that the network topologies generated represent a trade-off between optimizing transport efficiency, construction cost, and damage robustness and identify the Pareto-efficient front that evolution is expected to favor and select for. We show that the typical fluctuation length scale controls the position of the networks on the Pareto front and thus on the spectrum of venation phenotypes.
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Affiliation(s)
- Henrik Ronellenfitsch
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Eleni Katifori
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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35
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Deletion in the Promoter of PcPIN-L Affects the Polar Auxin Transport in Dwarf Pear (Pyrus communis L.). Sci Rep 2019; 9:18645. [PMID: 31819123 PMCID: PMC6901534 DOI: 10.1038/s41598-019-55195-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 11/25/2019] [Indexed: 12/31/2022] Open
Abstract
Dwarf cultivars or dwarfing rootstocks enable high-density planting and are therefore highly desirable in modern pear production. Previously, we found that the dwarf growth habit of pear is controlled by a single dominant gene PcDw. In this study, PcPIN-L (PCP021016) was cloned from dwarf-type and standard-type pears. PcPIN-L expression was significantly lower in the dwarf-type pears than in standard-type pears, which was caused by the CT repeat deletion in the promoter of dwarf-type pears. PcPIN-L overexpression in tobacco plants enhanced the growth of the stems and the roots. Notably, the indole acetic acid (IAA) content decreased in the shoot tips and increased in the stems of transgenic lines compared with wild type, which is consistent with the greater IAA content in the shoot tips and lower IAA content in the stems of dwarf-type pears than in standard-type pears. The CT repeat deletion in the promoter that causes a decrease in promoter activity is associated with lower PcPIN-L expression in the dwarf-type pears, which might limit the polar auxin transport and in turn result in the dwarf phenotype. Taken together, the results provide a novel dwarfing molecular mechanism in perennial woody plants.
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36
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Nakamasu A, Higaki T. Theoretical models for branch formation in plants. JOURNAL OF PLANT RESEARCH 2019; 132:325-333. [PMID: 31004242 PMCID: PMC7082385 DOI: 10.1007/s10265-019-01107-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Various branch architectures are observed in living organisms including plants. Branch formation has traditionally been an area of interest in the field of developmental biology, and theoretical approaches are now commonly used to understand the complex mechanisms involved. In this review article, we provide an overview of theoretical approaches including mathematical models and computer simulations for studying plant branch formation. These approaches cover a wide range of topics. In particular, we focus on the importance of positional information in branch formation, which has been especially revealed by theoretical research in plants including computations of developmental processes.
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Affiliation(s)
- Akiko Nakamasu
- International Research Organization for Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuou-ku, Kumamoto, 860-8555, Japan.
| | - Takumi Higaki
- International Research Organization for Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuou-ku, Kumamoto, 860-8555, Japan.
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37
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38
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Barbosa ICR, Hammes UZ, Schwechheimer C. Activation and Polarity Control of PIN-FORMED Auxin Transporters by Phosphorylation. TRENDS IN PLANT SCIENCE 2018; 23:523-538. [PMID: 29678589 DOI: 10.1016/j.tplants.2018.03.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/11/2018] [Accepted: 03/14/2018] [Indexed: 05/09/2023]
Abstract
Auxin controls almost every aspect of plant development. Auxin is distributed within the plant by passive diffusion and active cell-to-cell transport. PIN-FORMED (PIN) auxin efflux transporters are polarly distributed in the plasma membranes of many cells, and knowledge about their distribution can predict auxin transport and explain auxin distribution patterns, even in complex tissues. Recent studies have revealed that phosphorylation is essential for PIN activation, suggesting that PIN phosphorylation needs to be taken into account in understanding auxin transport. These findings also ask for a re-examination of previously proposed mechanisms for phosphorylation-dependent PIN polarity control. We provide a comprehensive summary of the current knowledge on PIN regulation by phosphorylation, and discuss possible mechanisms of PIN polarity control in the context of recent findings.
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Affiliation(s)
- Inês C R Barbosa
- Department of Plant Molecular Biology, Biophore Building, Unil-Sorge, Université de Lausanne, 1015 Lausanne, Switzerland; These authors contributed equally to this review article and are listed in alphabetical order
| | - Ulrich Z Hammes
- Plant Systems Biology, Technical University Munich, Emil-Ramann-Strasse 8, 85354 Freising, Germany; These authors contributed equally to this review article and are listed in alphabetical order
| | - Claus Schwechheimer
- Plant Systems Biology, Technical University Munich, Emil-Ramann-Strasse 8, 85354 Freising, Germany; These authors contributed equally to this review article and are listed in alphabetical order.
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39
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Fujita H, Kawaguchi M. Spatial regularity control of phyllotaxis pattern generated by the mutual interaction between auxin and PIN1. PLoS Comput Biol 2018; 14:e1006065. [PMID: 29614066 PMCID: PMC5882125 DOI: 10.1371/journal.pcbi.1006065] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/02/2018] [Indexed: 11/19/2022] Open
Abstract
Phyllotaxis, the arrangement of leaves on a plant stem, is well known because of its beautiful geometric configuration, which is derived from the constant spacing between leaf primordia. This phyllotaxis is established by mutual interaction between a diffusible plant hormone auxin and its efflux carrier PIN1, which cooperatively generate a regular pattern of auxin maxima, small regions with high auxin concentrations, leading to leaf primordia. However, the molecular mechanism of the regular pattern of auxin maxima is still largely unknown. To better understand how the phyllotaxis pattern is controlled, we investigated mathematical models based on the auxin-PIN1 interaction through linear stability analysis and numerical simulations, focusing on the spatial regularity control of auxin maxima. As in previous reports, we first confirmed that this spatial regularity can be reproduced by a highly simplified and abstract model. However, this model lacks the extracellular region and is not appropriate for considering the molecular mechanism. Thus, we investigated how auxin maxima patterns are affected under more realistic conditions. We found that the spatial regularity is eliminated by introducing the extracellular region, even in the presence of direct diffusion between cells or between extracellular spaces, and this strongly suggests the existence of an unknown molecular mechanism. To unravel this mechanism, we assumed a diffusible molecule to verify various feedback interactions with auxin-PIN1 dynamics. We revealed that regular patterns can be restored by a diffusible molecule that mediates the signaling from auxin to PIN1 polarization. Furthermore, as in the one-dimensional case, similar results are observed in the two-dimensional space. These results provide a great insight into the theoretical and molecular basis for understanding the phyllotaxis pattern. Our theoretical analysis strongly predicts a diffusible molecule that is pivotal for the phyllotaxis pattern but is yet to be determined experimentally.
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Affiliation(s)
- Hironori Fujita
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
- * E-mail:
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
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40
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Hernández-Hernández V, Barrio RA, Benítez M, Nakayama N, Romero-Arias JR, Villarreal C. A physico-genetic module for the polarisation of auxin efflux carriers PIN-FORMED (PIN). Phys Biol 2018; 15:036002. [PMID: 29393068 DOI: 10.1088/1478-3975/aaac99] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Intracellular polarisation of auxin efflux carriers is crucial for understanding how auxin gradients form in plants. The polarisation dynamics of auxin efflux carriers PIN-FORMED (PIN) depends on both biomechanical forces as well as chemical, molecular and genetic factors. Biomechanical forces have shown to affect the localisation of PIN transporters to the plasma membrane. We propose a physico-genetic module of PIN polarisation that integrates biomechanical, molecular, and cellular processes as well as their non-linear interactions. The module was implemented as a discrete Boolean model and then approximated to a continuous dynamic system, in order to explore the relative contribution of the factors mediating PIN polarisation at the scale of single cell. Our models recovered qualitative behaviours that have been experimentally observed and enable us to predict that, in the context of PIN polarisation, the effects of the mechanical forces can predominate over the activity of molecular factors such as the GTPase ROP6 and the ROP-INTERACTIVE CRIB MOTIF-CONTAINING PROTEIN RIC1.
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Affiliation(s)
- Valeria Hernández-Hernández
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico. Current Address: Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Lyon, France. Author to whom any correspondence should be addressed
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41
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Deb J, Bland HM, Østergaard L. Developmental cartography: coordination via hormonal and genetic interactions during gynoecium formation. CURRENT OPINION IN PLANT BIOLOGY 2018; 41:54-60. [PMID: 28961459 DOI: 10.1016/j.pbi.2017.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/01/2017] [Accepted: 09/05/2017] [Indexed: 05/06/2023]
Abstract
Development in multicellular organisms requires the establishment of tissue identity through polarity cues. The Arabidopsis gynoecium presents an excellent model to study this coordination, as it comprises a complex tissue structure which is established through multiple polarity systems. The gynoecium is derived from the fusion of two carpels and forms in the centre of the flower. Many regulators of carpel development also have roles in leaf development, emphasizing the evolutionary origin of carpels as modified leaves. The gynoecium can therefore be considered as having evolved from a simple setup followed by adjustment in tissue polarity to facilitate efficient reproduction. Here, we discuss concepts to understand how hormonal and genetic systems interact to pattern the gynoecium.
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Affiliation(s)
- Joyita Deb
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Heather M Bland
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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42
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Liu J, Moore S, Chen C, Lindsey K. Crosstalk Complexities between Auxin, Cytokinin, and Ethylene in Arabidopsis Root Development: From Experiments to Systems Modeling, and Back Again. MOLECULAR PLANT 2017; 10:1480-1496. [PMID: 29162416 DOI: 10.1016/j.molp.2017.11.002] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 05/23/2023]
Abstract
Understanding how hormones and genes interact to coordinate plant growth in a changing environment is a major challenge in plant developmental biology. Auxin, cytokinin, and ethylene are three important hormones that regulate many aspects of plant development. This review critically evaluates the crosstalk between the three hormones in Arabidopsis root development. We integrate a variety of experimental data into a crosstalk network, which reveals multiple layers of complexity in auxin, cytokinin, and ethylene crosstalk. In particular, data integration reveals an additional, largely overlooked link between the ethylene and cytokinin pathways, which acts through a phosphorelay mechanism. This proposed link addresses outstanding questions on whether ethylene application promotes or inhibits receptor kinase activity of the ethylene receptors. Elucidating the complexity in auxin, cytokinin, and ethylene crosstalk requires a combined experimental and systems modeling approach. We evaluate important modeling efforts for establishing how crosstalk between auxin, cytokinin, and ethylene regulates patterning in root development. We discuss how a novel methodology that iteratively combines experiments with systems modeling analysis is essential for elucidating the complexity in crosstalk of auxin, cytokinin, and ethylene in root development. Finally, we discuss the future challenges from a combined experimental and modeling perspective.
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Affiliation(s)
- Junli Liu
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Simon Moore
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Keith Lindsey
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK.
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43
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van den Berg T, Ten Tusscher KH. Auxin Information Processing; Partners and Interactions beyond the Usual Suspects. Int J Mol Sci 2017; 18:ijms18122585. [PMID: 29194409 PMCID: PMC5751188 DOI: 10.3390/ijms18122585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/20/2017] [Accepted: 11/24/2017] [Indexed: 12/20/2022] Open
Abstract
Auxin plays a major role in a variety of processes involved in plant developmental patterning and its adaptation to environmental conditions. Therefore, an important question is how specificity in auxin signalling is achieved, that is, how a single signalling molecule can carry so many different types of information. In recent years, many studies on auxin specificity have been published, unravelling increasingly more details on differential auxin sensitivity, expression domains and downstream partners of the auxin receptors (transport inhibitor response 1 (TIR1) and other auxin signaling F-box proteins (AFB)), transcriptional repressors that are degraded in response to auxin (AUX/IAA) and downstream auxin response factors (ARF) that together constitute the plant’s major auxin response pathways. These data are critical to explain how, in the same cells, different auxin levels may trigger different responses, as well as how in different spatial or temporal contexts similar auxin signals converge to different responses. However, these insights do not yet answer more complex questions regarding auxin specificity. As an example, they leave open the question of how similar sized auxin changes at similar locations result in different responses depending on the duration and spatial extent of the fluctuation in auxin levels. Similarly, it leaves unanswered how, in the case of certain tropisms, small differences in signal strength at both sides of a plant organ are converted into an instructive auxin asymmetry that enables a robust tropic response. Finally, it does not explain how, in certain cases, substantially different auxin levels become translated into similar cellular responses, while in other cases similar auxin levels, even when combined with similar auxin response machinery, may trigger different responses. In this review, we illustrate how considering the regulatory networks and contexts in which auxin signalling takes place helps answer these types of fundamental questions.
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Affiliation(s)
- Thea van den Berg
- Theoretical Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands.
| | - Kirsten H Ten Tusscher
- Theoretical Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands.
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44
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Ballaré CL, Pierik R. The shade-avoidance syndrome: multiple signals and ecological consequences. PLANT, CELL & ENVIRONMENT 2017; 40:2530-2543. [PMID: 28102548 DOI: 10.1111/pce.12914] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 05/18/2023]
Abstract
Plants use photoreceptor proteins to detect the proximity of other plants and to activate adaptive responses. Of these photoreceptors, phytochrome B (phyB), which is sensitive to changes in the red (R) to far-red (FR) ratio of sunlight, is the one that has been studied in greatest detail. The molecular connections between the proximity signal (low R:FR) and a model physiological response (increased elongation growth) have now been mapped in considerable detail in Arabidopsis seedlings. We briefly review our current understanding of these connections and discuss recent progress in establishing the roles of other photoreceptors in regulating growth-related pathways in response to competition cues. We also consider processes other than elongation that are controlled by photoreceptors and contribute to plant fitness under variable light conditions, including photoresponses that optimize the utilization of soil resources. In examining recent advances in the field, we highlight emerging roles of phyB as a major modulator of hormones related to plant immunity, in particular salicylic acid and jasmonic acid (JA). Recent attempts to manipulate connections between light signals and defence in Arabidopsis suggest that it might be possible to improve crop health at high planting densities by targeting links between phyB and JA signalling.
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Affiliation(s)
- Carlos L Ballaré
- IFEVA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Ave. San Martín 4453, C1417DSE, Buenos Aires, Argentina
- IIB-INTECH, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de San Martín, B1650HMP, Buenos Aires, Argentina
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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45
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Samodelov SL, Zurbriggen MD. Quantitatively Understanding Plant Signaling: Novel Theoretical-Experimental Approaches. TRENDS IN PLANT SCIENCE 2017; 22:685-704. [PMID: 28668509 DOI: 10.1016/j.tplants.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
With the need to respond to and integrate a multitude of external and internal stimuli, plant signaling is highly complex, exhibiting signaling component redundancy and high interconnectedness between individual pathways. We review here novel theoretical-experimental approaches in manipulating plant signaling towards the goal of a comprehensive understanding and targeted quantitative control of plant processes. We highlight approaches taken in the field of synthetic biology used in other systems and discuss their applicability in plants. Finally, we introduce existing tools for the quantitative analysis and monitoring of plant signaling and the integration of experimentally obtained quantitative data into mathematical models. Incorporating principles of synthetic biology into plant sciences more widely will lead this field forward in both fundamental and applied research.
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Affiliation(s)
- Sophia L Samodelov
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and Cluster of Excellence on Plant Sciences (CEPLAS), University of Düsseldorf, Düsseldorf, Germany.
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46
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Romero-Arias JR, Hernández-Hernández V, Benítez M, Alvarez-Buylla ER, Barrio RA. Model of polar auxin transport coupled to mechanical forces retrieves robust morphogenesis along the Arabidopsis root. Phys Rev E 2017; 95:032410. [PMID: 28415207 DOI: 10.1103/physreve.95.032410] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Indexed: 11/06/2022]
Abstract
Stem cells are identical in many scales, they share the same molecular composition, DNA, genes, and genetic networks, yet they should acquire different properties to form a functional tissue. Therefore, they must interact and get some external information from their environment, either spatial (dynamical fields) or temporal (lineage). In this paper we test to what extent coupled chemical and physical fields can underlie the cell's positional information during development. We choose the root apical meristem of Arabidopsis thaliana to model the emergence of cellular patterns. We built a model to study the dynamics and interactions between the cell divisions, the local auxin concentration, and physical elastic fields. Our model recovers important aspects of the self-organized and resilient behavior of the observed cellular patterns in the Arabidopsis root, in particular, the reverse fountain pattern observed in the auxin transport, the PIN-FORMED (protein family of auxin transporters) polarization pattern and the accumulation of auxin near the region of maximum curvature in a bent root. Our model may be extended to predict altered cellular patterns that are expected under various applied auxin treatments or modified physical growth conditions.
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Affiliation(s)
- J Roberto Romero-Arias
- Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 20-364, 01000 México Distrito Federal, Mexico.,Instituto de Matemáticas, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Juriquilla, Querétaro 76230, Mexico
| | - Valeria Hernández-Hernández
- Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, 04510 México Distrito Federal, Mexico.,Laboratoire Reproduction et Développement des Plantes, University of Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
| | - Mariana Benítez
- Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, 04510 México Distrito Federal, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 México Distrito Federal, Mexico
| | - Elena R Alvarez-Buylla
- Instituto de Ecología, Universidad Nacional Autónoma de México, Apartado Postal 70-275, 04510 México Distrito Federal, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 México Distrito Federal, Mexico
| | - Rafael A Barrio
- Instituto de Física, Universidad Nacional Autónoma de México, Apartado Postal 20-364, 01000 México Distrito Federal, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 México Distrito Federal, Mexico
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47
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Moore S, Liu J, Zhang X, Lindsey K. A recovery principle provides insight into auxin pattern control in the Arabidopsis root. Sci Rep 2017; 7:43004. [PMID: 28220889 PMCID: PMC5318957 DOI: 10.1038/srep43004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/18/2017] [Indexed: 11/08/2022] Open
Abstract
Regulated auxin patterning provides a key mechanism for controlling root growth and development. We have developed a data-driven mechanistic model using realistic root geometry and formulated a principle to theoretically investigate quantitative auxin pattern recovery following auxin transport perturbation. This principle reveals that auxin patterning is potentially controlled by multiple combinations of interlinked levels and localisation of influx and efflux carriers. We demonstrate that (1) when efflux carriers maintain polarity but change levels, maintaining the same auxin pattern requires non-uniform and polar distribution of influx carriers; (2) the emergence of the same auxin pattern, from different levels of influx carriers with the same nonpolar localisation, requires simultaneous modulation of efflux carrier level and polarity; and (3) multiple patterns of influx and efflux carriers for maintaining an auxin pattern do not have spatially proportional correlation. This reveals that auxin pattern formation requires coordination between influx and efflux carriers. We further show that the model makes various predictions that can be experimentally validated.
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Affiliation(s)
- Simon Moore
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Junli Liu
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Xiaoxian Zhang
- Department of Sustainable Soil and Grassland System, Rothamsted Research, Harpenden, Hertfordshire AL5 2GQ, UK
| | - Keith Lindsey
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
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48
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Qi J, Greb T. Cell polarity in plants: the Yin and Yang of cellular functions. CURRENT OPINION IN PLANT BIOLOGY 2017; 35:105-110. [PMID: 27918938 PMCID: PMC7212042 DOI: 10.1016/j.pbi.2016.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/17/2016] [Accepted: 11/22/2016] [Indexed: 05/03/2023]
Abstract
Spatial organization is fundamental for the performance of living organisms and is reflected in a distinct distribution of structures and molecules down to the subcellular level. In particular, eukaryotic cells harbor a vast range of possibilities for distributing organelles, the cytoskeleton or the extracellular matrix in an active and highly regulated manner. An asymmetric or polar distribution is rather the rule than the exception and often reflects a particular position or orientation of a cell within a multicellular body. Here, we highlight recent insights into the regulation of cell polarity in plants and reveal the interactive nature of underlying molecular processes.
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Affiliation(s)
- Jiyan Qi
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.
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49
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Fàbregas N, Formosa-Jordan P, Ibañes M, Caño-Delgado AI. Experimental and Theoretical Methods to Approach the Study of Vascular Patterning in the Plant Shoot. Methods Mol Biol 2017; 1544:3-19. [PMID: 28050824 DOI: 10.1007/978-1-4939-6722-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The plant vascular system provides transport and mechanical support functions that are essential for suitable plant growth and development. In Arabidopsis thaliana (Arabidopsis), the vascular tissues at the shoot inflorescence stems are disposed in organized vascular bundles. The vascular patterning emergence and development within the shoot inflorescence stems is under the control of plant growth regulators (De Rybel et al., Nat Rev Mol Cell Biol 17:30-40, 2016; Caño-Delgado et al., Annu Rev Cell Dev Biol 26:605-637, 2010). By using a combined approach of experimental methods for vascular tissues visualization and quantification together with theoretical methods through mathematical and computational modeling, we have reported that auxin transport and brassinosteroid signaling play complementary roles in the formation of the periodic vascular patterning in the shoot (Ibañes et al., Proc Natl Acad Sci U S A 106:13630-13635, 2009; Fàbregas et al., Plant Signal Behav 5:903-906, 2010; Fàbregas et al., PLoS Genet 11:e1005183, 2015). Here, we report the methodology for the interdisciplinary analysis of the shoot vascular patterning in the plant model Arabidopsis into a handle procedure for visualization, quantification, data analysis, and modeling implementation.
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Affiliation(s)
- Norma Fàbregas
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Pau Formosa-Jordan
- The Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Marta Ibañes
- Department of Condensed Matter Physics, University of Barcelona, Barcelona, Spain
| | - Ana I Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain.
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50
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Weijers D. Phyllotaxis: A Matthew Effect in Auxin Action. Curr Biol 2016; 26:R1233-R1235. [PMID: 27923132 DOI: 10.1016/j.cub.2016.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Local auxin concentration maxima promote organ initiation in the plant shoot meristem, but how auxin peaks are formed has remained unclear. A new study proposes a cellular Matthew effect, where auxin is pumped into those cells that have higher concentrations.
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Affiliation(s)
- Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands.
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