1
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Pukhovaya EM, Ramalho JJ, Weijers D. Polar targeting of proteins - a green perspective. J Cell Sci 2024; 137:jcs262068. [PMID: 39330548 DOI: 10.1242/jcs.262068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2024] Open
Abstract
Cell polarity - the asymmetric distribution of molecules and cell structures within the cell - is a feature that almost all cells possess. Even though the cytoskeleton and other intracellular organelles can have a direction and guide protein distribution, the plasma membrane is, in many cases, essential for the asymmetric localization of proteins because it helps to concentrate proteins and restrict their localization. Indeed, many proteins that exhibit asymmetric or polarized localization are either embedded in the PM or located close to it in the cellular cortex. Such proteins, which we refer to here as 'polar proteins', use various mechanisms of membrane targeting, including vesicle trafficking, direct phospholipid binding, or membrane anchoring mediated by post-translational modifications or binding to other proteins. These mechanisms are often shared with non-polar proteins, yet the unique combinations of several mechanisms or protein-specific factors assure the asymmetric distribution of polar proteins. Although there is a relatively detailed understanding of polar protein membrane targeting mechanisms in animal and yeast models, knowledge in plants is more fragmented and focused on a limited number of known polar proteins in different contexts. In this Review, we combine the current knowledge of membrane targeting mechanisms and factors for known plant transmembrane and cortical proteins and compare these with the mechanisms elucidated in non-plant systems. We classify the known factors as general or polarity specific, and we highlight areas where more knowledge is needed to construct an understanding of general polar targeting mechanisms in plants or to resolve controversies.
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Affiliation(s)
- Evgeniya M Pukhovaya
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - João Jacob Ramalho
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708WE, Wageningen, The Netherlands
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2
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Fiedler L, Friml J. Rapid auxin signaling: Unknowns old and new. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102443. [PMID: 37666097 DOI: 10.1016/j.pbi.2023.102443] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 09/06/2023]
Abstract
To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling.
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Affiliation(s)
- Lukáš Fiedler
- Institute of Science and Technology Austria (ISTA), 3400, Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology Austria (ISTA), 3400, Klosterneuburg, Austria.
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3
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Kiradjiev KB, Band LR. Multiscale Asymptotic Analysis Reveals How Cell Growth and Subcellular Compartments Affect Tissue-Scale Hormone Transport. Bull Math Biol 2023; 85:101. [PMID: 37702758 PMCID: PMC10499980 DOI: 10.1007/s11538-023-01199-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023]
Abstract
Determining how cell-scale processes lead to tissue-scale patterns is key to understanding how hormones and morphogens are distributed within biological tissues and control developmental processes. In this article, we use multiscale asymptotic analysis to derive a continuum approximation for hormone transport in a long file of cells to determine how subcellular compartments and cell growth and division affect tissue-scale hormone transport. Focusing our study on plant tissues, we begin by presenting a discrete multicellular ODE model tracking the hormone concentration in each cell's cytoplasm, subcellular vacuole, and surrounding apoplast, represented by separate compartments in the cell-file geometry. We allow the cells to grow at a rate that can depend both on space and time, accounting for both cytoplasmic and vacuolar expansion. Multiscale asymptotic analysis enables us to systematically derive the corresponding continuum model, obtaining an effective reaction-advection-diffusion equation and revealing how the effective diffusivity, effective advective velocity, and the effective sink term depend on the parameters in the cell-scale model. The continuum approximation reveals how subcellular compartments, such as vacuoles, can act as storage vessels, that significantly alter the effective properties of hormone transport, such as the effective diffusivity and the induced effective velocity. Furthermore, we show how cell growth and spatial variance across cell lengths affect the effective diffusivity and the induced effective velocity, and how these affect the tissue-scale hormone distribution. In particular, we find that cell growth naturally induces an effective velocity in the direction of growth, whereas spatial variance across cell lengths induces effective velocity due to the presence of an extra compartment, such as the apoplast and the vacuole, and variations in the relative sizes between the compartments across the file of cells. It is revealed that hormone transport is faster across cells of decreasing lengths than cells with increasing lengths. We also investigate the effect of cell division on transport dynamics, assuming that each cell divides as soon as it doubles in size, and find that increasing the time between successive cell divisions decreases the growth rate, which enhances the effect of cell division in slowing hormone transport. Motivated by recent experimental discoveries, we discuss particular applications for transport of gibberellic acid (GA), an important growth hormone, within the Arabidopsis root. The model reveals precisely how membrane proteins that mediate facilitated GA transport affect the effective tissue-scale transport. However, the results are general enough to be relevant to other plant hormones, or other substances that are transported in a similar way in any type of cells.
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Affiliation(s)
- K B Kiradjiev
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - L R Band
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
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4
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Scarpella E. Axes and polarities in leaf vein formation. PLANT PHYSIOLOGY 2023; 193:112-124. [PMID: 37261944 DOI: 10.1093/plphys/kiad321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 06/03/2023]
Abstract
For multicellular organisms to develop, cells must grow, divide, and differentiate along preferential or exclusive orientations or directions. Moreover, those orientations, or axes, and directions, or polarities, must be coordinated between cells within and between tissues. Therefore, how axes and polarities are coordinated between cells is a key question in biology. In animals, such coordination mainly depends on cell migration and direct interaction between proteins protruding from the plasma membrane. Both cell movements and direct cell-cell interactions are prevented in plants by cell walls that surround plant cells and keep them apart and in place. Therefore, plants have evolved unique mechanisms to coordinate their cell axes and polarities. Here I will discuss evidence suggesting that understanding how leaf veins form may uncover those unique mechanisms. Indeed, unlike previously thought, the cell-to-cell polar transport of the plant hormone auxin along developing veins cannot account for many features of vein patterning. Instead, those features can be accounted for by models of vein patterning that combine polar auxin transport with auxin diffusion through plasmodesmata along the axis of developing veins. Though it remains unclear whether such a combination of polar transport and axial diffusion of auxin can account for the formation of the variety of vein patterns found in plant leaves, evidence suggests that such a combined mechanism may control plant developmental processes beyond vein patterning.
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Affiliation(s)
- Enrico Scarpella
- Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton, AB T6G 2E9, Canada
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5
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Organ Patterning at the Shoot Apical Meristem (SAM): The Potential Role of the Vascular System. Symmetry (Basel) 2023. [DOI: 10.3390/sym15020364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Auxin, which is transported in the outermost cell layer, is one of the major players involved in plant organ initiation and positioning at the shoot apical meristem (SAM). However, recent studies have recognized the role of putative internal signals as an important factor collaborating with the well-described superficial pathway of organogenesis regulation. Different internal signals have been proposed; however, their nature and transport route have not been precisely determined. Therefore, in this mini-review, we aimed to summarize the current knowledge regarding the auxin-dependent regulation of organ positioning at the SAM and to discuss the vascular system as a potential route for internal signals. In addition, as regular organ patterning is a universal phenomenon, we focus on the role of the vasculature in this process in the major lineages of land plants, i.e., bryophytes, lycophytes, ferns, gymnosperms, and angiosperms.
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6
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ABP1-TMK auxin perception for global phosphorylation and auxin canalization. Nature 2022; 609:575-581. [PMID: 36071161 DOI: 10.1038/s41586-022-05187-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 08/03/2022] [Indexed: 12/22/2022]
Abstract
The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear1-3. Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades1,4. Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H+-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.
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7
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Pan L, Wang M, Yang Y, Chen C, Dai H, Zhang Z, Hua B, Miao M. Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant ( Cucurbita maxima). FRONTIERS IN PLANT SCIENCE 2022; 13:942004. [PMID: 35937359 PMCID: PMC9354748 DOI: 10.3389/fpls.2022.942004] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Atlantic Giant (AG) pumpkin (Cucurbita maxima) produces the world's largest fruit. Elucidating the molecular mechanism of AG fruit formation is of scientific and practical importance. In this research, genome-wide resequencing of an F2 population produced by a cross between AG and its small-fruit ancestor Hubbard was used to identify quantitative trait loci (QTLs) and candidate genes. Transgressive segregation of fruit size-related traits was observed in the F2 population, suggesting that fruit size was a quantitative trait controlled by multiple genes. A genetic map with an average physical distance of 154 kb per marker was constructed, and 13 QTLs related to fruit size were identified using bin-map construction. RNA sequencing analysis revealed that pathways associated with assimilate accumulation into the fruit, including carbohydrate metabolism, were significantly enriched in differentially expressed genes. According to the predicted impact of mutation on the biological function of certain proteins, 13 genes were selected as candidate genes associated with fruit size, among which two phytohormone-related genes, CmaCh17G011340 (a flavin-containing monooxygenase) and CmaCh04G029660 (a leucine-rich repeat protein kinase) were chosen for further investigation. Finally, one insertion-deletion (inDel) and three single nucleotide polymorphisms (SNPs) were successfully transformed to Kompetitive Allele-Specific PCR (KASP) markers. The novel QTLs and candidate genes identified provide insights into the genetic mechanism of large fruit formation of AG, and the genetic map and tightly linked KASP markers developed in this study can be employed for marker-assisted breeding to alter fruit size of C. maxima.
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Affiliation(s)
- Liu Pan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Min Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Yating Yang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Chen Chen
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Haibo Dai
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Zhiping Zhang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Bing Hua
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Minmin Miao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
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8
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Abstract
Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.
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Affiliation(s)
- Jiří Friml
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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9
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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: 9] [Impact Index Per Article: 4.5] [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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10
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Hajný J, Tan S, Friml J. Auxin canalization: From speculative models toward molecular players. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102174. [PMID: 35123880 DOI: 10.1016/j.pbi.2022.102174] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 05/12/2023]
Abstract
Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development.
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Affiliation(s)
- Jakub Hajný
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria; Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Olomouc, Czech Republic
| | - Shutang Tan
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria.
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11
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Antonovici CC, Peerdeman GY, Wolff HB, Merks RMH. Modeling Plant Tissue Development Using VirtualLeaf. Methods Mol Biol 2022; 2395:165-198. [PMID: 34822154 DOI: 10.1007/978-1-0716-1816-5_9] [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
Cell-based computational modeling and simulation are becoming invaluable tools in analyzing plant development. In a cell-based simulation model, the inputs are behaviors and dynamics of individual cells and the rules describing responses to signals from adjacent cells. The outputs are the growing tissues, shapes, and cell-differentiation patterns that emerge from the local, chemical, and biomechanical cell-cell interactions. In this updated and extended version of our previous chapter on VirtualLeaf (Merks and Guravage, Methods in Molecular Biology 959, 333-352), we present a step-by-step, practical tutorial for building cell-based simulations of plant development and for analyzing the influence of parameters on simulation outcomes by systematically changing the values of the parameters and analyzing each outcome. We show how to build a model of a growing tissue, a reaction-diffusion system on a growing domain, and an auxin transport model. Moreover, in addition to the previous publication, we demonstrate how to run a Turing system on a regular, rectangular lattice, and how to run parameter sweeps. The aim of VirtualLeaf is to make computational modeling more accessible to experimental plant biologists with relatively little computational background.
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Affiliation(s)
- Claudiu-Cristi Antonovici
- Mathematical Institute, Leiden University, Leiden, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Guacimo Y Peerdeman
- Mathematical Institute, Leiden University, Leiden, The Netherlands
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Faculty of Science and Technology, University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Harold B Wolff
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, VUmc, Amsterdam, The Netherlands
| | - Roeland M H Merks
- Mathematical Institute, Leiden University, Leiden, The Netherlands.
- Institute of Biology, Leiden University, Leiden, The Netherlands.
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12
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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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13
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Marconi M, Wabnik K. Shaping the Organ: A Biologist Guide to Quantitative Models of Plant Morphogenesis. FRONTIERS IN PLANT SCIENCE 2021; 12:746183. [PMID: 34675952 PMCID: PMC8523991 DOI: 10.3389/fpls.2021.746183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Organ morphogenesis is the process of shape acquisition initiated with a small reservoir of undifferentiated cells. In plants, morphogenesis is a complex endeavor that comprises a large number of interacting elements, including mechanical stimuli, biochemical signaling, and genetic prerequisites. Because of the large body of data being produced by modern laboratories, solving this complexity requires the application of computational techniques and analyses. In the last two decades, computational models combined with wet-lab experiments have advanced our understanding of plant organ morphogenesis. Here, we provide a comprehensive review of the most important achievements in the field of computational plant morphodynamics. We present a brief history from the earliest attempts to describe plant forms using algorithmic pattern generation to the evolution of quantitative cell-based models fueled by increasing computational power. We then provide an overview of the most common types of "digital plant" paradigms, and demonstrate how models benefit from diverse techniques used to describe cell growth mechanics. Finally, we highlight the development of computational frameworks designed to resolve organ shape complexity through integration of mechanical, biochemical, and genetic cues into a quantitative standardized and user-friendly environment.
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Affiliation(s)
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Pozuelo de Alarcón (Madrid), Spain
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14
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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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15
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Narasimhan M, Gallei M, Tan S, Johnson A, Verstraeten I, Li L, Rodriguez L, Han H, Himschoot E, Wang R, Vanneste S, Sánchez-Simarro J, Aniento F, Adamowski M, Friml J. Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking. PLANT PHYSIOLOGY 2021; 186:1122-1142. [PMID: 33734402 PMCID: PMC8195513 DOI: 10.1093/plphys/kiab134] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 01/23/2021] [Indexed: 05/08/2023]
Abstract
The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the auxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural indole-3-acetic acid (IAA) and synthetic naphthalene acetic acid (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network, rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using total internal reflection fluorescence microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus, contributing to its polarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments.
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Affiliation(s)
| | - Michelle Gallei
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
| | - Shutang Tan
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
| | - Alexander Johnson
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
| | - Inge Verstraeten
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
| | - Lanxin Li
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
| | - Lesia Rodriguez
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
| | - Huibin Han
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
| | - Ellie Himschoot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Ren Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Judit Sánchez-Simarro
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de Valencia, 46100 Burjassot, Spain
| | - Fernando Aniento
- Departamento de Bioquímica y Biología Molecular, Facultad de Farmacia, Universitat de Valencia, 46100 Burjassot, Spain
| | - Maciek Adamowski
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
| | - Jiří Friml
- Institute of Science and Technology (IST), Klosterneuburg 3400, Austria
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16
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Lavania D, Linh NM, Scarpella E. Of Cells, Strands, and Networks: Auxin and the Patterned Formation of the Vascular System. Cold Spring Harb Perspect Biol 2021; 13:cshperspect.a039958. [PMID: 33431582 DOI: 10.1101/cshperspect.a039958] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Throughout plant development, vascular cells continually form from within a population of seemingly equivalent cells. Vascular cells connect end to end to form continuous strands, and vascular strands connect at both or either end to form networks of exquisite complexity and mesmerizing beauty. Here we argue that experimental evidence gained over the past few decades implicates the plant hormone auxin-its production, transport, perception, and response-in all the steps that lead to the patterned formation of the plant vascular system, from the formation of vascular cells to their connection into vascular networks. We emphasize the organizing principles of the cell- and tissue-patterning process, rather than its molecular subtleties. In the picture that emerges, cells compete for an auxin-dependent, cell-polarizing signal; positive feedback between cell polarization and cell-to-cell movement of the polarizing signal leads to gradual selection of cell files; and selected cell files differentiate into vascular strands that drain the polarizing signal from the neighboring cells. Although the logic of the patterning process has become increasingly clear, the molecular details remain blurry; the future challenge will be to bring them into razor-sharp focus.
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Affiliation(s)
- Dhruv Lavania
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Nguyen Manh Linh
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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17
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Gelová Z, Gallei M, Pernisová M, Brunoud G, Zhang X, Glanc M, Li L, Michalko J, Pavlovičová Z, Verstraeten I, Han H, Hajný J, Hauschild R, Čovanová M, Zwiewka M, Hoermayer L, Fendrych M, Xu T, Vernoux T, Friml J. Developmental roles of Auxin Binding Protein 1 in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110750. [PMID: 33487339 DOI: 10.1016/j.plantsci.2020.110750] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Auxin is a major plant growth regulator, but current models on auxin perception and signaling cannot explain the whole plethora of auxin effects, in particular those associated with rapid responses. A possible candidate for a component of additional auxin perception mechanisms is the AUXIN BINDING PROTEIN 1 (ABP1), whose function in planta remains unclear. Here we combined expression analysis with gain- and loss-of-function approaches to analyze the role of ABP1 in plant development. ABP1 shows a broad expression largely overlapping with, but not regulated by, transcriptional auxin response activity. Furthermore, ABP1 activity is not essential for the transcriptional auxin signaling. Genetic in planta analysis revealed that abp1 loss-of-function mutants show largely normal development with minor defects in bolting. On the other hand, ABP1 gain-of-function alleles show a broad range of growth and developmental defects, including root and hypocotyl growth and bending, lateral root and leaf development, bolting, as well as response to heat stress. At the cellular level, ABP1 gain-of-function leads to impaired auxin effect on PIN polar distribution and affects BFA-sensitive PIN intracellular aggregation. The gain-of-function analysis suggests a broad, but still mechanistically unclear involvement of ABP1 in plant development, possibly masked in abp1 loss-of-function mutants by a functional redundancy.
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Affiliation(s)
- Zuzana Gelová
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Michelle Gallei
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Markéta Pernisová
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France; Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Géraldine Brunoud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Xixi Zhang
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria; Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Matouš Glanc
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria; Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 12844 Prague, Czech Republic
| | - Lanxin Li
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Jaroslav Michalko
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Zlata Pavlovičová
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Inge Verstraeten
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Huibin Han
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Jakub Hajný
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria; Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany & Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Robert Hauschild
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Milada Čovanová
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02 Praha 6, Czech Republic
| | - Marta Zwiewka
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lukas Hoermayer
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Matyáš Fendrych
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Tongda Xu
- FAFU-Joint Centre, Horticulture and Metabolic Biology Centre, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian, People's Republic of China
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Jiří Friml
- Institute of Science and Technology (IST), Am Campus 1, 3400 Klosterneuburg, Austria.
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18
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Ötvös K, Marconi M, Vega A, O’Brien J, Johnson A, Abualia R, Antonielli L, Montesinos JC, Zhang Y, Tan S, Cuesta C, Artner C, Bouguyon E, Gojon A, Friml J, Gutiérrez RA, Wabnik K, Benková E. Modulation of plant root growth by nitrogen source-defined regulation of polar auxin transport. EMBO J 2021; 40:e106862. [PMID: 33399250 PMCID: PMC7849315 DOI: 10.15252/embj.2020106862] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023] Open
Abstract
Availability of the essential macronutrient nitrogen in soil plays a critical role in plant growth, development, and impacts agricultural productivity. Plants have evolved different strategies for sensing and responding to heterogeneous nitrogen distribution. Modulation of root system architecture, including primary root growth and branching, is among the most essential plant adaptions to ensure adequate nitrogen acquisition. However, the immediate molecular pathways coordinating the adjustment of root growth in response to distinct nitrogen sources, such as nitrate or ammonium, are poorly understood. Here, we show that growth as manifested by cell division and elongation is synchronized by coordinated auxin flux between two adjacent outer tissue layers of the root. This coordination is achieved by nitrate-dependent dephosphorylation of the PIN2 auxin efflux carrier at a previously uncharacterized phosphorylation site, leading to subsequent PIN2 lateralization and thereby regulating auxin flow between adjacent tissues. A dynamic computer model based on our experimental data successfully recapitulates experimental observations. Our study provides mechanistic insights broadening our understanding of root growth mechanisms in dynamic environments.
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Affiliation(s)
- Krisztina Ötvös
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
- Bioresources UnitCenter for Health & BioresourcesAIT Austrian Institute of Technology GmbHTullnAustria
| | - Marco Marconi
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM‐INIA) Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
| | - Andrea Vega
- Pontifical Catholic University of ChileSantiagoChile
| | - Jose O’Brien
- Pontifical Catholic University of ChileSantiagoChile
| | - Alexander Johnson
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Rashed Abualia
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Livio Antonielli
- Bioresources UnitCenter for Health & BioresourcesAIT Austrian Institute of Technology GmbHTullnAustria
| | | | - Yuzhou Zhang
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Shutang Tan
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Candela Cuesta
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | - Christina Artner
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | | | - Alain Gojon
- BPMPCNRSINRAEInstitut AgroUniv MontpellierMontpellierFrance
| | - Jirí Friml
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
| | | | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM‐INIA) Universidad Politécnica de Madrid (UPM)—Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)MadridSpain
| | - Eva Benková
- Institute of Science and Technology (IST) AustriaKlosterneuburgAustria
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19
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Perianez-Rodriguez J, Rodriguez M, Marconi M, Bustillo-Avendaño E, Wachsman G, Sanchez-Corrionero A, De Gernier H, Cabrera J, Perez-Garcia P, Gude I, Saez A, Serrano-Ron L, Beeckman T, Benfey PN, Rodríguez-Patón A, Del Pozo JC, Wabnik K, Moreno-Risueno MA. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis. SCIENCE ADVANCES 2021; 7:eabd4722. [PMID: 33523850 PMCID: PMC7775764 DOI: 10.1126/sciadv.abd4722] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/06/2020] [Indexed: 05/19/2023]
Abstract
In Arabidopsis, the root clock regulates the spacing of lateral organs along the primary root through oscillating gene expression. The core molecular mechanism that drives the root clock periodicity and how it is modified by exogenous cues such as auxin and gravity remain unknown. We identified the key elements of the oscillator (AUXIN RESPONSE FACTOR 7, its auxin-sensitive inhibitor IAA18/POTENT, and auxin) that form a negative regulatory loop circuit in the oscillation zone. Through multilevel computer modeling fitted to experimental data, we explain how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing. Furthermore, gravistimulation experiments based on the model predictions show that external auxin stimuli can lead to entrainment of the root clock. Our work demonstrates the mechanism underlying a robust biological clock and how it can respond to external stimuli.
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Affiliation(s)
- Juan Perianez-Rodriguez
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Marcos Rodriguez
- Departamento de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Marco Marconi
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Estefano Bustillo-Avendaño
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Guy Wachsman
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Alvaro Sanchez-Corrionero
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Hugues De Gernier
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Javier Cabrera
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Pablo Perez-Garcia
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Inmaculada Gude
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Angela Saez
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Laura Serrano-Ron
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Tom Beeckman
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Philip N Benfey
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Juan Carlos Del Pozo
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Krzysztof Wabnik
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain.
| | - Miguel A Moreno-Risueno
- Centro de Biotecnología y Genómica de Plantas (Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria). Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain.
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20
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Hajný J, Prát T, Rydza N, Rodriguez L, Tan S, Verstraeten I, Domjan D, Mazur E, Smakowska-Luzan E, Smet W, Mor E, Nolf J, Yang B, Grunewald W, Molnár G, Belkhadir Y, De Rybel B, Friml J. Receptor kinase module targets PIN-dependent auxin transport during canalization. Science 2020; 370:550-557. [PMID: 33122378 PMCID: PMC7116426 DOI: 10.1126/science.aba3178] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 09/08/2020] [Indexed: 12/20/2022]
Abstract
Spontaneously arising channels that transport the phytohormone auxin provide positional cues for self-organizing aspects of plant development such as flexible vasculature regeneration or its patterning during leaf venation. The auxin canalization hypothesis proposes a feedback between auxin signaling and transport as the underlying mechanism, but molecular players await discovery. We identified part of the machinery that routes auxin transport. The auxin-regulated receptor CAMEL (Canalization-related Auxin-regulated Malectin-type RLK) together with CANAR (Canalization-related Receptor-like kinase) interact with and phosphorylate PIN auxin transporters. camel and canar mutants are impaired in PIN1 subcellular trafficking and auxin-mediated PIN polarization, which macroscopically manifests as defects in leaf venation and vasculature regeneration after wounding. The CAMEL-CANAR receptor complex is part of the auxin feedback that coordinates polarization of individual cells during auxin canalization.
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Affiliation(s)
- Jakub Hajný
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria
- Laboratory of Growth Regulators, The Czech Academy of Sciences, Institute of Experimental Botany and Palacký University, Šlechtitelů 27, CZ-78371 Olomouc, Czech Republic
| | - Tomáš Prát
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria
| | - Nikola Rydza
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Lesia Rodriguez
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria
| | - Shutang Tan
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria
| | - Inge Verstraeten
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria
| | - David Domjan
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria
| | - Ewa Mazur
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
| | - Elwira Smakowska-Luzan
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 Wageningen, the Netherlands
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Wouter Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Eliana Mor
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jonah Nolf
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - BaoJun Yang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wim Grunewald
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Gergely Molnár
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, (BOKU), Vienna, Austria
| | - Youssef Belkhadir
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jiří Friml
- Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria.
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21
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Zhang J, Mazur E, Balla J, Gallei M, Kalousek P, Medveďová Z, Li Y, Wang Y, Prát T, Vasileva M, Reinöhl V, Procházka S, Halouzka R, Tarkowski P, Luschnig C, Brewer PB, Friml J. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization. Nat Commun 2020; 11:3508. [PMID: 32665554 PMCID: PMC7360611 DOI: 10.1038/s41467-020-17252-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 06/15/2020] [Indexed: 11/27/2022] Open
Abstract
Directional transport of the phytohormone auxin is a versatile, plant-specific mechanism regulating many aspects of plant development. The recently identified plant hormones, strigolactones (SLs), are implicated in many plant traits; among others, they modify the phenotypic output of PIN-FORMED (PIN) auxin transporters for fine-tuning of growth and developmental responses. Here, we show in pea and Arabidopsis that SLs target processes dependent on the canalization of auxin flow, which involves auxin feedback on PIN subcellular distribution. D14 receptor- and MAX2 F-box-mediated SL signaling inhibits the formation of auxin-conducting channels after wounding or from artificial auxin sources, during vasculature de novo formation and regeneration. At the cellular level, SLs interfere with auxin effects on PIN polar targeting, constitutive PIN trafficking as well as clathrin-mediated endocytosis. Our results identify a non-transcriptional mechanism of SL action, uncoupling auxin feedback on PIN polarity and trafficking, thereby regulating vascular tissue formation and regeneration.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Ewa Mazur
- University of Silesia in Katowice, Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, Jagiellońska 28, 40-032, Katowice, Poland
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University (MU), 62500, Brno, Czech Republic
| | - Jozef Balla
- Central European Institute of Technology (CEITEC), Mendel University in Brno, Zemedelska 1, 61300, Brno, Czech Republic
- Department of Plant Biology, Mendel University in Brno, Zemedelska 1, 61300, Brno, Czech Republic
| | - Michelle Gallei
- Institute of Science and Technology (IST), Klosterneuburg, 3400, Austria
| | - Petr Kalousek
- Department of Plant Biology, Mendel University in Brno, Zemedelska 1, 61300, Brno, Czech Republic
| | - Zuzana Medveďová
- Central European Institute of Technology (CEITEC), Mendel University in Brno, Zemedelska 1, 61300, Brno, Czech Republic
| | - Yang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yaping Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Tomáš Prát
- Institute of Science and Technology (IST), Klosterneuburg, 3400, Austria
| | - Mina Vasileva
- Institute of Science and Technology (IST), Klosterneuburg, 3400, Austria
| | - Vilém Reinöhl
- Central European Institute of Technology (CEITEC), Mendel University in Brno, Zemedelska 1, 61300, Brno, Czech Republic
| | - Stanislav Procházka
- Central European Institute of Technology (CEITEC), Mendel University in Brno, Zemedelska 1, 61300, Brno, Czech Republic
| | - Rostislav Halouzka
- Central Laboratories and Research Support, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Petr Tarkowski
- Central Laboratories and Research Support, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Christian Luschnig
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190, Wien, Austria
| | - Philip B Brewer
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Precinct, The University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Jiří Friml
- Institute of Science and Technology (IST), Klosterneuburg, 3400, Austria.
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22
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Mazur E, Kulik I, Hajný J, Friml J. Auxin canalization and vascular tissue formation by TIR1/AFB-mediated auxin signaling in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:1375-1383. [PMID: 31971254 PMCID: PMC7318144 DOI: 10.1111/nph.16446] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/10/2020] [Indexed: 05/17/2023]
Abstract
Plant survival depends on vascular tissues, which originate in a self-organizing manner as strands of cells co-directionally transporting the plant hormone auxin. The latter phenomenon (also known as auxin canalization) is classically hypothesized to be regulated by auxin itself via the effect of this hormone on the polarity of its own intercellular transport. Correlative observations supported this concept, but molecular insights remain limited. In the current study, we established an experimental system based on the model Arabidopsis thaliana, which exhibits auxin transport channels and formation of vasculature strands in response to local auxin application. Our methodology permits the genetic analysis of auxin canalization under controllable experimental conditions. By utilizing this opportunity, we confirmed the dependence of auxin canalization on a PIN-dependent auxin transport and nuclear, TIR1/AFB-mediated auxin signaling. We also show that leaf venation and auxin-mediated PIN repolarization in the root require TIR1/AFB signaling. Further studies based on this experimental system are likely to yield better understanding of the mechanisms underlying auxin transport polarization in other developmental contexts.
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Affiliation(s)
- Ewa Mazur
- University of Silesia in KatowiceFaculty of Natural SciencesInstitute of Biology, Biotechnology and Environmental ProtectionKatowicePoland
- Mendel Centre for Plant Genomics and ProteomicsCentral European Institute of Technology (CEITEC)Masaryk UniversityCZ‐62‐500BrnoCzech Republic
| | - Ivan Kulik
- Institute of Science and Technology (IST)3400KlosterneuburgAustria
| | - Jakub Hajný
- Institute of Science and Technology (IST)3400KlosterneuburgAustria
- Laboratory of Growth Regulators and Department of Chemical Biology and GeneticsCentre of Region Haná for Biotechnological and Agricultural ResearchFaculty of SciencePalacký University and Institute of Experimental Botany ASCRŠlechtitelů 27783 71OlomoucCzech Republic
| | - Jiří Friml
- Institute of Science and Technology (IST)3400KlosterneuburgAustria
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23
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Mazur E, Gallei M, Adamowski M, Han H, Robert HS, Friml J. Clathrin-mediated trafficking and PIN trafficking are required for auxin canalization and vascular tissue formation in Arabidopsis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 293:110414. [PMID: 32081263 DOI: 10.1016/j.plantsci.2020.110414] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/10/2020] [Accepted: 01/11/2020] [Indexed: 06/10/2023]
Abstract
The flexible development of plants is characterized by a high capacity for post-embryonic organ formation and tissue regeneration, processes, which require tightly regulated intercellular communication and coordinated tissue (re-)polarization. The phytohormone auxin, the main driver for these processes, is able to establish polarized auxin transport channels, which are characterized by the expression and polar, subcellular localization of the PIN1 auxin transport proteins. These channels are demarcating the position of future vascular strands necessary for organ formation and tissue regeneration. Major progress has been made in the last years to understand how PINs can change their polarity in different contexts and thus guide auxin flow through the plant. However, it still remains elusive how auxin mediates the establishment of auxin conducting channels and the formation of vascular tissue and which cellular processes are involved. By the means of sophisticated regeneration experiments combined with local auxin applications in Arabidopsis thaliana inflorescence stems we show that (i) PIN subcellular dynamics, (ii) PIN internalization by clathrin-mediated trafficking and (iii) an intact actin cytoskeleton required for post-endocytic trafficking are indispensable for auxin channel formation, de novo vascular formation and vascular regeneration after wounding. These observations provide novel insights into cellular mechanism of coordinated tissue polarization during auxin canalization.
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Affiliation(s)
- Ewa Mazur
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Michelle Gallei
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Maciek Adamowski
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Huibin Han
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Hélène S Robert
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, 62500 Brno, Czech Republic
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria.
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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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Bu H, Yu W, Yuan H, Yue P, Wei Y, Wang A. Endogenous Auxin Content Contributes to Larger Size of Apple Fruit. FRONTIERS IN PLANT SCIENCE 2020; 11:592540. [PMID: 33519848 PMCID: PMC7841441 DOI: 10.3389/fpls.2020.592540] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/03/2020] [Indexed: 05/21/2023]
Abstract
Fruit size is an important economic trait that is controlled by multiple genes. However, the regulatory mechanism for fruit size remains poorly understood. A bud sport variety of "Longfeng" (LF) apple (Malus domestica) was identified and named "Grand Longfeng" (GLF). The fruit size of GLF is larger than that of LF, and both varieties are diploid. We found that the cell size in GLF fruit was larger than that of LF. Then, we compared the fruit transcriptomes of the two varieties using RNA-Seq technology. A total of 1166 differentially expressed genes (DEGs) were detected between GLF and LF fruits. The KEGG analysis revealed that the phytohormone pathway was the most enriched, in which most of the DEGs were related to auxin signaling. Moreover, the endogenous auxin levels of GLF fruit were higher than those of LF. The expressions of auxin synthetic genes, including MdTAR1 and MdYUCCA6, were higher in GLF fruit than LF. Collectively, our findings suggest that auxin plays an important role in fruit size development.
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Affiliation(s)
- Haidong Bu
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Wenquan Yu
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Hui Yuan
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Pengtao Yue
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yun Wei
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Aide Wang
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Aide Wang,
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26
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Bu H, Yu W, Yuan H, Yue P, Wei Y, Wang A. Endogenous Auxin Content Contributes to Larger Size of Apple Fruit. FRONTIERS IN PLANT SCIENCE 2020; 11:592540. [PMID: 33519848 DOI: 10.3389/fpls.2020.592540/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/03/2020] [Indexed: 05/21/2023]
Abstract
Fruit size is an important economic trait that is controlled by multiple genes. However, the regulatory mechanism for fruit size remains poorly understood. A bud sport variety of "Longfeng" (LF) apple (Malus domestica) was identified and named "Grand Longfeng" (GLF). The fruit size of GLF is larger than that of LF, and both varieties are diploid. We found that the cell size in GLF fruit was larger than that of LF. Then, we compared the fruit transcriptomes of the two varieties using RNA-Seq technology. A total of 1166 differentially expressed genes (DEGs) were detected between GLF and LF fruits. The KEGG analysis revealed that the phytohormone pathway was the most enriched, in which most of the DEGs were related to auxin signaling. Moreover, the endogenous auxin levels of GLF fruit were higher than those of LF. The expressions of auxin synthetic genes, including MdTAR1 and MdYUCCA6, were higher in GLF fruit than LF. Collectively, our findings suggest that auxin plays an important role in fruit size development.
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Affiliation(s)
- Haidong Bu
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Wenquan Yu
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Hui Yuan
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Pengtao Yue
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Yun Wei
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Aide Wang
- Key Laboratory of Fruit Postharvest Biology, College of Horticulture, Shenyang Agricultural University, Shenyang, China
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27
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Pałubicki W, Kokosza A, Burian A. Formal description of plant morphogenesis. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3601-3613. [PMID: 31290543 DOI: 10.1093/jxb/erz210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/14/2019] [Indexed: 06/09/2023]
Abstract
Plant morphogenesis may be characterized by complex feedback mechanisms between signals specifying growth and by the growth of the plant body itself. Comprehension of such feedback mechanisms is an ongoing research task and can be aided with formal descriptions of morphogenesis. In this review, we present a number of established mathematical paradigms that are useful to the formal representation of plant shape, and of biomechanical and biochemical signaling. Specifically, we discuss work from a range of research areas including plant biology, material sciences, fluid dynamics, and computer graphics. Treating plants as organized systems of information processing allows us to compare these different mathematical methods in terms of their expressive power of biological hypotheses. This is an attempt to bring together a large number of computational modeling concepts and make them accessible to the analytical as well as empirical student of plant morphogenesis.
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Affiliation(s)
- Wojtek Pałubicki
- Faculty of Mathematics and Computer Science, Adam Mickiewicz University, Umultowska, Poznań, Poland
| | - Andrzej Kokosza
- Faculty of Mathematics and Computer Science, Adam Mickiewicz University, Umultowska, Poznań, Poland
| | - Agata Burian
- Department of Biophysics and Morphogenesis of Plants, University of Silesia in Katowice, Jagiellońska, Katowice, Poland
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Toward a 3D model of phyllotaxis based on a biochemically plausible auxin-transport mechanism. PLoS Comput Biol 2019; 15:e1006896. [PMID: 30998674 PMCID: PMC6490938 DOI: 10.1371/journal.pcbi.1006896] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 04/30/2019] [Accepted: 02/20/2019] [Indexed: 11/19/2022] Open
Abstract
Polar auxin transport lies at the core of many self-organizing phenomena sustaining continuous plant organogenesis. In angiosperms, the shoot apical meristem is a potentially unique system in which the two main modes of auxin-driven patterning—convergence and canalization—co-occur in a coordinated manner and in a fully three-dimensional geometry. In the epidermal layer, convergence points form, from which auxin is canalized towards inner tissue. Each of these two patterning processes has been extensively investigated separately, but the integration of both in the shoot apical meristem remains poorly understood. We present here a first attempt of a three-dimensional model of auxin-driven patterning during phyllotaxis. We base our simulations on a biochemically plausible mechanism of auxin transport proposed by Cieslak et al. (2015) which generates both convergence and canalization patterns. We are able to reproduce most of the dynamics of PIN1 polarization in the meristem, and we explore how the epidermal and inner cell layers act in concert during phyllotaxis. In addition, we discuss the mechanism by which initiating veins connect to the already existing vascular system. The regularity of leaf arrangement around stems has long puzzled scientists. The key role played by the plant hormone auxin is now well established. On the surface of the tissue responsible for leaf formation, auxin accumulates at several points, from which new leaves eventually emerge. Auxin also guides the progression of new veins from the nascent leaves to the vascular system of the plant. Models of auxin transport have been developed to explain either auxin accumulation or auxin-driven venation. We propose the first three-dimensional model embracing both phenomena using a unifying mechanism of auxin transport. This integrative approach allows an assessment of our present knowledge on how auxin contributes to the early development of leaves. Our model reproduces many observations of auxin dynamics. It highlights how the inner and epidermal tissues act together to position new leaves. We also show that an additional, yet unknown, mechanism is required to attract new developing veins towards the main vasculature of the plant.
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29
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Advances in Understanding the Mechanism of Action of the Auxin Permease AUX1. Int J Mol Sci 2018; 19:ijms19113391. [PMID: 30380696 PMCID: PMC6275028 DOI: 10.3390/ijms19113391] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/19/2018] [Accepted: 10/24/2018] [Indexed: 01/08/2023] Open
Abstract
In over 40 years of research on the cellular uptake of auxin it is somewhat chastening that we have elaborated so little on the original kinetic descriptions of auxin uptake by plant cells made by Rubery and Sheldrake in 1974. Every aspect of that seminal work has been investigated in detail, and the uptake activity they measured is now known to be attributed to the AUX1/LAX family of permeases. Recent pharmacological studies have defined the substrate specificity of AUX1, biochemical studies have evaluated its permeability to auxin in plant cell membranes, and rigourous kinetic studies have confirmed the affinity of AUX1 for IAA and synthetic auxins. Advances in genome sequencing have provided a rich resource for informatic analysis of the ancestry of AUX1 and the LAX proteins and, along with models of topology, suggest mechanistic links to families of eukaryotic proton co-transporters for which crystal structures have been presented. The insights gained from all the accumulated research reflect the brilliance of Rubery and Sheldrake’s early work, but recent biochemical analyses are starting to advance further our understanding of this vitally important family of auxin transport proteins.
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30
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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: 7] [Impact Index Per Article: 1.2] [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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31
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Linh NM, Verna C, Scarpella E. Coordination of cell polarity and the patterning of leaf vein networks. CURRENT OPINION IN PLANT BIOLOGY 2018; 41:116-124. [PMID: 29278780 DOI: 10.1016/j.pbi.2017.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 09/12/2017] [Accepted: 09/15/2017] [Indexed: 06/07/2023]
Abstract
During development, the behavior of cells in tissues is coordinated along specific orientations or directions by coordinating the polar localization of components in those cells. The coordination of such cell polarity is perhaps nowhere more spectacular than in developing leaves, where the polarity of hundreds of cells is coordinated in the leaf epidermis and inner tissue to pattern vein networks. Available evidence suggests that the spectacular coordination of cell polarity that patterns vein networks is controlled by auxin transport and levels, and by genes that have been implicated in the polar localization of auxin transporters.
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Affiliation(s)
- Nguyen Manh Linh
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Carla Verna
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada.
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32
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WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity. PLoS Genet 2018; 14:e1007177. [PMID: 29377885 PMCID: PMC5805370 DOI: 10.1371/journal.pgen.1007177] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/08/2018] [Accepted: 12/29/2017] [Indexed: 11/19/2022] Open
Abstract
Auxin is unique among plant hormones due to its directional transport that is mediated by the polarly distributed PIN auxin transporters at the plasma membrane. The canalization hypothesis proposes that the auxin feedback on its polar flow is a crucial, plant-specific mechanism mediating multiple self-organizing developmental processes. Here, we used the auxin effect on the PIN polar localization in Arabidopsis thaliana roots as a proxy for the auxin feedback on the PIN polarity during canalization. We performed microarray experiments to find regulators of this process that act downstream of auxin. We identified genes that were transcriptionally regulated by auxin in an AXR3/IAA17- and ARF7/ARF19-dependent manner. Besides the known components of the PIN polarity, such as PID and PIP5K kinases, a number of potential new regulators were detected, among which the WRKY23 transcription factor, which was characterized in more detail. Gain- and loss-of-function mutants confirmed a role for WRKY23 in mediating the auxin effect on the PIN polarity. Accordingly, processes requiring auxin-mediated PIN polarity rearrangements, such as vascular tissue development during leaf venation, showed a higher WRKY23 expression and required the WRKY23 activity. Our results provide initial insights into the auxin transcriptional network acting upstream of PIN polarization and, potentially, canalization-mediated plant development. The plant hormone auxin belongs to the major plant-specific developmental regulators. It mediates or modifies almost all aspects of plant life. One of the fascinating features of the auxin action is its directional movement between cells, whose direction can be regulated by auxin signaling itself. This plant-specific feedback regulation has been proposed decades ago and allows for the self-organizing formation of distinct auxin channels shown to be crucial for processes, such as the regular pattern formation of leaf venation, organ formation, and regeneration of plant tissues. Despite the prominent importance of this so called auxin canalization process, the insight into the underlying molecular mechanism is very limited. Here, we identified a number of genes that are transcriptionally regulated and act downstream of the auxin signaling to mediate the auxin feedback on the polarized auxin transport. One of them is the WRKY23 transcription factor that has previously been unsuspected to play a role in this process. Our work provides the first insights into the transcriptional regulation of the auxin canalization and opens multiple avenues to further study this crucial process.
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Abad U, Sassi M, Traas J. Flower development: from morphodynamics to morphomechanics. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0545. [PMID: 28348258 PMCID: PMC5379030 DOI: 10.1098/rstb.2015.0545] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2016] [Indexed: 11/12/2022] Open
Abstract
The shoot apical meristem (SAM) is a small population of stem cells that continuously generates organs and tissues. We will discuss here flower formation at the SAM, which involves a complex network of regulatory genes and signalling molecules. A major downstream target of this network is the extracellular matrix or cell wall, which is a local determinant for both growth rates and growth directions. We will discuss here a number of recent studies aimed at analysing the link between cell wall structure and molecular regulation. This has involved multidisciplinary approaches including quantitative imaging, molecular genetics, computational biology and biophysics. A scenario emerges where molecular networks impact on both cell wall anisotropy and synthesis, thus causing the rapid outgrowth of organs at specific locations. More specifically, this involves two interdependent processes: the activation of wall remodelling enzymes and changes in microtubule dynamics.This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'.
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Affiliation(s)
- Ursula Abad
- Laboratory for Plant Reproduction and Development, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Massimiliano Sassi
- Laboratory for Plant Reproduction and Development, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Jan Traas
- Laboratory for Plant Reproduction and Development, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
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De Vos D, Dzhurakhalov A, Stijven S, Klosiewicz P, Beemster GTS, Broeckhove J. Virtual Plant Tissue: Building Blocks for Next-Generation Plant Growth Simulation. FRONTIERS IN PLANT SCIENCE 2017; 8:686. [PMID: 28523006 PMCID: PMC5415617 DOI: 10.3389/fpls.2017.00686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 04/13/2017] [Indexed: 05/11/2023]
Abstract
Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks. Multiple levels of model integration and coordination enable combining existing and new models from different sources, with diverse options in terms of input/output. Besides the core simulator the toolset also comprises a tissue editor for manipulating tissue geometry and cell, wall, and node attributes in an interactive manner. A parameter exploration tool is available to study parameter dependence of simulation results by distributing calculations over multiple systems. Availability: Virtual Plant Tissue is available as open source (EUPL license) on Bitbucket (https://bitbucket.org/vptissue/vptissue). The project has a website https://vptissue.bitbucket.io.
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Affiliation(s)
- Dirk De Vos
- Integrated Molecular Plant Physiology Research, Department of Biology, University of AntwerpAntwerp, Belgium
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
| | - Abdiravuf Dzhurakhalov
- Integrated Molecular Plant Physiology Research, Department of Biology, University of AntwerpAntwerp, Belgium
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
| | - Sean Stijven
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
| | - Przemyslaw Klosiewicz
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
| | - Gerrit T. S. Beemster
- Integrated Molecular Plant Physiology Research, Department of Biology, University of AntwerpAntwerp, Belgium
| | - Jan Broeckhove
- Modeling of Systems and Internet Communication, Department of Mathematics and Computer Science, University of AntwerpAntwerp, Belgium
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35
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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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36
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Morales-Tapia A, Cruz-Ramírez A. Computational Modeling of Auxin: A Foundation for Plant Engineering. FRONTIERS IN PLANT SCIENCE 2016; 7:1881. [PMID: 28066453 PMCID: PMC5168462 DOI: 10.3389/fpls.2016.01881] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/29/2016] [Indexed: 05/29/2023]
Abstract
Since the development of agriculture, humans have relied on the cultivation of plants to satisfy our increasing demand for food, natural products, and other raw materials. As we understand more about plant development, we can better manipulate plants to fulfill our particular needs. Auxins are a class of simple metabolites that coordinate many developmental activities like growth and the appearance of functional structures in plants. Computational modeling of auxin has proven to be an excellent tool in elucidating many mechanisms that underlie these developmental events. Due to the complexity of these mechanisms, current modeling efforts are concerned only with single phenomena focused on narrow spatial and developmental contexts; but a general model of plant development could be assembled by integrating the insights from all of them. In this perspective, we summarize the current collection of auxin-driven computational models, focusing on how they could come together into a single model for plant development. A model of this nature would allow researchers to test hypotheses in silico and yield accurate predictions about the behavior of a plant under a given set of physical and biochemical constraints. It would also provide a solid foundation toward the establishment of plant engineering, a proposed discipline intended to enable the design and production of plants that exhibit an arbitrarily defined set of features.
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Rakusová H, Abbas M, Han H, Song S, Robert HS, Friml J. Termination of Shoot Gravitropic Responses by Auxin Feedback on PIN3 Polarity. Curr Biol 2016; 26:3026-3032. [DOI: 10.1016/j.cub.2016.08.067] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/19/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022]
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38
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Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis. Sci Rep 2016; 6:33754. [PMID: 27649687 PMCID: PMC5030676 DOI: 10.1038/srep33754] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 06/06/2016] [Indexed: 01/10/2023] Open
Abstract
Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis.
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Abley K, Sauret-Güeto S, Marée AF, Coen E. Formation of polarity convergences underlying shoot outgrowths. eLife 2016; 5. [PMID: 27478985 PMCID: PMC4969039 DOI: 10.7554/elife.18165] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/28/2016] [Indexed: 11/13/2022] Open
Abstract
The development of outgrowths from plant shoots depends on formation of epidermal sites of cell polarity convergence with high intracellular auxin at their centre. A parsimonious model for generation of convergence sites is that cell polarity for the auxin transporter PIN1 orients up auxin gradients, as this spontaneously generates convergent alignments. Here we test predictions of this and other models for the patterns of auxin biosynthesis and import. Live imaging of outgrowths from kanadi1 kanadi2 Arabidopsis mutant leaves shows that they arise by formation of PIN1 convergence sites within a proximodistal polarity field. PIN1 polarities are oriented away from regions of high auxin biosynthesis enzyme expression, and towards regions of high auxin importer expression. Both expression patterns are required for normal outgrowth emergence, and may form part of a common module underlying shoot outgrowths. These findings are more consistent with models that spontaneously generate tandem rather than convergent alignments. DOI:http://dx.doi.org/10.7554/eLife.18165.001 Plants, unlike animals, are able to grow and develop throughout their lives. New leaves and flowers are made from outgrowths that constantly form at the tip of growing shoots. Groups of cells in the outer layer of the shoot tip arrange a protein called PIN1 so that it is more abundant on the cell surfaces that face towards the centre of the group. PIN1 transports a hormone called auxin out of plant cells and this “convergent” arrangement of PIN1 increases the levels of auxin in cells at the centre of the group, leading to the formation of a new outgrowth. However, it is not clear what causes these cells to position their PIN1 proteins in this way. Several hypotheses have been proposed to explain how convergent patterns of PIN1 form. For example, according to the “up-the-gradient” hypothesis, PIN1 is allocated to the end of a cell that is next to a cell with a higher level of auxin. Abley et al. have now compared predictions from computer models with new experimental data from a plant called Arabidopsis to evaluate three hypotheses for how convergent PIN1 patterns form. A computer model based on the up-the-gradient hypothesis naturally creates convergent PIN1 patterns, even if each cell starts off with the same level of auxin. On the other hand, models based on two other hypotheses generate tandem alignments of PIN1 so that auxin is transported in the same direction along lines of cells. Next, Abley et al. tested these models using mutant Arabidopsis plants that develop outgrowths from the lower surface of their leaves. These outgrowths form in a similar way to outgrowths at the growing shoot tip, but in a simpler context. The experiments show that the patterns of where auxin is produced in growing leaves were more compatible with the tandem alignment models than the up-the-gradient model. This suggests that plants use a tandem alignment mechanism to form convergences of PIN1 proteins that generate the local increases in auxin needed to make new outgrowths. This study only examined a single layer of cells on the plant surface. Other cell layers also show highly organised patterns of PIN1 proteins, so a future challenge is to extend the approach to study the entire 3D structure of new shoot outgrowths. DOI:http://dx.doi.org/10.7554/eLife.18165.002
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Affiliation(s)
- Katie Abley
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | | | - Enrico Coen
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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40
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Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discov 2016; 2:16018. [PMID: 27462465 PMCID: PMC4950145 DOI: 10.1038/celldisc.2016.18] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/11/2016] [Indexed: 01/24/2023] Open
Abstract
The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.
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41
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Galvan-Ampudia CS, Chaumeret AM, Godin C, Vernoux T. Phyllotaxis: from patterns of organogenesis at the meristem to shoot architecture. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:460-73. [PMID: 27199252 DOI: 10.1002/wdev.231] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 01/22/2023]
Abstract
The primary architecture of the aerial part of plants is controlled by the shoot apical meristem, a specialized tissue containing a stem cell niche. The iterative generation of new aerial organs, (leaves, lateral inflorescences, and flowers) at the meristem follows regular patterns, called phyllotaxis. Phyllotaxis has long been proposed to self-organize from the combined action of growth and of inhibitory fields blocking organogenesis in the vicinity of existing organs in the meristem. In this review, we will highlight how a combination of mathematical/computational modeling and experimental biology has demonstrated that the spatiotemporal distribution of the plant hormone auxin controls both organogenesis and the establishment of inhibitory fields. We will discuss recent advances showing that auxin likely acts through a combination of biochemical and mechanical regulatory mechanisms that control not only the pattern of organogenesis in the meristem but also postmeristematic growth, to shape the shoot. WIREs Dev Biol 2016, 5:460-473. doi: 10.1002/wdev.231 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Carlos S Galvan-Ampudia
- Laboratoire de Reproduction et Développement des plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, Lyon, France
| | - Anaïs M Chaumeret
- Laboratoire de Reproduction et Développement des plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, Lyon, France
| | - Christophe Godin
- Virtual Plants Plants INRIA/CIRAD/INRA Project Team, Montpellier, France
| | - Teva Vernoux
- Laboratoire de Reproduction et Développement des plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, Lyon, France
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42
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Grigolon S, Sollich P, Martin OC. Modelling the emergence of polarity patterns for the intercellular transport of auxin in plants. J R Soc Interface 2016; 12. [PMID: 25977961 DOI: 10.1098/rsif.2014.1223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The hormone auxin is actively transported throughout plants via protein machineries including the dedicated transporter known as PIN. The associated transport is ordered with nearby cells driving auxin flux in similar directions. Here, we provide a model of both the auxin transport and of the dynamics of cellular polarization based on flux sensing. Our main findings are: (i) spontaneous intracellular PIN polarization arises if PIN recycling dynamics are sufficiently nonlinear, (ii) there is no need for an auxin concentration gradient and (iii) ordered multi-cellular patterns of PIN polarization are favoured by molecular noise.
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43
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Draelants D, Avitabile D, Vanroose W. Localized auxin peaks in concentration-based transport models of the shoot apical meristem. J R Soc Interface 2016; 12:rsif.2014.1407. [PMID: 25878130 DOI: 10.1098/rsif.2014.1407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We study the formation of auxin peaks in a generic class of concentration-based auxin transport models, posed on static plant tissues. Using standard asymptotic analysis, we prove that, on bounded domains, auxin peaks are not formed via a Turing instability in the active transport parameter, but via simple corrections to the homogeneous steady state. When the active transport is small, the geometry of the tissue encodes the peaks' amplitude and location: peaks arise where cells have fewer neighbours, that is, at the boundary of the domain. We test our theory and perform numerical bifurcation analysis on two models that are known to generate auxin patterns for biologically plausible parameter values. In the same parameter regimes, we find that realistic tissues are capable of generating a multitude of stationary patterns, with a variable number of auxin peaks, that can be selected by different initial conditions or by quasi-static changes in the active transport parameter. The competition between active transport and production rate determines whether peaks remain localized or cover the entire domain. In particular, changes in the auxin production that are fast with respect to the cellular life cycle affect the auxin peak distribution, switching from localized spots to fully patterned states. We relate the occurrence of localized patterns to a snaking bifurcation structure, which is known to arise in a wide variety of nonlinear media, but has not yet been reported in plant models.
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Affiliation(s)
- Delphine Draelants
- Department of Mathematics and Computer Science, Universiteit Antwerpen, Middelheimlaan 1, 2020 Antwerpen, Belgium
| | - Daniele Avitabile
- Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Wim Vanroose
- Department of Mathematics and Computer Science, Universiteit Antwerpen, Middelheimlaan 1, 2020 Antwerpen, Belgium
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44
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Moore S, Zhang X, Mudge A, Rowe JH, Topping JF, Liu J, Lindsey K. Spatiotemporal modelling of hormonal crosstalk explains the level and patterning of hormones and gene expression in Arabidopsis thaliana wild-type and mutant roots. THE NEW PHYTOLOGIST 2015; 207:1110-22. [PMID: 25906686 PMCID: PMC4539600 DOI: 10.1111/nph.13421] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/20/2015] [Indexed: 05/08/2023]
Abstract
Patterning in Arabidopsis root development is coordinated via a localized auxin concentration maximum in the root tip, requiring the regulated expression of specific genes. However, little is known about how hormone and gene expression patterning is generated. Using a variety of experimental data, we develop a spatiotemporal hormonal crosstalk model that describes the integrated action of auxin, ethylene and cytokinin signalling, the POLARIS protein, and the functions of PIN and AUX1 auxin transporters. We also conduct novel experiments to confirm our modelling predictions. The model reproduces auxin patterning and trends in wild-type and mutants; reveals that coordinated PIN and AUX1 activities are required to generate correct auxin patterning; correctly predicts shoot to root auxin flux, auxin patterning in the aux1 mutant, the amounts of cytokinin, ethylene and PIN protein, and PIN protein patterning in wild-type and mutant roots. Modelling analysis further reveals how PIN protein patterning is related to the POLARIS protein through ethylene signalling. Modelling prediction of the patterning of POLARIS expression is confirmed experimentally. Our combined modelling and experimental analysis reveals that a hormonal crosstalk network regulates the emergence of patterns and levels of hormones and gene expression in wild-type and mutants.
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Affiliation(s)
- Simon Moore
- The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham UniversitySouth Road, Durham, DH1 3LE, UK
| | - Xiaoxian Zhang
- School of Engineering, The University of LiverpoolBrownlow Street, Liverpool, L69 3GQ, UK
| | - Anna Mudge
- The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham UniversitySouth Road, Durham, DH1 3LE, UK
| | - James H Rowe
- The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham UniversitySouth Road, Durham, DH1 3LE, UK
| | - Jennifer F Topping
- The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham UniversitySouth Road, Durham, DH1 3LE, UK
| | - Junli Liu
- The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham UniversitySouth Road, Durham, DH1 3LE, UK
| | - Keith Lindsey
- The Integrative Cell Biology Laboratory, School of Biological and Biomedical Sciences, Durham UniversitySouth Road, Durham, DH1 3LE, UK
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45
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Cieslak M, Runions A, Prusinkiewicz P. Auxin-driven patterning with unidirectional fluxes. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5083-102. [PMID: 26116915 PMCID: PMC4513925 DOI: 10.1093/jxb/erv262] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The plant hormone auxin plays an essential role in the patterning of plant structures. Biological hypotheses supported by computational models suggest that auxin may fulfil this role by regulating its own transport, but the plausibility of previously proposed models has been questioned. We applied the notion of unidirectional fluxes and the formalism of Petri nets to show that the key modes of auxin-driven patterning-the formation of convergence points and the formation of canals-can be implemented by biochemically plausible networks, with the fluxes measured by dedicated tally molecules or by efflux and influx carriers themselves. Common elements of these networks include a positive feedback of auxin efflux on the allocation of membrane-bound auxin efflux carriers (PIN proteins), and a modulation of this allocation by auxin in the extracellular space. Auxin concentration in the extracellular space is the only information exchanged by the cells. Canalization patterns are produced when auxin efflux and influx act antagonistically: an increase in auxin influx or concentration in the extracellular space decreases the abundance of efflux carriers in the adjacent segment of the membrane. In contrast, convergence points emerge in networks in which auxin efflux and influx act synergistically. A change in a single reaction rate may result in a dynamic switch between these modes, suggesting plausible molecular implementations of coordinated patterning of organ initials and vascular strands predicted by the dual polarization theory.
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Affiliation(s)
- Mikolaj Cieslak
- Department of Computer Science, University of Calgary, 2500 University Dr. N.W., Calgary, AB T2N 1N4, Canada
| | - Adam Runions
- Department of Computer Science, University of Calgary, 2500 University Dr. N.W., Calgary, AB T2N 1N4, Canada
| | - Przemyslaw Prusinkiewicz
- Department of Computer Science, University of Calgary, 2500 University Dr. N.W., Calgary, AB T2N 1N4, Canada
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46
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Růžička K, Ursache R, Hejátko J, Helariutta Y. Xylem development - from the cradle to the grave. THE NEW PHYTOLOGIST 2015; 207:519-35. [PMID: 25809158 DOI: 10.1111/nph.13383] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/21/2015] [Indexed: 05/06/2023]
Abstract
The development and growth of plants, as well as their successful adaptation to a variety of environments, is highly dependent on the conduction of water, nutrients and other important molecules throughout the plant body. Xylem is a specialized vascular tissue that serves as a conduit of water and minerals and provides mechanical support for upright growth. Wood, also known as secondary xylem, constitutes the major part of mature woody stems and roots. In the past two decades, a number of key factors including hormones, signal transducers and (post)transcriptional regulators have been shown to control xylem formation. We outline the main mechanisms shown to be essential for xylem development in various plant species, with an emphasis on Arabidopsis thaliana, as well as several tree species where xylem has a long history of investigation. We also summarize the processes which have been shown to be instrumental during xylem maturation. This includes mechanisms of cell wall formation and cell death which collectively complete xylem cell fate.
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Affiliation(s)
- Kamil Růžička
- Department of Functional Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 25, Brno, CZ-62500, Czech Republic
| | - Robertas Ursache
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
| | - Jan Hejátko
- Department of Functional Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 25, Brno, CZ-62500, Czech Republic
| | - Ykä Helariutta
- Sainsbury Laboratory, University of Cambridge, Bateman Street, Cambridge, CB2 1LR, UK
- Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland
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47
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Ahrazem O, Rubio-Moraga A, Trapero-Mozos A, Climent MFL, Gómez-Cadenas A, Gómez-Gómez L. Ectopic expression of a stress-inducible glycosyltransferase from saffron enhances salt and oxidative stress tolerance in Arabidopsis while alters anchor root formation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:60-73. [PMID: 25804810 DOI: 10.1016/j.plantsci.2015.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/09/2015] [Accepted: 02/11/2015] [Indexed: 05/03/2023]
Abstract
Glycosyltransferases play diverse roles in cellular metabolism by modifying the activities of regulatory metabolites. Three stress-regulated UDP-glucosyltransferase-encoding genes have been isolated from the stigmas of saffron, UGT85U1, UGT85U2 and UGT85V1, which belong to the UGT85 family that includes members associated with stress responses and cell cycle regulation. Arabidopsis constitutively expressing UGT85U1 exhibited and increased anchor root development. No differences were observed in the timing of root emergence, in leaf, stem and flower morphology or flowering time. However, salt and oxidative stress tolerance was enhanced in these plants. Levels of glycosylated compounds were measured in these plants and showed changes in the composition of several indole-derivatives. Moreover, auxin levels in the roots were higher compared to wild type. The expression of several key genes related to root development and auxin homeostasis, including CDKB2.1, CDKB2.2, PIN2, 3 and 4; TIR1, SHR, and CYCD6, were differentially regulated with an increase of expression level of SHR, CYCD6, CDKB2.1 and PIN2. The obtained results showed that UGT85U1 takes part in root growth regulation via auxin signal alteration and the modified expression of cell cycle-related genes, resulting in significantly improved survival during oxidative and salt stress treatments.
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Affiliation(s)
- Oussama Ahrazem
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain; Fundación Parque Científico y Tecnológico de Albacete, Spain
| | - Angela Rubio-Moraga
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | - Almudena Trapero-Mozos
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain
| | | | - Aurelio Gómez-Cadenas
- Universitat Jaume I, Department of Agricultural and Environmental Sciences, 12071 Castelló de la Plana, Spain
| | - Lourdes Gómez-Gómez
- Instituto Botánico, Departamento de Ciencia y Tecnología Agroforestal y Genética, Facultad de Farmacia, Universidad de Castilla-La Mancha, Campus Universitario s/n, 02071 Albacete, Spain.
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48
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Fàbregas N, Formosa-Jordan P, Confraria A, Siligato R, Alonso JM, Swarup R, Bennett MJ, Mähönen AP, Caño-Delgado AI, Ibañes M. Auxin influx carriers control vascular patterning and xylem differentiation in Arabidopsis thaliana. PLoS Genet 2015; 11:e1005183. [PMID: 25922946 PMCID: PMC4414528 DOI: 10.1371/journal.pgen.1005183] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/29/2015] [Indexed: 12/23/2022] Open
Abstract
Auxin is an essential hormone for plant growth and development. Auxin influx carriers AUX1/LAX transport auxin into the cell, while auxin efflux carriers PIN pump it out of the cell. It is well established that efflux carriers play an important role in the shoot vascular patterning, yet the contribution of influx carriers to the shoot vasculature remains unknown. Here, we combined theoretical and experimental approaches to decipher the role of auxin influx carriers in the patterning and differentiation of vascular tissues in the Arabidopsis inflorescence stem. Our theoretical analysis predicts that influx carriers facilitate periodic patterning and modulate the periodicity of auxin maxima. In agreement, we observed fewer and more spaced vascular bundles in quadruple mutants plants of the auxin influx carriers aux1lax1lax2lax3. Furthermore, we show AUX1/LAX carriers promote xylem differentiation in both the shoot and the root tissues. Influx carriers increase cytoplasmic auxin signaling, and thereby differentiation. In addition to this cytoplasmic role of auxin, our computational simulations propose a role for extracellular auxin as an inhibitor of xylem differentiation. Altogether, our study shows that auxin influx carriers AUX1/LAX regulate vascular patterning and differentiation in plants.
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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
- Department of Structure and Constituents of Matter, Faculty of Physics, University of Barcelona, Barcelona, Spain
| | - Ana Confraria
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Riccardo Siligato
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Jose M. Alonso
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Ranjan Swarup
- School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Nottingham, United Kingdom
| | - Malcolm J. Bennett
- School of Biosciences and Centre for Plant Integrative Biology, University of Nottingham, Nottingham, United Kingdom
| | - Ari Pekka Mähönen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Ana I. Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Marta Ibañes
- Department of Structure and Constituents of Matter, Faculty of Physics, University of Barcelona, Barcelona, Spain
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49
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Adamowski M, Friml J. PIN-dependent auxin transport: action, regulation, and evolution. THE PLANT CELL 2015; 27:20-32. [PMID: 25604445 PMCID: PMC4330589 DOI: 10.1105/tpc.114.134874] [Citation(s) in RCA: 492] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 12/01/2014] [Accepted: 01/05/2015] [Indexed: 05/18/2023]
Abstract
Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well.
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Affiliation(s)
- Maciek Adamowski
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Jiří Friml
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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50
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Livanos P, Giannoutsou E, Apostolakos P, Galatis B. Auxin as an inducer of asymmetrical division generating the subsidiary cells in stomatal complexes of Zea mays. PLANT SIGNALING & BEHAVIOR 2015; 10:e984531. [PMID: 25831267 PMCID: PMC4622748 DOI: 10.4161/15592324.2014.984531] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 09/20/2014] [Accepted: 09/23/2014] [Indexed: 05/05/2023]
Abstract
The data presented in this work revealed that in Zea mays the exogenously added auxins indole-3-acetic acid (IAA) and 1-napthaleneacetic acid (NAA), promoted the establishment of subsidiary cell mother cell (SMC) polarity and the subsequent subsidiary cell formation, while treatment with auxin transport inhibitors 2,3,5-triiodobenzoic acid (TIBA) and 1-napthoxyacetic acid (NOA) specifically blocked SMC polarization and asymmetrical division. Furthermore, in young guard cell mother cells (GMCs) the PIN1 auxin efflux carriers were mainly localized in the transverse GMC faces, while in the advanced GMCs they appeared both in the transverse and the lateral ones adjacent to SMCs. Considering that phosphatidyl-inositol-3-kinase (PI3K) is an active component of auxin signal transduction and that phospholipid signaling contributes in the establishment of polarity, treatments with the specific inhibitor of the PI3K LY294002 were carried out. The presence of LY294002 suppressed polarization of SMCs and prevented their asymmetrical division, whereas combined treatment with exogenously added NAA and LY294002 restricted the promotional auxin influence on subsidiary cell formation. These findings support the view that auxin is involved in Z. mays subsidiary cell formation, probably functioning as inducer of the asymmetrical SMC division. Collectively, the results obtained from treatments with auxin transport inhibitors and the appearance of PIN1 proteins in the lateral GMC faces indicate a local transfer of auxin from GMCs to SMCs. Moreover, auxin signal transduction seems to be mediated by the catalytic function of PI3K.
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Key Words
- AF, actin filament
- DIC, differential interference contrast
- GMC, guard cell mother cell
- IAA, indole-3-acetic acid
- MT, microtubule
- NAA, 1-napthaleneacetic acid
- NOA, 1-napthoxyacetic acid
- PDK, 3-phosphoinositide-dependent kinase
- PI3K, phosphatidyl-inositol-3-kinase
- PIN1
- PLC, phospholipase C
- PLD, phospholipase D
- ROP GTPases, Rho-like GTPases of plants
- SMC, subsidiary cell mother cell
- TIBA, 2,3,5-triiodobenzoic acid
- auxin carriers
- auxin signaling
- morphogenesis
- phosphatidyl-inositol-3-kinase
- polarity
- stomatal complexes
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Affiliation(s)
- Pantelis Livanos
- Department of Botany; Faculty of Biology; University of Athens; Athens, Greece
| | - Eleni Giannoutsou
- Department of Botany; Faculty of Biology; University of Athens; Athens, Greece
| | | | - Basil Galatis
- Department of Botany; Faculty of Biology; University of Athens; Athens, Greece
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