33 results on '"Wabnik, Krzysztof"'
Search Results
2. Core clock genes adjust growth cessation time to day-night switches in poplar
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Alique, Daniel, Redondo López, Arturo, González Schain, Nahuel, Allona, Isabel, Wabnik, Krzysztof, and Perales, Mariano
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- 2024
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3. The cold-induced factor CBF3 mediates root stem cell activity, regeneration, and developmental responses to cold
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Perez-Garcia, Pablo, Pucciariello, Ornella, Sanchez-Corrionero, Alvaro, Cabrera, Javier, del Barrio, Cristina, del Pozo, Juan Carlos, Perales, Mariano, Wabnik, Krzysztof, and Moreno-Risueno, Miguel A.
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- 2023
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4. Synchronization of gene expression across eukaryotic communities through chemical rhythms
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Pérez-García, Sara, García-Navarrete, Mario, Ruiz-Sanchis, Diego, Prieto-Navarro, Cristina, Avdovic, Merisa, Pucciariello, Ornella, and Wabnik, Krzysztof
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- 2021
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5. A Model of Differential Growth-Guided Apical Hook Formation in Plants
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Žádníková, Petra, Wabnik, Krzysztof, Abuzeineh, Anas, Gallemi, Marçal, Van Der Straeten, Dominique, Smith, Richard S., Inzé, Dirk, Friml, Jiří, Prusinkiewicz, Przemysław, and Benková, Eva
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- 2016
6. Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots
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Waidmann, Sascha, Ruiz Rosquete, Michel, Schöller, Maria, Sarkel, Elizabeth, Lindner, Heike, LaRue, Therese, Petřík, Ivan, Dünser, Kai, Martopawiro, Shanice, Sasidharan, Rashmi, Novak, Ondrej, Wabnik, Krzysztof, Dinneny, José R., and Kleine-Vehn, Jürgen
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- 2019
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7. Dynamic context-dependent regulation of auxin feedback signaling in synthetic gene circuits.
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Avdovic, Merisa, Garcia-Navarrete, Mario, Ruiz-Sanchis, Diego, and Wabnik, Krzysztof
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GENE regulatory networks ,SYNTHETIC genes ,AUXIN ,ARABIDOPSIS proteins ,PROTEOLYSIS ,PSYCHOLOGICAL feedback - Abstract
Phytohormone auxin plays a key role in regulating plant organogenesis. However, understanding the complex feedback signaling network that involves at least 29 proteins in Arabidopsis in the dynamic context remains a significant challenge. To address this, we transplanted an auxin-responsive feedback circuit responsible for plant organogenesis into yeast. By generating dynamic microfluidic conditions controlling gene expression, protein degradation, and binding affinity of auxin response factors to DNA, we illuminate feedback signal processing principles in hormone-driven gene expression. In particular, we recorded the regulatory mode shift between stimuli counting and rapid signal integration that is context-dependent. Overall, our study offers mechanistic insights into dynamic auxin response interplay trackable by synthetic gene circuits, thereby offering instructions for engineering plant architecture. [ABSTRACT FROM AUTHOR]
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- 2023
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8. Computer models of cell polarity establishment in plants.
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Marconi, Marco and Wabnik, Krzysztof
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Plant development is a complex task, and many processes involve changes in the asymmetric subcellular distribution of cell components that strongly depend on cell polarity. Cell polarity regulates anisotropic growth and polar localization of membrane proteins and helps to identify the cell's position relative to its neighbors within an organ. Cell polarity is critical in a variety of plant developmental processes, including embryogenesis, cell division, and response to external stimuli. The most conspicuous downstream effect of cell polarity is the polar transport of the phytohormone auxin, which is the only known hormone transported in a polar fashion in and out of cells by specialized exporters and importers. The biological processes behind the establishment of cell polarity are still unknown, and researchers have proposed several models that have been tested using computer simulations. The evolution of computer models has progressed in tandem with scientific discoveries, which have highlighted the importance of genetic, chemical, and mechanical input in determining cell polarity and regulating polarity-dependent processes such as anisotropic growth, protein subcellular localization, and the development of organ shapes. The purpose of this review is to provide a comprehensive overview of the current understanding of computer models of cell polarity establishment in plants, focusing on the molecular and cellular mechanisms, the proteins involved, and the current state of the field. [ABSTRACT FROM AUTHOR]
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- 2023
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9. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells
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Łangowski, Łukasz, Wabnik, Krzysztof, Li, Hongjiang, Vanneste, Steffen, Naramoto, Satoshi, Tanaka, Hirokazu, and Friml, Jiří
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- 2016
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10. Macroscopic control of cell electrophysiology through ion channel expression.
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García-Navarrete, Mario, Avdovic, Merisa, Pérez-Garcia, Sara, Sanchis, Diego Ruiz, and Wabnik, Krzysztof
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- 2022
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11. WOX5–IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis
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Tian, Huiyu, Wabnik, Krzysztof, Niu, Tiantian, Li, Hanbing, Yu, Qianqian, Pollmann, Stephan, Vanneste, Steffen, Govaerts, Willy, Rolčík, Jakub, Geisler, Markus, Friml, Jiří, and Ding, Zhaojun
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- 2014
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12. Gene expression trends and protein features effectively complement each other in gene function prediction
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Wabnik, Krzysztof, Hvidsten, Torgeir R., Kedzierska, Anna, Van Leene, Jelle, De Jaeger, Geert, Beemster, Gerrit T. S., Komorowski, Jan, and Kuiper, Martin T. R.
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- 2009
13. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth.
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Marconi, Marco, Gallemi, Marcal, Benkova, Eva, and Wabnik, Krzysztof
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- 2021
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14. Shaping the Organ: A Biologist Guide to Quantitative Models of Plant Morphogenesis.
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Marconi, Marco and Wabnik, Krzysztof
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BIOLOGISTS ,CELLULAR mechanics ,CELL growth ,PLANT morphogenesis ,FINITE element method - 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. [ABSTRACT FROM AUTHOR]
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- 2021
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15. Modulation of plant root growth by nitrogen source‐defined regulation of polar auxin transport.
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Ötvös, Krisztina, Marconi, Marco, Vega, Andrea, O'Brien, Jose, Johnson, Alexander, Abualia, Rashed, Antonielli, Livio, Montesinos, Juan Carlos, Zhang, Yuzhou, Tan, Shutang, Cuesta, Candela, Artner, Christina, Bouguyon, Eleonore, Gojon, Alain, Friml, Jirí, Gutiérrez, Rodrigo A., Wabnik, Krzysztof, and Benková, Eva
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PLANT growth ,AUXIN ,PLANT roots ,NITROGEN in soils ,ROOT growth ,NITROGEN ,ROOT development - 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. SYNOPSIS: Effective soil exploitation by plants depends on rapid adjustment of root systems to available nutrients. Here, root growth adaptation to distinct nitrogen sources is shown to involve modulation of auxin distribution via phosphorylation of the PIN2 auxin carrier. Nitrogen source type (nitrate vs. ammonium) differentially regulates cell elongation and division patterns in Arabidopsis root tip tissues.Nitrogen source type regulates directionality of auxin transport in the root tip.Root growth adjustment to nitrogen source is mediated by PIN2 phosphorylation at S439.PIN2 phosphorylation affects auxin flux via modulation of PIN2 polarized localization at the plasma membrane. [ABSTRACT FROM AUTHOR]
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- 2021
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16. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana.
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Li, Hongjiang, Wangenheim, Daniel, Zhang, Xixi, Tan, Shutang, Darwish‐Miranda, Nasser, Naramoto, Satoshi, Wabnik, Krzysztof, De Rycke, Riet, Kaufmann, Walter A., Gütl, Daniel, Tejos, Ricardo, Grones, Peter, Ke, Meiyu, Chen, Xu, Dettmer, Jan, and Friml, Jiří
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PERSONAL identification numbers ,THREE-dimensional imaging ,CELL membranes ,CELL anatomy - Abstract
Summary: Cell and tissue polarization is fundamental for plant growth and morphogenesis. The polar, cellular localization of Arabidopsis PIN‐FORMED (PIN) proteins is crucial for their function in directional auxin transport. The clustering of PIN polar cargoes within the plasma membrane has been proposed to be important for the maintenance of their polar distribution. However, the more detailed features of PIN clusters and the cellular requirements of cargo clustering remain unclear.Here, we characterized PIN clusters in detail by means of multiple advanced microscopy and quantification methods, such as 3D quantitative imaging or freeze‐fracture replica labeling. The size and aggregation types of PIN clusters were determined by electron microscopy at the nanometer level at different polar domains and at different developmental stages, revealing a strong preference for clustering at the polar domains.Pharmacological and genetic studies revealed that PIN clusters depend on phosphoinositol pathways, cytoskeletal structures and specific cell‐wall components as well as connections between the cell wall and the plasma membrane.This study identifies the role of different cellular processes and structures in polar cargo clustering and provides initial mechanistic insight into the maintenance of polarity in plants and other systems. [ABSTRACT FROM AUTHOR]
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- 2021
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17. Modeling auxin feedback signaling for polarized auxin transport in plant development
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Wabnik, Krzysztof, Govaerts, Willy, and Friml, Jiri
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fungi ,food and beverages ,Biology and Life Sciences - Abstract
Plants are fascinating biological systems with a great potential for adaption of their developmental programs to environmental cues. In contrast to animals, plants cannot run away and thus they had to develop specialized mechanisms to react to rapid changes in the environment. These plant-specific mechanisms including light perception, tropism and developmental reprogramming (de novo organ formation, tissue re-shaping), represent highly dynamic regulatory processes that are linked and intertwined on the molecular, cellular and tissue levels. The ultimate communication between these different levels is the key to understand how plants realize their developmental decisions. Cell signaling, tissue polarization, directional transport of signaling molecules within tissues are among those biological processes that allow for such multilevel organization in plant development. Nevertheless our understanding of these processes remains largely elusive. This doctoral thesis demonstrates the results of multidisciplinary studies at the interface between several scientific disciplines, including mathematics, computer science (under supervision of Prof. Willy Govaerts) and cell and developmental biology (under guidance of Prof. Jiří Friml). Therefore, I will utilize state-of-the-art mathematical and computational techniques combined with the most recent biological data to address cell and tissue polarities as well as graded distribution patterns of the plant phytohormone auxin, in the context of plant developmental flexibility. The main goal of the research presented herein was to explore general principles of auxin feedback regulation and its outstanding roles in auxin-driven plant development. A special focus was given to the combination of local auxin signaling cues (inside and outside of the cell), subcellular dynamics (trafficking of auxin carriers) and cell-type specific factors (spatial patterns of gene activity) to account for the developmental patterns observed in planta such as canalization of auxin transport, leaf venation patterning, tissue regeneration and establishment and maintenance of cell and tissue polarities. The core of the thesis will start with a general introduction to the models for auxin-mediated plant development and will be followed by presentation of various scientific results and their potential implications for hopefully better understanding of patterning mechanisms in plants. Finally, the summarizing chapter of this thesis aims to translate the results of these various studies to the more general concept of the local auxin feedback regulation in plants.
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- 2011
18. Model of Differential Growth-Guided Apical Hook Formation in Plants.
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Žádníková, Petra, Wabnik, Krzysztof, Abuzeineh, Anas, Gallemi, Marçal, Straeten, Dominique Van Der, Smith, Richard S., Inzé, Dirk, Friml, Jiří, Prusinkiewicz, Przemysław, and Benková, Eva
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CELL growth , *HOOKS , *ARABIDOPSIS thaliana , *CELL proliferation , *COMPUTER simulation - Abstract
Differential cell growth enables flexible organ bending in the presence of environmental signals such as light or gravity. A prominent example of the developmental processes based on differential cell growth is the formation of the apical hook that protects the fragile shoot apical meristem when it breaks through the soil during germination. Here, we combined in silico and in vivo approaches to identify a minimal mechanism producing auxin gradient-guided differential growth during the establishment of the apical hook in the model plant Arabidopsis thaliana. Computer simulation models based on experimental data demonstrate that asymmetric expression of the PIN-FORMED auxin efflux carrier at the concave (inner) versus convex (outer) side of the hook suffices to establish an auxin maximum in the epidermis at the concave side of the apical hook. Furthermore, we propose a mechanism that translates this maximum into differential growth, and thus curvature, of the apical hook. Through a combination of experimental and in silico computational approaches, we have identified the individual contributions of differential cell elongation and proliferation to defining the apical hook and reveal the role of auxin-ethylene crosstalk in balancing these two processes. [ABSTRACT FROM AUTHOR]
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- 2016
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19. Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants.
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Wabnik, Krzysztof, Robert, Hélène?S., Smith, Richard?S., and Friml, Jiří
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PLANT embryology , *PLANT regulators , *PLANT cells & tissues , *AUXIN , *PLANT growth - Abstract
Summary: The apical-basal axis of the early plant embryo determines the body plan of the adult organism. To establish a polarized embryonic axis, plants evolved a unique mechanism that involves directional, cell-to-cell transport of the growth regulator auxin. Auxin transport relies on PIN auxin transporters [1], whose polar subcellular localization determines the flow directionality. PIN-mediated auxin transport mediates the spatial and temporal activity of the auxin response machinery [2–7] that contributes to embryo patterning processes, including establishment of the apical (shoot) and basal (root) embryo poles [8]. However, little is known of upstream mechanisms guiding the (re)polarization of auxin fluxes during embryogenesis [9]. Here, we developed a model of plant embryogenesis that correctly generates emergent cell polarities and auxin-mediated sequential initiation of apical-basal axis of plant embryo. The model relies on two precisely localized auxin sources and a feedback between auxin and the polar, subcellular PIN transporter localization. Simulations reproduced PIN polarity and auxin distribution, as well as previously unknown polarization events during early embryogenesis. The spectrum of validated model predictions suggests that our model corresponds to a minimal mechanistic framework for initiation and orientation of the apical-basal axis to guide both embryonic and postembryonic plant development. [ABSTRACT FROM AUTHOR]
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- 2013
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20. Systems approaches to study root architecture dynamics.
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Cuesta, Candela, Wabnik, Krzysztof, and Benková, Eva
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The plant root system is essential for providing anchorage to the soil, supplying minerals and water, and synthesizing metabolites. It is a dynamic organ modulated by external cues such as environmental signals, water and nutrients availability, salinity and others. Lateral roots (LRs) are initiated from the primary root post-embryonically, after which they progress through discrete developmental stages which can be independently controlled, providing a high level of plasticity during root system formation. Within this review, main contributions are presented, from the classical forward genetic screens to the more recent high-throughput approaches, combined with computer model predictions, dissecting how LRs and thereby root system architecture is established and developed. [ABSTRACT FROM AUTHOR]
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- 2013
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21. Prototype cell-to-cell auxin transport mechanism by intracellular auxin compartmentalization
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Wabnik, Krzysztof, Kleine-Vehn, Jürgen, Govaerts, Willy, and Friml, Jiří
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PLANT cell compartmentation , *EFFECT of auxin on plants , *ENDOPLASMIC reticulum , *CELL membranes , *PROTOTYPES , *COMPUTER simulation , *CELL communication - Abstract
Carrier-dependent, intercellular auxin transport is central to the developmental patterning of higher plants (tracheophytes). The evolution of this polar auxin transport might be linked to the translocation of some PIN auxin efflux carriers from their presumably ancestral localization at the endoplasmic reticulum (ER) to the polar domains at the plasma membrane. Here we propose an eventually ancient mechanism of intercellular auxin distribution by ER-localized auxin transporters involving intracellular auxin retention and switch-like release from the ER. The proposed model integrates feedback circuits utilizing the conserved nuclear auxin signaling for the regulation of PIN transcription and a hypothetical ER-based signaling for the regulation of PIN-dependent transport activity at the ER. Computer simulations of the model revealed its plausibility for generating auxin channels and localized auxin maxima highlighting the possibility of this alternative mechanism for polar auxin transport. [Copyright &y& Elsevier]
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- 2011
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22. Recycling, clustering, and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane.
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Kleine‐Vehn, Jürgen, Wabnik, Krzysztof, Martinière, Alexandre, Łangowski, Łukasz, Willig, Katrin, Naramoto, Satoshi, Leitner, Johannes, Tanaka, Hirokazu, Jakobs, Stefan, Robert, Stéphanie, Luschnig, Christian, Govaerts, Willy, W Hell, Stefan, Runions, John, and Friml, Jiří
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Cell polarity reflected by asymmetric distribution of proteins at the plasma membrane is a fundamental feature of unicellular and multicellular organisms. It remains conceptually unclear how cell polarity is kept in cell wall-encapsulated plant cells. We have used super-resolution and semi-quantitative live-cell imaging in combination with pharmacological, genetic, and computational approaches to reveal insights into the mechanism of cell polarity maintenance in Arabidopsis thaliana.We show that polar-competent PIN transporters for the phytohormone auxin are delivered to the center of polar domains by super-polar recycling. Within the plasma membrane, PINs are recruited into non-mobile membrane clusters and their lateral diffusion is dramatically reduced, which ensures longer polar retention. At the circumventing edges of the polar domain, spatially defined internalization of escaped cargos occurs by clathrin-dependent endocytosis. Computer simulations confirm that the combination of these processes provides a robust mechanism for polarity maintenance in plant cells. Moreover, our study suggests that the regulation of lateral diffusion and spatially defined endocytosis, but not super-polar exocytosis have primary importance for PIN polarity maintenance. [ABSTRACT FROM AUTHOR]
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- 2011
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23. Cytokinin response factors regulate PIN-FORMED auxin transporters.
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Šimášková, Mária, O'Brien, José Antonio, Khan, Mamoona, Van Noorden, Giel, Ötvös, Krisztina, Vieten, Anne, De Clercq, Inge, Van Haperen, Johanna Maria Adriana, Cuesta, Candela, Hoyerová, Klára, Vanneste, Steffen, Marhavý, Peter, Wabnik, Krzysztof, Van Breusegem, Frank, Nowack, Moritz, Murphy, Angus, Friml, Jiří, Weijers, Dolf, Beeckman, Tom, and Benková, Eva
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- 2015
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24. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development.
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Chen, Qian, Liu, Yang, Maere, Steven, Lee, Eunkyoung, Van Isterdael, Gert, Xie, Zidian, Xuan, Wei, Lucas, Jessica, Vassileva, Valya, Kitakura, Saeko, Marhavý, Peter, Wabnik, Krzysztof, Geldner, Niko, Benková, Eva, Le, Jie, Fukaki, Hidehiro, Grotewold, Erich, Li, Chuanyou, Friml, Jiří, and Sack, Fred
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- 2015
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25. Synchronization of gene expression across eukaryotic communities through chemical rhythms
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Cristina Prieto-Navarro, Ornella Pucciariello, Krzysztof Wabnik, Diego Ruiz-Sanchis, Sara Pérez-García, Mario García-Navarrete, Merisa Avdovic, Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Pérez-García, Sara [0000-0003-0059-1181], García-Navarrete, Mario [0000-0002-1899-8206], Ruiz-Sanchis, Diego [0000-0002-2497-071X], Prieto-Navarro, Cristina [0000-0002-4202-1307], Avdovic, Merisa [0000-0002-7688-5541], Pucciariello, Ornella [0000-0002-5241-5385], Wabnik, Krzysztof [0000-0001-7263-0560], Pérez-García, Sara, García-Navarrete, Mario, Ruiz-Sanchis, Diego, Prieto-Navarro, Cristina, Avdovic, Merisa, Pucciariello, Ornella, and Wabnik, Krzysztof
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Biochemical Phenomena ,Science ,Saccharomyces cerevisiae ,Cell ,General Physics and Astronomy ,Gene Expression ,Microbial communities ,Computational biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,Rhythm ,Gene Expression Regulation, Fungal ,Gene expression ,Synchronization (computer science) ,medicine ,Synthetic biology ,Multidisciplinary ,biology ,Mechanism (biology) ,Small molecules ,Cell Cycle ,General Chemistry ,biology.organism_classification ,Yeast ,Repressor Proteins ,medicine.anatomical_structure ,Fungal ,Gene Expression Regulation ,Intercellular coupling - Abstract
10 Pág. Centro de Biotecnología y Genómica de Plantas (CBGP), The synchronization is a recurring phenomenon in neuroscience, ecology, human sciences, and biology. However, controlling synchronization in complex eukaryotic consortia on extended spatial-temporal scales remains a major challenge. Here, to address this issue we construct a minimal synthetic system that directly converts chemical signals into a coherent gene expression synchronized among eukaryotic communities through rate-dependent hysteresis. Guided by chemical rhythms, isolated colonies of yeast Saccharomyces cerevisiae oscillate in near-perfect synchrony despite the absence of intercellular coupling or intrinsic oscillations. Increased speed of chemical rhythms and incorporation of feedback in the system architecture can tune synchronization and precision of the cell responses in a growing cell collectives. This synchronization mechanism remain robust under stress in the two-strain consortia composed of toxin-sensitive and toxin-producing strains. The sensitive cells can maintain the spatial-temporal synchronization for extended periods under the rhythmic toxin dosages produced by killer cells. Our study provides a simple molecular framework for generating global coordination of eukaryotic gene expression through dynamic environment., This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to K.W.), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016-0672 (2017-2021) to K.W. via the CBGP). In the frame of SEV-2016-0672 funding M.A. received a PhD fellowship (SEV-2016-0672-18-3: PRE2018-084946) and O.P. is supported with a postdoctoral contract. K.W. was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to K.W.). UPM Plan Propio Predoctoral fellow finances M. G.N.
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- 2021
26. Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling.
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Wabnik, Krzysztof, Kleine‐Vehn, Jürgen, Balla, Jozef, Sauer, Michael, Naramoto, Satoshi, Reinöhl, Vilém, Merks, Roeland M H, Govaerts, Willy, and Friml, Jiří
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PLANT development , *MORPHOGENESIS , *REGENERATION (Botany) , *CHARACTERISTIC functions , *AUXIN - Abstract
Plant development is exceptionally flexible as manifested by its potential for organogenesis and regeneration, which are processes involving rearrangements of tissue polarities. Fundamental questions concern how individual cells can polarize in a coordinated manner to integrate into the multicellular context. In canalization models, the signaling molecule auxin acts as a polarizing cue, and feedback on the intercellular auxin flow is key for synchronized polarity rearrangements. We provide a novel mechanistic framework for canalization, based on up-to-date experimental data and minimal, biologically plausible assumptions. Our model combines the intracellular auxin signaling for expression of PINFORMED (PIN) auxin transporters and the theoretical postulation of extracellular auxin signaling for modulation of PIN subcellular dynamics. Computer simulations faithfully and robustly recapitulated the experimentally observed patterns of tissue polarity and asymmetric auxin distribution during formation and regeneration of vascular systems and during the competitive regulation of shoot branching by apical dominance. Additionally, our model generated new predictions that could be experimentally validated, highlighting a mechanistically conceivable explanation for the PIN polarization and canalization of the auxin flow in plants. [ABSTRACT FROM AUTHOR]
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- 2010
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27. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis
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Marcos Rodriguez, Marco Marconi, Javier Cabrera, Miguel A. Moreno-Risueno, Laura Serrano-Ron, Angela Saez, Tom Beeckman, Philip N. Benfey, Juan Carlos del Pozo, Alfonso Rodríguez-Patón, Krzysztof Wabnik, Inmaculada Gude, Hugues De Gernier, Alvaro Sanchez-Corrionero, Juan Perianez-Rodriguez, Estefano Bustillo-Avendaño, Pablo Perez-Garcia, Guy Wachsman, Ministerio de Economía y Competitividad (España), European Commission, Comunidad de Madrid, Research Foundation - Flanders, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Perianez-Rodriguez, Juan, Rodriguez, Marcos, Marconi, Marco, Bustillo-Avendaño, Estefano, Wachsman, Guy, Sanchez-Corrionero, Alvaro, De Gernier, Hugues, Cabrera, Javier, Perez-Garcia, Pablo, Gude, Inmaculada, Saez, Angela, Serrano-Ron, Laura, Beeckman, Tom, Benfey, Philip N, Rodríguez-Patón, Alfonso, Del Pozo, Juan Carlos, Wabnik, Krzysztof, Moreno-Risueno, Miguel A, Perianez-Rodriguez, Juan [0000-0003-1002-7111], Rodriguez, Marcos [0000-0003-3741-8593], Marconi, Marco [0000-0002-3457-1384], Bustillo-Avendaño, Estefano [0000-0002-1442-8791], Wachsman, Guy [0000-0002-0551-9333], Sanchez-Corrionero, Alvaro [0000-0001-5360-0294], De Gernier, Hugues [0000-0002-7644-3233], Cabrera, Javier [0000-0002-9277-4876], Perez-Garcia, Pablo [0000-0001-8595-8530], Gude, Inmaculada [0000-0002-3122-1688], Saez, Angela [0000-0002-9189-4737], Serrano-Ron, Laura [0000-0001-5180-6547], Beeckman, Tom [0000-0001-8656-2060], Benfey, Philip N [0000-0001-5302-758X], Rodríguez-Patón, Alfonso [0000-0001-7289-2114], Del Pozo, Juan Carlos [0000-0002-4113-457X], Wabnik, Krzysztof [0000-0001-7263-0560], and Moreno-Risueno, Miguel A [0000-0002-9794-1450]
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0106 biological sciences ,Cell division ,Digital storage ,PROTEINS ,Root (chord) ,CELL-DIVISION ,01 natural sciences ,Plants (botany) ,03 medical and health sciences ,DOMAIN-II ,Auxin ,Arabidopsis ,Timing circuits ,LENGTH ,TRAFFICKING ,RNA-SEQ ,Oscillating gene ,Research Articles ,Cell proliferation ,030304 developmental biology ,GENE-EXPRESSION ,chemistry.chemical_classification ,Physics ,0303 health sciences ,Multidisciplinary ,biology ,Oscillation ,Plant Sciences ,fungi ,SciAdv r-articles ,food and beverages ,Biology and Life Sciences ,Regulatory loop ,DEGRADATION ,biology.organism_classification ,OF-FUNCTION MUTATION ,chemistry ,Biophysics ,PATTERNS ,Gene expression ,Entrainment (chronobiology) ,010606 plant biology & botany ,Research Article - Abstract
CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 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., This work was funded by the Ministerio de Economía y Competitividad of Spain (MINECO) and/or the ERDF (BFU2016-80315-P to M.A.M.-R., BIO2017-82209-R to J.C.d.P., and TIN2016-81079-R to A.R.-P.), the Comunidad de Madrid and/or ERDF and ESF (2017-T1/BIO-5654 to K.W. and S2017/BMD-3691 to A.R.-P.), the Howard Hughes Medical Institute and the NIH (R35-GM131725 to P.N.B.), the Fonds Wetenschappelijk Onderzoek (FWO Flanders) (G022516N, G020918N, and G024118N to T.B.), and the “Severo Ochoa Program for Centres of Excellence in R&D” from the Agencia Estatal de Investigacion of Spain [SEV-2016-0672 (2017–2021)] to K.W., P.P.-G., and M.A.M.-R. through CBGP. M.M. was supported by a postdoctoral contract associated to SEV-2016-0672, E.B.-A. by Ayudante de Investigacion contract PEJ-2017-AI/BIO-7360 from the Comunidad de Madrid, A.S.-C. and L.S.-R. by FPI contracts from MINECO (BES-2014-068852 and BES-2017-080155, respectively), J.C. by a Juan de la Cierva contract from MINECO (FJCI-2016-28607), P.P.-G. by a Juan de la Cierva contract from MINECO (FJCI-2015-24905) and Programa Atraccion Talento from Comunidad Madrid (2017-T2/BIO-3453), A.S. by a Torres Quevedo contract from MINECO (PTQ-15-07915), and K.W. by program PGC2018-093387-A-I00 from the Ministerio de Ciencia e Innovacion (MICIU)
- Published
- 2021
28. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis.
- Author
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Perianez-Rodriguez, Juan, Rodriguez, Marcos, Marconi, Marco, Bustillo-Avendaño, Estefano, Wachsman, Guy, Sanchez-Corrionero, Alvaro, De Gernier, Hugues, Cabrera, Javier, Perez-Garcia, Pablo, Gude, Inmaculada, Saez, Angela, Serrano-Ron, Laura, Beeckman, Tom, Benfey, Philip N., RodrÃguez-PatÃn, Alfonso, del Pozo, Juan Carlos, Wabnik, Krzysztof, and Moreno-Risueno, Miguel A.
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AUXIN , *ARABIDOPSIS , *NUCLEOTIDE sequencing , *BOTANY , *GREEN fluorescent protein , *ROOT development - Abstract
The article presents research report on auxin-regulable oscillatory circuit drives the root clock in Arabidopsis. Topics include how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing; and time course analyses of in-phase gene oscillations in the mutant showed a persistent signal in the oscillation zone (OZ).
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- 2021
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29. Macroscopic control of cell electrophysiology through ion channel expression
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Sara Pérez-Garcia, Merisa Avdovic, Mario García-Navarrete, Diego Ruiz Sanchis, Krzysztof Wabnik, Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), García-Navarrete, Mario, Avdovic, Merisa, Pérez-Garcia, Sara, Ruiz Sanchis, Diego, and Wabnik, Krzysztof
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Potassium Channels ,General Immunology and Microbiology ,Aspirin ,General Neuroscience ,S. cerevisiae ,General Medicine ,Saccharomyces cerevisiae ,Synchronization ,Physics of living systems ,General Biochemistry, Genetics and Molecular Biology ,Cell Physiological Phenomena ,Electrophysiology ,Computational biology ,Bioelectricity ,Ion channels ,Auxin ,Systems biology ,Membrane potential - Abstract
15 Pág. Centro de Biotecnología y Genómica de Plantas, Cells convert electrical signals into chemical outputs to facilitate the active transport of information across larger distances. This electrical-to-chemical conversion requires a tightly regulated expression of ion channels. Alterations of ion channel expression provide landmarks of numerous pathological diseases, such as cardiac arrhythmia, epilepsy, or cancer. Although the activity of ion channels can be locally regulated by external light or chemical stimulus, it remains challenging to coordinate the expression of ion channels on extended spatial-temporal scales. Here, we engineered yeast Saccharomyces cerevisiae to read and convert chemical concentrations into a dynamic potassium channel expression. A synthetic dual-feedback circuit controls the expression of engineered potassium channels through phytohormones auxin and salicylate to produce a macroscopically coordinated pulses of the plasma membrane potential. Our study provides a compact experimental model to control electrical activity through gene expression in eukaryotic cell populations setting grounds for various cellular engineering, synthetic biology, and potential therapeutic applications., This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016-0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016-0672 funding MA received a PhD fellowship (SEV-2016-0672-18-3: PRE2018-084946). KW was supported by Programa Estatal de Generacion del Conocimiento y Forta lecimiento Cientıfico y Tecnologico del Sistema de I+D+I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). UPM Plan Propio Predoctoral fellow finances MGN
- Published
- 2022
30. Differential growth dynamics control aerial organ geometry.
- Author
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Peng, Ziyuan, Alique, Daniel, Xiong, Yuanyuan, Hu, Jinrong, Cao, Xiuwei, Lü, Shouqin, Long, Mian, Wang, Ying, Wabnik, Krzysztof, and Jiao, Yuling
- Subjects
- *
CELLULAR mechanics , *AUXIN , *CELL growth , *PLANT cell walls , *GENE expression , *ARABIDOPSIS thaliana ,LEAF growth - Abstract
How gene activities and biomechanics together direct organ shapes is poorly understood. Plant leaf and floral organs develop from highly similar initial structures and share similar gene expression patterns, yet they gain drastically different shapes later—flat and bilateral leaf primordia and radially symmetric floral primordia, respectively. We analyzed cellular growth patterns and gene expression in young leaves and flowers of Arabidopsis thaliana and found significant differences in cell growth rates, which correlate with convergence sites of phytohormone auxin that require polar auxin transport. In leaf primordia, the PRESSED - FLOWER -expressing middle domain grows faster than adjacent adaxial domain and coincides with auxin convergence. In contrast, in floral primordia, the LEAFY -expressing domain shows accelerated growth rates and pronounced auxin convergence. This distinct cell growth dynamics between leaf and flower requires changes in levels of cell-wall pectin de-methyl-esterification and mechanical properties of the cell wall. Data-driven computer model simulations at organ and cellular levels demonstrate that growth differences are central to obtaining distinct organ shape, corroborating in planta observations. Together, our study provides a mechanistic basis for the establishment of early aerial organ symmetries through local modulation of differential growth patterns with auxin and biomechanics. [Display omitted] • Leaf and floral primordia share similar gene expression and initial domain partition • Local growth-rate differences across domains explain primordia shape differences • Two primordia have different patterns of cell-wall rigidity and auxin convergence • When incorporating growth dynamics, models explain different organ shapes Peng et al. show that different growth dynamics determine the shape of plant aerial organs, leaf and floral primordia, which share similar initial geometry. Experiments and simulations are combined to link growth dynamics with biomechanics and polar auxin transport. [ABSTRACT FROM AUTHOR]
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- 2022
- Full Text
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31. PIN-LIKES Coordinate Brassinosteroid Signaling with Nuclear Auxin Input in Arabidopsis thaliana.
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Sun, Lin, Feraru, Elena, Feraru, Mugurel I., Waidmann, Sascha, Wang, Wenfei, Passaia, Gisele, Wang, Zhi-Yong, Wabnik, Krzysztof, and Kleine-Vehn, Jürgen
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- *
ARABIDOPSIS thaliana , *AUXIN , *ENDOPLASMIC reticulum , *PLANT development , *GROWTH regulators , *GENETIC testing - Abstract
Auxin and brassinosteroids (BR) are crucial growth regulators and display overlapping functions during plant development. Here, we reveal an alternative phytohormone crosstalk mechanism, revealing that BR signaling controls PIN-LIKES (PILS)-dependent nuclear abundance of auxin. We performed a forward genetic screen for imperial pils (imp) mutants that enhance the overexpression phenotypes of PILS5 putative intracellular auxin transport facilitator. Here, we report that the imp1 mutant is defective in the BR-receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1). Our set of data reveals that BR signaling transcriptionally and post-translationally represses the accumulation of PILS proteins at the endoplasmic reticulum, thereby increasing nuclear abundance and signaling of auxin. We demonstrate that this alternative phytohormonal crosstalk mechanism integrates BR signaling into auxin-dependent organ growth rates and likely has widespread importance for plant development. • Impaired BR perception enhances PILS5 overexpression phenotypes • BR signaling increases PILS protein turnover • BR signaling defines PILS-dependent nuclear abundance and signaling of auxin • PILS-dependent BR-auxin crosstalk affects organ growth Sun et al. reveal that BR signaling limits the accumulation of PILS proteins at the endoplasmic reticulum, thereby increasing nuclear abundance and signaling of auxin. This alternative phytohormonal crosstalk mechanism integrates BR signaling into auxin-dependent organ growth rates and likely has widespread importance for plant development. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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32. Polar auxin transport modulates early leaf flattening.
- Author
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Wang Q, Marconi M, Guan C, Wabnik K, and Jiao Y
- Subjects
- Meristem metabolism, Plant Leaves metabolism, Biological Transport genetics, Organogenesis, Plant, Gene Expression Regulation, Plant, Indoleacetic Acids metabolism, Solanum lycopersicum genetics, Solanum lycopersicum metabolism
- Abstract
The flattened leaf form is an important adaptation for efficient photosynthesis, and the developmental process of flattened leaves has been intensively studied. Classic microsurgery studies in potato and tomato suggest that the shoot apical meristem (SAM) communicates with the leaf primordia to promote leaf blade formation. More recently, it was found that polar auxin transport (PAT) could mediate this communication. However, it is unclear how the expression of leaf patterning genes is tailored by PAT routes originating from SAM. By combining experimental observations and computer model simulations, we show that microsurgical incisions and local inhibition of PAT in tomato interfere with auxin transport toward the leaf margins, reducing auxin response levels and altering the leaf blade shape. Importantly, oval auxin responses result in the bipolar expression of SlLAM1 that determines leaf blade formation. Furthermore, wounding caused by incisions promotes degradation of SlREV, a known regulator of leaf polarity. Additionally, computer simulations suggest that local auxin biosynthesis in early leaf primordia could remove necessity for external auxin supply originating from SAM, potentially explaining differences between species. Together, our findings establish how PAT near emerging leaf primordia determines spatial auxin patterning and refines SlLAM1 expression in the leaf margins to guide leaf flattening.
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- 2022
- Full Text
- View/download PDF
33. Feedback models for polarized auxin transport: an emerging trend.
- Author
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Wabnik K, Govaerts W, Friml J, and Kleine-Vehn J
- Subjects
- Arabidopsis metabolism, Biological Transport, Feedback, Physiological, Indoleacetic Acids chemistry, Plant Physiological Phenomena, Indoleacetic Acids metabolism, Models, Biological, Plants metabolism
- Abstract
The phytohormone auxin is vital to plant growth and development. A unique property of auxin among all other plant hormones is its cell-to-cell polar transport that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the substantial molecular insight into the cellular PIN polarization, the mechanistic understanding for developmentally and environmentally regulated PIN polarization is scarce. The long-standing belief that auxin modulates its own transport by means of a positive feedback mechanism has inspired both experimentalists and theoreticians for more than two decades. Recently, theoretical models for auxin-dependent patterning in plants include the feedback between auxin transport and the PIN protein localization. These computer models aid to assess the complexity of plant development by testing and predicting plausible scenarios for various developmental processes that occur in planta. Although the majority of these models rely on purely heuristic principles, the most recent mechanistic models tentatively integrate biologically testable components into known cellular processes that underlie the PIN polarity regulation. The existing and emerging computational approaches to describe PIN polarization are presented and discussed in the light of recent experimental data on the PIN polar targeting.
- Published
- 2011
- Full Text
- View/download PDF
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