128 results on '"Wabnik, Krzysztof"'
Search Results
2. Core clock genes adjust growth cessation time to day-night switches in poplar
- Author
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Alique, Daniel, Redondo López, Arturo, González Schain, Nahuel, Allona, Isabel, Wabnik, Krzysztof, and Perales, Mariano
- Published
- 2024
- Full Text
- View/download PDF
3. The cold-induced factor CBF3 mediates root stem cell activity, regeneration, and developmental responses to cold
- Author
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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
- Full Text
- View/download PDF
4. Core clock genes adjust growth cessation time to day-night switches in poplar
- Author
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Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Alique, Daniel [0000-0001-7869-9411], Redondo-López, Arturo [0000-0003-2037-5400], González Schain, Nahuel [0000-0003-2446-5825], Allona, Isabel [0000-0002-7012-2850], Wabnik, Krzysztof [0000-0001-7263-0560], Perales, Mariano [0000-0002-7351-8439], Alique, Daniel, Redondo-López, Arturo, González Schain, Nahuel, Allona, Isabel, Wabnik, Krzysztof, Perales, Mariano, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Ministerio de Universidades (España), Alique, Daniel [0000-0001-7869-9411], Redondo-López, Arturo [0000-0003-2037-5400], González Schain, Nahuel [0000-0003-2446-5825], Allona, Isabel [0000-0002-7012-2850], Wabnik, Krzysztof [0000-0001-7263-0560], Perales, Mariano [0000-0002-7351-8439], Alique, Daniel, Redondo-López, Arturo, González Schain, Nahuel, Allona, Isabel, Wabnik, Krzysztof, and Perales, Mariano
- Abstract
Poplar trees use photoperiod as a precise seasonal indicator, synchronizing plant phenology with the environment. Daylength cue determines FLOWERING LOCUS T 2 (FT2) daily expression, crucial for shoot apex development and establishment of the annual growing period. However, limited evidence exists for the molecular factors controlling FT2 transcription and the conservation with the photoperiodic control of Arabidopsis flowering. We demonstrate that FT2 expression mediates growth cessation response quantitatively, and we provide a minimal data-driven model linking core clock genes to FT2 daily levels. GIGANTEA (GI) emerges as a critical inducer of the FT2 activation window, time-bound by TIMING OF CAB EXPRESSION (TOC1) and LATE ELONGATED HYPOCOTYL (LHY2) repressions. CRISPR/Cas9 loss-of-function lines validate these roles, identifying TOC1 as a long-sought FT2 repressor. Additionally, model simulations predict that FT2 downregulation upon daylength shortening results from a progressive narrowing of this activation window, driven by the phase shift observed in the preceding clock genes. This circadian-mediated mechanism enables poplar to exploit FT2 levels as an accurate daylength-meter.
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- 2024
5. Two orthogonal differentiation gradients locally coordinate fruit morphogenesis
- Author
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Fonds de Recherche du Québec, Natural Sciences and Engineering Research Council of Canada, Comunidad de Madrid, Agencia Estatal de Investigación (España), Gómez-Felipe, Andrea [0000-0002-5647-0496], Branchini, Elvis [0000-0001-5826-7232], Wang, Binghan [0000-0003-0739-6741], Marconi, Marco [0000-0002-3457-1384], Stan, Teodora [0000-0001-6781-447X], Burkiewicz, Jérôme [0000-0001-6968-3506], de Folter, Stefan [0000-0003-4363-7274], Routier-Kierzkowska, Anne-Lise [0000-0003-0383-0811], Wabnik, Krzysztof [0000-0001-7263-0560], Kierzkowski, Daniel [0000-0002-1947-8691], Gómez-Felipe, Andrea, Branchini, Elvis, Wang, Binghan, Marconi, Marco, Bertrand-Rakusová, Hana, Stan, Teodora, Burkiewicz, Jérôme, de Folter, Stefan, Routier-Kierzkowska, Anne-Lise, Wabnik, Krzysztof, Kierzkowski, Daniel, Fonds de Recherche du Québec, Natural Sciences and Engineering Research Council of Canada, Comunidad de Madrid, Agencia Estatal de Investigación (España), Gómez-Felipe, Andrea [0000-0002-5647-0496], Branchini, Elvis [0000-0001-5826-7232], Wang, Binghan [0000-0003-0739-6741], Marconi, Marco [0000-0002-3457-1384], Stan, Teodora [0000-0001-6781-447X], Burkiewicz, Jérôme [0000-0001-6968-3506], de Folter, Stefan [0000-0003-4363-7274], Routier-Kierzkowska, Anne-Lise [0000-0003-0383-0811], Wabnik, Krzysztof [0000-0001-7263-0560], Kierzkowski, Daniel [0000-0002-1947-8691], Gómez-Felipe, Andrea, Branchini, Elvis, Wang, Binghan, Marconi, Marco, Bertrand-Rakusová, Hana, Stan, Teodora, Burkiewicz, Jérôme, de Folter, Stefan, Routier-Kierzkowska, Anne-Lise, Wabnik, Krzysztof, and Kierzkowski, Daniel
- Abstract
Morphogenesis requires the coordination of cellular behaviors along developmental axes. In plants, gradients of growth and differentiation are typically established along a single longitudinal primordium axis to control global organ shape. Yet, it remains unclear how these gradients are locally adjusted to regulate the formation of complex organs that consist of diverse tissue types. Here we combine quantitative live imaging at cellular resolution with genetics, and chemical treatments to understand the formation of Arabidopsis thaliana female reproductive organ (gynoecium). We show that, contrary to other aerial organs, gynoecium shape is determined by two orthogonal, time-shifted differentiation gradients. An early mediolateral gradient controls valve morphogenesis while a late, longitudinal gradient regulates style differentiation. Local, tissue-dependent action of these gradients serves to fine-tune the common developmental program governing organ morphogenesis to ensure the specialized function of the gynoecium.
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- 2024
6. 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
- Published
- 2021
- Full Text
- View/download PDF
7. Computer models of cell polarity establishment in plants
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Comunidad de Madrid, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Marconi, Marco [0000-0002-3457-1384], Wabnik, Krzysztof [0000-0001-7263-0560], Marconi, Marco, Wabnik, Krzysztof, Comunidad de Madrid, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Marconi, Marco [0000-0002-3457-1384], Wabnik, Krzysztof [0000-0001-7263-0560], Marconi, Marco, and Wabnik, Krzysztof
- Abstract
Plant development is a complex task, and many processes involve changes in the asymmetric subcellular distribution of cell components that strongly depend on cell polarity. Cell polarity regulates anisotropic growth and polar localization of membrane proteins and helps to identify the cell's position relative to its neighbors within an organ. Cell polarity is critical in a variety of plant developmental processes, including embryogenesis, cell division, and response to external stimuli. The most conspicuous downstream effect of cell polarity is the polar transport of the phytohormone auxin, which is the only known hormone transported in a polar fashion in and out of cells by specialized exporters and importers. The biological processes behind the establishment of cell polarity are still unknown, and researchers have proposed several models that have been tested using computer simulations. The evolution of computer models has progressed in tandem with scientific discoveries, which have highlighted the importance of genetic, chemical, and mechanical input in determining cell polarity and regulating polarity-dependent processes such as anisotropic growth, protein subcellular localization, and the development of organ shapes. The purpose of this review is to provide a comprehensive overview of the current understanding of computer models of cell polarity establishment in plants, focusing on the molecular and cellular mechanisms, the proteins involved, and the current state of the field.
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- 2023
8. Dynamic context-dependent regulation of auxin feedback signaling in synthetic gene circuits
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Comunidad de Madrid, Agencia Estatal de Investigación (España), Avdovic, Merisa [0000-0002-7688-5541], García-Navarrete, Mario [0000-0002-1899-8206], Ruiz-Sanchis, Diego [0000-0002-2497-071X], Wabnik, Krzysztof [0000-0001-7263-0560], Avdovic, Merisa, García-Navarrete, Mario, Ruiz-Sanchis, Diego, Wabnik, Krzysztof, Comunidad de Madrid, Agencia Estatal de Investigación (España), Avdovic, Merisa [0000-0002-7688-5541], García-Navarrete, Mario [0000-0002-1899-8206], Ruiz-Sanchis, Diego [0000-0002-2497-071X], Wabnik, Krzysztof [0000-0001-7263-0560], Avdovic, Merisa, García-Navarrete, Mario, Ruiz-Sanchis, Diego, and Wabnik, Krzysztof
- 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.
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- 2023
9. The cold-induced factor CBF3 mediates root stem cell activity, regeneration, and developmental responses to cold
- Author
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Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Comunidad de Madrid, Pucciariello, Ornella [0000-0002-5241-5385], Sanchez-Corrionero, Alvaro [0000-0001-5360-0294], Cabrera, Javier [0000-0002-9277-4876], del Barrio, Cristina [0000-0002-7829-2109], del Pozo, J. C. [0000-0002-4113-457X], Perales, Mariano [0000-0002-7351-8439], Wabnik, Krzysztof [0000-0001-7263-0560], Moreno-Risueño, Miguel Ángel [0000-0002-9794-1450], Pérez-García, Pablo, Pucciariello, Ornella, Sanchez-Corrionero, Alvaro, Cabrera, Javier, del Barrio, Cristina, del Pozo, J. C., Perales, Mariano, Wabnik, Krzysztof, Moreno-Risueño, Miguel Ángel, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Comunidad de Madrid, Pucciariello, Ornella [0000-0002-5241-5385], Sanchez-Corrionero, Alvaro [0000-0001-5360-0294], Cabrera, Javier [0000-0002-9277-4876], del Barrio, Cristina [0000-0002-7829-2109], del Pozo, J. C. [0000-0002-4113-457X], Perales, Mariano [0000-0002-7351-8439], Wabnik, Krzysztof [0000-0001-7263-0560], Moreno-Risueño, Miguel Ángel [0000-0002-9794-1450], Pérez-García, Pablo, Pucciariello, Ornella, Sanchez-Corrionero, Alvaro, Cabrera, Javier, del Barrio, Cristina, del Pozo, J. C., Perales, Mariano, Wabnik, Krzysztof, and Moreno-Risueño, Miguel Ángel
- Abstract
Plant growth and development involve the specification and regeneration of stem cell niches (SCNs). Although plants are exposed to disparate environmental conditions, how environmental cues affect developmental programs and stem cells is not well understood. Root stem cells are accommodated in meristems in SCNs around the quiescent center (QC), which maintains their activity. Using a combination of genetics and confocal microscopy to trace morphological defects and correlate them with changes in gene expression and protein levels, we show that the cold-induced transcription factor (TF) C-REPEAT BINDING FACTOR 3 (CBF3), which has previously been associated with cold acclimation, regulates root development, stem cell activity, and regeneration. CBF3 is integrated into the SHORT-ROOT (SHR) regulatory network, forming a feedback loop that maintains SHR expression. CBF3 is primarily expressed in the root endodermis, whereas the CBF3 protein is localized to other meristematic tissues, including root SCNs. Complementation of cbf3-1 using a wild-type CBF3 gene and a CBF3 fusion with reduced mobility show that CBF3 movement capacity is required for SCN patterning and regulates root growth. Notably, cold induces CBF3, affecting QC activity. Furthermore, exposure to moderate cold around 10°C-12°C promotes root regeneration and QC respecification in a CBF3-dependent manner during the recuperation period. By contrast, CBF3 does not appear to regulate stem cell survival, which has been associated with recuperation from more acute cold (∼4°C). We propose a role for CBF3 in mediating the molecular interrelationships among the cold response, stem cell activity, and development.
- Published
- 2023
10. Dynamic context-dependent regulation of auxin feedback signaling in synthetic gene circuits
- Author
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Avdovic, Merisa, primary, Garcia-Navarrete, Mario, additional, Ruiz-Sanchis, Diego, additional, and Wabnik, Krzysztof, additional
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- 2023
- Full Text
- View/download PDF
11. Computer models of cell polarity establishment in plants
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Marconi, Marco, primary and Wabnik, Krzysztof, additional
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- 2023
- Full Text
- View/download PDF
12. Macroscopic control of cell electrophysiology through ion channel expression
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Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), García-Navarrete, Mario [0000-0002-1899-8206], Avdovic, Merisa [0000-0002-7688-5541], Pérez-Garcia, Sara [0000-0003-0059-1181], Ruiz-Sanchis, Diego [0000-0002-2497-071X], Wabnik, Krzysztof [0000-0001-7263-0560], García-Navarrete, Mario, Avdovic, Merisa, Pérez-García, Sara, Ruiz-Sanchis, Diego, Wabnik, Krzysztof, Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), García-Navarrete, Mario [0000-0002-1899-8206], Avdovic, Merisa [0000-0002-7688-5541], Pérez-Garcia, Sara [0000-0003-0059-1181], Ruiz-Sanchis, Diego [0000-0002-2497-071X], Wabnik, Krzysztof [0000-0001-7263-0560], García-Navarrete, Mario, Avdovic, Merisa, Pérez-García, Sara, Ruiz-Sanchis, Diego, and Wabnik, Krzysztof
- Abstract
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.
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- 2022
13. Differential growth dynamics control aerial organ geometry
- Author
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Ministerio de Universidades (España), Comunidad de Madrid, Chinese Academy of Sciences, Centro de Biotecnología y Genómica de Plantas (España), K. C. Wong Magna Fund, Alique, Daniel [0000-0001-7869-9411], Lü, Shouqin [0000-0003-0704-4498], Long, Mian [0000-0003-0819-6186], Wabnik, Krzysztof [0000-0001-7263-0560], Jiao, Yuling [0000-0002-1189-1676], Peng, Ziyuan, Alique, Daniel, Xiong, Yuanyuan, Hu, Jinrong, Cao, Xiuwei, Lü, Shouqin, Long, Mian, Wang, Ying, Wabnik, Krzysztof, Jiao, Yuling, Ministerio de Universidades (España), Comunidad de Madrid, Chinese Academy of Sciences, Centro de Biotecnología y Genómica de Plantas (España), K. C. Wong Magna Fund, Alique, Daniel [0000-0001-7869-9411], Lü, Shouqin [0000-0003-0704-4498], Long, Mian [0000-0003-0819-6186], Wabnik, Krzysztof [0000-0001-7263-0560], Jiao, Yuling [0000-0002-1189-1676], Peng, Ziyuan, Alique, Daniel, Xiong, Yuanyuan, Hu, Jinrong, Cao, Xiuwei, Lü, Shouqin, Long, Mian, Wang, Ying, Wabnik, Krzysztof, and Jiao, Yuling
- 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.
- Published
- 2022
14. Polar auxin transport modulates early leaf flattening
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National Natural Science Foundation of China, K. C. Wong Magna Fund, Comunidad de Madrid, Ministerio de Ciencia, Innovación y Universidades (España), Wang, Qingqing [0000-0003-1303-697X], Marconi, Marco [0000-0002-3457-1384], Guan, Chunmei [0000-0001-7471-1276], Wabnik, Krzysztof [0000-0001-7263-0560], Jiao, Yuling [0000-0002-1189-1676], Wang, Qingqing, Marconi, Marco, Guan, Chunmei, Wabnik, Krzysztof, Jiao, Yuling, National Natural Science Foundation of China, K. C. Wong Magna Fund, Comunidad de Madrid, Ministerio de Ciencia, Innovación y Universidades (España), Wang, Qingqing [0000-0003-1303-697X], Marconi, Marco [0000-0002-3457-1384], Guan, Chunmei [0000-0001-7471-1276], Wabnik, Krzysztof [0000-0001-7263-0560], Jiao, Yuling [0000-0002-1189-1676], Wang, Qingqing, Marconi, Marco, Guan, Chunmei, Wabnik, Krzysztof, and Jiao, Yuling
- 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.
- Published
- 2022
15. 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
- Published
- 2016
16. 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
- Published
- 2019
- Full Text
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17. Polar auxin transport modulates early leaf flattening
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Wang, Qingqing, primary, Marconi, Marco, additional, Guan, Chunmei, additional, Wabnik, Krzysztof, additional, and Jiao, Yuling, additional
- Published
- 2022
- Full Text
- View/download PDF
18. Macroscopic control of cell electrophysiology through ion channel expression
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García-Navarrete, Mario, primary, Avdovic, Merisa, primary, Pérez-Garcia, Sara, primary, Ruiz Sanchis, Diego, additional, and Wabnik, Krzysztof, additional
- Published
- 2022
- Full Text
- View/download PDF
19. Differential growth dynamics control aerial organ geometry
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Peng, Ziyuan, primary, Alique, Daniel, additional, Xiong, Yuanyuan, additional, Hu, Jinrong, additional, Cao, Xiuwei, additional, Lü, Shouqin, additional, Long, Mian, additional, Wang, Ying, additional, Wabnik, Krzysztof, additional, and Jiao, Yuling, additional
- Published
- 2022
- Full Text
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20. Shaping the Organ: A Biologist Guide to Quantitative Models of Plant Morphogenesis
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Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Marconi, Marco [0000-0002-3457-1384], Wabnik, Krzysztof [0000-0001-7263-0560], Marconi, Marco, Wabnik, Krzysztof, Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia, Innovación y Universidades (España), Marconi, Marco [0000-0002-3457-1384], Wabnik, Krzysztof [0000-0001-7263-0560], Marconi, Marco, and Wabnik, Krzysztof
- 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.
- Published
- 2021
21. Synchronization of gene expression across eukaryotic communities through chemical rhythms
- Author
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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, Wabnik, Krzysztof, 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
- Abstract
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.
- Published
- 2021
22. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis
- Author
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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 [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, J. C. [0000-0002-4113-457X], Wabnik, Krzysztof [0000-0001-7263-0560], Moreno-Risueno, Miguel A [0000-0002-9794-1450], Perianez-Rodriguez, Juan, Rodriguez, Marcos, Marconi, Marco, Bustillo-Avendaño, Estefano, Wachsman, Guy, Sanchez-Corrionero, Alvaro, De Gernier, Hugues, Cabrera, Javier, Pérez-García, Pablo, Gude, Inmaculada, Saez, Angela, Serrano-Ron, Laura, Beeckman, Tom, Benfey, Philip N., Rodríguez-Patón, Alfonso, del Pozo, J. C., Wabnik, Krzysztof, Moreno-Risueño, Miguel Ángel, 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 [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, J. C. [0000-0002-4113-457X], Wabnik, Krzysztof [0000-0001-7263-0560], Moreno-Risueno, Miguel A [0000-0002-9794-1450], Perianez-Rodriguez, Juan, Rodriguez, Marcos, Marconi, Marco, Bustillo-Avendaño, Estefano, Wachsman, Guy, Sanchez-Corrionero, Alvaro, De Gernier, Hugues, Cabrera, Javier, Pérez-García, Pablo, Gude, Inmaculada, Saez, Angela, Serrano-Ron, Laura, Beeckman, Tom, Benfey, Philip N., Rodríguez-Patón, Alfonso, del Pozo, J. C., Wabnik, Krzysztof, and Moreno-Risueño, Miguel Ángel
- 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.
- Published
- 2021
23. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth
- Author
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Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Marconi, Marco [0000-0002-3457-1384], Gallemi, Marcal [0000-0003-4675-6893], Wabnik, Krzysztof [0000-0001-7263-0560], Marconi, Marco, Gallemí, Marçal, Benkova, Eva, Wabnik, Krzysztof, Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Marconi, Marco [0000-0002-3457-1384], Gallemi, Marcal [0000-0003-4675-6893], Wabnik, Krzysztof [0000-0001-7263-0560], Marconi, Marco, Gallemí, Marçal, Benkova, Eva, and Wabnik, Krzysztof
- 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.
- Published
- 2021
24. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells
- Author
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Łangowski, Łukasz, Wabnik, Krzysztof, Li, Hongjiang, Vanneste, Steffen, Naramoto, Satoshi, Tanaka, Hirokazu, and Friml, Jiří
- Published
- 2016
- Full Text
- View/download PDF
25. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth
- Author
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Marconi, Marco, primary, Gallemi, Marcal, additional, Benkova, Eva, additional, and Wabnik, Krzysztof, additional
- Published
- 2021
- Full Text
- View/download PDF
26. Shaping the Organ: A Biologist Guide to Quantitative Models of Plant Morphogenesis
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Marconi, Marco, primary and Wabnik, Krzysztof, additional
- Published
- 2021
- Full Text
- View/download PDF
27. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana
- Author
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Li, Hongjiang, von 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, Friml, Jiří, Li, Hongjiang, von 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
- Abstract
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.
- Published
- 2021
28. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis
- Author
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Moreno-Risueño, Miguel Ángel [0000-0002-9794-1450], Perianez-Rodriguez, Juan, Rodriguez, Marcos, Marconi, Marco, Bustillo-Avendaño, Estefano, Wachsman, Guy, Sanchez-Corrionero, Alvaro, DeGernier, Hugues, Cabrera, Javier, Pérez-García, Pablo, Gude, Inmaculada, Saez, Angela, Serrano-Ron, Laura, Beeckman, Tom, Benfey, Philip N., Rodríguez-Patón, Alfonso, del Pozo, J. C., Wabnik, Krzysztof, Moreno-Risueño, Miguel Ángel, Moreno-Risueño, Miguel Ángel [0000-0002-9794-1450], Perianez-Rodriguez, Juan, Rodriguez, Marcos, Marconi, Marco, Bustillo-Avendaño, Estefano, Wachsman, Guy, Sanchez-Corrionero, Alvaro, DeGernier, Hugues, Cabrera, Javier, Pérez-García, Pablo, Gude, Inmaculada, Saez, Angela, Serrano-Ron, Laura, Beeckman, Tom, Benfey, Philip N., Rodríguez-Patón, Alfonso, del Pozo, J. C., Wabnik, Krzysztof, and Moreno-Risueño, Miguel Ángel
- 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.
- Published
- 2021
29. Diseño e implementación de un sistema sintético de comunicación celular en Saccharomyces cerevisiae basado en histidina kinasas
- Author
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Wabnik, Krzysztof, Pollmann, Stephan, Ruiz Sanchis, Diego, Wabnik, Krzysztof, Pollmann, Stephan, and Ruiz Sanchis, Diego
- Abstract
El desarrollo de comunidades microbianas sintéticas es uno de los retos actuales dentro del campo de la biología sintética. El objetivo es diseñar de forma racional poblaciones microbianas que resuelvan, de forma cooperativa, problemas humanos o medioambientales. Para implementar comportamientos coordinados en estas poblaciones sintéticas, es necesario contar con sistemas de comunicación celular ortogonales y bien caracterizados. En trabajos previos, se han desarrollado receptores celulares artificiales basados en arquitecturas que ya existen en la naturaleza. Los sistemas de dos componentes son sistemas de transducción de señal altamente conservados y muy bien caracterizados, que se han utilizado previamente con este propósito en diferentes organismos huésped. En este trabajo intentamos implementar un sistema artificial de comunicación celular en Saccharomyces cerevisiae. Para ello, la histidina kinasa nativa Sln1 de levadura se modificó a dos niveles: a nivel de input, para hacerla sensible a un péptido sintético secretado por una cepa emisora, y a nivel de output, para desviar su señalización hacia una ruta ortogonal de origen bacteriano. No se obtuvo respuesta a través del mecanismo de activación que se había propuesto inicialmente, pero sí se obtuvieron niveles altos de señal al co-cultivar la cepa receptora con con células de S. cerevisiae BY4741 sin transformar. Experimentos posteriores sugieren que la activación está disparada por contacto directo entre células de ambas cepas, y posiblemente está mediada por proteínas de adhesión celular y señalización de estrés de pared. Proponemos un modelo que explica este comportamiento, donde la señalizaión nativa de Sln1 es desviada a una ruta paralela a través de nuestro sistema sintético. Estos resultados abren la puerta al desarrollo de un sensor de contacto celular, artificial y específico de cepa, que se podría usar para implementar comportamientos coordinados y espacialmente estructurados en sistemas sintéticos m
- Published
- 2021
30. 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
- Published
- 2014
- Full Text
- View/download PDF
31. PIN-LIKES Coordinate Brassinosteroid Signaling with Nuclear Auxin Input in Arabidopsis thaliana
- Author
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Sun, Lin, Feraru, Elena, Feraru, Mugurel I., Waidmann, Sascha, Wang, Wenfei, Passaia, Gisele, Wang, Zhi, Wabnik, Krzysztof, Kleine-Vehn, Juergen, Sun, Lin, Feraru, Elena, Feraru, Mugurel I., Waidmann, Sascha, Wang, Wenfei, Passaia, Gisele, Wang, Zhi, Wabnik, Krzysztof, and Kleine-Vehn, Juergen
- 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 crosstalkmechanism integrates BR signaling into auxin-dependent organ growth rates and likely has widespread importance for plant development.
- Published
- 2020
32. Modulation of plant root growth by nitrogen source‐defined regulation of polar auxin transport
- Author
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Ötvös, Krisztina, primary, Marconi, Marco, additional, Vega, Andrea, additional, O’Brien, Jose, additional, Johnson, Alexander, additional, Abualia, Rashed, additional, Antonielli, Livio, additional, Montesinos, Juan Carlos, additional, Zhang, Yuzhou, additional, Tan, Shutang, additional, Cuesta, Candela, additional, Artner, Christina, additional, Bouguyon, Eleonore, additional, Gojon, Alain, additional, Friml, Jirí, additional, Gutiérrez, Rodrigo A., additional, Wabnik, Krzysztof, additional, and Benková, Eva, additional
- Published
- 2021
- Full Text
- View/download PDF
33. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis
- Author
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Perianez-Rodriguez, Juan, primary, Rodriguez, Marcos, additional, Marconi, Marco, additional, Bustillo-Avendaño, Estefano, additional, Wachsman, Guy, additional, Sanchez-Corrionero, Alvaro, additional, De Gernier, Hugues, additional, Cabrera, Javier, additional, Perez-Garcia, Pablo, additional, Gude, Inmaculada, additional, Saez, Angela, additional, Serrano-Ron, Laura, additional, Beeckman, Tom, additional, Benfey, Philip N., additional, Rodríguez-Patón, Alfonso, additional, del Pozo, Juan Carlos, additional, Wabnik, Krzysztof, additional, and Moreno-Risueno, Miguel A., additional
- Published
- 2021
- Full Text
- View/download PDF
34. Cellular requirements for PIN polar cargo clustering in Arabidopsis thaliana
- Author
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Li, Hongjiang, primary, Wangenheim, Daniel, additional, Zhang, Xixi, additional, Tan, Shutang, additional, Darwish‐Miranda, Nasser, additional, Naramoto, Satoshi, additional, Wabnik, Krzysztof, additional, De Rycke, Riet, additional, Kaufmann, Walter A., additional, Gütl, Daniel, additional, Tejos, Ricardo, additional, Grones, Peter, additional, Ke, Meiyu, additional, Chen, Xu, additional, Dettmer, Jan, additional, and Friml, Jiří, additional
- Published
- 2020
- Full Text
- View/download PDF
35. PIN-LIKES Coordinate Brassinosteroid Signaling with Nuclear Auxin Input in Arabidopsis thaliana
- Author
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Sun, Lin, primary, Feraru, Elena, additional, Feraru, Mugurel I., additional, Waidmann, Sascha, additional, Wang, Wenfei, additional, Passaia, Gisele, additional, Wang, Zhi-Yong, additional, Wabnik, Krzysztof, additional, and Kleine-Vehn, Jürgen, additional
- Published
- 2020
- Full Text
- View/download PDF
36. Gene expression trends and protein features effectively complement each other in gene function prediction
- Author
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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.
- Published
- 2009
37. Cytokinin functions as an asymmetric and anti-gravitropic signal in lateral roots
- Author
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Sub Plant Ecophysiology, Plant Ecophysiology, 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., Kleine-Vehn, Jürgen, Sub Plant Ecophysiology, Plant Ecophysiology, 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
- Published
- 2019
38. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development
- Author
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Chen, Qian, primary, Liu, Yang, additional, Maere, Steven, additional, Lee, Eunkyoung, additional, Van Isterdael, Gert, additional, Xie, Zidian, additional, Xuan, Wei, additional, Lucas, Jessica, additional, Vassileva, Valya, additional, Kitakura, Saeko, additional, Marhavý, Peter, additional, Wabnik, Krzysztof, additional, Geldner, Niko, additional, Benková, Eva, additional, Le, Jie, additional, Fukaki, Hidehiro, additional, Grotewold, Erich, additional, Li, Chuanyou, additional, Friml, Jiří, additional, Sack, Fred, additional, Beeckman, Tom, additional, and Vanneste, Steffen, additional
- Published
- 2015
- Full Text
- View/download PDF
39. Cytokinin response factors regulate PIN-FORMED auxin transporters
- Author
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Šimášková, Mária, primary, O’Brien, José Antonio, additional, Khan, Mamoona, additional, Van Noorden, Giel, additional, Ötvös, Krisztina, additional, Vieten, Anne, additional, De Clercq, Inge, additional, Van Haperen, Johanna Maria Adriana, additional, Cuesta, Candela, additional, Hoyerová, Klára, additional, Vanneste, Steffen, additional, Marhavý, Peter, additional, Wabnik, Krzysztof, additional, Van Breusegem, Frank, additional, Nowack, Moritz, additional, Murphy, Angus, additional, Friml, Jiří, additional, Weijers, Dolf, additional, Beeckman, Tom, additional, and Benková, Eva, additional
- Published
- 2015
- Full Text
- View/download PDF
40. Modeling auxin feedback signaling for polarized auxin transport in plant development
- Author
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Wabnik, Krzysztof, Govaerts, Willy, and Friml, Jiri
- Subjects
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.
- Published
- 2011
41. Modeling Framework for the Establishment of the Apical-Basal Embryonic Axis in Plants
- Author
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Wabnik, Krzysztof, primary, Robert, Hélène S., additional, Smith, Richard S., additional, and Friml, Jiří, additional
- Published
- 2013
- Full Text
- View/download PDF
42. Systems approaches to study root architecture dynamics
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Cuesta, Candela, primary, Wabnik, Krzysztof, additional, and Benková, Eva, additional
- Published
- 2013
- Full Text
- View/download PDF
43. Model of Differential Growth-Guided Apical Hook Formation in Plants.
- Author
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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
- Subjects
- *
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]
- Published
- 2016
- Full Text
- View/download PDF
44. Recycling, clustering, and endocytosis jointly maintain PIN auxin carrier polarity at the plasma membrane
- Author
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Kleine‐Vehn, Jürgen, primary, Wabnik, Krzysztof, additional, Martinière, Alexandre, additional, Łangowski, Łukasz, additional, Willig, Katrin, additional, Naramoto, Satoshi, additional, Leitner, Johannes, additional, Tanaka, Hirokazu, additional, Jakobs, Stefan, additional, Robert, Stéphanie, additional, Luschnig, Christian, additional, Govaerts, Willy, additional, W Hell, Stefan, additional, Runions, John, additional, and Friml, Jiří, additional
- Published
- 2011
- Full Text
- View/download PDF
45. Emergence of tissue polarization from synergy of intracellular and extracellular auxin signaling
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Wabnik, Krzysztof, primary, Kleine‐Vehn, Jürgen, additional, Balla, Jozef, additional, Sauer, Michael, additional, Naramoto, Satoshi, additional, Reinöhl, Vilém, additional, Merks, Roeland M H, additional, Govaerts, Willy, additional, and Friml, Jiří, additional
- Published
- 2010
- Full Text
- View/download PDF
46. Gene expression trends and protein features effectively complement each other in gene function prediction
- Author
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Wabnik, Krzysztof, primary, Hvidsten, Torgeir R., additional, Kedzierska, Anna, additional, Van Leene, Jelle, additional, De Jaeger, Geert, additional, Beemster, Gerrit T. S., additional, Komorowski, Jan, additional, and Kuiper, Martin T. R., additional
- Published
- 2008
- Full Text
- View/download PDF
47. WOX5–IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in Arabidopsis
- Author
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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, Ding, Zhaojun, 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
- Abstract
In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5–IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5–IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation.
48. Synchronization of gene expression across eukaryotic communities through chemical rhythms
- Author
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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
49. An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis
- Author
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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]
- Subjects
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)
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- 2021
50. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth
- Author
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Eva Benková, Marco Marconi, Marçal Gallemí, Krzysztof Wabnik, Comunidad de Madrid, Agencia Estatal de Investigación (España), Ministerio de Ciencia e Innovación (España), Marconi, Marco [0000-0002-3457-1384], Gallemi, Marcal [0000-0003-4675-6893], Wabnik, Krzysztof [0000-0001-7263-0560], Marconi, Marco, Gallemi, Marcal, and Wabnik, Krzysztof
- Subjects
QH301-705.5 ,Polarity (physics) ,Science ,Systems biology ,Arabidopsis ,Plant Biology ,Models, Biological ,Plant Roots ,symmetry breaking ,General Biochemistry, Genetics and Molecular Biology ,Computational biology ,Computer model ,Auxin ,root meristem growth ,Cell polarity ,Biology (General) ,Anisotropy ,chemistry.chemical_classification ,Plant biology ,General Immunology and Microbiology ,biology ,General Neuroscience ,fungi ,Root meristem growth ,auxin transport ,food and beverages ,Cell Polarity ,Auxin transport ,Symmetry breaking ,General Medicine ,biology.organism_classification ,chemistry ,Models, Chemical ,A. thaliana ,Biophysics ,Medicine ,computer model ,Polar auxin transport ,Research Article ,Computational and Systems Biology - Abstract
36 Päg. Centro de Biotecnología y Genómica de Plantas (CBGP), 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., 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.M. 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-AI00) from MICIU (to K.W.). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).
- Published
- 2021
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