@article{1004, abstract = {The fundamental tasks of the root system are, besides anchoring, mediating interactions between plant and soil and providing the plant with water and nutrients. The architecture of the root system is controlled by endogenous mechanisms that constantly integrate environmental signals, such as availability of nutrients and water. Extremely important for efficient soil exploitation and survival under less favorable conditions is the developmental flexibility of the root system that is largely determined by its postembryonic branching capacity. Modulation of initiation and outgrowth of lateral roots provides roots with an exceptional plasticity, allows optimal adjustment to underground heterogeneity, and enables effective soil exploitation and use of resources. Here we discuss recent advances in understanding the molecular mechanisms that shape the plant root system and integrate external cues to adapt to the changing environment.}, author = {Ötvös, Krisztina and Benková, Eva}, issn = {0959437X}, journal = {Current Opinion in Genetics & Development}, pages = {82 -- 89}, publisher = {Elsevier}, title = {{Spatiotemporal mechanisms of root branching}}, doi = {10.1016/j.gde.2017.03.010}, volume = {45}, year = {2017}, } @article{946, abstract = {Roots navigate through soil integrating environmental signals to orient their growth. The Arabidopsis root is a widely used model for developmental, physiological and cell biological studies. Live imaging greatly aids these efforts, but the horizontal sample position and continuous root tip displacement present significant difficulties. Here, we develop a confocal microscope setup for vertical sample mounting and integrated directional illumination. We present TipTracker – a custom software for automatic tracking of diverse moving objects usable on various microscope setups. Combined, this enables observation of root tips growing along the natural gravity vector over prolonged periods of time, as well as the ability to induce rapid gravity or light stimulation. We also track migrating cells in the developing zebrafish embryo, demonstrating the utility of this system in the acquisition of high-resolution data sets of dynamic samples. We provide detailed descriptions of the tools enabling the easy implementation on other microscopes.}, author = {Von Wangenheim, Daniel and Hauschild, Robert and Fendrych, Matyas and Barone, Vanessa and Benková, Eva and Friml, Jirí}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{Live tracking of moving samples in confocal microscopy for vertically grown roots}}, doi = {10.7554/eLife.26792}, volume = {6}, year = {2017}, } @article{1024, abstract = {The history of auxin and cytokinin biology including the initial discoveries by father–son duo Charles Darwin and Francis Darwin (1880), and Gottlieb Haberlandt (1919) is a beautiful demonstration of unceasing continuity of research. Novel findings are integrated into existing hypotheses and models and deepen our understanding of biological principles. At the same time new questions are triggered and hand to hand with this new methodologies are developed to address these new challenges.}, author = {Hurny, Andrej and Benková, Eva}, issn = {10643745}, journal = {Auxins and Cytokinins in Plant Biology}, pages = {1 -- 29}, publisher = {Springer}, title = {{Methodological advances in auxin and cytokinin biology}}, doi = {10.1007/978-1-4939-6831-2_1}, volume = {1569}, year = {2017}, } @article{1081, abstract = {The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.}, author = {Łangowski, Łukasz and Wabnik, Krzysztof T and Li, Hongjiang and Vanneste, Steffen and Naramoto, Satoshi and Tanaka, Hirokazu and Friml, Jirí}, journal = {Cell Discovery}, publisher = {Nature Publishing Group}, title = {{Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells}}, doi = {10.1038/celldisc.2016.18}, volume = {2}, year = {2016}, } @article{1153, 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. © 2016 American Society of Plant Biologists. All rights reserved.}, author = {Žádníková, Petra and Wabnik, Krzysztof T and Abuzeineh, Anas and Gallemí, Marçal and Van Der Straeten, Dominique and Smith, Richard and Inze, Dirk and Friml, Jirí and Prusinkiewicz, Przemysław and Benková, Eva}, journal = {Plant Cell}, number = {10}, pages = {2464 -- 2477}, publisher = {American Society of Plant Biologists}, title = {{A model of differential growth guided apical hook formation in plants}}, doi = {10.1105/tpc.15.00569}, volume = {28}, year = {2016}, } @article{1185, abstract = {The developmental programme of the pistil is under the control of both auxin and cytokinin. Crosstalk between these factors converges on regulation of the auxin carrier PIN-FORMED 1 (PIN1). Here, we show that in the triple transcription factor mutant cytokinin response factor 2 (crf2) crf3 crf6 both pistil length and ovule number were reduced. PIN1 expression was also lower in the triple mutant and the phenotypes could not be rescued by exogenous cytokinin application. pin1 complementation studies using genomic PIN1 constructs showed that the pistil phenotypes were only rescued when the PCRE1 domain, to which CRFs bind, was present. Without this domain, pin mutants resemble the crf2 crf3 crf6 triple mutant, indicating the pivotal role of CRFs in auxin-cytokinin crosstalk.}, author = {Cucinotta, Mara and Manrique, Silvia and Guazzotti, Andrea and Quadrelli, Nadia and Mendes, Marta and Benková, Eva and Colombo, Lucia}, journal = {Development}, number = {23}, pages = {4419 -- 4424}, publisher = {Company of Biologists}, title = {{Cytokinin response factors integrate auxin and cytokinin pathways for female reproductive organ development}}, doi = {10.1242/dev.143545}, volume = {143}, year = {2016}, } @inbook{1210, abstract = {Mechanisms for cell protection are essential for survival of multicellular organisms. In plants, the apical hook, which is transiently formed in darkness when the germinating seedling penetrates towards the soil surface, plays such protective role and shields the vitally important shoot apical meristem and cotyledons from damage. The apical hook is formed by bending of the upper hypocotyl soon after germination, and it is maintained in a closed stage while the hypocotyl continues to penetrate through the soil and rapidly opens when exposed to light in proximity of the soil surface. To uncover the complex molecular network orchestrating this spatiotemporally tightly coordinated process, monitoring of the apical hook development in real time is indispensable. Here we describe an imaging platform that enables high-resolution kinetic analysis of this dynamic developmental process. © Springer Science+Business Media New York 2017.}, author = {Zhu, Qiang and Žádníková, Petra and Smet, Dajo and Van Der Straeten, Dominique and Benková, Eva}, booktitle = {Plant Hormones}, pages = {1 -- 8}, publisher = {Humana Press}, title = {{Real time analysis of the apical hook development}}, doi = {10.1007/978-1-4939-6469-7_1}, volume = {1497}, year = {2016}, } @article{1258, abstract = {When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling.}, author = {Gallemi Rovira, Marcal and Galstyan, Anahit and Paulišić, Sandi and Then, Christiane and Ferrández Ayela, Almudena and Lorenzo Orts, Laura and Roig Villanova, Irma and Wang, Xuewen and Micol, José and Ponce, Maria and Devlin, Paul and Martínez García, Jaime}, journal = {Development}, number = {9}, pages = {1623 -- 1631}, publisher = {Company of Biologists}, title = {{DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis}}, doi = {10.1242/dev.130211}, volume = {143}, year = {2016}, } @article{1264, abstract = {n contrast with the wealth of recent reports about the function of μ-adaptins and clathrin adaptor protein (AP) complexes, there is very little information about the motifs that determine the sorting of membrane proteins within clathrin-coated vesicles in plants. Here, we investigated putative sorting signals in the large cytosolic loop of the Arabidopsis (Arabidopsis thaliana) PIN-FORMED1 (PIN1) auxin transporter, which are involved in binding μ-adaptins and thus in PIN1 trafficking and localization. We found that Phe-165 and Tyr-280, Tyr-328, and Tyr-394 are involved in the binding of different μ-adaptins in vitro. However, only Phe-165, which binds μA(μ2)- and μD(μ3)-adaptin, was found to be essential for PIN1 trafficking and localization in vivo. The PIN1:GFP-F165A mutant showed reduced endocytosis but also localized to intracellular structures containing several layers of membranes and endoplasmic reticulum (ER) markers, suggesting that they correspond to ER or ER-derived membranes. While PIN1:GFP localized normally in a μA (μ2)-adaptin mutant, it accumulated in big intracellular structures containing LysoTracker in a μD (μ3)-adaptin mutant, consistent with previous results obtained with mutants of other subunits of the AP-3 complex. Our data suggest that Phe-165, through the binding of μA (μ2)- and μD (μ3)-adaptin, is important for PIN1 endocytosis and for PIN1 trafficking along the secretory pathway, respectively.}, author = {Sancho Andrés, Gloria and Soriano Ortega, Esther and Gao, Caiji and Bernabé Orts, Joan and Narasimhan, Madhumitha and Müller, Anna and Tejos, Ricardo and Jiang, Liwen and Friml, Jirí and Aniento, Fernando and Marcote, Maria}, journal = {Plant Physiology}, number = {3}, pages = {1965 -- 1982}, publisher = {American Society of Plant Biologists}, title = {{Sorting motifs involved in the trafficking and localization of the PIN1 auxin efflux carrier}}, doi = {10.1104/pp.16.00373}, volume = {171}, year = {2016}, } @article{1265, abstract = {Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical propertiesare modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed thatchanges in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patternedin hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principlefor the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology.}, author = {Elsayad, Kareem and Werner, Stephanie and Gallemi Rovira, Marcal and Kong, Jixiang and Guajardo, Edmundo and Zhang, Lijuan and Jaillais, Yvon and Greb, Thomas and Belkhadir, Youssef}, journal = {Science Signaling}, number = {435}, publisher = {American Association for the Advancement of Science}, title = {{Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging}}, doi = {10.1126/scisignal.aaf6326}, volume = {9}, year = {2016}, }