@article{1145, abstract = {Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure–function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. © 2016 The Authors}, author = {Nodzyński, Tomasz and Vanneste, Steffen and Zwiewka, Marta and Pernisová, Markéta and Hejátko, Jan and Friml, Jirí}, journal = {Molecular Plant}, number = {11}, pages = {1504 -- 1519}, publisher = {Cell Press}, title = {{Enquiry into the topology of plasma membrane localized PIN auxin transport components}}, doi = {10.1016/j.molp.2016.08.010}, volume = {9}, year = {2016}, } @article{1147, abstract = {Apical dominance is one of the fundamental developmental phenomena in plant biology, which determines the overall architecture of aerial plant parts. Here we show apex decapitation activated competition for dominance in adjacent upper and lower axillary buds. A two-nodal-bud pea (Pisum sativum L.) was used as a model system to monitor and assess auxin flow, auxin transport channels, and dormancy and initiation status of axillary buds. Auxin flow was manipulated by lateral stem wounds or chemically by auxin efflux inhibitors 2,3,5-triiodobenzoic acid (TIBA), 1-N-naphtylphtalamic acid (NPA), or protein synthesis inhibitor cycloheximide (CHX) treatments, which served to interfere with axillary bud competition. Redirecting auxin flow to different points influenced which bud formed the outgrowing and dominant shoot. The obtained results proved that competition between upper and lower axillary buds as secondary auxin sources is based on the same auxin canalization principle that operates between the shoot apex and axillary bud. © The Author(s) 2016.}, author = {Balla, Jozef and Medved'Ová, Zuzana and Kalousek, Petr and Matiješčuková, Natálie and Friml, Jirí and Reinöhl, Vilém and Procházka, Stanislav}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Auxin flow mediated competition between axillary buds to restore apical dominance}}, doi = {10.1038/srep35955}, volume = {6}, year = {2016}, } @article{1151, abstract = {Tissue patterning in multicellular organisms is the output of precise spatio–temporal regulation of gene expression coupled with changes in hormone dynamics. In plants, the hormone auxin regulates growth and development at every stage of a plant’s life cycle. Auxin signaling occurs through binding of the auxin molecule to a TIR1/AFB F-box ubiquitin ligase, allowing interaction with Aux/IAA transcriptional repressor proteins. These are subsequently ubiquitinated and degraded via the 26S proteasome, leading to derepression of auxin response factors (ARFs). How auxin is able to elicit such a diverse range of developmental responses through a single signaling module has not yet been resolved. Here we present an alternative auxin-sensing mechanism in which the ARF ARF3/ETTIN controls gene expression through interactions with process-specific transcription factors. This noncanonical hormonesensing mechanism exhibits strong preference for the naturally occurring auxin indole 3-acetic acid (IAA) and is important for coordinating growth and patterning in diverse developmental contexts such as gynoecium morphogenesis, lateral root emergence, ovule development, and primary branch formation. Disrupting this IAA-sensing ability induces morphological aberrations with consequences for plant fitness. Therefore, our findings introduce a novel transcription factor-based mechanism of hormone perception in plants. © 2016 Simonini et al.}, author = {Simonini, Sara and Deb, Joyita and Moubayidin, Laila and Stephenson, Pauline and Valluru, Manoj and Freire Rios, Alejandra and Sorefan, Karim and Weijers, Dolf and Friml, Jirí and Östergaard, Lars}, journal = {Genes and Development}, number = {20}, pages = {2286 -- 2296}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{A noncanonical auxin sensing mechanism is required for organ morphogenesis in arabidopsis}}, doi = {10.1101/gad.285361.116}, volume = {30}, 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{1212, abstract = {Plants adjust their growth according to gravity. Gravitropism involves gravity perception, signal transduction, and asymmetric growth response, with organ bending as a consequence [1]. Asymmetric growth results from the asymmetric distribution of the plant-specific signaling molecule auxin [2] that is generated by lateral transport, mediated in the hypocotyl predominantly by the auxin transporter PIN-FORMED3 (PIN3) [3–5]. Gravity stimulation polarizes PIN3 to the bottom sides of endodermal cells, correlating with increased auxin accumulation in adjacent tissues at the lower side of the stimulated organ, where auxin induces cell elongation and, hence, organ bending. A curvature response allows the hypocotyl to resume straight growth at a defined angle [6], implying that at some point auxin symmetry is restored to prevent overbending. Here, we present initial insights into cellular and molecular mechanisms that lead to the termination of the tropic response. We identified an auxin feedback on PIN3 polarization as underlying mechanism that restores symmetry of the PIN3-dependent auxin flow. Thus, two mechanistically distinct PIN3 polarization events redirect auxin fluxes at different time points of the gravity response: first, gravity-mediated redirection of PIN3-mediated auxin flow toward the lower hypocotyl side, where auxin gradually accumulates and promotes growth, and later PIN3 polarization to the opposite cell side, depleting this auxin maximum to end the bending. Accordingly, genetic or pharmacological interference with the late PIN3 polarization prevents termination of the response and leads to hypocotyl overbending. This observation reveals a role of auxin feedback on PIN polarity in the termination of the tropic response. © 2016 Elsevier Ltd}, author = {Rakusová, Hana and Abbas, Mohamad and Han, Huibin and Song, Siyuan and Robert, Hélène and Friml, Jirí}, journal = {Current Biology}, number = {22}, pages = {3026 -- 3032}, publisher = {Cell Press}, title = {{Termination of shoot gravitropic responses by auxin feedback on PIN3 polarity}}, doi = {10.1016/j.cub.2016.08.067}, volume = {26}, year = {2016}, } @article{1221, abstract = {The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in plants. Since decades ago, it has been the prime receptor candidate for the plant hormone auxin with a plethora of described functions in auxin signaling and development. The developmental importance of ABP1 has recently been questioned by identification of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes under normal growth conditions. In this study, we examined the contradiction between the normal growth and development of the abp1 knock-outs and the strong morphological defects observed in three different ethanol-inducible abp1 knock-down mutants ( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out vs. abp1 knock-down crosses we show that the strong morphological defects that were believed to be the result of conditional down-regulation of ABP1 can be reproduced also in the absence of the functional ABP1 protein. This data suggests that the phenotypes in abp1 knock-down lines are due to the off-target effects and asks for further reflections on the biological function of ABP1 or alternative explanations for the missing phenotypic defects in the abp1 loss-of-function alleles.}, author = {Michalko, Jaroslav and Glanc, Matous and Perrot Rechenmann, Catherine and Friml, Jirí}, journal = {F1000 Research }, publisher = {F1000 Research}, title = {{Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein}}, doi = {10.12688/f1000research.7654.1}, volume = {5}, year = {2016}, } @article{1238, abstract = {The dynamic localization of endosomal compartments labeled with targeted fluorescent protein tags is routinely followed by time lapse fluorescence microscopy approaches and single particle tracking algorithms. In this way trajectories of individual endosomes can be mapped and linked to physiological processes as cell growth. However, other aspects of dynamic behavior including endosomal interactions are difficult to follow in this manner. Therefore, we characterized the localization and dynamic properties of early and late endosomes throughout the entire course of root hair formation by means of spinning disc time lapse imaging and post-acquisition automated multitracking and quantitative analysis. Our results show differential motile behavior of early and late endosomes and interactions of late endosomes that may be specified to particular root hair domains. Detailed data analysis revealed a particular transient interaction between late endosomes—termed herein as dancing-endosomes—which is not concluding to vesicular fusion. Endosomes preferentially located in the root hair tip interacted as dancing-endosomes and traveled short distances during this interaction. Finally, sizes of early and late endosomes were addressed by means of super-resolution structured illumination microscopy (SIM) to corroborate measurements on the spinning disc. This is a first study providing quantitative microscopic data on dynamic spatio-temporal interactions of endosomes during root hair tip growth.}, author = {Von Wangenheim, Daniel and Rosero, Amparo and Komis, George and Šamajová, Olga and Ovečka, Miroslav and Voigt, Boris and Šamaj, Jozef}, journal = {Frontiers in Plant Science}, number = {JAN2016}, publisher = {Frontiers Research Foundation}, title = {{Endosomal interactions during root hair growth}}, doi = {10.3389/fpls.2015.01262}, volume = {6}, year = {2016}, } @article{1247, abstract = {The shaping of organs in plants depends on the intercellular flow of the phytohormone auxin, of which the directional signaling is determined by the polar subcellular localization of PIN-FORMED (PIN) auxin transport proteins. Phosphorylation dynamics of PIN proteins are affected by the protein phosphatase 2A (PP2A) and the PINOID kinase, which act antagonistically to mediate their apical-basal polar delivery. Here, we identified the ROTUNDA3 (RON3) protein as a regulator of the PP2A phosphatase activity in Arabidopsis thaliana. The RON3 gene was map-based cloned starting from the ron3-1 leaf mutant and found to be a unique, plant-specific gene coding for a protein with high and dispersed proline content. The ron3-1 and ron3-2 mutant phenotypes [i.e., reduced apical dominance, primary root length, lateral root emergence, and growth; increased ectopic stages II, IV, and V lateral root primordia; decreased auxin maxima in indole-3-acetic acid (IAA)-treated root apical meristems; hypergravitropic root growth and response; increased IAA levels in shoot apices; and reduced auxin accumulation in root meristems] support a role for RON3 in auxin biology. The affinity-purified PP2A complex with RON3 as bait suggested that RON3 might act in PIN transporter trafficking. Indeed, pharmacological interference with vesicle trafficking processes revealed that single ron3-2 and double ron3-2 rcn1 mutants have altered PIN polarity and endocytosis in specific cells. Our data indicate that RON3 contributes to auxin-mediated development by playing a role in PIN recycling and polarity establishment through regulation of the PP2A complex activity.}, author = {Karampelias, Michael and Neyt, Pia and De Groeve, Steven and Aesaert, Stijn and Coussens, Griet and Rolčík, Jakub and Bruno, Leonardo and De Winne, Nancy and Van Minnebruggen, Annemie and Van Montagu, Marc and Ponce, Maria and Micol, José and Friml, Jirí and De Jaeger, Geert and Van Lijsebettens, Mieke}, journal = {PNAS}, number = {10}, pages = {2768 -- 2773}, publisher = {National Academy of Sciences}, title = {{ROTUNDA3 function in plant development by phosphatase 2A-mediated regulation of auxin transporter recycling}}, doi = {10.1073/pnas.1501343112}, volume = {113}, year = {2016}, } @article{1251, abstract = {Plant growth and architecture is regulated by the polar distribution of the hormone auxin. Polarity and flexibility of this process is provided by constant cycling of auxin transporter vesicles along actin filaments, coordinated by a positive auxinactin feedback loop. Both polar auxin transport and vesicle cycling are inhibited by synthetic auxin transport inhibitors, such as 1-Nnaphthylphthalamic acid (NPA), counteracting the effect of auxin; however, underlying targets and mechanisms are unclear. Using NMR, we map the NPA binding surface on the Arabidopsis thaliana ABCB chaperone TWISTED DWARF1 (TWD1).We identify ACTIN7 as a relevant, although likely indirect, TWD1 interactor, and show TWD1-dependent regulation of actin filament organization and dynamics and that TWD1 is required for NPA-mediated actin cytoskeleton remodeling. The TWD1-ACTIN7 axis controls plasma membrane presence of efflux transporters, and as a consequence act7 and twd1 share developmental and physiological phenotypes indicative of defects in auxin transport. These can be phenocopied by NPA treatment or by chemical actin (de)stabilization. We provide evidence that TWD1 determines downstreamlocations of auxin efflux transporters by adjusting actin filament debundling and dynamizing processes and mediating NPA action on the latter. This function appears to be evolutionary conserved since TWD1 expression in budding yeast alters actin polarization and cell polarity and provides NPA sensitivity.}, author = {Zhu, Jinsheng and Bailly, Aurélien and Zwiewka, Marta and Sovero, Valpuri and Di Donato, Martin and Ge, Pei and Oehri, Jacqueline and Aryal, Bibek and Hao, Pengchao and Linnert, Miriam and Burgardt, Noelia and Lücke, Christian and Weiwad, Matthias and Michel, Max and Weiergräber, Oliver and Pollmann, Stephan and Azzarello, Elisa and Mancuso, Stefano and Ferro, Noel and Fukao, Yoichiro and Hoffmann, Céline and Wedlich Söldner, Roland and Friml, Jirí and Thomas, Clément and Geisler, Markus}, journal = {Plant Cell}, number = {4}, pages = {930 -- 948}, publisher = {American Society of Plant Biologists}, title = {{TWISTED DWARF1 mediates the action of auxin transport inhibitors on actin cytoskeleton dynamics}}, doi = {10.1105/tpc.15.00726}, volume = {28}, 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{1277, abstract = {The Arabidopsis thaliana endogenous elicitor peptides (AtPeps) are released into the apoplast after cellular damage caused by pathogens or wounding to induce innate immunity by direct binding to the membrane-localized leucine-rich repeat receptor kinases, PEP RECEPTOR1 (PEPR1) and PEPR2. Although the PEPR-mediated signaling components and responses have been studied extensively, the contributions of the subcellular localization and dynamics of the active PEPRs remain largely unknown. We used live-cell imaging of the fluorescently labeled and bioactive pep1 to visualize the intracellular behavior of the PEPRs in the Arabidopsis root meristem. We found that AtPep1 decorated the plasma membrane (PM) in a receptor-dependent manner and cointernalized with PEPRs. Trafficking of the AtPep1-PEPR1 complexes to the vacuole required neither the trans-Golgi network/early endosome (TGN/EE)-localized vacuolar H+ -ATPase activity nor the function of the brefeldin A-sensitive ADP-ribosylation factor-guanine exchange factors (ARF-GEFs). In addition, AtPep1 and different TGN/EE markers colocalized only rarely, implying that the intracellular route of this receptor-ligand pair is largely independent of the TGN/EE. Inducible overexpression of the Arabidopsis clathrin coat disassembly factor, Auxilin2, which inhibits clathrin-mediated endocytosis (CME), impaired the AtPep1-PEPR1 internalization and compromised AtPep1-mediated responses. Our results show that clathrin function at the PM is required to induce plant defense responses, likely through CME of cell surface-located signaling components. }, author = {Ortiz Morea, Fausto and Savatin, Daniel and Dejonghe, Wim and Kumar, Rahul and Luo, Yu and Adamowski, Maciek and Van Begin, Jos and Dressano, Keini and De Oliveira, Guilherme and Zhao, Xiuyang and Lu, Qing and Madder, Annemieke and Friml, Jirí and De Moura, Daniel and Russinova, Eugenia}, journal = {PNAS}, number = {39}, pages = {11028 -- 11033}, publisher = {National Academy of Sciences}, title = {{Danger-associated peptide signaling in Arabidopsis requires clathrin}}, doi = {10.1073/pnas.1605588113}, volume = {113}, year = {2016}, } @article{1344, abstract = {Despite being composed of immobile cells, plants reorient along directional stimuli. The hormone auxin is redistributed in stimulated organs leading to differential growth and bending. Auxin application triggers rapid cell wall acidification and elongation of aerial organs of plants, but the molecular players mediating these effects are still controversial. Here we use genetically-encoded pH and auxin signaling sensors, pharmacological and genetic manipulations available for Arabidopsis etiolated hypocotyls to clarify how auxin is perceived and the downstream growth executed. We show that auxin-induced acidification occurs by local activation of H+-ATPases, which in the context of gravity response is restricted to the lower organ side. This auxin-stimulated acidification and growth require TIR1/AFB-Aux/IAA nuclear auxin perception. In addition, auxin-induced gene transcription and specifically SAUR proteins are crucial downstream mediators of this growth. Our study provides strong experimental support for the acid growth theory and clarified the contribution of the upstream auxin perception mechanisms.}, author = {Fendrych, Matyas and Leung, Jeffrey and Friml, Jirí}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{TIR1 AFB Aux IAA auxin perception mediates rapid cell wall acidification and growth of Arabidopsis hypocotyls}}, doi = {10.7554/eLife.19048}, volume = {5}, year = {2016}, } @article{1345, abstract = {The electrostatic charge at the inner surface of the plasma membrane is strongly negative in higher organisms. A new study shows that phosphatidylinositol-4-phosphate plays a critical role in establishing plasma membrane surface charge in Arabidopsis, which regulates the correct localization of signalling components.}, author = {Molnar, Gergely and Fendrych, Matyas and Friml, Jirí}, journal = {Nature Plants}, publisher = {Nature Publishing Group}, title = {{Plasma membrane: Negative attraction}}, doi = {10.1038/nplants.2016.102}, volume = {2}, year = {2016}, } @article{1372, abstract = {Redirection of intercellular auxin fluxes via relocalization of the PIN-FORMED 3 (PIN3) and PIN7 auxin efflux carriers has been suggested to be necessary for the root gravitropic response. Cytokinins have also been proposed to play a role in controlling root gravitropism, but conclusive evidence is lacking. We present a detailed study of the dynamics of root bending early after gravistimulation, which revealed a delayed gravitropic response in transgenic lines with depleted endogenous cytokinins (Pro35S:AtCKX) and cytokinin signaling mutants. Pro35S:AtCKX lines, as well as a cytokinin receptor mutant ahk3, showed aberrations in the auxin response distribution in columella cells consistent with defects in the auxin transport machinery. Using in vivo real-time imaging of PIN3-GFP and PIN7-GFP in AtCKX3 overexpression and ahk3 backgrounds, we observed wild-type-like relocalization of PIN proteins in the columella early after gravistimulation, with gravity-induced relocalization of PIN7 faster than that of PIN3. Nonetheless, the cellular distribution of PIN3 and PIN7 and expression of PIN7 and the auxin influx carrier AUX1 was affected in AtCKX overexpression lines. Based on the retained cytokinin sensitivity in pin3 pin4 pin7 mutant, we propose the AUX1-mediated auxin transport rather than columella-located PIN proteins as a target of endogenous cytokinins in the control of root gravitropism.}, author = {Pernisová, Markéta and Prat, Tomas and Grones, Peter and Haruštiaková, Danka and Matonohova, Martina and Spíchal, Lukáš and Nodzyński, Tomasz and Friml, Jirí and Hejátko, Jan}, journal = {New Phytologist}, number = {2}, pages = {497 -- 509}, publisher = {Wiley-Blackwell}, title = {{Cytokinins influence root gravitropism via differential regulation of auxin transporter expression and localization in Arabidopsis}}, doi = {10.1111/nph.14049}, volume = {212}, year = {2016}, } @article{1410, abstract = {The pollen grains arise after meiosis of pollen mother cells within the anthers. A series of complex structural changes follows, generating mature pollen grains capable of performing the double fertilization of the female megasporophyte. Several signaling molecules, including hormones and lipids, have been involved in the regulation and appropriate control of pollen development. Phosphatidylinositol 4-phophate 5-kinases (PIP5K), which catalyze the biosynthesis of the phosphoinositide PtdIns(4,5)P2, are important for tip polar growth of root hairs and pollen tubes, embryo development, vegetative plant growth, and responses to the environment. Here, we report a role of PIP5Ks during microgametogenesis. PIP5K1 and PIP5K2 are expressed during early stages of pollen development and their transcriptional activity respond to auxin in pollen grains. Early male gametophytic lethality to certain grade was observed in both pip5k1-/- and pip5k2-/- single mutants. The number of pip5k mutant alleles is directly related to the frequency of aborted pollen grains suggesting the two genes are involved in the same function. Indeed PIP5K1 and PIP5K2 are functionally redundant since homozygous double mutants did not render viable pollen grains. The loss of function of PIP5K1 and PIP5K2results in defects in vacuole morphology in pollen at the later stages and epidermal root cells. Our results show that PIP5K1, PIP5K2 and phosphoinositide signaling are important cues for early developmental stages and vacuole formation during microgametogenesis.}, author = {Ugalde, José and Rodríguez Furlán, Cecilia and De Rycke, Riet and Norambuena, Lorena and Friml, Jirí and León, Gabriel and Tejos, Ricardo}, journal = {Plant Science}, pages = {10 -- 19}, publisher = {Elsevier}, title = {{Phosphatidylinositol 4-phosphate 5-kinases 1 and 2 are involved in the regulation of vacuole morphology during Arabidopsis thaliana pollen development}}, doi = {10.1016/j.plantsci.2016.05.014}, volume = {250}, year = {2016}, } @article{1417, abstract = {Plant development mediated by the phytohormone auxin depends on tightly controlled cellular auxin levels at its target tissue that are largely established by intercellular and intracellular auxin transport mediated by PIN auxin transporters. Among the eight members of the Arabidopsis PIN family, PIN6 is the least characterized candidate. In this study we generated functional, fluorescent protein-tagged PIN6 proteins and performed comprehensive analysis of their subcellular localization and also performed a detailed functional characterization of PIN6 and its developmental roles. The localization study of PIN6 revealed a dual localization at the plasma membrane (PM) and endoplasmic reticulum (ER). Transport and metabolic profiling assays in cultured cells and Arabidopsis strongly suggest that PIN6 mediates both auxin transport across the PM and intracellular auxin homeostasis, including the regulation of free auxin and auxin conjugates levels. As evidenced by the loss- and gain-of-function analysis, the complex function of PIN6 in auxin transport and homeostasis is required for auxin distribution during lateral and adventitious root organogenesis and for progression of these developmental processes. These results illustrate a unique position of PIN6 within the family of PIN auxin transporters and further add complexity to the developmentally crucial process of auxin transport.}, author = {Simon, Sibu and Skůpa, Petr and Viaene, Tom and Zwiewka, Marta and Tejos, Ricardo and Klíma, Petr and Čarná, Mária and Rolčík, Jakub and De Rycke, Riet and Moreno, Ignacio and Dobrev, Petre and Orellana, Ariel and Zažímalová, Eva and Friml, Jirí}, journal = {New Phytologist}, number = {1}, pages = {65 -- 74}, publisher = {Wiley-Blackwell}, title = {{PIN6 auxin transporter at endoplasmic reticulum and plasma membrane mediates auxin homeostasis and organogenesis in Arabidopsis}}, doi = {10.1111/nph.14019}, volume = {211}, year = {2016}, } @article{1482, abstract = {Plants have the ability to continously generate new organs by maintaining populations of stem cells throught their lives. The shoot apical meristem (SAM) provides a stable environment for the maintenance of stem cells. All cells inside the SAM divide, yet boundaries and patterns are maintained. Experimental evidence indicates that patterning is independent of cell lineage, thus a dynamic self-regulatory mechanism is required. A pivotal role in the organization of the SAM is played by the WUSCHEL gene (WUS). An important question in this regard is that how WUS expression is positioned in the SAM via a cell-lineage independent signaling mechanism. In this study we demonstrate via mathematical modeling that a combination of an inhibitor of the Cytokinin (CK) receptor, Arabidopsis histidine kinase 4 (AHK4) and two morphogens originating from the top cell layer, can plausibly account for the cell lineage-independent centering of WUS expression within SAM. Furthermore, our laser ablation and microsurgical experiments support the hypothesis that patterning in SAM occurs at the level of CK reception and signaling. The model suggests that the interplay between CK signaling, WUS/CLV feedback loop and boundary signals can account for positioning of the WUS expression, and provides directions for further experimental investigation.}, author = {Adibi, Milad and Yoshida, Saiko and Weijers, Dolf and Fleck, Christian}, journal = {PLoS One}, number = {2}, publisher = {Public Library of Science}, title = {{Centering the organizing center in the Arabidopsis thaliana shoot apical meristem by a combination of cytokinin signaling and self-organization}}, doi = {10.1371/journal.pone.0147830}, volume = {11}, year = {2016}, } @article{1484, author = {Chen, Xu and Wu, Shuang and Liu, Zengyu and Friml, Jiřĺ}, journal = {Trends in Cell Biology}, number = {6}, pages = {409 -- 419}, publisher = {Cell Press}, title = {{Environmental and endogenous control of cortical microtubule orientation}}, doi = {10.1016/j.tcb.2016.02.003}, volume = {26}, year = {2016}, } @article{1641, abstract = {The plant hormone auxin (indole-3-acetic acid) is a major regulator of plant growth and development including embryo and root patterning, lateral organ formation and growth responses to environmental stimuli. Auxin is directionally transported from cell to cell by the action of specific auxin influx [AUXIN-RESISTANT1 (AUX1)] and efflux [PIN-FORMED (PIN)] transport regulators, whose polar, subcellular localizations are aligned with the direction of the auxin flow. Auxin itself regulates its own transport by modulation of the expression and subcellular localization of the auxin transporters. Increased auxin levels promote the transcription of PIN2 and AUX1 genes as well as stabilize PIN proteins at the plasma membrane, whereas prolonged auxin exposure increases the turnover of PIN proteins and their degradation in the vacuole. In this study, we applied a forward genetic approach, to identify molecular components playing a role in the auxin-mediated degradation. We generated EMS-mutagenized Arabidopsis PIN2::PIN2:GFP, AUX1::AUX1:YFP eir1aux1 populations and designed a screen for mutants with persistently strong fluorescent signals of the tagged PIN2 and AUX1 after prolonged treatment with the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D). This approach yielded novel auxin degradation mutants defective in trafficking and degradation of PIN2 and AUX1 proteins and established a role for auxin-mediated degradation in plant development.}, author = {Zemová, Radka and Zwiewka, Marta and Bielach, Agnieszka and Robert, Hélène and Friml, Jirí}, journal = {Journal of Plant Growth Regulation}, number = {2}, pages = {465 -- 476}, publisher = {Springer}, title = {{A forward genetic screen for new regulators of auxin mediated degradation of auxin transport proteins in Arabidopsis thaliana}}, doi = {10.1007/s00344-015-9553-2}, volume = {35}, year = {2016}, } @article{1346, abstract = {ATP production requires the establishment of an electrochemical proton gradient across the inner mitochondrial membrane. Mitochondrial uncouplers dissipate this proton gradient and disrupt numerous cellular processes, including vesicular trafficking, mainly through energy depletion. Here we show that Endosidin9 (ES9), a novel mitochondrial uncoupler, is a potent inhibitor of clathrin-mediated endocytosis (CME) in different systems and that ES9 induces inhibition of CME not because of its effect on cellular ATP, but rather due to its protonophore activity that leads to cytoplasm acidification. We show that the known tyrosine kinase inhibitor tyrphostinA23, which is routinely used to block CME, displays similar properties, thus questioning its use as a specific inhibitor of cargo recognition by the AP-2 adaptor complex via tyrosine motif-based endocytosis signals. Furthermore, we show that cytoplasm acidification dramatically affects the dynamics and recruitment of clathrin and associated adaptors, and leads to reduction of phosphatidylinositol 4,5-biphosphate from the plasma membrane.}, author = {Dejonghe, Wim and Kuenen, Sabine and Mylle, Evelien and Vasileva, Mina K and Keech, Olivier and Viotti, Corrado and Swerts, Jef and Fendrych, Matyas and Ortiz Morea, Fausto and Mishev, Kiril and Delang, Simon and Scholl, Stefan and Zarza, Xavier and Heilmann, Mareike and Kourelis, Jiorgos and Kasprowicz, Jaroslaw and Nguyen, Le and Drozdzecki, Andrzej and Van Houtte, Isabelle and Szatmári, Anna and Majda, Mateusz and Baisa, Gary and Bednarek, Sebastian and Robert, Stéphanie and Audenaert, Dominique and Testerink, Christa and Munnik, Teun and Van Damme, Daniël and Heilmann, Ingo and Schumacher, Karin and Winne, Johan and Friml, Jirí and Verstreken, Patrik and Russinova, Eugenia}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification}}, doi = {10.1038/ncomms11710}, volume = {7}, year = {2016}, } @article{510, abstract = {The CLE (CLAVATA3/Embryo Surrounding Region-related) peptides are small secreted signaling peptides that are primarily involved in the regulation of stem cell homeostasis in different plant meristems. Particularly, the characterization of the CLE41-PXY/TDR signaling pathway has greatly advanced our understanding on the potential roles of CLE peptides in vascular development and wood formation. Nevertheless, our knowledge on this gene family in a tree species is limited. In a recent study, we reported on a systematically investigation of the CLE gene family in Populus trichocarpa . The potential roles of PtCLE genes were studied by comparative analysis and transcriptional pro fi ling. Among fi fty PtCLE members, many PtCLE proteins share identical CLE motifs or contain the same CLE motif as that of AtCLEs, while PtCLE genes exhibited either comparable or distinct expression patterns comparing to their Arabidopsis counterparts. These fi ndings indicate the existence of both functional conservation and functional divergence between PtCLEs and their AtCLE orthologues. Our results provide valuable resources for future functional investigations of these critical signaling molecules in woody plants. }, author = {Liu, Zhijun and Yang, Nan and Lv, Yanting and Pan, Lixia and Lv, Shuo and Han, Huibin and Wang, Guodong}, journal = {Plant Signaling & Behavior}, number = {6}, publisher = {Taylor & Francis}, title = {{The CLE gene family in Populus trichocarpa}}, doi = {10.1080/15592324.2016.1191734}, volume = {11}, year = {2016}, } @article{1274, abstract = {Synchronized tissue polarization during regeneration or de novo vascular tissue formation is a plant-specific example of intercellular communication and coordinated development. According to the canalization hypothesis, the plant hormone auxin serves as polarizing signal that mediates directional channel formation underlying the spatio-temporal vasculature patterning. A necessary part of canalization is a positive feedback between auxin signaling and polarity of the intercellular auxin flow. The cellular and molecular mechanisms of this process are still poorly understood, not the least, because of a lack of a suitable model system. We show that the main genetic model plant, Arabidopsis (Arabidopsis thaliana) can be used to study the canalization during vascular cambium regeneration and new vasculature formation. We monitored localized auxin responses, directional auxin-transport channels formation, and establishment of new vascular cambium polarity during regenerative processes after stem wounding. The increased auxin response above and around the wound preceded the formation of PIN1 auxin transporter-marked channels from the primarily homogenous tissue and the transient, gradual changes in PIN1 localization preceded the polarity of newly formed vascular tissue. Thus, Arabidopsis is a useful model for studies of coordinated tissue polarization and vasculature formation after wounding allowing for genetic and mechanistic dissection of the canalization hypothesis.}, author = {Mazur, Ewa and Benková, Eva and Friml, Jirí}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Vascular cambium regeneration and vessel formation in wounded inflorescence stems of Arabidopsis}}, doi = {10.1038/srep33754}, volume = {6}, year = {2016}, } @article{1383, abstract = {In plants, vacuolar H+-ATPase (V-ATPase) activity acidifies both the trans-Golgi network/early endosome (TGN/EE) and the vacuole. This dual V-ATPase function has impeded our understanding of how the pH homeostasis within the plant TGN/EE controls exo- and endocytosis. Here, we show that the weak V-ATPase mutant deetiolated3 (det3) displayed a pH increase in the TGN/EE, but not in the vacuole, strongly impairing secretion and recycling of the brassinosteroid receptor and the cellulose synthase complexes to the plasma membrane, in contrast to mutants lacking tonoplast-localized V-ATPase activity only. The brassinosteroid insensitivity and the cellulose deficiency defects in det3 were tightly correlated with reduced Golgi and TGN/EE motility. Thus, our results provide strong evidence that acidification of the TGN/EE, but not of the vacuole, is indispensable for functional secretion and recycling in plants.}, author = {Yu, Luo and Scholl, Stefan and Doering, Anett and Yi, Zhang and Irani, Niloufer and Di Rubbo, Simone and Neumetzler, Lutz and Krishnamoorthy, Praveen and Van Houtte, Isabelle and Mylle, Evelien and Bischoff, Volker and Vernhettes, Samantha and Winne, Johan and Friml, Jirí and Stierhof, York and Schumacher, Karin and Persson, Staffan and Russinova, Eugenia}, journal = {Nature Plants}, number = {7}, publisher = {Nature Publishing Group}, title = {{V-ATPase activity in the TGN/EE is required for exocytosis and recycling in Arabidopsis}}, doi = {10.1038/nplants.2015.94}, volume = {1}, year = {2015}, } @article{1532, abstract = {Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels.}, author = {Yang, Huaiyu and Von Der Fecht Bartenbach, Jenny and Friml, Jirí and Lohmann, Jan and Neuhäuser, Benjamin and Ludewig, Uwe}, issn = {1445-4408}, journal = {Functional Plant Biology}, number = {3}, pages = {239 -- 251}, publisher = {CSIRO}, title = {{Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source}}, doi = {10.1071/FP14171}, volume = {42}, year = {2015}, } @article{1534, abstract = {PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.}, author = {Wang, Hongzhe and Yang, Kezhen and Zou, Junjie and Zhu, Lingling and Xie, Zidian and Morita, Miyoterao and Tasaka, Masao and Friml, Jirí and Grotewold, Erich and Beeckman, Tom and Vanneste, Steffen and Sack, Fred and Le, Jie}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism}}, doi = {10.1038/ncomms9822}, volume = {6}, year = {2015}, } @article{1536, abstract = {Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil.}, author = {Sasse, Joëlle and Simon, Sibu and Gübeli, Christian and Liu, Guowei and Cheng, Xi and Friml, Jirí and Bouwmeester, Harro and Martinoia, Enrico and Borghi, Lorenzo}, journal = {Current Biology}, number = {5}, pages = {647 -- 655}, publisher = {Cell Press}, title = {{Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport}}, doi = {10.1016/j.cub.2015.01.015}, volume = {25}, year = {2015}, } @article{1543, abstract = {A plethora of diverse programmed cell death (PCD) processes has been described in living organisms. In animals and plants, different forms of PCD play crucial roles in development, immunity, and responses to the environment. While the molecular control of some animal PCD forms such as apoptosis is known in great detail, we still know comparatively little about the regulation of the diverse types of plant PCD. In part, this deficiency in molecular understanding is caused by the lack of reliable reporters to detect PCD processes. Here, we addressed this issue by using a combination of bioinformatics approaches to identify commonly regulated genes during diverse plant PCD processes in Arabidopsis (Arabidopsis thaliana). Our results indicate that the transcriptional signatures of developmentally controlled cell death are largely distinct from the ones associated with environmentally induced cell death. Moreover, different cases of developmental PCD share a set of cell death-associated genes. Most of these genes are evolutionary conserved within the green plant lineage, arguing for an evolutionary conserved core machinery of developmental PCD. Based on this information, we established an array of specific promoter-reporter lines for developmental PCD in Arabidopsis. These PCD indicators represent a powerful resource that can be used in addition to established morphological and biochemical methods to detect and analyze PCD processes in vivo and in planta.}, author = {Olvera Carrillo, Yadira and Van Bel, Michiel and Van Hautegem, Tom and Fendrych, Matyas and Huysmans, Marlies and Šimášková, Mária and Van Durme, Matthias and Buscaill, Pierre and Rivas, Susana and Coll, Núria and Coppens, Frederik and Maere, Steven and Nowack, Moritz}, journal = {Plant Physiology}, number = {4}, pages = {2684 -- 2699}, publisher = {American Society of Plant Biologists}, title = {{A conserved core of programmed cell death indicator genes discriminates developmentally and environmentally induced programmed cell death in plants}}, doi = {10.1104/pp.15.00769}, volume = {169}, year = {2015}, } @article{1556, abstract = {The elongator complex subunit 2 (ELP2) protein, one subunit of an evolutionarily conserved histone acetyltransferase complex, has been shown to participate in leaf patterning, plant immune and abiotic stress responses in Arabidopsis thaliana. Here, its role in root development was explored. Compared to the wild type, the elp2 mutant exhibited an accelerated differentiation of its root stem cells and cell division was more active in its quiescent centre (QC). The key transcription factors responsible for maintaining root stem cell and QC identity, such as AP2 transcription factors PLT1 (PLETHORA1) and PLT2 (PLETHORA2), GRAS transcription factors such as SCR (SCARECROW) and SHR (SHORT ROOT) and WUSCHEL-RELATED HOMEOBOX5 transcription factor WOX5, were all strongly down-regulated in the mutant. On the other hand, expression of the G2/M transition activator CYCB1 was substantially induced in elp2. The auxin efflux transporters PIN1 and PIN2 showed decreased protein levels and PIN1 also displayed mild polarity alterations in elp2, which resulted in a reduced auxin content in the root tip. Either the acetylation or methylation level of each of these genes differed between the mutant and the wild type, suggesting that the ELP2 regulation of root development involves the epigenetic modification of a range of transcription factors and other developmental regulators.}, author = {Jia, Yuebin and Tian, Huiyu and Li, Hongjiang and Yu, Qianqian and Wang, Lei and Friml, Jirí and Ding, Zhaojun}, journal = {Journal of Experimental Botany}, number = {15}, pages = {4631 -- 4642}, publisher = {Oxford University Press}, title = {{The Arabidopsis thaliana elongator complex subunit 2 epigenetically affects root development}}, doi = {10.1093/jxb/erv230}, volume = {66}, year = {2015}, } @article{1558, abstract = {CyclophilinAis a conserved peptidyl-prolyl cis-trans isomerase (PPIase) best known as the cellular receptor of the immunosuppressant cyclosporine A. Despite significant effort, evidence of developmental functions of cyclophilin A in non-plant systems has remained obscure. Mutations in a tomato (Solanum lycopersicum) cyclophilin A ortholog, DIAGEOTROPICA (DGT), have been shown to abolish the organogenesis of lateral roots; however, a mechanistic explanation of the phenotype is lacking. Here, we show that the dgt mutant lacks auxin maxima relevant to priming and specification of lateral root founder cells. DGT is expressed in shoot and root, and localizes to both the nucleus and cytoplasm during lateral root organogenesis. Mutation of ENTIRE/ IAA9, a member of the auxin-responsive Aux/IAA protein family of transcriptional repressors, partially restores the inability of dgt to initiate lateral root primordia but not the primordia outgrowth. By comparison, grafting of a wild-type scion restores the process of lateral root formation, consistent with participation of a mobile signal. Antibodies do not detect movement of the DGT protein into the dgt rootstock; however, experiments with radiolabeled auxin and an auxin-specific microelectrode demonstrate abnormal auxin fluxes. Functional studies of DGT in heterologous yeast and tobacco-leaf auxin-transport systems demonstrate that DGT negatively regulates PIN-FORMED (PIN) auxin efflux transporters by affecting their plasma membrane localization. Studies in tomato support complex effects of the dgt mutation on PIN expression level, expression domain and plasma membrane localization. Our data demonstrate that DGT regulates auxin transport in lateral root formation.}, author = {Ivanchenko, Maria and Zhu, Jinsheng and Wang, Bangjun and Medvecka, Eva and Du, Yunlong and Azzarello, Elisa and Mancuso, Stefano and Megraw, Molly and Filichkin, Sergei and Dubrovsky, Joseph and Friml, Jirí and Geisler, Markus}, journal = {Development}, number = {4}, pages = {712 -- 721}, publisher = {Company of Biologists}, title = {{The cyclophilin a DIAGEOTROPICA gene affects auxin transport in both root and shoot to control lateral root formation}}, doi = {10.1242/dev.113225}, volume = {142}, year = {2015}, } @article{1554, abstract = {The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set of fluorescent reporters that allow sensitive and semiquantitative readout of auxin responses at cellular resolution in Arabidopsis thaliana. These generic tools are suitable for any transformable plant species.}, author = {Liao, Cheyang and Smet, Wouter and Brunoud, Géraldine and Yoshida, Saiko and Vernoux, Teva and Weijers, Dolf}, journal = {Nature Methods}, number = {3}, pages = {207 -- 210}, publisher = {Nature Publishing Group}, title = {{Reporters for sensitive and quantitative measurement of auxin response}}, doi = {10.1038/nmeth.3279}, volume = {12}, year = {2015}, } @article{1562, abstract = {The plant hormone auxin is a key regulator of plant growth and development. Auxin levels are sensed and interpreted by distinct receptor systems that activate a broad range of cellular responses. The Auxin-Binding Protein1 (ABP1) that has been identified based on its ability to bind auxin with high affinity is a prime candidate for the extracellular receptor responsible for mediating a range of auxin effects, in particular, the fast non-transcriptional ones. Contradictory genetic studies suggested prominent or no importance of ABP1 in many developmental processes. However, how crucial the role of auxin binding to ABP1 is for its functions has not been addressed. Here, we show that the auxin-binding pocket of ABP1 is essential for its gain-of-function cellular and developmental roles. In total, 16 different abp1 mutants were prepared that possessed substitutions in the metal core or in the hydrophobic amino acids of the auxin-binding pocket as well as neutral mutations. Their analysis revealed that an intact auxin-binding pocket is a prerequisite for ABP1 to activate downstream components of the ABP1 signalling pathway, such as Rho of Plants (ROPs) and to mediate the clathrin association with membranes for endocytosis regulation. In planta analyses demonstrated the importance of the auxin binding pocket for all known ABP1-mediated postembryonic developmental processes, including morphology of leaf epidermal cells, root growth and root meristem activity, and vascular tissue differentiation. Taken together, these findings suggest that auxin binding to ABP1 is central to its function, supporting the role of ABP1 as auxin receptor.}, author = {Grones, Peter and Chen, Xu and Simon, Sibu and Kaufmann, Walter and De Rycke, Riet and Nodzyński, Tomasz and Zažímalová, Eva and Friml, Jirí}, journal = {Journal of Experimental Botany}, number = {16}, pages = {5055 -- 5065}, publisher = {Oxford University Press}, title = {{Auxin-binding pocket of ABP1 is crucial for its gain-of-function cellular and developmental roles}}, doi = {10.1093/jxb/erv177}, volume = {66}, year = {2015}, } @article{1574, abstract = {Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level.}, author = {Chen, Qian and Liu, Yang and Maere, Steven and Lee, Eunkyoung and Van Isterdael, Gert and Xie, Zidian and Xuan, Wei and Lucas, Jessica and Vassileva, Valya and Kitakura, Saeko and Marhavy, Peter and Wabnik, Krzysztof T and Geldner, Niko and Benková, Eva and Le, Jie and Fukaki, Hidehiro and Grotewold, Erich and Li, Chuanyou and Friml, Jirí and Sack, Fred and Beeckman, Tom and Vanneste, Steffen}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development}}, doi = {10.1038/ncomms9821}, volume = {6}, year = {2015}, } @article{1569, abstract = {Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development.}, author = {Doyle, Siamsa and Haegera, Ash and Vain, Thomas and Rigala, Adeline and Viotti, Corrado and Łangowskaa, Małgorzata and Maa, Qian and Friml, Jirí and Raikhel, Natasha and Hickse, Glenn and Robert, Stéphanie}, journal = {PNAS}, number = {7}, pages = {E806 -- E815}, publisher = {National Academy of Sciences}, title = {{An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana}}, doi = {10.1073/pnas.1424856112}, volume = {112}, year = {2015}, } @article{1640, abstract = {Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.}, author = {Šimášková, Mária and O'Brien, José and Khan-Djamei, Mamoona and Van Noorden, Giel and Ötvös, Krisztina and Vieten, Anne and De Clercq, Inge and Van Haperen, Johanna and Cuesta, Candela and Hoyerová, Klára and Vanneste, Steffen and Marhavy, Peter and Wabnik, Krzysztof T and Van Breusegem, Frank and Nowack, Moritz and Murphy, Angus and Friml, Jiřĺ and Weijers, Dolf and Beeckman, Tom and Benková, Eva}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Cytokinin response factors regulate PIN-FORMED auxin transporters}}, doi = {10.1038/ncomms9717}, volume = {6}, year = {2015}, } @article{1819, abstract = {The sessile life style of plants creates the need to deal with an often adverse environment, in which water availability can change on a daily basis, challenging the cellular physiology and integrity. Changes in osmotic conditions disrupt the equilibrium of the plasma membrane: hypoosmotic conditions increase and hyperosmotic environment decrease the cell volume. Here, we show that short-term extracellular osmotic treatments are closely followed by a shift in the balance between endocytosis and exocytosis in root meristem cells. Acute hyperosmotic treatments (ionic and nonionic) enhance clathrin-mediated endocytosis simultaneously attenuating exocytosis, whereas hypoosmotic treatments have the opposite effects. In addition to clathrin recruitment to the plasma membrane, components of early endocytic trafficking are essential during hyperosmotic stress responses. Consequently, growth of seedlings defective in elements of clathrin or early endocytic machinery is more sensitive to hyperosmotic treatments. We also found that the endocytotic response to a change of osmotic status in the environment is dominant over the presumably evolutionary more recent regulatory effect of plant hormones, such as auxin. These results imply that osmotic perturbation influences the balance between endocytosis and exocytosis acting through clathrin-mediated endocytosis. We propose that tension on the plasma membrane determines the addition or removal of membranes at the cell surface, thus preserving cell integrity.}, author = {Zwiewka, Marta and Nodzyński, Tomasz and Robert, Stéphanie and Vanneste, Steffen and Friml, Jiřĺ}, journal = {Molecular Plant}, number = {8}, pages = {1175 -- 1187}, publisher = {Elsevier}, title = {{Osmotic stress modulates the balance between exocytosis and clathrin mediated endocytosis in Arabidopsis thaliana}}, doi = {10.1016/j.molp.2015.03.007}, volume = {8}, year = {2015}, } @article{1849, abstract = {Cell polarity is a fundamental property of pro- and eukaryotic cells. It is necessary for coordination of cell division, cell morphogenesis and signaling processes. How polarity is generated and maintained is a complex issue governed by interconnected feed-back regulations between small GTPase signaling and membrane tension-based signaling that controls membrane trafficking, and cytoskeleton organization and dynamics. Here, we will review the potential role for calcium as a crucial signal that connects and coordinates the respective processes during polarization processes in plants. This article is part of a Special Issue entitled: 13th European Symposium on Calcium.}, author = {Himschoot, Ellie and Beeckman, Tom and Friml, Jiřĺ and Vanneste, Steffen}, journal = {Biochimica et Biophysica Acta - Molecular Cell Research}, number = {9}, pages = {2168 -- 2172}, publisher = {Elsevier}, title = {{Calcium is an organizer of cell polarity in plants}}, doi = {10.1016/j.bbamcr.2015.02.017}, volume = {1853}, year = {2015}, } @article{1847, author = {Grones, Peter and Friml, Jiřĺ}, journal = {Molecular Plant}, number = {3}, pages = {356 -- 358}, publisher = {Elsevier}, title = {{ABP1: Finally docking}}, doi = {10.1016/j.molp.2014.12.013}, volume = {8}, year = {2015}, } @article{1865, abstract = {The plant hormone auxin and its directional transport are known to play a crucial role in defining the embryonic axis and subsequent development of the body plan. Although the role of PIN auxin efflux transporters has been clearly assigned during embryonic shoot and root specification, the role of the auxin influx carriers AUX1 and LIKE-AUX1 (LAX) proteins is not well established. Here, we used chemical and genetic tools on Brassica napus microspore-derived embryos and Arabidopsis thaliana zygotic embryos, and demonstrate that AUX1, LAX1 and LAX2 are required for both shoot and root pole formation, in concert with PIN efflux carriers. Furthermore, we uncovered a positive-feedback loop betweenMONOPTEROS(ARF5)-dependent auxin signalling and auxin transport. ThisMONOPTEROSdependent transcriptional regulation of auxin influx (AUX1, LAX1 and LAX2) and auxin efflux (PIN1 and PIN4) carriers by MONOPTEROS helps to maintain proper auxin transport to the root tip. These results indicate that auxin-dependent cell specification during embryo development requires balanced auxin transport involving both influx and efflux mechanisms, and that this transport is maintained by a positive transcriptional feedback on auxin signalling.}, author = {Robert, Hélène and Grunewald, Wim and Sauer, Michael and Cannoot, Bernard and Soriano, Mercedes and Swarup, Ranjan and Weijers, Dolf and Bennett, Malcolm and Boutilier, Kim and Friml, Jirí}, journal = {Development}, number = {4}, pages = {702 -- 711}, publisher = {Company of Biologists}, title = {{Plant embryogenesis requires AUX/LAX-mediated auxin influx}}, doi = {10.1242/dev.115832}, volume = {142}, year = {2015}, } @article{1871, abstract = {The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction.}, author = {Grones, Peter and Friml, Jirí}, journal = {Journal of Cell Science}, number = {1}, pages = {1 -- 7}, publisher = {Company of Biologists}, title = {{Auxin transporters and binding proteins at a glance}}, doi = {10.1242/jcs.159418}, volume = {128}, year = {2015}, } @article{1879, abstract = {When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions.}, author = {Kremer, A and Lippens, Stefaan and Bartunkova, Sonia and Asselbergh, Bob and Blanpain, Cendric and Fendrych, Matyas and Goossens, A and Holt, Matthew and Janssens, Sophie and Krols, Michiel and Larsimont, Jean and Mc Guire, Conor and Nowack, Moritz and Saelens, Xavier and Schertel, Andreas and Schepens, B and Slezak, M and Timmerman, Vincent and Theunis, Clara and Van Brempt, Ronald and Visser, Y and Guérin, Christophe}, journal = {Journal of Microscopy}, number = {2}, pages = {80 -- 96}, publisher = {Wiley-Blackwell}, title = {{Developing 3D SEM in a broad biological context}}, doi = {10.1111/jmi.12211}, volume = {259}, year = {2015}, } @article{1878, abstract = {Petrocoptis is a small genus of chasmophytic plants endemic to the Iberian Peninsula, with some localized populations in the French Pyrenees. Within the genus, a dozen species have been recognized based on morphological diversity, most of them with limited distribution area, in small populations and frequently with potential threats to their survival. To date, however, a molecular evaluation of the current systematic treatments has not been carried out. The aim of the present study is to infer phylogenetic relationships among its subordinate taxa by using plastidial rps16 intron and nuclear internal transcribed spacer (ITS) DNA sequences; and evaluate the phylogenetic placement of the genus Petrocoptis within the family Caryophyllaceae. The monophyly of Petrocoptis is supported by both ITS and rps16 intron sequence analyses. Furthermore, time estimates using BEAST analyses indicate a Middle to Late Miocene diversification (10.59 Myr, 6.44–15.26 Myr highest posterior densities [HPD], for ITS; 14.30 Myr, 8.61–21.00 Myr HPD, for rps16 intron).}, author = {Cires Rodriguez, Eduardo and Prieto, José}, journal = {Journal of Plant Research}, number = {2}, pages = {223 -- 238}, publisher = {Springer}, title = {{Phylogenetic relationships of Petrocoptis A. Braun ex Endl. (Caryophyllaceae), a discussed genus from the Iberian Peninsula}}, doi = {10.1007/s10265-014-0691-6}, volume = {128}, year = {2015}, } @article{1944, author = {Rakusová, Hana and Fendrych, Matyas and Friml, Jirí}, journal = {Current Opinion in Plant Biology}, number = {2}, pages = {116 -- 123}, publisher = {Elsevier}, title = {{Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants}}, doi = {10.1016/j.pbi.2014.12.002}, volume = {23}, year = {2015}, } @article{532, abstract = {Ethylene is a gaseous phytohormone that plays vital roles in plant growth and development. Previous studies uncovered EIN2 as an essential signal transducer linking ethylene perception on ER to transcriptional regulation in the nucleus through a “cleave and shuttle” model. In this study, we report another mechanism of EIN2-mediated ethylene signaling, whereby EIN2 imposes the translational repression of EBF1 and EBF2 mRNA. We find that the EBF1/2 3′ UTRs mediate EIN2-directed translational repression and identify multiple poly-uridylates (PolyU) motifs as functional cis elements of 3′ UTRs. Furthermore, we demonstrate that ethylene induces EIN2 to associate with 3′ UTRs and target EBF1/2 mRNA to cytoplasmic processing-body (P-body) through interacting with multiple P-body factors, including EIN5 and PABs. Our study illustrates translational regulation as a key step in ethylene signaling and presents mRNA 3′ UTR functioning as a “signal transducer” to sense and relay cellular signaling in plants.}, author = {Li, Wenyang and Ma, Mengdi and Feng, Ying and Li, Hongjiang and Wang, Yichuan and Ma, Yutong and Li, Mingzhe and An, Fengying and Guo, Hongwei}, journal = {Cell}, number = {3}, pages = {670 -- 683}, publisher = {Cell Press}, title = {{EIN2-directed translational regulation of ethylene signaling in arabidopsis}}, doi = {10.1016/j.cell.2015.09.037}, volume = {163}, year = {2015}, } @article{1591, abstract = {Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well.}, author = {Adamowski, Maciek and Friml, Jirí}, journal = {Plant Cell}, number = {1}, pages = {20 -- 32}, publisher = {American Society of Plant Biologists}, title = {{PIN-dependent auxin transport: Action, regulation, and evolution}}, doi = {10.1105/tpc.114.134874}, volume = {27}, year = {2015}, } @article{1509, abstract = {The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.}, author = {Michalko, Jaroslav and Dravecka, Marta and Bollenbach, Tobias and Friml, Jirí}, journal = {F1000 Research }, publisher = {F1000 Research}, title = {{Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene}}, doi = {10.12688/f1000research.7143.1}, volume = {4}, year = {2015}, } @inbook{1806, abstract = {The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants.}, author = {Baster, Pawel and Friml, Jiří}, booktitle = {Auxin and Its Role in Plant Development}, editor = {Zažímalová, Eva and Petrášek, Jan and Benková, Eva}, pages = {143 -- 170}, publisher = {Springer}, title = {{Auxin on the road navigated by cellular PIN polarity}}, doi = {10.1007/978-3-7091-1526-8_8}, year = {2014}, } @article{1852, abstract = {To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner.}, author = {Sassi, Massimiliano and Ali, Olivier and Boudon, Frédéric and Cloarec, Gladys and Abad, Ursula and Cellier, Coralie and Chen, Xu and Gilles, Benjamin and Milani, Pascale and Friml, Jirí and Vernoux, Teva and Godin, Christophe and Hamant, Olivier and Traas, Jan}, journal = {Current Biology}, number = {19}, pages = {2335 -- 2342}, publisher = {Cell Press}, title = {{An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis}}, doi = {10.1016/j.cub.2014.08.036}, volume = {24}, year = {2014}, } @article{1862, abstract = {The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses.}, author = {Chen, Xu and Grandont, Laurie and Li, Hongjiang and Hauschild, Robert and Paque, Sébastien and Abuzeineh, Anas and Rakusova, Hana and Benková, Eva and Perrot Rechenmann, Catherine and Friml, Jirí}, issn = {1476-4687}, journal = {Nature}, number = {729}, pages = {90 -- 93}, publisher = {Nature Publishing Group}, title = {{Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules}}, doi = {10.1038/nature13889}, volume = {516}, year = {2014}, } @article{1893, abstract = {Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.}, author = {Nováková, Petra and Hirsch, Sibylle and Feraru, Elena and Tejos, Ricardo and Van Wijk, Ringo and Viaene, Tom and Heilmann, Mareike and Lerche, Jennifer and De Rycke, Riet and Feraru, Mugurel and Grones, Peter and Van Montagu, Marc and Heilmann, Ingo and Munnik, Teun and Friml, Jirí}, journal = {PNAS}, number = {7}, pages = {2818 -- 2823}, publisher = {National Academy of Sciences}, title = {{SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis}}, doi = {10.1073/pnas.1324264111}, volume = {111}, year = {2014}, } @article{1897, abstract = {GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants.}, author = {Naramoto, Satoshi and Otegui, Marisa and Kutsuna, Natsumaro and De Rycke, Riet and Dainobu, Tomoko and Karampelias, Michael and Fujimoto, Masaru and Feraru, Elena and Miki, Daisuke and Fukuda, Hiroo and Nakano, Akihiko and Friml, Jirí}, journal = {Plant Cell}, number = {7}, pages = {3062 -- 3076}, publisher = {American Society of Plant Biologists}, title = {{Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis}}, doi = {10.1105/tpc.114.125880}, volume = {26}, year = {2014}, } @article{1901, 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.}, author = {Tian, Huiyu and Wabnik, Krzysztof T and Niu, Tiantian and Li, Hongjiang and Yu, Qianqian and Pollmann, Stephan and Vanneste, Steffen and Govaerts, Willy and Rolčík, Jakub and Geisler, Markus and Friml, Jirí and Ding, Zhaojun}, journal = {Molecular Plant}, number = {2}, pages = {277 -- 289}, publisher = {Oxford University Press}, title = {{WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis}}, doi = {10.1093/mp/sst118}, volume = {7}, year = {2014}, } @article{1917, abstract = {Auxin-binding protein 1 (ABP1) was discovered nearly 40 years ago and was shown to be essential for plant development and morphogenesis, but its mode of action remains unclear. Here, we report that the plasma membrane-localized transmembrane kinase (TMK) receptor-like kinases interact with ABP1 and transduce auxin signal to activate plasma membrane-associated ROPs [Rho-like guanosine triphosphatases (GTPase) from plants], leading to changes in the cytoskeleton and the shape of leaf pavement cells in Arabidopsis. The interaction between ABP1 and TMK at the cell surface is induced by auxin and requires ABP1 sensing of auxin. These findings show that TMK proteins and ABP1 form a cell surface auxin perception complex that activates ROP signaling pathways, regulating nontranscriptional cytoplasmic responses and associated fundamental processes.}, author = {Xu, Tongda and Dai, Ning and Chen, Jisheng and Nagawa, Shingo and Cao, Min and Li, Hongjiang and Zhou, Zimin and Chen, Xu and De Rycke, Riet and Rakusová, Hana and Wang, Wen and Jones, Alan and Friml, Jirí and Patterson, Sara and Bleecker, Anthony and Yang, Zhenbiao}, journal = {Science}, number = {6174}, pages = {1025 -- 1028}, publisher = {American Association for the Advancement of Science}, title = {{Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling}}, doi = {10.1126/science.1245125}, volume = {343}, year = {2014}, } @article{1915, abstract = {ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small GTPases that function as essential molecular switches to control diverse cellular processes including cytoskeleton organization, cell polarization, cytokinesis, cell differentiation and vesicle trafficking. Although the machineries of vesicle trafficking and cell polarity in plants have been individually well addressed, how ROPs co-ordinate those processes is still largely unclear. Recent progress has been made towards an understanding of the coordination of ROP signalling and trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both root and leaf pavement cells. PIN transporters constantly shuttle between the endosomal compartments and the polar plasma membrane domains, therefore the modulation of PIN-dependent auxin transport between cells is a main developmental output of ROP-regulated vesicle trafficking. The present review focuses on these cellular mechanisms, especially the integration of ROP-based vesicle trafficking and plant cell polarity.}, author = {Chen, Xu and Friml, Jirí}, issn = {1470-8752}, journal = {Biochemical Society Transactions}, number = {1}, pages = {212 -- 218}, publisher = {Portland Press}, title = {{Rho-GTPase-regulated vesicle trafficking in plant cell polarity}}, doi = {10.1042/BST20130269}, volume = {42}, year = {2014}, } @article{1914, abstract = {Targeting membrane proteins for degradation requires the sequential action of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally conserved among kingdoms, plants lack the essential ESCRT-0 components. A new report closes this gap by identifying a novel protein family that substitutes for ESCRT-0 function in plants.}, author = {Sauer, Michael and Friml, Jirí}, journal = {Current Biology}, number = {1}, pages = {R27 -- R29}, publisher = {Cell Press}, title = {{Plant biology: Gatekeepers of the road to protein perdition}}, doi = {10.1016/j.cub.2013.11.019}, volume = {24}, year = {2014}, } @article{1921, abstract = {Cell polarity manifested by asymmetric distribution of cargoes, such as receptors and transporters, within the plasma membrane (PM) is crucial for essential functions in multicellular organisms. In plants, cell polarity (re)establishment is intimately linked to patterning processes. Despite the importance of cell polarity, its underlying mechanisms are still largely unknown, including the definition and distinctiveness of the polar domains within the PM. Here, we show in Arabidopsis thaliana that the signaling membrane components, the phosphoinositides phosphatidylinositol 4-phosphate (PtdIns4P) and phosphatidylinositol 4, 5-bisphosphate [PtdIns(4, 5)P2] as well as PtdIns4P 5-kinases mediating their interconversion, are specifically enriched at apical and basal polar plasma membrane domains. The PtdIns4P 5-kinases PIP5K1 and PIP5K2 are redundantly required for polar localization of specifically apical and basal cargoes, such as PIN-FORMED transporters for the plant hormone auxin. As a consequence of the polarity defects, instructive auxin gradients as well as embryonic and postembryonic patterning are severely compromised. Furthermore, auxin itself regulates PIP5K transcription and PtdIns4P and PtdIns(4, 5)P2 levels, in particular their association with polar PM domains. Our results provide insight into the polar domain-delineating mechanisms in plant cells that depend on apical and basal distribution of membrane lipids and are essential for embryonic and postembryonic patterning.}, author = {Tejos, Ricardo and Sauer, Michael and Vanneste, Steffen and Palacios-Gomez, MiriamPalacios and Li, Hongjiang and Heilmann, Mareike and Van Wijk, Ringo and Vermeer, Joop and Heilmann, Ingo and Munnik, Teun and Friml, Jirí}, journal = {Plant Cell}, number = {5}, pages = {2114 -- 2128}, publisher = {American Society of Plant Biologists}, title = {{Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis}}, doi = {10.1105/tpc.114.126185}, volume = {26}, year = {2014}, } @article{1924, abstract = {Stomata are two-celled valves that control epidermal pores whose spacing optimizes shoot-atmosphere gas exchange. They develop from protodermal cells after unequal divisions followed by an equal division and differentiation. The concentration of the hormone auxin, a master plant developmental regulator, is tightly controlled in time and space, but its role, if any, in stomatal formation is obscure. Here dynamic changes of auxin activity during stomatal development are monitored using auxin input (DII-VENUS) and output (DR5:VENUS) markers by time-lapse imaging. A decrease in auxin levels in the smaller daughter cell after unequal division presages the acquisition of a guard mother cell fate whose equal division produces the two guard cells. Thus, stomatal patterning requires auxin pathway control of stem cell compartment size, as well as auxin depletion that triggers a developmental switch from unequal to equal division.}, author = {Le, Jie and Liu, Xuguang and Yang, Kezhen and Chen, Xiaolan and Zhu, Lingling and Wang, Hongzhe and Wang, Ming and Vanneste, Steffen and Morita, Miyo and Tasaka, Masao and Ding, Zhaojun and Friml, Jirí and Beeckman, Tom and Sack, Fred}, journal = {Nature Communications}, publisher = {Nature Publishing Group}, title = {{Auxin transport and activity regulate stomatal patterning and development}}, doi = {10.1038/ncomms4090}, volume = {5}, year = {2014}, } @article{1934, abstract = {The plant hormones auxin and cytokinin mutually coordinate their activities to control various aspects of development [1-9], and their crosstalk occurs at multiple levels [10, 11]. Cytokinin-mediated modulation of auxin transport provides an efficient means to regulate auxin distribution in plant organs. Here, we demonstrate that cytokinin does not merely control the overall auxin flow capacity, but might also act as a polarizing cue and control the auxin stream directionality during plant organogenesis. Cytokinin enhances the PIN-FORMED1 (PIN1) auxin transporter depletion at specific polar domains, thus rearranging the cellular PIN polarities and directly regulating the auxin flow direction. This selective cytokinin sensitivity correlates with the PIN protein phosphorylation degree. PIN1 phosphomimicking mutations, as well as enhanced phosphorylation in plants with modulated activities of PIN-specific kinases and phosphatases, desensitize PIN1 to cytokinin. Our results reveal conceptually novel, cytokinin-driven polarization mechanism that operates in developmental processes involving rapid auxin stream redirection, such as lateral root organogenesis, in which a gradual PIN polarity switch defines the growth axis of the newly formed organ.}, author = {Marhavy, Peter and Duclercq, Jérôme and Weller, Benjamin and Feraru, Elena and Bielach, Agnieszka and Offringa, Remko and Friml, Jirí and Schwechheimer, Claus and Murphy, Angus and Benková, Eva}, journal = {Current Biology}, number = {9}, pages = {1031 -- 1037}, publisher = {Cell Press}, title = {{Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis}}, doi = {10.1016/j.cub.2014.04.002}, volume = {24}, year = {2014}, } @article{1996, abstract = {Auxin polar transport, local maxima, and gradients have become an importantmodel system for studying self-organization. Auxin distribution is regulated by auxin-dependent positive feedback loops that are not well-understood at the molecular level. Previously, we showed the involvement of the RHO of Plants (ROP) effector INTERACTOR of CONSTITUTIVELY active ROP 1 (ICR1) in regulation of auxin transport and that ICR1 levels are posttranscriptionally repressed at the site of maximum auxin accumulation at the root tip. Here, we show that bimodal regulation of ICR1 levels by auxin is essential for regulating formation of auxin local maxima and gradients. ICR1 levels increase concomitant with increase in auxin response in lateral root primordia, cotyledon tips, and provascular tissues. However, in the embryo hypophysis and root meristem, when auxin exceeds critical levels, ICR1 is rapidly destabilized by an SCF(TIR1/AFB) [SKP, Cullin, F-box (transport inhibitor response 1/auxin signaling F-box protein)]-dependent auxin signaling mechanism. Furthermore, ectopic expression of ICR1 in the embryo hypophysis resulted in reduction of auxin accumulation and concomitant root growth arrest. ICR1 disappeared during root regeneration and lateral root initiation concomitantly with the formation of a local auxin maximum in response to external auxin treatments and transiently after gravitropic stimulation. Destabilization of ICR1 was impaired after inhibition of auxin transport and signaling, proteasome function, and protein synthesis. A mathematical model based on these findings shows that an in vivo-like auxin distribution, rootward auxin flux, and shootward reflux can be simulated without assuming preexisting tissue polarity. Our experimental results and mathematical modeling indicate that regulation of auxin distribution is tightly associated with auxin-dependent ICR1 levels.}, author = {Hazak, Ora and Obolski, Uri and Prat, Tomas and Friml, Jiří and Hadany, Lilach and Yalovsky, Shaul}, journal = {PNAS}, number = {50}, pages = {E5471 -- E5479}, publisher = {National Academy of Sciences}, title = {{Bimodal regulation of ICR1 levels generates self-organizing auxin distribution}}, doi = {10.1073/pnas.1413918111}, volume = {111}, year = {2014}, } @article{1994, abstract = {The emergence and radiation of multicellular land plants was driven by crucial innovations to their body plans [1]. The directional transport of the phytohormone auxin represents a key, plant-specific mechanism for polarization and patterning in complex seed plants [2-5]. Here, we show that already in the early diverging land plant lineage, as exemplified by the moss Physcomitrella patens, auxin transport by PIN transporters is operational and diversified into ER-localized and plasma membrane-localized PIN proteins. Gain-of-function and loss-of-function analyses revealed that PIN-dependent intercellular auxin transport in Physcomitrella mediates crucial developmental transitions in tip-growing filaments and waves of polarization and differentiation in leaf-like structures. Plasma membrane PIN proteins localize in a polar manner to the tips of moss filaments, revealing an unexpected relation between polarization mechanisms in moss tip-growing cells and multicellular tissues of seed plants. Our results trace the origins of polarization and auxin-mediated patterning mechanisms and highlight the crucial role of polarized auxin transport during the evolution of multicellular land plants.}, author = {Viaene, Tom and Landberg, Katarina and Thelander, Mattias and Medvecka, Eva and Pederson, Eric and Feraru, Elena and Cooper, Endymion and Karimi, Mansour and Delwiche, Charles and Ljung, Karin and Geisler, Markus and Sundberg, Eva and Friml, Jirí}, journal = {Current Biology}, number = {23}, pages = {2786 -- 2791}, publisher = {Cell Press}, title = {{Directional auxin transport mechanisms in early diverging land plants}}, doi = {10.1016/j.cub.2014.09.056}, volume = {24}, year = {2014}, } @article{2061, abstract = {Development of cambium and its activity is important for our knowledge of the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model plant for such a kind of study. Thus, this paper reports on cellular events taking place in the interfascicular regions of inflorescence stems of A. thaliana, leading to the development of interfascicular cambium from differentiated interfascicular parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation, PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane and periclinal divisions. Distribution of auxin was observed to be higher in differentiating into cambium parenchyma cells compared to cells within the pith and cortex. Expression of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of PIN1 was already established in the cells prior to their periclinal division. These cellular events initiated within parenchyma cells adjacent to the vascular bundles and successively extended from that point towards the middle region of the interfascicular area, located between neighboring vascular bundles. The final consequence of which was the closure of the cambial ring within the stem. Changes in the chemical composition of IPC walls were also detected and included changes of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs). In summary, results presented in this paper describe interfascicular cambium ontogenesis in terms of successive cellular events in the interfascicular regions of inflorescence stems of Arabidopsis.}, author = {Mazur, Ewa and Kurczyñska, Ewa and Friml, Jiří}, journal = {Protoplasma}, number = {5}, pages = {1125 -- 1139}, publisher = {Springer}, title = {{Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis}}, doi = {10.1007/s00709-014-0620-5}, volume = {251}, year = {2014}, } @article{2188, abstract = {Although plant and animal cells use a similar core mechanism to deliver proteins to the plasma membrane, their different lifestyle, body organization and specific cell structures resulted in the acquisition of regulatory mechanisms that vary in the two kingdoms. In particular, cell polarity regulators do not seem to be conserved, because genes encoding key components are absent in plant genomes. In plants, the broad knowledge on polarity derives from the study of auxin transporters, the PIN-FORMED proteins, in the model plant Arabidopsis thaliana. In animals, much information is provided from the study of polarity in epithelial cells that exhibit basolateral and luminal apical polarities, separated by tight junctions. In this review, we summarize the similarities and differences of the polarization mechanisms between plants and animals and survey the main genetic approaches that have been used to characterize new genes involved in polarity establishment in plants, including the frequently used forward and reverse genetics screens as well as a novel chemical genetics approach that is expected to overcome the limitation of classical genetics methods.}, author = {Kania, Urszula and Fendrych, Matyas and Friml, Jiřĺ}, journal = {Open Biology}, number = {APRIL}, publisher = {Royal Society}, title = {{Polar delivery in plants; commonalities and differences to animal epithelial cells}}, doi = {10.1098/rsob.140017}, volume = {4}, year = {2014}, } @article{2223, abstract = {Correct positioning of membrane proteins is an essential process in eukaryotic organisms. The plant hormone auxin is distributed through intercellular transport and triggers various cellular responses. Auxin transporters of the PIN-FORMED (PIN) family localize asymmetrically at the plasma membrane (PM) and mediate the directional transport of auxin between cells. A fungal toxin, brefeldin A (BFA), inhibits a subset of guanine nucleotide exchange factors for ADP-ribosylation factor small GTPases (ARF GEFs) including GNOM, which plays a major role in localization of PIN1 predominantly to the basal side of the PM. The Arabidopsis genome encodes 19 ARF-related putative GTPases. However, ARF components involved in PIN1 localization have been genetically poorly defined. Using a fluorescence imaging-based forward genetic approach, we identified an Arabidopsis mutant, bfa-visualized exocytic trafficking defective1 (bex1), in which PM localization of PIN1-green fluorescent protein (GFP) as well as development is hypersensitive to BFA. We found that in bex1 a member of the ARF1 gene family, ARF1A1C, was mutated. ARF1A1C localizes to the trans-Golgi network/early endosome and Golgi apparatus, acts synergistically to BEN1/MIN7 ARF GEF and is important for PIN recycling to the PM. Consistent with the developmental importance of PIN proteins, functional interference with ARF1 resulted in an impaired auxin response gradient and various developmental defects including embryonic patterning defects and growth arrest. Our results show that ARF1A1C is essential for recycling of PIN auxin transporters and for various auxin-dependent developmental processes.}, author = {Tanaka, Hirokazu and Nodzyński, Tomasz and Kitakura, Saeko and Feraru, Mugurel and Sasabe, Michiko and Ishikawa, Tomomi and Kleine Vehn, Jürgen and Kakimoto, Tatsuo and Friml, Jirí}, issn = {00320781}, journal = {Plant and Cell Physiology}, number = {4}, pages = {737 -- 749}, publisher = {Oxford University Press}, title = {{BEX1/ARF1A1C is required for BFA-sensitive recycling of PIN auxin transporters and auxin-mediated development in arabidopsis}}, doi = {10.1093/pcp/pct196}, volume = {55}, year = {2014}, } @article{2222, abstract = {Leaf venation develops complex patterns in angiosperms, but the mechanism underlying this process is largely unknown. To elucidate the molecular mechanisms governing vein pattern formation, we previously isolated vascular network defective (van) mutants that displayed venation discontinuities. Here, we report the phenotypic analysis of van4 mutants, and we identify and characterize the VAN4 gene. Detailed phenotypic analysis shows that van4 mutants are defective in procambium cell differentiation and subsequent vascular cell differentiation. Reduced shoot and root cell growth is observed in van4 mutants, suggesting that VAN4 function is important for cell growth and the establishment of venation continuity. Consistent with these phenotypes, the VAN4 gene is strongly expressed in vascular and meristematic cells. VAN4 encodes a putative TRS120, which is a known guanine nucleotide exchange factor (GEF) for Rab GTPase involved in regulating vesicle transport, and a known tethering factor that determines the specificity of membrane fusion. VAN4 protein localizes at the trans-Golgi network/early endosome (TGN/EE). Aberrant recycling of the auxin efflux carrier PIN proteins is observed in van4 mutants. These results suggest that VAN4-mediated exocytosis at the TGN plays important roles in plant vascular development and cell growth in shoot and root. Our identification of VAN4 as a putative TRS120 shows that Rab GTPases are crucial (in addition to ARF GTPases) for continuous vascular development, and provides further evidence for the importance of vesicle transport in leaf vascular formation.}, author = {Naramoto, Satoshi and Nodzyński, Tomasz and Dainobu, Tomoko and Takatsuka, Hirotomo and Okada, Teruyo and Friml, Jirí and Fukuda, Hiroo}, issn = {00320781}, journal = {Plant and Cell Physiology}, number = {4}, pages = {750 -- 763}, publisher = {Oxford University Press}, title = {{VAN4 encodes a putative TRS120 that is required for normal cell growth and vein development in arabidopsis}}, doi = {10.1093/pcp/pcu012}, volume = {55}, year = {2014}, } @article{2227, abstract = {The Balkan Peninsula, characterized by high rates of endemism, is recognised as one of the most diverse and species-rich areas of Europe. However, little is known about the origin of Balkan endemics. The present study addresses the phylogenetic position of the Balkan endemic Ranunculus wettsteinii, as well as its taxonomic status and relationship with the widespread R. parnassiifolius, based on nuclear DNA (internal transcribed spacer, ITS) and plastid regions (rpl32-trnL, rps16-trnQ, trnK-matK and ycf6-psbM). Maximum parsimony and Bayesian inference analyses revealed a well-supported clade formed by accessions of R. wettsteinii. Furthermore, our phylogenetic and network analyses supported previous hypotheses of a likely allopolyploid origin for R. wettsteinii between R. montenegrinus and R. parnassiifolius, with the latter as the maternal parent.}, author = {Cires Rodriguez, Eduardo and Baltisberger, Matthias and Cuesta, Candela and Vargas, Pablo and Prieto, José}, issn = {14396092}, journal = {Organisms Diversity and Evolution}, number = {1}, pages = {1 -- 10}, publisher = {Springer}, title = {{Allopolyploid origin of the Balkan endemic Ranunculus wettsteinii (Ranunculaceae) inferred from nuclear and plastid DNA sequences}}, doi = {10.1007/s13127-013-0150-6}, volume = {14}, year = {2014}, } @article{2240, abstract = {Clathrin-mediated endocytosis is the major mechanism for eukaryotic plasma membrane-based proteome turn-over. In plants, clathrin-mediated endocytosis is essential for physiology and development, but the identification and organization of the machinery operating this process remains largely obscure. Here, we identified an eight-core-component protein complex, the TPLATE complex, essential for plant growth via its role as major adaptor module for clathrin-mediated endocytosis. This complex consists of evolutionarily unique proteins that associate closely with core endocytic elements. The TPLATE complex is recruited as dynamic foci at the plasma membrane preceding recruitment of adaptor protein complex 2, clathrin, and dynamin-related proteins. Reduced function of different complex components severely impaired internalization of assorted endocytic cargoes, demonstrating its pivotal role in clathrin-mediated endocytosis. Taken together, the TPLATE complex is an early endocytic module representing a unique evolutionary plant adaptation of the canonical eukaryotic pathway for clathrin-mediated endocytosis.}, author = {Gadeyne, Astrid and Sánchez Rodríguez, Clara and Vanneste, Steffen and Di Rubbo, Simone and Zauber, Henrik and Vanneste, Kevin and Van Leene, Jelle and De Winne, Nancy and Eeckhout, Dominique and Persiau, Geert and Van De Slijke, Eveline and Cannoot, Bernard and Vercruysse, Leen and Mayers, Jonathan and Adamowski, Maciek and Kania, Urszula and Ehrlich, Matthias and Schweighofer, Alois and Ketelaar, Tijs and Maere, Steven and Bednarek, Sebastian and Friml, Jirí and Gevaert, Kris and Witters, Erwin and Russinova, Eugenia and Persson, Staffan and De Jaeger, Geert and Van Damme, Daniël}, issn = {00928674}, journal = {Cell}, number = {4}, pages = {691 -- 704}, publisher = {Cell Press}, title = {{The TPLATE adaptor complex drives clathrin-mediated endocytosis in plants}}, doi = {10.1016/j.cell.2014.01.039}, volume = {156}, year = {2014}, } @inbook{2245, abstract = {Exogenous application of biologically important molecules for plant growth promotion and/or regulation is very common both in plant research and horticulture. Plant hormones such as auxins and cytokinins are classes of compounds which are often applied exogenously. Nevertheless, plants possess a well-established machinery to regulate the active pool of exogenously applied compounds by converting them to metabolites and conjugates. Consequently, it is often very useful to know the in vivo status of applied compounds to connect them with some of the regulatory events in plant developmental processes. The in vivo status of applied compounds can be measured by incubating plants with radiolabeled compounds, followed by extraction, purification, and HPLC metabolic profiling of plant extracts. Recently we have used this method to characterize the intracellularly localized PIN protein, PIN5. Here we explain the method in detail, with a focus on general application. }, author = {Simon, Sibu and Skůpa, Petr and Dobrev, Petre and Petrášek, Jan and Zažímalová, Eva and Friml, Jirí}, booktitle = {Plant Chemical Genomics}, editor = {Hicks, Glenn and Robert, Stéphanie}, issn = {10643745}, pages = {255 -- 264}, publisher = {Springer}, title = {{Analyzing the in vivo status of exogenously applied auxins: A HPLC-based method to characterize the intracellularly localized auxin transporters}}, doi = {10.1007/978-1-62703-592-7_23}, volume = {1056}, year = {2014}, } @article{2253, abstract = {Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation.}, author = {Bailly, Aurélien and Wang, Bangjun and Zwiewka, Marta and Pollmann, Stephan and Schenck, Daniel and Lüthen, Hartwig and Schulz, Alexander and Friml, Jirí and Geisler, Markus}, issn = {09607412}, journal = {Plant Journal}, number = {1}, pages = {108 -- 118}, publisher = {Wiley-Blackwell}, title = {{Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth}}, doi = {10.1111/tpj.12369}, volume = {77}, year = {2014}, } @article{2249, abstract = {The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes.}, author = {Chen, Yani and Aung, Kyaw and Rolčík, Jakub and Walicki, Kathryn and Friml, Jirí and Brandizzí, Federica}, issn = {09607412}, journal = {Plant Journal}, number = {1}, pages = {97 -- 107}, publisher = {Wiley-Blackwell}, title = {{Inter-regulation of the unfolded protein response and auxin signaling}}, doi = {10.1111/tpj.12373}, volume = {77}, year = {2014}, } @phdthesis{1402, abstract = {Phosphatidylinositol (Ptdlns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, Ptdlns3P and Ptdlns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vauolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with Ptdlns3P, the presumable product of their activity. in SAC gain- and loss-of-function mutants, the levels of Ptdlns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with Ptdlns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.}, author = {Marhavá, Petra}, issn = {2663-337X}, pages = {90}, publisher = {Institute of Science and Technology Austria}, title = {{Molecular mechanisms of patterning and subcellular trafficking in Arabidopsis thaliana}}, year = {2014}, } @article{10895, abstract = {Due to their sessile lifestyles, plants need to deal with the limitations and stresses imposed by the changing environment. Plants cope with these by a remarkable developmental flexibility, which is embedded in their strategy to survive. Plants can adjust their size, shape and number of organs, bend according to gravity and light, and regenerate tissues that were damaged, utilizing a coordinating, intercellular signal, the plant hormone, auxin. Another versatile signal is the cation, Ca2+, which is a crucial second messenger for many rapid cellular processes during responses to a wide range of endogenous and environmental signals, such as hormones, light, drought stress and others. Auxin is a good candidate for one of these Ca2+-activating signals. However, the role of auxin-induced Ca2+ signaling is poorly understood. Here, we will provide an overview of possible developmental and physiological roles, as well as mechanisms underlying the interconnection of Ca2+ and auxin signaling. }, author = {Vanneste, Steffen and Friml, Jiří}, issn = {2223-7747}, journal = {Plants}, keywords = {Plant Science, Ecology, Ecology, Evolution, Behavior and Systematics}, number = {4}, pages = {650--675}, publisher = {MDPI}, title = {{Calcium: The missing link in auxin action}}, doi = {10.3390/plants2040650}, volume = {2}, year = {2013}, } @article{2290, abstract = {The plant hormone indole-acetic acid (auxin) is essential for many aspects of plant development. Auxin-mediated growth regulation typically involves the establishment of an auxin concentration gradient mediated by polarly localized auxin transporters. The localization of auxin carriers and their amount at the plasma membrane are controlled by membrane trafficking processes such as secretion, endocytosis, and recycling. In contrast to endocytosis or recycling, how the secretory pathway mediates the localization of auxin carriers is not well understood. In this study we have used the differential cell elongation process during apical hook development to elucidate the mechanisms underlying the post-Golgi trafficking of auxin carriers in Arabidopsis. We show that differential cell elongation during apical hook development is defective in Arabidopsis mutant echidna (ech). ECH protein is required for the trans-Golgi network (TGN)-mediated trafficking of the auxin influx carrier AUX1 to the plasma membrane. In contrast, ech mutation only marginally perturbs the trafficking of the highly related auxin influx carrier LIKE-AUX1-3 or the auxin efflux carrier PIN-FORMED-3, both also involved in hook development. Electron tomography reveals that the trafficking defects in ech mutant are associated with the perturbation of secretory vesicle genesis from the TGN. Our results identify differential mechanisms for the post-Golgi trafficking of de novo-synthesized auxin carriers to plasma membrane from the TGN and reveal how trafficking of auxin influx carriers mediates the control of differential cell elongation in apical hook development.}, author = {Boutté, Yohann and Jonsson, Kristoffer and Mcfarlane, Heather and Johnson, Errin and Gendre, Delphine and Swarup, Ranjan and Friml, Jirí and Samuels, Lacey and Robert, Stéphanie and Bhalerao, Rishikesh}, journal = {PNAS}, number = {40}, pages = {16259 -- 16264}, publisher = {National Academy of Sciences}, title = {{ECHIDNA mediated post Golgi trafficking of auxin carriers for differential cell elongation}}, doi = {10.1073/pnas.1309057110}, volume = {110}, year = {2013}, } @article{2443, abstract = {The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.}, author = {Simon, Sibu and Kubeš, Martin and Baster, Pawel and Robert, Stéphanie and Dobrev, Petre and Friml, Jirí and Petrášek, Jan and Zažímalová, Eva}, journal = {New Phytologist}, number = {4}, pages = {1034 -- 1048}, publisher = {Wiley}, title = {{Defining the selectivity of processes along the auxin response chain: A study using auxin analogues}}, doi = {10.1111/nph.12437}, volume = {200}, year = {2013}, } @article{2449, abstract = {Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. }, author = {Nodzyński, Tomasz and Feraru, Murguel and Hirsch, Sibylle and De Rycke, Riet and Nicuales, Claudiu and Van Leene, Jelle and De Jaeger, Geert and Vanneste, Steffen and Friml, Jirí}, journal = {Molecular Plant}, number = {6}, pages = {1849 -- 1862}, publisher = {Cell Press}, title = {{Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis}}, doi = {10.1093/mp/sst044}, volume = {6}, year = {2013}, } @article{2472, abstract = {Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.}, author = {Cazzonelli, Christopher and Vanstraelen, Marleen and Simon, Sibu and Yin, Kuide and Carron Arthur, Ashley and Nisar, Nazia and Tarle, Gauri and Cuttriss, Abby and Searle, Iain and Benková, Eva and Mathesius, Ulrike and Masle, Josette and Friml, Jirí and Pogson, Barry}, journal = {PLoS One}, number = {7}, publisher = {Public Library of Science}, title = {{Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development}}, doi = {10.1371/journal.pone.0070069}, volume = {8}, year = {2013}, } @article{2470, abstract = {Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients.}, author = {Čovanová, Milada and Sauer, Michael and Rychtář, Jan and Friml, Jirí and Petrášek, Jan and Zažímalová, Eva}, journal = {PLoS One}, number = {7}, publisher = {Public Library of Science}, title = {{Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells}}, doi = {10.1371/journal.pone.0070050}, volume = {8}, year = {2013}, } @article{2808, abstract = {In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/ STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of organ morphogenesis and to show that reproductive organ development in P. patens is highly organized and that organ phyllotaxis differs between vegetative and reproductive development. Using the PpSHI1 and PpSHI2 reporter and knockout lines, the auxin reporters GmGH3pro:GUS and PpPINApro:GFP-GUS, and the auxin-conjugating transgene PpSHI2pro:IAAL, we could show that the PpSHI genes, and by inference also auxin, play important roles for reproductive organ development in moss. The PpSHI genes are required for the apical opening of the reproductive organs, the final differentiation of the egg cell, and the progression of canal cells into a cell death program. The apical cells of the archegonium, the canal cells, and the egg cell are also sites of auxin responsiveness and are affected by reduced levels of active auxin, suggesting that auxin mediates PpSHI function in the reproductive organs.}, author = {Landberg, Katarina and Pederson, Eric and Viaene, Tom and Bozorg, Behruz and Friml, Jirí and Jönsson, Henrik and Thelander, Mattias and Sundberg, Eva}, journal = {Plant Physiology}, number = {3}, pages = {1406 -- 1419}, publisher = {American Society of Plant Biologists}, title = {{The moss physcomitrella patens reproductive organ development is highly organized, affected by the two SHI/STY genes and by the level of active auxin in the SHI/STY expression domain}}, doi = {10.1104/pp.113.214023}, volume = {162}, year = {2013}, } @article{2821, abstract = {Many key aspects of plant development are regulated by the polarized transport of the phytohormone auxin. Cellular auxin efflux, the rate-limiting step in this process, has been shown to rely on the coordinated action of PIN-formed (PIN) and B-type ATP binding cassette (ABCB) carriers. Here, we report that polar auxin transport in the Arabidopsis thaliana root also requires the action of a Major Facilitator Superfamily (MFS) transporter, Zinc-Induced Facilitator-Like 1 (ZIFL1). Sequencing, promoter-reporter, and fluorescent protein fusion experiments indicate that the full-length ZIFL1.1 protein and a truncated splice isoform, ZIFL1.3, localize to the tonoplast of root cells and the plasma membrane of leaf stomatal guard cells, respectively. Using reverse genetics, we show that the ZIFL1.1 transporter regulates various root auxin-related processes, while the ZIFL1.3 isoform mediates drought tolerance by regulating stomatal closure. Auxin transport and immunolocalization assays demonstrate that ZIFL1.1 indirectly modulates cellular auxin efflux during shootward auxin transport at the root tip, likely by regulating plasma membrane PIN2 abundance. Finally, heterologous expression in yeast revealed that ZIFL1.1 and ZIFL1.3 share H+-coupled K+ transport activity. Thus, by determining the subcellular and tissue distribution of two isoforms, alternative splicing dictates a dual function for the ZIFL1 transporter. We propose that this MFS carrier regulates stomatal movements and polar auxin transport by modulating potassium and proton fluxes in Arabidopsis cells.}, author = {Remy, Estelle and Cabrito, Tânia and Baster, Pawel and Batista, Rita and Teixeira, Miguel and Friml, Jirí and Sá Correia, Isabel and Duque, Paula}, journal = {Plant Cell}, number = {3}, pages = {901 -- 926}, publisher = {American Society of Plant Biologists}, title = {{A major facilitator superfamily transporter plays a dual role in polar auxin transport and drought stress tolerance in Arabidopsis}}, doi = {10.1105/tpc.113.110353}, volume = {25}, year = {2013}, } @article{2827, abstract = {Removal of cargos from the cell surface via endocytosis is an efficient mechanism to regulate activities of plasma membrane (PM)-resident proteins, such as receptors or transporters. Salicylic acid (SA) is an important plant hormone that is traditionally associated with pathogen defense. Here, we describe an unanticipated effect of SA on subcellular endocytic cycling of proteins. Both exogenous treatments and endogenously enhanced SA levels repressed endocytosis of different PM proteins. The SA effect on endocytosis did not involve transcription or known components of the SA signaling pathway for transcriptional regulation. SA likely targets an endocytic mechanism that involves the coat protein clathrin, because SA interfered with the clathrin incidence at the PM and clathrin-deficient mutants were less sensitive to the impact of SA on the auxin distribution and root bending during the gravitropic response. By contrast, SA did not affect the ligand-induced endocytosis of the FLAGELLIN SENSING2 (FLS2) receptor during pathogen responses. Our data suggest that the established SA impact on transcription in plant immunity and the nontranscriptional effect of SA on clathrin-mediated endocytosis are independent mechanisms by which SA regulates distinct aspects of plant physiology.}, author = {Du, Yunlong and Tejos, Ricardo and Beck, Martina and Himschoot, Ellie and Li, Hongjiang and Robatzek, Silke and Vanneste, Steffen and Friml, Jirí}, journal = {PNAS}, number = {19}, pages = {7946 -- 7951}, publisher = {National Academy of Sciences}, title = {{Salicylic acid interferes with clathrin-mediated endocytic protein trafficking}}, doi = {10.1073/pnas.1220205110}, volume = {110}, year = {2013}, } @article{2832, abstract = {PIN-FORMED (PIN) proteins localize asymmetrically at the plasma membrane and mediate intercellular polar transport of the plant hormone auxin that is crucial for a multitude of developmental processes in plants. PIN localization is under extensive control by environmental or developmental cues, but mechanisms regulating PIN localization are not fully understood. Here we show that early endosomal components ARF GEF BEN1 and newly identified Sec1/Munc18 family protein BEN2 are involved in distinct steps of early endosomal trafficking. BEN1 and BEN2 are collectively required for polar PIN localization, for their dynamic repolarization, and consequently for auxin activity gradient formation and auxin-related developmental processes including embryonic patterning, organogenesis, and vasculature venation patterning. These results show that early endosomal trafficking is crucial for cell polarity and auxin-dependent regulation of plant architecture.}, author = {Tanaka, Hirokazu and Kitakura, Saeko and Rakusová, Hana and Uemura, Tomohiro and Feraru, Mugurel and De Rycke, Riet and Robert, Stéphanie and Kakimoto, Tatsuo and Friml, Jirí}, journal = {PLoS Genetics}, number = {5}, publisher = {Public Library of Science}, title = {{Cell polarity and patterning by PIN trafficking through early endosomal compartments in arabidopsis thaliana}}, doi = {10.1371/journal.pgen.1003540}, volume = {9}, year = {2013}, } @article{2835, abstract = {The phytohormone auxin regulates virtually every aspect of plant development. To identify new genes involved in auxin activity, a genetic screen was performed for Arabidopsis (Arabidopsis thaliana) mutants with altered expression of the auxin-responsive reporter DR5rev:GFP. One of the mutants recovered in the screen, designated as weak auxin response3 (wxr3), exhibits much lower DR5rev:GFP expression when treated with the synthetic auxin 2,4-dichlorophenoxyacetic acid and displays severe defects in root development. The wxr3 mutant decreases polar auxin transport and results in a disruption of the asymmetric auxin distribution. The levels of the auxin transporters AUXIN1 and PIN-FORMED are dramatically reduced in the wxr3 root tip. Molecular analyses demonstrate that WXR3 is ROOT ULTRAVIOLET B-SENSITIVE1 (RUS1), a member of the conserved Domain of Unknown Function647 protein family found in diverse eukaryotic organisms. Our data suggest that RUS1/WXR3 plays an essential role in the regulation of polar auxin transport by maintaining the proper level of auxin transporters on the plasma membrane.}, author = {Yu, Hong and Karampelias, Michael and Robert, Stéphanie and Peer, Wendy and Swarup, Ranjan and Ye, Songqing and Ge, Lei and Cohen, Jerry and Murphy, Angus and Friml, Jirí and Estelle, Mark}, journal = {Plant Physiology}, number = {2}, pages = {965 -- 976}, publisher = {American Society of Plant Biologists}, title = {{Root ultraviolet b-sensitive1/weak auxin response3 is essential for polar auxin transport in arabidopsis}}, doi = {10.1104/pp.113.217018}, volume = {162}, year = {2013}, } @article{2844, abstract = {As soon as a seed germinates, plant growth relates to gravity to ensure that the root penetrates the soil and the shoot expands aerially. Whereas mechanisms of positive and negative orthogravitropism of primary roots and shoots are relatively well understood [1-3], lateral organs often show more complex growth behavior [4]. Lateral roots (LRs) seemingly suppress positive gravitropic growth and show a defined gravitropic set-point angle (GSA) that allows radial expansion of the root system (plagiotropism) [3, 4]. Despite its eminent importance for root architecture, it so far remains completely unknown how lateral organs partially suppress positive orthogravitropism. Here we show that the phytohormone auxin steers GSA formation and limits positive orthogravitropism in LR. Low and high auxin levels/signaling lead to radial or axial root systems, respectively. At a cellular level, it is the auxin transport-dependent regulation of asymmetric growth in the elongation zone that determines GSA. Our data suggest that strong repression of PIN4/PIN7 and transient PIN3 expression limit auxin redistribution in young LR columella cells. We conclude that PIN activity, by temporally limiting the asymmetric auxin fluxes in the tip of LRs, induces transient, differential growth responses in the elongation zone and, consequently, controls root architecture.}, author = {Rosquete, Michel and Von Wangenheim, Daniel and Marhavy, Peter and Barbez, Elke and Stelzer, Ernst and Benková, Eva and Maizel, Alexis and Kleine Vehn, Jürgen}, journal = {Current Biology}, number = {9}, pages = {817 -- 822}, publisher = {Cell Press}, title = {{An auxin transport mechanism restricts positive orthogravitropism in lateral roots}}, doi = {10.1016/j.cub.2013.03.064}, volume = {23}, year = {2013}, } @article{2883, abstract = {Plant architecture is influenced by the polar, cell-to-cell transport of auxin that is primarily provided and regulated by plasma membrane efflux catalysts of the PIN-FORMED and B family of ABC transporter (ABCB) classes. The latter were shown to require the functionality of the FK506 binding protein42 TWISTED DWARF1 (TWD1), although underlying mechanisms are unclear. By genetic manipulation of TWD1 expression, we show here that TWD1 affects shootward root auxin reflux and, thus, downstream developmental traits, such as epidermal twisting and gravitropism of the root. Using immunological assays, we demonstrate a predominant lateral, mainly outward-facing, plasma membrane location for TWD1 in the root epidermis characterized by the lateral marker ABC transporter G36/PLEIOTROPIC DRUG-RESISTANCE8/PENETRATION3. At these epidermal plasma membrane domains, TWD1 colocalizes with nonpolar ABCB1. In planta bioluminescence resonance energy transfer analysis was used to verify specific ABC transporter B1 (ABCB1)-TWD1 interaction. Our data support a model in which TWD1 promotes lateral ABCB-mediated auxin efflux via protein-protein interaction at the plasma membrane, minimizing reflux from the root apoplast into the cytoplasm.}, author = {Wang, Bangjun and Bailly, Aurélien and Zwiewk, Marta and Henrichs, Sina and Azzarello, Elisa and Mancuso, Stefano and Maeshima, Masayoshi and Friml, Jirí and Schulz, Alexander and Geisler, Markus}, journal = {Plant Cell}, number = {1}, pages = {202 -- 214}, publisher = {American Society of Plant Biologists}, title = {{Arabidopsis TWISTED DWARF1 functionally interacts with auxin exporter ABCB1 on the root plasma membrane}}, doi = {10.1105/tpc.112.105999}, volume = {25}, year = {2013}, } @article{2882, abstract = {Gravitropic bending of plant organs is mediated by an asymmetric signaling of the plant hormone auxin between the upper and lower side of the respective organ. Here, we show that also another plant hormone, gibberellic acid (GA), shows asymmetric action during gravitropic responses. Immunodetection using an antibody against GA and monitoring GA signaling output by downstream degradation of DELLA proteins revealed an asymmetric GA distribution and response with the maximum at the lower side of gravistimulated roots. Genetic or pharmacological manipulation of GA levels or response affects gravity-mediated auxin redistribution and root bending response. The higher GA levels at the lower side of the root correlate with increased amounts of PIN-FORMED2 (PIN2) auxin transporter at the plasma membrane. The observed increase in PIN2 stability is caused by a specific GA effect on trafficking of PIN proteins to lytic vacuoles that presumably occurs downstream of brefeldin A-sensitive endosomes. Our results suggest that asymmetric auxin distribution instructive for gravity-induced differential growth is consolidated by the asymmetric action of GA that stabilizes the PIN-dependent auxin stream along the lower side of gravistimulated roots.}, author = {Löfke, Christian and Zwiewka, Marta and Heilmann, Ingo and Van Montagu, Marc and Teichmann, Thomas and Friml, Jirí}, journal = {PNAS}, number = {9}, pages = {3627 -- 3632}, publisher = {National Academy of Sciences}, title = {{Asymmetric gibberellin signaling regulates vacuolar trafficking of PIN auxin transporters during root gravitropism}}, doi = {10.1073/pnas.1300107110}, volume = {110}, year = {2013}, } @article{2919, abstract = {The distribution of the phytohormone auxin regulates many aspects of plant development including growth response to gravity. Gravitropic root curvature involves coordinated and asymmetric cell elongation between the lower and upper side of the root, mediated by differential cellular auxin levels. The asymmetry in the auxin distribution is established and maintained by a spatio-temporal regulation of the PIN-FORMED (PIN) auxin transporter activity. We provide novel insights into the complex regulation of PIN abundance and activity during root gravitropism. We show that PIN2 turnover is differentially regulated on the upper and lower side of gravistimulated roots by distinct but partially overlapping auxin feedback mechanisms. In addition to regulating transcription and clathrin-mediated internalization, auxin also controls PIN abundance at the plasma membrane by promoting their vacuolar targeting and degradation. This effect of elevated auxin levels requires the activity of SKP-Cullin-F-box TIR1/AFB (SCF TIR1/AFB)-dependent pathway. Importantly, also suboptimal auxin levels mediate PIN degradation utilizing the same signalling pathway. These feedback mechanisms are functionally important during gravitropic response and ensure fine-tuning of auxin fluxes for maintaining as well as terminating asymmetric growth.}, author = {Baster, Pawel and Robert, Stéphanie and Kleine Vehn, Jürgen and Vanneste, Steffen and Kania, Urszula and Grunewald, Wim and De Rybel, Bert and Beeckman, Tom and Friml, Jirí}, journal = {EMBO Journal}, number = {2}, pages = {260 -- 274}, publisher = {Wiley-Blackwell}, title = {{SCF^TIR1 AFB-auxin signalling regulates PIN vacuolar trafficking and auxin fluxes during root gravitropism}}, doi = {10.1038/emboj.2012.310}, volume = {32}, year = {2013}, } @article{509, abstract = {Clathrin-mediated endocytosis (CME) regulates many aspects of plant development, including hormone signaling and responses to environmental stresses. Despite the importance of this process, the machinery that regulates CME in plants is largely unknown. In mammals, the heterotetrameric ADAPTOR PROTEIN COMPLEX-2 (AP-2) is required for the formation of clathrin-coated vesicles at the plasma membrane (PM). Although the existence of AP-2 has been predicted in Arabidopsis thaliana, the biochemistry and functionality of the complex is still uncharacterized. Here, we identified all the subunits of the Arabidopsis AP-2 by tandem affinity purification and found that one of the large AP-2 subunits, AP2A1, localized at the PM and interacted with clathrin. Furthermore, endocytosis of the leucine-rich repeat receptor kinase, BRASSINOSTEROID INSENSITIVE1 (BRI1), was shown to depend on AP-2. Knockdown of the two Arabidopsis AP2A genes or overexpression of a dominant-negative version of the medium AP-2 subunit, AP2M, impaired BRI1 endocytosis and enhanced the brassinosteroid signaling. Our data reveal that the CME machinery in Arabidopsis is evolutionarily conserved and that AP-2 functions in receptormediated endocytosis. }, author = {Di Rubbo, Simone and Irani, Niloufer and Kim, Soo and Xu, Zheng and Gadeyne, Astrid and Dejonghe, Wim and Vanhoutte, Isabelle and Persiau, Geert and Eeckhout, Dominique and Simon, Sibu and Song, Kyungyoung and Kleine Vehn, Jürgen and Friml, Jirí and De Jaeger, Geert and Van Damme, Daniël and Hwang, Inhwan and Russinova, Eugenia}, journal = {Plant Cell}, number = {8}, pages = {2986 -- 2997}, publisher = {American Society of Plant Biologists}, title = {{The clathrin adaptor complex AP-2 mediates endocytosis of brassinosteroid INSENSITIVE1 in arabidopsis}}, doi = {10.1105/tpc.113.114058}, volume = {25}, year = {2013}, } @article{507, abstract = {Fertilization in flowering plants requires the temporal and spatial coordination of many developmental processes, including pollen production, anther dehiscence, ovule production, and pollen tube elongation. However, it remains elusive as to how this coordination occurs during reproduction. Here, we present evidence that endocytosis, involving heterotetrameric adaptor protein complex 2 (AP-2), plays a crucial role in fertilization. An Arabidopsis thaliana mutant ap2m displays multiple defects in pollen production and viability, as well as elongation of staminal filaments and pollen tubes, all of which are pivotal processes needed for fertilization. Of these abnormalities, the defects in elongation of staminal filaments and pollen tubes were partially rescued by exogenous auxin. Moreover, DR5rev:GFP (for green fluorescent protein) expression was greatly reduced in filaments and anthers in ap2m mutant plants. At the cellular level, ap2m mutants displayed defects in both endocytosis of N-(3-triethylammonium-propyl)-4- (4-diethylaminophenylhexatrienyl) pyridinium dibromide, a lypophilic dye used as an endocytosis marker, and polar localization of auxin-efflux carrier PIN FORMED2 (PIN2) in the stamen filaments. Moreover, these defects were phenocopied by treatment with Tyrphostin A23, an inhibitor of endocytosis. Based on these results, we propose that AP-2-dependent endocytosis plays a crucial role in coordinating the multiple developmental aspects of male reproductive organs by modulating cellular auxin level through the regulation of the amount and polarity of PINs.}, author = {Kim, Soo and Xu, Zheng and Song, Kyungyoung and Kim, Dae and Kang, Hyangju and Reichardt, Ilka and Sohn, Eun and Friml, Jirí and Juergens, Gerd and Hwang, Inhwan}, journal = {Plant Cell}, number = {8}, pages = {2970 -- 2985}, publisher = {American Society of Plant Biologists}, title = {{Adaptor protein complex 2-mediated endocytosis is crucial for male reproductive organ development in arabidopsis}}, doi = {10.1105/tpc.113.114264}, volume = {25}, year = {2013}, } @article{511, abstract = {The native auxin, indole-3-acetic acid (IAA), is a major regulator of plant growth and development. Its nonuniform distribution between cells and tissues underlies the spatiotemporal coordination of many developmental events and responses to environmental stimuli. The regulation of auxin gradients and the formation of auxin maxima/minima most likely involve the regulation of both metabolic and transport processes. In this article, we have demonstrated that 2-oxindole-3-acetic acid (oxIAA) is a major primary IAA catabolite formed in Arabidopsis thaliana root tissues. OxIAA had little biological activity and was formed rapidly and irreversibly in response to increases in auxin levels. We further showed that there is cell type-specific regulation of oxIAA levels in the Arabidopsis root apex. We propose that oxIAA is an important element in the regulation of output from auxin gradients and, therefore, in the regulation of auxin homeostasis and response mechanisms.}, author = {Pěnčík, Aleš and Simonovik, Biljana and Petersson, Sara and Henyková, Eva and Simon, Sibu and Greenham, Kathleen and Zhang, Yi and Kowalczyk, Mariusz and Estelle, Mark and Zažímalová, Eva and Novák, Ondřej and Sandberg, Göran and Ljung, Karin}, journal = {Plant Cell}, number = {10}, pages = {3858 -- 3870}, publisher = {American Society of Plant Biologists}, title = {{Regulation of auxin homeostasis and gradients in Arabidopsis roots through the formation of the indole-3-acetic acid catabolite 2-oxindole-3-acetic acid}}, doi = {10.1105/tpc.113.114421}, volume = {25}, year = {2013}, } @article{516, abstract = {In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin‐responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue‐specific transcriptional regulation of cell‐identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin‐response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome‐level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.}, author = {Bargmann, Bastiaan and Vanneste, Steffen and Krouk, Gabriel and Nawy, Tal and Efroni, Idan and Shani, Eilon and Choe, Goh and Friml, Jirí and Bergmann, Dominique and Estelle, Mark and Birnbaum, Kenneth}, journal = {Molecular Systems Biology}, number = {1}, publisher = {Nature Publishing Group}, title = {{A map of cell type‐specific auxin responses}}, doi = {10.1038/msb.2013.40}, volume = {9}, year = {2013}, } @article{528, abstract = {Establishment of the embryonic axis foreshadows the main body axis of adults both in plants and in animals, but underlying mechanisms are considered distinct. Plants utilize directional, cell-to-cell transport of the growth hormone auxin [1, 2] to generate an asymmetric auxin response that specifies the embryonic apical-basal axis [3-6]. The auxin flow directionality depends on the polarized subcellular localization of PIN-FORMED (PIN) auxin transporters [7, 8]. It remains unknown which mechanisms and spatial cues guide cell polarization and axis orientation in early embryos. Herein, we provide conceptually novel insights into the formation of embryonic axis in Arabidopsis by identifying a crucial role of localized tryptophan-dependent auxin biosynthesis [9-12]. Local auxin production at the base of young embryos and the accompanying PIN7-mediated auxin flow toward the proembryo are required for the apical auxin response maximum and the specification of apical embryonic structures. Later in embryogenesis, the precisely timed onset of localized apical auxin biosynthesis mediates PIN1 polarization, basal auxin response maximum, and specification of the root pole. Thus, the tight spatiotemporal control of distinct local auxin sources provides a necessary, non-cell-autonomous trigger for the coordinated cell polarization and subsequent apical-basal axis orientation during embryogenesis and, presumably, also for other polarization events during postembryonic plant life [13, 14].}, author = {Robert, Hélène and Grones, Peter and Stepanova, Anna and Robles, Linda and Lokerse, Annemarie and Alonso, Jose and Weijers, Dolf and Friml, Jirí}, journal = {Current Biology}, number = {24}, pages = {2506 -- 2512}, publisher = {Cell Press}, title = {{Local auxin sources orient the apical basal axis in arabidopsis embryos}}, doi = {10.1016/j.cub.2013.09.039}, volume = {23}, year = {2013}, } @article{527, abstract = {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.}, author = {Wabnik, Krzysztof T and Robert, Hélène and Smith, Richard and Friml, Jirí}, journal = {Current Biology}, number = {24}, pages = {2513 -- 2518}, publisher = {Cell Press}, title = {{Modeling framework for the establishment of the apical-basal embryonic axis in plants}}, doi = {10.1016/j.cub.2013.10.038}, volume = {23}, year = {2013}, } @article{2448, abstract = {Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots.}, author = {Remy, Estelle and Baster, Pawel and Friml, Jirí and Duque, Paula}, journal = {Plant Signaling & Behavior}, number = {10}, publisher = {Taylor & Francis}, title = {{ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip}}, doi = {10.4161/psb.25688}, volume = {8}, year = {2013}, }