Rast-Somssich MI,Žádníková P, Schmid S, Kieffer M, Kepinski S, Simon R The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin Journal of Experimental Botany 68 2741-2755, 2017
DOI:10.1093/jxb/erx131
View abstract
Plant growth and development of new organs depend on the continuous activity of the meristems. In the shoot, patterns of organ initiation are determined by PINFORMED (PIN)-dependent auxin distribution, while the undifferentiated state of meristem cells requires activity of KNOTTED LIKE HOMEOBOX (KNOX) transcription factors. Cell proliferation and differentiation of the root meristem are regulated by the largely antagonistic functions of auxin and cytokinins. It has previously been shown that the transcription factor JAGGED LATERAL ORGANS (JLO), a member of the LATERAL ORGAN BOUNDARY DOMAIN (LBD) family, coordinates KNOX and PIN expression in the shoot and promotes root meristem growth. Here we show that JLO is required for the establishment of the root stem cell niche, where it interacts with the auxin/PLETHORA pathway. Auxin signaling involves the AUX/IAA co-repressor proteins, ARF transcription factors and F-box receptors of the TIR1/AFB1–5 family. Because jlo mutants fail to degrade the AUX/IAA protein BODENLOS, root meristem development is inhibited. We also demonstrate that the expression levels of two auxin receptors, TIR1 and AFB1, are controlled by JLO dosage, and that the shoot and root defects of jlo mutants are alleviatedin jlo plants expressing TIR1 and AFB1 from a transgene. The finding that the auxin sensitivity of a plant can be differentially regulated through control of auxin receptor expression can explain how different developmental processes can be integrated by the activity of a key transcription factor.
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Roychoudhry S, Kieffer M, Del Bianco M, Liao CY, Weijers D, Kepinski S The developmental and environmental regulation of gravitropic setpoint angle in Arabidopsis and bean Scientific Reports 7, 2017
DOI:10.1038/srep42664
View abstract
© The Author(s) 2017. Root and shoot branches are major determinants of plant form and critical for the effective capture of resources below and above ground. These branches are often maintained at specific angles with respect to gravity, known as gravitropic set point angles (GSAs). We have previously shown that the mechanism permitting the maintenance of non-vertical GSAs is highly auxin-dependent and here we investigate the developmental and environmental regulation of root and shoot branch GSA. We show that nitrogen and phosphorous deficiency have opposing, auxin signalling-dependent effects on lateral root GSA in Arabidopsis: while low nitrate induces less vertical lateral root GSA, phosphate deficiency results in a more vertical lateral root growth angle, a finding that contrasts with the previously reported growth angle response of bean adventitious roots. We find that this root-class-specific discrepancy in GSA response to low phosphorus is mirrored by similar differences in growth angle response to auxin treatment between these root types. Finally we show that both shaded, low red/far-red light conditions and high temperature induce more vertical growth in Arabidopsis shoot branches. We discuss the significance of these findings in the context of efforts to improve crop performance via the manipulation of root and shoot branch growth angle.
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Wang R, Zhang Y, Kieffer M, Yu H, Kepinski S, Estelle M Corrigendum: HSP90 regulates temperature-dependent seedling growth in Arabidopsis by stabilizing the auxin co-receptor F-box protein TIR1 Nature Communications 7, 2016
DOI:10.1038/ncomms11677
Wang R, Zhang Y, Kieffer M, Yu H, Kepinski S, Estelle M HSP90 regulates temperature-dependent seedling growth in Arabidopsis by stabilizing the auxin co-receptor F-box protein TIR1 Nature Communications 7, 2016
DOI:10.1038/ncomms10269
View abstract
© 2016, Nature Publishing Group. All rights reserved. Recent studies have revealed that a mild increase in environmental temperature stimulates the growth of Arabidopsis seedlings by promoting biosynthesis of the plant hormone auxin. However, little is known about the role of other factors in thisprocess. In this report, we show that increased temperature promotes rapid accumulation of the TIR1 auxin co-receptor, an effect that is dependent on the molecular chaperone HSP90. In addition, we show that HSP90 and the co-chaperone SGT1 each interact with TIR1, confirming that TIR1 is an HSP90 client. Inhibition of HSP90 activity results in degradation of TIR1 and interestingly, defects in a range of auxin-mediated growth processes at lower as well as higher temperatures. Our results indicate that HSP90 and SGT1 integrate temperature and auxin signalling in order to regulate plant growth ina changing environment.
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Roychoudhry S, Kepinski S Analysis of gravitropic setpoint angle control in arabidopsis, 2015
DOI:10.1007/978-1-4939-2697-8_4
View abstract
© Springer Science+Business Media New York 2015. All right reserved. The history of research on gravitropism has been largely confined to the primary root-shoot axis and to understanding how the typically vertical orientation observed there is maintained. Many lateral organs are gravitropic too andare often held at specific non-vertical angles relative to gravity. These so-called gravitropic setpoint angles (GSAs) are intriguing because their maintenance requires that root and shoot lateral organs are able to effect tropic growth both with and against the gravity vector. This chapter describes methods and considerations relevant to the investigation of mechanisms underlying GSA control.
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Roychoudhry S, Kepinski S Shoot and root branch growth angle control - the wonderfulness of lateralness. Current Opinion in Plant Biology 23 124-131, 2015
DOI:10.1016/j.pbi.2014.12.004
View abstract
The overall shape of plants, the space they occupy above and below ground, is determined principally by the number, length, and angle of their lateral branches. The function of these shoot and root branches is to hold leaves and other organs to the sun, and below ground, to provide anchorage and facilitate the uptake of water and nutrients. While in some respects lateral roots and shoots can be considered mere iterations of the primary root-shoot axis, in others there are fundamental differences in their biology, perhaps most conspicuously in the regulation their angle of growth. Here we discuss recent advances in the understanding of the control of branch growth angle, one of the most important but least understood components of the wonderful diversity of plant form observed throughout nature.
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Lee S, Sundaram S, Armitage L, Evans JP, Hawkes T, Kepinski S, Ferro N, Napier RM Defining binding efficiency and specificity of auxins for SCF(TIR1/AFB)-Aux/IAA co-receptor complex formation. ACS Chemical Biology 9 673-682, 2014
DOI:10.1021/cb400618m
View abstract
Structure-activity profiles for the phytohormone auxin have been collected for over 70 years, and a number of synthetic auxins are used in agriculture. Auxin classification schemes and binding models followed from understanding auxin structures. However, all of the data came from whole plant bioassays, meaning the output was the integral of many different processes. The discovery of Transport Inhibitor-Response 1 (TIR1) and the Auxin F-Box (AFB) proteins as sites of auxin perception and the role of auxin as molecular glue in the assembly of co-receptor complexes has allowed the development of a definitive quantitative structure-activity relationship for TIR1 and AFB5. Factorial analysis of binding activities offered two uncorrelated factors associated with binding efficiency and binding selectivity. The six maximum-likelihood estimators of Efficiency are changes in the overlap matrixes, inferring that Efficiency is related to the volume of the electronic system. Using the subset of compounds that bound strongly, chemometric analyses based on quantum chemical calculations and similarity and self-similarity indices yielded three classes of Specificity that relate to differential binding. Specificity may not be defined by any one specific atom or position and is influenced by coulomb matrixes, suggesting that it is driven by electrostatic forces. These analyses give the first receptor-specific classification of auxins and indicate that AFB5 is the preferred site for a number of auxinic herbicides by allowing interactions with analogues having van der Waals surfaces larger than that of indole-3-acetic acid. The quality factors are also examined in terms of long-standing models for the mechanism of auxin binding.
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Boer DR, Freire-Rios A, van den Berg WAM, Saaki T, Manfield IW, Kepinski S, López-Vidrieo I, Franco-Zorrilla JM, de Vries SC, Solano R, Weijers D, Coll M Structural basis for DNA binding specificity by the auxin-dependent ARF transcription factors. Cell 156 577-589, 2014
DOI:10.1016/j.cell.2013.12.027
View abstract
Auxin regulates numerous plant developmental processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs), yet the mechanistic basis for generating specificity in auxin response is unknown. Here, we address this question by solving high-resolution crystal structures of the pivotal Arabidopsis developmental regulator ARF5/MONOPTEROS (MP), its divergent paralog ARF1, and a complex of ARF1 and a generic auxin response DNA element (AuxRE). We show that ARF DNA-binding domains also homodimerize to generate cooperative DNA binding, which is critical for in vivo ARF5/MP function. Strikingly, DNA-contacting residues are conserved between ARFs, and we discover that monomers have the same intrinsic specificity. ARF1 and ARF5 homodimers, however, differ in spacing tolerated between binding sites. Our data identify the DNA-binding domain as an ARF dimerization domain, suggest that ARF dimers bind complex sites as molecular calipers with ARF-specific spacing preference, and provide an atomic-scale mechanistic model for specificity in auxin response.
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Roychoudhry S, Del Bianco M, Kieffer M, Kepinski S Auxin controls gravitropic setpoint angle in higher plant lateral branches. Current Biology 23 1497-1504, 2013
DOI:10.1016/j.cub.2013.06.034
View abstract
Lateral branches in higher plants are often maintained at specific angles with respect to gravity, a quantity known as the gravitropic setpoint angle (GSA) [1]. Despite the importance of GSA control as a fundamental determinant of plant form, the mechanisms underlying gravity-dependent angled growth are not known. Here we address the central questions of how stable isotropic growth of a branch at a nonvertical angle is maintained and of how the value of that angle is set. We show that nonvertical lateral root and shoot branches are distinguished from the primary axis by the existence of an auxin-dependent antigravitropic offset mechanism that operates in tension with gravitropic response to generate angled isotropic growth. Further, we show that the GSA of lateral roots and shoots is dependent upon the magnitude of the antigravitropic offset component. Finally, we show that auxin specifies GSA values dynamically throughout development by regulating the magnitude of the antigravitropic offset component via TIR1/AFB-Aux/IAA-ARF-dependent auxin signaling within the gravity-sensing cells of the root and shoot. The involvement of auxin in controlling GSA is yet another example of auxin's remarkable capacity to self-organize in development [2] and provides a conceptual framework for understanding the specification of GSA throughout nature.
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De Rybel B, Audenaert D, Xuan W, Overvoorde P, Strader LC, Kepinski S, Hoye R, Brisbois R, Parizot B, Vanneste S, Liu X, Gilday A, Graham IA, Nguyen L, Jansen L, Njo MF, Inzé D, Bartel B, Beeckman T A role for the root cap in root branching revealed by the non-auxin probe naxillin. Nat Chem Biol 8 798-805, 2012
DOI:10.1038/nchembio.1044
View abstract
The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture.
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Hayashi K-I, Neve J, Hirose M, Kuboki A, Shimada Y, Kepinski S, Nozaki H Rational design of an auxin antagonist of the SCF(TIR1) auxin receptor complex. ACS Chem Biol 7 590-598, 2012
DOI:10.1021/cb200404c
View abstract
The plant hormone auxin is a master regulator of plant growth and development. By regulating rates of cell division and elongation and triggering specific patterning events, indole 3-acetic acid (IAA) regulates almost every aspect of plant development. The perception of auxin involves the formation of a ternary complex consisting of an F-box protein of the TIR1/AFB family of auxin receptors, the auxin molecule, and a member the Aux/IAA family of co-repressor proteins. In this study, we identified a potent auxin antagonist,α-(phenylethyl-2-oxo)-IAA, as a lead compound for TIR1/AFB receptors by in silico virtual screening. This molecule was used as the basis for the development of a more potent TIR1 antagonist, auxinole (α-[2,4-dimethylphenylethyl-2-oxo]-IAA), using a structure-based drug design approach. Auxinole binds TIR1 to block the formation of the TIR1-IAA-Aux/IAA complex and so inhibits auxin-responsive gene expression. Molecular docking analysis indicates that the phenyl ring in auxinole would strongly interact with Phe82 of TIR1, a residue that is crucial for Aux/IAA recognition. Consistent with thispredicted mode of action, auxinole competitively inhibits various auxin responses in planta. Additionally, auxinole blocks auxin responses of the moss Physcomitrella patens, suggesting activity over a broad range of species. Our works not only substantiates the utility of chemical tools for plant biology but also demonstrates a new class of small molecule inhibitor of protein-protein interactions common to mechanisms of perception of other plant hormones, such as jasmonate, gibberellin, and abscisic acid.
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Brunoud G, Wells DM, Oliva M, Larrieu A, Mirabet V, Burrow AH, Beeckman T, Kepinski S, Traas J, Bennett MJ, Vernoux T A novel sensor to map auxin response and distribution at high spatio-temporal resolution. Nature 482 103-106, 2012
DOI:10.1038/nature10791
View abstract
Auxin is a key plant morphogenetic signal but tools to analyse dynamically its distribution and signalling during development are still limited. Auxin perception directly triggers the degradation of Aux/IAA repressor proteins. Here we describe a novel Aux/IAA-based auxin signalling sensor termed DII-VENUS that was engineered in the model plant Arabidopsis thaliana. The VENUS fast maturing form of yellow fluorescent protein was fused in-frame to the Aux/IAA auxin-interaction domain (termed domain II; DII) and expressed under a constitutive promoter. We initially show that DII-VENUS abundance is dependent on auxin, its TIR1/AFBs co-receptors and proteasome activities. Next, we demonstrate that DII-VENUS provides a map of relative auxin distribution at cellular resolution in different tissues. DII-VENUS is also rapidly degraded in response to auxin and we used it to visualize dynamic changes in cellular auxin distribution successfully during two developmental responses, the root gravitropic response and lateral organ production at the shoot apex. Our results illustrate the value of developing response input sensors such as DII-VENUS to provide high-resolution spatio-temporal information about hormone distribution and response during plant growth and development.
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Bridge LJ, Mirams GR, Kieffer ML, King JR, Kepinski S Distinguishing possible mechanisms for auxin-mediated developmental control in Arabidopsis: models with two Aux/IAA and ARF proteins, and two target gene-sets. Math Biosci 235 32-44, 2012
DOI:10.1016/j.mbs.2011.10.005
View abstract
New models of gene transcriptional responses to auxin signalling in Arabidopsis are presented. This work extends a previous model of auxin signalling to include networks of gene-sets which may control developmental responses along auxin gradients. Key elements of this new study include models of signalling pathways and networks involving two Aux-IAA proteins (IAAs), auxin response factors (ARFs) and gene targets. Hypotheses for the gene network topologies which may be involved in developmental responses have been tested against experimental observations for root hair growth in particular. In studying these models, we provide a framework for the analysis of auxin signalling with multiple IAAs and ARFs, and discuss the implications of bistability in such systems.
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Calderón Villalobos LIA, Lee S, De Oliveira C, Ivetac A, Brandt W, Armitage L, Sheard LB, Tan X, Parry G, Mao H, Zheng N, Napier R, Kepinski S, Estelle M A combinatorial TIR1/AFB-Aux/IAA co-receptor system for differential sensing of auxin Nature Chemical Biology 8 477-485, 2012
DOI:10.1038/nchembio.926
View abstract
The plant hormone auxin regulates virtually every aspect of plant growth and development. Auxin acts by binding the F-box protein transport inhibitor response 1 (TIR1) and promotes the degradation of the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) transcriptional repressors. Here we show that efficient auxin binding requires assembly of an auxin co-receptor complex consisting of TIR1 and an Aux/IAA protein. Heterologous experiments in yeast and quantitative IAA binding assays using purified proteins showed that different combinations of TIR1 and Aux/IAA proteins form co-receptor complexes with a wide range of auxin-binding affinities. Auxin affinity seems to be largely determined by the Aux/IAA. As there are 6 TIR1/AUXIN SIGNALING F-BOX proteins (AFBs) and 29 Aux/IAA proteins in Arabidopsis thaliana, combinatorial interactions may result in many co-receptors with distinct auxin-sensing properties. We also demonstrate that the AFB5-Aux/IAA co-receptor selectively binds the auxinic herbicide picloram. This co-receptor system broadens the effective concentration range of the hormone and may contribute to the complexity of auxin response.© 2012 Nature America, Inc. All rights reserved.
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Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guedon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J The auxin signalling network translates dynamic input into robust patterning at the shoot apex MOL SYST BIOL 7, 2011
DOI:10.1038/msb.2011.39
Brown LA, O'Leary-Steele C, Brookes P, Armitage L, Kepinski S, Warriner SL, Baker A A small molecule with differential effects on the PTS1 and PTS2 peroxisome matrix import pathways PLANT J 65 980-990, 2011
DOI:10.1111/j.1365-313X.2010.04473.x
Del Bianco M, Kepinski S Context, specificity, and self-organization in auxin response. Cold Spring Harb Perspect Biol 3 a001578-, 2011
DOI:10.1101/cshperspect.a001578
View abstract
Auxin is a simple molecule with a remarkable ability to control plant growth, differentiation, and morphogenesis. The mechanistic basis for this versatility appears to stem from the highly complex nature of the networks regulating auxin metabolism, transport and response. These heavily feedback-regulated and inter-dependent mechanisms are complicated in structure and complex in operation giving rise to a system with self-organizing properties capable of generating highly context-specific responses to auxin as a single, generic signal.
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Kieffer M, Neve J, Kepinski S Defining auxin response contexts in plant development CURR OPIN PLANT BIOL 13 12-20, 2010
DOI:10.1016/j.pbi.2009.10.006
De Rybel B, Audenaert D, Beeckman T, Kepinski S The Past, Present, and Future of Chemical Biology in Auxin Research ACS CHEM BIOL 4 987-998, 2009
DOI:10.1021/cb9001624
Kepinski S Pull-down assays for plant hormone research. Methods Mol Biol 495 61-80, 2009
DOI:10.1007/978-1-59745-477-3_6
View abstract
Hormonal signals are transduced (and sometimes perceived) by protein-protein interactions. Understanding these interactions is therefore crucial to understanding the network of signalling components as a whole. Often, genetic analysis serves up a selection of players that may or may not interact directly to carry the signal in question and further insight inevitably leads to some sort of biochemistry. Using the example of the auxin-regulated interaction between the auxin receptor TIR1 and the Aux/IAA repressor proteins, this chapter deals with some of this biochemistry, describing a very simple assay for looking at which proteins are interacting, and if and how those interactions are regulated.
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Hayashi K, Tan X, Zheng N, Hatate T, Kimura Y, Kepinski S, Nozaki H Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling P NATL ACAD SCI USA 105 5632-5637, 2008
Kepinski S The anatomy of auxin perception BIOESSAYS 29 953-956, 2007
DOI:10.1002/bies.20657
Kepinski S Integrating hormone signaling and patterning mechanisms in plant development CURR OPIN PLANT BIOL 9 28-34, 2006
DOI:10.1016/j.pbi.2005.11.001
Yamazoe A, Hayashi K, Kepinski S, Leyser O, Nozaki H Characterization of terfestatin A, a new specific inhibitor for auxin signaling PLANT PHYSIOL 139 779-789, 2005
Kepinski S, Leyser O The Arabidopsis F-box protein TIR1 is an auxin receptor NATURE 435 446-451, 2005
DOI:10.1038/nature03542
Kepinski S, Leyser O Plant development: auxin in loops. Curr Biol 15 R208-R210, 2005
DOI:10.1016/j.cub.2005.03.012
View abstract
Concentration gradients of the hormone auxin are associated with various patterning events in plants. Recent work has refined our picture of the complex and dynamic system of auxin transport underlying the formation of these gradients.
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Kepinski S, Leyser O Auxin-induced SCFTIR1-Aux/IAA interaction involves stable modification of the SCFTIR1 complex P NATL ACAD SCI USA 101 12381-12386, 2004
DOI:10.1073/pnas.0402868101
Kepinski S, Leyser O SCF-mediated proteolysis and negative regulation in ethylene signaling. Cell 115 647-648, 2003
View abstract
Ethylene is an important hormonal regulator of plant growth that acts by regulating gene expression. In this issue of Cell, Guo and Ecker, and Potuschak et al., show that ethylene increases the abundance of the transcription factor EIN3, an activator of ethylene-inducible genes, by relieving its SCF-mediated destruction.
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Kepinski S, Leyser O Plant development: an axis of auxin. Nature 426 132-135, 2003
DOI:10.1038/426132b
Kepinski S, Leyser O An axis of auxin Nature 426 132-135, 2003
View abstract
Embryos have two distinct ends, which become apparent early on. Quite how this initial polarity is sustained in plant embryos has been unclear. Step forward the agent provocateur of plant development - auxin.
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Kepinski S, Leyser O Ubiquitination and auxin signaling: A degrading story PLANT CELL 14 S81-S95, 2002
DOI:10.1105/tpc.010447
Gray WM, Kepinski S, Rouse D, Leyser O, Estelle M Auxin regulates SCFTIR1-dependent degradation of AUX/IAA proteins NATURE 414 271-276, 2001