Robert, Stéphanie - Regulation of plant cell shape acquisition

@article{liu_drought_2026,
	title = {A drought stress-induced {MYB} transcription factor regulates pavement cell shape in leaves of {European} aspen ({Populus} tremula)},
	volume = {251},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.71399},
	doi = {10.1111/nph.71399},
	abstract = {MYB305a promoter expression increases in pavement cells as they grow and acquire their complex shape.},
	language = {en},
	number = {5},
	urldate = {2026-08-17},
	journal = {New Phytologist},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Liu, Sijia and Doyle, Siamsa M. and Robinson, Kathryn M. and Rahneshan, Zahra and Street, Nathaniel R. and Robert, Stéphanie},
	month = sep,
	year = {2026},
	keywords = {Cell Shape, Droughts, European aspen (Populus tremula), GWAS, Gene Expression Regulation, Plant, Genome-Wide Association Study, Plant Leaves, Plant Proteins, Populus, Promoter Regions, Genetic, Stress, Physiological, Transcription Factors, cell shape, drought, leaf pavement cells},
	pages = {2688--2705},
}

MYB305a promoter expression increases in pavement cells as they grow and acquire their complex shape.

@article{devi_art_2026,
	title = {The art of interdigitation: {Current} views on pavement cell shape acquisition},
	volume = {91},
	issn = {1369-5266},
	shorttitle = {The art of interdigitation},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526626000233},
	doi = {10.1016/j.pbi.2026.102880},
	abstract = {Cell shape acquisition is a central feature of morphogenesis, governing tissue organization, organ development, and organismal architecture. In vascular plants, leaf epidermal cells often adopt wavy, interlocking geometries, creating intricate jigsaw puzzle-like patterns. These complex shapes, which develop from simple polyhedral progenitors, provide an excellent model for investigating the mechanisms driving cell shape acquisition. Lobed, interdigitated pavement cells contribute to planar leaf expansion and mechanical stability. Recent advances reveal that the coordination of cell wall remodeling, cytoskeletal organization, and mechanical forces underlies the emergence of lobes (outgrowths) and necks (indentations) that stabilize the tissue and support organ growth. Biomechanical models further demonstrate how spatial modulation of wall stiffness and cytoskeletal dynamics drive interdigitated growth, while phytohormone signaling and communication among neighboring cells fine-tune patterning across the epidermal layer. Here, we bring together current insights into the mechanical, molecular and signaling frameworks that shape pavement cell morphogenesis and highlight key knowledge gaps and future research directions.},
	urldate = {2026-03-27},
	journal = {Current Opinion in Plant Biology},
	author = {Devi, Loitongbam Lorinda and Kumar, Vinod and Ratnakaram, Hemamshu and Lin, Mengzhuo and Robert, Stéphanie},
	month = jun,
	year = {2026},
	pages = {102880},
}

Cell shape acquisition is a central feature of morphogenesis, governing tissue organization, organ development, and organismal architecture. In vascular plants, leaf epidermal cells often adopt wavy, interlocking geometries, creating intricate jigsaw puzzle-like patterns. These complex shapes, which develop from simple polyhedral progenitors, provide an excellent model for investigating the mechanisms driving cell shape acquisition. Lobed, interdigitated pavement cells contribute to planar leaf expansion and mechanical stability. Recent advances reveal that the coordination of cell wall remodeling, cytoskeletal organization, and mechanical forces underlies the emergence of lobes (outgrowths) and necks (indentations) that stabilize the tissue and support organ growth. Biomechanical models further demonstrate how spatial modulation of wall stiffness and cytoskeletal dynamics drive interdigitated growth, while phytohormone signaling and communication among neighboring cells fine-tune patterning across the epidermal layer. Here, we bring together current insights into the mechanical, molecular and signaling frameworks that shape pavement cell morphogenesis and highlight key knowledge gaps and future research directions.

@article{yadav_primary_2026,
	title = {The primary beta-galactosidase {BGAL10} modulates pavement cell shape acquisition in {Arabidopsis}},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erag320},
	doi = {10.1093/jxb/erag320},
	abstract = {Cell shape acquisition is a fundamental biological process that allows cells to establish and maintain morphologies adapted to their specialised functions while preserving tissue integrity. In plants, this process is strongly influenced by the presence of the cell wall, a dynamic extracellular network of polysaccharides and proteins that surrounds the plasma membrane and physically connects neighbouring cells. By constraining and directing cellular expansion, the cell wall plays a central role in controlling cell shape. In Arabidopsis leaves, epidermal pavement cells adopt a characteristic jigsaw-puzzle–like morphology through the formation of interdigitating lobes and necks, providing a powerful model system for dissecting the mechanisms underlying complex plant cell shape acquisition. Here, we demonstrate the involvement of the glycoside hydrolase BETA-GALACTOSIDASE 10 (BGAL10) in pavement cell morphogenesis. Using high-resolution time-series imaging, we analysed cell growth dynamics alongside the spatial expression and subcellular localisation of BGAL10, revealing a prominent role for BGAL10 in mature cells, particularly at curved regions of the cell wall along pavement cell lobes. Furthermore, Brillouin microscopy revealed altered mechanical properties in the bgal10-1 mutant, most notably at lobe–indentation interfaces and cell junctions. Together, our results indicate that BGAL10 fine-tunes lobe outgrowth, likely through modification of the hemicellulose matrix, thereby regulating cell wall extensibility and mechanical stress distribution during pavement cell shape acquisition.},
	urldate = {2026-07-07},
	journal = {Journal of Experimental Botany},
	author = {Yadav, Sandeep and Kumar, Vinod and Heymans, Adrien and Sabooni, Nasrin and Jobert, François and Lin, Mengzhuo and Grones, Peter and Bacete, Laura and Robert, Stéphanie},
	month = jul,
	year = {2026},
	pages = {erag320},
}

Cell shape acquisition is a fundamental biological process that allows cells to establish and maintain morphologies adapted to their specialised functions while preserving tissue integrity. In plants, this process is strongly influenced by the presence of the cell wall, a dynamic extracellular network of polysaccharides and proteins that surrounds the plasma membrane and physically connects neighbouring cells. By constraining and directing cellular expansion, the cell wall plays a central role in controlling cell shape. In Arabidopsis leaves, epidermal pavement cells adopt a characteristic jigsaw-puzzle–like morphology through the formation of interdigitating lobes and necks, providing a powerful model system for dissecting the mechanisms underlying complex plant cell shape acquisition. Here, we demonstrate the involvement of the glycoside hydrolase BETA-GALACTOSIDASE 10 (BGAL10) in pavement cell morphogenesis. Using high-resolution time-series imaging, we analysed cell growth dynamics alongside the spatial expression and subcellular localisation of BGAL10, revealing a prominent role for BGAL10 in mature cells, particularly at curved regions of the cell wall along pavement cell lobes. Furthermore, Brillouin microscopy revealed altered mechanical properties in the bgal10-1 mutant, most notably at lobe–indentation interfaces and cell junctions. Together, our results indicate that BGAL10 fine-tunes lobe outgrowth, likely through modification of the hemicellulose matrix, thereby regulating cell wall extensibility and mechanical stress distribution during pavement cell shape acquisition.

@article{ma_rack1a_2025,
	title = {{RACK1A} positively regulates opening of the apical hook in {Arabidopsis} thaliana via suppression of its auxin response gradient},
	volume = {122},
	url = {https://www.pnas.org/doi/10.1073/pnas.2407224122},
	doi = {10.1073/pnas.2407224122},
	abstract = {Apical hook development is an ideal model for studying differential growth in plants and is controlled by complex phytohormonal crosstalk, with auxin being the major player. Here, we identified a bioactive small molecule that decelerates apical hook opening in Arabidopsis thaliana. Our genetic studies suggest that this molecule enhances or maintains the auxin maximum found in the inner hook side and requires certain auxin signaling components to modulate apical hook opening. Using biochemical approaches, we then revealed the WD40 repeat scaffold protein RECEPTOR FOR ACTIVATED C KINASE 1A (RACK1A) as a direct target of this compound. We present data in support of RACK1A playing a positive role in apical hook opening by activating specific auxin signaling mechanisms and negatively regulating the differential auxin response gradient across the hook, thereby adjusting differential cell growth, an essential process for organ structure and function in plants.},
	number = {30},
	urldate = {2025-07-25},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Ma, Qian and Liu, Sijia and Doyle, Siamsa M. and Raggi, Sara and Pařízková, Barbora and Barange, Deepak Kumar and Ratnakaram, Hemamshu and Wilkinson, Edward G. and Crespo Garcia, Isidro and Bygdell, Joakim and Wingsle, Gunnar and Boer, Dirk Roeland and Strader, Lucia C. and Almqvist, Fredrik and Novák, Ondřej and Robert, Stéphanie},
	month = jul,
	year = {2025},
	pages = {e2407224122},
}

Apical hook development is an ideal model for studying differential growth in plants and is controlled by complex phytohormonal crosstalk, with auxin being the major player. Here, we identified a bioactive small molecule that decelerates apical hook opening in Arabidopsis thaliana. Our genetic studies suggest that this molecule enhances or maintains the auxin maximum found in the inner hook side and requires certain auxin signaling components to modulate apical hook opening. Using biochemical approaches, we then revealed the WD40 repeat scaffold protein RECEPTOR FOR ACTIVATED C KINASE 1A (RACK1A) as a direct target of this compound. We present data in support of RACK1A playing a positive role in apical hook opening by activating specific auxin signaling mechanisms and negatively regulating the differential auxin response gradient across the hook, thereby adjusting differential cell growth, an essential process for organ structure and function in plants.

@article{kumar_shape_2025,
	title = {“{Shape} of {Cell}”—{An} {Auxin} and {Cell} {Wall} {Duet}},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70294},
	doi = {10.1111/ppl.70294},
	abstract = {Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.},
	language = {en},
	number = {3},
	urldate = {2025-06-13},
	journal = {Physiologia Plantarum},
	author = {Kumar, Vinod and Yadav, Sandeep and Heymans, Adrien and Robert, Stéphanie},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70294},
	keywords = {auxin, cell shape, cell wall, cytoskeleton, mechanical stress},
	pages = {e70294},
}

Understanding the mechanisms underlying cell shape acquisition is of fundamental importance in plant science, as this process ultimately defines the structure and function of plant organs. Plants produce cells of diverse shapes and sizes, including pavement cells and stomata of leaves, elongated epidermal cells of the hypocotyl, and cells with outgrowths such as root hairs, and so forth. Plant cells experience mechanical forces of variable magnitude during their development and interaction with neighboring cells and the surrounding environment. From the time of cytokinesis, they are encaged in a complex cell wall matrix, which offers mechanical support and enables directional growth and a differential rate of expansion towards adjacent cells via its mechanochemical heterogeneity. The phytohormone auxin is well characterized for its role in cell expansion and cell elasticity. The interaction between dynamic auxin redistribution and the mechanical properties of the cell wall within tissues drives the development of specific cell shapes. Here, we focus on the regulatory feedback loop involving auxin activity, its influence on cell wall chemistry and mechanical properties, and the coordination of cell shape formation. Integrating insights from molecular and cell biology, biophysics, and computational modeling, we explore the mechanistic link between auxin signaling and cell wall dynamics in shaping plant cells.

@article{lorrai_cell_2024,
	title = {Cell wall integrity modulates {HOOKLESS1} and {PHYTOCHROME} {INTERACTING} {FACTOR4} expression controlling apical hook formation},
	volume = {196},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiae370},
	doi = {10.1093/plphys/kiae370},
	abstract = {Formation of the apical hook in etiolated dicot seedlings results from differential growth in the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) play an important role. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development are still unclear. Here, we show that etiolated seedlings of the Arabidopsis (Arabidopsis thaliana) quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS1 (HLS1) and PHYTOCHROME INTERACTING FACTOR4 (PIF4), which are positive regulators of hook formation. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 and PIF4 expression. Exogenous GAs, loss of DELLA proteins, or HLS1 overexpression partially restore hook development in qua2 and isx-treated seedlings. Interestingly, increased agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook formation, asymmetric auxin maxima, and PIF4 and HLS1 expression. Analyses of plants expressing a Förster resonance energy transfer-based GA sensor indicate that isx reduces accumulation of GAs in the apical hook region in a turgor-dependent manner. Lack of the cell wall integrity sensor THESEUS 1, which modulates turgor loss point, restores hook formation in qua2 and isx-treated seedlings. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4-HLS1 signaling module to control differential cell elongation during hook formation.},
	number = {2},
	urldate = {2024-10-04},
	journal = {Plant Physiology},
	author = {Lorrai, Riccardo and Erguvan, Özer and Raggi, Sara and Jonsson, Kristoffer and Široká, Jitka and Tarkowská, Danuše and Novák, Ondřej and Griffiths, Jayne and Jones, Alexander M and Verger, Stéphane and Robert, Stéphanie and Ferrari, Simone},
	month = oct,
	year = {2024},
	pages = {1562--1578},
}

Formation of the apical hook in etiolated dicot seedlings results from differential growth in the hypocotyl apex and is tightly controlled by environmental cues and hormones, among which auxin and gibberellins (GAs) play an important role. Cell expansion is tightly regulated by the cell wall, but whether and how feedback from this structure contributes to hook development are still unclear. Here, we show that etiolated seedlings of the Arabidopsis (Arabidopsis thaliana) quasimodo2-1 (qua2) mutant, defective in pectin biosynthesis, display severe defects in apical hook formation and maintenance, accompanied by loss of asymmetric auxin maxima and differential cell expansion. Moreover, qua2 seedlings show reduced expression of HOOKLESS1 (HLS1) and PHYTOCHROME INTERACTING FACTOR4 (PIF4), which are positive regulators of hook formation. Treatment of wild-type seedlings with the cellulose inhibitor isoxaben (isx) also prevents hook development and represses HLS1 and PIF4 expression. Exogenous GAs, loss of DELLA proteins, or HLS1 overexpression partially restore hook development in qua2 and isx-treated seedlings. Interestingly, increased agar concentration in the medium restores, both in qua2 and isx-treated seedlings, hook formation, asymmetric auxin maxima, and PIF4 and HLS1 expression. Analyses of plants expressing a Förster resonance energy transfer-based GA sensor indicate that isx reduces accumulation of GAs in the apical hook region in a turgor-dependent manner. Lack of the cell wall integrity sensor THESEUS 1, which modulates turgor loss point, restores hook formation in qua2 and isx-treated seedlings. We propose that turgor-dependent signals link changes in cell wall integrity to the PIF4-HLS1 signaling module to control differential cell elongation during hook formation.

@article{jaillais_guidelines_2024,
	title = {Guidelines for naming and studying plasma membrane domains in plants},
	volume = {10},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-024-01742-8},
	doi = {10.1038/s41477-024-01742-8},
	language = {en},
	number = {8},
	urldate = {2024-08-30},
	journal = {Nature Plants},
	author = {Jaillais, Yvon and Bayer, Emmanuelle and Bergmann, Dominique C. and Botella, Miguel A. and Boutté, Yohann and Bozkurt, Tolga O. and Caillaud, Marie-Cecile and Germain, Véronique and Grossmann, Guido and Heilmann, Ingo and Hemsley, Piers A. and Kirchhelle, Charlotte and Martinière, Alexandre and Miao, Yansong and Mongrand, Sebastien and Müller, Sabine and Noack, Lise C. and Oda, Yoshihisa and Ott, Thomas and Pan, Xue and Pleskot, Roman and Potocky, Martin and Robert, Stéphanie and Rodriguez, Clara Sanchez and Simon-Plas, Françoise and Russinova, Eugenia and Van Damme, Daniel and Van Norman, Jaimie M. and Weijers, Dolf and Yalovsky, Shaul and Yang, Zhenbiao and Zelazny, Enric and Gronnier, Julien},
	month = aug,
	year = {2024},
	pages = {1172--1183},
}

@article{jobert_auxin_2023,
	title = {Auxin as an architect of the pectin matrix},
	volume = {74},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad174},
	doi = {10.1093/jxb/erad174},
	abstract = {Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.},
	number = {22},
	urldate = {2023-12-08},
	journal = {Journal of Experimental Botany},
	author = {Jobert, François and Yadav, Sandeep and Robert, Stéphanie},
	month = dec,
	year = {2023},
	pages = {6933--6949},
}

Auxin is a versatile plant growth regulator that triggers multiple signalling pathways at different spatial and temporal resolutions. A plant cell is surrounded by the cell wall, a complex and dynamic network of polysaccharides. The cell wall needs to be rigid to provide mechanical support and protection and highly flexible to allow cell growth and shape acquisition. The modification of the pectin components, among other processes, is a mechanism by which auxin activity alters the mechanical properties of the cell wall. Auxin signalling precisely controls the transcriptional output of several genes encoding pectin remodelling enzymes, their local activity, pectin deposition, and modulation in different developmental contexts. This review examines the mechanism of auxin activity in regulating pectin chemistry at organ, cellular, and subcellular levels across diverse plant species. Moreover, we ask questions that remain to be addressed to fully understand the interplay between auxin and pectin in plant growth and development.

@article{zukauskaite_new_2023,
	title = {New {PEO}-{IAA}-{Inspired} {Anti}-{Auxins}: {Synthesis}, {Biological} {Activity}, and {Possible} {Application} in {Hemp} ({Cannabis} {Sativa} {L}.) {Micropropagation}},
	issn = {1435-8107},
	shorttitle = {New {PEO}-{IAA}-{Inspired} {Anti}-{Auxins}},
	url = {https://doi.org/10.1007/s00344-023-11031-x},
	doi = {10.1007/s00344-023-11031-x},
	abstract = {Auxins play an important role in plant physiology and are involved in numerous aspects of plant development, such as cell division, elongation and differentiation, fruit development, and phototropic response. In addition, through their antagonistic interaction with cytokinins, auxins play a key role in the regulation of root growth and apical dominance. Thanks to this capacity to determine plant architecture, natural and synthetic auxins have been successfully employed to obtain more economically advantageous plants. The crosstalk between auxins and cytokinins determines plant development and thus is of particular importance in the field of plant micropropagation, where the ratios between these two phytohormones need to be tightly controlled to achieve proper rooting and shoot generation. Previously reported anti-auxin PEO-IAA, which blocks auxin signalling through binding to TIR1 receptor and inhibiting the expression of auxin-responsive genes, has been successfully used to facilitate hemp micropropagation. Herein, we report a set of new PEO-IAA-inspired anti-auxins capable of antagonizing auxin responses in vivo. The capacity of these compounds to bind to the TIR1 receptor was confirmed in vitro by SPR analysis. Using DESI-MSI analysis, we evaluated the uptake and distribution of the compounds at the whole plant level. Finally, we characterized the effect of the compounds on the organogenesis of hemp explants, where they showed to be able to improve beneficial morphological traits, such as the balanced growth of all the produced shoots and enhanced bud proliferation.},
	language = {en},
	urldate = {2023-06-09},
	journal = {Journal of Plant Growth Regulation},
	author = {Žukauskaitė, Asta and Saiz-Fernández, Iñigo and Bieleszová, Kristýna and Iškauskienė, Monika and Zhang, Chao and Smýkalová, Iva and Dzedulionytė, Karolina and Kubeš, Martin F. and Sedlářová, Michaela and Pařízková, Barbora and Pavlović, Iva and Vain, Thomas and Petřík, Ivan and Malinauskienė, Vida and Šačkus, Algirdas and Strnad, Miroslav and Robert, Stéphanie and Napier, Richard and Novák, Ondřej and Doležal, Karel},
	month = may,
	year = {2023},
	keywords = {Anti-auxin, Arabidopsis thaliana, DESI-MSI analysis, Indole-3-acetic acid (IAA), Multiple shoot culture, SPR analysis},
}

Auxins play an important role in plant physiology and are involved in numerous aspects of plant development, such as cell division, elongation and differentiation, fruit development, and phototropic response. In addition, through their antagonistic interaction with cytokinins, auxins play a key role in the regulation of root growth and apical dominance. Thanks to this capacity to determine plant architecture, natural and synthetic auxins have been successfully employed to obtain more economically advantageous plants. The crosstalk between auxins and cytokinins determines plant development and thus is of particular importance in the field of plant micropropagation, where the ratios between these two phytohormones need to be tightly controlled to achieve proper rooting and shoot generation. Previously reported anti-auxin PEO-IAA, which blocks auxin signalling through binding to TIR1 receptor and inhibiting the expression of auxin-responsive genes, has been successfully used to facilitate hemp micropropagation. Herein, we report a set of new PEO-IAA-inspired anti-auxins capable of antagonizing auxin responses in vivo. The capacity of these compounds to bind to the TIR1 receptor was confirmed in vitro by SPR analysis. Using DESI-MSI analysis, we evaluated the uptake and distribution of the compounds at the whole plant level. Finally, we characterized the effect of the compounds on the organogenesis of hemp explants, where they showed to be able to improve beneficial morphological traits, such as the balanced growth of all the produced shoots and enhanced bud proliferation.

@article{jobert_auxin_2022,
	title = {Auxin triggers pectin modification during rootlet emergence in white lupin},
	volume = {112},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15993},
	doi = {10.1111/tpj.15993},
	abstract = {Emergence of secondary roots through parental tissue is a highly controlled developmental process. Although the model plant Arabidopsis has been useful to uncover the predominant role of auxin in this process, its simple root structure is not representative of how emergence takes place in most plants, which display more complex root anatomy. White lupin is a legume crop producing structures called cluster roots, where closely spaced rootlets emerge synchronously. Rootlet primordia push their way through several cortical cell layers while maintaining the parent root integrity, reflecting more generally the lateral root emergence process in most multilayered species. In this study, we showed that lupin rootlet emergence is associated with an upregulation of cell wall pectin modifying and degrading genes under the active control of auxin. Among them, we identified LaPG3, a polygalacturonase gene typically expressed in cells surrounding the rootlet primordium and we showed that its downregulation delays emergence. Immunolabeling of pectin epitopes and their quantification uncovered a gradual pectin demethylesterification in the emergence zone, which was further enhanced by auxin treatment, revealing a direct hormonal control of cell wall properties. We also report rhamnogalacturonan-I modifications affecting cortical cells that undergo separation as a consequence of primordium outgrowth. In conclusion, we describe a model of how external tissues in front of rootlet primordia display cell wall modifications to allow for the passage of newly formed rootlets.},
	language = {en},
	number = {5},
	urldate = {2022-12-09},
	journal = {The Plant Journal},
	author = {Jobert, François and Soriano, Alexandre and Brottier, Laurent and Casset, Célia and Divol, Fanchon and Safran, Josip and Lefebvre, Valérie and Pelloux, Jérôme and Robert, Stéphanie and Péret, Benjamin},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.15993},
	keywords = {Auxin, Cell wall, Lupinus albus (white lupin), Pectin, Root development, auxin, cell wall, pectin, root development},
	pages = {1127--1140},
}

Emergence of secondary roots through parental tissue is a highly controlled developmental process. Although the model plant Arabidopsis has been useful to uncover the predominant role of auxin in this process, its simple root structure is not representative of how emergence takes place in most plants, which display more complex root anatomy. White lupin is a legume crop producing structures called cluster roots, where closely spaced rootlets emerge synchronously. Rootlet primordia push their way through several cortical cell layers while maintaining the parent root integrity, reflecting more generally the lateral root emergence process in most multilayered species. In this study, we showed that lupin rootlet emergence is associated with an upregulation of cell wall pectin modifying and degrading genes under the active control of auxin. Among them, we identified LaPG3, a polygalacturonase gene typically expressed in cells surrounding the rootlet primordium and we showed that its downregulation delays emergence. Immunolabeling of pectin epitopes and their quantification uncovered a gradual pectin demethylesterification in the emergence zone, which was further enhanced by auxin treatment, revealing a direct hormonal control of cell wall properties. We also report rhamnogalacturonan-I modifications affecting cortical cells that undergo separation as a consequence of primordium outgrowth. In conclusion, we describe a model of how external tissues in front of rootlet primordia display cell wall modifications to allow for the passage of newly formed rootlets.

@article{zuch_cell_2022,
	title = {Cell biology of the leaf epidermis: {Fate} specification, morphogenesis, and coordination},
	volume = {34},
	issn = {1040-4651},
	shorttitle = {Cell biology of the leaf epidermis},
	url = {https://doi.org/10.1093/plcell/koab250},
	doi = {10/gpjfdq},
	abstract = {As the outermost layer of plants, the epidermis serves as a critical interface between plants and the environment. During leaf development, the differentiation of specialized epidermal cell types, including stomatal guard cells, pavement cells, and trichomes, occurs simultaneously, each providing unique and pivotal functions for plant growth and survival. Decades of molecular-genetic and physiological studies have unraveled key players and hormone signaling specifying epidermal differentiation. However, most studies focus on only one cell type at a time, and how these distinct cell types coordinate as a unit is far from well-comprehended. Here we provide a review on the current knowledge of regulatory mechanisms underpinning the fate specification, differentiation, morphogenesis, and positioning of these specialized cell types. Emphasis is given to their shared developmental origins, fate flexibility, as well as cell cycle and hormonal controls. Furthermore, we discuss computational modeling approaches to integrate how mechanical properties of individual epidermal cell types and entire tissue/organ properties mutually influence each other. We hope to illuminate the underlying mechanisms coordinating the cell differentiation that ultimately generate a functional leaf epidermis.},
	number = {1},
	urldate = {2022-02-14},
	journal = {The Plant Cell},
	author = {Zuch, Daniel T and Doyle, Siamsa M and Majda, Mateusz and Smith, Richard S and Robert, Stéphanie and Torii, Keiko U},
	month = jan,
	year = {2022},
	pages = {209--227},
}

As the outermost layer of plants, the epidermis serves as a critical interface between plants and the environment. During leaf development, the differentiation of specialized epidermal cell types, including stomatal guard cells, pavement cells, and trichomes, occurs simultaneously, each providing unique and pivotal functions for plant growth and survival. Decades of molecular-genetic and physiological studies have unraveled key players and hormone signaling specifying epidermal differentiation. However, most studies focus on only one cell type at a time, and how these distinct cell types coordinate as a unit is far from well-comprehended. Here we provide a review on the current knowledge of regulatory mechanisms underpinning the fate specification, differentiation, morphogenesis, and positioning of these specialized cell types. Emphasis is given to their shared developmental origins, fate flexibility, as well as cell cycle and hormonal controls. Furthermore, we discuss computational modeling approaches to integrate how mechanical properties of individual epidermal cell types and entire tissue/organ properties mutually influence each other. We hope to illuminate the underlying mechanisms coordinating the cell differentiation that ultimately generate a functional leaf epidermis.

@article{rigal_network_2021,
	title = {A network of stress-related genes regulates hypocotyl elongation downstream of selective auxin perception},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab269},
	doi = {10.1093/plphys/kiab269},
	abstract = {The plant hormone auxin, a master coordinator of development, regulates hypocotyl elongation during seedling growth. We previously identified the synthetic molecule RubNeddin 1 (RN1), which induces degradation of the AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors INDOLE-3-ACETIC ACID-INDUCIBLE3 (IAA3) and IAA7 in planta and strongly promotes hypocotyl elongation. In the present study, we show that despite the structural similarity of RN1 to the synthetic auxin 2,4-dichlorophenoxyacetic-acid (2,4-D), direct treatments with these compounds in Arabidopsis (Arabidopsis thaliana) result in distinct effects, possibly due to enhanced uptake of RN1 and low-level, chronic release of 2,4-D from RN1 in planta. We confirm RN1-induced hypocotyl elongation occurs via specific TRANSPORT INHIBITOR RESISTANT1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) receptor-mediated auxin signaling involving TIR1, AFB2, and AFB5. Using a transcriptome profiling strategy and candidate gene approach, we identify the genes ZINC FINGER OF ARABIDOPSIS THALIANA10 (ZAT10), ARABIDOPSIS TOXICOS EN LEVADURA31 (ATL31), and WRKY DNA-BINDING PROTEIN33 (WRKY33) as being rapidly upregulated by RN1, despite being downregulated by 2,4-D treatment. RN1-induced expression of these genes also occurs via TIR1/AFB-mediated auxin signaling. Our results suggest both hypocotyl elongation and transcription of these genes are induced by RN1 via the promoted degradation of the AUX/IAA transcriptional repressor IAA7. Moreover, these three genes, which are known to be stress-related, act in an inter-dependent transcriptional regulatory network controlling hypocotyl elongation. Together, our results suggest ZAT10, ATL31, and WRKY33 take part in a common gene network regulating hypocotyl elongation in Arabidopsis downstream of a selective auxin perception module likely involving TIR1, AFB2, and AFB5 and inducing the degradation of IAA7.},
	number = {1},
	urldate = {2021-10-15},
	journal = {Plant Physiology},
	author = {Rigal, Adeline and Doyle, Siamsa M. and Ritter, Andrés and Raggi, Sara and Vain, Thomas and O’Brien, José Antonio and Goossens, Alain and Pauwels, Laurens and Robert, Stéphanie},
	month = sep,
	year = {2021},
	pages = {430--445},
}

The plant hormone auxin, a master coordinator of development, regulates hypocotyl elongation during seedling growth. We previously identified the synthetic molecule RubNeddin 1 (RN1), which induces degradation of the AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors INDOLE-3-ACETIC ACID-INDUCIBLE3 (IAA3) and IAA7 in planta and strongly promotes hypocotyl elongation. In the present study, we show that despite the structural similarity of RN1 to the synthetic auxin 2,4-dichlorophenoxyacetic-acid (2,4-D), direct treatments with these compounds in Arabidopsis (Arabidopsis thaliana) result in distinct effects, possibly due to enhanced uptake of RN1 and low-level, chronic release of 2,4-D from RN1 in planta. We confirm RN1-induced hypocotyl elongation occurs via specific TRANSPORT INHIBITOR RESISTANT1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) receptor-mediated auxin signaling involving TIR1, AFB2, and AFB5. Using a transcriptome profiling strategy and candidate gene approach, we identify the genes ZINC FINGER OF ARABIDOPSIS THALIANA10 (ZAT10), ARABIDOPSIS TOXICOS EN LEVADURA31 (ATL31), and WRKY DNA-BINDING PROTEIN33 (WRKY33) as being rapidly upregulated by RN1, despite being downregulated by 2,4-D treatment. RN1-induced expression of these genes also occurs via TIR1/AFB-mediated auxin signaling. Our results suggest both hypocotyl elongation and transcription of these genes are induced by RN1 via the promoted degradation of the AUX/IAA transcriptional repressor IAA7. Moreover, these three genes, which are known to be stress-related, act in an inter-dependent transcriptional regulatory network controlling hypocotyl elongation. Together, our results suggest ZAT10, ATL31, and WRKY33 take part in a common gene network regulating hypocotyl elongation in Arabidopsis downstream of a selective auxin perception module likely involving TIR1, AFB2, and AFB5 and inducing the degradation of IAA7.

@article{parizkova_new_2021,
	title = {New fluorescent auxin probes visualise tissue‐specific and subcellular distributions of auxin in {Arabidopsis}},
	volume = {230},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17183},
	doi = {10/gkcr7d},
	language = {en},
	number = {2},
	urldate = {2021-06-03},
	journal = {New Phytologist},
	author = {Pařízková, Barbora and Žukauskaitė, Asta and Vain, Thomas and Grones, Peter and Raggi, Sara and Kubeš, Martin F. and Kieffer, Martin and Doyle, Siamsa M. and Strnad, Miroslav and Kepinski, Stefan and Napier, Richard and Doležal, Karel and Robert, Stéphanie and Novák, Ondřej},
	month = apr,
	year = {2021},
	pages = {535--549},
}

@article{otvos_pickle_2021,
	title = {Pickle {Recruits} {Retinoblastoma} {Related} 1 to {Control} {Lateral} {Root} {Formation} in {Arabidopsis}},
	volume = {22},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1422-0067/22/8/3862},
	doi = {10.3390/ijms22083862},
	abstract = {Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.},
	language = {en},
	number = {8},
	urldate = {2021-07-01},
	journal = {International Journal of Molecular Sciences},
	author = {Ötvös, Krisztina and Miskolczi, Pál and Marhavý, Peter and Cruz-Ramírez, Alfredo and Benková, Eva and Robert, Stéphanie and Bakó, László},
	month = jan,
	year = {2021},
	keywords = {\textit{de novo} organogenesis, auxin signaling, chromatin remodeling},
	pages = {3862},
}

Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.

@article{liu_solving_2021,
	title = {Solving the {Puzzle} of {Shape} {Regulation} in {Plant} {Epidermal} {Pavement} {Cells}},
	volume = {72},
	issn = {1543-5008},
	url = {https://www.annualreviews.org/doi/10.1146/annurev-arplant-080720-081920},
	doi = {10/gkzfvc},
	abstract = {The plant epidermis serves many essential functions, including interactions with the environment, protection, mechanical strength, and regulation of tissue and organ growth. To achieve these functions, specialized epidermal cells develop into particular shapes. These include the intriguing interdigitated jigsaw puzzle shape of cotyledon and leaf pavement cells seen in many species, the precise functions of which remain rather obscure. Although pavement cell shape regulation is complex and still a long way from being fully understood, the roles of the cell wall, mechanical stresses, cytoskeleton, cytoskeletal regulatory proteins, and phytohormones are becoming clearer. Here, we provide a review of this current knowledge of pavement cell morphogenesis, generated from a wealth of experimental evidence and assisted by computational modeling approaches. We also discuss the evolution and potential functions of pavement cell interdigitation. Throughout the review, we highlight some of the thought-provoking controversies and creative theories surrounding the formation of the curious puzzle shape of these cells.},
	number = {1},
	urldate = {2021-06-21},
	journal = {Annual Review of Plant Biology},
	author = {Liu, Sijia and Jobert, François and Rahneshan, Zahra and Doyle, Siamsa M. and Robert, Stéphanie},
	month = jun,
	year = {2021},
	pages = {525--550},
}

The plant epidermis serves many essential functions, including interactions with the environment, protection, mechanical strength, and regulation of tissue and organ growth. To achieve these functions, specialized epidermal cells develop into particular shapes. These include the intriguing interdigitated jigsaw puzzle shape of cotyledon and leaf pavement cells seen in many species, the precise functions of which remain rather obscure. Although pavement cell shape regulation is complex and still a long way from being fully understood, the roles of the cell wall, mechanical stresses, cytoskeleton, cytoskeletal regulatory proteins, and phytohormones are becoming clearer. Here, we provide a review of this current knowledge of pavement cell morphogenesis, generated from a wealth of experimental evidence and assisted by computational modeling approaches. We also discuss the evolution and potential functions of pavement cell interdigitation. Throughout the review, we highlight some of the thought-provoking controversies and creative theories surrounding the formation of the curious puzzle shape of these cells.

@article{woude_chemical_2021,
	title = {The chemical compound ‘{Heatin}’ stimulates hypocotyl elongation and interferes with the {Arabidopsis} {NIT1}‐subfamily of nitrilases},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15250},
	doi = {10/gkcr8m},
	language = {en},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Woude, Lennard and Piotrowski, Markus and Klaasse, Gruson and Paulus, Judith K. and Krahn, Daniel and Ninck, Sabrina and Kaschani, Farnusch and Kaiser, Markus and Novák, Ondřej and Ljung, Karin and Bulder, Suzanne and Verk, Marcel and Snoek, Basten L. and Fiers, Martijn and Martin, Nathaniel I. and Hoorn, Renier A. L. and Robert, Stéphanie and Smeekens, Sjef and Zanten, Martijn},
	month = may,
	year = {2021},
	pages = {tpj.15250},
}

@incollection{raggi_auxin_2020,
	title = {Auxin},
	isbn = {978-1-119-35725-4},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119357254.ch5},
	doi = {10.1002/9781119357254.ch5},
	abstract = {As synthetic auxins are valuable tools for dissecting the chemistry and biology of auxin, it is important to understand the mechanisms of their transport compared to indole-3-acetic acid (IAA). The discovery of auxin was followed by enthusiastic attempts to synthesize more plant growth-promoting substances similar to IAA. The formation of auxin gradients is essential for many different developmental events such as specification of apical and basal axes in the embryo, maintenance of meristematic activity, formation of leaves, lateral roots, flowers and hypocotyls, and root bending. The application of structurally different auxin-like molecules, together with the development of molecular biology and biochemical techniques, has deepened the understanding of how auxin works and what its characteristics are. Furthermore, the use of small molecules as tools to perturb the complex pathways of auxin metabolism, transport and signalling has greatly assisted our journey of understanding.},
	language = {en},
	urldate = {2021-12-09},
	booktitle = {The {Chemical} {Biology} of {Plant} {Biostimulants}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Raggi, Sara and Doyle, Siamsa M. and Robert, Stéphanie},
	year = {2020},
	note = {Section: 5
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119357254.ch5},
	keywords = {auxin biology, auxin chemistry, auxin gradient, auxin metabolism, indole-3-acetic acid, plant growth-promoting substances, synthetic auxins},
	pages = {123--153},
}

As synthetic auxins are valuable tools for dissecting the chemistry and biology of auxin, it is important to understand the mechanisms of their transport compared to indole-3-acetic acid (IAA). The discovery of auxin was followed by enthusiastic attempts to synthesize more plant growth-promoting substances similar to IAA. The formation of auxin gradients is essential for many different developmental events such as specification of apical and basal axes in the embryo, maintenance of meristematic activity, formation of leaves, lateral roots, flowers and hypocotyls, and root bending. The application of structurally different auxin-like molecules, together with the development of molecular biology and biochemical techniques, has deepened the understanding of how auxin works and what its characteristics are. Furthermore, the use of small molecules as tools to perturb the complex pathways of auxin metabolism, transport and signalling has greatly assisted our journey of understanding.

@incollection{raggi_auxin_2020,
	title = {Auxin: at the crossroads between chemistry and biology},
	isbn = {978-1-119-35725-4},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119357254.ch5},
	abstract = {As synthetic auxins are valuable tools for dissecting the chemistry and biology of auxin, it is important to understand the mechanisms of their transport compared to indole-3-acetic acid (IAA). The discovery of auxin was followed by enthusiastic attempts to synthesize more plant growth-promoting substances similar to IAA. The formation of auxin gradients is essential for many different developmental events such as specification of apical and basal axes in the embryo, maintenance of meristematic activity, formation of leaves, lateral roots, flowers and hypocotyls, and root bending. The application of structurally different auxin-like molecules, together with the development of molecular biology and biochemical techniques, has deepened the understanding of how auxin works and what its characteristics are. Furthermore, the use of small molecules as tools to perturb the complex pathways of auxin metabolism, transport and signalling has greatly assisted our journey of understanding.},
	language = {en},
	urldate = {2021-10-21},
	booktitle = {The {Chemical} {Biology} of {Plant} {Biostimulants}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Raggi, Sara and Doyle, Siamsa M. and Robert, Stéphanie},
	year = {2020},
	keywords = {auxin biology, auxin chemistry, auxin gradient, auxin metabolism, indole-3-acetic acid, plant growth-promoting substances, synthetic auxins},
	pages = {123--153},
}

As synthetic auxins are valuable tools for dissecting the chemistry and biology of auxin, it is important to understand the mechanisms of their transport compared to indole-3-acetic acid (IAA). The discovery of auxin was followed by enthusiastic attempts to synthesize more plant growth-promoting substances similar to IAA. The formation of auxin gradients is essential for many different developmental events such as specification of apical and basal axes in the embryo, maintenance of meristematic activity, formation of leaves, lateral roots, flowers and hypocotyls, and root bending. The application of structurally different auxin-like molecules, together with the development of molecular biology and biochemical techniques, has deepened the understanding of how auxin works and what its characteristics are. Furthermore, the use of small molecules as tools to perturb the complex pathways of auxin metabolism, transport and signalling has greatly assisted our journey of understanding.

@article{antoniadi_cell-surface_2020,
	title = {Cell-surface receptors enable perception of extracellular cytokinins},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-17700-9},
	doi = {10.1038/s41467-020-17700-9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Antoniadi, Ioanna and Novák, Ondřej and Gelová, Zuzana and Johnson, Alexander and Plíhal, Ondřej and Simerský, Radim and Mik, Václav and Vain, Thomas and Mateo-Bonmatí, Eduardo and Karady, Michal and Pernisová, Markéta and Plačková, Lenka and Opassathian, Korawit and Hejátko, Jan and Robert, Stéphanie and Friml, Jiří and Doležal, Karel and Ljung, Karin and Turnbull, Colin},
	month = dec,
	year = {2020},
	pages = {4284},
}

@article{grones_fluctuating_2020,
	title = {Fluctuating auxin response gradients determine pavement cell-shape acquisition},
	volume = {117},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2007400117},
	doi = {10.1073/pnas.2007400117},
	abstract = {Puzzle-shaped pavement cells provide a powerful model system to investigate the cellular and subcellular processes underlying complex cell-shape determination in plants. To better understand pavement cell-shape acquisition and the role of auxin in this process, we focused on the spirals of young stomatal lineage ground cells of
              Arabidopsis
              leaf epidermis. The predictability of lobe formation in these cells allowed us to demonstrate that the auxin response gradient forms within the cells of the spiral and fluctuates based on the particular stage of lobe development. We revealed that specific localization of auxin transporters at the different membranes of these young cells changes during the course of lobe formation, suggesting that these fluctuating auxin response gradients are orchestrated via auxin transport to control lobe formation and determine pavement cell shape.},
	language = {en},
	number = {27},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Grones, Peter and Majda, Mateusz and Doyle, Siamsa M. and Van Damme, Daniël and Robert, Stéphanie},
	month = jul,
	year = {2020},
	pages = {16027--16034},
}

Puzzle-shaped pavement cells provide a powerful model system to investigate the cellular and subcellular processes underlying complex cell-shape determination in plants. To better understand pavement cell-shape acquisition and the role of auxin in this process, we focused on the spirals of young stomatal lineage ground cells of Arabidopsis leaf epidermis. The predictability of lobe formation in these cells allowed us to demonstrate that the auxin response gradient forms within the cells of the spiral and fluctuates based on the particular stage of lobe development. We revealed that specific localization of auxin transporters at the different membranes of these young cells changes during the course of lobe formation, suggesting that these fluctuating auxin response gradients are orchestrated via auxin transport to control lobe formation and determine pavement cell shape.

@article{raggi_polar_2020,
	title = {Polar expedition: mechanisms for protein polar localization},
	volume = {53},
	issn = {13695266},
	shorttitle = {Polar expedition},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526619301165},
	doi = {10.1016/j.pbi.2019.12.001},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Raggi, Sara and Demes, Elsa and Liu, Sijia and Verger, Stéphane and Robert, Stéphanie},
	month = feb,
	year = {2020},
	pages = {134--140},
}

@article{smith_cep5_2020,
	title = {The {CEP5} {Peptide} {Promotes} {Abiotic} {Stress} {Tolerance}, {As} {Revealed} by {Quantitative} {Proteomics}, and {Attenuates} the {AUX}/{IAA} {Equilibrium} in {Arabidopsis}},
	volume = {19},
	issn = {15359476},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1535947620349604},
	doi = {10.1074/mcp.RA119.001826},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Molecular \& Cellular Proteomics},
	author = {Smith, Stephanie and Zhu, Shanshuo and Joos, Lisa and Roberts, Ianto and Nikonorova, Natalia and Vu, Lam Dai and Stes, Elisabeth and Cho, Hyunwoo and Larrieu, Antoine and Xuan, Wei and Goodall, Benjamin and van de Cotte, Brigitte and Waite, Jessic Marie and Rigal, Adeline and Ramans Harborough, Sigurd and Persiau, Geert and Vanneste, Steffen and Kirschner, Gwendolyn K. and Vandermarliere, Elien and Martens, Lennart and Stahl, Yvonne and Audenaert, Dominique and Friml, Jirí and Felix, Georg and Simon, Rüdiger and Bennett, Malcolm J. and Bishopp, Anthony and De Jaeger, Geert and Ljung, Karin and Kepinski, Stefan and Robert, Stephanie and Nemhauser, Jennifer and Hwang, Ildoo and Gevaert, Kris and Beeckman, Tom and De Smet, Ive},
	month = aug,
	year = {2020},
	pages = {1248--1262},
}

@article{doyle_role_2019,
	title = {A role for the auxin precursor anthranilic acid in root gravitropism via regulation of {PIN}-{FORMED} protein polarity and relocalisation in {Arabidopsis}},
	volume = {223},
	issn = {0028-646X, 1469-8137},
	shorttitle = {A role for the auxin precursor anthranilic acid in root gravitropism via regulation of {PIN}-{FORMED} protein polarity and relocalisation in {Arabidopsis}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15877},
	doi = {10.1111/nph.15877},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Doyle, Siamsa M. and Rigal, Adeline and Grones, Peter and Karady, Michal and Barange, Deepak K. and Majda, Mateusz and Pařízková, Barbora and Karampelias, Michael and Zwiewka, Marta and Pěnčík, Aleš and Almqvist, Fredrik and Ljung, Karin and Novák, Ondřej and Robert, Stéphanie},
	month = aug,
	year = {2019},
	pages = {1420--1432},
}

@article{dauphinee_chemical_2019,
	title = {Chemical {Screening} {Pipeline} for {Identification} of {Specific} {Plant} {Autophagy} {Modulators}},
	volume = {181},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/181/3/855-866/6044914},
	doi = {10/ghwwjc},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Dauphinee, Adrian N. and Cardoso, Catarina and Dalman, Kerstin and Ohlsson, Jonas A. and Fick, Stina Berglund and Robert, Stéphanie and Hicks, Glenn R. and Bozhkov, Peter V. and Minina, Elena A.},
	month = nov,
	year = {2019},
	pages = {855--866},
}

@article{grones_force-ing_2019,
	title = {{FORCE}-ing the shape},
	volume = {52},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526618301833},
	doi = {10/gjctf8},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Grones, Peter and Raggi, Sara and Robert, Stéphanie},
	month = dec,
	year = {2019},
	pages = {1--6},
}

@article{majda_mechanical_2019,
	title = {Mechanical {Asymmetry} of the {Cell} {Wall} {Predicts} {Changes} in {Pavement} {Cell} {Geometry}},
	volume = {50},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580719304873},
	doi = {10/gf6sqg},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Developmental Cell},
	author = {Majda, Mateusz and Krupinski, Pawel and Jönsson, Henrik and Hamant, Olivier and Robert, Stéphanie},
	month = jul,
	year = {2019},
	pages = {9--10},
}

@article{bieleszova_new_2019,
	title = {New fluorescently labeled auxins exhibit promising anti-auxin activity},
	volume = {48},
	issn = {18716784},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1871678417305721},
	doi = {10.1016/j.nbt.2018.06.003},
	language = {en},
	urldate = {2021-06-07},
	journal = {New Biotechnology},
	author = {Bieleszová, Kristýna and Pařízková, Barbora and Kubeš, Martin and Husičková, Alexandra and Kubala, Martin and Ma, Qian and Sedlářová, Michaela and Robert, Stéphanie and Doležal, Karel and Strnad, Miroslav and Novák, Ondřej and Žukauskaitė, Asta},
	month = jan,
	year = {2019},
	pages = {44--52},
}

@article{vain_selective_2019,
	title = {Selective auxin agonists induce specific {AUX}/{IAA} protein degradation to modulate plant development},
	volume = {116},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1809037116},
	doi = {10/gfxjp6},
	abstract = {Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCF
              TIR1/AFB
              functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Vain, Thomas and Raggi, Sara and Ferro, Noel and Barange, Deepak Kumar and Kieffer, Martin and Ma, Qian and Doyle, Siamsa M. and Thelander, Mattias and Pařízková, Barbora and Novák, Ondřej and Ismail, Alexandre and Enquist, Per-Anders and Rigal, Adeline and Łangowska, Małgorzata and Ramans Harborough, Sigurd and Zhang, Yi and Ljung, Karin and Callis, Judy and Almqvist, Fredrik and Kepinski, Stefan and Estelle, Mark and Pauwels, Laurens and Robert, Stéphanie},
	month = mar,
	year = {2019},
	pages = {6463--6472},
}

Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCF TIR1/AFB functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.

@article{ma_auxin_2018,
	title = {Auxin signaling: a big question to be addressed by small molecules},
	volume = {69},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Auxin signaling},
	url = {https://academic.oup.com/jxb/article/69/2/313/4641657},
	doi = {10/gct4mb},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Ma, Qian and Grones, Peter and Robert, Stéphanie},
	month = jan,
	year = {2018},
	pages = {313--328},
}

@article{kania_inhibitor_2018,
	title = {The {Inhibitor} {Endosidin} 4 {Targets} {SEC7} {Domain}-{Type} {ARF} {GTPase} {Exchange} {Factors} and {Interferes} with {Subcellular} {Trafficking} in {Eukaryotes}},
	volume = {30},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/30/10/2553-2572/6099476},
	doi = {10.1105/tpc.18.00127},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Kania, Urszula and Nodzyński, Tomasz and Lu, Qing and Hicks, Glenn R. and Nerinckx, Wim and Mishev, Kiril and Peurois, François and Cherfils, Jacqueline and De Rycke, Riet and Grones, Peter and Robert, Stéphanie and Russinova, Eugenia and Friml, Jiří},
	month = oct,
	year = {2018},
	pages = {2553--2572},
}

@article{majda_role_2018,
	title = {The {Role} of {Auxin} in {Cell} {Wall} {Expansion}},
	volume = {19},
	issn = {1422-0067},
	url = {http://www.mdpi.com/1422-0067/19/4/951},
	doi = {10.3390/ijms19040951},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {International Journal of Molecular Sciences},
	author = {Majda, Mateusz and Robert, Stéphanie},
	month = mar,
	year = {2018},
	pages = {951},
}

@article{liu_vacuole_2018,
	title = {Vacuole {Integrity} {Maintained} by {DUF300} {Proteins} {Is} {Required} for {Brassinosteroid} {Signaling} {Regulation}},
	volume = {11},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S1674205217303854},
	doi = {10/gdbfj5},
	abstract = {Brassinosteroid (BR) hormone signaling controls multiple processes during plant growth and development and is initiated at the plasma membrane through the receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1) together with co-receptors such as BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1). BRI1 abundance is regulated by endosomal recycling and vacuolar targeting, but the role of vacuole-related proteins in BR receptor dynamics and BR responses remains elusive. Here, we show that the absence of two DUF300 domain-containing tonoplast proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1), causes vacuole morphology defects, growth inhibition, and constitutive activation of BR signaling. Intriguingly, tonoplast accumulation of BAK1 was substantially increased and appeared causally linked to enhanced BRI1 trafficking and degradation in laz1 laz1h1 plants. Since unrelated vacuole mutants exhibited normal BR responses, our findings indicate that DUF300 proteins play distinct roles in the regulation of BR signaling by maintaining vacuole integrity required to balance subcellular BAK1 pools and BR receptor distribution.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Molecular Plant},
	author = {Liu, Qinsong and Vain, Thomas and Viotti, Corrado and Doyle, Siamsa M. and Tarkowská, Danuše and Novák, Ondřej and Zipfel, Cyril and Sitbon, Folke and Robert, Stéphanie and Hofius, Daniel},
	month = apr,
	year = {2018},
	keywords = {DUF300 proteins, brassinosteroid signaling, tonoplast, vacuole integrity},
	pages = {553--567},
}

Brassinosteroid (BR) hormone signaling controls multiple processes during plant growth and development and is initiated at the plasma membrane through the receptor kinase BRASSINOSTEROID INSENSITIVE1 (BRI1) together with co-receptors such as BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1). BRI1 abundance is regulated by endosomal recycling and vacuolar targeting, but the role of vacuole-related proteins in BR receptor dynamics and BR responses remains elusive. Here, we show that the absence of two DUF300 domain-containing tonoplast proteins, LAZARUS1 (LAZ1) and LAZ1 HOMOLOG1 (LAZ1H1), causes vacuole morphology defects, growth inhibition, and constitutive activation of BR signaling. Intriguingly, tonoplast accumulation of BAK1 was substantially increased and appeared causally linked to enhanced BRI1 trafficking and degradation in laz1 laz1h1 plants. Since unrelated vacuole mutants exhibited normal BR responses, our findings indicate that DUF300 proteins play distinct roles in the regulation of BR signaling by maintaining vacuole integrity required to balance subcellular BAK1 pools and BR receptor distribution.

@article{vernoux_auxin_2017,
	title = {Auxin 2016: a burst of auxin in the warm south of {China}},
	volume = {144},
	issn = {1477-9129, 0950-1991},
	shorttitle = {Auxin 2016},
	url = {https://journals.biologists.com/dev/article/144/4/533/48302/Auxin-2016-a-burst-of-auxin-in-the-warm-south-of},
	doi = {10.1242/dev.144790},
	abstract = {The luxurious vegetation at Sanya, the most southern location in China on the island of Hainan, provided a perfect environment for the ‘Auxin 2016’ meeting in October. As we review here, participants from all around the world discussed the latest advances in auxin transport, metabolism and signaling pathways, highlighting how auxin acts during plant development and in response to the environment in combination with other hormones. The meeting also provided a rich perspective on the evolution of the role of auxin, from algae to higher plants.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Vernoux, Teva and Robert, Stéphanie},
	month = feb,
	year = {2017},
	pages = {533--540},
}

The luxurious vegetation at Sanya, the most southern location in China on the island of Hainan, provided a perfect environment for the ‘Auxin 2016’ meeting in October. As we review here, participants from all around the world discussed the latest advances in auxin transport, metabolism and signaling pathways, highlighting how auxin acts during plant development and in response to the environment in combination with other hormones. The meeting also provided a rich perspective on the evolution of the role of auxin, from algae to higher plants.

@article{majda_mechanochemical_2017,
	title = {Mechanochemical {Polarization} of {Contiguous} {Cell} {Walls} {Shapes} {Plant} {Pavement} {Cells}},
	volume = {43},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580717308304},
	doi = {10/gcjnxj},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Developmental Cell},
	author = {Majda, Mateusz and Grones, Peter and Sintorn, Ida-Maria and Vain, Thomas and Milani, Pascale and Krupinski, Pawel and Zagórska-Marek, Beata and Viotti, Corrado and Jönsson, Henrik and Mellerowicz, Ewa J. and Hamant, Olivier and Robert, Stéphanie},
	month = nov,
	year = {2017},
	pages = {290--304.e4},
}

@article{poxson_regulating_2017,
	title = {Regulating plant physiology with organic electronics},
	volume = {114},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1617758114},
	doi = {10.1073/pnas.1617758114},
	abstract = {The organic electronic ion pump (OEIP) provides flow-free and accurate delivery of small signaling compounds at high spatiotemporal resolution. To date, the application of OEIPs has been limited to delivery of nonaromatic molecules to mammalian systems, particularly for neuroscience applications. However, many long-standing questions in plant biology remain unanswered due to a lack of technology that precisely delivers plant hormones, based on cyclic alkanes or aromatic structures, to regulate plant physiology. Here, we report the employment of OEIPs for the delivery of the plant hormone auxin to induce differential concentration gradients and modulate plant physiology. We fabricated OEIP devices based on a synthesized dendritic polyelectrolyte that enables electrophoretic transport of aromatic substances. Delivery of auxin to transgenic
              Arabidopsis thaliana
              seedlings in vivo was monitored in real time via dynamic fluorescent auxin-response reporters and induced physiological responses in roots. Our results provide a starting point for technologies enabling direct, rapid, and dynamic electronic interaction with the biochemical regulation systems of plants.},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Poxson, David J. and Karady, Michal and Gabrielsson, Roger and Alkattan, Aziz Y. and Gustavsson, Anna and Doyle, Siamsa M. and Robert, Stéphanie and Ljung, Karin and Grebe, Markus and Simon, Daniel T. and Berggren, Magnus},
	month = may,
	year = {2017},
	pages = {4597--4602},
}

The organic electronic ion pump (OEIP) provides flow-free and accurate delivery of small signaling compounds at high spatiotemporal resolution. To date, the application of OEIPs has been limited to delivery of nonaromatic molecules to mammalian systems, particularly for neuroscience applications. However, many long-standing questions in plant biology remain unanswered due to a lack of technology that precisely delivers plant hormones, based on cyclic alkanes or aromatic structures, to regulate plant physiology. Here, we report the employment of OEIPs for the delivery of the plant hormone auxin to induce differential concentration gradients and modulate plant physiology. We fabricated OEIP devices based on a synthesized dendritic polyelectrolyte that enables electrophoretic transport of aromatic substances. Delivery of auxin to transgenic Arabidopsis thaliana seedlings in vivo was monitored in real time via dynamic fluorescent auxin-response reporters and induced physiological responses in roots. Our results provide a starting point for technologies enabling direct, rapid, and dynamic electronic interaction with the biochemical regulation systems of plants.

@article{eyer_24-d_2016,
	title = {2,4-{D} and {IAA} {Amino} {Acid} {Conjugates} {Show} {Distinct} {Metabolism} in {Arabidopsis}},
	volume = {11},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0159269},
	doi = {10/gbpkvw},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {PLOS ONE},
	author = {Eyer, Luděk and Vain, Thomas and Pařízková, Barbora and Oklestkova, Jana and Barbez, Elke and Kozubíková, Hana and Pospíšil, Tomáš and Wierzbicka, Roksana and Kleine-Vehn, Jürgen and Fránek, Milan and Strnad, Miroslav and Robert, Stéphanie and Novak, Ondrej},
	editor = {Rahman, Abidur},
	month = jul,
	year = {2016},
	pages = {e0159269},
}

@article{jiskrova_extra-_2016,
	title = {Extra- and intracellular distribution of cytokinins in the leaves of monocots and dicots},
	volume = {33},
	issn = {18716784},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1871678416000029},
	doi = {10.1016/j.nbt.2015.12.010},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {New Biotechnology},
	author = {Jiskrová, Eva and Novák, Ondřej and Pospíšilová, Hana and Holubová, Katarína and Karády, Michal and Galuszka, Petr and Robert, Stéphanie and Frébort, Ivo},
	month = sep,
	year = {2016},
	pages = {735--742},
}

@article{dejonghe_mitochondrial_2016,
	title = {Mitochondrial uncouplers inhibit clathrin-mediated endocytosis largely through cytoplasmic acidification},
	volume = {7},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms11710},
	doi = {10/f3r3j2},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Dejonghe, Wim and Kuenen, Sabine and Mylle, Evelien and Vasileva, Mina and Keech, Olivier and Viotti, Corrado and Swerts, Jef and Fendrych, Matyáš and Ortiz-Morea, Fausto Andres and Mishev, Kiril and Delang, Simon and Scholl, Stefan and Zarza, Xavier and Heilmann, Mareike and Kourelis, Jiorgos and Kasprowicz, Jaroslaw and Nguyen, Le Son Long and Drozdzecki, Andrzej and Van Houtte, Isabelle and Szatmári, Anna-Mária and Majda, Mateusz and Baisa, Gary and Bednarek, Sebastian York 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, Jiří and Verstreken, Patrik and Russinova, Eugenia},
	month = sep,
	year = {2016},
	pages = {11710},
}

@article{doyle_early_2015,
	title = {An early secretory pathway mediated by {GNOM}-{LIKE} 1 and {GNOM} is essential for basal polarity establishment in {Arabidopsis} thaliana},
	volume = {112},
	issn = {1091-6490 (Electronic) 0027-8424 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25646449},
	doi = {10.1073/pnas.1424856112},
	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.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Proc Natl Acad Sci U S A},
	author = {Doyle, S. M. and Haeger, A. and Vain, T. and Rigal, A. and Viotti, C. and Langowska, M. and Ma, Q. and Friml, J. and Raikhel, N. V. and Hicks, G. R. and Robert, S.},
	month = feb,
	year = {2015},
	note = {Edition: 2015/02/04},
	keywords = {Arabidopsis Proteins/metabolism/*physiology, Arabidopsis/growth \& development/*physiology, Endocytosis, Guanine Nucleotide Exchange Factors/*physiology, Membrane Transport Proteins/metabolism, PIN auxin transporters, Protein Transport, chemical genomics, endomembrane trafficking, plasma membrane protein polarity},
	pages = {E806--15},
}

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.

@incollection{estevez_live_2015,
	address = {New York, NY},
	title = {Live {Cell} {Imaging} of {FM4}-64, a {Tool} for {Tracing} the {Endocytic} {Pathways} in {Arabidopsis} {Root} {Cells}},
	volume = {1242},
	isbn = {978-1-4939-1901-7 978-1-4939-1902-4},
	url = {http://link.springer.com/10.1007/978-1-4939-1902-4_9},
	doi = {10.1007/978-1-4939-1902-4_9},
	urldate = {2021-06-08},
	booktitle = {Plant {Cell} {Expansion}},
	publisher = {Springer New York},
	author = {Rigal, Adeline and Doyle, Siamsa M. and Robert, Stéphanie},
	editor = {Estevez, José M.},
	year = {2015},
	note = {Series Title: Methods in Molecular Biology},
	pages = {93--103},
}

@article{zwiewka_osmotic_2015,
	title = {Osmotic {Stress} {Modulates} the {Balance} between {Exocytosis} and {Clathrin}-{Mediated} {Endocytosis} in {Arabidopsis} thaliana},
	volume = {8},
	issn = {1752-9867 (Electronic) 1674-2052 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25795554},
	doi = {10.1016/j.molp.2015.03.007},
	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.},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Mol Plant},
	author = {Zwiewka, M. and Nodzynski, T. and Robert, S. and Vanneste, S. and Friml, J.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/03/22},
	keywords = {*Endocytosis/drug effects, *Exocytosis/drug effects, *Osmotic Pressure/drug effects, Adaptation, Physiological/drug effects, Arabidopsis Proteins/metabolism, Arabidopsis/*cytology/drug effects/*metabolism, Cell Membrane/drug effects/metabolism, Clathrin/*metabolism, Gene Knockdown Techniques, Indoleacetic Acids/pharmacology, Mutation/genetics, auxin, clathrin-mediated endocytosis, osmotic stress, protein trafficking},
	pages = {1175--87},
}

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.

@article{doyle_small_2015,
	title = {Small molecules unravel complex interplay between auxin biology and endomembrane trafficking},
	volume = {66},
	issn = {1460-2431 (Electronic) 0022-0957 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25911743},
	doi = {10/f3p4ct},
	abstract = {The establishment and maintenance of controlled auxin gradients within plant tissues are essential for a multitude of developmental processes. Auxin gradient formation is co-ordinated via local biosynthesis and transport. Cell to cell auxin transport is facilitated and precisely regulated by complex endomembrane trafficking mechanisms that target auxin carrier proteins to their final destinations. In turn, auxin and cross-talk with other phytohormones regulate the endomembrane trafficking of auxin carriers. Dissecting such rapid and complicated processes is challenging for classical genetic experiments due to trafficking pathway diversity, gene functional redundancy, and lethality in loss-of-function mutants. Many of these difficulties can be bypassed via the use of small molecules to modify or disrupt the function or localization of proteins. Here, we will review examples of the knowledge acquired by the use of such chemical tools in this field, outlining the advantages afforded by chemical biology approaches.},
	language = {en},
	number = {16},
	urldate = {2021-06-07},
	journal = {J Exp Bot},
	author = {Doyle, S. M. and Vain, T. and Robert, S.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/04/26},
	keywords = {*Signal Transduction, Auxin carriers, Carrier Proteins/*metabolism, Indoleacetic Acids/*metabolism, Plant Growth Regulators/*metabolism, Plant Proteins/*metabolism, Protein Transport, auxin gradients, auxin transport, chemical biology, endomembrane trafficking, phytohormones.},
	pages = {4971--82},
}

The establishment and maintenance of controlled auxin gradients within plant tissues are essential for a multitude of developmental processes. Auxin gradient formation is co-ordinated via local biosynthesis and transport. Cell to cell auxin transport is facilitated and precisely regulated by complex endomembrane trafficking mechanisms that target auxin carrier proteins to their final destinations. In turn, auxin and cross-talk with other phytohormones regulate the endomembrane trafficking of auxin carriers. Dissecting such rapid and complicated processes is challenging for classical genetic experiments due to trafficking pathway diversity, gene functional redundancy, and lethality in loss-of-function mutants. Many of these difficulties can be bypassed via the use of small molecules to modify or disrupt the function or localization of proteins. Here, we will review examples of the knowledge acquired by the use of such chemical tools in this field, outlining the advantages afforded by chemical biology approaches.

@article{ma_auxin_2014,
	title = {Auxin biology revealed by small molecules},
	volume = {151},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12128},
	doi = {10/f3p65j},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Ma, Qian and Robert, Stéphanie},
	month = may,
	year = {2014},
	pages = {25--42},
}

@article{vain_cellulase_2014,
	title = {The {Cellulase} {KORRIGAN} {Is} {Part} of the {Cellulose} {Synthase} {Complex}},
	volume = {165},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/165/4/1521/6113133},
	doi = {10/gkgdgm},
	abstract = {Abstract
            Plant growth and organ formation depend on the oriented deposition of load-bearing cellulose microfibrils in the cell wall. Cellulose is synthesized by a large relative molecular weight cellulose synthase complex (CSC), which comprises at least three distinct cellulose synthases. Cellulose synthesis in plants or bacteria also requires the activity of an endo-1,4-β-d-glucanase, the exact function of which in the synthesis process is not known. Here, we show, to our knowledge for the first time, that a leaky mutation in the Arabidopsis (Arabidopsis thaliana) membrane-bound endo-1,4-β-d-glucanase KORRIGAN1 (KOR1) not only caused reduced CSC movement in the plasma membrane but also a reduced cellulose synthesis inhibitor-induced accumulation of CSCs in intracellular compartments. This suggests a role for KOR1 both in the synthesis of cellulose microfibrils and in the intracellular trafficking of CSCs. Next, we used a multidisciplinary approach, including live cell imaging, gel filtration chromatography analysis, split ubiquitin assays in yeast (Saccharomyces cerevisiae NMY51), and bimolecular fluorescence complementation, to show that, in contrast to previous observations, KOR1 is an integral part of the primary cell wall CSC in the plasma membrane.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Vain, Thomas and Crowell, Elizabeth Faris and Timpano, Hélène and Biot, Eric and Desprez, Thierry and Mansoori, Nasim and Trindade, Luisa M. and Pagant, Silvère and Robert, Stéphanie and Höfte, Herman and Gonneau, Martine and Vernhettes, Samantha},
	month = aug,
	year = {2014},
	pages = {1521--1532},
}

Abstract Plant growth and organ formation depend on the oriented deposition of load-bearing cellulose microfibrils in the cell wall. Cellulose is synthesized by a large relative molecular weight cellulose synthase complex (CSC), which comprises at least three distinct cellulose synthases. Cellulose synthesis in plants or bacteria also requires the activity of an endo-1,4-β-d-glucanase, the exact function of which in the synthesis process is not known. Here, we show, to our knowledge for the first time, that a leaky mutation in the Arabidopsis (Arabidopsis thaliana) membrane-bound endo-1,4-β-d-glucanase KORRIGAN1 (KOR1) not only caused reduced CSC movement in the plasma membrane but also a reduced cellulose synthesis inhibitor-induced accumulation of CSCs in intracellular compartments. This suggests a role for KOR1 both in the synthesis of cellulose microfibrils and in the intracellular trafficking of CSCs. Next, we used a multidisciplinary approach, including live cell imaging, gel filtration chromatography analysis, split ubiquitin assays in yeast (Saccharomyces cerevisiae NMY51), and bimolecular fluorescence complementation, to show that, in contrast to previous observations, KOR1 is an integral part of the primary cell wall CSC in the plasma membrane.

@article{paudyal_trafficking_2014,
	title = {Trafficking modulator {TENin1} inhibits endocytosis, causes endomembrane protein accumulation at the pre-vacuolar compartment and impairs gravitropic response in {Arabidopsis} thaliana},
	volume = {460},
	issn = {0264-6021, 1470-8728},
	url = {https://portlandpress.com/biochemj/article/460/2/177/46675/Trafficking-modulator-TENin1-inhibits-endocytosis},
	doi = {10/f3m25k},
	abstract = {In the present study a detailed characterization of a small molecule inhibitor of protein trafficking and gravitropic response is described. We also identified two Arabidopsis thaliana ecotypes that display resistance to this compound. The ecotypes and chemical provide useful tool to investigate protein trafficking.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Biochemical Journal},
	author = {Paudyal, Rupesh and Jamaluddin, Adam and Warren, James P. and Doyle, Siamsa M. and Robert, Stéphanie and Warriner, Stuart L. and Baker, Alison},
	month = jun,
	year = {2014},
	pages = {177--185},
}

In the present study a detailed characterization of a small molecule inhibitor of protein trafficking and gravitropic response is described. We also identified two Arabidopsis thaliana ecotypes that display resistance to this compound. The ecotypes and chemical provide useful tool to investigate protein trafficking.

@article{rigal_unraveling_2014,
	title = {Unraveling plant hormone signaling through the use of small molecules},
	volume = {5},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2014.00373/full},
	doi = {10/f3m3b6},
	abstract = {Plants have acquired the capacity to grow continuously and adjust their morphology in response to endogenous and external signals, leading to a high architectural plasticity. The dynamic and differential distribution of phytohormones is an essential factor in these developmental changes. Phytohormone perception is a fast but complex process modulating specific developmental reprogramming. In recent years, chemical genomics or the use of small molecules to modulate target protein function has emerged as a powerful strategy to study complex biological processes in plants such as hormone signaling. Small molecules can be applied in a conditional, dose-dependent and reversible manner, with the advantage of circumventing the limitations of lethality and functional redundancy inherent to traditional mutant screens. High-throughput screening of diverse chemical libraries has led to the identification of bioactive molecules able to induce plant hormone-related phenotypes. Characterization of the cognate targets and pathways of those molecules has allowed the identification of novel regulatory components, providing new insights into the molecular mechanisms of plant hormone signaling. An extensive structure-activity relationship (SAR) analysis of the natural phytohormones, their designed synthetic analogues and newly identified bioactive molecules has led to the determination of the structural requirements essential for their bioactivity. In this review, we will summarize the so far identified small molecules and their structural variants targeting specific phytohormone signaling pathways. We will highlight how the SAR analyses have enabled better interrogation of the molecular mechanisms of phytohormone responses. Finally, we will discuss how labeled/tagged hormone analogues can be exploited, as compelling tools to better understand hormone signaling and transport mechanisms.},
	language = {English},
	urldate = {2021-06-08},
	journal = {Frontiers in Plant Science},
	publisher = {Frontiers},
	author = {Rigal, Adeline and Ma, Qian and Robert, Stéphanie},
	year = {2014},
	keywords = {agonists and antagonists, hormone signaling, labeled molecule, phytohormones, structure-activity relationship},
}

Plants have acquired the capacity to grow continuously and adjust their morphology in response to endogenous and external signals, leading to a high architectural plasticity. The dynamic and differential distribution of phytohormones is an essential factor in these developmental changes. Phytohormone perception is a fast but complex process modulating specific developmental reprogramming. In recent years, chemical genomics or the use of small molecules to modulate target protein function has emerged as a powerful strategy to study complex biological processes in plants such as hormone signaling. Small molecules can be applied in a conditional, dose-dependent and reversible manner, with the advantage of circumventing the limitations of lethality and functional redundancy inherent to traditional mutant screens. High-throughput screening of diverse chemical libraries has led to the identification of bioactive molecules able to induce plant hormone-related phenotypes. Characterization of the cognate targets and pathways of those molecules has allowed the identification of novel regulatory components, providing new insights into the molecular mechanisms of plant hormone signaling. An extensive structure-activity relationship (SAR) analysis of the natural phytohormones, their designed synthetic analogues and newly identified bioactive molecules has led to the determination of the structural requirements essential for their bioactivity. In this review, we will summarize the so far identified small molecules and their structural variants targeting specific phytohormone signaling pathways. We will highlight how the SAR analyses have enabled better interrogation of the molecular mechanisms of phytohormone responses. Finally, we will discuss how labeled/tagged hormone analogues can be exploited, as compelling tools to better understand hormone signaling and transport mechanisms.

@incollection{hicks_using_2014,
	address = {Totowa, NJ},
	title = {Using a {Reverse} {Genetics} {Approach} to {Investigate} {Small}-{Molecule} {Activity}},
	volume = {1056},
	isbn = {978-1-62703-591-0 978-1-62703-592-7},
	url = {http://link.springer.com/10.1007/978-1-62703-592-7_6},
	doi = {10.1007/978-1-62703-592-7_6},
	urldate = {2021-06-08},
	booktitle = {Plant {Chemical} {Genomics}},
	publisher = {Humana Press},
	author = {Doyle, Siamsa M. and Robert, Stéphanie},
	editor = {Hicks, Glenn R and Robert, Stéphanie},
	year = {2014},
	note = {Series Title: Methods in Molecular Biology},
	pages = {51--62},
}

@article{le_hir_abcg9_2013,
	title = {{ABCG9}, {ABCG11} and {ABCG14} {ABC} transporters are required for vascular development in {Arabidopsis}},
	volume = {76},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12334},
	doi = {10/f22xd4},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Le Hir, Rozenn and Sorin, Clément and Chakraborti, Dipankar and Moritz, Thomas and Schaller, Hubert and Tellier, Frédérique and Robert, Stéphanie and Morin, Halima and Bakó, Laszlo and Bellini, Catherine},
	month = dec,
	year = {2013},
	pages = {811--824},
}

@article{sauer_auxin_2013,
	title = {Auxin: simply complicated},
	volume = {64},
	issn = {1460-2431, 0022-0957},
	shorttitle = {Auxin},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ert139},
	doi = {10/f3pxg2},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Sauer, Michael and Robert, Stéphanie and Kleine-Vehn, Jürgen},
	month = jun,
	year = {2013},
	pages = {2565--2577},
}

@article{tanaka_cell_2013,
	title = {Cell {Polarity} and {Patterning} by {PIN} {Trafficking} through {Early} {Endosomal} {Compartments} in {Arabidopsis} thaliana},
	volume = {9},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1003540},
	doi = {10/gbc9jh},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {PLoS Genetics},
	author = {Tanaka, Hirokazu and Kitakura, Saeko and Rakusová, Hana and Uemura, Tomohiro and Feraru, Mugurel I. and De Rycke, Riet and Robert, Stéphanie and Kakimoto, Tatsuo and Friml, Jiří},
	editor = {Luschnig, Christian},
	month = may,
	year = {2013},
	pages = {e1003540},
}

@article{simon_defining_2013,
	title = {Defining the selectivity of processes along the auxin response chain: a study using auxin analogues},
	volume = {200},
	issn = {0028-646X, 1469-8137},
	shorttitle = {Defining the selectivity of processes along the auxin response chain},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12437},
	doi = {10/f3p46z},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Simon, Sibu and Kubeš, Martin and Baster, Pawel and Robert, Stéphanie and Dobrev, Petre Ivanov and Friml, Jiří and Petrášek, Jan and Zažímalová, Eva},
	month = dec,
	year = {2013},
	pages = {1034--1048},
}

@article{boutte_echidna-mediated_2013,
	title = {{ECHIDNA}-mediated post-{Golgi} trafficking of auxin carriers for differential cell elongation},
	volume = {110},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1309057110},
	doi = {10/f2z6v9},
	language = {en},
	number = {40},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Boutte, Y. and Jonsson, K. and McFarlane, H. E. and Johnson, E. and Gendre, D. and Swarup, R. and Friml, J. and Samuels, L. and Robert, S. and Bhalerao, Rishikesh P.},
	month = oct,
	year = {2013},
	pages = {16259--16264},
}

@article{yu_root_2013,
	title = {{ROOT} {ULTRAVIOLET} {B}-{SENSITIVE1}/{WEAK} {AUXIN} {RESPONSE3} {Is} {Essential} for {Polar} {Auxin} {Transport} in {Arabidopsis}},
	volume = {162},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/162/2/965/6110776},
	doi = {10/f3rt2n},
	abstract = {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.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Yu, Hong and Karampelias, Michael and Robert, Stephanie and Peer, Wendy Ann and Swarup, Ranjan and Ye, Songqing and Ge, Lei and Cohen, Jerry and Murphy, Angus and Friml, Jirí and Estelle, Mark},
	month = may,
	year = {2013},
	pages = {965--976},
}

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.

@article{moschou_caspase-related_2013,
	title = {The {Caspase}-{Related} {Protease} {Separase} ({EXTRA} {SPINDLE} {POLES}) {Regulates} {Cell} {Polarity} and {Cytokinesis} in {Arabidopsis}[{C}][{W}]},
	volume = {25},
	issn = {1040-4651},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3723619/},
	doi = {10/f24kgw},
	abstract = {Separase is responsible for segregation of daughter chromatids during cell division in all eukaryotes. Here it is reported that in addition to regulating chromatid segregation, the plant homolog of separase regulates vesicle trafficking essential for the cytokinesis and establishment of cell polarity during tissue and organ patterning., Vesicle trafficking plays an important role in cell division, establishment of cell polarity, and translation of environmental cues to developmental responses. However, the molecular mechanisms regulating vesicle trafficking remain poorly understood. Here, we report that the evolutionarily conserved caspase-related protease separase (EXTRA SPINDLE POLES [ESP]) is required for the establishment of cell polarity and cytokinesis in Arabidopsis
thaliana. At the cellular level, separase colocalizes with microtubules and RabA2a (for RAS GENES FROM RAT BRAINA2a) GTPase-positive structures. Separase facilitates polar targeting of the auxin efflux carrier PIN-FORMED2 (PIN2) to the rootward side of the root cortex cells. Plants with the radially swollen4 (rsw4) allele with compromised separase activity, in addition to mitotic failure, display isotropic cell growth, perturbation of auxin gradient formation, slower gravitropic response in roots, and cytokinetic failure. Measurements of the dynamics of vesicle markers on the cell plate revealed an overall reduction of the delivery rates of KNOLLE and RabA2a GTPase in separase-deficient roots. Furthermore, dissociation of the clathrin light chain, a protein that plays major role in the formation of coated vesicles, was slower in rsw4 than in the control. Our results demonstrate that separase is a key regulator of vesicle trafficking, which is indispensable for cytokinesis and the establishment of cell polarity.},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Moschou, Panagiotis N. and Smertenko, Andrei P. and Minina, Elena A. and Fukada, Kazutake and Savenkov, Eugene I. and Robert, Stephanie and Hussey, Patrick J. and Bozhkov, Peter V.},
	month = jun,
	year = {2013},
	pages = {2171--2186},
}

Separase is responsible for segregation of daughter chromatids during cell division in all eukaryotes. Here it is reported that in addition to regulating chromatid segregation, the plant homolog of separase regulates vesicle trafficking essential for the cytokinesis and establishment of cell polarity during tissue and organ patterning., Vesicle trafficking plays an important role in cell division, establishment of cell polarity, and translation of environmental cues to developmental responses. However, the molecular mechanisms regulating vesicle trafficking remain poorly understood. Here, we report that the evolutionarily conserved caspase-related protease separase (EXTRA SPINDLE POLES [ESP]) is required for the establishment of cell polarity and cytokinesis in Arabidopsis thaliana. At the cellular level, separase colocalizes with microtubules and RabA2a (for RAS GENES FROM RAT BRAINA2a) GTPase-positive structures. Separase facilitates polar targeting of the auxin efflux carrier PIN-FORMED2 (PIN2) to the rootward side of the root cortex cells. Plants with the radially swollen4 (rsw4) allele with compromised separase activity, in addition to mitotic failure, display isotropic cell growth, perturbation of auxin gradient formation, slower gravitropic response in roots, and cytokinetic failure. Measurements of the dynamics of vesicle markers on the cell plate revealed an overall reduction of the delivery rates of KNOLLE and RabA2a GTPase in separase-deficient roots. Furthermore, dissociation of the clathrin light chain, a protein that plays major role in the formation of coated vesicles, was slower in rsw4 than in the control. Our results demonstrate that separase is a key regulator of vesicle trafficking, which is indispensable for cytokinesis and the establishment of cell polarity.

@incollection{audenaert_use_2013,
	address = {Hoboken, NJ},
	title = {The {Use} of {Chemical} {Biology} to {Study} {Plant} {Cellular} {Processes}: {Subcellular} {Trafficking}},
	isbn = {978-1-118-74292-1 978-0-470-94669-5},
	shorttitle = {The {Use} of {Chemical} {Biology} to {Study} {Plant} {Cellular} {Processes}},
	url = {http://doi.wiley.com/10.1002/9781118742921.ch5.2},
	doi = {10.1002/9781118742921.ch5.2},
	language = {en},
	urldate = {2021-06-08},
	booktitle = {Plant {Chemical} {Biology}},
	publisher = {John Wiley \& Sons, Inc},
	author = {Haeger, Ash and Łangowska, Malgorzata and Robert, Stéphanie},
	editor = {Audenaert, Dominique and Overvoorde, Paul},
	month = nov,
	year = {2013},
	pages = {218--231},
}

@article{chen_abp1_2012,
	title = {{ABP1} and {ROP6} {GTPase} {Signaling} {Regulate} {Clathrin}-{Mediated} {Endocytosis} in {Arabidopsis} {Roots}},
	volume = {22},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982212005738},
	doi = {10/f35br9},
	language = {en},
	number = {14},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Chen, Xu and Naramoto, Satoshi and Robert, Stéphanie and Tejos, Ricardo and Löfke, Christian and Lin, Deshu and Yang, Zhenbiao and Friml, Jiří},
	month = jul,
	year = {2012},
	pages = {1326--1332},
}

@article{baster_scftir1afb-auxin_2012,
	title = {{SCFTIR1}/{AFB}-auxin signalling regulates {PIN} vacuolar trafficking and auxin fluxes during root gravitropism},
	volume = {32},
	issn = {0261-4189, 1460-2075},
	url = {http://emboj.embopress.org/cgi/doi/10.1038/emboj.2012.310},
	doi = {10/f3m3cc},
	number = {2},
	urldate = {2021-06-08},
	journal = {The EMBO Journal},
	author = {Baster, Paweł 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, Jiří},
	month = dec,
	year = {2012},
	pages = {260--274},
}

@article{kitakura_clathrin_2011,
	title = {Clathrin {Mediates} {Endocytosis} and {Polar} {Distribution} of {PIN} {Auxin} {Transporters} in \textit{{Arabidopsis}}},
	volume = {23},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/23/5/1920/6097062},
	doi = {10/bdwh3s},
	abstract = {Abstract
            Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrin-mediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type–specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants.},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Kitakura, Saeko and Vanneste, Steffen and Robert, Stéphanie and Löfke, Christian and Teichmann, Thomas and Tanaka, Hirokazu and Friml, Jiří},
	month = may,
	year = {2011},
	pages = {1920--1931},
}

Abstract Endocytosis is a crucial mechanism by which eukaryotic cells internalize extracellular and plasma membrane material, and it is required for a multitude of cellular and developmental processes in unicellular and multicellular organisms. In animals and yeast, the best characterized pathway for endocytosis depends on the function of the vesicle coat protein clathrin. Clathrin-mediated endocytosis has recently been demonstrated also in plant cells, but its physiological and developmental roles remain unclear. Here, we assessed the roles of the clathrin-mediated mechanism of endocytosis in plants by genetic means. We interfered with clathrin heavy chain (CHC) function through mutants and dominant-negative approaches in Arabidopsis thaliana and established tools to manipulate clathrin function in a cell type–specific manner. The chc2 single mutants and dominant-negative CHC1 (HUB) transgenic lines were defective in bulk endocytosis as well as in internalization of prominent plasma membrane proteins. Interference with clathrin-mediated endocytosis led to defects in constitutive endocytic recycling of PIN auxin transporters and their polar distribution in embryos and roots. Consistent with this, these lines had altered auxin distribution patterns and associated auxin transport-related phenotypes, such as aberrant embryo patterning, imperfect cotyledon specification, agravitropic growth, and impaired lateral root organogenesis. Together, these data demonstrate a fundamental role for clathrin function in cell polarity, growth, patterning, and organogenesis in plants.

@article{drakakaki_clusters_2011,
	chapter = {Biological Sciences},
	title = {Clusters of bioactive compounds target dynamic endomembrane networks in vivo},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/43/17850},
	doi = {10/bf5jvk},
	abstract = {Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery.},
	language = {en},
	number = {43},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {National Academy of Sciences},
	author = {Drakakaki, Georgia and Robert, Stéphanie and Szatmari, Anna-Maria and Brown, Michelle Q. and Nagawa, Shingo and Damme, Daniel Van and Leonard, Marilyn and Yang, Zhenbiao and Girke, Thomas and Schmid, Sandra L. and Russinova, Eugenia and Friml, Jiří and Raikhel, Natasha V. and Hicks, Glenn R.},
	month = oct,
	year = {2011},
	keywords = {chemical genomics, endosidin, endosome, high content screen},
	pages = {17850--17855},
}

Endomembrane trafficking relies on the coordination of a highly complex, dynamic network of intracellular vesicles. Understanding the network will require a dissection of cargo and vesicle dynamics at the cellular level in vivo. This is also a key to establishing a link between vesicular networks and their functional roles in development. We used a high-content intracellular screen to discover small molecules targeting endomembrane trafficking in vivo in a complex eukaryote, Arabidopsis thaliana. Tens of thousands of molecules were prescreened and a selected subset was interrogated against a panel of plasma membrane (PM) and other endomembrane compartment markers to identify molecules that altered vesicle trafficking. The extensive image dataset was transformed by a flexible algorithm into a marker-by-phenotype-by-treatment time matrix and revealed groups of molecules that induced similar subcellular fingerprints (clusters). This matrix provides a platform for a systems view of trafficking. Molecules from distinct clusters presented avenues and enabled an entry point to dissect recycling at the PM, vacuolar sorting, and cell-plate maturation. Bioactivity in human cells indicated the value of the approach to identifying small molecules that are active in diverse organisms for biology and drug discovery.

@article{barberon_monoubiquitin-dependent_2011,
	title = {Monoubiquitin-dependent endocytosis of the {IRON}-{REGULATED} {TRANSPORTER} 1 ({IRT1}) transporter controls iron uptake in plants},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1100659108},
	doi = {10/dw2prg},
	language = {en},
	number = {32},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Barberon, Marie and Zelazny, Enric and Robert, Stéphanie and Conéjéro, Geneviève and Curie, Cathy and Friml, Jìří and Vert, Grégory},
	month = aug,
	year = {2011},
	pages = {E450--E458},
}

@article{kleinevehn_recycling_2011,
	title = {Recycling, clustering, and endocytosis jointly maintain {PIN} auxin carrier polarity at the plasma membrane},
	volume = {7},
	issn = {1744-4292, 1744-4292},
	url = {https://onlinelibrary.wiley.com/doi/10.1038/msb.2011.72},
	doi = {10/d9hncd},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Molecular Systems Biology},
	author = {Kleine‐Vehn, Jürgen and Wabnik, Krzysztof and Martinière, Alexandre and Łangowski, Łukasz and Willig, Katrin and Naramoto, Satoshi and Leitner, Johannes and Tanaka, Hirokazu and Jakobs, Stefan and Robert, Stéphanie and Luschnig, Christian and Govaerts, Willy and W Hell, Stefan and Runions, John and Friml, Jiří},
	month = jan,
	year = {2011},
	pages = {540},
}

@article{robert_abp1_2010,
	title = {{ABP1} mediates auxin inhibition of clathrin-dependent endocytosis in {Arabidopsis}},
	volume = {143},
	issn = {1097-4172},
	doi = {10/b86r8c},
	abstract = {Spatial distribution of the plant hormone auxin regulates multiple aspects of plant development. These self-regulating auxin gradients are established by the action of PIN auxin transporters, whose activity is regulated by their constitutive cycling between the plasma membrane and endosomes. Here, we show that auxin signaling by the auxin receptor AUXIN-BINDING PROTEIN 1 (ABP1) inhibits the clathrin-mediated internalization of PIN proteins. ABP1 acts as a positive factor in clathrin recruitment to the plasma membrane, thereby promoting endocytosis. Auxin binding to ABP1 interferes with this action and leads to the inhibition of clathrin-mediated endocytosis. Our study demonstrates that ABP1 mediates a nontranscriptional auxin signaling that regulates the evolutionarily conserved process of clathrin-mediated endocytosis and suggests that this signaling may be essential for the developmentally important feedback of auxin on its own transport.},
	language = {eng},
	number = {1},
	journal = {Cell},
	author = {Robert, Stéphanie and Kleine-Vehn, Jürgen and Barbez, Elke and Sauer, Michael and Paciorek, Tomasz and Baster, Pawel and Vanneste, Steffen and Zhang, Jing and Simon, Sibu and Čovanová, Milada and Hayashi, Kenichiro and Dhonukshe, Pankaj and Yang, Zhenbiao and Bednarek, Sebastian Y. and Jones, Alan M. and Luschnig, Christian and Aniento, Fernando and Zažímalová, Eva and Friml, Jiří},
	month = oct,
	year = {2010},
	keywords = {Arabidopsis, Arabidopsis Proteins, Cell Membrane, Clathrin, Endocytosis, Indoleacetic Acids, Membrane Transport Proteins, Plant Proteins, Receptors, Cell Surface},
	pages = {111--121},
}

Spatial distribution of the plant hormone auxin regulates multiple aspects of plant development. These self-regulating auxin gradients are established by the action of PIN auxin transporters, whose activity is regulated by their constitutive cycling between the plasma membrane and endosomes. Here, we show that auxin signaling by the auxin receptor AUXIN-BINDING PROTEIN 1 (ABP1) inhibits the clathrin-mediated internalization of PIN proteins. ABP1 acts as a positive factor in clathrin recruitment to the plasma membrane, thereby promoting endocytosis. Auxin binding to ABP1 interferes with this action and leads to the inhibition of clathrin-mediated endocytosis. Our study demonstrates that ABP1 mediates a nontranscriptional auxin signaling that regulates the evolutionarily conserved process of clathrin-mediated endocytosis and suggests that this signaling may be essential for the developmentally important feedback of auxin on its own transport.

@article{naramoto_adp-ribosylation_2010,
	title = {{ADP}-ribosylation factor machinery mediates endocytosis in plant cells},
	volume = {107},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1016260107},
	doi = {10/cwst7p},
	language = {en},
	number = {50},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Naramoto, S. and Kleine-Vehn, J. and Robert, S. and Fujimoto, M. and Dainobu, T. and Paciorek, T. and Ueda, T. and Nakano, A. and Van Montagu, M. C. E. and Fukuda, H. and Friml, J.},
	month = dec,
	year = {2010},
	pages = {21890--21895},
}

@article{ge_arabidopsis_2010,
	title = {Arabidopsis {ROOT} {UVB} {SENSITIVE2}/{WEAK} {AUXIN} {RESPONSE1} {Is} {Required} for {Polar} {Auxin} {Transport}},
	volume = {22},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.110.074195},
	doi = {10/brs5hr},
	abstract = {Auxin is an essential phytohormone that regulates many aspects of plant development. To identify new genes that function in auxin signaling, we performed a genetic screen for Arabidopsis thaliana mutants with an alteration in the expression of the auxin-responsive reporter DR5rev:GFP (for green fluorescent protein). One of the mutants recovered in this screen, called weak auxin response1 (wxr1), has a defect in auxin response and exhibits a variety of auxin-related growth defects in the root. Polar auxin transport is reduced in wxr1 seedlings, resulting in auxin accumulation in the hypocotyl and cotyledons and a reduction in auxin levels in the root apex. In addition, the levels of the PIN auxin transport proteins are reduced in the wxr1 root. We also show that WXR1 is ROOT UV-B SENSITIVE2 (RUS2), a member of the broadly conserved DUF647 domain protein family found in diverse eukaryotic organisms. Our data indicate that RUS2/WXR1 is required for auxin transport and to maintain the normal levels of PIN proteins in the root.},
	number = {6},
	urldate = {2021-06-21},
	journal = {The Plant Cell},
	author = {Ge, L. and Peer, W. and Robert, S. and Swarup, R. and Ye, S. and Prigge, M. and Cohen, J.D. and Friml, J. and Murphy, A. and Tang, D. and Estelle, M.},
	month = jun,
	year = {2010},
	pages = {1749--1761},
}

Auxin is an essential phytohormone that regulates many aspects of plant development. To identify new genes that function in auxin signaling, we performed a genetic screen for Arabidopsis thaliana mutants with an alteration in the expression of the auxin-responsive reporter DR5rev:GFP (for green fluorescent protein). One of the mutants recovered in this screen, called weak auxin response1 (wxr1), has a defect in auxin response and exhibits a variety of auxin-related growth defects in the root. Polar auxin transport is reduced in wxr1 seedlings, resulting in auxin accumulation in the hypocotyl and cotyledons and a reduction in auxin levels in the root apex. In addition, the levels of the PIN auxin transport proteins are reduced in the wxr1 root. We also show that WXR1 is ROOT UV-B SENSITIVE2 (RUS2), a member of the broadly conserved DUF647 domain protein family found in diverse eukaryotic organisms. Our data indicate that RUS2/WXR1 is required for auxin transport and to maintain the normal levels of PIN proteins in the root.

@article{drakakaki_chemical_2009,
	title = {Chemical dissection of endosomal pathways},
	volume = {4},
	issn = {1559-2316},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634075/},
	abstract = {Membrane trafficking and associated signal transduction pathways are critical for plant development and responses to environment. These transduction pathways, including those for brassinosteroids and auxins, require endocytosis to endosomes and recycling back to the plasma membrane. A major challenge toward understanding these processes and their biological roles has been the highly dynamic nature of endomembrane trafficking. To effectively study endocytosis and recycling, which occur in a time frame of minutes, bioactive chemicals provide a powerful and exacting tool. Pharmacological inhibitors such as Brefeldin A (BFA) and the newly identified Endosidin 1 (ES1) have been used to define endosome compartments. ES1 is a clear example of the ability of chemicals to dissect even distinct subpopulations of endosomes involved in trafficking and signal transduction. The ability to characterize and dissect such highly dynamic pathways in a temporal and spatial manner is possible only using pharmacological reagents which can act rapidly and reversibly.},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Signaling \& Behavior},
	author = {Drakakaki, Georgia and Robert, Stéphanie and Raikhel, Natasha V and Hicks, Glenn R},
	month = jan,
	year = {2009},
	pages = {57--62},
}

Membrane trafficking and associated signal transduction pathways are critical for plant development and responses to environment. These transduction pathways, including those for brassinosteroids and auxins, require endocytosis to endosomes and recycling back to the plasma membrane. A major challenge toward understanding these processes and their biological roles has been the highly dynamic nature of endomembrane trafficking. To effectively study endocytosis and recycling, which occur in a time frame of minutes, bioactive chemicals provide a powerful and exacting tool. Pharmacological inhibitors such as Brefeldin A (BFA) and the newly identified Endosidin 1 (ES1) have been used to define endosome compartments. ES1 is a clear example of the ability of chemicals to dissect even distinct subpopulations of endosomes involved in trafficking and signal transduction. The ability to characterize and dissect such highly dynamic pathways in a temporal and spatial manner is possible only using pharmacological reagents which can act rapidly and reversibly.

@article{robert_powerful_2009,
	title = {Powerful partners: {Arabidopsis} and chemical genomics},
	volume = {7},
	issn = {1543-8120},
	shorttitle = {Powerful partners},
	doi = {10/fwnm6m},
	abstract = {Chemical genomics (i.e. genomics scale chemical genetics) approaches capitalize on the ability of low molecular mass molecules to modify biological processes. Such molecules are used to modify the activity of a protein or a pathway in a manner that it is tunable and reversible. Bioactive chemicals resulting from forward or reverse chemical screens can be useful in understanding and dissecting complex biological processes due to the essentially limitless variation in structure and activities inherent in chemical space. A major advantage of this approach as a powerful addition to conventional plant genetics is the fact that chemical genomics can address loss-of-function lethality and redundancy. Furthermore, the ability of chemicals to be added at will and to act quickly can permit the study of processes that are highly dynamic such as endomembrane trafficking. An important aspect of utilizing small molecules effectively is to characterize bioactive chemicals in detail including an understanding of structure-activity relationships and the identification of active and inactive analogs. Bioactive chemicals can be useful as reagents to probe biological pathways directly. However, the identification of cognate targets and their pathways is also informative and can be achieved by screens for genetic resistance or hypersensitivity in Arabidopsis thaliana or other organisms from which the results can be translated to plants. In addition, there are approaches utilizing "tagged" chemical libraries that possess reactive moieties permitting the immobilization of active compounds. This opens the possibility for biochemical purification of putative cognate targets. We will review approaches to screen for bioactive chemicals that affect biological processes in Arabidopsis and provide several examples of the power and challenges inherent in this new approach in plant biology.},
	language = {eng},
	journal = {The Arabidopsis Book},
	author = {Robert, Stéphanie and Raikhel, Natasha V. and Hicks, Glenn R.},
	year = {2009},
	pages = {e0109},
}

Chemical genomics (i.e. genomics scale chemical genetics) approaches capitalize on the ability of low molecular mass molecules to modify biological processes. Such molecules are used to modify the activity of a protein or a pathway in a manner that it is tunable and reversible. Bioactive chemicals resulting from forward or reverse chemical screens can be useful in understanding and dissecting complex biological processes due to the essentially limitless variation in structure and activities inherent in chemical space. A major advantage of this approach as a powerful addition to conventional plant genetics is the fact that chemical genomics can address loss-of-function lethality and redundancy. Furthermore, the ability of chemicals to be added at will and to act quickly can permit the study of processes that are highly dynamic such as endomembrane trafficking. An important aspect of utilizing small molecules effectively is to characterize bioactive chemicals in detail including an understanding of structure-activity relationships and the identification of active and inactive analogs. Bioactive chemicals can be useful as reagents to probe biological pathways directly. However, the identification of cognate targets and their pathways is also informative and can be achieved by screens for genetic resistance or hypersensitivity in Arabidopsis thaliana or other organisms from which the results can be translated to plants. In addition, there are approaches utilizing "tagged" chemical libraries that possess reactive moieties permitting the immobilization of active compounds. This opens the possibility for biochemical purification of putative cognate targets. We will review approaches to screen for bioactive chemicals that affect biological processes in Arabidopsis and provide several examples of the power and challenges inherent in this new approach in plant biology.

@article{robert_endosidin1_2008,
	chapter = {Biological Sciences},
	title = {Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor {BRI1} and the auxin transporters {PIN2} and {AUX1}},
	volume = {105},
	copyright = {© 2008 by The National Academy of Sciences of the USA},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/105/24/8464},
	doi = {10/ck5x78},
	abstract = {Although it is known that proteins are delivered to and recycled from the plasma membrane (PM) via endosomes, the nature of the compartments and pathways responsible for cargo and vesicle sorting and cellular signaling is poorly understood. To define and dissect specific recycling pathways, chemical effectors of proteins involved in vesicle trafficking, especially through endosomes, would be invaluable. Thus, we identified chemicals affecting essential steps in PM/endosome trafficking, using the intensely localized PM transport at the tips of germinating pollen tubes. The basic mechanisms of this localized growth are likely similar to those of non-tip growing cells in seedlings. The compound endosidin 1 (ES1) interfered selectively with endocytosis in seedlings, providing a unique tool to dissect recycling pathways. ES1 treatment induced the rapid agglomeration of the auxin translocators PIN2 and AUX1 and the brassinosteroid receptor BRI1 into distinct endomembrane compartments termed “endosidin bodies”; however, the markers PIN1, PIN7, and other PM proteins were unaffected. Endosidin bodies were defined by the syntaxin SYP61 and the V-ATPase subunit VHA-a1, two trans-Golgi network (TGN)/endosomal proteins. Interestingly, brassinosteroid (BR)-induced gene expression was inhibited by ES1 and treated seedlings displayed a brassinolide (BL)-insensitive phenotype similar to a bri1 loss-of-function mutant. No effect was detected in auxin signaling. Thus, PIN2, AUX1, and BRI1 use interactive pathways involving an early SYP61/VHA-a1 endosomal compartment.},
	language = {en},
	number = {24},
	urldate = {2021-06-10},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {National Academy of Sciences},
	author = {Robert, Stéphanie and Chary, S. Narasimha and Drakakaki, Georgia and Li, Shundai and Yang, Zhenbiao and Raikhel, Natasha V. and Hicks, Glenn R.},
	month = jun,
	year = {2008},
	keywords = {Arabidopsis, chemical genomics, endosome, prieurianin},
	pages = {8464--8469},
}

Although it is known that proteins are delivered to and recycled from the plasma membrane (PM) via endosomes, the nature of the compartments and pathways responsible for cargo and vesicle sorting and cellular signaling is poorly understood. To define and dissect specific recycling pathways, chemical effectors of proteins involved in vesicle trafficking, especially through endosomes, would be invaluable. Thus, we identified chemicals affecting essential steps in PM/endosome trafficking, using the intensely localized PM transport at the tips of germinating pollen tubes. The basic mechanisms of this localized growth are likely similar to those of non-tip growing cells in seedlings. The compound endosidin 1 (ES1) interfered selectively with endocytosis in seedlings, providing a unique tool to dissect recycling pathways. ES1 treatment induced the rapid agglomeration of the auxin translocators PIN2 and AUX1 and the brassinosteroid receptor BRI1 into distinct endomembrane compartments termed “endosidin bodies”; however, the markers PIN1, PIN7, and other PM proteins were unaffected. Endosidin bodies were defined by the syntaxin SYP61 and the V-ATPase subunit VHA-a1, two trans-Golgi network (TGN)/endosomal proteins. Interestingly, brassinosteroid (BR)-induced gene expression was inhibited by ES1 and treated seedlings displayed a brassinolide (BL)-insensitive phenotype similar to a bri1 loss-of-function mutant. No effect was detected in auxin signaling. Thus, PIN2, AUX1, and BRI1 use interactive pathways involving an early SYP61/VHA-a1 endosomal compartment.

@article{sanmartin_divergent_2007,
	title = {Divergent functions of {VTI12} and {VTI11} in trafficking to storage and lytic vacuoles in {Arabidopsis}},
	volume = {104},
	issn = {0027-8424},
	doi = {10/bt2khm},
	abstract = {The protein storage vacuole (PSV) is a plant-specific organelle that accumulates reserve proteins, one of the main agricultural products obtained from crops. Despite the importance of this process, the cellular machinery required for transport and accumulation of storage proteins remains largely unknown. Interfering with transport to PSVs has been shown to result in secretion of cargo. Therefore, secretion of a suitable marker could be used as an assay to identify mutants in this pathway. CLV3, a negative regulator of shoot stem cell proliferation, is an extracellular ligand that is rendered inactive when targeted to vacuoles. We devised an assay where trafficking mutants secrete engineered vacuolar CLV3 and show reduced meristems, a phenotype easily detected by visual inspection of plants. We tested this scheme in plants expressing VAC2, a fusion of CLV3 to the vacuolar sorting signal from the storage protein barley lectin. In this way, we determined that trafficking of VAC2 requires the SNARE VTI12 but not its close homologue, the conditionally redundant VTI11 protein. Furthermore, a vti12 mutant is specifically altered in transport of storage proteins, whereas a vti11 mutant is affected in transport of a lytic vacuole marker. These results demonstrate the specialization of VTI12 and VTI11 in mediating trafficking to storage and lytic vacuoles, respectively. Moreover, they validate the VAC2 secretion assay as a simple method to isolate genes that mediate trafficking to the PSV.},
	language = {eng},
	number = {9},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Sanmartín, Maite and Ordóñez, Angel and Sohn, Eun Ju and Robert, Stephanie and Sánchez-Serrano, José Juán and Surpin, Marci A. and Raikhel, Natasha V. and Rojo, Enrique},
	month = feb,
	year = {2007},
	keywords = {Arabidopsis, Arabidopsis Proteins, Microscopy, Fluorescence, Plant Lectins, Protein Transport, Qb-SNARE Proteins, Vacuoles},
	pages = {3645--3650},
}

The protein storage vacuole (PSV) is a plant-specific organelle that accumulates reserve proteins, one of the main agricultural products obtained from crops. Despite the importance of this process, the cellular machinery required for transport and accumulation of storage proteins remains largely unknown. Interfering with transport to PSVs has been shown to result in secretion of cargo. Therefore, secretion of a suitable marker could be used as an assay to identify mutants in this pathway. CLV3, a negative regulator of shoot stem cell proliferation, is an extracellular ligand that is rendered inactive when targeted to vacuoles. We devised an assay where trafficking mutants secrete engineered vacuolar CLV3 and show reduced meristems, a phenotype easily detected by visual inspection of plants. We tested this scheme in plants expressing VAC2, a fusion of CLV3 to the vacuolar sorting signal from the storage protein barley lectin. In this way, we determined that trafficking of VAC2 requires the SNARE VTI12 but not its close homologue, the conditionally redundant VTI11 protein. Furthermore, a vti12 mutant is specifically altered in transport of storage proteins, whereas a vti11 mutant is affected in transport of a lytic vacuole marker. These results demonstrate the specialization of VTI12 and VTI11 in mediating trafficking to storage and lytic vacuoles, respectively. Moreover, they validate the VAC2 secretion assay as a simple method to isolate genes that mediate trafficking to the PSV.

@article{robert_isolation_2007,
	title = {Isolation of intact vacuoles from {Arabidopsis} rosette leaf–derived protoplasts},
	volume = {2},
	copyright = {2007 Nature Publishing Group},
	issn = {1750-2799},
	url = {https://www.nature.com/articles/nprot.2007.26},
	doi = {10/c58qb9},
	abstract = {Vacuoles are very prominent compartments within plant cells, and understanding of their function relies on knowledge of their content. Here, we present a simple vacuole purification protocol that was successfully used for large-scale isolation of vacuoles, free of significant contamination from other endomembrane compartments. This method is based on osmotic and thermal disruption of mesophyl-derived Arabidopsis protoplasts, followed by a density gradient fractionation of the cellular content. The whole procedure, including protoplast isolation, takes approximately 6 h.},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {Nature Protocols},
	publisher = {Nature Publishing Group},
	author = {Robert, Stéphanie and Zouhar, Jan and Carter, Clay and Raikhel, Natasha},
	month = feb,
	year = {2007},
	note = {Number: 2},
	pages = {259--262},
}

Vacuoles are very prominent compartments within plant cells, and understanding of their function relies on knowledge of their content. Here, we present a simple vacuole purification protocol that was successfully used for large-scale isolation of vacuoles, free of significant contamination from other endomembrane compartments. This method is based on osmotic and thermal disruption of mesophyl-derived Arabidopsis protoplasts, followed by a density gradient fractionation of the cellular content. The whole procedure, including protoplast isolation, takes approximately 6 h.

@article{drakakaki_arabidopsis_2006,
	title = {Arabidopsis {Reversibly} {Glycosylated} {Polypeptides} 1 and 2 {Are} {Essential} for {Pollen} {Development}},
	volume = {142},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.106.086363},
	doi = {10.1104/pp.106.086363},
	abstract = {Reversibly glycosylated polypeptides (RGPs) have been implicated in polysaccharide biosynthesis. To date, to our knowledge, no direct evidence exists for the involvement of RGPs in a particular biochemical process. The Arabidopsis (Arabidopsis thaliana) genome contains five RGP genes out of which RGP1 and RGP2 share the highest sequence identity. We characterized the native expression pattern of Arabidopsis RGP1 and RGP2 and used reverse genetics to investigate their respective functions. Although both genes are ubiquitously expressed, the highest levels are observed in actively growing tissues and in mature pollen, in particular. RGPs showed cytoplasmic and transient association with Golgi. In addition, both proteins colocalized in the same compartments and coimmunoprecipitated from plant cell extracts. Single-gene disruptions did not show any obvious morphological defects under greenhouse conditions, whereas the double-insertion mutant could not be recovered. We present evidence that the double mutant is lethal and demonstrate the critical role of RGPs, particularly in pollen development. Detailed analysis demonstrated that mutant pollen development is associated with abnormally enlarged vacuoles and a poorly defined inner cell wall layer, which consequently results in disintegration of the pollen structure during pollen mitosis I. Taken together, our results indicate that RGP1 and RGP2 are required during microspore development and pollen mitosis, either affecting cell division and/or vacuolar integrity.},
	number = {4},
	urldate = {2021-10-21},
	journal = {Plant Physiology},
	author = {Drakakaki, Georgia and Zabotina, Olga and Delgado, Ivan and Robert, Stéphanie and Keegstra, Kenneth and Raikhel, Natasha},
	month = dec,
	year = {2006},
	pages = {1480--1492},
}

Reversibly glycosylated polypeptides (RGPs) have been implicated in polysaccharide biosynthesis. To date, to our knowledge, no direct evidence exists for the involvement of RGPs in a particular biochemical process. The Arabidopsis (Arabidopsis thaliana) genome contains five RGP genes out of which RGP1 and RGP2 share the highest sequence identity. We characterized the native expression pattern of Arabidopsis RGP1 and RGP2 and used reverse genetics to investigate their respective functions. Although both genes are ubiquitously expressed, the highest levels are observed in actively growing tissues and in mature pollen, in particular. RGPs showed cytoplasmic and transient association with Golgi. In addition, both proteins colocalized in the same compartments and coimmunoprecipitated from plant cell extracts. Single-gene disruptions did not show any obvious morphological defects under greenhouse conditions, whereas the double-insertion mutant could not be recovered. We present evidence that the double mutant is lethal and demonstrate the critical role of RGPs, particularly in pollen development. Detailed analysis demonstrated that mutant pollen development is associated with abnormally enlarged vacuoles and a poorly defined inner cell wall layer, which consequently results in disintegration of the pollen structure during pollen mitosis I. Taken together, our results indicate that RGP1 and RGP2 are required during microspore development and pollen mitosis, either affecting cell division and/or vacuolar integrity.

@article{robert_arabidopsis_2005,
	title = {An {Arabidopsis} {Endo}-1,4-β-d-{Glucanase} {Involved} in {Cellulose} {Synthesis} {Undergoes} {Regulated} {Intracellular} {Cycling}},
	volume = {17},
	issn = {1040-4651},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1315376/},
	doi = {10.1105/tpc.105.036228},
	abstract = {The synthesis of cellulose microfibrils requires the presence of a membrane-bound endo-1,4-β-d-glucanase, KORRIGAN1 (KOR1). Although the exact biochemical role of KOR1 in cellulose synthesis is unknown, we used the protein as a marker to explore the potential involvement of subcellular transport processes in cellulose synthesis. Using immunofluorescence and a green fluorescent protein (GFP)–KOR1 fusion that complemented the phenotype conferred by the kor1-1 mutant, we investigated the distribution of KOR1 in epidermal cells in the root meristem. KOR1 was localized in intracellular compartments corresponding to a heterogeneous population of organelles, which comprised the Golgi apparatus, FM4-64–labeled compartments referred to as early endosomes, and, in the case of GFP-KOR1, the tonoplast. Inhibition of cellulose synthesis by isoxaben promoted a net redistribution of GFP-KOR1 toward a homogeneous population of compartments, distinct from early endosomes, which were concentrated close to the plasma membrane facing the root surface. A redistribution of GFP-KOR1 away from early endosomes was also observed in the same cells at later stages of cell elongation. A subpopulation of GFP-KOR1–containing compartments followed trajectories along the plasma membrane, and this motility required intact microtubules. These observations demonstrate that the deposition of cellulose, like chitin synthesis in yeast, involves the regulated intracellular cycling of at least one enzyme required for its synthesis.},
	number = {12},
	urldate = {2021-10-21},
	journal = {The Plant Cell},
	author = {Robert, Stéphanie and Bichet, Adeline and Grandjean, Olivier and Kierzkowski, Daniel and Satiat-Jeunemaître, Béatrice and Pelletier, Sandra and Hauser, Marie-Theres and Höfte, Herman and Vernhettes, Samantha},
	month = dec,
	year = {2005},
	pages = {3378--3389},
}

The synthesis of cellulose microfibrils requires the presence of a membrane-bound endo-1,4-β-d-glucanase, KORRIGAN1 (KOR1). Although the exact biochemical role of KOR1 in cellulose synthesis is unknown, we used the protein as a marker to explore the potential involvement of subcellular transport processes in cellulose synthesis. Using immunofluorescence and a green fluorescent protein (GFP)–KOR1 fusion that complemented the phenotype conferred by the kor1-1 mutant, we investigated the distribution of KOR1 in epidermal cells in the root meristem. KOR1 was localized in intracellular compartments corresponding to a heterogeneous population of organelles, which comprised the Golgi apparatus, FM4-64–labeled compartments referred to as early endosomes, and, in the case of GFP-KOR1, the tonoplast. Inhibition of cellulose synthesis by isoxaben promoted a net redistribution of GFP-KOR1 toward a homogeneous population of compartments, distinct from early endosomes, which were concentrated close to the plasma membrane facing the root surface. A redistribution of GFP-KOR1 away from early endosomes was also observed in the same cells at later stages of cell elongation. A subpopulation of GFP-KOR1–containing compartments followed trajectories along the plasma membrane, and this motility required intact microtubules. These observations demonstrate that the deposition of cellulose, like chitin synthesis in yeast, involves the regulated intracellular cycling of at least one enzyme required for its synthesis.

@article{robert_mechanism_2004,
	title = {The mechanism and regulation of cellulose synthesis in primary walls: lessons from cellulose-deficient {Arabidopsis} mutants},
	volume = {11},
	issn = {1572-882X},
	shorttitle = {The mechanism and regulation of cellulose synthesis in primary walls},
	url = {https://doi.org/10.1023/B:CELL.0000046415.45774.80},
	doi = {10/ftnsm7},
	abstract = {Cellulose-deficient Arabidopsis mutants were identified using FT-IR microspectroscopy. The study of these mutants not only led to the identification of actors in cellulose synthesis, but also provided insights in the organization of the hexameric terminal complex from CESA mutants and identified unsuspected accessory proteins with so far unknown roles in the synthesis and/or assembly of cellulose microfibrils. Finally, mutant analysis established a role for protein glycosylation in cellulose synthesis and provided new perspectives on the developmental regulation of cell wall synthesis and the role that cellulose synthesis plays in the control of cell elongation.},
	language = {en},
	number = {3},
	urldate = {2021-06-15},
	journal = {Cellulose},
	author = {Robert, Stéphanie and Mouille, Grégory and Höfte, Herman},
	month = sep,
	year = {2004},
	pages = {351--364},
}

Cellulose-deficient Arabidopsis mutants were identified using FT-IR microspectroscopy. The study of these mutants not only led to the identification of actors in cellulose synthesis, but also provided insights in the organization of the hexameric terminal complex from CESA mutants and identified unsuspected accessory proteins with so far unknown roles in the synthesis and/or assembly of cellulose microfibrils. Finally, mutant analysis established a role for protein glycosylation in cellulose synthesis and provided new perspectives on the developmental regulation of cell wall synthesis and the role that cellulose synthesis plays in the control of cell elongation.