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The transcription factor BRI1-EMS-SUPRESSOR 1 (BES1) is a master regulator of brassinosteroid (BR)-regulated gene expression. BES1 together with BRASSINAZOLE-RESISTANT 1 (BZR1) drive activated or repressed expression of several genes, and have a prominent role in negative regulation of BR synthesis. Here, we report that BES1 interaction with TOPLESS (TPL), via its ERF-associated amphiphilic repression (EAR) motif, is essential for BES1-mediated control of organ boundary formation in the shoot apical meristem and the regulation of quiescent center (QC) cell division in roots. We show that TPL binds via BES1 to the promoters of the CUC3 and BRAVO targets and suppresses their expression. Ectopic expression of TPL leads to similar organ boundary defects and alterations in QC cell division rate to the bes1-d mutation, while bes1-d defects are suppressed by the dominant interfering protein encoded by tpl-1, with these effects respectively correlating with changes in CUC3 and BRAVO expression. Together, our data unveil a pivotal role of the co-repressor TPL in the shoot and root meristems, which relies on its interaction with BES1 and regulation of BES1 target gene expression., C.M. was initially supported by a Juan de la Cierva contract from the Spanish Ministry of Science and Innovation (Ministerio de Ciencia e Innovación). This work was supported by grants BIO2011-30546 and BIO2014-60064-R from the Spanish Ministry of Economy and Competitiveness (Ministerio de Economía y Competitividad, MINECO). The A.I.C.-D. laboratory is funded by a BIO2013-43873 grant from MINECO and by a European Research Council Consolidator Grant (ERC-2015-CoG-683163).

Summary Plants are able to orient their growth according to gravity, which ultimately controls both shoot and root architecture.1 Gravitropism is a dynamic process whereby gravistimulation induces the asymmetric distribution of the plant hormone auxin, leading to asymmetric growth, organ bending, and subsequent reset of auxin distribution back to the original pre-gravistimulation situation.1, 2, 3 Differential auxin accumulation during the gravitropic response depends on the activity of polarly localized PIN-FORMED (PIN) auxin-efflux carriers.1, 2, 3, 4 In particular, the timing of this dynamic response is regulated by PIN2,5,6 but the underlying molecular mechanisms are poorly understood. Here, we show that MEMBRANE ASSOCIATED KINASE REGULATOR2 (MAKR2) controls the pace of the root gravitropic response. We found that MAKR2 is required for the PIN2 asymmetry during gravitropism by acting as a negative regulator of the cell-surface signaling mediated by the receptor-like kinase TRANSMEMBRANE KINASE1 (TMK1).2,7, 8, 9, 10 Furthermore, we show that the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner. Our findings suggest that the timing of the root gravitropic response is orchestrated by the reversible inhibition of the TMK1 signaling pathway at the cell surface., Graphical Abstract, Highlights • MAKR2 is co-expressed with PIN2 and regulates the pace of root gravitropism • MAKR2 controls PIN2 asymmetric accumulation at the root level during gravitropism • MAKR2 binds to and is a negative regulator of the TMK1 receptor kinase • Auxin antagonizes the MAKR2 inhibition of TMK1 by delocalizing MAKR2 in the cytosol, Marquès-Bueno, Armengot et al. show that the unstructured protein MAKR2 controls the dynamics of the root gravitropic response by acting as a negative regulator of the TMK1 receptor kinase. In addition, the MAKR2 inhibitory effect on TMK1 signaling is antagonized by auxin itself, which triggers rapid MAKR2 membrane dissociation in a TMK1-dependent manner.

Understanding how reactive oxygen species (ROS) are sensed could help engineer plants with better stress responses that are relying on the production of ROS. Here, we summarize the latest research in ROS signaling with focus on the discovery by Wu et al. of a leucine-rich repeat receptor kinase (LRR-RK) as a hydrogen peroxide (H2O2) sensor., A.I.C.-D. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 683163). A.I.C-D. is a recipient of a grant (FEDER-BIO2016-78150-P) funded by the Spanish Ministry of Economy and Competitiveness-National Research Agency, and the European Regional Development Fund. A.P-R. is recipient of a PhD fellowship funded by the Spanish Ministry of Economy and Competitiveness-National Research Agency and the European Social Fund (BES-2016-077106) from the ‘Severo Ochoa Programme for Centers of Excellence in R&D’ 2016–2019 from the Ministerio de Ciencia e Innovación (SEV-2015-0533) in the A.I.C-D. laboratory. We also acknowledge the support from the CERCA Programme/Generalitat de Catalunya.

Understanding stem cell regulatory circuits is the next challenge in plant biology, as these cells are essential for tissue growth and organ regeneration in response to stress. In the Arabidopsis primary root apex, stem cell-specific transcription factors BRAVO and WOX5 co-localize in the quiescent centre (QC) cells, where they commonly repress cell division so that these cells can act as a reservoir to replenish surrounding stem cells, yet their molecular connection remains unknown. Genetic and biochemical analysis indicates that BRAVO and WOX5 form a transcription factor complex that modulates gene expression in the QC cells to preserve overall root growth and architecture. Furthermore, by using mathematical modelling we establish that BRAVO uses the WOX5/BRAVO complex to promote WOX5 activity in the stem cells. Our results unveil the importance of transcriptional regulatory circuits in plant stem cell development., A.I.C-D. is a recipient of a BIO2016-78955 grant from the Spanish Ministry of Economy and Competitiveness and a European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163). I.B-P. is funded by the FPU15/02822 grant from the Spanish Ministry of Education, Culture and Sport; N.B. by the FI-DGR 2016FI_B 00472 grant from the AGAUR, Generalitat de Catalunya; and A.P-R. by the SEV-2015-0533 from the Severo Ochoa Programme for Centers of Excellence in R&D. M.I. and J.M. acknowledge support from the Spanish Ministry of Economy and Competitiveness and FEDER (EU) through grant FIS2015-66503-C3-3-P, from Ministerio de Ciencia, Innovación y Universidades / Agencia Estatal de Investigación / Fondo Europeo de Desarrollo Regional, Unión Europea through grant PGC2018-101896-B-I00 and from the Generalitat de Catalunya through Grup de Recerca Consolidat 2014 SGR 878 and 2017 SGR 1061. J.M. is funded by the Spanish Ministry of Education through BES-2016-078218. Y.S. and R.C.D. were funded by the Deutsche Forschungsgesellschaft (DFG) (grant STA12/12 1-1). A.I.C.-D.–A.C. collaboration was funded by the European Regional Development Funds and Marie Curie IRSES Project DEANN (PIRSES-GA-2013-612583). CRAG is funded by “Severo Ochoa Programme” from Centers of Excellence in R&D 2016-2019 (SEV-2015-485 0533).

Brassinosteroids (BRs) are steroid hormones that play crucial roles in plant growth, development and adaptation to shifting environmental conditions. Our current understanding of the origin, evolution and functional significance of BRs is influenced by a double-edged bias: most we know stems from studies on a single species and, on the flip side, dearth of information from a phylogenetically broad and significant array of land plants precludes well-grounded comparisons. Here, we provide an update on BR presence and sensing along land plant evolution. Furthermore, a comprehensive search in all major plant lineages reveals the widespread presence of BR-receptor related sequences, suggesting that steroid-related signals may have been functional early in the evolution of land plants., A.I.C.D. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 683163). A.I.C.D. is a recipient of a grant (FEDER-BIO2016-78150-P) funded by the Spanish Ministry of Economy and Competitiveness-National Research Agency, and the European Regional Development Fund. M.F.G. PhD thesis is funded by the FPU fellowship (FPU16/06952) funded by the Ministry of Education, Culture and Sports, in A.I.C.D. laboratory. M.M.B. have received funding from ERC-2015-CoG-683163 granted to the A.I.C.D. laboratory. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D 2016-2019 (SEV-2015-0533)” and by the CERCA Programme/Generalitat de Catalunya. S.M.G. is a recipient of a grant from Agencia Nacional de Promoción Científica y Tecnológica, Argentina (PICT2016-2234).

Drought alone causes more annual loss in crop yield than all pathogens combined. To adapt to moisture gradients in soil, plants alter their physiology, modify root growth and architecture, and close stomata on their aboveground segments. These tissue-specific responses modify the flux of cellular signals, resulting in early flowering or stunted growth and, often, reduced yield. Physiological and molecular analyses of the model plant Arabidopsis thaliana have identified phytohormone signaling as key for regulating the response to drought or water insufficiency. Here we discuss how engineering hormone signaling in specific cells and cellular domains can facilitate improved plant responses to drought. We explore current knowledge and future questions central to the quest to produce high-yield, drought-resistant crops., A.I.C.-D. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement 683163). A.I.C.-D. is a recipient of a BIO2016-78150-P grant funded by the Spanish Ministry of Economy and Competitiveness and Agencia Estatal de Investigación (MINECO/AEI) and Fondo Europeo de Desarrollo Regional (FEDER). A.G. has received funding by a postdoctoral fellowship from the “Severo Ochoa Programme for Centers of Excellence in R&D” 2016–2019 from the Ministerio de Ciencia e Innovación (SEV-2015-0533). A.G. and A.R.-M. have received funding from ERC-2015-CoG–683163 granted to the A.I.C.-D. laboratory. A.R.-M. is a predoctoral fellow from Fundación Tatiana Pérez de Guzmán el Bueno. This work was supported by the CERCA Programme/Generalitat de Catalunya.

Drought is the primary cause of agricultural loss globally, and represents a major threat to food security. Currently, plant biotechnology stands as one of the most promising fields when it comes to developing crops that are able to produce high yields in water-limited conditions. From studies of Arabidopsis thaliana whole plants, the main response mechanisms to drought stress have been uncovered, and multiple drought resistance genes have already been engineered into crops. So far, most plants with enhanced drought resistance have displayed reduced crop yield, meaning that there is still a need to search for novel approaches that can uncouple drought resistance from plant growth. Our laboratory has recently shown that the receptors of brassinosteroid (BR) hormones use tissue-specific pathways to mediate different developmental responses during root growth. In Arabidopsis, we found that increasing BR receptors in the vascular plant tissues confers resistance to drought without penalizing growth, opening up an exceptional opportunity to investigate the mechanisms that confer drought resistance with cellular specificity in plants. In this review, we provide an overview of the most promising phenotypical drought traits that could be improved biotechnologically to obtain drought-tolerant cereals. In addition, we discuss how current genome editing technologies could help to identify and manipulate novel genes that might grant resistance to drought stress. In the upcoming years, we expect that sustainable solutions for enhancing crop production in water-limited environments will be identified through joint efforts., AIC-D is a recipient of a BIO2016-78150-P grant funded by the Spanish Ministry of Economy and Competitiveness and Agencia Estatal de Investigación (MINECO/AEI) and Fondo Europeo de Desarrollo Regional (FEDER), and a European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163). JBF-M is supported by the grant 2017SGR718 from Secretaria d’Universitats i Recerca del Departament d’Empresa i Coneixement de la Generalitat de Catalunya and by the ERC- 2015-CoG – 683163 granted to the AIC-D laboratory. AR-M is a predoctoral fellow from Fundación Tatiana Pérez de Guzmán el Bueno. DB-E and DM are funded by the ERC-2015-CoG – 683163 granted to the AIC-D laboratory. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No 683163). This work was supported by the CERCA Programme from the Generalitat de Catalunya. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness (MINECO), through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016-2019 (SEV-2015-0533).

Brassinosteroids (BRs) play essential roles in growth and development in seed plants;1 disturbances in BR homeostasis lead to altered mitotic activity in meristems2,3 and organ boundaries4,5 and to changes in meristem determinacy.6 An intricate signaling cascade linking the perception of BRs at the plasma membrane to the regulation of master transcriptional regulators belonging to the BEH, for BES1 homologues, family7 has been described in great detail in model angiosperms. Homologs of these transcription factors are present in streptophyte algae and in land plant lineages where BR signaling or function is absent or has not yet been characterized. The genome of the bryophyte Marchantia polymorpha does not encode for BR receptors but includes one close ortholog of Arabidopsis thaliana BRI1-EMS-SUPPRESSOR 1 (AtBES1)8 and Arabidopsis thaliana BRASSINAZOLE-RESISTANT 1 (AtBZR1),9 MpBES1. Altered levels of MpBES1 severely compromised cell division and differentiation, resulting in stunted thalli that failed to differentiate adult tissues and reproductive organs. The transcriptome of Mpbes1 knockout plants revealed a significant overlap with homologous functions controlled by AtBES1 and AtBZR1, suggesting that members of this gene family share a subset of common targets. Indeed, MpBES1 behaved as a gain-of-function substitute of AtBES1/AtBZR1 when expressed in Arabidopsis, probably because it mediates conserved functions but evades the regulatory mechanisms that native counterparts are subject to. Our results show that this family of transcription factors plays an ancestral role in the control of cell division and differentiation in plants and that BR signaling likely co-opted this function and imposed additional regulatory checkpoints upon it., M.A.M. and F.L.-E. received funding from FEDER-BIO2016-78150-P and PIRSES-GA-2013-612583. M.G.-H. is supported by the National Agency for the Promotion of Science and Technology (ANPCyT, Argentina). M.M.-B., D.B.-E., and F.L.-E. are funded by ERC-2015-CoG–683163 granted to A.I.C.-D. A.P.-R. is recipient of a PhD fellowship from the “Severo Ochoa Programme for Centers of Excellence in R&D” 2016–2019 from the Ministerio de Ciencia e Innovación, Spain (SEV-2015-0533). We acknowledge financial support from the Spanish Ministry of Science and Innovation-State Research Agency (AEI), through the “Severo Ochoa Programme for Centres of Excellence in R&D” SEV-2015-0533 and CEX2019-000902-S, and support from the CERCA Programme/Generalitat de Catalunya. S.M.-G. is a member of the National Research Council of Science and Technology (CONICET, Argentina); work in his laboratory was supported by a grant from ANPCyT (PICT2016-2234). A.I.C.-D. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 683163).

Brassinosteroids (BRs) are steroid hormones that are essential for plant growth and development. These hormones control the division, elongation and differentiation of various cell types throughout the entire plant life cycle. Our current understanding of the BR signaling pathway has mostly been obtained from studies using Arabidopsis thaliana as a model. In this context, the membrane steroid receptor BRI1 (BRASSINOSTEROID INSENSITIVE 1) binds directly to the BR ligand, triggering a signal cascade in the cytoplasm that leads to the transcription of BR-responsive genes that drive cellular growth. However, recent studies of the primary root have revealed distinct BR signaling pathways in different cell types and have highlighted cell-specific roles for BR signaling in controlling adaptation to stress. In this Review, we summarize our current knowledge of the spatiotemporal control of BR action in plant growth and development, focusing on BR functions in primary root development and growth, in stem cell self-renewal and death, and in plant adaption to environmental stress., A.P.-R. is recipient of a PhD fellowship from the “Severo Ochoa Programme for Centers of Excellence in R&D” 2016-2019 from the Ministerio de Ciencia e Innovación (SEV-2015-0533). A.G. is a recipient of a post-doctoral fellowship from the “Severo Ochoa Programme for Centers of Excellence in R&D” 2016-2019 from the Ministerio de Ciencia e Innovación (SEV-2015-0533). I.B.-P. is funded by a grant from the Ministerio de Educación, Cultura y Deporte (FPU15/02822). N.B. is funded by a grant from the Agència de Gestió d'Ajuts Universitaris i de Recerca, Generalitat de Catalunya (FI-DGR 2016FI_B 00472). M.I. acknowledges support from the Ministerio de Economía y Competitividad (Spain) and FEDER (European Regional Development Fund of the European Union) (FIS2015-66503-C3-3-P) and from the Generalitat de Catalunya through Grup de Recerca Consolidat (2017 SGR 1061). A.I.C.-D. is recipient of a grant from the Ministerio de Economía y Competitividad (BIO2013-43873) and of an ERC Consolidator Grant from the European Research Council (ERC-2015-CoG – 683163).

Brassinosteroids (BRs) are essential hormones for plant growth and development that are perceived at the plasma membrane by a group of Leucine-Rich Repeat Receptor-Like Kinases (LRR–RLKs) of the BRASSINOSTEROID INSENSITIVE 1 (BRI1) family. The BRI1 receptor was first discovered by genetic screenings based on the dwarfism of BR-deficient plants. There are three BRI1 homologs, named BRI1-like 1, 2 and 3 (BRLs), yet only BRL1 and BRL3 behave as functional BR receptors. Whereas the BRI1 pathway operates in the majority of cells to promote growth, BRL receptor signaling operates under specific spatiotemporal constraints. Despite a wealth of information on the BRI1 pathway, data on specific BRL pathways and their biological relevance is just starting to emerge. Here, we systematically compare BRLs with BRI1 to identify any differences that could account for specific receptor functions. Understanding how vascular and cell-specific BRL receptors orchestrate plant development and adaptation to the environment will help shed light on membrane signaling and cell communication in plants, while opening up novel possibilities to improve stress adaptation without penalizing growth., A.I.C-D. is a recipient of a Spanish Ministry of Economy and Competitiveness and a European Research Council (FEDER-BIO2016-78150-), ERC Consolidator Grant (ERC-2015-CoG – 683163). F.L.E. PhD thesis is funded by the FEDER-BIO2016-78150-P grant in A.I.C-D laboratory.

Plant roots grow due to cell division in the meristem and subsequent cell elongation and differentiation, a tightly coordinated process that ensures growth and adaptation to the changing environment. How the newly formed cells decide to stop elongating becoming fully differentiated is not yet understood. To address this question, we established a novel approach that combines the quantitative phenotypic variability of wild-type Arabidopsis roots with computational data from mathematical models. Our analyses reveal that primary root growth is consistent with a Sizer mechanism, in which cells sense their length and stop elongating when reaching a threshold value. The local expression of brassinosteroid receptors only in the meristem is sufficient to set this value. Analysis of roots insensitive to BR signaling and of roots with gibberellin biosynthesis inhibited suggests distinct roles of these hormones on cell expansion termination. Overall, our study underscores the value of using computational modeling together with quantitative data to understand root growth., M.I. acknowledges support from the Ministerio de Economía y Competitividad (Spain) and Fondo Europeo de Desarrollo Regional FEDER (EU) through grant FIS2015-66503-C3-3-P (MINECO/FEDER), from MINECO through FIS2012-37655-C02-02 and FIS2009-13360-C03-01, and from the Generalitat de Catalunya through Grup de Recerca Consolidat 2014 SGR 878. A.I.C.-D. is a recipient of BIO2016-78955 and BIO2013-43873 grants from the Spanish Ministry of Economy and Competitiveness (MINECO), of an ERC Consolidator Grant (ERC-2015-CoG—683163) from the European Research Council, and has funding from Developing an European American NGS Network (DEANN) from FP7-PEOPLE-2013-IRSES (2015–2017). M.G.-G. was the recipient of a postdoctoral contract from BIO2010-16673 grant from the Spanish Ministry of Economy and Competitiveness, J.V.B was funded by FI PhD fellowship from Generalitat de Catalunya, and I.P was funded by a JAE-CSIC PhD fellowship in A. I.C.-D. laboratory. A.P.-R. is a recipient of a PhD fellowship from the “Severo Ochoa Programme for Centers of Excellence in R&D” 2016–2019 (SEV-2015-0533)” in A.I.C-D. laboratory.

Mathematical modeling of biological processes is a useful tool to draw conclusions that are contained in the data, but not directly reachable, as well as to make predictions and select the most efficient follow-up experiments. Here we outline a method to model systems of a few proteins that interact transcriptionally and/or posttranscriptionally, by representing the system as Ordinary Differential Equations and to study the model dynamics and stationary states. We exemplify this method by focusing on the regulation by the brassinosteroid (BR) signaling component BRASSINOSTEROID INSENSITIVE1 ETHYL METHYL SULFONATE SUPPRESSOR1 (BES1) of BRAVO, a quiescence-regulating transcription factor expressed in the quiescent cells of Arabidopsis thaliana roots. The method to extract the stationary states and the dynamics is provided as a Mathematica code and requires basic knowledge of the Mathematica software to be executed., D.F. and M.I. acknowledge support from the Ministerio de Economía y Competitividad (Spain) and FEDER (EU) through grant FIS2015-66503-C3-3-P and from the Generalitat de Catalunya through Grup de Recerca Consolidat 2014 SGR 878. AIC-D acknowledges financial support from the Spanish Ministry of Economy and Competitiveness, through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV-2015-0533). AIC-D is a recipient of a BIO2013-43873 grant from the Spanish Ministry of Economy and Competitiveness and European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163).

Roots anchor plants to the soil and are essential for a successful plant growth and adaptation to the environment. Research on the primary root in the plant model system Arabidopsis thaliana has yielded important advances in the molecular and cellular understanding of root growth and development. Several studies have uncovered how the hormones brassinosteroids (BRs) control cell cycle and differentiation programs through different cell-specific signaling pathways that are key for root growth and development. Currently, an important challenge resides in the translation of the current knowledge on Arabidopsis roots into agronomically valuable species to improve the agricultural production and to meet the food security goals of the millennium. In this chapter, we characterize the primary root apex of the cereal Sorghum bicolor (L. Moench) (sorghum), analyze the physiological response of sorghum roots to BRs, and examine the phylogeny of the BRASSINOSTEROID INSENSITIVE1-like receptor family in Arabidopsis and its orthologous genes in sorghum. Overall, we support the use of sorghum as a suitable crop model species for the study of BR signaling in root growth and development. The methods presented enable any laboratory worldwide to use sorghum primary roots as a favorite organ for the study of growth and development in crops., We acknowledge the financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016–2019 (SEV-2015-0533).” N.F. is indebted to the “Fundación Renta Corporation” charity and F.L-E and D.B-E. are funded by a BIO2013-43873 grant and a “Retos Colaboración” project (RTC-2014-1916-2) from the Spanish Ministry of Economy and Competitiveness, respectively. A.I.C.-D. is the recipient of a European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163).

The plant vascular system provides transport and mechanical support functions that are essential for suitable plant growth and development. In Arabidopsis thaliana (Arabidopsis), the vascular tissues at the shoot inflorescence stems are disposed in organized vascular bundles. The vascular patterning emergence and development within the shoot inflorescence stems is under the control of plant growth regulators (De Rybel et al., Nat Rev Mol Cell Biol 17:30–40, 2016; Caño-Delgado et al., Annu Rev Cell Dev Biol 26:605–637, 2010). By using a combined approach of experimental methods for vascular tissues visualization and quantification together with theoretical methods through mathematical and computational modeling, we have reported that auxin transport and brassinosteroid signaling play complementary roles in the formation of the periodic vascular patterning in the shoot (Ibañes et al., Proc Natl Acad Sci U S A 106:13630–13635, 2009; Fàbregas et al., Plant Signal Behav 5:903–906, 2010; Fàbregas et al., PLoS Genet 11:e1005183, 2015). Here, we report the methodology for the interdisciplinary analysis of the shoot vascular patterning in the plant model Arabidopsis into a handle procedure for visualization, quantification, data analysis, and modeling implementation., We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness, through the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016–2019 (SEV‐2015‐0533)”. N.F. is funded by “Fundación RENTA CORPORACIÓN” charity in A.C.-D. Lab. P.F.-J. acknowledges the postdoctoral fellowship provided by the Herchel Smith Foundation. P.F.-J and M.I. acknowledge support from the Spanish Ministry of Economy and Competitiveness through grants FIS2012-37655-C02-02 and FIS2015-66503-C3-3-P and to the Generalitat de Catalunya through Projecte Consolidat 2014 SGR 878. A.I.C.-D. lab is funded by a BIO2013-43873 grant from the Spanish Ministry of Economy and Competitiveness, and the European Research Council by the ERC Consolidator Grant (ERC-2015-CoG—683163).

Brassinosteroid (BR) hormones are essential for plant growth and development. In Arabidopsis, the general understanding of BR signaling has been greatly attained by genetic and biochemical approaches that led to the identification of central BR signaling components, from the BRI1 receptor at the plasma membrane to downstream acting BR-regulated BRZ1 and BES1 transcription factors in the nuclei. Recently, an emerging trend is being established to further advance our understanding of the BR signaling pathway in plant development. Scientists have turned on the microscope lens turret to revisit the pleiotropic phenotypes of the BR mutants at a higher magnification, uncovering novel and specific cellular defects in the plant. In-depth phenotypic analysis in combination with the search for cell-specific signaling components that are responsible for those particular defects in the mutants are leading to: (1) definition of novel roles for BRs in vascular development, (2) unraveling BR function in cell division through quantitative analysis of Arabidopsis root growth, (3) establishment of a molecular connection between known patterning and BR-signaling components in organ boundary and stomata development and (4) development of novel strategies toward the identification of BR signaling components with spatiotemporal resolution. In this review, we highlight the importance of these emerging studies to investigate the spatiotemporal control of BR pathways in plant development., N. F. is funded by an FI PhD fellowship from the Generalitat de Catalunya. A. I. C. -D. is recipient of a Marie-Curie Initial Training Network ‘BRAVISSIMO’ (Grant PITN-GA-2008-215118) and a from the Spanish Ministry of Education and Science (BIO2010/00505).

Brassinosteroid (BR) hormones are primarily perceived at the cell surface by the leucine-rich repeat receptor-like kinase BRASSINOSTEROID INSENSITIVE1 (BRI1). In Arabidopsis thaliana, BRI1 has two close homologs, BRI1-LIKE1 (BRL1) and BRL3, respectively, which are expressed in the vascular tissues and regulate shoot vascular development. Here, we identify novel components of the BRL3 receptor complex in planta by immunoprecipitation and mass spectrometry analysis. Whereas BRI1 ASSOCIATED KINASE1 (BAK1) and several other known BRI1 interactors coimmunoprecipitated with BRL3, no evidence was found of a direct interaction between BRI1 and BRL3. In addition, we confirmed that BAK1 interacts with the BRL1 receptor by coimmunoprecipitation and fluorescence microscopy analysis. Importantly, genetic analysis of brl1 brl3 bak1-3 triple mutants revealed that BAK1, BRL1, and BRL3 signaling modulate root growth and development by contributing to the cellular activities of provascular and quiescent center cells. This provides functional relevance to the observed protein–protein interactions of the BRL3 signalosome. Overall, our study demonstrates that cell-specific BR receptor complexes can be assembled to perform different cellular activities during plant root growth, while highlighting that immunoprecipitation of leucine-rich repeat receptor kinases in plants is a powerful approach for unveiling signaling mechanisms with cellular resolution in plant development., S.D.C., T.E.N., and M.B.G. are funded by grants from the U.S. National Science Foundation (MCB-1021363 and DBI-1126244). N.F. is funded by an Formació de personal Investigador PhD fellowship from the Generalitat de Catalunya. A.I.C.-D. and S.d.V. are recipients of a Marie-Curie Initial Training Network “BRAVISSIMO” (Grant PITN-GA-2008-215118). S.d.V. was a sabbatical professor funded by AGAUR (Generalitat de Catalunya) in A.I.C.-D.'s lab. A.I.C.-D. is funded by a grant from the Spanish Ministry of Education and Science (BIO2010/00505).

Brassinosteroid (BR) hormones control plant growth through acting on both cell expansion and division. Here, we examined the role of BRs in leaf growth using the Arabidopsis BR-deficient mutant constitutive photomorphogenesis and dwarfism (cpd). We show that the reduced size of cpd leaf blades is a result of a decrease in cell size and number, as well as in venation length and complexity. Kinematic growth analysis and tissue-specific marker gene expression revealed that the leaf phenotype of cpd is associated with a prolonged cell division phase and delayed differentiation. cpd-leaf-rescue experiments and leaf growth analysis of BR biosynthesis and signaling gain-of-function mutants showed that BR production and BR receptor-dependent signaling differentially control the balance between cell division and expansion in the leaf. Investigation of cell cycle markers in leaves of cpd revealed the accumulation of mitotic proteins independent of transcription. This correlated with an increase in cyclin-dependent kinase activity, suggesting a role for BRs in control of mitosis., This work was supported by the FP7 Marie-Curie Initial Training Network ‘BRAVISSIMO’ (PITN-GA-2008-215118; E.R. and A.C-D), the Belgian Science Policy (BELSPO) (M.K.Z.) and the Agency for Innovation by Science and Technology (IWT) (who awarded a postdoctoral fellowship to M.K.Z., a pre-doctoral fellowship to S.D. and a ‘Strategisch Basisonderzoek’ grant (no. 60839) to C.B.). A.C-D. receives funding through grants from the Spanish Ministry of Science and Innovation (BIO2008/00505).

Brassinosteroid (BR) hormones are important regulators of plant growth and development. Recent studies revealed the cell-specific role of BRs in vascular and stem cell development by the action of cell-specific BR receptor complexes and downstream signaling components in Arabidopsis thaliana. Despite the importance of spatiotemporal regulation of hormone signaling in the control of plant vascular development, the mechanisms that confer cellular specificity to BR receptors within the vascular cells are not yet understood. The present work shows that BRI1-like receptor genes 1 and 3 (BRL1 and BRL3) are differently regulated by BRs. By using promoter deletion constructs of BRL1 and BRL3 fused to GFP/GUS (green fluorescent protein/β-glucuronidase) reporters in Arabidopsis, analysis of their cell-specific expression and regulation by BRs in the root apex has been carried out. We found that BRL3 expression is finely modulated by BRs in different root cell types, whereas the location of BRL1 appears to be independent of this hormone. Physiological and genetic analysis show a BR-dependent expression of BRL3 in the root meristem. In particular, BRL3 expression requires active BES1, a central transcriptional effector within the BRI1 pathway. ChIP analysis showed that BES1 directly binds to the BRRE present in the BRL3 promoter region, modulating its transcription in different subsets of cells of the root apex. Overall our study reveals the existence of a cell-specific negative feedback loop from BRI1-mediated BES1 transcription factor to BRL3 in phloem cells, while contributing to a general understanding of the spatial control of steroid signaling in plant development., RL was funded by the FWF Erwin Schrödinger Stipendum from Austria (J 3019-B16), and JES-H was supported by the Department of Innovation, Universities and Enterprise of the Generalitat de Catalunya, the European Social Fund FI Fellowship (AGAUR: FI-2006, Resolució EDU/3600/2006; FI-2008, Resolució IUE/2658/2007, and BE-DGR2010) in the Laboratory of AC-D. We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness, through the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV‐2015‐0533). AIC-D is a recipient of a BIO2013-43873 grant from the Spanish Ministry of Economy and Competitiveness an European Research Council, ERC Consolidator Grant (ERC-2015-CoG – 683163).

Receptor-mediated endocytosis is an integral part of signal transduction as it mediates signal attenuation and provides spatial and temporal dimensions to signaling events. One of the best-studied leucine-rich repeat receptor-like kinases in plants, BRASSINOSTEROID INSENSITIVE 1 (BRI1), perceives its ligand, the brassinosteroid (BR) hormone, at the cell surface and is constitutively endocytosed. However, the importance of endocytosis for BR signaling remains unclear. Here we developed a bioactive, fluorescent BR analog, Alexa Fluor 647-castasterone (AFCS), and visualized the endocytosis of BRI1-AFCS complexes in living Arabidopsis thaliana cells. Impairment of endocytosis dependent on clathrin and the guanine nucleotide exchange factor for ARF GTPases (ARF-GEF) GNOM enhanced BR signaling by retaining active BRI1-ligand complexes at the plasma membrane. Increasing the trans-Golgi network/early endosome pool of BRI1-BR complexes did not affect BR signaling. Our findings provide what is to our knowledge the first visualization of receptor-ligand complexes in plants and reveal clathrin- and ARF-GEF-dependent endocytic regulation of BR signaling from the plasma membrane.

International audience; Global climate change and a growing population require tackling the reduction in arable land and improving biomass production and seed yield per area under varying conditions. One of these conditions is suboptimal water availability. Here, we review some of the classical approaches to dealing with plant response to drought stress and we evaluate how research on RECEPTOR-LIKE KINASES (RLKs) can contribute to improving plant performance under drought stress. RLKs are considered as key regulators of plant architecture and growth behavior, but they also function in defense and stress responses. The available literature and analyses of available transcript profiling data indeed suggest that RLKs can play an important role in optimizing plant responses to drought stress. In addition, RLK pathways are ideal targets for nontransgenic approaches, such as synthetic molecules, providing a novel strategy to manipulate their activity and supporting translational studies from model species, such as Arabidopsis thaliana, to economically useful crops.

Mapping centromere distribution in complete organs is a key step towards establishing how this couples to organ development and cell functions. In this context, quantitative microscopy tools play a key role, as they allow a precise measurement of centromere presence at both individual cell and whole organ levels. This work introduces PloidyQuantX, an imaging tool that operates on confocal microscopy image stacks. Tested on imagery obtained from whole-mount centromere Q-FISH of the Arabidopsis thaliana primary root, PloidyQuantX incorporates interactive segmentation and image analysis modules that allow quantifying the number of centromeres present in each cell nucleus, thus creating maps of centromere distribution in cells across the whole organ. Moreover, the presented tool also allows rendering three-dimensional models of each individual root cell, which makes it possible to relate their internal topology to specific cell functions.

Auxin is an essential hormone for plant growth and development. Auxin influx carriers AUX1/LAX transport auxin into the cell, while auxin efflux carriers PIN pump it out of the cell. It is well established that efflux carriers play an important role in the shoot vascular patterning, yet the contribution of influx carriers to the shoot vasculature remains unknown. Here, we combined theoretical and experimental approaches to decipher the role of auxin influx carriers in the patterning and differentiation of vascular tissues in the Arabidopsis inflorescence stem. Our theoretical analysis predicts that influx carriers facilitate periodic patterning and modulate the periodicity of auxin maxima. In agreement, we observed fewer and more spaced vascular bundles in quadruple mutants plants of the auxin influx carriers aux1lax1lax2lax3. Furthermore, we show AUX1/LAX carriers promote xylem differentiation in both the shoot and the root tissues. Influx carriers increase cytoplasmic auxin signaling, and thereby differentiation. In addition to this cytoplasmic role of auxin, our computational simulations propose a role for extracellular auxin as an inhibitor of xylem differentiation. Altogether, our study shows that auxin influx carriers AUX1/LAX regulate vascular patterning and differentiation in plants., NF is funded by an FI PhD fellowship from the Generalitat de Catalunya. PFJ acknowledges the FPU grant (FPU-AP2008-03325) funded by the Spanish Ministry of Education (2009–2011) and the Spanish Ministry of Education, Culture and Sports (2011–2013). AC is funded by a post-doctoral fellowship from Fundação para a Ciência e Tecnologia (SFRH/BPD/47280/2008). AICD is a recipient of a Marie-Curie Initial Training Network “BRAVISSIMO” (Grant PITN-GA- 2008- 215118). This work is supported by the Spanish Ministry of Science and Innovation through grants FIS2012-37655-C02-02 (PFJ and MI), FIS2009-13360-C03-01 (PFJ and MI), BIO2010-16673 (NF, AC and AICD) and BIO2013-43873 Grant Excellence to AICD, the Generalitat de Catalunya through grants 2009 SGR 0014 and 2014 SGR 878 (PFJ and MI), the Academy of Finland and the University of Helsinki (RSi and APM), Integrative Life Science Doctoral Program (RSi) and National Science Foundation Grant DBI0820755 (JMA). RSw. and MJB acknowledge the BBSRC and EPSRC for funding.

Telomeres are specialized nucleoprotein caps that protect chromosome ends assuring cell division. Single-cell telomere quantification in animals established a critical role for telomerase in stem cells, yet, in plants, telomere-length quantification has been reported only at the organ level. Here, a quantitative analysis of telomere length of single cells in Arabidopsis root apex uncovered a heterogeneous telomere-length distribution of different cell lineages showing the longest telomeres at the stem cells. The defects in meristem and stem cell renewal observed in tert mutants demonstrate that telomere lengthening by TERT sets a replicative limit in the root meristem. Conversely, the long telomeres of the columella cells and the premature stem cell differentiation plt1,2 mutants suggest that differentiation can prevent telomere erosion. Overall, our results indicate that telomere dynamics are coupled to meristem activity and continuous growth, disclosing a critical association between telomere length, stem cell function, and the extended lifespan of plants., This work was supported by NIH R01-GM065383 to D.E.S. Research in the M.A.B. lab is funded by European Research Council (ERC) Project TEL STEM CELL (GA#232854), European Union FP7 Projects 2007-A-20088 (MARK-AGE) and 2010-259749 (EuroBATS), Spanish Ministry of Economy and Competitiveness Projects SAF2008-05384 and CSD2007-00017, Regional of Government of Madrid Project S2010/BMD-2303 (ReCaRe), AXA Research Fund (Life Risks Project), and Lilly 2010 Preclinical Biomedicine Research Award and Fundación Botín (Spain). M.I. acknowledges support from the Spanish Ministry of Science and Innovation through grant FIS2012-37655-C02-02 and to the Generalitat de Catalunya through grant 2014 SGR 878. A.I.C.-D. is funded by the Spanish Ministry of Economy and Competitiveness (BIO2010-16673 and BIO2013-43873) and a Marie-Curie Initial Training Network (grant no. PITN-GA-2008-215118). M.-P.G.-G. was the recipient of a postdoctoral contract from BIO2010-16673 and an EMBO short-term fellowship and I.P. is funded by a JAE-CSIC PhD fellowship in the A.I.C.-D. laboratory.

Both animals and plants use steroids as signalling molecules during growth and development. Animal steroids are principally recognized by members of the nuclear receptor superfamily of transcription factors. In plants, BRI1, a leucine-rich repeat (LRR) receptor kinase localized to the plasma membrane, is a critical component of a receptor complex for brassinosteroids. Here, we present the first evidence for direct binding of active brassinosteroids to BRI1 using a biotin-tagged photoaffinity castasterone (BPCS), a biosynthetic precursor of brassinolide (the most active of the brassinosteroids). Binding studies using BPCS, (3)H-labelled brassinolide and recombinant BRI1 fragments show that the minimal binding domain for brassinosteroids consists of a 70-amino acid island domain (ID) located between LRR21 and LRR22 in the extracellular domain of BRI1, together with the carboxy-terminal flanking LRR (ID-LRR22). Our results demonstrate that brassinosteroids bind directly to the 94 amino acids comprising ID-LRR22 in the extracellular domain of BRI1, and define a new binding domain for steroid hormones.

Referred to by: Josep Vilarrasa-Blasi, Mary-Paz González-García, David Frigola, Norma Fàbregas-Vallvé, Konstantinos G. Alexiou, Nuria López-Bigas, Susana Rivas, Alain Jauneau, Jan U. Lohmann, Philip N. Benfey, Marta Ibañes, Ana I. Caño-Delgado Regulation of Plant Stem Cell Quiescence by a Brassinosteroid Signaling Module Developmental Cell, Volume 33, Issue 2, 20 April 2015, Pages 238., The quiescent center (QC) maintains the activity of the surrounding stem cells within the root stem cell niche, yet specific molecular players sustaining the low rate of QC cell division remain poorly understood. Here, we identified a R2R3-MYB transcription factor, BRAVO (BRASSINOSTEROIDS AT VASCULAR AND ORGANIZING CENTER), acting as a cell-specific repressor of QC divisions in the primary root of Arabidopsis. Ectopic BRAVO expression restricts overall root growth and ceases root regeneration upon damage of the stem cells, demonstrating the role of BRAVO in counteracting Brassinosteroid (BR)-mediated cell division in the QC cells. Interestingly, BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo, creating a switch that modulates QC divisions at the root stem cell niche. Together, our results define a mechanism for BR-mediated regulation of stem cell quiescence in plants., J.V.-B. and N.F.-V. are funded by FI PhD fellowship from the Generalitat de Catalunya (GC) in the A.I.C.-D. laboratory. J.V.-B. received a short-term fellowship (BE1-00924) in the Lohmann (J.U.L.) laboratory supported by the SFB873 of the DFG. Research by D.F and M.I. is funded by FIS2012-37655-C02-02 by the Spanish Ministry de Economy and Competitiveness and 2009SGR14 from GC, and D.F. has a PhD fellowship (FPU-AP2009-3736). S.R. is funded by the Laboratoire d’Excellence (LABEX) TULIP (ANR-10-LABX-41). M.-P.G.-G. received a “Juan de la Cierva” postdoctoral contract from the Spanish Ministry of Science in the Ana Caño (A.I.C.-D.) laboratory, and an HFSP short-term fellowship in the Benfey (P.N.B.) laboratory. P.N.B. is funded by NSF Arabidopsis 2010 grant. Work in the Ana Caño (A.I.C.-D.) laboratory is funded by a BIO2010/007 grant from the Spanish Ministry of Innovation and Science and a Marie-Curie Initial Training Network “BRAVISSIMO” (grant no. PITN-GA-2008-215118).

Protein phosphatases with Kelch-like domains (PPKL) are members of the phosphoprotein phosphatases family present only in plants and alveolates. PPKL have been described as positive effectors of brassinosteroid (BR) signaling in plants. Most of the evidence supporting this role has been gathered using one of the four homologs in Arabidopsis (Arabidopsis thaliana), BRASSINOSTEROID-INSENSITIVE1 SUPPRESSOR (BSU1). We reappraised the roles of the other three members of the family, BSL1, BSL2, and BSL3, through phylogenetic, functional, and genetic analyses. We show that BSL1 and BSL2/BSL3 belong to two ancient evolutionary clades that have been highly conserved in land plants. In contrast, BSU1-type genes are exclusively found in the Brassicaceae and display a remarkable sequence divergence, even among closely related species. Simultaneous loss of function of the close paralogs BSL2 and BSL3 brings about a peculiar array of phenotypic alterations, but with marginal effects on BR signaling; loss of function of BSL1 is, in turn, phenotypically silent. Still, the products of these three genes account for the bulk of PPKL-related activity in Arabidopsis and together have an essential role in the early stages of development that BSU1 is unable to supplement. Our results underline the functional relevance of BSL phosphatases in plants and suggest that BSL2/BSL3 and BSU1 may have contrasting effects on BR signaling. Given that BSU1-type genes have likely undergone a functional shift and are phylogenetically restricted, we caution that inferences based on these genes to the whole family or to other species may be misleading., This work was supported by the Agencia Nacional de Promoción Científica y Tecnológica (grant no. PICT–38012) and the Consejo Nacional de Investigaciones Científicas y Técnicas (grant no. PIP–414) to S.M.-G.

Fruits represent an important part of the human diet and show extensive variation in size and shape between and within cultivated species. The genetic basis of such variation has been studied most extensively in tomato, where currently six quantitative trait loci (QTLs) involving these traits have been fine-mapped and the genes underlying the QTLs identified. The genes responsible for the cloned QTLs belong to families with a few to many members. FASCIATED is encoded by a member of the YABBY family, CNR/FW2.2 by a member of the Cell Number Regulator family, SlKLUH/FW3.2 by a cytochrome P450 of the 78A class (CYP78A), LOCULE NUMBER by a member of the WOX family including WUSCHEL, OVATE by a member of the Ovate Family Proteins (OFP), and SUN by a member of the IQ domain family. A high portion of the history and current diversity in fruit morphology among tomato cultivars can be explained by modifications at four of these cloned QTLs. In melon, a number of QTLs involved in fruit morphology have been mapped, but the molecular basis for these QTLs is unknown. In the present review, we examine the current knowledge on the molecular basis of fruit morphology in tomato and transfer that information in order to define candidate genes of melon fruit shape and size QTLs. We hypothesize that different members of the gene families identified in tomato may have a role in the regulation of fruit morphology in other species. We anchored the published melon QTL map on the genome sequence and identified the melon family members of the six cloned tomato QTLs in the genome. We investigated the co-localization of melon fruit morphology QTLs and the candidate genes. We found that QTLs for fruit weight co-localized frequently with members of the CNR/FW2.2 and KLUH/FW3.2 families, as well as co-localizations between OFP family members and fruit-shape QTLs, making this family the most suitable to explain fruit shape variation among melon accessions., This research was supported in part by grant AGL2012-40130-C02-02 for the Spanish Ministry of Economy and Competitiveness (MINECO) to AJM. Research in the van der Knaap laboratory is supported by NSF IOS 0922661.

Active gibberellins (GAs) are endogenous factors that regulate plant growth and development in a dose-dependent fashion. Mutant plants that are GA deficient, or exhibit reduced GA responses, display a characteristic dwarf phenotype. Extragenic suppressor analysis has resulted in the isolation of Arabidopsis mutations, which partially suppress the dwarf phenotype conferred by GA deficiency and reduced GA-response mutations. Here we describe detailed studies of the effects of two of these suppressors,spy-7 and gar2–1, on several different GA-responsive growth processes (seed germination, vegetative growth, stem elongation, chlorophyll accumulation, and flowering) and on the in planta amounts of active and inactive GA species. The results of these experiments show that spy-7 and gar2–1affect the GA dose-response relationship for a wide range of GA responses and suggest that all GA-regulated processes are controlled through a negatively acting GA-signaling pathway.

Two recent studies disclose the interaction between brassinosteroids (BRs) and cell-identity genes in establishing organ boundaries. BR signaling is downregulated by LATERAL ORGAN BOUNDARIES (LOB), whereas active BR signaling prevents LATERAL ORGAN FUSION1 (LOF1) and CUP SHAPED COTYLEDON (CUC) expression in the growing primordia, pointing to cell-specific hormone signaling as part of the mechanisms controlling fate acquisition., A.C-D is funded by a Marie-Curie Initial Training Network ‘BRAVISSIMO’ (grant no. PITN-GA-2008-215118). Work in the authors’ laboratories is also supported by grants BIO2010-00505 and BIO2010-15071 from the Spanish Ministry of Science.

Background Melon (Cucumis melo L.) is a commercially important fruit crop that is cultivated worldwide. The melon research community has recently benefited from the determination of a complete draft genome sequence and the development of associated genomic tools, which have allowed us to focus on small RNAs (sRNAs). These are short, non-coding RNAs 21-24 nucleotides in length with diverse physiological roles. In plants, they regulate gene expression and heterochromatin assembly, and control protection against virus infection. Much remains to be learned about the role of sRNAs in melon. Results We constructed 10 sRNA libraries from two stages of developing ovaries, fruits and photosynthetic cotyledons infected with viruses, and carried out high-throughput pyrosequencing. We catalogued and analysed the melon sRNAs, resulting in the identification of 26 known miRNA families (many conserved with other species), the prediction of 84 melon-specific miRNA candidates, the identification of trans-acting siRNAs, and the identification of chloroplast, mitochondrion and transposon-derived sRNAs. In silico analysis revealed more than 400 potential targets for the conserved and novel miRNAs. Conclusion We have discovered and analysed a large number of conserved and melon-specific sRNAs, including miRNAs and their potential target genes. This provides insight into the composition and function of the melon small RNAome, and paves the way towards an understanding of sRNA-mediated processes that regulate melon fruit development and melon-virus interactions., This work was supported by grants AGL2009-07552/AGR, BIO2006-13107 (Ministerio de Ciencia e Innovación, Spain) and MELONOMICS (Fundación Genoma España, Spain).

Background Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited. Result We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences. Conclusion The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns., This work was supported by Research Grant Award No. IS-4223-09C from BARD, the United States-Israel Binational Agricultural Research and Development Fund, and by SNC Laboratoire ASL, de Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fitó S.A., Seminis Vegetable Seeds Inc, Syngenta Seeds B.V., Takii and Company Ltd, Vilmorin and Cie S.A. and Zeraim Gedera Ltd (all of them as part of the support to ICuGI). CC was supported by CNRS ERL 8196.

Plant vascular tissues, the conduits of water, nutrients, and small molecules, play important roles in plant growth and development. Vascular tissues have allowed plants to successfully adapt to various environmental conditions since they evolved 450 Mya. The majority of plant biomass, an important source of renewable energy, comes from the xylem of the vascular tissues. Efforts have been made to identify the underlying mechanisms of cell specification and patterning of plant vascular tissues and their proliferation. The formation of the plant vascular system is a complex process that integrates signaling and gene regulation at transcriptional and posttranscriptional levels. Recently, a wealth of molecular genetic studies and the advent of cell biology and genomic tools have enabled important progress toward understanding its underlying mechanisms. Here, we provide a comprehensive review of the cell and developmental processes of plant vascular tissue and resources recently available for studying them that will enable the discovery of new ways to develop sustainable energy using plant biomass., This work was supported by the Boyce Thompson Institute and a National Science Foundation grant (IOS0818071) to J.Y.L., by a Grant-in-Aid for Scientific Research of Japan (Grant 21027031) to T.D., and by the Spanish Ministry of Science and Innovation (BIO2008/00505/) and the EU Marie Curie Initial Training Networks (ITN) FP7-PEOPLE-2007 to A.C.-D.

15 pages, 4 figures, 3 tables, 1 appendix, 3 additional files., Background: Melon (Cucumis melo) is a horticultural specie of significant nutritional value, which belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. Its small genome of approx. 450 Mb coupled to the high genetic diversity has prompted the development of genetic tools in the last decade. However, the unprecedented existence of a transcriptomic approaches in melon, highlight the importance of designing new tools for high-throughput analysis of gene expression., Results: We report the construction of an oligo-based microarray using a total of 17,510 unigenes derived from 33,418 high-quality melon ESTs. This chip is particularly enriched with genes that are expressed in fruit and during interaction with pathogens. Hybridizations for three independent experiments allowed the characterization of global gene expression profiles during fruit ripening, as well as in response to viral and fungal infections in plant cotyledons and roots, respectively. Microarray construction, statistical analyses and validation together with functional-enrichment analysis are presented in this study., Conclusion: The platform validation and enrichment analyses shown in our study indicate that this oligo-based microarray is amenable for future genetic and functional genomic studies of a wide range of experimental conditions in melon., This work was supported by grants from the Spanish Ministry of Education and Science (BIO2005/007 to A.C-D; GEN2003-20237-C06 and AGL2006-08069/ AGR to M.A.A.). W.D., C.R. and D. G-I. are recipients of CRAG and "Juan de la Cierva" postdoctoral contracts from the Spanish Ministry of Education and Science. S.M-G was funded by PIV2 program (AGAUR; Generalitat de Catalunya, Spain). A.M-C and J.V. are PhD students funded by I3P program (CSIC; Spain) in A.I. C-D laboratory. A.I. C-D is funded by a HFSPO/Career Development Award (CDA2004/007). A.I. C-D is a "Ramón y Cajal" researcher from the Spanish Ministry of Education and Science.

The plant vascular system provides transport and support capabilities that are essential for plant growth and development, yet the mechanisms directing the arrangement of vascular bundles within the shoot inflorescence stem remain unknown. We used computational and experimental biology to evaluate the role of auxin and brassinosteroid hormones in vascular patterning in Arabidopsis. We show that periodic auxin maxima controlled by polar transport and not overall auxin levels underlie vascular bundle spacing, whereas brassinosteroids modulate bundle number by promoting early procambial divisions. Overall, this study demonstrates that auxin polar transport coupled to brassinosteroid signaling is required to determine the radial pattern of vascular bundles in shoots., M.I. and A.I.C.-D. acknowledge financial support from the Spanish Ministry of Science and Innovation (“Ramón y Cajal” program). N.F. is funded by a “Generalitat de Catalunya” PhD fellowship. This work was supported by Spanish Ministry of Science and Innovation Grants BIO2005/0047 and BIO2008/00505 (to A.I.C.-D.) and FIS2006/05019 and FIS2006-11452-C03-01 ( M.I.); U.S. National Science Foundation Grant IOS-0649389 (to J.C.); and by Human Frontiers Science Program Organization Award CDA2004/007 (to A.I.C.-D.). J.C. is an investigator of the Howard Hughes Medical Institute.

This article is available from: http://www.biomedcentral.com/1471-2164/8/306, [Background] Melon (Cucumis melo L.) is one of the most important fleshy fruits for fresh consumption. Despite this, few genomic resources exist for this species. To facilitate the discovery of genes involved in essential traits, such as fruit development, fruit maturation and disease resistance, and to speed up the process of breeding new and better adapted melon varieties, we have produced a large collection of expressed sequence tags (ESTs) from eight normalized cDNA libraries from different tissues in different physiological conditions., [Results] We determined over 30,000 ESTs that were clustered into 16,637 non-redundant sequences or unigenes, comprising 6,023 tentative consensus sequences (contigs) and 10,614 unclustered sequences (singletons). Many potential molecular markers were identified in the melon dataset: 1,052 potential simple sequence repeats (SSRs) and 356 single nucleotide polymorphisms (SNPs) were found. Sixty-nine percent of the melon unigenes showed a significant similarity with proteins in databases. Functional classification of the unigenes was carried out following the Gene Ontology scheme. In total, 9,402 unigenes were mapped to one or more ontology. Remarkably, the distributions of melon and Arabidopsis unigenes followed similar tendencies, suggesting that the melon dataset is representative of the whole melon transcriptome. Bioinformatic analyses primarily focused on potential precursors of melon micro RNAs (miRNAs) in the melon dataset, but many other genes potentially controlling disease resistance and fruit quality traits were also identified. Patterns of transcript accumulation were characterised by Real-Time-qPCR for 20 of these genes., [Conclusion] The collection of ESTs characterised here represents a substantial increase on the genetic information available for melon. A database (MELOGEN) which contains all EST sequences, contig images and several tools for analysis and data mining has been created. This set of sequences constitutes also the basis for an oligo-based microarray for melon that is being used in experiments to further analyse the melon transcriptome., This work was supported by grants from Ministerio de Educación y Ciencia (Spain) (GEN2003-20237-C06) and Consejería de Educación y Cultura (Región de Murcia, Spain) (BIO2005/04-6436). Wim Deleu, Cristina Roig and Daniel Gonzalez-Ibeas are recipient of a postdoctoral fellowship from the Centre de Recerca en Agrigenòmica CSIC-IRTA (Spain), a Juan de la Cierva grant from Ministerio de Educación y Ciencia (Spain) and a predoctoral fellowship from Ministerio de Educación y Ciencia (Spain), respectively.

Plant steroid hormones, brassinosteroids (BRs), are perceived by the plasma membrane-localized leucine-rich-repeat-receptor kinase BRI1. Based on sequence similarity, we have identified three members of the BRI1 family, named BRL1, BRL2 and BRL3. BRL1 and BRL3, but not BRL2, encode functional BR receptors that bind brassinolide, the most active BR, with high affinity. In agreement, only BRL1 and BRL3 can rescue bri1 mutants when expressed under the control of the BRI1 promoter. While BRI1 is ubiquitously expressed in growing cells, the expression of BRL1 and BRL3 is restricted to non-overlapping subsets of vascular cells. Loss-of-function of brl1 causes abnormal phloem:xylem differentiation ratios and enhances the vascular defects of a weak bri1 mutant. bri1 brl1 brl3 triple mutants enhance bri1 dwarfism and also exhibit abnormal vascular differentiation. Thus, Arabidopsis contains a small number of BR receptors that have specific functions in cell growth and vascular differentiation. Fil: Caño Delgado, Ana. Salk Institute. Plant Biology Laboratory; Estados Unidos. Howard Hughes Medical Institute; Estados Unidos Fil: Yin, Yanhai. Howard Hughes Medical Institute; Estados Unidos. Salk Institute. Plant Biology Laboratory; Estados Unidos Fil: Yu, Cong. University of Michigan; Estados Unidos Fil: Vafeados, Dionne. Howard Hughes Medical Institute; Estados Unidos. Salk Institute. Plant Biology Laboratory; Estados Unidos Fil: Mora Garcia, Santiago. Howard Hughes Medical Institute; Estados Unidos. Salk Institute. Plant Biology Laboratory; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Cheng, Jin Chen. University of Michigan; Estados Unidos Fil: Nam, Kyoung Hee. University of Michigan; Estados Unidos Fil: Li, Jianming. University of Michigan; Estados Unidos Fil: Chory, Joanne. Salk Institute. Plant Biology Laboratory; Estados Unidos. Howard Hughes Medical Institute; Estados Unidos

Perception of the plant steroid hormone brassinolide (BL) by the membrane-associated receptor kinase BRI1 triggers the dephosphorylation and accumulation in the nucleus of the transcriptional modulators BES1 and BZR1. We identified bsu1-1D as a dominant suppressor of bri1 in A abidopsis. BSU1 encodes a nuclear-localized serine-threonine protein phosphatase with an N-terminal Kelch-repeat domain, and is preferentially expressed in elongating cells. BSU1 is able to modulate the phosphorylation state of BES1, counter acting the action of the glycogen synthase kinase-3 BIN2, and leading to inc eased steady-state levels of dephosphorylated BES1. BSU1 belongs to a small gene family; loss-of-function analyses unravel the extent of functional overlap among members of the family and confirm the role of these phosphatases in the control of cell elongation by BL. Our data indicate that BES1 is subject to antagonistic phosphorylation and dephosphorylation reactions in the nucleus, which fine-tune the amplitude of the response to BL. Fil: Mora Garcia, Santiago. Salk Institute. Plant Biology Laboratory; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina. Howard Hughes Medical Institute; Estados Unidos Fil: Vert, Gregory. Howard Hughes Medical Institute; Estados Unidos. Salk Institute. Plant Biology Laboratory; Estados Unidos Fil: Yin, Yanhai. Howard Hughes Medical Institute; Estados Unidos. Salk Institute. Plant Biology Laboratory; Estados Unidos Fil: Caño Delgado, Ana. Howard Hughes Medical Institute; Estados Unidos. Salk Institute. Plant Biology Laboratory; Estados Unidos Fil: Cheong, Hyeonsook. Howard Hughes Medical Institute; Estados Unidos. Salk Institute. Plant Biology Laboratory; Estados Unidos Fil: Chory, Joanne. Howard Hughes Medical Institute; Estados Unidos. Salk Institute. Plant Biology Laboratory; Estados Unidos

In Arabidopsis thaliana brassinosteroid (BR), perception is mediated by two Leu-rich repeat receptor-like kinases, BRASSINOSTEROID INSENSITIVE1 (BRI1) and BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) (Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR-like KINASE3 [AtSERK3]). Genetic, biochemical, and yeast (Saccharomyces cerevisiae) interaction studies suggested that the BRI1-BAK1 receptor complex initiates BR signaling, but the role of the BAK1 receptor is still not clear. Using transient expression in protoplasts of BRI1 and AtSERK3 fused to cyan and yellow fluorescent green fluorescent protein variants allowed us to localize each receptor independently in vivo. We show that 11311111, but not AtSERK3, homodimerizes in the plasma membrane, whereas BRI1 and AtSERK3 preferentially heterodimerize in the endosomes. Coexpression of BRI1 and AtSERK3 results in a change of the steady state distribution of both receptors because of accelerated endocytosis. Endocytic vesicles contain either BRI1 or AtSERK3 alone or both. We propose that the AtSERK3 protein is involved in changing the equilibrium between plasma membrane-located BRI1 homodimers and endocytosed BRI1-AtSERK3 heterodimers.

The cell wall determines the shape of plant cells and is also the primary interface for pathogen interactions. The structure of the cell wall can be modified in response to developmental and environmental cues, for example to strengthen the wall and to create barriers to pathogen ingress. The ectopic lignin 1-1 and 1-2 (eli1-1 and eli1-2) mutations lead to an aberrant deposition of lignin, a complex phenylpropanoid polymer. We show that the eli1 mutants occur in the cellulose synthase gene CESA3 in Arabidopsis thaliana and cause reduced cellulose synthesis, providing further evidence for the function of multiple CESA subunits in cellulose synthesis. We show that reduced levels of cellulose synthesis, caused by mutations in cellulose synthase genes and in genes affecting cell expansion, activate lignin synthesis and defense responses through jasmonate and ethylene and other signaling pathways. These observations suggest that mechanisms monitoring cell wall integrity can activate lignification and defense responses.

Mutants with altered patterns of lignification have been identified in a population of mutagenised Arabidopsis seedlings. One of the mutants exhibited ectopic lignification (eli) of cells throughout the plant that never normally lignify. The reduced expansion of eli1 cells resulted in a stunted phenotype, and xylem cells were misshapen and failed to differentiate into continuous strands, causing a disorganized xylem. Analysis of phenotypes associated with double mutants of eli1 lit (lion’s tail), a cell expansion mutant, indicated that the primary defect in eli1 plants may be inappropriate initiation of secondary wall formation and subsequent aberrant lignification of cells caused by altered cell expansion. Related ectopic lignification phenotypes were also observed in other cell expansion mutants, suggesting a mechanism that senses cell size and controls subsequent secondary wall formation. Interactions between eli1 and wol (woodenleg), a mutant altering xylem cell specification, revealed a role for ELI1 in promoting formation of continuous xylem strands, and demonstrated that ELI1 functions during cell elongation zone in the primary root and other tissues.

Resumen del póster presentado al Congreso 'At the Forefront of Plant Research', celebrado en Barcelona (España) del 6 al 8 de mayo de 2019., Root analysis is essential for both academic and agricultural research. Despite the great advances in root phenotyping and imaging, calculating root length is still performed manually and involves considerable amounts of labor and time. To overcome these limitations, we have developed MyROOT, a software for the semi-automatic quantification of root growth of seedlings growing directly in agar plates. Our method automatically determines the scale from the image of the plate, and subsequently measures the root length of the individual plants. To this aim, MyROOT combines a bottom-up root tracking approach with a hypocotyl detection algorithm. At the same time as providing accurate root measurements, MyROOT also significantly minimizes the user intervention required during the process. Using Arabidopsis, we tested MyROOT with seedlings from different growth stages and experimental conditions. Upon comparing the data obtained using this software with that of manual root measurements, we found a high correlation between both methods (R2 = 0.997). When compared to previous developed softwares with similar features (BRAT and EZ-Rhizo), MyROOT offers an improved accuracy in root length measurements. Thus, MyROOT will be of great aid to the plant science community by permitting high-throughput root length measurements while saving on both labor and time.

Stem cell regeneration is crucial for both cell turnover and tissue healing in multicellular organisms. In Arabidopsis roots, a reduced group of cells known as the quiescent center (QC) act as a cell reservoir for surrounding stem cells during both normal growth and in response to external damage. Although cells of the QC have a very low mitotic activity, plant hormones such as brassinosteroids (BRs) can promote QC divisions. Here, we used a tissue-specific strategy to investigate the spatial signaling requirements of BR-mediated QC divisions. We generated stem cell niche-specific receptor knockout lines by placing an artificial microRNA against BRI1 (BRASSINOSTEROID INSENSITIVE 1) under the control of the QC-specific promoter WOX5. Additionally, QC-specific knock-in lines for BRI1 and its downstream transcription factor BES1 (BRI1-EMS-SUPPRESOR1) were also created using the WOX5 promoter. By analyzing the roots of these lines, we show that BES1-mediated signaling cell-autonomously promotes QC divisions, that BRI1 is essential for sensing nearby inputs and triggering QC divisions and that DNA damage promotes BR-dependent paracrine signaling in the stem cell niche as a prerequisite to stem cell replenishment., Summary: Quiescent cell division at the stem cell niche is activated by exogenous brassinosteroid signals and points to the brassinosteroid hormone as a limiting factor for stem cell division.