GRANAR, a new computational tool to better understand the functional importance of root anatomy, bioRxiv, 2019-05-23
AbstractRoot hydraulic conductivity is an important determinant of plant water uptake capacity. In particular, the root radial conductivity is often thought to be a limiting factor along the water pathways between the soil and the leaf. The root radial conductivity is itself defined by cell scale hydraulic properties and anatomical features. However, quantifying the influence of anatomical features on the radial conductivity remains challenging due to complex, and time-consuming, experimental procedures.We present a new computation tool, the Generator of Root ANAtomy in R (GRANAR) that can be used to rapidly generate digital versions of root anatomical networks. GRANAR uses a limited set of root anatomical parameters, easily acquired with existing image analysis tools. The generated anatomical network can then be used in combination with hydraulic models to estimate the corresponding hydraulic properties.We used GRANAR to re-analyse large maize (Zea mays) anatomical datasets from the literature. Our model was successful at creating virtual anatomies for each experimental observation. We also used GRANAR to generate anatomies not observed experimentally, over wider ranges of anatomical parameters. The generated anatomies were then used to estimate the corresponding radial conductivities with the hydraulic model MECHA. This enabled us to quantify the effect of individual anatomical features on the root radial conductivity. In particular, our simulations highlight the large importance of the width of the stele and the cortex.GRANAR is an open-source project available here <jatsext-link xmlnsxlink=httpwww.w3.org1999xlink ext-link-type=uri xlinkhref=httpgranar.github.io>httpgranar.github.io<jatsext-link>One-Sentence summaryGenerator of Root ANAtomy in R (GRANAR) is a new open-source computational tool that can be used to rapidly generate digital versions of root anatomical networks.
biorxiv plant-biology 0-100-users 2019Proximity labeling of protein complexes and cell type-specific organellar proteomes in Arabidopsis enabled by TurboID, bioRxiv, 2019-05-13
AbstractDefining specific protein interactions and spatially or temporally restricted local proteomes improves our understanding of all cellular processes, but obtaining such data is challenging, especially for rare proteins, cell types, or events. Proximity labeling enables discovery of protein neighborhoods defining functional complexes andor organellar protein compositions. Recent technological improvements, namely two highly active biotin ligase variants (TurboID and miniTurboID), allowed us to address two challenging questions in plants (1) what are in vivo partners of a low abundant key developmental transcription factor and (2) what is the nuclear proteome of a rare cell type? Proteins identified with FAMA-TurboID include known interactors of this stomatal transcription factor and novel proteins that could facilitate its activator and repressor functions. Directing TurboID to stomatal nuclei enabled purification of cell type- and subcellular compartment-specific proteins. Broad tests of TurboID and miniTurboID in Arabidopsis and N. benthamiana and versatile vectors enable customization by plant researchers.
biorxiv plant-biology 100-200-users 2019The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons, bioRxiv, 2019-04-24
AbstractMADS-box transcription factors are ubiquitous in eukaryotic organisms and play major roles during plant development. Nevertheless, their function in seed development remains largely unknown. Here we show that the imprinted Arabidopsis thaliana MADS-box TF PHERES1 (PHE1) is a master regulator of paternally expressed imprinted genes, as well as of non-imprinted key regulators of endosperm development. PHE1 binding sites show distinct epigenetic modifications on maternal and paternal alleles, correlating with parental-specific transcriptional activity. Importantly, we show that the CArG-box-like DNA-binding motifs bound by PHE1 have been distributed by RCHelitron transposable elements. Our data provide an example of molecular domestication of these elements, which by distributing PHE1 binding sites throughout the genome, have facilitated the recruitment of crucial endosperm regulators into a single transcriptional network.
biorxiv plant-biology 0-100-users 2019Chitin perception in plasmodesmata identifies subcellular, context-specific immune signalling in plants, bioRxiv, 2019-04-17
AbstractThe plasma membrane (PM) that lines plasmodesmata has a distinct protein and lipid composition, underpinning specific regulation of these connections between cells. The plasmodesmal PM can integrate extracellular signals differently from the cellular PM, but it is not known how this specificity is established or how a single stimulus can trigger independent signalling cascades in neighbouring membrane domains. Here we have used the fungal elicitor chitin to investigate signal integration and responses at the plasmodesmal PM. We found that the plasmodesmal PM employs a receptor complex composed of the LysM receptors LYM2 and LYK4 which respectively change their location and interactions in response to chitin. Downstream, signalling is transmitted via a specific phosphorylation signature of an NADPH oxidase and localised callose synthesis that causes plasmodesmata closure. This demonstrates the plasmodesmal PM deploys both plasmodesmata-specific components and differential activation of PM-common components to independently integrate an immune signal.
biorxiv plant-biology 0-100-users 2019Protein engineering expands the effector recognition profile of a rice NLR immune receptor, bioRxiv, 2019-04-16
AbstractPlant NLR receptors detect pathogen effectors and initiate an immune response. Since their discovery, NLRs have been the focus of protein engineering to improve disease resistance. However, this has proven challenging, in part due to their narrow response specificity. Here, we used structure-guided engineering to expand the response profile of the rice NLR Pikp to variants of the rice blast pathogen effector AVR-Pik. A mutation located within an effector binding interface of the integrated Pikp-HMA domain increased the binding affinity for AVR-Pik variants in vitro and in vivo. This translates to an expanded cell death response to AVR-Pik variants previously unrecognized by Pikp in planta. Structures of the engineered Pikp-HMA in complex with AVR-Pik variants revealed the mechanism of expanded recognition. These results provide a proof-of-concept that protein engineering can improve the utility of plant NLR receptors where direct interaction between effectors and NLRs is established, particularly via integrated domains.
biorxiv plant-biology 0-100-users 2019PBS3 is the missing link in plant-specific isochorismate-derived salicylic acid biosynthesis, bioRxiv, 2019-04-05
AbstractThe phytohormone salicylic acid (SA) is a central regulator of plant immunity. Despite such functional importance, our knowledge of its biosynthesis is incomplete. Previous work showed that SA is synthesized from chorismic acid in plastids. The bulk of pathogen-induced SA derives from isochorismate generated by the catalytic activity of ISOCHORISMATE SYNTHASE1 (ICS1). How and in which cellular compartment isochorismate is converted to SA is unknown. Here we show that the pathway downstream of isochorismate requires only two additional proteins the plastidial isochorismate exporter ENHANCED DISEASE SUSCEPTIBILITY5 (EDS5) and the cytosolic amido-transferase AvrPphB SUSCEPTIBLE3 (PBS3). PBS3 catalyzes the conjugation of glutamate to isochorismate. The reaction product isochorismate-9-glutamate spontaneously decomposes into enolpyruvyl-N-glutamate and SA. This previously unknown reaction mechanism appears to be conserved throughout the plant kingdom.One Sentence SummarySalicylic acid is synthesized via isochorismate-9-glutamate by PBS3.
biorxiv plant-biology 0-100-users 2019