Oomycete interactions with plants: infection strategies and resistance principles.

The Oomycota include many economically significant microbial pathogens of crop species. Understanding the mechanisms by which oomycetes infect plants and identifying methods to provide durable resistance are major research goals. Over the last few years, many elicitors that trigger plant immunity have been identified, as well as host genes that mediate susceptibility to oomycete pathogens. The mechanisms behind these processes have subsequently been investigated and many new discoveries made, marking a period of exciting research in the oomycete pathology field. This review provides an introduction to our current knowledge of the pathogenic mechanisms used by oomycetes, including elicitors and effectors, plus an overview of the major principles of host resistance: the established R gene hypothesis and the more recently defined susceptibility (S) gene model. Future directions for development of oomycete-resistant plants are discussed, along with ways that recent discoveries in the field of oomycete-plant interactions are generating novel means of studying how pathogen and symbiont colonizations overlap.The authors acknowledge funding from the Gatsby Charitable Foundation (GAT3273/GLD). SF and SS acknowledge funding by the Royal Society. SF would also like to acknowledge personal funding from The Morley Agricultural Foundation and The Felix Cobbold Trust.This is the accepted manuscript. The final version is available at http://mmbr.asm.org/content/79/3/263.abstract

Pour une démocratie socio-environnementale : cadre pour une plate-forme participative « transition écologique »

Contribution publiée in Penser une démocratie alimentaire Volume II – Proposition Lascaux entre ressources naturelles et besoins fondamentaux, F. Collart Dutilleul et T. Bréger (dir), Inida, San José, 2014, pp. 87-111.International audienceL’anthropocène triomphant actuel, avec ses forçages environnementaux et sociaux, est à l’origine de l’accélération des dégradations des milieux de vie sur Terre et de l’accentuation des tensions sociales et géopolitiques. Passer à un anthropocène de gestion équitable, informé et sobre vis-à-vis de toutes les ressources et dans tous les secteurs d’activité (slow anthropocene), impose une analyse préalable sur l’ensemble des activités et des rapports humains. Cette transition dite « écologique », mais en réalité à la fois sociétale et écologique, est tout sauf un ajustement technique de secteurs dits prioritaires et technocratiques. Elle est avant tout culturelle, politique et philosophique au sens propre du terme. Elle est un horizon pour des trajectoires de développement humain, pour des constructions sociales et économiques, censées redéfinir socialement richesse, bien-être, travail etc. La dénomination « transition écologique » est largement véhiculée, mais ses bases conceptuelles ne sont pas entièrement acquises ni même élaborées. Dans ce contexte, les étudiants en première année de Master BioSciences à l’Ecole Normale Supérieure (ENS) de Lyon ont préparé une première étude analytique de ce changement radical et global de société pour mieux comprendre dans quelle société ils souhaitent vivre, en donnant du sens aux activités humaines présentes et à venir. Une trentaine de dossiers sur divers secteurs d’activités et acteurs de la société ont été produits et ont servis de support à cette synthèse. Plus largement, le but est de construire un socle conceptuel et une plate-forme de travail sur lesquels les questions de fond, mais aussi opérationnelles, peuvent être posées et étudiées en permanence. Cette démarche participative est ouverte à la collectivité sur le site http://institutmichelserres.ens-lyon.fr/

Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors

BACKGROUND: Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped in understanding how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce. RESULTS: We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features. CONCLUSIONS: These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection-relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.This work was supported by the Gatsby Charitable Foundation (RG62472), by the Royal Society (RG69135) and by the European Research Council (ERC-2014-STG, H2020, 637537)

Contrôle du phosphatidylinositol-4,5-biphosphate [PI(4,5)P2] par des phosphatases

Phosphoinositides are low abundant anionic membrane phospholipids. Their relative accumulation in thecytosolic leaflet of the plasma membrane and of various internal membranes in eukaryotic cells generates alandmark code. Especially, phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] was only reported in theplasma membrane in yeast, Metazoan and plant cells so far.Here, we used Arabidopsis thaliana (thale cress) as model organism to study PI(4,5)P2. In suppressor of actin 9(sac9) mutant, in which PI(4,5)P2 and phosphatidylinositol 4-phosphate (PI4P) balance is skewed, weobserved anomalous presence of PI(4,5)P2 in subcortical endo-compartments did not co-localise with anyorganelle marker tested. We therefore show that proper patterning of PI(4,5)P2 requires AtSAC9 in plantcells. Besides, we also observed that AtSAC9 localises to endosomes, and that sac9 mutant displays defectsin vesicular trafficking, showing AtSAC9 implication in this process, possibly through proper patterningof PI(4,5)P2.We also developed an inducible genetic system that allows unprecedented fast and specific depletion ofPI(4,5)P2 from the plasma membrane of plant cells. We also describe a transient system depleting PI4P.Both systems will enable to assess the role of PI(4,5)P2 and PI4P for cellular processes and plantdevelopment and can be amended to investigate various additional biological mechanims.Les phosphoinositides sont des lipides membranaires anioniques peu abondants .Leurs concentrations relatives dans les feuillets cytosoliques de la membrane plasmique et de certaines membranes internes des cellules eucaryotes constituent des signatures moléculaires. Le phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2 ] en particulier a pour l’instant seulement été détecté à la membrane plasmique dans les cellules de levure, animales ou végétales.Nous avons utilisé l’organisme modèle Arabidopsis thaliana (Arabette des dames) pour étudier le PI(4,5)P2. Dans un mutant perte de fonction où l’équilibre entre PI(4,5)P2 et phosphatidylinositol-4-phosphate (PI4P) est modifié, nous avons observé la présence anormale de PI(4,5)P2 dans des compartiments intracellulaires qui n’ont co-localisé avec aucun marqueur d’organite testé. Par conséquent, la protéine codée par le gène muté est nécessaire à la restriction du PI(4,5)P2 à la membrane plasmique dans la cellule végétale. De plus, nous avons aussi constaté que cette protéine est présente sur des endosomes, et que le trafic vésiculaire est perturbé dans le mutant dont elle est absente, montrant que la protéine est impliquée dans ce processus, potentiellement via le contrôle de la distribution subcellulaire du PI(4,5)P2.Nous avons par ailleurs développé un système génétique inductible, sans équivalent à ce jour, appauvrissant rapidement et spécifiquement en PI(4,5)P2 la membrane plasmique des cellules végétales. Nous présentons également un système génétique transitoire déplétant le PI4P. Ces deux systèmes permettent d’étudier le rôle du PI(4,5)P2 et du PI4P dans les cellules végétales et le développement végétal. Ils peuvent être adaptés pour étudier différents processus biologiques

Experimental manipulation of phosphoinositide lipids: from cells to organisms

International audiencePhosphoinositides (PIs) play critical roles in various cellular, physiological, developmental, pathological and infectious processes. They are signaling phospholipids that can affect every aspect of membrane biology, including protein function (e.g., recruitment, activity), membrane physicochemical properties (e.g., curvature, surface charges, packing), and the generation of second messengers. PIs act at very precise locations within the cell in a dosedependent manner, and their local concentration can vary drastically during signaling and trafficking. Techniques able to manipulate PI amounts acutely and with subcellular accuracy are thus paramount to understand the role of these lipids in vivo. Here, we review these methods and emphasize the approaches recently developed to perturb PI levels in multicellular organisms. Phosphoinositides (PIs) constitute a dynamic and interlinked network of landmark lipids in cellular membranes PIs are phosphorylated derivatives from the glycerophospholipid phosphatidylinositol (PtdIns) [1]. The inositol head group can be phosphorylated in position three, four or five, forming up to seven distinct species of phosphorylated PtdIns, collectively known as phosphoinositide

iDePP: a genetically encoded system for the inducible depletion of PI(4,5)P 2 in Arabidopsis thaliana

Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ] is a low abundant lipid present at the plasma membrane of eukaryotic cells. Extensive studies in animal cells revealed the pleiotropic functions of PI(4,5)P 2 . In plant cells, PI(4,5)P 2 is involved in various cellular processes including the regulation of cell polarity and tip growth, clathrin-mediated endocytosis, polar auxin transport, actin dynamics or membrane-contact sites. To date, most studies investigating the role of PI(4,5)P 2 in plants have relied on mutants lacking enzymes responsible for PI(4,5)P 2 synthesis and degradation. However, such genetic perturbations only allow steady-state analysis of plants undergoing their life cycle in PI(4,5)P 2 deficient conditions and the corresponding mutants are likely to induce a range of non-causal (untargeted) effects driven by compensatory mechanisms. In addition, there are no small molecule inhibitors that are available in plants to specifically block the production of this lipid. Thus, there is currently no system to fine tune PI(4,5)P 2 content in plant cells. Here we report a genetically encoded and inducible synthetic system, iDePP (Inducible De pletion of P I(4,5)P 2 in P lants), that efficiently removes PI(4,5)P 2 from the plasma membrane in different organs of Arabidopsis thaliana , including root meristem, root hair and shoot apical meristem. We show that iDePP allows the inducible depletion of PI(4,5)P 2 in less than three hours. Using this strategy, we reveal that PI(4,5)P 2 is critical for cortical microtubule organization. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P 2 in given cellular or developmental responses but also to evaluate the importance of this lipid in protein localization.Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is a low abundant lipid present at the plasma membrane of eukaryotic cells. Extensive studies in animal cells revealed the pleiotropic functions of PI(4,5)P2. In plant cells, PI(4,5)P2 is involved in various cellular processes including the regulation of cell polarity and tip growth, clathrin-mediated endocytosis, polar auxin transport, actin dynamics or membrane-contact sites. To date, most studies investigating the role of PI(4,5)P2 in plants have relied on mutants lacking enzymes responsible for PI(4,5)P2 synthesis and degradation. However, such genetic perturbations only allow steady-state analysis of plants undergoing their life cycle in PI(4,5)P2 deficient conditions and the corresponding mutants are likely to induce a range of non-causal (untargeted) effects driven by compensatory mechanisms. In addition, there are no small molecule inhibitors that are available in plants to specifically block the production of this lipid. Thus, there is currently no system to fine tune PI(4,5)P2 content in plant cells. Here we report a genetically encoded and inducible synthetic system, iDePP (Inducible Depletion of PI(4,5)P2 in Plants), that efficiently removes PI(4,5)P2 from the plasma membrane in different organs of Arabidopsis thaliana, including root meristem, root hair and shoot apical meristem. We show that iDePP allows the inducible depletion of PI(4,5)P2 in less than three hours. Using this strategy, we reveal that PI(4,5)P2 is critical for cortical microtubule organization. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P2 in given cellular or developmental responses but also to evaluate the importance of this lipid in protein localization

Inducible depletion of PI(4,5)P2 by the synthetic iDePP system in Arabidopsis

International audiencePI(4,5)P-2 is importantly involved in a broad array of cellular processes, including polar auxin transport, vesicle trafficking and anisotropic cell growth. An inducible system is developed in Arabidopsis to conduct tunable depletion of PI(4,5)P-2 and reveal new roles of this membrane lipid.Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P-2) is a low-abundance membrane lipid essential for plasma membrane function(1,2). In plants, mutations in phosphatidylinositol 4-phosphate (PI4P) 5-kinases (PIP5K) suggest that PI(4,5)P-2 production is involved in development, immunity and reproduction(3-5). However, phospholipid synthesis is highly intricate(6). It is thus likely that steady-state depletion of PI(4,5)P-2 triggers confounding indirect effects. Furthermore, inducible tools available in plants allow PI(4,5)P-2 to increase(7-9) but not decrease, and no PIP5K inhibitors are available. Here, we introduce iDePP (inducible depletion of PI(4,5)P-2 in plants), a system for the inducible and tunable depletion of PI(4,5)P-2 in plants in less than three hours. Using this strategy, we confirm that PI(4,5)P-2 is critical for various aspects of plant development, including root growth, root-hair elongation and organ initiation. We show that PI(4,5)P-2 is required to recruit various endocytic proteins, including AP2-mu, to the plasma membrane, and thus to regulate clathrin-mediated endocytosis. Finally, we find that inducible PI(4,5)P-2 perturbation impacts the dynamics of the actin cytoskeleton as well as microtubule anisotropy. Together, we propose that iDePP is a simple and efficient genetic tool to test the importance of PI(4,5)P-2 in given cellular or developmental responses, and also to evaluate the importance of this lipid in protein localization

The Arabidopsis SAC9 Enzyme defines a cortical population of early endosomes and restricts PI(4,5)P 2 to the Plasma Membrane

Membranes lipids, and especially phosphoinositides, are differentially enriched within the eukaryotic endomembrane system. This generates a landmark code by modulating the properties of each membrane. Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 ] specifically accumulates at the plasma membrane in yeast, animal and plant cells, where it regulates a wide range of cellular processes including endocytosis. However, the functional consequences of mispatterning PI(4,5)P 2 in plants are unknown. Here, we functionally characterized the phosphoinositide phosphatase SUPPRESSOR OF ACTIN9 ( SAC9 ) in Arabidopsis thaliana (Arabidopsis). We found that SAC9 depletion led to the ectopic localization of PI(4,5)P 2 on cortical intracellular compartments, which depends on PI4P and PI(4,5)P 2 production at the plasma membrane. SAC9 localizes to a subpopulation of trans -Golgi Network/early endosomes that are spatially restricted to a region close to the cell cortex and that are coated with clathrin. Furthermore, it interacts and colocalizes with the endocytic component Src Homology 3 Domain Protein 2 (SH3P2). In the absence of SAC9, SH3P2 localization is altered and the clathrin mediated endocytosis rate is significantly reduced. Thus, SAC9 is required to maintain efficient endocytic uptake, highlighting the importance of restricting the PI(4,5)P 2 pool at the plasma membrane for the proper regulation of endocytosis in plants. One-sentence summary SAC9 prevents the accumulation of PI(4,5)P 2 along the endocytic pathway in plants and thereby contributes to the clathrin mediated endocytosis process at the plasma membrane via its interaction with SH3P

Arabidopsis ADR1 helper NLR immune receptors localize and function at the plasma membrane in a phospholipid dependent manner

International audienceActivation of nucleotide-binding leucine-rich repeat receptors (NLRs) results in immunity and a localized cell death. NLR cell death activity requires oligomerization and in some cases plasma membrane (PM) localization. The exact mechanisms underlying PM localization of NLRs lacking predicted transmembrane domains or recognizable lipidation motifs remain elusive.We used confocal microscopy, genetically encoded molecular tools and protein-lipid overlay assays to determine whether PM localization of members of the Arabidopsis HeLo-/RPW8-like domain ‘helper’ NLR (RNL) family is mediated by the interaction with negatively charged phospholipids of the PM.Our results show that PM localization and stability of some RNLs and one CC-type NLR (CNL) depend on the direct interaction with PM phospholipids. Depletion of phosphatidylinositol-4-phosphate from the PM led to a mis-localization of the analyzed NLRs and consequently inhibited their cell death activity. We further demonstrate homo- and hetero-association of members of the RNL family. Our results provide new insights into the molecular mechanism of NLR localization and defines an important role of phospholipids for CNL and RNL PM localization and consequently, for their function.We propose that RNLs interact with anionic PM phospholipids and that RNL-mediated cell death and immune responses happen at the P

A Combinatorial Lipid Code Shapes the Electrostatic Landscape of Plant Endomembranes

International audienceMembrane surface charge is critical for the transient, yet specific recruitment of proteins with polybasic regions to certain organelles. In eukaryotes, the plasma membrane (PM) is the most electronegative compartment of the cell, which specifies its identity. As such, membrane electrostatics is a central parameter in signaling, intracellular trafficking, and polarity. Here, we explore which are the lipids that control membrane electrostatics using plants as a model. We show that phosphatidylinositol-4-phosphate (PI4P), phosphatidic acidic (PA), and phosphatidylserine (PS) are separately required to generate the electrostatic signature of the plant PM. In addition, we reveal the existence of an electrostatic territory that is organized as a gradient along the endocytic pathway and is controlled by PS/PI4P combination. Altogether, we propose that combinatorial lipid composition of the cytosolic leaflet of organelles not only defines the electrostatic territory but also distinguishes different functional compartments within this territory by specifying their varying surface charges