Team Leader : Véronique Decroocq (veronique.decroocq@inrae.fr)

Team description and research objectives :

Plant viruses are ubiquitous and highly diverse obligate pathogens which can severely affect crops and are difficult to control. They are also an underestimated part of natural ecosystems and represent half of emerging plant pathogens. The multidisciplinary Plant Viruses (Viro) team brings together expertise in plant virology, genetics and genomics, cellular biology, biochemistry and bioinformatics. In a translational approach, it develops efforts to understand the diversity and the functioning of these agents and strategies to control them. The team is near exclusively focused on RNA viruses, which represent about 80% of known plant viruses and its project centers primarily on two major research themes: (i) identifying mechanisms and factors controlling plant-virus interactions and (ii) developing and using tools to describe and analyze viral diversity. Each of these themes has both cognitive and applicative aspects. The applicative aspects deal principally with the development and use of resistant plants (plant virus-interactions) and with viral diagnostics and aetiology (virus diversity). The two themes are interconnected as knowledge of viral diversity is often a useful entrypoint for plant-virus interaction studies.

Research topics :

The research activity of the Plant Virology team is structured in four strongly interacting topics, which reinforce and complement each other. Two technological platforms, « Viral indexing by sequencing » and « Viral vectors » are supported by these research activities.

1 - Analysis of viral diversity at different scales and translational research applications: etiology, diagnostics, taxonomy

Contacts :
Thierry Candresse (thierry.candresse@inrae.fr) - Armelle Marais-Colombel (armelle.marais-colombel@inrae.fr)

Viruses are undoubtedly the most diverse biological agents. They are also individually highly variable and their error-prone replication endows them with very high evolutionary potential. These characteristics have a number of practical implications for control efforts, from difficulties encountered identifying and detecting disease agents to host resistance instability. Our team is actively engaged in the diagnostics and viral characterization field, with particular emphasis on the use of high-throughput sequencing (HTS). We have put major emphasis on the use of HTS for the solving of aetiology problems and on the translation of HTS into practical diagnostics.

In recent years, we have made a significant contribution to the characterization of the grapevine virome in the context of collaborative projects with growers organization; This effort is now being extended by two PNDV (National Vineyard Deterioration Plan) projects and extended to the mycovirome (fungal viruses) associated with grapevine. Likewise, the virome of Prunus fruit trees is being characterized in genetic resources collections as part of a PhD supported through the European Marie Curie InextVir training network. This should lead to an optimized inclusiveness of the PCR detection primers currently used for viral diagnosis in these species. The viral indexing by sequencing platform operated by the team is open to all stakeholders in the phytosanitary field and supports collaborative projects involving a large number of crops. These actions lead to the characterization of viral populations, the identification and characterization of the agents responsible for diseases of unknown etiology and the development of efficient diagnostic tools. This know-how was recently mobilized to contribute to the PNRI (national research and innovation plan) on beet virus diseases and to a PPR (Priority Research Program) project aiming to reduce dependence of cereal crops to insecticides used to control the aphids vectors of viral diseases.

Over the years, these virus characterization activities have generated a collection of reference viral isolates housed in our high-level containment greenhouse, leading to our participation to the Q-Collect EU 7th Framework Program project. This collection has now been integrated into the EU-funded EVA-Global (European Virus Archive) infrastructure project, which aims to increase the number and quality standards of viral isolates and facilitate their distribution.

While they can be applied to isolated plants for diagnostic purposes, HTS approaches can also be applied to plant populations, with the goal to identify all plant viruses in a given environment and gain an understanding of viral ecology. Our efforts in viral metagenomics have two objectives. The first is methodological and has resulted, for example, in the development of the VirAnnot pipeline, allowing for the first time to reproducibly estimate a virome specific richness. The second concerns the description and comparison of phytoviromes in different environments and, in viral ecology approaches, the understanding of the factors structuring phytoviral populations in time and space or the identification of virus fluxes between the wild and cultivated compartments of agroecosystems. These studies have highlighted the complexity and diversity of viromes associated with plants, and demonstrated their highly dynamic nature. These efforts are being pursued within the framework of the European Marie Curie InextVir training network and of the ANR Phytovirus project coordinated by P. Roumagnac (CIRAD Montpellier)

2 - Functional analysis of plant-Potyvirus molecular interactions

• To invade plants, plant viruses reroute host cellular functions for their own benefits. The completion of the viral cycle results from a complex interplay between virus- and host-encoded factors, also called susceptibility factors. In this scheme, absence or non-adequacy of a single susceptibility factor leads to full or partial resistance to viruses.
  Our first aim is to identify such factors and to decipher the underlying interaction mechanism(s) through functional studies

Contact : Sylvie German-Retana (sylvie.german-retana@inrae.fr)

Plasmodesmata (PD) are symplasmic tunnels between cells that are the gateway for plant virus movement. Plant virus genome encodes a class of proteins called Movement Protein that interact with host proteins to modify the PD for cell-to-cell movement. Our aim is to identify new plant factors involved in potyvirus cell-to-cell movement. This key-step of the viral infection is considered to be a major putative obstacle to viral exponential expansion in the plant by generating population bottlenecks and thus, an excellent target for resistance.

Plasmodesmata (PD) are structures unique to plants, crucial for the communication between the cells. To invade the whole plant, viruses move through the PD to enter in the neighboring cells. Then they reach the sieve elements where they are transported within the source-to-sink flow of photo-assimilates and are unloaded from sieve elements into sink tissues. Underlying mechanisms of cell-to-cell movement of potyviruses are still little documented.

Plasmodesmic factors potentially involved in the movement of potyviruses in the plant have been identified and are in the process of being validated (ANR PotyMove contract). Remorin, a protein localized at lipid rafts, specific sites of the plasma membrane, is involved in the regulation of the permeability of plasmodesmas. As part of an INRA-CNRS collaboration (Team Sébastien Mongrand, LBM Bordeaux), we have shown that Remorine is involved in the control of the movement of a plant virus, the potato virus X (PVX, potexvirus). The perspectives are to understand how post-translational modifications of this phosphoprotein could regulate its interaction with proteins necessary for the integration of a signal and the establishment by the cell of responses to viruses, and in particular potyviruses.

Monitoring of the movement of GFP-tagged potyvirus in Arabidopsis thaliana (Photos taken under UV). Foci of infection observed on inoculated leaves 6 days after incoulation (A and B). Observation of virus propagation in upper leaves 12 days after inoculation (C and D)

In parallel, we are developing a new project with Claire Brehelin’s team (CNRS, LBM-Bordeaux) that aims at understanding the roles of leaf Lipid Droplets (LDs) in the infection cycle of potyviruses (RoLiPV project). LDs are unique spherical organelles involved in energy production, membrane biogenesis and stress signaling purposes. Those dynamic organelles were recently shown to be high-jacked by animal viruses for their replication complexes formation through cellular endomembrane recruitment. Animal and plant viruses (including potyviruses) both share the capacity to induce the proliferation of host endomembranes for their replication, suggesting that plant viruses may also usurp LDs. This study will represent one of the very rare studies performed on the role of plant LDs during a viral biotic stress.

• The engine of virus adaptation, in particular their ability to bypass resistance in the host plant, is based on a modulation of the structure-function relationship between their protein factors.
  Our second goal is to explore the molecular mechanisms that govern viral adaptation.

Contacts : Guillaume Lafforgue (guillaume.lafforgue@inrae.fr) - Thierry Michon (thierry.michon@inrae.fr)

The high mutation frequency of viruses boosts their evolutionary potential and compromises the durability of host resistance. Certain viral proteins have so-called intrinsically disordered regions (IDR) which do not have a stable structure, but which nevertheless fulfill important functions in the infectious cycle of the virus. These structurally unconstrained IDRs have a mutational robustness which could facilitate the adaptation of the virus to its host. By combining experimental evolutionary approaches in plants and biochemical methods, we evaluated the contribution of IDRs to bypassing host resistance. Our experimental data, obtained in vivo, allow for the first time, to support the hypothesis that IDRs can directly modulate the adaptability of viruses.

3 - Analysis of the plant's response to potyviruses in multi-stress conditions: genetic basis of tolerance

Contact : Valérie Schurdi-Levraud (valerie.schurdi-levraud@inrae.fr)

Viral infection is one of the most alarming biotic threats in crops due to the impact of climate change on the spatial and temporal distribution of vectors and viruses. Global changes, in particular the increase in the frequency of high temperature periods, are thus expected to favour the redistribution of many plant pathogens and the emergence of new pathogens and/or strains. In addition, heat has been shown to largely suppress the defence responses and signalling elements produced by the plant during a viral infection. In this context, understanding the response of plants to viral infection under abiotic constraints such as temperature rise is of great importance for finding sustainable agricultural solutions.

So far, particularly with regard to biotic stresses, resistance has been considered the best response. However, it has the disadvantage of producing selection pressure on pathogen populations, contributing to its overcome. It is, moreover, often associated with a yield penalty related to the trade-off between resistance and growth.

With the objective of sustainable agriculture, the question of tolerance to multiple stresses is therefore crucial. Plant stress tolerance can be defined as a compromise between stress response and growth maintenance. We are therefore researching the genetic and functional bases of this response.  We are interested in the pathosystem between the model plant Arabidopsis thaliana and the turnip mosaic virus (TuMV). Under outdoor conditions, this interaction reveals a genetic architecture that is more complex than under controlled conditions, highlighting new loci involved in the interaction using pan-genomic analysis (GWA mapping). We have also investigated the metabolic changes associated with viral infection in the field (F. collaborations. Roux INRAE LIPM Toulouse, J. Bergelson U. Chicago USA and Y. Gibon, Meta team, UMR 1332 BF P).  Certain metabolites appear as markers of the interaction. This pioneering study underlines the interest of analysing plant-virus interactions in the complex context of multi-stress that plants are confronted with under natural conditions. The approach will be extended to a study on tomato and  wheat. We will also be interested in multiple biotic interactions.

4 - Genetics, genomics and translational research in stone fruit species: transforming the knowledge acquired on plant-virus interactions into resistance strategies

Contact : Véronique Decroocq (veronique.decroocq@inrae.fr)

Our main objective is the acquisition of knowledge and the development of biotechnological and genetic tools for lasting resistance to PPV (Plum pox virus), the causative agent of plum pox in stone fruit species (Prunus species such as peach, apricot, almond). This is a major challenge for a quarantine pathogen that infects perennial host plants.

To this end, we have implemented a series of complementary strategies which use the latest advances in metagenomics in these woody species as well as the knowledge acquired on plant-virus interactions. To this end, we have assembled a unique botanical collection of more than 1,000 accessions of wild and cultivated apricot and almond trees. We have sequenced the genome of more than 500 of these accessions and assembled de novo, the apricot genome in collaboration with the Center de BioInformatique de Bordeaux.

In parallel, we initiated an association studies to elucidate the genetic architecture of resistance to PPV in cultivated apricot trees (Mariette et al, 2016). This approach is currently being extended to natural populations of apricot trees. In view of the originality of this plant material, and the data generated, we were lead to wonder about the origin of the cultivated apricot tree and the impact of domestication on plant-virus interactions.

The second strategy that we are pursuing consists in looking for mutations in the genes for susceptibility to plum pox within the natural or artificial diversity of Prunus (the so-called Eco-TILLING or TILLING approaches). First, we showed, in the Arabidopsis thaliana model, that CPGK (Poque et al, 2015), and the isoforms of the translation initiation complex, eIF4F (eIFiso4E and eIFiso4G), were key interactors during PPV infection (Decroocq et al, 2006; Nicaise et al, 2007). Transgenic Japanese plum trees in which the expression of different forms of these susceptibility factors confirmed the major role of one of the two copies of eIFiso4G in the viral infection. Since most stone fruit varieties are susceptible to PPV, we postulate that susceptibility alleles are predominant in cultivated germplasm. Accordingly, our current approach is to screen our botanical collection of Prunus as well as collections of cultivated varieties of peach, apricot, almond and plum, for rare mutations affecting the susceptibility factors to plum pox. We have more recently included in the study a population of 3000 mutagenized peach trees (by the agent EMS) which is currently screened by TILLING and we are developing genome editing tools to produce non-functional copies of these factors. of sensitivity to the plum pox.

In the future, we plan to extend similar translational research approaches to other agronomic traits of interest (resistance to other pathogens, to abiotic stress, etc.) and to other cultivated Prunus species. We want to optimize a rapid transfer of this knowledge, tools and plant material, to stone fruit breeding programs