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UMR 1332 Biologie du Fruit et Pathologie

Plant Virology Team

Team leader : Thierry Candresse, DR1 INRA, UMR 1332 BFP Director, thierry.candresse@inra.fr

Team description and research objectives :

The research activity of the Plant Virology team focuses on RNA plant viruses and in particular on Potyviruses, the largest and most economically damaging genus of plant viruses. The overall objective is to better understand these agents and their interactions with their host plants. In a translational research approach, this allows us to propose new tools or new strategies to fight plant viruses: detection and characterization techniques (phytodiagnostic ...), development of resistant plants...

These multidisciplinary efforts benefit from the complementary skills of team members (virology, molecular biology, biochemistry, genetics and genomics) and from a wide network of national and international collaborations.

Research topics :

The research activity of the Plant Virology team is structured in five strongly interacting topics, which reinforce and complement each other.

1 - Etiology, diagnosis and characterization of agents or viral metagenomes 

Our team has recognized know-how and expertise on viral diseases of fruit trees. Our efforts aim to better understand the virus infecting these plants (or other host plants, often through collaborations) and to develop new approaches for the discovery, characterization, detection of viruses and for the analysis of their diversity.

A recent development concerns the use of high throughput sequencing techniques. These approaches are developed for diagnostic purposes, in particular with the development of a service platform performing NGS-based viral indexing, but also for the study of the phytoviral metagenome in various plant populations or ecosystems.. Our metagenomic approaches are conducted in temperate settings affected by human activity (agricultural environments) but also, in frame of the French ANR Evince and Genoscope MetaGKer projects, in the constrained and non-anthropized Kerguelen Islands environment.

Right : Val Studer : one of the sampling sites for phytoviral metagenome analysis in the Kerguelen islands

Val Studer : un des sites d’échantillonnage du métagénome phytoviral aux Iles Kerguelen

2 - Identification of host factors involved in plant-potyvirus interactions

We have shown that Arabidopsis is an excellent biological system for the study of host responses to potyviruses and for the identification, by reverse genetics, of recessive genes conferring resistance to viruses (susceptibility genes). In order to identify the genetic bases of phenotypic responses to viral infection, we rely on classical genetics but also, more recently, on association genetics, for the analysis of qualitative and quantitative responses in the Arabidopsis-PPV and Arabidopsis-Lettuce mosaic virus (LMV) pathosystems.

These efforts will be extended through the Plant KBBE COBRA project. In parallel, studies aimed at mapping the determinants of quantitative resistance to PPV in susceptible Prunus (apricot, peach) and supported by the European FP7 project SharCo led to the identification of markers linked to the major resistance locus. These results are the starting point of another FP7European project, MARS (involving 9 laboratories and 8 SMEs), which aims to implement marker-assisted selection in apricot, at European level. These results have recently been enriched by genome-wide approaches in apricot (ANR ABRIWG Chair of Excellence), which also benefit from the results of the peach genome initiative. These association studies are being extended to wild apricot populations and to related species, peach and almond, using plant materials collected as part of the FP7 Marie Curie project STONE.

Symptoms caused by PPV in Arabidopsis thaliana. The plant on the left is healthy

Symptoms caused by PPV in Arabidopsis thaliana. The plant on the left is healthy

3 - Functional analysis of molecular plant-potyvirus interactions

We develop a multidisciplinary approach (molecular and cellular biology, biochemistry, viral reverse genetics...) to identify the cellular or viral partners involved and to analyze the mechanisms underlying the action of host factors playing a key role in plant-Potyvirus interactions.

This work is developed on two main aspects, the role of translation initiation factors eIF4E and eIF4G in sensitivity of plants to Potyviruses and the identification of host factors involved in the long-distance movement of Potyviruses The recruitment of eIF4E and eIF4G (or their isoforms) appears to be a prerequisite for the success of infection not only by Potyvirus but also by viruses belonging to many other viral genera.

eIF(iso)4G1 but not eIF4G or eIF(iso)4G2 is necessary for successful PPV infection in Arabidopsis thaliana

eIF(iso)4G1 but not eIF4G or eIF(iso)4G2 is necessary for successful PPV infection in Arabidopsis thaliana

Schematic representation of the involvement of cellular factors in the translation initiation process

Schematic representation of the involvement of cellular factors in the translation initiation process

Our aim is to decipher the complex web of interactions between these cellular factors and various viral proteins (VPg, CI, HC-Pro) and to understand their contribution to the infection process. We also analyze the mechanisms involved in the overcoming of the eIF4E-mediated resistance to LMV in lettuce.

The viral proteins involved in these interactions have a high proportion of intrinsically disordered domains (IDDS), which likely confer the plasticity needed for their multifunctionality. Using potyvirus models, we seek to experimentally evaluate whether these IDDs confer a selective advantage and are evolutionarily favored.

4 - Development of new strategies for antiviral resistance – Biosafety

This line of research aims to transfer in practice knowledge gained on the identity and function of host factors involved in plant-potyvirus interactions.

We focus on the development of new strategies of resistance to Plum pox virus in Prunus (peach, apricot, plum ...) and are supported by the European FP7 projects SharCo, Stone and MARS (both coordinated by our team) and by national funding (FranceAgriMer ...). These studies use different approaches, from conventional breeding (mapping of resistance determinants for the development of marker-assisted selection) to transgenesis for resistance. We also develop the targeted exploration of natural (Ecotilling) or induced (Tilling) genetic diversity in susceptible Prunus species.

In this context, a recent development is the establishment of a collection of over 3000 peach Tilling mutants. Work on the use of "pathogen-derived resistance" through transgenesis has led to the development of the PPV-resistant Honeysweet plum variety (collaboration with the USDA).

Current efforts, in the framework of the European FP7 Interest Network, are also aimed at gaining a better understanding of the mechanisms and effectiveness of silencing induced by small RNAs (siRNAs and miRNAs) and of the stability and durability of resistances to PPV thus obtained.

Fruits of the plum pox-resistant transgenic plum variety Honeysweet

Fruits of the plum pox-resistant transgenic plum variety Honeysweet

5 - Plant viruses applications in nanotechnology

The highly ordered protein backbone of viruses can be exploited to control the positioning of macromolecules for various nanotechnological applications, such as enzymes chip design, amplification of immune responses or molecular therapy. In collaboration with the molecular electronics laboratory of the University Paris Diderot and CNRS, we develop various molecular "Velcros" to control the topology of presentation of enzymes on Potyvirus particles to reconstruct redox cascades on these nanostructures.

The use of Z33, a peptide derived from Staphylococus aureus protein A, to adsorb various proteins on to virus particles surface

The use of Z33, a peptide derived from Staphylococus aureus protein A, to adsorb various proteins on to virus particles surface. Z33 specifically interacts with antibodies constant fragment. Z33 (red) was fuzzed  to GFP (Green Fluorescent  Protein) in green. This way, GFP or any other proteins may be bound along the particle through the interaction between Z33 and an antibody directed against the virus surface (orange).