When attacked by a pathogen, plants are able to set up defense mechanisms that will slow down more or less effectively, and sometimes stop the infection completely. These inducible defenses include, for example, the production of molecules with antimicrobial properties, such as molecules of the glucosinolate and isoflavone family. A plant defense mechanism called hypersensitive response relies on the rapid self-destruction of plant cells bordering the point of infection (Fig. 1). By radically modifying the pathogen's environment, the hypersensitive response can completely inhibit the infection and stop the disease completely. This is called complete resistance or qualitative resistance. The hypersensitive response is particularly effective against biotrophic pathogens, which can only complete their infectious cycle in a living host (Fig. 1). Moreover, the triggering of the hypersensitive response requires the recognition of specific molecules of certain pathogen genotypes by dedicated plant receptor proteins. This form of defence is thus controlled by a more or less elaborate key-lock mechanism that is reconstituted only when plant-pathogen pairs with compatible keys and locks are present (Fig. 2). Varietal selection is often aimed at favouring plants capable of recognising genotypes of pathogens common in agricultural environments. Minor variations in the "molecular key" carried by the pathogen may nevertheless render the plant detection system inoperative (pathogen evading resistance). On the other hand, many pathogens are able to complete their infectious cycle in dead host tissue, and necrotrophic agents will even actively induce host cell death to complete their cycle (Fig. 1). Consequently, the hypersensitive response and the resulting complete resistance remain exceptional phenomena in nature.
Figure 1: Some plant disease symptoms indicative of the molecular mechanisms governing plant-pathogen interaction. (A) Typical hypersensitive reaction (dead cells surrounded by a yellowish halo) on a leaf of A. thaliana leading to the confinement of pathogenic bacteria in a limited area of the leaf, then to their destruction. (B) Young sunflower seedling infected with the downy mildew oomycete Plasmopara halstedii, forming white sporangia on the surface. Infected tissues remain alive and green in response to this biotrophic pathogen. (C) Sunflower plant infected with the white rot fungus Sclerotinia sclerotiorum. The infected plant organs die rapidly, producing brownish lesions characteristic of a necrotrophic interaction
In the absence of qualitative resistance, a phenotype of partial or incomplete resistance is often observed, resulting in a reduction of symptoms rather than absence of disease on a given plant. At the level of plant populations, this phenomenon results in a continuous distribution of resistance levels and is referred to as quantitative disease resistance (QDR, Fig. 2). The emergence of a qualitative or quantitative resistance phenotype depends on the genotype of the pathogen and the plant genotype, according to the molecular key lock model mentioned above, but also on environmental conditions (soil and climate conditions and other microorganisms present). Thus, understanding the nature and regulation of the biological processes that contribute to the quantitative resistance phenotype is essential for optimizing the durability of plant resistance in the face of the evolutionary power of pathogen populations and variations in environmental conditions.
The genetic architecture of the resistance trait studied is often rich in information on the evolutionary and functional constraints that weigh on plant immunity, but is sometimes difficult to approach. The mapping of quantitative resistance loci typically leads to the identification of multiple quantitative trait loci (QTLs) of low to moderate effect, explaining between 5 and 30% of the phenotypic variance. In theory, qualitative resistance is therefore distinguished by the possibility of obtaining complete resistance by the introduction of a single gene (known as "resistance" or "R" gene) into a sensitive genetic background, whereas the introduction of a quantitative resistance gene will only confer partial resistance. In practice, however, some R genes may only confer partial resistance depending on the allele considered, the environmental conditions or the genotype of the pathogen under study (Fig. 2). Conversely, a quantitative resistance phenotype may appear binary (resistant/sensitive typical of qualitative resistance) if the plant population under study lacks diversity, if environmental conditions erase phenotypic differences, or if the precision and resolution of the phenotyping methodology is insufficient. Functional characterization of resistance QTLs therefore requires robust and accurate technologies to (i) map quantitative resistance loci on the plant genome and (ii) assess the phenotypic contribution of a gene or allele to the resistance locus.
Figure 2. Different forms of plant resistance. These are characterized by the distribution of the resistance phenotype within a host population (resistance-sensitive binary or continuum), as well as by the architecture of the genetic bases involved. Molecules produced by the pathogen are shown in brown, molecules produced by the plant are shown in green. In the gene network, each circle represents a gene of the plant. The dotted lines represent interactions between the elements of the network. The "other external signals" correspond to signals from the environment that are independent of the pathogen, such as light intensity, humidity, etc. The "other external signals" correspond to signals from the environment that are independent of the pathogen, such as light intensity, humidity, etc.
Genome evolution in filamentous plant pathogens: why bigger can be better. www.nature.com/articles/nrmicro2790
Resistance to phytopathogens e tutti quanti: placing plant quantitative disease resistance on the map. bsppjournals.onlinelibrary.wiley.com/doi/full/10.1111/mpp.12138
Advances on plant-pathogen interactions from molecular toward systems biology perspectives. onlinelibrary.wiley.com/doi/full/10.1111/tpj.13429
Silent control: microbial plant pathogens evade host immunity without coding sequence changes. academic.oup.com/femsre/advance-article/doi/10.1093/femsre/fuab002/6095737
Sclerotinia, the hard-hitting mold
The white and stem mold pathogen Sclerotinia sclerotiorum is a generalist fungal pathogen, infecting a broad range of host species (>400) in nature. Its name comes from the from Ancient Greek σκληρός (sklērós) which means “hard", by reference to the hard and melanized resting structures called sclerotia that it forms. This greek word also means "tough”, which accurately reflects how Sclerotinia behave with plants. It is among the most devastating plant pathogens worldwide and causes disease on many crops including soybean, rapeseed, sunflower and most vegetables. Solutions for the genetic control of the disease are very limited in most crops. S. Sclerotiorum naturally infects wild and cultivated Brassica species, including the model plant Arabidopsis thaliana which shows quantitative disease resistance when challenged by Sclerotinia.
A majority of studies on plant interactions with fungal pathogens over the last years have focused on tightly coupled host-pathogen interactions. For instance the powdery mildew fungus Blumeria graminis, the cereal rust fungi of the Puccinia spp., and the corn smut fungus Ustilago maydis are among the most studied fungal pathogens and are obligate biotrophic pathogens restricted to a single host genus. Such pairwise interactions only represents a fraction of plant-fungal pathogen interactions encountered in nature and a number of broad host range fungal pathogens also are major threats for food security. Understanding how broad host range pathogens successfully infect multiple plant lineages is a major challenge in plant pathology.
Among Leotiomycete, the grey mold fungus Botrytis cinerea and the white mold fungus Sclerotinia sclerotiorum stand out for having a remarkably broad host range, encompassing over 200 species. Each of these pathogens causes yearly several hundred millions of US dollars crop losses worldwide. They are considered as typical necrotrophs, secreting an arsenal of cell wall-degrading enzymes and toxins to kill host cells and derive energy. Host plants typically exhibit quantitative disease resistance (QDR) to B. cinerea and S. sclerotiorum, leading to a reduction rather than absence of disease. How these generalist fungal pathogens cause disease and what are the genetic bases of plant QDR is still poorly understood and a major focus of our research.
Figure 3. The plant pathogenic fungus Sclerotinia sclerotiorum.
Emerging Trends in Molecular Interactions between Plants and the Broad Host Range Fungal Pathogens Botrytis cinerea and Sclerotinia sclerotiorum. www.frontiersin.org/articles/10.3389/fpls.2016.00422/full
Shifts in diversification rates and host jump frequencies shaped the diversity of host range among Sclerotiniaceae fungal plant pathogens. onlinelibrary.wiley.com/doi/full/10.1111/mec.14523
Codon optimization underpins generalist parasitism in fungi. elifesciences.org/articles/22472
Intercellular cooperation in a fungal plant pathogen facilitates host colonization. www.pnas.org/content/116/8/3193.long
Characterization of molecular mechanisms underlying Arabidopsis quantitative immunity to the fungus Sclerotinia sclerotiorum
Using worldwide Arabidopsis thaliana populations, we documented extensive variation in quantitative immunity to S. sclerotiorum, opening the way to the molecular characterization of plant and pathogen determinants underlying this interaction. The overall objectives of this project are to identify which plant genes are involved in quantitative immunity to Sclerotinia and understand how they contribute to disease resistance ?
For this, we are developing notably genome wide association mapping, functional genetics, transcriptomics and high throughput quantitative phenotyping approaches.
A) The range of symptoms on Arabidopsis thaliana leaves inoculated by S. sclerotiorum with an illustration of image processing used to quantify disease.
B) Molecular structure of a fungal protein predicted to facilitate host colonization.
C) Genome wide association mapping of plant genes contributing to quantitative disease resistance, with a world map indicating the origin of plant accessions used.
Selected recent publications :
Le Roux C, Huet G, Jauneau A, Camborde L, Trémousaygue D, Kraut A, Zhou B, Levaillant M, Adachi H, Yoshioka H, Raffaele S, Berthomé R, Couté Y, Parker JE, Deslandes L. A receptor pair with an integrated decoy converts pathogen disabling of transcription factors to immunity. Cell. 2015 May 21;161(5):1074-88.
Roux F, Voisin D, Badet T, Balagué C, Barlet X, Huard-Chauveau C, Roby D, Raffaele S. Resistance to phytopathogens e tutti quanti: placing plant quantitative disease resistance on the map. Mol Plant Pathol. 2014 Jun;15(5):427-32.
Bozkurt TO, Richardson A, Dagdas YF, Mongrand S, Kamoun S, Raffaele S. The Plant Membrane-Associated REMORIN1.3 Accumulates in Discrete Perihaustorial Domains and Enhances Susceptibility to Phytophthora infestans. Plant Physiol. 2014 May 7;165(3):1005-1018.
Contact : Sylvain Raffaele
Thigmoimmunity: contribution of mechanical signal perception to quantitative immunity against Sclerotinia
During their interaction with plants, and prior to plant tissue penetration or degradation, fungal pathogens develop important mechanical loads susceptible to emit Mechanical loads are due to the tremendous turgor pressure created by water in the vacuole of appressoria and fungal cell wall mechanical preperties. This mechanical stress is generally sufficient to penetrte plant cells. Mechanosensing occurs at the plant cell level and relies on the internal mechanical state of the cell.
Recent studies demonstrated the link between mechanosensing and plant immune response to B. cinerea in Arabidopsis thaliana: plants submitted to MS exhibited higher resistance to fungal infection suggesting a priming effect operated by sterile mechanosensing. Future work should aim at addressing whether mechanosensing for fungal contact or penetration per se, in addition to PAMP perception, leads to enhanced plant immunity.
Mechanoperception and thigmomorphogenesis at INRA
Selected recent publications :
Mbengue M, Navaud O, Peyraud R, Barascud M, Badet T, Vincent R, Barbacci A, Raffaele S. Emerging Trends in Molecular Interactions between Plants and the Broad Host Range Fungal Pathogens Botrytis cinerea and Sclerotinia sclerotiorum. Front Plant Sci. 2016 Mar 31;7:422.
Barbacci A, Magnenet V, Lahaye M. Thermodynamical journey in plant biology. Front Plant Sci. 2015 Jun 30;6:481.
Contact : Adelin Barbacci
Fungal adaptations to plant quantitative immunity
Fungal plant pathogens are major and rising threats for global food security and environment sustainability. Generalist fungal pathogens such as S. sclerotiorum, infecting a broad range of host species in nature, are among the most devastating plant pathogens worldwide. The range of hosts that pathogens can infect in nature is a key determinant of the emergence and spread of diseases. How pathogens evolve the ability to infect many diverse hosts remains enigmatic. Through this project, we are addressing the following questions: What are the mechanisms used by Sclerotinia to colonize its hosts? What are the evolutionary processes that shaped the extent fungal virulence and plant immunity processes ? This work relies mostly on comparative genomics, transcriptomics, phylogeny, and systems biology approaches.
Figure legend :
A) S. sclerotiorum colonizing an Arabidopsis leaf imaged using a strain expressing the green fluorescent protein.
B) A Circos diagram illustrating comparative genomics of fungal species related to S. sclerotiorum.
C) A phylogenetic tree of fungi from the Sclerotiniaceae family.
Selected recent publications :
Dong S, Raffaele S, Kamoun S. The two-speed genomes of filamentous pathogens: waltz with plants. Curr Opin Genet Dev. 2015 Dec;35:57-65. doi: 10.1016/j.gde.2015.09.001.
Badet T, Peyraud R, Raffaele S. Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae. Front Plant Sci. 2015 Sep 24;6:776.
Guyon K, Balagué C, Roby D, Raffaele S. Secretome analysis reveals effector candidates associated with broad host range necrotrophy in the fungal plant pathogen Sclerotinia sclerotiorum. BMC Genomics. 2014 May 4;15:336.
Contact : Sylvain Raffaele
Bruno Grezes-Besset; Biogemma Mondonville
Fabrice Roux; LIPM Toulouse
Sébastien Mongrand; LBM Bordeaux
John P. Clarkson; University of Warwick (UK)
Richard P. Oliver, Mark Derbyshire, Matthew Denton-Giles; Curtin University (Aus)
Lone Buschwaldt; University of Saskatchewan (Can)
Jan van Kan, Michael Siedl; Wageningen University (NL)
Sophien Kamoun; The Sainsbury Laboratory Norwich (UK)
Jean-Charles Portais, Pierre Millard; LISBP Toulouse
Ludovic Cottret, Lucas Marmiesse; LIPM Toulouse
Contract ANR-Investissement d’Avenir LabEx TULIP, 2011-2020, Coordinators ROBY Dominique /Danchin Etienne, 9 000 k€
Contract Marie Curie CIG grant – European commission FP7, « Identification of Sclerotinia sclerotiorum Effector Proteins mediating virulence on Arabidopsis thaliana ecotypes (SEPAraTE) », 2013-17, Coordinator Sylvain Raffaele, 100 k€
Contract ERC Starting Grant Conseil Européen « Understanding White mold disease quantitative resistance using natural variation (VariWhiM) », scientific coordinator Sylvain Raffaele, 2013-2018, 1500 k€.
TULIP “New Frontiers” project “Virulence function and evolution of Sclerotinia signals manipulating plant RNA silencing pathways (ScleRNAi)”, Coordinator S. Raffaele, 2014-16, 119 k€.
Contract ANR RIPOSTE “Exploitation of pathogen quantitative resistance diversity to improve disease tolerance in crops”, Coordinator D. Roby, 2014-2018, 248 k€.
Project Plant Health & Environment Division INRA – SPE. “Identification of genetic factors underlying potential disease outbreaks of the bacterial pathogen Xanthomonas campestris” PI : Fabrice Roux, 2016 – 2017, 40k€.