Approaches towards disease resistance to filamentous pathogens

In the co-evolutionary arms race between plants and pathogens, plants have developed a multifaceted armory consisting of diverse defence responses, such as the production of antimicrobial compounds and the activation of immunity via specific receptors. This work examines the use of the phytoalexin capsidiol and synthetic NLR immune receptors as disease resistance approaches against oomycete and fungal plant pathogens. The production of phytoalexins constitutes an important aspect of plant defence. Capsidiol, a pepper phytoalexin, differentially inhibits the growth of two Phytophthora species, the late-blight pathogen P. infestans and the vegetable pathogen P. capsici. The differential effect of capsidiol towards these two oomycetes was determined and quantified. I also monitored intraspecific variation among various P. infestans isolates in their sensitivity towards capsidiol. Plant defence machinery also involves intracellular immune receptors of the Nucleotidebinding Leucine-rich Repeat-containing protein family (NLRs). NLRs typically recognize pathogen effector proteins with avirulence activities, leading to a response known as effector-triggered immunity (ETI). R3a and I2 are orthologous NLRs from potato and tomato responding to effectors of P. infestans and the wilt fungus Fusarium oxysporum f. sp. lycopersici, respectively. Yet, particular races of these pathogens have evolved stealthy effectors that evade recognition by R3a and I2. I assessed whether previously identified mutations in R3a, with expanded response specificities to Phytophthora spp. effectors, can be transferred to I2 with similar beneficial effects. I recovered I2 mutants with expanded response spectrum to effectors from both P. infestans and F. oxysporum f. sp. lycopersici. Infection assays in both transient and stable transgenic systems suggested this expanded response correlates with resistance. I finally investigated whether the I2 locus is a determinant of tomato resistance against P. infestans. Overall, these findings generate new insights into the molecular interactions underlying plants response to pathogens, and open up applied perspectives for sustainable crop disease resistance

Emerging oomycete threats to plants and animals

Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases to both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture, and natural ecosystems. They include the plant pathogens Phytophthora infestans, Phytophthora palmivora, Phytophthora ramorum, Plasmopara obducens, and the animal pathogens Aphanomyces invadans, Saprolegnia parasitica, and Halioticida noduliformans. For each species, we describe its pathology, importance, and impact, discuss why it is an emerging threat, and briefly review current research activities

Gene expression polymorphism underpins evasion of host immunity in an asexual lineage of the Irish potato famine pathogen

BACKGROUND: Outbreaks caused by asexual lineages of fungal and oomycete pathogens are a continuing threat to crops, wild animals and natural ecosystems (Fisher MC, Henk DA, Briggs CJ, Brownstein JS, Madoff LC, McCraw SL, Gurr SJ, Nature 484:186-194, 2012; Kupferschmidt K, Science 337:636-638, 2012). However, the mechanisms underlying genome evolution and phenotypic plasticity in asexual eukaryotic microbes remain poorly understood (Seidl MF, Thomma BP, BioEssays 36:335-345, 2014). Ever since the 19th century Irish famine, the oomycete Phytophthora infestans has caused recurrent outbreaks on potato and tomato crops that have been primarily caused by the successive rise and migration of pandemic asexual lineages (Goodwin SB, Cohen BA, Fry WE, Proc Natl Acad Sci USA 91:11591-11595, 1994; Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10:e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Cooke DEL, Cano LM, Raffaele S, Bain RA, Cooke LR, Etherington GJ, Deahl KL, Farrer RA, Gilroy EM, Goss EM, et al. PLoS Pathog 8:e1002940, 2012). However, the dynamics of genome evolution within these clonal lineages have not been determined. The objective of this study was to use a comparative genomics and transcriptomics approach to determine the molecular mechanisms that underpin phenotypic variation within a clonal lineage of P. infestans. RESULTS: Here, we reveal patterns of genomic and gene expression variation within a P. infestans asexual lineage by comparing strains belonging to the South American EC-1 clone that has dominated Andean populations since the 1990s (Yoshida K, Burbano HA, Krause J, Thines M, Weigel D, Kamoun S, PLoS Pathog 10e1004028, 2014; Yoshida K, Schuenemann VJ, Cano LM, Pais M, Mishra B, Sharma R, Lanz C, Martin FN, Kamoun S, Krause J, et al. eLife 2:e00731, 2013; Delgado RA, Monteros-Altamirano AR, Li Y, Visser RGF, van der Lee TAJ, Vosman B, Plant Pathol 62:1081-1088, 2013; Forbes GA, Escobar XC, Ayala CC, Revelo J, Ordonez ME, Fry BA, Doucett K, Fry WE, Phytopathology 87:375-380, 1997; Oyarzun PJ, Pozo A, Ordonez ME, Doucett K, Forbes GA, Phytopathology 88:265-271, 1998). We detected numerous examples of structural variation, nucleotide polymorphisms and loss of heterozygosity within the EC-1 clone. Remarkably, 17 genes are not expressed in one of the two EC-1 isolates despite apparent absence of sequence polymorphisms. Among these, silencing of an effector gene was associated with evasion of disease resistance conferred by a potato immune receptor. CONCLUSIONS: Our findings highlight the molecular changes underpinning the exceptional genetic and phenotypic plasticity associated with host adaptation in a pandemic clonal lineage of a eukaryotic plant pathogen. We observed that the asexual P. infestans lineage EC-1 can exhibit phenotypic plasticity in the absence of apparent genetic mutations resulting in virulence on a potato carrying the Rpi-vnt1.1 gene. Such variant alleles may be epialleles that arose through epigenetic changes in the underlying genes

Variation in capsidiol sensitivity between Phytophthora infestans and Phytophthora capsici is consistent with their host range.

Plants protect themselves against a variety of invading pathogenic organisms via sophisticated defence mechanisms. These responses include deployment of specialized antimicrobial compounds, such as phytoalexins, that rapidly accumulate at pathogen infection sites. However, the extent to which these compounds contribute to species-level resistance and their spectrum of action remain poorly understood. Capsidiol, a defense related phytoalexin, is produced by several solanaceous plants including pepper and tobacco during microbial attack. Interestingly, capsidiol differentially affects growth and germination of the oomycete pathogens Phytophthora infestans and Phytophthora capsici, although the underlying molecular mechanisms remain unknown. In this study we revisited the differential effect of capsidiol on P. infestans and P. capsici, using highly pure capsidiol preparations obtained from yeast engineered to express the capsidiol biosynthetic pathway. Taking advantage of transgenic Phytophthora strains expressing fluorescent markers, we developed a fluorescence-based method to determine the differential effect of capsidiol on Phytophtora growth. Using these assays, we confirm major differences in capsidiol sensitivity between P. infestans and P. capsici and demonstrate that capsidiol alters the growth behaviour of both Phytophthora species. Finally, we report intraspecific variation within P. infestans isolates towards capsidiol tolerance pointing to an arms race between the plant and the pathogens in deployment of defence related phytoalexins

Plant immunity switched from bacteria to virus

A plant immune receptor is engineered to recognize viruses rather than bacteria

Growth behaviour of <i>P. capsici</i> tdtom, after 10 days of exposure to different capsidiol concentrations.

<p>The experiment was performed 3 times.</p

Scatter plots correlating 0D600 and capsidiol concentration.

<p>The plots illustrate growth of <i>P. infestans</i> 88069td (A) and <i>P. capsici</i> tdtom (B) strains over time for a maximum of 10 days. The experiment was performed 3 times.</p

Scatter plots correlating fluorescence intensity and capsidiol concentration.

<p>The plots illustrate fluorescence intensity of <i>P. infestans</i> 88069td (A) and <i>P. capsici</i> tdtom (B) strains over time for a maximum of 10 days. The experiment was performed 3 times.</p

Provenance of <i>Phytophthora</i> samples.

<p>Provenance of <i>Phytophthora</i> samples.</p

Capsidiol inhibits <i>P. infestans</i> growth reversibly.

<p>(A) Growth inhibition assay of <i>P. infestans</i> after 10 days of exposure of mycelial plugs to capsidiol. (B) Restoration of growth after washing treatment. Green line indicates the point after which the washing treatment was applied. The experiment was performed 3 times. Picture was taken 10 days after the washing and 20 days after initial exposure to capsidiol.</p