Computational Prediction and Molecular Characterization of an Oomycete Effector and the Cognate Arabidopsis Resistance Gene

Hyaloperonospora arabidopsidis (Hpa) is an obligate biotroph oomycete pathogen of the model plant Arabidopsis thaliana and contains a large set of effector proteins that are translocated to the host to exert virulence functions or trigger immune responses. These effectors are characterized by conserved amino-terminal translocation sequences and highly divergent carboxyl-terminal functional domains. The availability of the Hpa genome sequence allowed the computational prediction of effectors and the development of effector delivery systems enabled validation of the predicted effectors in Arabidopsis. In this study, we identified a novel effector ATR39-1 by computational methods, which was found to trigger a resistance response in the Arabidopsis ecotype Weiningen (Wei-0). The allelic variant of this effector, ATR39-2, is not recognized, and two amino acid residues were identified and shown to be critical for this loss of recognition. The resistance protein responsible for recognition of the ATR39-1 effector in Arabidopsis is RPP39 and was identified by map-based cloning. RPP39 is a member of the CC-NBS-LRR family of resistance proteins and requires the signaling gene NDR1 for full activity. Recognition of ATR39-1 in Wei-0 does not inhibit growth of Hpa strains expressing the effector, suggesting complex mechanisms of pathogen evasion of recognition, and is similar to what has been shown in several other cases of plant-oomycete interactions. Identification of this resistance gene/effector pair adds to our knowledge of plant resistance mechanisms and provides the basis for further functional analyses. Author Summary: Oomycete plant pathogens are among the most devastating agricultural pests and employ arsenals of effector proteins to manipulate their plant hosts. Some of these effectors, however, are recognized in the plant and trigger an immune response. Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on the model plant Arabidopsis thaliana and this interaction has been developed as a model system for oomycete pathogenesis. Here, we employ computational predictions to identify a novel effector ATR39-1, which is highly conserved among different Hpa isolates. A two amino acid-insertion in the alternative allele ATR39-2 correlated with evasion of recognition. We identified the corresponding resistance gene RPP39 and found that the signaling gene NDR1 is required to establish full resistance. Recognition of ATR39-1 by RPP39 in the plant did not inhibit growth of the oomycete, suggesting that complex mechanisms exist to prevent effector recognition. Knowledge of such novel resistance interactions provides the backbone of our understanding of plant resistance mechanisms and will aid in the further dissection of plant immunity.