Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement¹. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth largest food crop and a critical alternative to the major cereal crops for feeding the world’s population¹. Current annual worldwide potato crop losses due to late blight are conservatively estimated at $6.7 billion². Management of this devastating pathogen is challenged by its remarkable speed of adaptation to control strategies such as genetically resistant cultivars^3,4. Here we report the sequence of the P. infestans genome, which at ∼ 240 megabases (Mb) is by far the largest and most complex genome sequenced so far in the chromalveolates. Its expansion results from a proliferation of repetitive DNA accounting for ∼ 74% of the genome. Comparison with two other Phytophthora genomes showed rapid turnover and extensive expansion of specific families of secreted disease effector proteins, including many genes that are induced during infection or are predicted to have activities that alter host physiology. These fast-evolving effector genes are localized to highly dynamic and expanded regions of the P. infestans genome. This probably plays a crucial part in the rapid adaptability of the pathogen to host plants and underpins its evolutionary potential.

Fungal and oomycete plant pathogens translocate effector proteins into host cells to establish infection. However, virulence targets and modes of action of their effectors are unknown. Effector AVR3a from potato blight pathogen Phytophthora infestans is translocated into host cells and occurs in two forms: AVR3a ^KI , which is detected by potato resistance protein R3a, strongly suppresses infestin 1 (INF1)-triggered cell death (ICD), whereas AVR3a ^EM , which evades recognition by R3a, weakly suppresses host ICD. Here we show that AVR3a interacts with and stabilizes host U-box E3 ligase CMPG1, which is required for ICD. In contrast, AVR3a ^KI/Y147del , a mutant with a deleted C-terminal tyrosine residue that fails to suppress ICD, cannot interact with or stabilize CMPG1. CMPG1 is stabilized by the inhibitors MG132 and epoxomicin, indicating that it is degraded by the 26S proteasome. CMPG1 is degraded during ICD. However, it is stabilized by mutations in the U-box that prevent its E3 ligase activity. In stabilizing CMPG1, AVR3a thus modifies its normal activity. Remarkably, given the potential for hundreds of effector genes in the P. infestans genome, silencing Avr3a compromises P. infestans pathogenicity, suggesting that AVR3a is essential for virulence. Interestingly, Avr3a silencing can be complemented by in planta expression of Avr3a ^KI or Avr3a ^EM but not the Avr3a ^KI/Y147del mutant. Our data provide genetic evidence that AVR3a is an essential virulence factor that targets and stabilizes the plant E3 ligase CMPG1, potentially to prevent host cell death during the biotrophic phase of infection.

Summary: The RXLR cytoplasmic effector AVR3a of Phytophthora infestans confers avirulence on potato plants carrying the R3a gene. Two alleles of Avr3a encode secreted proteins that differ in only three amino acid residues, two of which are in the mature protein. Avirulent isolates carry the Avr3a allele, which encodes AVR3a^KI (containing amino acids C¹⁹, K⁸⁰ and I¹⁰³), whereas virulent isolates express only the virulence allele avr3a, encoding AVR3a^EM (S¹⁹, E⁸⁰ and M¹⁰³). Only the AVR3a^KI protein is recognized inside the plant cytoplasm where it triggers R3a‐mediated hypersensitivity. Similar to other oomycete avirulence proteins, AVR3a^KI carries a signal peptide followed by a conserved motif centered on the consensus RXLR sequence that is functionally similar to a host cell‐targeting signal of malaria parasites. The interaction between Avr3a and R3a can be reconstructed by their transient co‐expression in Nicotiana benthamiana. We exploited the N. benthamiana experimental system to further characterize the Avr3a–R3a interaction. R3a activation by AVR3a^KI is dependent on the ubiquitin ligase‐associated protein SGT1 and heat‐shock protein HSP90. The AVR3a^KI and AVR3a^EM proteins are equally stable in planta, suggesting that the difference in R3a‐mediated death cannot be attributed to AVR3a^EM protein instability. AVR3a^KI is able to suppress cell death induced by the elicitin INF1 of P. infestans, suggesting a possible virulence function for this protein. Structure–function experiments indicated that the 75‐amino acid C‐terminal half of AVR3a^KI, which excludes the RXLR region, is sufficient for avirulence and suppression functions, consistent with the view that the N‐terminal region of AVR3a^KI and other RXLR effectors is involved in secretion and targeting but is not required for effector activity. We also found that both polymorphic amino acids, K⁸⁰ and I¹⁰³, of mature AVR3a contribute to the effector functions.