A functional study of the Phytophthora infestans Avr3a alleles and paralogs

  • Zulkifli Ahmad Seman

    Student thesis: Doctoral ThesisDoctor of Philosophy


    Late Blight disease, caused by Phytophthora infestans, is the most significant threat to potato production world-wide. Identifying and deploying more durable host resistance to P. infestans is a promising way forward to sustain the production of potato. To achieve this goal, it is important to seek key pathogen components that are essential for infection and which, upon detection by the host, trigger a resistance response. One such potential key pathogen molecule is the RXLR-containing effector Avr3a. Avr3a is highly up-regulated during infection and is also required for P. infestans pathogenicity. To date, all P. infestans isolates studied contain Avr3a alleles E80M103 and/or K80I103. However, a study of Avr3a diversity in the Toluca Valley, Mexico, has identified additional alleles such as K80I103L139, K80I103H133, E80M103H133 and E80M103G124. Functional studies of these alleles were conducted as part of this thesis, which also include the Avr3a paralogs Pex147-2 and Pex147-3.

    By examining the amino acid changes in relation to the established protein structure, it was determined that all alterations within the Avr3a variants occur at surface exposed amino acids. The change R124G that leads to Avr3aEMG is located in the a-helix loop 3 and the changes Q133H and M139L (Avr3aKIH, Avr3aEMH and Avr3aKIL) locate to a helix 4. Whereas amino acid substitutions in PEX147-3 only affect surface exposed residues, amino acid changes that occur in PEX147-2 involves a ‘buried’ amino acid that is key to structure and stability. Indeed, with the exception of PEX147-2, all Avr3a variants and PEX147-3 are stable upon transient expression in planta and in yeast cells.

    In terms of host recognition, the protein products of the Avr3a alleles derived from Avr3aKI are recognised by the cognate host resistance gene product R3a whereas those derived from Avr3aEM evade recognition. Similarly, PEX147-3 is recognised by R3a but PEX147-2 is not. In addition to host recognition, virulence functions of these alleles and paralogs have been elucidated. INF1 and AVR4/CF-4 induced cell death responses, which are dependent on the host defence protein CMPG1, are suppressed by Avr3aKI, Avr3aKIH, Avr3aKIL, Avr3aEM and Avr3aEMG but not by Avr3aEMH. All Avr3a variants interact with and stabilise the host E3 ubiquitin ligase CMPG1 to various degrees in planta and this interaction was found to be weakest for Avr3aEMH. Interestingly, PEX147-3, which did not interact with or stabilise CMPG1, could only suppress INF1 cell death but not CF-4/AVR4 elicited responses.

    A P. infestans isolate, CS12, which was stably silenced for Avr3aEM expression and subsequently shown to be compromised in virulence on the normally susceptible host Nicotiana benthamiana, was used for in planta complementation studies. As shown previously, upon transient expression in planta prior to infection with C12, Avr3aKI and Avr3aEM successfully restore pathogenicity. Similar levels of virulence re-establishment were only observed for Avr3KI derived alleles Avr3aKIH and Avr3aKIL but not for alleles derived from Avr3aEM. This study concludes that Avr3aEM is currently the only form of the essential effector that is fully functional and evades recognition by the known resistance gene product R3a. This functionality is the likely reason that 70% of all studied isolates in the Toluca Valley are homozygous for Avr3aEM. This form of the effector is therefore a suitable target for identifying more durable resistances.
    Date of Award2013
    Original languageEnglish
    SponsorsMalaysian Agricultural Research and Development Institute
    SupervisorPaul Birch (Supervisor) & Ingo Hein (Supervisor)


    • Avr3a effector
    • Phytophthora infestans

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