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Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors

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  • Mark C. Derbyshire

    (Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University)

  • Sylvain Raffaele

    (Laboratoire des Interactions Plantes Micro-organismes Environnement (LIPME), INRAE, CNRS, Université de Toulouse)

Abstract

Pathogens secrete effector proteins to subvert host physiology and cause disease. Effectors are engaged in a molecular arms race with the host resulting in conflicting evolutionary constraints to manipulate host cells without triggering immune responses. The molecular mechanisms allowing effectors to be at the same time robust and evolvable remain largely enigmatic. Here, we show that 62 conserved structure-related families encompass the majority of fungal orphan effector candidates in the Pezizomycotina subphylum. These effectors diversified through changes in patterns of thermodynamic frustration at surface residues. The underlying mutations tended to increase the robustness of the overall effector protein structure while switching potential binding interfaces. This mechanism could explain how conserved effector families maintained biological activity over long evolutionary timespans in different host environments and provides a model for the emergence of sequence-unrelated effector families with conserved structures.

Suggested Citation

  • Mark C. Derbyshire & Sylvain Raffaele, 2023. "Surface frustration re-patterning underlies the structural landscape and evolvability of fungal orphan candidate effectors," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-40949-9
    DOI: 10.1038/s41467-023-40949-9
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    1. Kathryn Tunyasuvunakool & Jonas Adler & Zachary Wu & Tim Green & Michal Zielinski & Augustin Žídek & Alex Bridgland & Andrew Cowie & Clemens Meyer & Agata Laydon & Sameer Velankar & Gerard J. Kleywegt, 2021. "Highly accurate protein structure prediction for the human proteome," Nature, Nature, vol. 596(7873), pages 590-596, August.
    2. Karine de Guillen & Diana Ortiz-Vallejo & Jérome Gracy & Elisabeth Fournier & Thomas Kroj & André Padilla, 2015. "Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi," PLOS Pathogens, Public Library of Science, vol. 11(10), pages 1-27, October.
    3. Brian J. Haas & Sophien Kamoun & Michael C. Zody & Rays H. Y. Jiang & Robert E. Handsaker & Liliana M. Cano & Manfred Grabherr & Chinnappa D. Kodira & Sylvain Raffaele & Trudy Torto-Alalibo & Tolga O., 2009. "Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans," Nature, Nature, vol. 461(7262), pages 393-398, September.
    4. John Jumper & Richard Evans & Alexander Pritzel & Tim Green & Michael Figurnov & Olaf Ronneberger & Kathryn Tunyasuvunakool & Russ Bates & Augustin Žídek & Anna Potapenko & Alex Bridgland & Clemens Me, 2021. "Highly accurate protein structure prediction with AlphaFold," Nature, Nature, vol. 596(7873), pages 583-589, August.
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