Exploring a diverse world of effector domains and amyloid signaling motifs in fungal NLR proteins.

Autor: Wojciechowski JW; Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland., Tekoglu E; Biyomühendislik Bölümü, Yıldız Teknik Üniversitesi, İstanbul, Turkey.; Wydział Chemiczny, Politechnika Wrocławska, Poland., Gąsior-Głogowska M; Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland., Coustou V; Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux, France., Szulc N; Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland., Szefczyk M; Katedra Chemii Bioorganicznej, Wydział Chemiczny, Politechnika Wrocławska, Wrocław, Poland., Kopaczyńska M; Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland., Saupe SJ; Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, Bordeaux, France., Dyrka W; Katedra Inżynierii Biomedycznej, Wydział Podstawowych Problemów Techniki, Politechnika Wrocławska, Wrocław, Poland.
Jazyk: angličtina
Zdroj: PLoS computational biology [PLoS Comput Biol] 2022 Dec 21; Vol. 18 (12), pp. e1010787. Date of Electronic Publication: 2022 Dec 21 (Print Publication: 2022).
DOI: 10.1371/journal.pcbi.1010787
Abstrakt: NLR proteins are intracellular receptors constituting a conserved component of the innate immune system of cellular organisms. In fungi, NLRs are characterized by high diversity of architectures and presence of amyloid signaling. Here, we explore the diverse world of effector and signaling domains of fungal NLRs using state-of-the-art bioinformatic methods including MMseqs2 for fast clustering, probabilistic context-free grammars for sequence analysis, and AlphaFold2 deep neural networks for structure prediction. In addition to substantially improving the overall annotation, especially in basidiomycetes, the study identifies novel domains and reveals the structural similarity of MLKL-related HeLo- and Goodbye-like domains forming the most abundant superfamily of fungal NLR effectors. Moreover, compared to previous studies, we found several times more amyloid motif instances, including novel families, and validated aggregating and prion-forming properties of the most abundant of them in vitro and in vivo. Also, through an extensive in silico search, the NLR-associated amyloid signaling was identified in basidiomycetes. The emerging picture highlights similarities and differences in the NLR architectures and amyloid signaling in ascomycetes, basidiomycetes and other branches of life.
Competing Interests: The authors have declared that no competing interests exist.
(Copyright: © 2022 Wojciechowski et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
Databáze: MEDLINE
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