Zinc-finger (ZiF) fold secreted effectors form a functionally diverse family across lineages of the blast fungus Magnaporthe oryzae

PLoS Pathogens, Год журнала: 2024, Номер 20(6), С. e1012277 - e1012277

Опубликована: Июнь 17, 2024

Filamentous plant pathogens deliver effector proteins into host cells to suppress defence responses and manipulate metabolic processes support colonization. Understanding the evolution molecular function of these effectors provides knowledge about pathogenesis can suggest novel strategies reduce damage caused by pathogens. However, are highly variable, share weak sequence similarity and, although they be grouped according their structure, only a few structurally conserved families have been functionally characterized date. Here, we demonstrate that Zinc-finger fold (ZiF) secreted form diverse family in blast fungus Magnaporthe oryzae . This relies on motif for protein stability is ubiquitously present lineages infecting 13 different species, forming tribes. Homologs canonical ZiF effector, AVR-Pii, from rice isolates multiple M lineages. Wheat strains also possess an AVR-Pii like allele binds Exo70 activates immune receptor Pii. Furthermore, tribes may vary bind to, indicating functional diversification intricate effector/host interactome. Altogether, uncovered new with common has diversified work expands our understanding diversity effectors, basis ultimately facilitate development sources pathogen resistance.

Язык: Английский

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The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies

eLife, Год журнала: 2024, Номер 12

Опубликована: Фев. 27, 2024

Plant pathogens secrete proteins, known as effectors, that function in the apoplast or inside plant cells to promote virulence. Effector recognition by cell-surface cytosolic receptors results activation of defence pathways and immunity. Despite their importance, our general understanding fungal effector immunity remains poor. One complication often associated with effectors is high sequence diversity lack identifiable motifs precluding prediction structure function. In recent years, several studies have demonstrated can be grouped into structural classes, despite significant variation existence across taxonomic groups. Using protein X-ray crystallography, we identify a new class hidden within secreted xylem (SIX) from Fusarium oxysporum f. sp. lycopersici ( Fol ). The recognised Avr1 (SIX4) Avr3 (SIX1) represent founding members dual-domain (FOLD) class, containing two distinct domains. AlphaFold2, predicted full SIX repertoire show SIX6 SIX13 are also FOLD which validated experimentally for SIX6. Based on comparisons, present three divisions fungi expanded symbionts. Further comparisons demonstrate secretes adopt limited number folds during infection tomato. This analysis revealed relationship between transcriptionally co-regulated pairs. We make use understand its I receptor, leads disease resistance study represents an important advance Fol- tomato, extension plant–fungal interactions, will assist development novel control engineering strategies combat pathogens.

Язык: Английский

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Effector proteins of Funneliformis mosseae BR221: unravelling plant-fungal interactions through reference-based transcriptome analysis, in vitro validation, and protein‒protein docking studies

BMC Genomics, Год журнала: 2025, Номер 26(1)

Опубликована: Янв. 16, 2025

Язык: Английский

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Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution

Опубликована: Фев. 21, 2025

Phytopathogens secrete effector molecules to manipulate host immunity and metabolism. Recent advances in structural genomics have identified fungal families whose members adopt similar folds despite sequence divergence, highlighting their importance virulence immune evasion. To extend the scope of comparative structure-guided analysis more evolutionarily distant phytopathogens with lifestyles, we used AlphaFold2 predict 3D structures secretome from selected plasmodiophorid, oomycete, gall-forming pathogens. Clustering protein based on homology revealed species-specific expansions a low abundance known orphan families. We novel sequence- unrelated but structurally (SUSS) clusters, rich conserved motifs such as ’CCG’ ’RAYH’. demonstrate that these likely play central role maintaining overall fold. also SUSS cluster adopting nucleoside hydrolase-like fold among various microbes. Notably, ankyrin proteins were significantly expanded plasmodiophorids, most being highly expressed during clubroot disease, suggesting pathogenicity. Altogether, this study our understanding landscapes microbes provides valuable resource for broadening phylogenomic studies across diverse phytopathogens.

Язык: Английский

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Structure-guided secretome analysis of gall-forming microbes offers insights into effector diversity and evolution

Опубликована: Фев. 21, 2025

Phytopathogens secrete effector molecules to manipulate host immunity and metabolism. Recent advances in structural genomics have identified fungal families whose members adopt similar folds despite sequence divergence, highlighting their importance virulence immune evasion. To extend the scope of comparative structure-guided analysis more evolutionarily distant phytopathogens with lifestyles, we used AlphaFold2 predict 3D structures secretome from selected plasmodiophorid, oomycete, gall-forming pathogens. Clustering protein based on homology revealed species-specific expansions a low abundance known orphan families. We novel sequence- unrelated but structurally (SUSS) clusters, rich conserved motifs such as ’CCG’ ’RAYH’. demonstrate that these likely play central role maintaining overall fold. also SUSS cluster adopting nucleoside hydrolase-like fold among various microbes. Notably, ankyrin proteins were significantly expanded plasmodiophorids, most being highly expressed during clubroot disease, suggesting pathogenicity. Altogether, this study our understanding landscapes microbes provides valuable resource for broadening phylogenomic studies across diverse phytopathogens.

Язык: Английский

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Structure‐guided insights into the biology of fungal effectors

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Март 25, 2025

Phytopathogenic fungi cause enormous yield losses in many crops, threatening both agricultural production and global food security. To infect plants, they secrete effectors targeting various cellular processes the host. Putative effector genes are numerous fungal genomes, generally encode proteins with no sequence homology to each other or known domains. Recent studies have elucidated predicted three-dimensional structures of from a wide diversity plant pathogenic fungi, revealing limited number conserved folds. Effectors very diverse amino acid sequences can thereby be grouped into families based on structural homology. Some different some expanded specific taxa. Here, we describe features these discuss recent advances predicting new families. We highlight contribution analyses deepen our understanding function evolution effectors. also prospects offered by modeling for studying virulence targets plants.

Язык: Английский

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Mucoromycotina ‘fine root endophytes’: a new molecular model for plant–fungal mutualisms?

Trends in Plant Science, Год журнала: 2023, Номер 29(6), С. 650 - 661

Опубликована: Дек. 14, 2023

Язык: Английский

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EVO-MPMI: From fundamental science to practical applications

Current Opinion in Plant Biology, Год журнала: 2023, Номер 76, С. 102469 - 102469

Опубликована: Сен. 30, 2023

Язык: Английский

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Strain-specific evolution and host-specific regulation of transposable elements in the model plant symbiont Rhizophagus irregularis

G3 Genes Genomes Genetics, Год журнала: 2024, Номер 14(5)

Опубликована: Март 20, 2024

Abstract Transposable elements (TEs) are repetitive DNA that can create genome structure and regulation variability. The of Rhizophagus irregularis, a widely studied arbuscular mycorrhizal fungus (AMF), comprises ∼50% sequences include TEs. Despite their abundance, two-thirds TEs remain unclassified, among AMF life stages remains unknown. Here, we aimed to improve our understanding TE diversity in this model species by curating repeat datasets obtained from chromosome-level assemblies investigating expression across multiple conditions. Our analyses uncovered new superfamilies families symbiont revealed significant differences how these evolve both within between R. irregularis strains. With curated annotation, also found the number upregulated colonized roots is 4 times higher than extraradical mycelium, overall differs depending on plant host. This work provides fine-scale view evolution symbionts highlights transcriptional dynamism specificity during host–microbe interactions. We provide Hidden Markov Model profiles domains for future manual curation uncharacterized (https://github.com/jordana-olive/TE-manual-curation/tree/main).

Язык: Английский

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Integrating Large-Scale Protein Structure Prediction into Human Genetics Research

Annual Review of Genomics and Human Genetics, Год журнала: 2024, Номер 25(1), С. 123 - 140

Опубликована: Апрель 15, 2024

The last five years have seen impressive progress in deep learning models applied to protein research. Most notably, sequence-based structure predictions transformative gains the form of AlphaFold2 and related approaches. Millions missense variants human population lack annotations, these computational methods are a valuable means prioritize for further analysis. Here, we review recent prediction variants, with particular emphasis on their implications genetics health. Improved structures facilitates annotations impact stability, protein–protein interaction interfaces, small-molecule binding pockets. Moreover, it contributes study host–pathogen interactions characterization function. As genome sequencing large cohorts becomes increasingly prevalent, believe that better integration state-of-the-art informatics technologies into research is paramount importance.

Язык: Английский

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