Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses

Nature Microbiology, Год журнала: 2023, Номер 8(1), С. 174 - 187

Опубликована: Янв. 5, 2023

Elucidating the similarity and diversity of pathogen effectors is critical to understand their evolution across fungal phytopathogens. However, rapid divergence that diminishes sequence similarities between putatively homologous has largely concealed roots effector evolution. Here we modelled structures 26,653 secreted proteins from 14 agriculturally important phytopathogens, six non-pathogenic fungi one oomycete with AlphaFold 2. With 18,000 successfully predicted folds, performed structure-guided comparative analyses on two aspects evolution: uniquely expanded sequence-unrelated structurally similar (SUSS) families common folds present species. Extreme expansion lineage-specific SUSS was found only in several obligate biotrophs, Blumeria graminis Puccinia graminis. The highly were source conserved motifs, such as Y/F/WxC motif. We identified new classes include known virulence factors, AvrSr35, AvrSr50 Tin2. Structural comparisons revealed structural further diversify through domain duplications fusion disordered stretches. Putatively sub- neo-functionalized could reconverge regulation, expanding functional pools infection cycle. also evidence many have originated ancestral fungi. Collectively, our study highlights diverse mechanisms supports divergent a major force driving proteins.

Язык: Английский

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A new family of structurally conserved fungal effectors displays epistatic interactions with plant resistance proteins

PLoS Pathogens, Год журнала: 2022, Номер 18(7), С. e1010664 - e1010664

Опубликована: Июль 6, 2022

Recognition of a pathogen avirulence (AVR) effector protein by cognate plant resistance (R) triggers set immune responses that render the resistant. Pathogens can escape this so-called Effector-Triggered Immunity (ETI) different mechanisms including deletion or loss-of-function mutation AVR gene, incorporation point mutations allow recognition to be evaded while maintaining virulence function, and acquisition new effectors suppress recognition. The Dothideomycete Leptosphaeria maculans, causal agent oilseed rape stem canker, is one few fungal pathogens where suppression ETI an has been demonstrated. Indeed, AvrLm4-7 suppresses Rlm3- Rlm9-mediated triggered AvrLm3 AvrLm5-9, respectively. presence does not impede AvrLm5-9 expression, three proteins do appear physically interact. To decipher epistatic interaction between these L. maculans effectors, we determined crystal structure obtained 3D model AvrLm3, based on Ecp11-1, homologous candidate from Fulvia fulva. Despite lack sequence similarity, are structural analogues (structure previously characterized). Structure-informed database searches identified larger number putative among candidates, AvrLmS-Lep2, all produced during early stages infection, as well candidates other phytopathogenic fungi. These named LARS (for AviRulence Suppressing) effectors. Remarkably, transformants expressing analogues, immunity in several genotypes carrying Rlm3. Furthermore, could suppressed AvrLm4-7. results suggest Ecp11-1 shares common activity with within host which detected Rlm3, sufficiently close recognized

Язык: Английский

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Structural polymorphisms within a common powdery mildew effector scaffold as a driver of coevolution with cereal immune receptors

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(32)

Опубликована: Июль 31, 2023

In plants, host-pathogen coevolution often manifests in reciprocal, adaptive genetic changes through variations host nucleotide-binding leucine-rich repeat immune receptors (NLRs) and virulence-promoting pathogen effectors. grass powdery mildew (PM) fungi, an extreme expansion of a RNase-like effector family, termed RALPH, dominates the repertoire, with some members recognized as avirulence (AVR) effectors by cereal NLR receptors. We report structures sequence-unrelated barley PM AVR

Язык: Английский

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

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Авг. 28, 2023

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

Язык: Английский

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The N-terminal domains of NLR immune receptors exhibit structural and functional similarities across divergent plant lineages

The Plant Cell, Год журнала: 2024, Номер 36(7), С. 2491 - 2511

Опубликована: Апрель 10, 2024

Abstract Nucleotide-binding domain and leucine-rich repeat (NLR) proteins are a prominent class of intracellular immune receptors in plants. However, our understanding plant NLR structure function is limited to the evolutionarily young flowering clade. Here, we describe an extended spectrum diversity across divergent lineages demonstrate structural functional similarities N-terminal domains that trigger responses. We show broadly distributed coiled-coil (CC) toll/interleukin-1 receptor (TIR) families nonflowering plants retain immune-related functions through translineage activation cell death angiosperm Nicotiana benthamiana. further examined CC subfamily specific uncovered essential MAEPL motif functionally comparable with motifs resistosome-forming CC-NLRs. Consistent conserved role immunity, ectopic CCMAEPL liverwort Marchantia polymorpha led profound growth inhibition, defense gene activation, signatures death. Moreover, comparative transcriptomic analyses activity delineated common CC-mediated program shared Collectively, findings highlight ancestral nature NLR-mediated immunity during evolution dates its origin at least ∼500 million years ago.

Язык: Английский

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Optimization of a CRISPR-Cas9 in vitro protocol for targeting the SIX9 gene of Fusarium oxysporum f.sp. cubense race 1 associated with banana Fusarium wilt

Frontiers in Plant Science, Год журнала: 2025, Номер 16

Опубликована: Март 10, 2025

Introduction Fusarium wilt of bananas ( Musa spp.), a threat to sustainable banana production worldwide, necessitates immediate action control the disease. The current strategies are centered on preventing its spread or developing resistant varieties. However, very little is known about genetic machinery used by fungus infect and kill plants. Therefore, research should focused also in understanding plant-pathogen molecular interaction targeting virulent genes for knock-out Fusarium. This study aims standardize gene editing protocol using CRISPR Cas9 technology oxysporum f.sp. cubense race 1 (Foc1); specifically, induce targeted mutations particular effector gene, SIX9, Foc1. Methods An vitro was optimized protein target SIX9 testing two gRNAs, expression purification Cas9, included plasmids pHis-parallel1 pMJ922, E. coli BL21 Rosetta, independently. Results demonstrated that produced exhibits high enzymatic activity, comparable commercial standard. These findings underscore robustness in-house enzyme highlight suitability future biotechnological applications. Discussion facilitates recombinant enabling use various experimental settings accelerating editing, an area significant relevance today. will support studies banana-Fusarium identifying candidate disease resistance plant, lack virulence pathogen, establishing function SIX proteins evaluating fungus’s infection capacity through pathogenicity assays.

Язык: Английский

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The Venturia inaequalis effector repertoire is dominated by expanded families with predicted structural similarity, but unrelated sequence, to avirulence proteins from other plant-pathogenic fungi

BMC Biology, Год журнала: 2022, Номер 20(1)

Опубликована: Ноя. 3, 2022

Abstract Background Scab, caused by the biotrophic fungus Venturia inaequalis , is most economically important disease of apples worldwide. During infection, V. occupies subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many these effectors are expected be non-enzymatic proteins, some which can recognized corresponding resistance proteins activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding roles that effector play in promoting growth well activating, suppressing, or circumventing protein-mediated defences apple, required. Results We generated first comprehensive RNA-seq transcriptome during colonization apple. Analysis this revealed five temporal waves gene expression peaked early, mid, mid-late infection. While number genes encoding secreted, proteinaceous candidates (ECs) varied each wave, belonged Spectral clustering based on sequence similarity determined majority ECs expanded protein families. gain insights into function, tertiary structures were predicted using AlphaFold2. Strikingly, despite an absence similarity, have structural from including members MAX, LARS, ToxA and FOLD In addition, several ECs, EC family AvrLm6 Leptosphaeria maculans adopt KP6-like fold. Thus, fold represent another shared among fungi. Conclusions Our study reveals transcriptomic profile underpinning provides enriched list investigated for avirulence. Furthermore, our supports idea numerous sequence-unrelated across fungi share common folds. doing so, gives weight hypothesis fungal evolved ancestral through duplication, followed diversification, produce but structurally similar proteins.

Язык: Английский

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Molecular plant immunity against biotrophic, hemibiotrophic, and necrotrophic fungi

Essays in Biochemistry, Год журнала: 2022, Номер 66(5), С. 581 - 593

Опубликована: Май 19, 2022

Pathogenic fungi use diverse infection strategies to obtain nutrients from plants. Biotrophic feed only on living plant tissue, whereas necrotrophic kill host cells extract nutrients. To prevent disease, plants need distinguish between pathogens with different life cycles, as a successful defense against biotroph, which often involves programmed cell-death around the site of infection, is not an appropriate response some necrotrophs. Plants utilize vast collection extracellular and intracellular receptors detect signatures pathogen attack. In turn, are under strong selection mask or avoid certain receptor responses while enhancing manipulating other promote virulence. this review, we focus involved in resistance fungal highlight, examples, how strategy can determine if recognition effective at preventing disease.

Язык: Английский

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The structural landscape and diversity of Pyricularia oryzae MAX effectors revisited

PLoS Pathogens, Год журнала: 2024, Номер 20(5), С. e1012176 - e1012176

Опубликована: Май 6, 2024

Magnaporthe AVRs and ToxB-like (MAX) effectors constitute a family of secreted virulence proteins in the fungus Pyricularia oryzae (syn . oryzae) , which causes blast disease on numerous cereals grasses. In spite high sequence divergence, MAX share common fold characterized by ß-sandwich core stabilized conserved disulfide bond. this study, we investigated structural landscape diversity within effector repertoire P Combining experimental protein structure determination silico modeling validated presence domain 77 out 94 groups orthologs (OG) identified previous population genomic study. Four novel structures determined NMR were remarkably good agreement with AlphaFold2 (AF2) predictions. Based comparison AF2-generated 3D models propose classification superfamily 20 that vary canonical fold, bond patterns, additional secondary N- C-terminal extensions. About one-third members remain singletons, without strong relationship to other effectors. Analysis surface properties AF2 also highlights variability at level, potentially reflecting wide their functions host targets.

Язык: Английский

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Computational and In silico study of novel fungicides against combating root rot, gray mold, fusarium wilt, and cereal rust

PLoS ONE, Год журнала: 2025, Номер 20(1), С. e0316606 - e0316606

Опубликована: Янв. 31, 2025

The exploration of potential candidates for fungicides against four fungal proteins that cause some vital plant diseases, namely Phytophthora capsici, Botrytis cinerea, Fusarium oxysporum f. sp. lycopersici, and Puccinia graminis tritici, was conducted using in silico, molecular docking simulations, dynamic (MD) simulation selecting the nature binding affinity with actives sites proteins. First all, DFT employed to optimize geometry, get prepared optimized ligand. From data, chemical descriptors were calculated. Next, two tools, such as AutoDock by PyRx Molecular Docking Glide from Schrödinger suite, used convey score, ligand protein interactions main proteases, instance 7VEM, 8H6Q, 8EBB, 7XDS having name pathogens: respectively. In case auto dock PyRx, L01, L03, L04, L13, L14, L17, L18, L19 demonstrated significantly higher affinities pathogens. Surprisingly, it is conveyed L03 illustrated highest score three L09 8H6Q. However, MD performed check validation calculation procedure stability docked complex accounting RMSD, RMSF, SASA, Radius gyration (Rg), Protein secondary structure elements (SSE), Ramachandran plot which confirm so high, number calculating hydrogen bonds more than good enough, a result concluded valid. Finally, Difenoconazole (L03) has been considered most promising antifungal drug evaluated studies.

Язык: Английский

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