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

Published: Feb. 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.

Language: Английский

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

Published: Feb. 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.

Language: Английский

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The first single-cell sequencing of Plasmodiophora brassicae reveals genetic diversity and clonal dynamics

Frontiers in Microbiology, Journal Year: 2025, Volume and Issue: 16

Published: April 22, 2025

Clubroot, caused by the obligate Chromist pathogen Plasmodiophora brassicae, is an important disease of brassica crops but little known about its reproductive biology. We enzymatically removed cell walls from dormant spores to generate protoplasts, enabling first single-cell sequencing P. brassicae with DNA free host and soil microbial contamination. Analysis 4,000 protoplasts a single root showed moderate genetic diversity, 2-5 distinct genotypes. A more detailed analysis 500 cells indicated presence seven genotypes, accounting for rare haplotypes. This level diversity in supports other indications that there high field populations brassicae. These results support hypothesis balancing selection maintains multiple genotypes within population. complicates use single-gene resistance sources clubroot management explains short durability resistance. The predominance strong indication reproduction predominantly clonal. whole genome plant pathogen.

Language: Английский

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Arabidopsis ecotype screening reveals novel sources of clubroot resistance and insights into resistance inheritance

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: April 16, 2025

ABSTRACT Clubroot, caused by Plasmodiophora brassicae , poses a persistent threat to Brassicaceae crops, particularly in regions where resistant cultivars are under strong selection pressure. To identify new sources of resistance and better understand the underlying genetic mechanisms, we evaluated 60 Arabidopsis thaliana ecotypes against highly virulent Canadian pathotype 3A. Using stringent phenotyping criteria, pathogen DNA quantification, survival analysis, identified eight ecotypes, including two novel sources, Marce-1 DraII-6. DraII-6 exhibited exceptionally low disease symptoms high rate. While gene RPB1/WeiTsing was present most its expression significantly elevated at early infection stages, suggesting potential role suppression. However, analysis F1 F2 progeny from × Col-0 cross revealed recessive pattern, supporting hypothesis that RPB1 alone may not be sufficient confer clubroot Our findings highlight complexity need for further research into regulation networks beyond RPB1, context translating Arabidopsis-based insights Brassica crops. GRAPHICAL Natural variability response The abstract also celebrates first author, Melaine Gonzalez-Garcia, who is submitting this manuscript just one week before welcoming her child.

Language: Английский

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A telomere‐to‐telomere gap‐free assembly integrating multi‐omics uncovers the genetic mechanism of fruit quality and important agronomic trait associations in pomegranate

Plant Biotechnology Journal, Journal Year: 2025, Volume and Issue: unknown

Published: May 3, 2025

Summary Pomegranate is an important perennial fruit tree distributed worldwide. Reference genomes with gaps and limit gene identification controlling agronomic traits hinder its functional genomics genetic improvements. Here, we reported a telomere‐to‐telomere (T2T) gap‐free genome assembly of the distinctive cultivar ‘Moshiliu’. The Moshiliu reference was assembled into eight chromosomes without gaps, totalling ~366.71 Mb, 32 158 predicted protein‐coding genes. All 16 telomeres centromeres were characterized; combined FISH analysis, revealed atypical telomere units in pomegranate as TTTTAGGG. Furthermore, total loci associated 15 identified based on GWAS 146 accessions. Gene editing biochemical experiments demonstrated that 37.2‐Kb unique chromosome translocation disrupting coding domain sequence PgANS responsible for anthocyanin‐less, knockout exhibited defect anthocyanin production; repeat expansion promoter PgANR may affected expression, resulting black peel; notably, G → A transversion located at 166‐bp PgNST3 , which caused E56K mutation protein, closely linked soft‐seed trait. Overexpression tomato presented smaller softer seed coats. eliminated binding ability to PgMYB46 promoter, subsequently thickness inner coat soft‐seeded pomegranates. Collectively, validated genome, genes CRISPR‐Cas9‐mediated system all provided invaluable resources precise breeding.

Language: Английский

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Dual RNA-seq reveals distinct families of co-regulated and structurally conserved effectors in Botrytis cinerea infection of Arabidopsis thaliana

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Oct. 21, 2024

Botrytis cinerea is a broad-host-range pathogen causing gray mold disease and significant yield losses of numerous crops. However, the mechanisms underlying its rapid invasion efficient killing plant cells remain unclear. In this study, we elucidated dynamics B. infection in Arabidopsis thaliana by live cell imaging dual RNA sequencing. We found extensive transcriptional reprogramming events both host, which involved metabolic pathways, signaling cascades, regulation. For pathogen, identified 591 candidate effector proteins (CEPs) comprehensively analyzed their co-expression, sequence similarity, structural conservation. The results revealed temporal co-regulation patterns these CEPs, indicating coordinated deployment effectors during infection. Through functional screening 48 selected CEPs Nicotiana benthamiana, 11 death-inducing (CDIPs) cinerea. findings provide important insights into biology driving pathogenesis. involves prominent role CDIPs host death. This work highlights changes gene expression associated with disease, underscoring importance diverse repertoire crucial for successful

Language: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 3, 2024

ABSTRACT 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 lifestyle, 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 nucleoside hydrolase-like fold, structurally homologous bacterial HopQ1, be conserved among various microbes. also novel sequence-unrelated but (SUSS) clusters, rich motifs. Notably, ankyrin proteins were significantly expanded plasmodiophorids, AlphaFold-Multimer screening revealing MAP kinase pathway as major target these proteins. Altogether, this study our understanding landscapes microbes provides valuable resource for broadening phylogenomic studies across diverse phytopathogens.

Language: Английский

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