Dual-RNA-sequencing to elucidate the interactions between sorghum and Colletotrichum sublineola DOI Creative Commons
Saddie Vela, Emily S. A. Wolf, Jeffrey A. Rollins

et al.

Frontiers in Fungal Biology, Journal Year: 2024, Volume and Issue: 5

Published: Aug. 16, 2024

In warm and humid regions, the productivity of sorghum is significantly limited by fungal hemibiotrophic pathogen Colletotrichum sublineola , causal agent anthracnose, a problematic disease ( Sorghum bicolor (L.) Moench) that can result in grain biomass yield losses up to 50%. Despite available genomic resources both host pathogen, molecular basis sorghum− C. interactions are poorly understood. By employing dual-RNA sequencing approach, crosstalk between be elucidated. this study, we examined transcriptomes four resistant accessions from association panel (SAP) at varying time points post-infection with . Approximately 0.3% 93% reads mapped genomes respectively. Expression profiling vitro versus planta 1-, 3-, 5-days (dpi) indicated genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), membrane transporters increased expression during transition biotrophic necrotrophic phase (3 dpi). The hallmark pathogen-associated pattern (PAMP)-triggered immunity includes production reactive oxygen species (ROS) phytoalexins. majority effector candidates were predicted localized apoplast, where they could interfere PAMP-triggered response, specifically ROS signaling pathway. critical factors influencing pathogenicity identified study useful resource for subsequent genetic experiments aimed validating their contributions virulence. This comprehensive not only provides better understanding biology but also supports long-term goal developing cultivars.

Language: Английский

Integrating Large-Scale Protein Structure Prediction into Human Genetics Research DOI
Miguel Marrero, Jürgen Jänes, Delora Baptista

et al.

Annual Review of Genomics and Human Genetics, Journal Year: 2024, Volume and Issue: 25(1), P. 123 - 140

Published: April 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.

Language: Английский

Citations

1
Zymoseptoria tritici proteins structurally related to UmV-KP4 and UmV-KP6 are toxic to fungi, and define novel structural families of fungal effectors DOI Creative Commons
Karine de Guillen, Léa Mammri, Jérôme Gracy

et al.

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

Published: Oct. 16, 2024

Abstract Fungal effectors play crucial roles in plant infection. Despite low sequence identity, were recently classified into structural families. In this study, we have elucidated the structures of Zt-NIP1 and Mycgr3-91409 wheat fungal pathogen Zymoseptoria tritici, using X-ray crystallography NMR. These displayed a homology with, respectively, KP4 KP6α killer toxins, from UmV dsRNA viruses infecting corn Ustilago maydis . Consequently, renamed Zt-KP4-1 Zt-KP6-1. Orthologs paralogs Zt-KP6-1 identified , but not other fungi, except Ecp2 related to Zt-KP4-1. Assessment biological activities revealed their toxicity fungi such as Botrytis cinerea Z. tritici wheat. A novel pipeline relying on Foldseek cysteine-pattern constrained HMM searches AlphaFold2 predicted Uniprot generated comprehensive inventory KP6 proteins plants. structure-based classification these four three super This provided far-reaching hypotheses function evolution. unifying framework highlights power structure determination for effectors, functional investigation.

Language: Английский

Citations

1
The structural repertoire of Fusarium oxysporum f. sp. lycopersici effectors revealed by experimental and computational studies DOI Open Access
Daniel S. Yu, Megan A. Outram, Ashley Smith

et al.

Published: Jan. 30, 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 d ual-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.

Language: Английский

Citations

1
Secreted in Xylem 6 (SIX6) Mediates Fusarium oxysporum f. sp. fragariae Race 1 Avirulence on FW1-Resistant Strawberry Cultivars DOI Creative Commons
Christine Jade Dilla-Ermita,

Polly Goldman,

Amy Anchieta

et al.

Molecular Plant-Microbe Interactions, Journal Year: 2024, Volume and Issue: 37(6), P. 530 - 541

Published: March 29, 2024

Fusarium oxysporum f. sp. fragariae (Fof) race 1 is avirulent on cultivars with the dominant resistance gene FW1, while Fof 2 virulent FW1-resistant cultivars. We hypothesized there was a gene-for-gene interaction between at FW1 locus and an avirulence (AvrFW1) in 1. To identify candidate AvrFW1, we compared genomes of 24 three isolates. found one that present 1, absent 2, highly expressed planta, homologous to known effector, secreted xylem 6 (SIX6). knocked out SIX6 two isolates by recombination. All knockout transformants (ΔSIX6) gained virulence FW1/fw1 cultivars, whereas ectopic wildtype remained avirulent. ΔSIX6 were quantitatively less Fronteras San Andreas than fw1/fw1 Seedlings from × population genotyped for tested susceptibility isolate. Results suggested additional minor-effect quantitative genes could be locus. This work demonstrates acts as factor interacting The identification AvrFW1 enables surveillance provides insight into mechanisms FW1-mediated resistance. [Formula: see text] Copyright © 2024 Author(s). open access article distributed under CC BY-NC-ND 4.0 International license.

Language: Английский

Citations

1
Dual-RNA-sequencing to elucidate the interactions between sorghum and Colletotrichum sublineola DOI Creative Commons
Saddie Vela, Emily S. A. Wolf, Jeffrey A. Rollins

et al.

Frontiers in Fungal Biology, Journal Year: 2024, Volume and Issue: 5

Published: Aug. 16, 2024

In warm and humid regions, the productivity of sorghum is significantly limited by fungal hemibiotrophic pathogen Colletotrichum sublineola , causal agent anthracnose, a problematic disease ( Sorghum bicolor (L.) Moench) that can result in grain biomass yield losses up to 50%. Despite available genomic resources both host pathogen, molecular basis sorghum− C. interactions are poorly understood. By employing dual-RNA sequencing approach, crosstalk between be elucidated. this study, we examined transcriptomes four resistant accessions from association panel (SAP) at varying time points post-infection with . Approximately 0.3% 93% reads mapped genomes respectively. Expression profiling vitro versus planta 1-, 3-, 5-days (dpi) indicated genes encoding secreted candidate effectors, carbohydrate-active enzymes (CAZymes), membrane transporters increased expression during transition biotrophic necrotrophic phase (3 dpi). The hallmark pathogen-associated pattern (PAMP)-triggered immunity includes production reactive oxygen species (ROS) phytoalexins. majority effector candidates were predicted localized apoplast, where they could interfere PAMP-triggered response, specifically ROS signaling pathway. critical factors influencing pathogenicity identified study useful resource for subsequent genetic experiments aimed validating their contributions virulence. This comprehensive not only provides better understanding biology but also supports long-term goal developing cultivars.

Language: Английский

Citations

1