Bioinformatic prediction of plant–pathogenicity effector proteins of fungi

Jones, Darcy A. B.; Bertazzoni, Stefania; Turo, Chala; Syme, Robert A.; Hane, James K.

doi:10.1016/j.mib.2018.01.017

Cited by 76 publications

(76 citation statements)

References 57 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Effector features are still complicated to evidence because of very few conserved domains (Jones, Bertazzoni, Turo, Syme, & Hane, 2018;Sperschneider et al, 2016). One way to increase the detection of candidate effectors is the analysis of the predicted subcellular compartments the proteins are predicted to be addressed to.…”

Section: Dynamics Of the Wheat-f Graminearum Dual Proteome Illustrmentioning

confidence: 99%

Time‐resolved dissection of the molecular crosstalk driving Fusarium head blight in wheat provides new insights into host susceptibility determinism

Fabre

Vignassa

Urbach

et al. 2019

Plant Cell & Environment

View full text Add to dashboard Cite

Fungal plant diseases are controlled by a complex molecular dialogue that involves pathogen effectors able to manipulate plant susceptibility factors at the earliest stages of the interaction. By probing the wheat–Fusarium graminearum pathosystem, we profiled the coregulations of the fungal and plant proteins shaping the molecular responses of a 96‐hr‐long infection's dynamics. Although no symptoms were yet detectable, fungal biomass swiftly increased along with an extremely diverse set of secreted proteins and candidate effectors supposed to target key plant organelles. Some showed to be early accumulated during the interaction or already present in spores, otherwise stored in germinating spores and detectable in an in vitro F. graminearum exudate. Wheat responses were swiftly set up and were evidenced before any visible symptom. Significant wheat protein abundance changes co‐occurred along with the accumulation of putative secreted fungal proteins and predicted effectors. Regulated wheat proteins were closely connected to basal cellular processes occurring during spikelet ontogeny, and particular coregulation patterns were evidenced between chloroplast proteins and fungal proteins harbouring a predicted chloroplast transit peptide. The described plant and fungal coordinated responses provide a resourceful set of data and expand our understanding of the wheat–F. graminearum interaction.

show abstract

Section: Dynamics Of the Wheat-f Graminearum Dual Proteome Illustrmentioning

confidence: 99%

Time‐resolved dissection of the molecular crosstalk driving Fusarium head blight in wheat provides new insights into host susceptibility determinism

Fabre

Vignassa

Urbach

et al. 2019

Plant Cell & Environment

View full text Add to dashboard Cite

show abstract

“…Effector prediction from microbial pathogen genomes is based on the premise that effector proteins are secreted to the site of action in the plant-pathogen interaction and therefore carry a signal peptide. Furthermore, effector proteins are generally of small size and often carry a proportionally high number of cysteine residues to counter the highly reducing environment of the plant apoplast (Jones et al, 2018). Effector proteins are subject to constant evolution of primary structure while maintaining secondary and tertiary structural elements in order to modify surface chemical properties and topography.…”

Section: Discussionmentioning

confidence: 99%

“…The presence of a predicted signal peptide for secretion to the apoplast and a lack of homologous sequences among other species are further key signatures for necrotrophic effectors of apoplastic plant pathogenic fungi. Computational approaches have been developed to predict effectors from genomic sequences (Sonah et al, 2016;Jones et al, 2018) and EffectorP is a useful program that rates the likelihood of a protein sequence encoding an effector using a machine-learning approach with validated effectors as training data (Sperschneider et al, 2016(Sperschneider et al, , 2018. In addition, secondary metabolites botcinic acid and botrydial are known phytotoxic compounds with established roles in plant disease for other Botrytis species and it is not known whether these compounds contribute to plant diseases caused by B. fabae (Collado and Viaud, 2016).…”

Section: Introductionmentioning

confidence: 99%

Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean (Vicia faba L.)

et al. 2020

View full text Add to dashboard Cite

Chocolate spot is a major fungal disease of faba bean caused by the ascomycete fungus, Botrytis fabae. B. fabae is also implicated in botrytis gray mold disease in lentils, along with B. cinerea. Here we have isolated and characterized two B. fabae isolates from chocolate spot lesions on faba bean leaves. In plant disease assays on faba bean and lentil, B. fabae was more aggressive than B. cinerea and we observed variation in susceptibility among a small set of cultivars for both plant hosts. Using light microscopy, we observed a spreading, generalized necrosis response in faba bean toward B. fabae. In contrast, the plant response to B. cinerea was localized to epidermal cells underlying germinated spores and appressoria. In addition to the species characterization of B. fabae, we produced genome assemblies for both B. fabae isolates using Illumina sequencing. Genome sequencing coverage and assembly size for B. fabae isolates, were 27x and 45x, and 43.2 and 44.5 Mb, respectively. Following genome assembly and annotation, carbohydrate-active enzyme (CAZymes) and effector genes were predicted. There were no major differences in the numbers of each of the major classes of CAZymes. We predicted 29 effector genes for B. fabae, and using the same selection criteria for B. cinerea, we predicted 34 putative effector genes. For five of the predicted effector genes, the pairwise dN/dS ratio between orthologs from B. fabae and B. cinerea was greater than 1.0, suggesting positive selection and the potential evolution of molecular mechanisms for host specificity in B. fabae. Furthermore, a homology search of secondary metabolite clusters revealed the absence of the B. cinerea phytotoxin botrydial and several other uncharacterized secondary metabolite biosynthesis genes from B. fabae. Although there were no obvious differences in the number or proportional representation of different transposable element classes, the overall proportion of AT-rich DNA sequence in B. fabae was double that of B. cinerea.

show abstract

“…El análisis de las secuencias genómicas también ha permitido avanzar en la identificación de efectores. Se sabe que algunas de estas proteínas presentan características estructurales similares: en el caso de los Oomycota, a través de métodos bioinformáticos de enriquecimiento especiales es posible predecir secretomas de otras especies de oomycetes (Jones, Bertazzoni, Turo, Syme & Hane, 2018). Sin embargo, en los hongos estas secuencias son mucho menos conservadas y su predicción se dificulta.…”

unclassified

“…Sin embargo, en los hongos estas secuencias son mucho menos conservadas y su predicción se dificulta. Los métodos ac-tuales de predicción génica generalmente son asistidos por una combinación de estrategias in silico y apoyados por alineamientos a partir de secuencias de transcritos obtenidos con RNA-seq (Joshi, Megha, Basu, Rahman & Kav, 2016;Jones et al, 2018).…”

unclassified

Genómica de hongos fitopatógenos como herramienta para el desarrollo de estrategias de manejo

Romero

2019

Rev. colomb. biotecnol.

View full text Add to dashboard Cite

Los patógenos más devastadores de los cultivos agrícolas son los hongos, su manejo ha variado en el tiempo, este se ha dado de acuerdo al desarrollo del conocimiento de cada época y a la cultura. En las últimas dos décadas el desarrollo vertiginoso de las plataformas de secuenciación masiva y la bioinformática ha permitido la generación cientos de secuencias de genomas completos de hongos incluidos los fitopatógenos, abriendo la puerta para mejorar estrategias de manejo existentes y generar nuevas.Los hongos son considerados los patógenos más devastadores de las plantas causando el 60% de las pérdidas, a pesar de que solo el 10% de los hasta ahora descritos puede colonizar plantas vivas (Aslam et al., 2017); es decir, solo un pequeño número es considerado patógeno de especies vegetales. El manejo de enfermedades causadas por estos, en cultivos de importancia económica, siempre ha sido un reto que afrontar por el hombre desde la aparición misma de la agricultura. Las estrategias se han dado de acuerdo al desarrollo del conocimiento de cada época y a la cultura. Los primeros reportes escritos de enfermedades son mencionados en algunos textos griegos antiguos de Homero (1000 años a.C.); también aparecen en el antiguo testamento (750 años a.C.) y fueron documentadas de manera similar a como se abordaron las guerras y las enfermedades humanas. Los primeros agentes causales a los que se les atribuyeron las pérdidas de los cultivos fueron las divinidades a manera de castigo, y el manejo se daba a través de ofrecimiento de sacrificios a los dioses para que se apaciguaran y de esta forma evitar el daño de los cultivos a causa de mildeos, royas entre otras plagas. También los textos de Homero señalan la posibilidad de manejarlas con el uso del azufre, y Demócrito (470 años a.C.) recomendaba el uso de aceite de oliva para contrarrestar los tizones (Agrios, 2005).

show abstract

Bioinformatic prediction of plant–pathogenicity effector proteins of fungi

Cited by 76 publications

References 57 publications

Time‐resolved dissection of the molecular crosstalk driving Fusarium head blight in wheat provides new insights into host susceptibility determinism

Time‐resolved dissection of the molecular crosstalk driving Fusarium head blight in wheat provides new insights into host susceptibility determinism

Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean (Vicia faba L.)

Genómica de hongos fitopatógenos como herramienta para el desarrollo de estrategias de manejo

Contact Info

Product

Resources

About