An Interspecies Comparative Analysis of the Predicted Secretomes of the Necrotrophic Plant Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Abstract

Phytopathogenic fungi form intimate associations with host plant species and cause disease. To be successful, fungal pathogens communicate with a susceptible host through the secretion of proteinaceous effectors, hydrolytic enzymes and metabolites. Sclerotinia sclerotiorum and Botrytis cinerea are economically important necrotrophic fungal pathogens that cause disease on numerous crop species. Here, a powerful bioinformatics pipeline was used to predict the refined S. sclerotiorum and B. cinerea secretomes, identifying 432 and 499 proteins respectively. Analyses focusing on S. sclerotiorum revealed that 16% of the secretome encoding genes resided in small, sequence heterogeneous, gene clusters that were distributed over 13 of the 16 predicted chromosomes. Functional analyses highlighted the importance of plant cell hydrolysis, oxidation-reduction processes and the redox state to the S. sclerotiorum and B. cinerea secretomes and potentially host infection. Only 8% of the predicted proteins were distinct between the two secretomes. In contrast to S. sclerotiorum, the B. cinerea secretome lacked CFEM- or LysM-containing proteins. The 115 fungal and oomycete genome comparison identified 30 proteins specific to S. sclerotiorum and B. cinerea, plus 11 proteins specific to S. sclerotiorum and 32 proteins specific to B. cinerea. Expressed sequence tag (EST) and proteomic analyses showed that 246 S. sclerotiorum secretome encoding genes had EST support, including 101 which were only expressed in vitro and 49 which were only expressed in planta, whilst 42 predicted proteins were experimentally proven to be secreted. These detailed in silico analyses of two important necrotrophic pathogens will permit informed choices to be made when candidate effector proteins are selected for function analyses in planta.

Conservation and expansion of a necrosis‐inducing small secreted protein family from host‐variable phytopathogens of the Sclerotiniaceae

“…Guyon et al () predicted the secretome of S. sclerotiorum ( n = 488) with a specific focus on secreted proteins expressed in planta (SPEPs). Heard et al () developed a rigorous prediction model to produce a “refined” secretome for both B. cinerea ( n = 499) and S. sclerotiorum ( n = 432). A total of 75% of the predicted SPEP sequences, 91% of the “refined” B. cinerea secretome, and 93% of the “refined” S. sclerotiorum secretome matched proteins within the C. camelliae secretome described here.…”

Small RNAs from the plant pathogenic fungus Sclerotinia sclerotiorum highlight host candidate genes associated with quantitative disease resistance

“…Nevertheless, effector genes may also be associated with repeat sequences in necrotrophic fungi and fungi with a broad host range (Dallery et al , ; Laurent et al , ; Syme et al , ; Wang et al , ). Secretome analyses highlighted a number of candidate effector‐like proteins in the genome of S. sclerotiorum (Badet et al , ; Derbyshire et al , ; Guyon et al , ; Heard et al , ). These predicted effector genes associate with repeat sequences (Derbyshire et al , ; Guyon et al , ) and show a high degree of codon adaptation (Badet et al ., ).…”

Partner communication and role of nutrients in the arbuscular mycorrhizal symbiosis

“…A large majority (95%) of R. irregularis secreted proteins (SPs) is conserved in the related species R. clarus , whereas only 194 of 872 (22%) of R. irregularis SPs show similarity with those from Gigaspora rosea , a distantly related AMF (Sędzielewska Toro & Brachmann, ; Kamel et al ., ). The AMF secretome therefore seems to be characterized by the prevalence of lineage‐specific proteins, which is in agreement with data obtained from comparative analyses in other fungal groups including parasitic, mutualistic or saprotrophic fungi (Schirawski et al ., ; Heard et al ., ; Pellegrin et al ., ). Secretome variations have been ascribed to several factors such as phylogenetic history, life style as well as host specificity.…”