Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes

Abstract

IntroductionThe fungal secretome comprise diverse proteins that are involved in various aspects of fungal lifestyles, including adaptation to ecological niches and environmental interactions. The aim of this study was to investigate the composition and activity of fungal secretomes in mycoparasitic and beneficial fungal-plant interactions.MethodsWe used six Clonostachys spp. that exhibit saprotrophic, mycotrophic and plant endophytic lifestyles. Genome-wide analyses was performed to investigate the composition, diversity, evolution and gene expression of Clonostachys secretomes in relation to their potential role in mycoparasitic and endophytic lifestyles.Results and discussionOur analyses showed that the predicted secretomes of the analyzed species comprised between 7 and 8% of the respective proteomes. Mining of transcriptome data collected during previous studies showed that 18% of the genes encoding predicted secreted proteins were upregulated during the interactions with the mycohosts Fusarium graminearum and Helminthosporium solani. Functional annotation of the predicted secretomes revealed that the most represented protease family was subclass S8A (11–14% of the total), which include members that are shown to be involved in the response to nematodes and mycohosts. Conversely, the most numerous lipases and carbohydrate-active enzyme (CAZyme) groups appeared to be potentially involved in eliciting defense responses in the plants. For example, analysis of gene family evolution identified nine CAZyme orthogroups evolving for gene gains (p ≤ 0.05), predicted to be involved in hemicellulose degradation, potentially producing plant defense-inducing oligomers. Moreover, 8–10% of the secretomes was composed of cysteine-enriched proteins, including hydrophobins, important for root colonization. Effectors were more numerous, comprising 35–37% of the secretomes, where certain members belonged to seven orthogroups evolving for gene gains and were induced during the C. rosea response to F. graminearum or H. solani. Furthermore, the considered Clonostachys spp. possessed high numbers of proteins containing Common in Fungal Extracellular Membranes (CFEM) modules, known for their role in fungal virulence. Overall, this study improves our understanding of Clonostachys spp. adaptation to diverse ecological niches and establishes a basis for future investigation aiming at sustainable biocontrol of plant diseases.

Dicer-mediated RNA silencing is the key regulatory mechanism in the biocontrol fungusClonostachys rosea-wheat interactions

“…The biological processes in the genes upregulated during Cr-Wr interactions mostly referred to an increase in the catabolism in many types of carbohydrates, and they included “carbohydrate catabolic process” (GO:0016052) and “polysaccharide catabolic process” (GO:0000272). This can be attributed to the fact that 229 of the upregulated genes were coding for putative CAZymes, and the majority of them (163) was reported as secreted in previous study (Piombo et al 2023). Among the CAZymes, 134 were glycoside hydrolases, and 87 of them had CBM domain, the most frequent of which was CBM1, present in 55 proteins Even if glycoside hydrolases were the most common type of CAZyme, the most numerous single class was AA9 (21 genes), involved in the degradation of cellulose.…”

“…Since many genes coding for CAZymes and effectors were upregulated during Cr-Wr, we wanted to know if their expression is DCL-mediated. The expression of 54 CAZymes genes was significantly downregulated in C. rosea DCL deletion strains during the interaction with wheat roots compared to the WT, 32 of which were predicted to be secreted in a previous work (Piombo et al, 2023). (Supplementary table 7).…”

“…are known to have a much higher number of AA9 in their secretome, compared with Trichoderma spp. (Piombo et al 2023). In summary, the result highlighted that the interaction mechanisms between beneficial fungi and host plants depend on the interactions organisms and the experimental conditions.…”

Diversity and antioxidant activity of endophytic fungi isolated from salam (Syzygium polyanthum)

“…This fungus lives in many types of habitats, with the highest frequency found in the soil. Therefore, as an excellent mycoparasite, C. rosea exhibits strong biological control capabilities against many fungal, nematode, and insect-plant pathogens (Piombo et al 2023;Song et al 2023;Venkatesan et al 2023). This behavior is according to the activation of several mechanisms, such as secreted enzymes to degrade the cell wall, antifungal secondary metabolites production, and plant defense systems induction.…”

Identification and Characterization of a Predominant Hydrophobin in the Edible Mushroom Grifola frondosa

“…All HFBs are able to self-assemble into suprastructural organization, with highly ordered amphipathic layers occurring in the conidia or aerial hyphal surfaces that assist the filamentous fungi to fulfill life activities and various fungal processes, such as hyphal growth [11], primordium differentiation [12,13], and fruiting body development [12,14,15]. These proteins are also associated with sporulation and sexual development [5,[16][17][18], as well as the capacity to become pathogenic [19][20][21][22].…”