The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey

Abstract

Clonostachys rosea is a necrotrophic mycoparasitic fungus, used for biological control of plant pathogenic fungi. A better understanding of the underlying mechanisms resulting in successful biocontrol is important for knowledge‐based improvements of the application and use of biocontrol in agricultural production systems. Transcriptomic analyses revealed that C. rosea responded with both common and specific gene expression during interactions with the fungal prey species Botrytis cinerea and Fusarium graminearum. Genes predicted to encode proteins involved in membrane transport, biosynthesis of secondary metabolites and carbohydrate‐active enzymes were induced during the mycoparasitic attack. Predicted major facilitator superfamily (MFS) transporters constituted 54% of the induced genes, and detailed phylogenetic and evolutionary analyses showed that a majority of these genes belonged to MFS gene families evolving under selection for increased paralog numbers, with predicted functions in drug resistance and transport of carbohydrates and small organic compounds. Sequence analysis of MFS transporters from family 2.A.1.3.65 identified rapidly evolving loop regions forming the entry to the transport tunnel, indicating changes in substrate specificity as a target for selection. Deletion of the MFS transporter gene mfs464 resulted in mutants with increased growth inhibitory activity against F. graminearum, providing evidence for a function in interspecific fungal interactions. In summary, we show that the mycoparasite C. rosea can distinguish between fungal prey species and modulate its transcriptomic responses accordingly. Gene expression data emphasize the importance of secondary metabolites in mycoparasitic interactions.

Functional analysis of polyketide synthase genes in the biocontrol fungus Clonostachys rosea

“…rosea interacting with B. cinerea or F. graminearum revealed both common and species-specific responses in PKS gene expression. This is in line with a recent transcriptome analysis of C. rosea during interactions with B. cinerea or F. graminearum where genes predicted to encode proteins particularly involved in membrane transport and secondary metabolite biosynthesis were differentially expressed towards the two fungi 26 . The pks9 gene was reported by Nygren et al .…”

“…This limited knowledge on production of secondary metabolites in C. rosea is in sharp contrast to the predicted gene content of its genome. The C. rosea strain IK726 genome contains high numbers of genes encoding PKSs (31 genes), non-ribosomal peptide synthetases (NRPSs, 17 genes), ABC (90 genes) and MFS (634 genes) membrane transporters 25 , 26 . Functional studies indeed confirmed the role of several ABC and MFS transporters in antagonism, xenobiotic tolerance and in biocontrol by mediating efflux of endogenous or exogenous metabolites in C. rosea 10 , 11 , 26 – 28 .…”

Biology and applications of Clonostachys rosea

“…Moreover, several transcriptomes of C. rosea were sequenced under interaction with Fusarium graminearum, Botrytis cinerea, Helminthosporium solani and Sclerotinia sclerotiorum, respectively. Therefore, plenty of biocontrol-related genes in C. rosea were obtained (Kosawang et al 2014;Sun et al 2015aSun et al , 2015bLysøe et al 2017;Demissie et al 2018;Nygren et al 2018). Genes encoding nonribosomal peptide synthetase, transcription factor, transaldolase, ABC transporter, zearalenone lactonohydrolase and hydrophobin were verified to be involved in C. rosea against fungal plant pathogens through gene deletion (Dubey et al 2014;Kosawang et al 2014;Dubey et al 2016;Liu et al 2016;Sun et al 2018;Iqbal et al 2019).…”

Use of Competitive Filamentous Fungi as an Alternative Approach for Mycotoxin Risk Reduction in Staple Cereals: State of Art and Future Perspectives

“…When transcriptomic analyses were performed with the aim to better understand the underlying mechanisms resulting in the successful biocontrol activity of C. rosea, both common and specific gene expression was detected during interactions with F. graminearum. Genes encoding proteins involved in membrane transport, biosynthesis of secondary metabolites and carbohydrate-active enzymes were induced during the mycoparasitic attack as well as facilitator superfamily (MFS) transporters (54% of the induced genes), with predicted functions in drug resistance and transport of carbohydrates and small organic compounds [137].…”