The ectomycorrhizal fungus Pisolithus microcarpus encodes a microRNA involved in cross-kingdom gene silencing during symbiosis

Abstract

Small RNAs (sRNAs) are known to regulate pathogenic plant–microbe interactions. Emerging evidence from the study of these model systems suggests that microRNAs (miRNAs) can be translocated between microbes and plants to facilitate symbiosis. The roles of sRNAs in mutualistic mycorrhizal fungal interactions, however, are largely unknown. In this study, we characterized miRNAs encoded by the ectomycorrhizal fungus Pisolithus microcarpus and investigated their expression during mutualistic interaction with Eucalyptus grandis. Using sRNA sequencing data and in situ miRNA detection, a novel fungal miRNA, Pmic_miR-8, was found to be transported into E. grandis roots after interaction with P. microcarpus. Further characterization experiments demonstrate that inhibition of Pmic_miR-8 negatively impacts the maintenance of mycorrhizal roots in E. grandis, while supplementation of Pmic_miR-8 led to deeper integration of the fungus into plant tissues. Target prediction and experimental testing suggest that Pmic_miR-8 may target the host NB-ARC domain containing transcripts, suggesting a potential role for this miRNA in subverting host signaling to stabilize the symbiotic interaction. Altogether, we provide evidence of previously undescribed cross-kingdom sRNA transfer from ectomycorrhizal fungi to plant roots, shedding light onto the involvement of miRNAs during the developmental process of mutualistic symbioses.

Systemic silencing and DNA methylation of a host reporter gene induced by a beneficial fungal root endophyte

“…Indeed, RdDM is essential in Arabidopsis to establish a beneficial relationship with the root-colonizing Trichoderma atroviride while DNA methylation and histone modifications are required for plant priming by the beneficial fungus against B. cinerea (Rebolledo-Prudencio et al ., 2021). Importantly, it was just recently shown that during the mutualistic interaction of the ectomycorrhizal fungus Pisolithus microcarpus with Eucalyptus grandis , a fungal miRNA, Pmic_miR-8, targets the host NB-ARC domain containing transcripts in a cross-kingdom RNAi manner (Wong-Bajracharya et al ., 2022). Reminiscent of this, an in silico study predicted that the beneficial arbuscular mycorrhizal fungi Rhizophagus irregularis produces sRNAs that have 237 candidate targets in the host plant Medicago truncatula , including specific mRNAs known to be modulated in roots upon AMF colonization (Silvestri et al ., 2019).…”

Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation

“…Recently, the miRNA, Pmic_miR-8, was found to be transported from a fungal symbiont, Pisolithus microcarpus , to the roots of its symbiotic host, Eucalyptus grandis ( Wong-Bajracharya et al., 2022 ). Pmic_miR-8 may inhibit the host transcripts encoding an NB-ARC domain-containing disease resistance protein, to stabilize the symbiotic interaction ( Wong-Bajracharya et al., 2022 ).…”

Site-specific analysis reveals candidate cross-kingdom small RNAs, tRNA and rRNA fragments, and signs of fungal RNA phasing in the barley-powdery mildew interaction

“…A special case of inter-organismal communication is the exchange of information between organisms of different taxa. Examples of this phenomenon in the area of plant-microbe interactions comprise mutually advantageous symbioses and diseases caused by pathogenic fungi (1, 2). Gene regulation by non-coding small RNAs (sRNAs) can play an important role in the context of such plant-microbe encounters (1).…”