Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea

Abstract

Coprinopsis cinerea is a model mushroom particularly suited for the study of fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) have been extensively studied in animals and plants for their essential roles in post-transcriptional regulation of gene expression, miRNAs in fungi are less well characterized and their potential roles in controlling mushroom development remain unknown. To identify miRNA-like RNAs (milRNAs) in C. cinerea and explore their expression patterns during the early developmental transition of mushroom development, small RNA libraries of vegetative mycelium and primordium were generated and putative milRNA candidates were identified following the standards of miRNA prediction in animals and plants. Two out of 22 novel predicted milRNAs, cci-milR-12c and cci-milR-13e-5p, were validated by northern blot and stem-loop reverse transcription real-time PCR. Cci-milR-12c was differentially expressed whereas the expression levels of cci-milR-13e-5p were similar in the two developmental stages. Target prediction of the validated milRNAs resulted in genes associated with fruiting body development, including pheromone, hydrophobin, cytochrome P450, and protein kinase. Essential genes for miRNA biogenesis, including three coding for Dicer-like (DCL), one for Argonaute (AGO), one for AGO-like and one for quelling deficient-2 (QDE-2) proteins, were also identified in the C. cinerea genome. Phylogenetic analysis showed that the DCL and AGO proteins of C. cinerea were more closely related to those in other basidiomycetes and ascomycetes than to those in animals and plants. Taken together, our findings provided the first evidence for milRNAs in the model mushroom and their potential roles in regulating fruiting body development. New information on the evolutionary relationship of milRNA biogenesis proteins across kingdoms has also provided new insights for guiding further functional and evolutionary studies of miRNAs.

Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi

“…2014 ). Argonaute-family proteins were developmentally regulated in all nine species, suggesting RNA interference as a widespread regulatory mechanism of CM morphogenesis, consistent with recent reports on individual species ( Lau et al. 2018 ; Shao et al.…”

Comparative genomics reveals unique wood‐decay strategies and fruiting body development in the Schizophyllaceae

“…Fruiting body production is a highly integrated developmental process triggered by a changing environment, such as a drop in temperature, nutrient depletion or shifts in light conditions (Kües & Liu, ; Kües & Navarro‐González, ; Sakamoto et al ., ). It results from the concerted expression of structural and regulatory genes (Martin et al ., ; Stajich et al ., ; Ohm et al ., ; Muraguchi et al ., ; Nagy et al ., ; Lau et al ., ) as well as other processes, such as alternative splicing (Gehrmann et al ., ; Krizsán et al ., ), allele‐specific gene expression (Gehrmann et al ., ) and probably selective protein modification (Pelkmans et al ., ; Krizsán et al ., ). Known structural genes include ones coding for hydrophobins (Lugones et al ., ; Wösten et al ., ; Bayry et al ., ), lectins (Cooper et al ., ; Boulianne et al ., ; Hassan et al ., ) and several cell wall chitin and glucan‐active CAZymes (Wessels, ; Fukuda et al ., ; Konno & Sakamoto, ; Sakamoto et al ., ), and probably include genes for cerato‐platanins, which are expansin‐like proteins (Sipos et al ., ; Krizsán et al ., ), among others.…”

The Evolutionary Significance of RNAi in the Fungal Kingdom

“…milRNAs have also been studied in other organisms. Coprinopsis cinerea , a model mushroom, produces milRNAs implicated in development and fruiting body formation [ 47 ]; moreover, in F. graminearum , milRNAs were initially found not only in asexual phases [ 107 ] but also in sexual stages later on [ 46 ], where they seem to have an important role in the regulation of sexual development. As described above, F. graminearum also produces ex-siRNAs [ 45 ].…”