Endogenous short RNAs generated by Dicer 2 and RNA-dependent RNA polymerase 1 regulate mRNAs in the basal fungus Mucor circinelloides

Abstract

Endogenous short RNAs (esRNAs) play diverse roles in eukaryotes and usually are produced from double-stranded RNA (dsRNA) by Dicer. esRNAs are grouped into different classes based on biogenesis and function but not all classes are present in all three eukaryotic kingdoms. The esRNA register of fungi is poorly described compared to other eukaryotes and it is not clear what esRNA classes are present in this kingdom and whether they regulate the expression of protein coding genes. However, evidence that some dicer mutant fungi display altered phenotypes suggests that esRNAs play an important role in fungi. Here, we show that the basal fungus Mucor circinelloides produces new classes of esRNAs that map to exons and regulate the expression of many protein coding genes. The largest class of these exonic-siRNAs (ex-siRNAs) are generated by RNA-dependent RNA Polymerase 1 (RdRP1) and dicer-like 2 (DCL2) and target the mRNAs of protein coding genes from which they were produced. Our results expand the range of esRNAs in eukaryotes and reveal a new role for esRNAs in fungi.

The Genomes of Three Uneven Siblings: Footprints of the Lifestyles of Three Trichoderma Species

“…Sequencing of sRNAs from many species of fungi has led to the discovery of many classes of them, e.g., siRNAs in Schizosaccharomyces pombe, Saccharomyces castellii, Candida albicans, Cryptococcus neoformans, and Magnaporthe oryzae; qiRNAs (QDE-2-interacting RNAs) in N. crassa; priRNAs (primal small RNAs) in S. pombe; ex-siRNAs (exonic-siRNAs) in Mucor circinelloides and T. atroviride; disiRNAs (Dicer-independent small interfering RNAs) in N. crassa, and milRNAs (miRNAslike small RNAs) in N. crassa, Sclerotinia sclerotiorum, Metharizium anisopliae, C. neoformans, and T. reesei. The functional role of some of these classes of sRNAs has been proven, but for many others it still remains to be shown (50,(55)(56)(57)(58)(59)(60)(61)(62)(63)(64)(65)(66)(67). For T. atroviride, however, a functional characterization of the components of the RNAi machinery is already available.…”

“…To determine the differentiation of the cellulase machineries between T. atroviride, T. reesei, and T. virens, the protein sequences of Trichoderma ␤-glucosidases and cellulases from GH families 1,3,5,6,7,12,45,61, and 74 (xyloglucanase) were compared and analyzed in detail. Protein similarities between T. atroviride, T. reesei, and T. virens were in a similar range for all tested enzymes associated with cellulose degradation (see Fig.…”

RNA Interference in Fungi: Pathways, Functions, and Applications

“…circinelloides is a basal fungus of the clade zygomycete that has become an important fungal model system for RNAi and sRNA production. Transformation of M. circinelloides with self-replicative plasmids or with vectors for expression of inverted repeat transgenes results in activation of gene silencing pathways and production of sRNAs of two distinct sizes, 21 nt and 25 nt (26,(67)(68)(69). Of the two Dicer proteins, DCL-2 plays the major role in siRNA generation (26).…”

“…Of the two Dicer proteins, DCL-2 plays the major role in siRNA generation (26). Mucor has two RdRPs, and RdRP1 is required for transgene-induced gene silencing (68).…”

Qipgene inFusarium oxysporumis required for normal hyphae morphology and virulence

“…Based on their RNA precursors and biogenesis mechanisms, these small RNAs can be divided into various types in fungi, including QDE-2-interacting small RNAs (qiRNAs), microRNA-like RNAs (milRNAs), Dicer-independent small interfering RNAs (disiRNAs), small interfering RNAs (siRNAs), long terminal repeat retrotransposon-siRNAs (LTR-siRNAs) and tRNA-derived RNA fragments (tRFs) (Jöchl et al 2008; Lee et al 2009; Nicolas et al 2010; Nunes et al 2011). The maturation of small RNAs in the RNA-silencing pathway is dependent on the RNase III ribonuclease Dicer, RNA-dependent RNA polymerases (RdRps) and Argonaute proteins (Lee et al 2010).…”