A Non-canonical RNA Silencing Pathway Promotes mRNA Degradation in Basal Fungi

Abstract

The increasing knowledge on the functional relevance of endogenous small RNAs (esRNAs) as riboregulators has stimulated the identification and characterization of these molecules in numerous eukaryotes. In the basal fungus Mucor circinelloides, an emerging opportunistic human pathogen, esRNAs that regulate the expression of many protein coding genes have been described. These esRNAs share common machinery for their biogenesis consisting of an RNase III endonuclease Dicer, a single Argonaute protein and two RNA-dependent RNA polymerases. We show in this study that, besides participating in this canonical dicer-dependent RNA interference (RNAi) pathway, the rdrp genes are involved in a novel dicer-independent degradation process of endogenous mRNAs. The analysis of esRNAs accumulated in wild type and silencing mutants demonstrates that this new rdrp-dependent dicer-independent regulatory pathway, which does not produce sRNA molecules of discrete sizes, controls the expression of target genes promoting the specific degradation of mRNAs by a previously unknown RNase. This pathway mainly regulates conserved genes involved in metabolism and cellular processes and signaling, such as those required for heme biosynthesis, and controls responses to specific environmental signals. Searching the Mucor genome for candidate RNases to participate in this pathway, and functional analysis of the corresponding knockout mutants, identified a new protein, R3B2. This RNase III-like protein presents unique domain architecture, it is specifically found in basal fungi and, besides its relevant role in the rdrp-dependent dicer-independent pathway, it is also involved in the canonical dicer-dependent RNAi pathway, highlighting its crucial role in the biogenesis and function of regulatory esRNAs. The involvement of RdRPs in RNA degradation could represent the first evolutionary step towards the development of an RNAi mechanism and constitutes a genetic link between mRNA degradation and post-transcriptional gene silencing.

A non-canonical RNA degradation pathway suppresses RNAi-dependent epimutations in the human fungal pathogen Mucor circinelloides

“…In fact, two novel and unusual mechanisms have been recently reported in the human fungal pathogen Mucor circinelloides that differ from the canonical exogenously or endogenously activated RNAi pathways described previously [6, 7]. These are an RNAi-dependent epimutation pathway [4] and an RdRP-dependent Dicer-independent degradation cascade that acts on endogenous mRNA [5]. These discoveries position M .…”

“…Quelling, meiotic silencing by unpaired DNA (MSUD), and sex induced silencing (SIS) are distinct RNAi pathways that have been described in Neurospora crassa and Cryptococcus neoformans , respectively, and new RNAi pathways are still being discovered in other fungi [4, 5]. In fact, two novel and unusual mechanisms have been recently reported in the human fungal pathogen Mucor circinelloides that differ from the canonical exogenously or endogenously activated RNAi pathways described previously [6, 7].…”

“…As mentioned above, a recently published study described a novel RdRP-dependent Dicer-independent degradation mechanism for endogenous mRNA [5]. This unusual Dicer-independent regulatory pathway controls the expression of conserved and highly expressed genes via specific degradation of the corresponding target mRNAs.…”

“…A new RNase III-like protein named R3B2 has been found to function as the primary RNase protein in this pathway instead of Dicer. R3B2 is also involved in the canonical RNAi pathway, likely by functioning in combination with the Dicer proteins [5], although its specific role in this pathway is still unknown. How R3B2 discriminates between both pathways is also unknown.…”

Non-coding RNA-mediated epigenetic regulation of liver fibrosis

“…These modifications result in a variable expression of identical genetic information based on the surrounding conditions leading to enhanced expression or silencing of genes [58,59]. Both miRs and LncRNAs modulate gene expression through mechanisms that will be discussed in detail below.…”