Abstract
Epimutations in fungal pathogens are emerging as novel phenomena that could explain the fast-developing resistance to antifungal drugs and other stresses. These epimutations are generated by RNA interference (RNAi) mechanisms that transiently silence specific genes to overcome stressful stimuli. The early-diverging fungus Mucor circinelloides exercises a fine control over two interacting RNAi pathways to produce epimutants: the canonical RNAi pathway and a new RNAi degradative pathway. The latter is considered a non-canonical RNAi pathway (NCRIP) because it relies on RNA-dependent RNA polymerases (RdRPs) and a novel ribonuclease III-like named R3B2 to degrade target transcripts. Here in this work, we uncovered the role of NCRIP in regulating virulence processes and transposon movements through key components of the pathway, RdRP1 and R3B2. Mutants in these genes are unable to launch a proper virulence response to macrophage phagocytosis, resulting in a decreased virulence potential. The transcriptomic profile of rdrp1Δ and r3b2Δ mutants revealed a pre-exposure adaptation to the stressful phagosomal environment even when the strains are not confronted by macrophages. These results suggest that NCRIP represses key targets during regular growth and releases its control when a stressful environment challenges the fungus. NCRIP interacts with the RNAi canonical core to protect genome stability by controlling the expression of centromeric retrotransposable elements. In the absence of NCRIP, these retrotransposons are robustly repressed by the canonical RNAi machinery; thus, supporting the antagonistic role of NCRIP in containing the epimutational pathway. Both interacting RNAi pathways might be essential to govern host-pathogen interactions through transient adaptations, contributing to the unique traits of the emerging infection mucormycosis.
Highlights
Mucorales are a group of ancient fungi that are emerging as a new source of pathogens causing the fungal infection mucormycosis
A non-canonical RNA interference (RNAi) pathway in Mucorales strain co-cultured with mouse macrophages)
Small RNA raw data corresponding to the wild-type and mutant strains grown during 48 h in rich medium were available to the public through the following NCBI SRA run accession numbers: SRR039123, SRR836082, SRR039128, SRR039126, and SRR1576768 (r3b2Δ mutant strain)
Summary
Mucorales are a group of ancient fungi that are emerging as a new source of pathogens causing the fungal infection mucormycosis This infectious disease is increasing the focus of recent studies due to its high mortality rates, which can reach up to 90% in cases of disseminated infection [1,2]. The elevated mortality rate is a direct connection to a lack of effective antifungal treatments, a consequence of the unusual resistance observed in these fungi In this regard, a novel RNAi-dependent epimutational mechanism of drug resistance has been described in M. circinelloides [3]. A novel RNAi-dependent epimutational mechanism of drug resistance has been described in M. circinelloides [3] In this mechanism, M. circinelloides generates strains resistant to the antifungal drug FK506 after only four days of exposure. The epimutational drug resistance in M. circinelloides is becoming clinically relevant because epimutants can emerge upon exposure to other antifungal drugs [4], and they exhibit organ-specific stability during in vivo infection [5]
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