The interaction of fungi with the environment orchestrated by RNAi

Abstract

The fungal kingdom has been key in the investigation of the biogenesis and function of small RNAs (sRNAs). The discovery of phenomena such as quelling in Neurospora crassa represents pioneering work in the identification of the main elements of the RNA interference (RNAi) machinery. Recent discoveries in the regulatory mechanisms in some yeast and filamentous fungi are helping us reach a deeper understanding of the transcriptional and post-transcriptional gene-silencing mechanisms involved in genome protection against viral infections, DNA damage and transposon activity. Although most of these mechanisms are reasonably well understood, their role in the physiology, response to the environment and interaction of fungi with other organisms had remained elusive. Nevertheless, studies in fungi such as Mucor circinelloides, Magnaporthe oryzae, Cryptococcus neoformans, Trichoderma atroviride, Botrytis cinerea and others have started to shed light on the relevance of the RNAi pathway. In these fungi gene regulation by RNAi is important for growth, reproduction, control of viral infections and transposon activity, as well as in the development of antibiotic resistance and interactions with their hosts. Moreover, the increasing number of reports of the discovery of microRNA-like RNAs in fungi under different conditions highlights the importance of fungi as models for understanding adaptation to the environment using regulation by sRNAs. The goal of this review is to provide the reader with an up-to-date overview of the importance of RNAi in the interaction of fungi with their environment.

In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant

“…Among the population of Rir -sRNA-generating loci, 10 were predicted as miRNA-like. So far, miRNA-like have been identified in several fungi belonging to Ascomycota and Basidiomycota phyla but not in the basal fungus M. circinelloides [13, 69, 70]. This is the first evidence of miRNA-like occurrence in the Mucoromycota group.…”

“…Since no miRNA-like database is currently available for fungal sequences, analysis for homolog sequences could not be done in an automated way. Remarkably, based on the current literature, unlike other eukaryotes, miRNA-like sequences are not conserved among fungi belonging to different genera [70]. Interestingly, three miRNA-like are up-regulated in the intraradical phase, which could lead to the hypothesis of miRNA-like AMF genes required to manipulate fungal or host plant gene expression; however, further analyses are necessary to confirm their possible functional role.…”

Genome-wide exonic small interference RNA-mediated gene silencing regulates sexual reproduction in the homothallic fungus Fusarium graminearum

“…MSUD detects unpaired DNA regions during meiosis and leads to siRNA production for gene silencing in the heterothallic fungus N . crassa [ 26 , 62 ]. In a recent study, naturally unpaired regions between two mating partners were predicted to be major sources for ex-siRNAs in the heterothallic fungus N .…”

Chilling Stress Triggers VvAgo1-Mediated miRNA-Like RNA Biogenesis in Volvariella volvacea

“…Recent findings in the regulation of gene expression in response to their environment by small RNAs in fungi have led to the understanding of the regulatory processes better to survive environmental stresses, which also represents an enormous potential for application in the fields of medicine and agriculture (Villalobos-Escobedo et al, 2016). The related genes in the VvAgo1-mediated RNAi pathways have the potential to be the new target genes for reducing cryogenic autolysis.…”