Identification and Functional Demonstration of miRNAs in the Fungus Cryptococcus neoformans

Abstract

microRNAs (miRNAs), endogenous posttranscriptional repressors by base-pairing of their cognate mRNAs in plants and animals, have mostly been thought lost in the kingdom of fungi. Here, we report the identification of miRNAs from the fungus Cryptococcus neoformans. With bioinformatics and Northern blotting approaches, we found that these miRNAs and their hairpin precursors were present in this fungus. The size of miR1 and miR2 is 22 nt and 18 nt, respectively. The precursors are about ∼70 nt in length that is close to mammalian pre-miRNAs. Characteristic features of miRNAs are also found in miR1/2. We demonstrated that the identified miRNAs, miR1 and miR2, caused transgene silencing via the canonical RNAi pathway. Bioinformantics analysis helps to reveal a number of identical sequences of the miR1/2 in transposable elements (TEs) and pseudogenes, prompting us to think that fungal miRNAs might be involved in the regulation of the activity of transposons and the expression of pseudogenes. This study identified functional miRNAs in C. neoformans, and sheds light on the diversity and evolutionary origin of eukaryotic miRNAs.

Extracellular vesicle-mediated export of fungal RNA

“…S. cerevisiae ), and functional in most filamentous fungi50515253. C. neoformans bears a fully functional RNAi machinery, including Argonaute proteins, Dicer and the RNA-dependent RNA polymerase5455. In this organism, RNAi-dependent mechanisms are involved in the sex-induced silencing of transgenes during the sexual stage of the fungus55.…”

“…In this organism, RNAi-dependent mechanisms are involved in the sex-induced silencing of transgenes during the sexual stage of the fungus55. In addition, C. neoformans miRNA and pre-miRNA may be similar to their mammalian counterparts5455. In C. albicans , the RNAi machinery includes a noncanonical Dicer, and small-RNA molecule preparations from this species are enriched in 22-mer sequences56.…”

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.…”

The identification of microRNAs in Ganoderma lingzhi sporocarp

“…Previously, it was generally accepted that miRNA and miRNA-like did not exist in fungus. In recent years, the small RNAs, especially miRNA-like small RNAs, were widely studied in fungal species based on the deep sequencing technology, such as Fusarium oxysporum (Schumann et al 2013;Chen et al 2014), Cryptococcus neoformans (Jiang et al 2012), Trichoderma reesei (Kang et al 2013), Penicillium marneffei (Lau et al 2013), Neurospora crassa , Sclerotinia sclerotiorum (Zhou et al 2012a), and Metarhizium anisopliae (Zhou et al 2012b).…”