MicroRNA-like RNA Functions Are Required for the Biosynthesis of Active Compounds in the Medicinal Fungus Sanghuangporus vaninii

• Published in: Microbiology spectrum 2022-12, Vol.10 (6), p.e0021922-e0021922
• Main Authors: Zhou, Qiumei, Yin, Xuebing, Zhang, Hanghang, Wang, Yulong
• Format: Article
• Language: English
• Subjects: Argonaute; Basidiomycota - metabolism; Dicer; Gene Expression Regulation, Fungal; Genetics and Molecular Biology; microRNA-like RNA; MicroRNAs - genetics; MicroRNAs - metabolism; Research Article; RNA Interference; RNA, Fungal - genetics; RNA, Fungal - metabolism; RNA-dependent RNA polymerase; Sanghuangporus vaninii; spray-induced gene silencing
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/spectrum.00219-22

miRNA-like RNAs (milRNAs) have been recognized as sequence-specific regulators of posttranscriptional regulation of gene expression in eukaryotes. However, the functions of hundreds of fungal milRNAs in the biosynthesis of metabolic components are obscure. produces diverse bioactive compounds and is widely used in Asian countries. Here, genes encoding two Dicers, four Argonautes, and four RdRPs were identified and characterized in . Due to the lack of an efficient gene manipulation system, the efficacy of spray-induced gene silencing (SIGS) was determined in which showed efficient double-stranded RNA (dsRNA) uptake and gene silencing efficiency. SIGS-mediated gene knockdown showed that SVRDRP-3, SVRDRP-4, SVDICER-1, and SVDICER-2 were critical for mycelial biomass, flavonoid, triterpenoid, and polysaccharide production. Illumina deep sequencing was performed to characterize the milRNAs from mycelium and fruiting body. A total of 31 milRNAs were identified, out of which, , , and were - and -dependent milRNAs. Importantly, SIGS-mediated overexpression of and resulted in significant changes in the yields of flavonoids, triterpenoids, and polysaccharides. Further analysis showed that these milRNA target genes encoding the retrotransposon-derived protein PEG1 and histone-lysine N-methyltransferase were potentially downregulated in the milRNA overexpressing strain. Our results revealed that has high external dsRNA and small RNA uptake efficiency and that milRNAs may play crucial regulatory roles in the biosynthesis of bioactive compounds. Fungi can take up environmental RNA that can silence fungal genes with RNA interference, which prompts the development of SIGS. Efficient dsRNA and milRNA uptake in , successful dsRNA-targeted gene block, and the increase in intracellular miRNA abundance showed that SIGS technology is an effective and powerful tool for the functional dissection of fungal genes and millRNAs. We found that the RdRP, Dicer, and Argonaute genes are critical for mycelial biomass and bioactive compound production. Our study also demonstrated that overexpressed SVRDRP-4- and SVDICER-1-dependent milRNAs ( and ) led to significant changes in the yields of the three active compounds. This study not only provides the first report on SIGS-based gene and milRNA function exploration, but also provides a theoretical platform for exploration of the functions of milRNAs involved in biosynthesis of metabolic compounds in fungi.