Abundant and Selective RNA-Editing Events in the Medicinal Mushroom Ganoderma lucidum

Abstract

RNA editing is a widespread, post-transcriptional molecular phenomenon that diversifies hereditary information across various organisms. However, little is known about genome-scale RNA editing in fungi. In this study, we screened for fungal RNA editing sites at the genomic level in Ganoderma lucidum, a valuable medicinal fungus. On the basis of our pipeline that predicted the editing sites from genomic and transcriptomic data, a total of 8906 possible RNA-editing sites were identified within the G. lucidum genome, including the exon and intron sequences and the 59-/39-untranslated regions of 2991 genes and the intergenic regions. The major editing types included C-to-U, A-to-G, G-to-A, and U-to-C conversions. Four putative RNA-editing enzymes were identified, including three adenosine deaminases acting on transfer RNA and a deoxycytidylate deaminase. The genes containing RNA-editing sites were functionally classified by the Kyoto Encyclopedia of Genes and Genomes enrichment and gene ontology analysis. The key functional groupings enriched for RNA-editing sites included laccase genes involved in lignin degradation, key enzymes involved in triterpenoid biosynthesis, and transcription factors. A total of 97 putative editing sites were randomly selected and validated by using PCR and Sanger sequencing. We presented an accurate and large-scale identification of RNA-editing events in G. lucidum, providing global and quantitative cataloging of RNA editing in the fungal genome. This study will shed light on the role of transcriptional plasticity in the growth and development of G. lucidum, as well as its adaptation to the environment and the regulation of valuable secondary metabolite pathways. RNA editing is a post-transcriptional process that can enhance the diversity of gene products by altering RNA sequences. This can involve site-specific nucleotide modifications, nucleotide insertions/deletions, and nucleotide substitutions (Gott and Emeson 2000;Bass 2002;Farajollahi and Maas 2010). RNA editing can affect messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs, and small regulatory RNAs present in all cellular compartments and has been described in a wide range of organisms from viruses to fungi, mammals, and plants ( Gott and Emeson 2000;Gott 2003;Kawahara et al. 2007). The prevalent RNA-editing pathways in higher eukaryotes involves the deamination of cytidine (C) to create uridine (U) and deamination of adenosine (A) to create inosine (I) (Bass 2002;Gott 2003). The editing process generally involves a specificity factor (RNA or protein) that recognizes the editing site, as well as an enzyme, occasionally with other accessory factors, that catalyzes the reaction (Bass 2002). The functions of RNA editing include regulation of gene expression, increasing protein diversity and reversion of the effect of mutations in the genome (Gott and Emeson 2000;Gott 2003). In many cases, RNA editing is essential for correcting protein production (Young 1990) or for modulating the functional properties of proteins...

Cell lineage inference from SNP and scRNA-Seq data

“…In the neuron data, we found 26 such genes associated with the 35 predicted SNPs. The most significant GO terms associated with these 26 genes are "Regulation of protein depolymerization" (p − v al ue = 1.32 × 10 −4 , F D R = 1) and "Regulation of protein complex disassembly" (p − v al ue = 1.98 × 10 −4 , F D R = 1), which are consistent with the potential protein degradation related functions of RNA-editing previously reported by study (Zhu et al, 2014). In the Liver data, we found 42 genes associated with the 54 predicted SNPs.…”

“…Third, the identified SNPs significantly overlap known RNA-editing sites reported in RADAR database (Picardi et al, 2016). Fourth, many reside in genes that are known to be associated with processes that are regulated by RNA-editing such as protein degradation (Zhu et al, 2014).…”

Carbon metabolism, transcriptome and RNA editome in developmental paths differentiation ofCoprinopsis cinerea

“…Our results show that RNA editing not only occurs in fruiting, but also other developmental paths. Similar to the stage-specific and substrate-specific RNA editing studies on basidiomycetes, editing events in C. cinerea regulate the genes in carbohydrate metabolism and cell structure formation (37, 38). All these results emphasize the functional similarity of RNA editing in regulating carbohydrate metabolism, and further, the essential role of carbon metabolism in fungal development.…”

“…As a special kind of transcriptional modification, RNA editing has been widely found in all domains of life and showed significant impacts on diverging the transcriptome and proteome (73–76). In fungi, developmentally regulated for sexual reproduction and evolutionarily conserved across genus are two main patterns of RNA editing events (35, 37, 38). Our results show that RNA editing not only occurs in fruiting, but also other developmental paths.…”

Serotonin and conditioning: Focus on Pavlovian psychostimulant drug conditioning

“…Furthermore, this type of genetic subtraction manipulation affects the expression of the 5-HT receptors throughout the brain. Recent developments in selective gene editing may obviate much of the above criticism; however, this new technological breakthrough does not have sufficient experimental exploration to allow sufficient basis for evaluating this more advanced tool in the manipulation of serotonin or other transmitter receptors [59,60].…”