Stage-Specific A-to-I RNA Editing in the Wheat Scab Fungus Fusarium graminearum

Yeasts and filamentous fungi do not have ADAR orthologs and are believed to lack A-to-I RNA editing, which is the most prevalent editing of mRNA in animals.  However, during this study with the PUK1 pseudo-kinase gene important for sexual reproduction in Fusarium graminearum, we found that two tandem stop codons UA¹⁸³¹G UA¹⁸³⁴G in its kinase domain were changed to UG¹⁸³¹G UG¹⁸³⁴G by RNA editing in perithecia.  To confirm A-to-I editing of PUK1 transcripts, strand-specific RNA-Seq data were generated with RNA isolated from conidia, hyphae, and perithecia.  PUK1 transcripts were almost specifically expressed in perithecia and 90% of them were edited to UG¹⁸³¹G UG¹⁸³⁴G.  Genome-wide analysis identified 27,301 perithecium-specific A-to-I editing sites.  Unlike those in animals, 70.5% of A-to-I editing sites in F. graminearum occur in coding regions and over two-thirds of them result in amino acid changes, including editing of 45 PUK1-like pseudogenes with stop codons in ORFs.  PUK1 orthologs and a number of other genes also displayed stage-specific expression and editing in Neurospora crassa and F. verticillioides.  Furthermore, F. graminearum differs from animals in the sequence-preference and structure-selectivity of A-to-I editing sites.  Whereas As embedded in RNA stems are targeted by ADARs, RNA editing in F. graminearum preferentially targets As in hairpin loops, which is similar to the anticodon loop of tRNA targeted by ADATs.  Overall, our results showed that A-to-I editing occurs specifically during sexual reproduction and mainly in the coding regions in filamentous ascomycetes, involving adenine deamination mechanisms distinct from metazoan ADARs.