A-to-I RNA editing is developmentally regulated and generally adaptive for sexual reproduction in <i>Neurospora crassa</i>.

Abstract

Although fungi lack adenosine deaminase acting on RNA (ADAR) enzymes, adenosine to inosine (A-to-I) RNA editing was reported recently in <i>Fusarium graminearum</i> during sexual reproduction. In this study, we profiled the A-to-I editing landscape and characterized its functional and adaptive properties in the model filamentous fungus <i>Neurospora crassa</i> A total of 40,677 A-to-I editing sites were identified, and approximately half of them displayed stage-specific editing or editing levels at different sexual stages. RNA-sequencing analysis with the Δ<i>stc</i>-1 and Δ<i>sad</i>-1 mutants confirmed A-to-I editing occurred before ascus development but became more prevalent during ascosporogenesis. Besides fungal-specific sequence and secondary structure preference, 63.5% of A-to-I editing sites were in the coding regions and 81.3% of them resulted in nonsynonymous recoding, resulting in a significant increase in the proteome complexity. Many genes involved in RNA silencing, DNA methylation, and histone modifications had extensive recoding, including <i>sad</i>-1, <i>sms</i>-3, <i>qde</i>-1, and <i>dim</i>-2. Fifty pseudogenes harbor premature stop codons that require A-to-I editing to encode full-length proteins. Unlike in humans, nonsynonymous editing events in <i>N. crassa</i> are generally beneficial and favored by positive selection. Almost half of the nonsynonymous editing sites in <i>N. crassa</i> are conserved and edited in <i>Neurospora tetrasperma</i> Furthermore, hundreds of them are conserved in <i>F. graminearum</i> and had higher editing levels. Two unknown genes with editing sites conserved between <i>Neurospora</i> and <i>Fusarium</i> were experimentally shown to be important for ascosporogenesis. This study comprehensively analyzed A-to-I editing in <i>N. crassa</i> and showed that RNA editing is stage-specific and generally adaptive, and may be functionally related to repeat induced point mutation and meiotic silencing by unpaired DNA.