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Genome Res. 2016 Apr;26(4):499-509. doi: 10.1101/gr.199877.115. Epub 2016 Mar 2.

Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes.

Author information

1
State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China;
2
College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China;
3
Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA.
4
State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA.

Abstract

Yeasts and filamentous fungi do not have adenosine deaminase acting on RNA (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(FGRRES_01058) pseudokinase gene important for sexual reproduction in Fusarium graminearum, we found that two tandem stop codons, UA(1831)GUA(1834)G, in its kinase domain were changed to UG(1831)GUG(1834)G 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 was almost specifically expressed in perithecia, and 90% of transcripts were edited to UG(1831)GUG(1834)G. Genome-wide analysis identified 26,056 perithecium-specific A-to-I editing sites. Unlike those in animals, 70.5% of A-to-I editing sites inF. graminearum occur in coding regions, and more than two-thirds of them result in amino acid changes, including editing of 69PUK1-like pseudogenes with stop codons in ORFs.PUK1orthologs and other pseudogenes 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 A's embedded in RNA stems are targeted by ADARs, RNA editing inF. graminearum preferentially targets A's in hairpin loops, which is similar to the anticodon loop of tRNA targeted by adenosine deaminases acting on tRNA (ADATs). Overall, our results showed that A-to-I RNA editing occurs specifically during sexual reproduction and mainly in the coding regions in filamentous ascomycetes, involving adenosine deamination mechanisms distinct from metazoan ADARs.

PMID:
26934920
PMCID:
PMC4817773
DOI:
10.1101/gr.199877.115
[Indexed for MEDLINE]
Free PMC Article

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