Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes.
Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes.
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DOI：
10.1101/gr.199877.115
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发表时间：
2016-04
期刊：
影响因子：
7
通讯作者：
Xu JR
中科院分区：
文献类型：
--
作者：
Liu H;Wang Q;He Y;Chen L;Hao C;Jiang C;Li Y;Dai Y;Kang Z;Xu JR
酵母和丝状真菌不具有作用于RNA（阿达尔）直系同源物的腺苷脱氨酶，并且被认为缺乏A至I RNA编辑，这是动物中最普遍的mRNA编辑。然而，在对禾谷镰刀菌PUK 1（FGRRES_01058）假激酶基因的研究中，我们发现其激酶结构域中的两个串联终止密码子UA 1831 GUA 1834 G在包皮中通过RNA编辑被改变为UG 1831 GUG 1834 G。为了确认PUK 1转录物的A至I编辑，用从分生孢子、菌丝和孢子囊分离的RNA生成链特异性RNA-seq数据。PUK 1几乎特异性地在包皮中表达，并且90%的转录本被编辑为UG 1831 GUG 1834 G。全基因组分析鉴定了26，056个子囊壳特异性A-to-I编辑位点。与动物不同，F.禾谷镰刀菌的突变发生在编码区，其中超过三分之二的突变导致了氨基酸的改变，包括在ORF中编辑了69个具有终止密码子的PUK 1样假基因。PUK 1同源基因和其他假基因在粗糙脉孢菌和F.轮枝状此外，F.禾谷镰刀菌与动物的不同之处在于A-to-I编辑位点的序列偏好性和结构选择性。然而，嵌入RNA茎中的A是ADAR的目标，F中的RNA编辑。禾谷镰刀菌优先靶向发夹环中的A，这类似于作用于tRNA的腺苷脱氨酶（ADAT）靶向的tRNA的反密码子环。总的来说，我们的研究结果表明，A到I RNA编辑专门发生在有性生殖过程中，主要是在丝状子囊菌的编码区，涉及腺苷脱氨机制不同于后生动物ADAR。
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, UA1831GUA1834G, in its kinase domain were changed to UG1831GUG1834G 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 UG1831GUG1834G. 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 in F. graminearum occur in coding regions, and more than two-thirds of them result in amino acid changes, including editing of 69 PUK1-like pseudogenes with stop codons in ORFs. PUK1 orthologs 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 in F. 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.