Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea
Discovery of microRNA-like RNAs during early fruiting body development in the model mushroom Coprinopsis cinerea
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DOI：
10.1371/journal.pone.0198234
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发表时间：
2018-09-19
期刊：
影响因子：
3.7
通讯作者：
Kwan, Hoi Shan
中科院分区：
文献类型：
--
作者：
Lau, Amy Yuet Ting;Cheng, Xuanjin;Kwan, Hoi Shan
灰盖鬼伞（Coprinopsis cinerea）是一种模式蘑菇，特别适合于研究真菌子实体发育和真菌多细胞性的进化。虽然microRNA（miRNAs）在动物和植物中因其在基因表达的转录后调节中的重要作用而被广泛研究，但真菌中的miRNAs的特征不太清楚，并且它们在控制蘑菇发育中的潜在作用仍然未知。为了鉴定C.为了研究其在蘑菇发育的早期发育转变过程中的表达模式，产生了营养菌丝体和原基的小RNA文库，并按照动物和植物中miRNA预测的标准鉴定了推定的milRNA候选物。通过北方印迹和茎环逆转录实时PCR验证了22个新预测的milRNA中的两个，cci-milR-12 c和cci-milR-13 e-5 p。在两个发育阶段中，cci-milR-12 c差异表达，而cci-milR-13 e-5 p的表达水平相似。验证的milRNA的靶预测产生与子实体发育相关的基因，包括信息素、疏水蛋白、细胞色素P450和蛋白激酶。在C.灰葡萄基因组系统进化分析表明，C.灰霉病菌与其它担子菌和子囊菌的亲缘关系较近，而与动植物的亲缘关系较远。综上所述，我们的发现为模型蘑菇中的milRNA及其在调节子实体发育中的潜在作用提供了第一个证据。关于跨界milRNA生物发生蛋白进化关系的新信息也为指导进一步的miRNAs功能和进化研究提供了新的见解。
Coprinopsis cinerea is a model mushroom particularly suited for the study of fungal fruiting body development and the evolution of multicellularity in fungi. While microRNAs (miRNAs) have been extensively studied in animals and plants for their essential roles in post-transcriptional regulation of gene expression, miRNAs in fungi are less well characterized and their potential roles in controlling mushroom development remain unknown. To identify miRNA-like RNAs (milRNAs) in C. cinerea and explore their expression patterns during the early developmental transition of mushroom development, small RNA libraries of vegetative mycelium and primordium were generated and putative milRNA candidates were identified following the standards of miRNA prediction in animals and plants. Two out of 22 novel predicted milRNAs, cci-milR-12c and cci-milR-13e-5p, were validated by northern blot and stem-loop reverse transcription real-time PCR. Cci-milR-12c was differentially expressed whereas the expression levels of cci-milR-13e-5p were similar in the two developmental stages. Target prediction of the validated milRNAs resulted in genes associated with fruiting body development, including pheromone, hydrophobin, cytochrome P450, and protein kinase. Essential genes for miRNA biogenesis, including three coding for Dicer-like (DCL), one for Argonaute (AGO), one for AGO-like and one for quelling deficient-2 (QDE-2) proteins, were also identified in the C. cinerea genome. Phylogenetic analysis showed that the DCL and AGO proteins of C. cinerea were more closely related to those in other basidiomycetes and ascomycetes than to those in animals and plants. Taken together, our findings provided the first evidence for milRNAs in the model mushroom and their potential roles in regulating fruiting body development. New information on the evolutionary relationship of milRNA biogenesis proteins across kingdoms has also provided new insights for guiding further functional and evolutionary studies of miRNAs.