Identification of microRNA-Like RNAs in the Filamentous Fungus Trichoderma reesei by Solexa Sequencing
Identification of microRNA-Like RNAs in the Filamentous Fungus Trichoderma reesei by Solexa Sequencing
复制标题
通过 Solexa 测序鉴定丝状真菌里氏木霉中的 microRNA 样 RNA
DOI：
10.1371/journal.pone.0076288
复制
发表时间：
2013-10-02
期刊：
影响因子：
3.7
通讯作者：
Gou, Deming
中科院分区：
文献类型：
--
作者：
Kang, Kang;Zhong, Jiasheng;Gou, Deming
microRNAs （miRNAs）是一种非编码小rna (sRNAs)，能够负向调节基因表达。近年来，在几种丝状真菌中发现了类似microrna的小rna (milRNAs)，但在里氏木霉（Trichoderma reesei）这种能分泌大量水解酶的工业丝状真菌中尚未发现。为了探索milRNA在T. reesei中的存在并评估其在纤维素诱导下的表达情况，我们构建了T. reesei纤维素诱导（in）和非诱导（CON）两个sRNA文库，并利用Solexa测序技术对其进行了测序。从IN和CON样品中分别获得了726和631个srna。全局表达分析显示，在两种条件下，T. reesei中sRNAs的表达存在广泛差异。基于短发夹结构分析，共鉴定出13个预测mirnas。通过RT-qPCR进一步验证深度测序获得的milRNA谱。计算分析预测了一些与许多过程相关的潜在靶标，包括酶表达的调节。褐条霉milRNA的存在和差异表达提示milRNA可能在褐条霉生长和纤维素酶诱导中发挥作用。该工作为进一步研究真菌mirrna的功能及其产业化应用奠定了基础。
microRNAs (miRNAs) are non-coding small RNAs (sRNAs) capable of negatively regulating gene expression. Recently, microRNA-like small RNAs (milRNAs) were discovered in several filamentous fungi but not yet in Trichoderma reesei, an industrial filamentous fungus that can secrete abundant hydrolases. To explore the presence of milRNA in T. reesei and evaluate their expression under induction of cellulose, two T. reesei sRNA libraries of cellulose induction (IN) and non-induction (CON) were generated and sequenced using Solexa sequencing technology. A total of 726 and 631 sRNAs were obtained from the IN and CON samples, respectively. Global expression analysis showed an extensively differential expression of sRNAs in T. reesei under the two conditions. Thirteen predicted milRNAs were identified in T. reesei based on the short hairpin structure analysis. The milRNA profiles obtained in deep sequencing were further validated by RT-qPCR assay. Computational analysis predicted a number of potential targets relating to many processes including regulation of enzyme expression. The presence and differential expression of T. reesei milRNAs imply that milRNA might play a role in T. reesei growth and cellulase induction. This work lays foundation for further functional study of fungal milRNAs and their industrial application.