College of Life Sciences, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, China ; College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
PLoS One. 2013 Oct 2;8(10):e76288. doi: 10.1371/journal.pone.0076288. eCollection 2013.
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.
microRNAs (miRNAs) 是一类非编码的小 RNA（sRNA），能够负向调控基因表达。最近，在几种丝状真菌中发现了 miRNA 样小 RNA（milRNAs），但在工业丝状真菌里氏木霉中尚未发现，里氏木霉能够分泌丰富的水解酶。为了探究 milRNA 在里氏木霉中的存在，并评估其在纤维素诱导下的表达情况，我们构建了里氏木霉纤维素诱导（IN）和非诱导（CON）的两个 sRNA 文库，并使用 Solexa 测序技术进行测序。从 IN 和 CON 样品中分别获得了 726 条和 631 条 sRNA。全局表达分析显示，在这两种条件下，里氏木霉中的 sRNA 表达广泛存在差异。基于短发夹结构分析，在里氏木霉中鉴定出了 13 个预测的 milRNAs。通过 RT-qPCR 实验进一步验证了深度测序获得的 milRNA 图谱。计算分析预测了许多与酶表达调控等多个过程相关的潜在靶标。里氏木霉 milRNAs 的存在和差异表达表明，milRNA 可能在里氏木霉的生长和纤维素酶诱导中发挥作用。这项工作为进一步研究真菌 milRNAs 的功能及其工业应用奠定了基础。
