Identification of microRNA-Like RNAs in the filamentous fungus Trichoderma reesei by solexa sequencing

Kang Kang; Jiasheng Zhong; Liang Jiang; Gang Liu; Christine Yuan Gou; Qiong Wu; You Wang; Jun Luo; Deming Gou

doi:10.1371/journal.pone.0076288

Identification of microRNA-Like RNAs in the filamentous fungus Trichoderma reesei by solexa sequencing

PLoS One. 2013 Oct 2;8(10):e76288. doi: 10.1371/journal.pone.0076288. eCollection 2013.

Authors

Kang Kang¹, Jiasheng Zhong, Liang Jiang, Gang Liu, Christine Yuan Gou, Qiong Wu, You Wang, Jun Luo, Deming Gou

Affiliation

¹ 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.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling
Gene Expression Regulation, Fungal
High-Throughput Nucleotide Sequencing*
MicroRNAs / chemistry
MicroRNAs / genetics*
Nucleic Acid Conformation
RNA, Fungal / chemistry
RNA, Fungal / genetics*
Trichoderma / genetics*
Trichoderma / growth & development

Substances

MicroRNAs
RNA, Fungal

Grants and funding

This study was supported in part by National Basic Research Program of China (973 Program, 2012CB124701); National Natural Science Foundation of China No. 81170047, 81370151 (to D.G.); Shenzhen overseas high-level talents innovation program No.YFZZ20111009 (to D.G.); Shenzhen Municipal Basic Research Program No.JC201006010725A (to D.G.); Shenzhen Municipal Basic Research Program No. JCYJ20130329120507746 (to K.K.); and Postdoctoral Science Foundation of China No. 2013M542203 (to K.K.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.