Viral Infection Induces Expression of Novel Phased MicroRNAs from Conserved Cellular MicroRNA Precursors

PLoS Pathogens

Hong Zheng¹  Liping Wei¹  Yi Li¹  Jiayao Zhang²  Ge Gao³  Peng Du³  Jianguo Wu³  Shuqi Zhao⁴ 

[1] Center for Bioinformatics, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China;Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China;Peking-Yale Joint Center for Plant Molecular Genetics and Agrobiotechnology, The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China;School of Statistics, Renmin University of China, Beijing, China

关键词: MicroRNAs;    Rice;    Small interfering RNAs;    RNA sequencing;    RNA viruses;    Sequence databases;    Small nucleolar RNAs;    cDNA libraries;   

DOI  :  10.1371/journal.ppat.1002176

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

RNA silencing, mediated by small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs), is a potent antiviral or antibacterial mechanism, besides regulating normal cellular gene expression critical for development and physiology. To gain insights into host small RNA metabolism under infections by different viruses, we used Solexa/Illumina deep sequencing to characterize the small RNA profiles of rice plants infected by two distinct viruses, Rice dwarf virus (RDV, dsRNA virus) and Rice stripe virus (RSV, a negative sense and ambisense RNA virus), respectively, as compared with those from non-infected plants. Our analyses showed that RSV infection enhanced the accumulation of some rice miRNA*s, but not their corresponding miRNAs, as well as accumulation of phased siRNAs from a particular precursor. Furthermore, RSV infection also induced the expression of novel miRNAs in a phased pattern from several conserved miRNA precursors. In comparison, no such changes in host small RNA expression was observed in RDV-infected rice plants. Significantly RSV infection elevated the expression levels of selective OsDCLs and OsAGOs, whereas RDV infection only affected the expression of certain OsRDRs. Our results provide a comparative analysis, via deep sequencing, of changes in the small RNA profiles and in the genes of RNA silencing machinery induced by different viruses in a natural and economically important crop host plant. They uncover new mechanisms and complexity of virus-host interactions that may have important implications for further studies on the evolution of cellular small RNA biogenesis that impact pathogen infection, pathogenesis, as well as organismal development.

【 授权许可】

CC BY