Abstract
RNA silencing is a conserved surveillance mechanism against viruses in plants. It is mediated by Dicer-like (DCL) proteins producing small interfering RNAs (siRNAs), which guide specific Argonaute (AGO)-containing complexes to inactivate viral genomes and may promote the silencing of host mRNAs. In this study, we obtained the profile of virus-derived siRNAs (vsiRNAs) from Sugarcane mosaic virus (SCMV) in infected maize (Zea mays L.) plants by deep sequencing. Our data showed that vsiRNAs which derived almost equally from sense and antisense SCMV RNA strands accumulated preferentially as 21- and 22-nucleotide (nt) species and had an adenosine bias at the 5′-terminus. The single-nucleotide resolution maps revealed that vsiRNAs were almost continuously but heterogeneously distributed throughout the SCMV genome and the hotspots of sense and antisense strands were mainly distributed in the HC-Pro coding region. Moreover, dozens of host transcripts targeted by vsiRNAs were predicted, several of which encode putative proteins involved in ribosome biogenesis and in biotic and abiotic stresses. We also found that ZmDCL2 mRNAs were up-regulated in SCMV-infected maize plants, which may be the cause of abundant 22-nt vsiRNAs production. However, ZmDCL4 mRNAs were down-regulated slightly regardless of the most abundant 21-nt vsiRNAs. Our results also showed that SCMV infection induced the accumulation of AGO2 mRNAs, which may indicate a role for AGO2 in antiviral defense. To our knowledge, this is the first report on vsiRNAs in maize plants.
Highlights
RNA silencing is a conserved antiviral defense mechanism in plants
It was reported that RDR1 and RDR6 exhibited specificity in targeting the genome sequences of Cucumber mosaic virus (CMV) in amplifying viral secondary small interfering RNAs (siRNAs) [13]. virus-derived small interfering RNAs (vsiRNAs) are associated with specific AGO complexes to function in RNA silencing [22,23,24,25]
The results indicated that the accumulation of ZmDCL2 mRNA was significantly up-regulated, while ZmDCL4 was down-regulated and there were no significant differences in the levels of ZmDCL1, ZmDCL3a and ZmDCL3b mRNAs between mock- and SCMVinoculated maize plants (Figure 4A)
Summary
RNA silencing is a conserved antiviral defense mechanism in plants. The antiviral silencing can be triggered by viral doublestranded RNA (dsRNA) and highly structured single-stranded RNA (ssRNA), which can be recognized and cleaved by Dicer-like (DCL) proteins and processed into virus-derived small interfering RNAs (vsiRNAs) that vary in length from 21 to 24 nucleotides (nt) in virus-infected plants [1,2,3,4]. PLOS ONE | www.plosone.org vsiRNAs Produced in SCMV-Infected Maize components involved in RNA silencing participate in antiviral defense in plants, including dsRNA-binding protein 4 (DRB4), suppressor of gene silencing 3 (SGS3) and HUA ENHANCER 1 (HEN1) [11,22,35,36,37,38,39]. Co-expression assay demonstrated that the HC-Pro encoded by SCMV suppressed the RNA silencing induced by sense RNA and dsRNA, and down-regulated the accumulation of RDR6 mRNA [48]. These results suggested that RDR1 and RDR6 may be involved in SCMV infection and plant antiviral defense. The relative accumulation level of ZmDCLs and ZmAGO2 mRNAs in SCMVinfected maize plants were detected
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