Characterization of Small Interfering RNAs Derived from Sugarcane Mosaic Virus in Infected Maize Plants by Deep Sequencing

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.

Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection

“…7), while for 21-22 nt vsRNAs the enrichment was not significant, even if preference for 5 terminal A and U was observed (not shown). Preference for A/U terminal nucleotides compared to G/C was described in previous vsRNA analyses, for instance for RSV in rice and N. benthamiana plants (Yan et al, 2010;Xu et al, 2012), tomato yellow leaf curl China virus in tomato (Yang et al, 2011), potato virus Y in potato (Naveed et al, 2014), sugarcane mosaic virus in maize (Xia et al, 2014), and TSWV in tomato and N. benthamiana (Mitter et al, 2013;Margaria et al, 2015a). Preferential sorting of small RNAs into AGO complexes has been shown to be directed by the 5 terminal nucleotide (Takeda et al, 2008;Mi et al, 2008;Mallory and Vaucheret, 2010).…”

A Violaxanthin Deepoxidase Interacts with a Viral Suppressor of RNA Silencing to Inhibit Virus Amplification

“…The probes were labeled, and the blots were probed and washed as reported previously (Xia et al, 2016). Approximately 30-mg total RNA samples were prepared to detect GFP siRNAs, and the blots were probed and washed as described previously (Xia et al, 2014). Probe sequences used for detection of the GFP siRNAs are shown in Supplemental Table S3.…”

Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana

“…Analysis of vsRNAs accumulation in cotton infected by cotton leaf roll dwarf virus (a single-stranded positive sense RNA virus containing six open reading frames) showed equivalent amounts of sense and antisense vsRNAs (Silva et al, 2011), as also Table 1 for specific treatments. observed in maize infected by sugarcane mosaic virus (Xia et al, 2014). DsRNA-like secondary structures within the single-stranded viral RNA, have been reported to likely be the main source of vsRNAs; in other cases, dsRNA replication-intermediates could be the source of vsRNAs, thus resulting in equal amounts of sense and antisense sRNA reads (Molnar et al, 2005;Szittya et al, 2010;Wang et al, 2010;Pantaleo et al, 2010).…”