Abstract
BackgroundSatellite RNAs (satRNAs), virus parasites, are exclusively associated with plant virus infection and have attracted much interest over the last 3 decades. Upon virus infection, virus-specific small interfering RNAs (vsiRNAs) are produced by dicer-like (DCL) endoribonucleases for anti-viral defense. The composition of vsiRNAs has been studied extensively; however, studies of satRNA-derived siRNAs (satsiRNAs) or siRNA profiles after satRNA co-infection are limited. Here, we report on the small RNA profiles associated with infection with Bamboo mosaic virus (BaMV) and its two satellite RNAs (satBaMVs) in Nicotiana benthamiana and Arabidopsis thaliana.Methodology/Principal FindingsLeaves of N. benthamiana or A. thaliana inoculated with water, BaMV alone or co-inoculated with interfering or noninterfering satBaMV were collected for RNA extraction, then large-scale Solexa sequencing. Up to about 20% of total siRNAs as BaMV-specific siRNAs were accumulated in highly susceptible N. benthamiana leaves inoculated with BaMV alone or co-inoculated with noninterfering satBaMV; however, only about 0.1% of vsiRNAs were produced in plants co-infected with interfering satBaMV. The abundant region of siRNA distribution along BaMV and satBaMV genomes differed by host but not by co-infection with satBaMV. Most of the BaMV and satBaMV siRNAs were 21 or 22 nt, of both (+) and (−) polarities; however, a higher proportion of 22-nt BaMV and satBaMV siRNAs were generated in N. benthamiana than in A. thaliana. Furthermore, the proportion of non-viral 24-nt siRNAs was greatly increased in N. benthamiana after virus infection.Conclusions/SignificanceThe overall composition of vsiRNAs and satsiRNAs in the infected plants reflect the combined action of virus, satRNA and different DCLs in host plants. Our findings suggest that the structure and/or sequence demands of various DCLs in different hosts may result in differential susceptibility to the same virus. DCL2 producing 24-nt siRNAs under biotic stresses may play a vital role in the antiviral mechanism in N. benthamiana.
Highlights
RNA silencing is a sequence-specific gene regulatory mechanism involved in development, maintenance of genome integrity and cellular defense against virus infection in plants and animals [1,2,3,4,5]
In Bamboo mosaic virus (BaMV)-inoculated or BSF4 co-inoculated N. benthamiana, BaMV Small interfering RNAs (siRNAs) were barely detected in the inoculated leaves, and BaMV siRNAs were not detected in the BSL6 co-inoculated leaves (Figure 1A)
The level of siRNAs derived from BSF4 was substantial in the co-inoculated and systemic leaves; neither BaMV nor satBaMV siRNAs could be detected in BaMV-infected and BSL6-co-infected inoculated or systemic leaves of N. benthamiana (Figures 1A and 1B), probably because of the low accumulation of both BaMV and satBaMV in the BSL6-co-inoculated plants
Summary
RNA silencing is a sequence-specific gene regulatory mechanism involved in development, maintenance of genome integrity and cellular defense against virus infection in plants and animals [1,2,3,4,5]. Small interfering RNAs (siRNAs), diverse in size, sequence, biogenesis and biological actions, are the key mediators of RNA silencing [6]. The model plant Arabidopsis thaliana contains four DICER-like proteins (DCLs) faithfully generating size-specific siRNAs from both endogenous and exogenous dsRNA precursors [9]. Virus-specific small interfering RNAs (vsiRNAs) are produced by dicer-like (DCL) endoribonucleases for anti-viral defense. We report on the small RNA profiles associated with infection with Bamboo mosaic virus (BaMV) and its two satellite RNAs (satBaMVs) in Nicotiana benthamiana and Arabidopsis thaliana
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