Background Small RNA-mediated gene silencing plays evolutionarily conserved roles in gene regulation and defense against invasive nucleic acids. Virus-derived small interfering RNAs (vsiRNAs) are one of the key elements involved in RNA silencing-based antiviral activities in plant and insect. vsiRNAs produced after viruses infecting hosts from a single kingdom (i.e., plant or animal) are well described. In contrast, vsiRNAs derived from viruses capable of infecting both plants and their insect vectors have not been characterized. Methodology/Principal Findings We examined Rice stripe virus (RSV)-derived small interfering RNAs in three different hosts, Oryza sativa, Nicotiana benthamiana and a natural RSV transmitting vector Laodelphgax striatellus, through deep sequencing. Our results show that large amounts of vsiRNAs generated in these hosts after RSV infection. The vsiRNAs from N. benthamiana and L. striatellus mapped equally to the genomic- and antigenomic-strand of RSV RNAs. They showed, however, a significant bias in those from O. sativa. Furthermore, our results demonstrate that the number and size distributions of vsiRNAs in the three hosts were very different. In O. sativa and N. benthamiana, most vsiRNAs were mapped to the discrete regions in the RSV genome sequence, and most of the vsiRNAs from these two hosts were generated from RSV genomic RNAs 3 and 4. In contrast, the vsiRNAs identified in L. striatellus distributed uniformly along the whole genome of RSV. We have also shown that silencing Agronaute 2 in L. striatellus enhanced RSV accumulation in this host. Conclusions/Significance Our study demonstrates that the core RNA-induced gene silencing (RNAi) machinery is present in L. striatellus. We also provide evidence that the RNAi-mediated immunity against RSV is present in L. striatellus. We propose that a common small RNA-mediated virus defense mechanism exists in both helipterum insects and plants, but the vsiRNAs are generated differentially in different hosts.
References
[1]
Hohn T (2007) Plant virus transmission from the insect point of view. Proc Natl Acad Sci U S A 104: 17905–17906.
Galiana-Arnoux D, Dostert C, Schneemann A, Hoffmann JA, Imler JL (2006) Essential function in vivo for Dicer-2 in host defense against RNA viruses in drosophila. Nat Immunol 7: 590–597.
[4]
Wang XH, Aliyari R, Li WX, Li HW, Kim K, et al. (2006) RNA interference directs innate immunity against viruses in adult Drosophila. Science 312: 452–454.
[5]
Luan JB, Li JM, Varela N, Wang YL, Li FF, et al. (2011) Global analysis of the transcriptional response of whitefly to Tomato yellow leaf curl China virus reveals the relationship of coevolved adaptations. J Virol 85: 3330–3340.
[6]
Ding SW, Voinnet O (2007) Antiviral immunity directed by small RNAs. Cell 130: 413–426.
[7]
Brodersen P, Voinnet O (2006) The diversity of RNA silencing pathways in plants. Trends Genet 22: 268–280.
[8]
Mi S, Cai T, Hu Y, Chen Y, Hodges E, et al. (2008) Sorting of small RNAs into Arabidopsis argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133: 116–127.
[9]
Bouche N, Lauressergues D, Gasciolli V, Vaucheret H (2006) An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs. EMBO J 25: 3347–3356.
[10]
Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, et al. (2006) Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313: 68–71.
[11]
Fusaro AF, Matthew L, Smith NA, Curtin SJ, Dedic-Hagan J, et al. (2006) RNA interference-inducing hairpin RNAs in plants act through the viral defence pathway. EMBO Rep 7: 1168–1175.
[12]
Diaz-Pendon JA, Li F, Li WX, Ding SW (2007) Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell 19: 2053–2063.
[13]
van Rij RP, Saleh MC, Berry B, Foo C, Houk A, et al. (2006) The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes Dev 20: 2985–2995.
[14]
Li J, Chen Q, Lin Y, Jiang T, Wu G, et al. (2011) RNA interference in Nilaparvata lugens (Homoptera: Delphacidae) based on dsRNA ingestion. Pest Manag Sci 67: 852–859.
[15]
Wei TY, Yang JG, Liao FR, Gao FL, Lu LM, et al. (2009) Genetic diversity and population structure of Rice stripe virus in China. J Gen Virol 90: 1025–1034.
[16]
Sun F, Yuan X, Zhou T, Fan YJ, Zhou YJ (2011) Arabidopsis is susceptible to Rice stripe virus Infections. Journal of Phytopathology 159: 767–772.
[17]
Hibino H (1996) Biology and epidemiology of rice viruses. Annu Rev Phytopathol 34: 249–274.
[18]
Falk BW, Tsai JH (1998) Biology and molecular biology of viruses in the genus Tenuivirus. Annual Review of Phytopathology 36: 139–163.
[19]
Li S, Xiong RY, Wang XF, Zhou YJ (2011) Five proteins of Laodelphax striatellus are potentially involved in the interactions between Rice stripe virus and vector. Plos One 6.
[20]
Goodin MM, Zaitlin D, Naidu RA, Lommel SA (2008) Nicotiana benthamiana: its history and future as a model for plant-pathogen interactions. Mol Plant Microbe Interact 21: 1015–1026.
[21]
Yan F, Zhang H, Adams MJ, Yang J, Peng J, et al. (2010) Characterization of siRNAs derived from Rice stripe virus in infected rice plants by deep sequencing. Arch Virol 155: 935–940.
[22]
Yang X, Wang Y, Guo W, Xie Y, Xie Q, et al. (2011) Characterization of small interfering RNAs derived from the geminivirus/betasatellite complex using deep sequencing. Plos One 6: e16928.
[23]
Hamera S, Song X, Su L, Chen X, Fang R (2012) Cucumber mosaic virus suppressor 2b binds to AGO4-related small RNAs and impairs AGO4 activities. Plant J 69: 104–115.
[24]
Seto AG, Kingston RE, Lau NC (2007) The coming of age for Piwi proteins. Mol Cell 26: 603–609.
[25]
Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nature Reviews Genetics 10: 94–108.
[26]
Smardon A, Spoerke JM, Stacey SC, Klein ME, Mackin N, et al. (2000) EGO-1 is related to RNA-directed RNA polymerase and functions in germ-line development and RNA interference in C. elegans. Curr Biol 10: 169–178.
[27]
Sijen T, Fleenor J, Simmer F, Thijssen KL, Parrish S, et al. (2001) On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107: 465–476.
[28]
Simmer F, Tijsterman M, Parrish S, Koushika SP, Nonet ML, et al. (2002) Loss of the putative RNA-directed RNA polymerase RRF-3 makes C. elegans hypersensitive to RNAi. Curr Biol 12: 1317–1319.
[29]
Raja P, Sanville BC, Buchmann RC, Bisaro DM (2008) Viral genome methylation as an epigenetic defense against geminiviruses. J Virol 82: 8997–9007.
[30]
Akbergenov R, Si-Ammour A, Blevins T, Amin I, Kutter C, et al. (2006) Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Research 34: 462–471.
[31]
Takeda A, Iwasaki S, Watanabe T, Utsumi M, Watanabe Y (2008) The mechanism selecting the guide strand from small RNA duplexes is different among argonaute proteins. Plant Cell Physiol 49: 493–500.
[32]
Wu L, Zhang Q, Zhou H, Ni F, Wu X, et al. (2009) Rice microRNA effector complexes and targets. Plant Cell 21: 3421–3435.
[33]
Qu F, Ye X, Morris TJ (2008) Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A 105: 14732–14737.
[34]
Morel JB, Godon C, Mourrain P, Beclin C, Boutet S, et al. (2002) Fertile hypomorphic ARGONAUTE (ago1) mutants impaired in post-transcriptional gene silencing and virus resistance. Plant Cell 14: 629–639.
[35]
Tomari Y, Du T, Zamore PD (2007) Sorting of Drosophila small silencing RNAs. Cell 130: 299–308.
[36]
Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD (2010) Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16: 43–56.
[37]
Falk BW, Klaassen VA, Tsai JH (1989) Complementary DNA cloning and hybridization analysis of Maize stripe virus RNAs. Virology 173: 338–342.
[38]
Wang XB, Wu Q, Ito T, Cillo F, Li WX, et al. (2010) RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci U S A 107: 484–489.
[39]
Siu RW, Fragkoudis R, Simmonds P, Donald CL, Chase-Topping ME, et al. (2011) Antiviral RNA interference responses induced by Semliki forest virus infection of mosquito cells: characterization, origin, and frequency-dependent functions of virus-derived small interfering RNAs. J Virol 85: 2907–2917.
[40]
Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Research 36: W70–74.
[41]
Jiang L, Qian D, Zheng H, Meng LY, Chen J, et al. (2012) RNA-dependent RNA polymerase 6 of rice (Oryza sativa) plays role in host defense against negative-strand RNA virus, Rice stripe virus. Virus Res 163: 512–519.
[42]
Xue J, Bao YY, Li BL, Cheng YB, Peng ZY, et al. (2010) Transcriptome analysis of the brown planthopper Nilaparvata lugens. Plos One 5: e14233.
[43]
Xu Y, Zhou W, Zhou Y, Wu J, Zhou X (2012) Transcriptome and comparative gene expression analysis of Sogatella furcifera (Horvath) in response to Southern rice black-streaked dwarf virus. Plos One 7: e36238.
[44]
Xiong R, Wu J, Zhou Y, Zhou X (2008) Identification of a movement protein of the tenuivirus Rice stripe virus. J Virol 82: 12304–12311.
[45]
Li R, Yu C, Li Y, Lam TW, Yiu SM, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966–1967.
[46]
Xiong R, Wu J, Zhou Y, Zhou X (2009) Characterization and subcellular localization of an RNA silencing suppressor encoded by Rice stripe tenuivirus. Virology 387: 29–40.
[47]
Zhang F, Guo H, Zheng H, Zhou T, Zhou Y, et al. (2010) Massively parallel pyrosequencing-based transcriptome analyses of small brown planthopper (Laodelphax striatellus), a vector insect transmitting rice stripe virus (RSV). Bmc Genomics 11: 303.
