RNA Interference: A Versatile Tool for Functional Genomics and Unraveling the Genes Required for Viral Disease Resistance in Plants

Main Article Content

Tushar Ranjan
Namaste Kumari
Sangita Sahni
Bishun Deo Prasad

Abstract

Virus-induced gene silencing (VIGS) is a powerful reverse genetics technology used to unravel the functions of genes. It uses viruses as vectors to carry targeted plant genes. The virus vector is used to induce RNA-mediated silencing of a gene or genes in the host plant. The process of silencing is triggered by dsRNA molecules, the mechanism is explained in this chapter. Over the years a large number of viruses have been modified for use as VIGS vectors and a list of these vectors is also included. As the name suggests, virus-induced gene silencing uses the host plant’s natural defense mechanisms against viral infection to silence plant genes. VIGS is methodologically simple and is widely used to determine gene functions, including disease resistance, abiotic stress, biosynthesis of secondary metabolites and signal transduction pathways. Here, we made an attempt to describe the basic underlying molecular mechanism of VIGS, the methodology and various experimental requirements, as well as its advantages and disadvantages. Finally, we discuss the future prospects of VIGS in relation to CRISPR/Cas9 technology. Besides using it to overexpress or silence genes, VIGS has emerged as the preferred delivery system for the cutting edge CRISPR/Cas9 genome editing technology.

Keywords:
RNAi, virus-induced gene silencing (VIGS), plant virus, CRISPR/Cas system.

Article Details

How to Cite
Ranjan, T., Kumari, N., Sahni, S., & Prasad, B. (2019). RNA Interference: A Versatile Tool for Functional Genomics and Unraveling the Genes Required for Viral Disease Resistance in Plants. Current Journal of Applied Science and Technology, 35(5), 1-20. https://doi.org/10.9734/cjast/2019/v35i530197
Section
Review Article

References

Napoli C, Lemieux C, Jorgensen R. Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell. 1990;2(4):279–289.

Ecker JR, Davis RW. Inhibition of gene expression in plant cells by expression of antisense RNA. Proc Natl Acad Sci USA. 1986;83(15):5372–5376.

Romano N, Macino G. Quelling: Transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol. 1992;6(22):3343-3353.

Van Blokland R, Vander Geest N, Mol JNM, Kooter JM. Transgene-mediated suppression of chalcone synthase expression in Petunia hybrida results from an increase in RNA turnover. Plant J. 1994;6(6):861–877.

Covey S, Al-Kaff N, Lángara A, Turner D. Plants combat infection by gene silencing. Nature. 1997;385(6619):781–782.

Ratcliff F, Harrison B, Baulcombe D. A similarity between viral defense and gene silencing in plants. Science. 1997; 276(5318):1558–1560.

Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998;391(6669):806–11.

Guo S, Kemphues K. Par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell. 1995;81(4):611–620.

Pal-Bhadra M, Bhadra U, Birchler J. Cosuppression in Drosophila: Gene silencing of Alcohol dehydrogenase by white-Adh transgenes is Polycomb dependent. Cell. 1997;90(3):479–490.

Tabara H, Sarkissian M, Kelly WG, Fleenor J, Grishok A, Timmons L, Fire A, Mello CC. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell. 1999;99(2):123-132.

Hamilton AJ, Baulcombe DC. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science. 1999; 286(5441):950-952.

Hammond SM, Bernstein E, Beach D, Hannon GJ. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature. 2000; 404(6775):293-6.

Zamore PD, Tuschl T, Sharp PA, Bartel DP. RNAi: Double-stranded RNA directs the ATP dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell. 2000; 101(1):25-33.

Tomari Y, Zamore PD. Perspective: Machines for RNAi. Genes Dev. 2005;19: 517–529.

Meister G, Tuschl T. Mechanisms of gene silencing by double-stranded RNA. Nature. 2004;431:343-349.

Cenik ES, Fukunaga R, Lu G, Dutcher R, Wang Y, Tanaka Hall TM, Zamore PD. "Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease. Mol. Cell. 2011; 42(2):172–84.

Zhang H, Kolb F, Jaskiewicz L, Westhof E, Filipowicz W. Single processing center models for human Dicer and bacterial RNase III. Cell. 2004;118:57–68.

Tomari Y, Matranga C, Haley B, Martinez N, Zamore PD. A protein sensor for siRNA asymmetry. Science. 2004;306:1377-1380.

Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. Structural basis for double-stranded RNA processing by dicer. Science. 2006; 311(5758):195–198.

Tabara H, Yigit E, Siomi H, Mello CC. The dsRNA binding protein RDE-4 interacts with RDE-1, DCR-1, and a DExH-box helicase to direct RNAi in C. elegans. Cell. 2002;109:861-871.

Höck J, Weinmann L, Ender C, Rüdel S, Kremmer E, Raabe M, Urlaub H, Meister G. Proteomic and functional analysis of Argonaute-containing mRNA-protein complexes in human cells. EMBO Rep. 2007;8(11):1052-1060.

Martinez J, Patkaniowska A, Urlaub H, Lührmann R, Tuschl T. Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell. 2002;110 (5):563-574.

Pham JW, Pellino JL, Lee YS, Carthew RW, Sontheimer EJ. A Dicer-2-dependent 80s complex cleaves targeted mRNAs during RNAi in Drosophila. Cell. 2004; 117(1):83-94.

Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell. 2005;123:631–640.

Rivas FV, Tolia NH, Song JJ, Aragon JP, Liu J, Hannon GJ, Joshua-Tor L. Purified Argonaute 2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol. 2005;12(4):340-349.

Vaucheret H. Plant argonautes. Trends Plant Sci. 2008;13(7):350-358.

Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell. 2001;106(1):23-34.

Hutvagner G, Simard MJ. Argonaute proteins: Key players in RNA silencing. Nature Reviews Molecular Cell Biology. 2000;9(1):22–32.

Ding SW. RNA-based antiviral immunity. Nat Rev Immunol. 2010;10:632–644.

Yigit E, Batista PJ, Bei Y, Pang KM, Chen CC, Tolia NH, Joshua-Tor L, Mitani S, Simard MJ, Mello CC. Analysis of the C. elegans Argonaute family reveals that distinct Argonautes act sequentially during RNAi. Cell. 2006;127:747–757.

Meins F, Si-Ammour A, Blevins T. RNA silencing systems and their relevance to plant development. Annual Review of Cell and Developmental Biology. 2005;21(1): 297–318.

Aravin AA, Hannon GJ, Brennecke J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science. 2007;318:761–764.

Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 2008;322:1387–1392.

Tang G. siRNA and miRNA: an insight into RISCs. Trends in Biochemical Sciences. 2002;30(2):106–114.

Meister G, Landthaler M, Patkaniowska A, Dorsett Yair, Teng G, Tuschl T. Human Argonaute2 Mediates RNA Cleavage Targeted by miRNAs and siRNAs. Molecular Cell. 2004;15(2):185–197.

Richard WC, Sontheimer EJ. Origins and Mechanisms of miRNAs and siRNAs. Cell. 2009;136(4):642–655.

Filipowicz W, Jaskiewicz L, Kolb FA, Pillai SR. Post-transcriptional gene silencing by siRNAs and miRNAs. Current Opinion in Structural Biology. 2005;15:331–341.

Lippman Z, Martienssen R. The role of RNA interference in heterochromatic silencing. Nature. 2004;431:364-370.

Hannon GJ, Rossi JJ. Unlocking the potential of the human genome with RNA interference. Nature. 2004;431(7006):371-378.

Lund E, Güttinger S, Calado A, Dahlberg JE, Kutay U. Nuclear export of microRNA precursors. Science. 2004;303 (5654):95-98.

Hammond SM. Dicing and slicing: the core machinery of the RNA interference pathway. FEBS Lett. 2005;579(26):5822-5829.

Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2004;2(5): E104.

Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell. 2003;115:209-216.

Nykanen A, Haley B, Zamore PD. ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell. 2001;107(3):309-321.

Elbashir SM, Lendeckel W, Tuschl T. RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev. 2001;15(2): 188-200.

Duan CG, Wang CH, Guo HS. Application of RNA silencing to plant disease resistance. Silence. 2012;3(1):5.

Liu J, Valencia-Sanchez MA, Hannon GJ, Parker R. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat Cell Biol. 2005; 7(7):719-723.

Sen GL, Blau HM. Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat Cell Biol. 2005;7(6):633-636.

Mette MF, Aufsatz W, Vander-Winden J, Matzke MA, Matzke AJ. Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 2000;19(19):5194-201.

Wassenegger M, Heimes S, Riedel L, Sänger HL. RNA-directed de novo methylation of genomic sequences in plants. Cell. 1994;76(3):567-576.

Baulcombe D. RNA silencing in plants. Nature. 2004;431:356-363.

Vargason JM, Szittya G, Burgyan J, Tanaka HTM. Size selective recognition of siRNA by an RNA silencing suppressor. Cell. 2003;115:799-811.

Silhavy D, Molnár A, Lucioli A, Szittya G, Hornyik C, Tavazza M, Burgyán J. A viral protein suppresses RNA silencing and binds silencing-generated, 21- to 25-nucleotide double-stranded RNAs. EMBO J. 2002;21:3070-3080.

Dunoyer P, Brosnan CA, Schott G, Wang Y, Jay F, Alioua A, Himber C, Voinnet O. An endogenous, systemic RNAi pathway in plants. EMBO J. 2010;29:1699-1712.

Chen HY, Yang J, Lin C, Yuan YA. Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b. EMBO Rep. 2008;9:754-760.

Azevedo J, Garcia D, Pontier D, Ohnesorge S, Yu A, Garcia S, Braun L, Bergdoll M, Hakimi MA, Lagrange T, Voinnet O. Argonaute quenching and global changes in Dicer homeostasis caused by a pathogen-encoded GW repeat protein. Genes Dev. 2010;24:904-915.

Van Kammen A. Virus-induced gene silencing in infected and transgenic plants. Trends Plant Sci. 1997;2:409-411.

Baulcombe D. Fast forward genetics based on virusinduced gene silencing. Curr. Opin. Plant Biol. 1999;2:109-113.

Ruiz MT, Voinnet O, Baulcombe DC. Initiation and maintenance of virus-induced gene silencing. Plant Cell. 1998;10:937– 946.

Voinnet O. RNA silencing as a plant immune system against viruses. Trends Genet. 2001;17(8):449-459.

Brigneti G, Voinnet O, Li WX, Ji L, Ding SW, Baulcombe DC. Viral pathogenicity determinants are suppressors of transgene silencing in Nicotiana benthamiana. EMBO J. 1998;17(22):6739–6746.

Kjemtrup S, Sampson KS, Peele CG, Nguyen LV, Conkling MV, Thompson WF, Robertson D. Gene silencing from plant DNA carried by a Geminivirus. Plant J. 1998;91–100.

Peele C, Jordan CV, Muangsan N, Turnage M, Egelkrout E, Eagle P, Hanley-Bowdoin L, Robertson D. Silencing of a meristematic gene using geminivirus-derived vectors. Plant J. 2001;24:357–366.

Abel PP, Nelson RS, De B, Hoffmann N, Rogers SG, Fraley RT, Beachy RN. Delay of disease development in transgenic plants that express the tobacco mosaic virus coat protein gene. Science. 1986; 232:738–743.

Bucher E, Lohuis D, van Poppel PM, Geerts-Dimitriadou C, Goldbach R, Prins M. Multiple virus resistance at a high frequency using a single transgene construct. J Gen Virol. 2006;87:3697–3701.

Himber C, Dunoyer P, Moissiard G, Ritzenthaler C, Voinnet O. Transitivitydependent and-independent cell-to-cell movement of RNA silencing. EMBO J. 2003;22:4523–4533.

Schwab R. Highly specific gene silencing by Artificial MicroRNAs in arabidopsis. Plant Cell. 2006;18:1121–1133.

Liu Y, Schiff M, Dinesh-Kumar SP. Virus-induced gene silencing in tomato. The Plant Journal. 2003;31(6):777–786.

Ratcliff F, Mart´ın-Hern´andez AM, Baulcombe DC. Tobacco rattle virus as a vector for analysis of gene function by silencing. The Plant Journal. 2001;25(2): 237–245.

Fofana BF, Sangar´e A, Collier R, Taylor C, Fauquet CM. A geminivirus-induced gene silencing system for gene function validation in cassava. Plant Molecular Biology. 2004;56(4):613–624.

Tao X, Zhou X. A modified viral satellite DNA that suppresses gene expression in plants. The Plant Journal. 2004;38(5): 850–860.

Matzke MA, Birchler JA. RNAi-mediated pathways in the nucleus. Nat Rev Genet. 2005;6:24-35.