Skip to main content
SpringerLink
Log in

Suppressor to Survival: RNAi as a Molecular Weapon in Arms Race Between Virus and Host

  • Chapter
  • First Online:
RNA-Based Technologies for Functional Genomics in Plants

Part of the book series: Concepts and Strategies in Plant Sciences ((CSPS))

  • 479 Accesses

Abstract

The sessile nature of the plant kingdom has developed various defense strategies in response to viral attack with different degrees of success. RNA silencing is an essential part of the cellular mechanism that controls transcription and plays an important role in defense against virus infection. Viruses evade the plant defense strategy, by encoding various “suppressor” molecules, which interact with the small RNA species or the components of host RNA silencing machinery. The present chapter aims to compile the plant defense strategies with the help of small RNA-omics and their mode of action involved during plant–pathogen interactions. Finally, we discuss the specific applications of the RNAi-based strategies and various suppression proteins used during the counterattack of plant viruses.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Agrawal N, Dasaradhi P, Mohmmed A, Malhotra P, Bhatnagar RK, Mukherjee SK (2003) RNA interference: biology, mechanism, and applications. Microbiol Mol Biol Rev 67(4):657–685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Anandalakshmi R, Marathe R, Ge X, Herr JM, Mau C, Mallory A, Pruss G, Bowman L, Vance VB (2000) A calmodulin-related protein that suppresses posttranscriptional gene silencing in plants. Science 290(5489):142–144

    Article  CAS  PubMed  Google Scholar 

  • Anandalakshmi R, Pruss GJ, Ge X, Marathe R, Mallory AC, Smith TH, Vance VB (1998) A viral suppressor of gene silencing in plants. Proc Natl Acad Sci 95(22):13079–13084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Andolfo G, Ferriello F, Tardella L, Ferrarini A, Sigillo L, Frusciante L, Ercolano MR (2014) Tomato genome-wide transcriptional responses to Fusarium wilt and Tomato Mosaic Virus. PLoS ONE 9(5):e94963. https://doi.org/10.1371/journal.pone.0094963

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baltes NJ, Hummel AW, Konecna E, Cegan R, Bruns AN, Bisaro DM, Voytas DF (2015) Conferring resistance to geminiviruses with the CRISPR–Cas prokaryotic immune system. Nature Plants 1(10):15145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barta A, Sommergruber K, Thompson D, Hartmuth K, Matzke MA, Matzke AJ (1986) The expression of a nopaline synthase—human growth hormone chimaeric gene in transformed tobacco and sunflower callus tissue. Plant Mol Biol 6(5):347–357

    Article  CAS  PubMed  Google Scholar 

  • Baulcombe D (2002) RNA silencing. Curr Biol 12(3):R82–R84

    Article  CAS  PubMed  Google Scholar 

  • Baulcombe D (2004) RNA silencing in plants. Nature 431(7006):356

    Article  CAS  PubMed  Google Scholar 

  • Baulcombe DC (1999) Fast forward genetics based on virus-induced gene silencing. Curr Opin Plant Biol 2(2):109–113

    Article  CAS  PubMed  Google Scholar 

  • Baumberger N, Baulcombe D (2005) Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits microRNAs and short interfering RNAs. Proc Natl Acad Sci 102(33):11928–11933

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berezovski MV, Khan N (2013) Quantitative analysis of microRNA in blood serum with protein-facilitated affinity capillary electrophoresis. In: Nucleic acid detection. Springer, pp 245–259

    Google Scholar 

  • Bisaro DM (2006) Silencing suppression by geminivirus proteins. Virology 344(1):158–168

    Article  CAS  PubMed  Google Scholar 

  • Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu J-K (2005) Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123(7):1279–1291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bortolamiol D, Pazhouhandeh M, Ziegler-Graff V (2008) Viral suppression of RNA silencing by destabilization of ARGONAUTE 1. Plant Signaling Behav 3(9):657–659

    Article  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bucher E, Sijen T, de Haan P, Goldbach R, Prins M (2003) Negative-strand tospoviruses and tenuiviruses carry a gene for a suppressor of gene silencing at analogous genomic positions. J Virol 77(2):1329–1336

    Google Scholar 

  • Buchmann RC, Asad S, Wolf JN, Mohannath G, Bisaro DM (2009) Geminivirus AL2 and L2 proteins suppress transcriptional gene silencing and cause genome-wide reductions in cytosine methylation. J Virol 83(10):5005–5013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cao X, Zhou P, Zhang X, Zhu S, Zhong X, Xiao Q, Ding B, Li Y (2005) Identification of an RNA silencing suppressor from a plant double-stranded RNA virus. J Virol 79(20):13018–13027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Carrington JC, Kasschau KD, Johansen LK (2001) Activation and suppression of RNA silencing by plant viruses. Virology 281(1):1–5

    Article  CAS  PubMed  Google Scholar 

  • Castillo-Gonzalez C et al. (2015) Geminivirus-encoded TrAP suppressor inhibits the histone methyltransferase SUVH4/KYP to counter host defense Elife 4:e06671. https://doi.org/10.7554/elife.06671

  • Chapman EJ, Prokhnevsky AI, Gopinath K, Dolja VV, Carrington JC (2004) Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. Genes Dev 18(10):1179–1186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen HY, Yang J, Lin C, Yuan YA (2008) Structural basis for RNA-silencing suppression by Tomato aspermy virus protein 2b. EMBO Rep 9(8):754–760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chu L, Robinson DK (2001) Industrial choices for protein production by large-scale cell culture. Curr Opin Biotechnol 12(2):180–187

    Article  CAS  PubMed  Google Scholar 

  • Constantin GD, Krath BN, MacFarlane SA, Nicolaisen M, Johansen IE, Lund OS (2004) Virus-induced gene silencing as a tool for functional genomics in a legume species. Plant J 40(4):622–631

    Article  CAS  PubMed  Google Scholar 

  • Curaba J, Chen X (2008) Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6. J Biol Chem 283(6):3059–3066

    Article  CAS  PubMed  Google Scholar 

  • Davies KM (2007) Genetic modification of plant metabolism for human health benefits. Mutat Res, Fundam Mol Mech Mutagen 622(1–2):122–137

    Article  CAS  Google Scholar 

  • Day A, Bejarano E, Buck K, Burrell M, Lichtenstein C (1991) Expression of an antisense viral gene in transgenic tobacco confers resistance to the DNA virus tomato golden mosaic virus. Proc Natl Acad Sci 88(15):6721–6725

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, Voinnet O (2006) Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313(5783):68–71

    Article  CAS  PubMed  Google Scholar 

  • Diaz-Pendon JA, Li F, Li W-X, Ding S-W (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(6):2053–2063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding S-W, Voinnet O (2007) Antiviral immunity directed by small RNAs. Cell 130(3):413–426

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding XS, Schneider WL, Chaluvadi SR, Mian MR, Nelson RS (2006) Characterization of a Brome mosaic virus strain and its use as a vector for gene silencing in monocotyledonous hosts. Mol Plant Microbe Interact 19(11):1229–1239

    Article  CAS  PubMed  Google Scholar 

  • Dong X, van Wezel R, Stanley J, Hong Y (2003) Functional characterization of the nuclear localization signal for a suppressor of posttranscriptional gene silencing. J Virol 77(12):7026–7033

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duan CG, Fang YY, Zhou BJ, Zhao JH, Hou W-N, Zhu H, Ding SW, Guo HS (2012) Suppression of Arabidopsis ARGONAUTE1-mediated slicing, transgene-induced RNA silencing, and DNA methylation by distinct domains of the Cucumber mosaic virus 2b protein. Plant Cell 24(1):259–274

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dunoyer P, Brosnan CA, Schott G, Wang Y, Jay F, Alioua A, Himber C, Voinnet O (2010) Retracted: An endogenous, systemic RNAi pathway in plants. EMBO J 29(10):1699–1712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dunoyer P, Lecellier C-H, Parizotto EA, Himber C, Voinnet O (2004) RETRACTED: Probing the MicroRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing. Plant Cell 16(5):1235–1250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dunoyer P, Voinnet O (2005) The complex interplay between plant viruses and host RNA-silencing pathways. Curr Opin Plant Biol 8(4):415–423

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Elmayan T, Vaucheret H (1996) Expression of single copies of a strongly expressed 35S transgene can be silenced post-transcriptionally. Plant J 9(6):787–797

    Article  CAS  Google Scholar 

  • Fang X, Qi Y (2016) RNAi in plants: an Argonaute-centered view. Plant Cell 28(2):272–285

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fischer R, Emans N (2000) Molecular farming of pharmaceutical proteins. Transgenic Res 9(4–5):279–299

    Article  CAS  PubMed  Google Scholar 

  • Garcia-Ruiz H, Takeda A, Chapman EJ, Sullivan CM, Fahlgren N, Brempelis KJ, Carrington JC (2010) Arabidopsis RNA-dependent RNA polymerases and dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection. Plant Cell 22(2):481–496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10(2):94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gosselé V, Faché I, Meulewaeter F, Cornelissen M, Metzlaff M (2002) SVISS—a novel transient gene silencing system for gene function discovery and validation in tobacco plants. Plant J 32:859–866

    Article  PubMed  Google Scholar 

  • Goto K, Kobori T, Kosaka Y, Natsuaki T, Masuta C (2007) Characterization of silencing suppressor 2b of cucumber mosaic virus based on examination of its small RNA-binding abilities. Plant Cell Physiol 48(7):1050–1060

    Article  CAS  PubMed  Google Scholar 

  • Gu L, Knipple DC (2013) Recent advances in RNA interference research in insects: implications for future insect pest management strategies. Crop Protection 45:36–40

    Article  CAS  Google Scholar 

  • Gustafson AM, Allen E, Givan S, Smith D, Carrington JC, Kasschau KD (2005) ASRP: the Arabidopsis small RNA project database. Nucleic Acids Res 33(suppl_1):D637–D640

    CAS  PubMed  Google Scholar 

  • Haan Pd, Gielen JJL, Prins M, Wijkamp IG, Schepen Av, Peters D, van Grinsven MQJM, Goldbach R (1992) Characterization of RNA–mediated resistance to tomato spotted wilt virus in transgenic tobacco plants. Bio/Technology 10(10): 1133–1137. https://doi.org/10.1038/nbt1092-1133

  • Haas G, Azevedo J, Moissiard G, Geldreich A, Himber C, Bureau M, Fukuhara T, Keller M, Voinnet O (2008) Nuclear import of CaMV P6 is required for infection and suppression of the RNA silencing factor DRB4. EMBO J 27(15):2102–2112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hamilton A, Voinnet O, Chappell L, Baulcombe D (2002) Two classes of short interfering RNA in RNA silencing. EMBO J 21(17):4671–4679

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ (2001) Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293(5532):1146–1150

    Article  CAS  PubMed  Google Scholar 

  • Hao L, Wang H, Sunter G, Bisaro DM (2003) Geminivirus AL2 and L2 proteins interact with and inactivate SNF1 kinase. Plant Cell 15(4):1034–1048

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hartitz MD, Sunter G, Bisaro DM (1999) The tomato golden mosaic virus transactivator (TrAP) is a single-stranded DNA and zinc-binding phosphoprotein with an acidic activation domain. Virology 263(1):1–14

    Article  CAS  PubMed  Google Scholar 

  • Havelda Z, Hornyik C, Crescenzi A, Burgyán J (2003) In situ characterization of Cymbidium Ringspot Tombusvirus infection-induced posttranscriptional gene silencing in Nicotiana benthamiana. J Virol 77(10):6082–6086

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Havelda Z, Hornyik C, Válóczi A, Burgyán J (2005) Defective interfering RNA hinders the activity of a tombusvirus-encoded posttranscriptional gene silencing suppressor. J Virol 79(1):450–457

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holzberg S, Brosio P, Gross C, Pogue GP (2002) Barley stripe mosaic virus-induced gene silencing in a monocot plant. Plant J 30:315–327

    Article  CAS  PubMed  Google Scholar 

  • Huang C, Xie Y, Zhou X (2009) Efficient virus-induced gene silencing in plants using a modified geminivirus DNA1 component. Plant Biotechnol J 7(3):254–265. https://doi.org/10.1111/j.14677652.2008.00395.x

    Article  CAS  PubMed  Google Scholar 

  • Hutvagner G, Simard MJ (2008) Argonaute proteins: key players in RNA silencing. Nat Rev Mol Cell Biol 9(1):22–32

    Article  CAS  PubMed  Google Scholar 

  • Jeon EJ et al (2017) rgs-CaM detects and counteracts viral RNA silencing suppressors in plant immune priming. J Virol:91. https://doi.org/10.1128/jvi.00761-17

  • Ji X, Zhang H, Zhang Y, Wang Y, Gao C (2015) Establishing a CRISPR–Cas-like immune system conferring DNA virus resistance in plants. Nature Plants 1(10):15144

    Article  CAS  PubMed  Google Scholar 

  • Ji Y, Schuster DJ, Scott JW (2007) Ty-3, a begomovirus resistance locus near the Tomato yellow leaf curl virus resistance locus Ty-1 on chromosome 6 of tomato. Mol Breeding 20(3):271–284

    Article  CAS  Google Scholar 

  • Johansen LK, Carrington JC (2001) Silencing on the spot: Induction and suppression of RNA silencing in the Agrobacterium-mediated transient expression system. Plant Physiol 126(3):930–938

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Karjee S, Minhas A, Sood V, Ponia SS, Banerjea AC, Chow VT, Mukherjee SK, Lal SK (2010) The 7a accessory protein of severe acute respiratory syndrome coronavirus acts as an RNA silencing suppressor. J Virol 84(19):10395–10401

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kasschau KD, Carrington JC (1998) A counterdefensive strategy of plant viruses: suppression of posttranscriptional gene silencing. Cell 95(4):461–470

    Article  CAS  PubMed  Google Scholar 

  • Kasschau KD, Xie Z, Allen E, Llave C, Chapman EJ, Krizan KA, Carrington JC (2003) P1/HC-Pro, a viral suppressor of RNA silencing, interferes with Arabidopsis development and miRNA function. Dev Cell 4(2):205–217

    Article  CAS  PubMed  Google Scholar 

  • Khraiwesh B, Zhu J-K, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1819(2):137–148

    Article  CAS  Google Scholar 

  • Kumagai MH, Donson J, Della-Cioppa G, Harvey D, Hanley K, Grill L (1995) Cytoplasmic inhibition of carotenoid biosynthesis with virus-derived RNA. Proc Natl Acad Sci 92(5):1679–1683

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar V, Mishra SK, Rahman J, Taneja J, Sundaresan G, Mishra NS, Mukherjee SK (2015) Mungbean yellow mosaic Indian virus encoded AC2 protein suppresses RNA silencing by inhibiting Arabidopsis RDR6 and AGO1 activities. Virology 486:158–172

    Article  CAS  PubMed  Google Scholar 

  • Kumar RV (2019) Plant antiviral immunity against geminiviruses and viral counter-defense for survival. Frontiers Microbiol 10:1460. https://doi.org/10.3389/fmicb.2019.01460

    Article  Google Scholar 

  • Lacomme C, Hrubikova K, Hein I (2003) Enhancement of virus-induced gene silencing through viral-based production of inverted-repeats. Plant J 34:543–553

    Article  CAS  PubMed  Google Scholar 

  • Lakatos L, Csorba T, Pantaleo V, Chapman EJ, Carrington JC, Liu YP, Dolja VV, Calvino LF, López-Moya JJ, Burgyán J (2006) Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors. EMBO J 25(12):2768–2780

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Legg J, Thresh J (2000) Cassava mosaic virus disease in East Africa: a dynamic disease in a changing environment. Virus Res 71(1–2):135–149

    Article  CAS  PubMed  Google Scholar 

  • Li ZH, Zhou XP, Zhang X, Xie Y (2004) Molecular characterization of tomato-infecting begomoviruses in Yunnan. China Arch Virol 149:1721–1732

    CAS  PubMed  Google Scholar 

  • Li K, Wu G, Li M et al (2018) Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus. Virol J 15:138. https://doi.org/10.1186/s12985-018-1044-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li WX, Ding SW (2001) Viral suppressors of RNA silencing. Curr Opin Biotechnol 12(2):150–154

    Article  CAS  PubMed  Google Scholar 

  • Lindbo JA, Dougherty WG (1992) Untranslatable transcripts of the tobacco etch virus coat protein gene sequence can interfere with tobacco etch virus replication in transgenic plants and protoplasts. Virology 189(2):725–733

    Article  CAS  PubMed  Google Scholar 

  • Lindbo JA, Silva-Rosales L, Proebsting WM, Dougherty WG (1993) Induction of a highly specific antiviral state in transgenic plants: implications for regulation of gene expression and virus resistance. Plant Cell 5(12):1749–1759

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC, Green PJ (2005) Elucidation of the small RNA component of the transcriptome. Science 309(5740):1567–1569

    Article  CAS  PubMed  Google Scholar 

  • Lu R, Folimonov A, Shintaku M, Li WX, Falk BW, Dawson WO, Ding SW (2004) Three distinct suppressors of RNA silencing encoded by a 20-kb viral RNA genome. Proc Natl Acad Sci 101(44):15742–15747

    Google Scholar 

  • Lucy AP, Guo HS, Li WX, Ding SW (2000) Suppression of post-transcriptional gene silencing by a plant viral protein localized in the nucleus. EMBO J 19(7):1672–1680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mallory AC, Ely L, Smith TH, Marathe R, Anandalakshmi R, Fagard M, Vaucheret H, Pruss G, Bowman L, Vance VB (2001) HC-Pro suppression of transgene silencing eliminates the small RNAs but not transgene methylation or the mobile signal. Plant Cell 13(3):571–583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mangwende T, Wang M-L, Borth W, Hu J, Moore PH, Mirkov TE, Albert HH (2009) The P0 gene of Sugarcane yellow leaf virus encodes an RNA silencing suppressor with unique activities. Virology 384(1):38–50

    Article  CAS  PubMed  Google Scholar 

  • Mérai Z, Kerényi Z, Kertész S, Magna M, Lakatos L, Silhavy D (2006) Double-stranded RNA binding may be a general plant RNA viral strategy to suppress RNA silencing. J Virol 80(12):5747–5756

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mishra NS, Mukherjee SK (2007) A peep into the plant miRNA world. Open Plant Sci J 1:1–9

    Article  CAS  Google Scholar 

  • Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC (2010) Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells. Science 328(5980):872–875

    Article  CAS  PubMed  Google Scholar 

  • Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133(1):128–141

    Article  CAS  PubMed  Google Scholar 

  • Naim F, Nakasugi K, Crowhurst RN, Hilario E, Zwart AB, Hellens RP, Taylor JM, Waterhouse PM, Wood CC (2012) Advanced engineering of lipid metabolism in Nicotiana benthamiana using a draft genome and the V2 viral silencing-suppressor protein. PLoS ONE 7(12):e52717

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Naqvi AR, Choudhury NR, Mukherjee SK, Haq QMR (2011) In silico analysis reveals that several tomato microRNA/microRNA∗ sequences exhibit propensity to bind to tomato leaf curl virus (ToLCV) associated genomes and most of their encoded open reading frames (ORFs). Plant Physiol Biochem 49(1):13–17

    Article  CAS  PubMed  Google Scholar 

  • Naqvi AR, Haq QM, Mukherjee SK (2010) MicroRNA profiling of tomato leaf curl new delhi virus (tolcndv) infected tomato leaves indicates that deregulation of mir159/319 and mir172 might be linked with leaf curl disease. Virology J 7(1):281

    Article  CAS  Google Scholar 

  • Nayak A, Tassetto M, Kunitomi M, Andino R (2013) RNA interference-mediated intrinsic antiviral immunity in invertebrates. In: Intrinsic immunity. Springer, pp 183–200

    Google Scholar 

  • Niu Q-W, Lin S-S, Reyes JL, Chen K-C, Wu H-W, Yeh S-D, Chua N-H (2006) Expression of artificial microRNAs in transgenic Arabidopsis thaliana confers virus resistance. Nat Biotechnol 24(11):1420

    Article  CAS  PubMed  Google Scholar 

  • Niu S, Wang B, Guo X, Yu J, Wang X, Xu K, Zhai Y, Wang J, Liu Z (2009) Identification of two RNA silencing suppressors from banana bunchy top virus. Adv Virol 154(11):1775

    CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Ossowski S, Schwab R, Weigel D (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J 53(4):674–690

    Article  CAS  PubMed  Google Scholar 

  • Pandey P, Choudhury NR, Mukherjee SK (2009) A geminiviral amplicon (VA) derived from Tomato leaf curl virus (ToLCV) can replicate in a wide variety of plant species and also acts as a VIGS vector. Virol J 6:152. https://doi.org/10.1186/1743-422X-6-152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peele C, Jordan CV, Muangsan N, Turnage M, Egelkrout E, Eagle P, Hanley-Bowdoin L, Robertson D (2001) Silencing of a meristematic gene using geminivirus-derived vectors. Plant J 27(4):357–366. https://doi.org/10.1046/j.1365-313x.2001.01080.x

    Article  CAS  PubMed  Google Scholar 

  • Pfeffer S, Dunoyer P, Heim F, Richards KE, Jonard G, Ziegler-Graff V (2002) P0 of beet Western yellows virus is a suppressor of posttranscriptional gene silencing. J Virol 76:6815–6824

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pradhan B, Naqvi AR, Saraf S, Mukherjee SK, Dey N (2015) Prediction and characterization of Tomato leaf curl New Delhi virus (ToLCNDV) responsive novel microRNAs in Solanum lycopersicum. Virus Res 195:183–195

    Article  CAS  PubMed  Google Scholar 

  • Praveen S, Ramesh S, Mishra AK, Koundal V, Palukaitis P (2010) Silencing potential of viral derived RNAi constructs in Tomato leaf curl virus-AC4 gene suppression in tomato. Transgenic Res 19(1):45–55

    Article  CAS  PubMed  Google Scholar 

  • Pruss G, Ge X, Shi XM, Carrington JC, Vance VB (1997) Plant viral synergism: the potyviral genome encodes a broad-range pathogenicity enhancer that transactivates replication of heterologous viruses. Plant Cell 9(6):859–868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pumplin N, Voinnet O (2013) RNA silencing suppression by plant pathogens: defence, counter-defence and counter-counter-defence. Nat Rev Microbiol 11(11):745

    Article  CAS  PubMed  Google Scholar 

  • Qu F, Ren T, Morris TJ (2003) The coat protein of turnip crinkle virus suppresses posttranscriptional gene silencing at an early initiation step. J Virol 77:511–522

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ramesh S, Mishra A, Praveen S (2007) Hairpin RNA-mediated strategies for silencing of tomato leaf curl virus AC1 and AC4 genes for effective resistance in plants. Oligonucleotides 17(2):251–257

    Article  CAS  PubMed  Google Scholar 

  • Ratcliff F, Harrison BD, Baulcombe DC (1997) A Similarity Between Viral Defense and Gene Silencing in Plants. Science 276(5318):1558–1560. https://doi.org/10.1126/science.276.5318.1558

    Article  CAS  PubMed  Google Scholar 

  • Ratcliff FG, MacFarlane SA, Baulcombe DC (1999) Gene silencing without DNA: RNA-mediated cross-protection between viruses. Plant Cell 11(7):1207–1215

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ratcliff F, Martin-Hernandez AM, Baulcombe DC (2001) Tobacco rattle virus as a vector for analysis of gene function by silencing. Plant J 25:237–245

    Article  CAS  PubMed  Google Scholar 

  • Reed JC, Kasschau KD, Prokhnevsky AI, Gopinath K, Pogue GP, Carrington JC, Dolja VV (2003) Suppressor of RNA silencing encoded by Beet yellows virus. Virology 306:203–209

    Article  CAS  PubMed  Google Scholar 

  • Reinhart BJ, Bartel DP (2002) Small RNAs correspond to centromere heterochromatic repeats. Science 297(5588):1831

    Article  CAS  PubMed  Google Scholar 

  • Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110(4):513–520

    Article  CAS  PubMed  Google Scholar 

  • Rogers K, Chen X (2013) Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 25(7):2383–2399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roth A, Breaker RR (2004) Selection in vitro of allosteric ribozymes. In: Ribozymes and siRNA Protocols. Springer, pp 145–164

    Google Scholar 

  • Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510

    Article  CAS  PubMed  Google Scholar 

  • Ruiz MT, Voinnet O, Baulcombe DC (1998) Initiation and maintenance of virus-induced gene silencing. Plant Cell 10(6):937–946

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sablok G, Pérez-Quintero ÁL, Hassan M, Tatarinova TV, López C (2011) Artificial microRNAs (amiRNAs) engineering–On how microRNA-based silencing methods have affected current plant silencing research. Biochem Biophys Res Commun 406(3):315–319

    Article  CAS  PubMed  Google Scholar 

  • Schiebel W, Pélissier T, Riedel L, Thalmeir S, Schiebel R, Kempe D, Lottspeich F, Sänger HL, Wassenegger M (1998) Isolation of an RNA-directed RNA polymerase–specific cDNA clone from tomato. Plant Cell 10(12):2087–2101

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sharma N, Prasad M (2017) An insight into plant–Tomato leaf curl New Delhi virus interaction. The Nucleus 60(3):335–348

    Article  Google Scholar 

  • Shi B-J, Palukaitis P, Symons RH (2002) Differential virulence by strains of Cucumber mosaic virus is mediated by the 2b gene. Mol Plant Microbe Interact 15(9):947–955

    Article  CAS  PubMed  Google Scholar 

  • Shimura H, Fukagawa T, Meguro A, Yamada H, Oh-hira M, Sano S, Masuta C (2008) A strategy for screening an inhibitor of viral silencing suppressors, which attenuates symptom development of plant viruses. FEBS Lett 582(29):4047–4052

    Article  CAS  PubMed  Google Scholar 

  • Silhavy D, Burgyán J (2004) Effects and side-effects of viral RNA silencing suppressors on short RNAs. Trends Plant Sci 9(2):76–83

    Article  CAS  PubMed  Google Scholar 

  • Silhavy D, Molnár A, Lucioli A, Szittya G, Hornyik C, Tavazza M, Burgyán J (2002) A viral protein suppresses RNA silencing and binds silencing-generated, 21-to 25-nucleotide double-stranded RNAs. EMBO J 21(12):3070–3080

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sindhu AS, Maier TR, Mitchum MG, Hussey RS, Davis EL, Baum TJ (2008) Effective and specific in planta RNAi in cyst nematodes: expression interference of four parasitism genes reduces parasitic success. J Exp Bot 60(1):315–324

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Singh A, Taneja J, Dasgupta I, Mukherjee SK (2015) Development of plants resistant to tomato geminiviruses using artificial trans-acting small interfering RNA. Molecular Plant Pathol 16(7):724–734

    Article  CAS  Google Scholar 

  • Singh G, Popli S, Hari Y, Malhotra P, Mukherjee S, Bhatnagar RK (2009) Suppression of RNA silencing by Flock house virus B2 protein is mediated through its interaction with the PAZ domain of Dicer. FASEB J 23(6):1845–1857

    Article  CAS  PubMed  Google Scholar 

  • Sudarshana MR, Plesha MA, Uratsu SL, Falk BW, Dandekar AM, Huang TK, McDonald KA (2006) A chemically inducible cucumber mosaic virus amplicon (2008) 136–142 141 system for expression of heterologous proteins in plant tissues. Plant Biotechnol J 4:551–559

    CAS  PubMed  Google Scholar 

  • Sundaresan G, Das SS, Tripathi A, Mukherjee SK, Sanan-Mishra N (2020) Evaluating the strength of RNA silencing suppressor proteins encoded by two geminiviruses using assay based on reversal of GFP silencing. Australas Plant Pathol 49(2):95–106

    Article  CAS  Google Scholar 

  • Takeda A, Sugiyama K, Nagano H, Mori M, Kaido M, Mise K et al (2002) Identification of a novel RNA silencing suppressor, NSs protein of Tomato spotted wilt virus. FEBS Lett 532:75–79

    Article  CAS  PubMed  Google Scholar 

  • Tao X, Zhou X (2004) A modified viral satellite DNA that suppresses gene expression in plants. Plant J 38:850–860. https://doi.org/10.1111/j.1365-313X.2004.02087.x

    Article  CAS  PubMed  Google Scholar 

  • Tang G, Reinhart BJ, Bartel DP, Zamore PD (2003) A biochemical framework for RNA silencing in plants. Genes Dev 17(1):49–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • tenOever BR (2016) The evolution of antiviral defense systems. Cell Host Microbe 19(2):142

    Article  CAS  PubMed  Google Scholar 

  • Teotia S, Singh D, Tang G (2017) DNA Methylation in Plants by microRNAs. In: Rajewsky N, Jurga S, Barciszewski J (eds) Plant Epigenetics. Springer International Publishing, Cham, pp 247–262. https://doi.org/10.1007/978-3-319-55520-1_13

  • Thomas CL, Leh V, Lederer C, Maule AJ (2003) Turnip crinkle virus coat protein mediates suppression of RNA silencing in Nicotiana benthamiana. Virology 306:33–41

    Article  CAS  PubMed  Google Scholar 

  • Tiwari M, Sharma D, Trivedi PK (2014) Artificial microRNA mediated gene silencing in plants: progress and perspectives. Plant Mol Biol 86(1–2):1–18

    Article  CAS  PubMed  Google Scholar 

  • Turnage MA, Muangsan N, Peele CG, Robertson D (2002) Geminivirus-based vectors for gene silencing in Arabidopsis. Plant J 30(1):107–114. https://doi.org/10.1046/j.1365-313x.2002.01261.x

    Article  CAS  PubMed  Google Scholar 

  • Uprichard SL (2005) The therapeutic potential of RNA interference. FEBS Lett 579(26):5996–6007

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Van der Krol AR, Mur LA, Beld M, Mol J, Stuitje AR (1990) Flavonoid genes in petunia: addition of a limited number of gene copies may lead to a suppression of gene expression. Plant Cell 2(4):291–299

    PubMed  PubMed Central  Google Scholar 

  • Van Vu T, Choudhury NR, Mukherjee SK (2013) Transgenic tomato plants expressing artificial microRNAs for silencing the pre-coat and coat proteins of a begomovirus, Tomato leaf curl New Delhi virus, show tolerance to virus infection. Virus Res 172(1–2):35–45

    Article  CAS  PubMed  Google Scholar 

  • Vanitharani R, Chellappan P, Pita JS, Fauquet CM (2004) Differential roles of AC2 and AC4 of cassava geminiviruses in mediating synergism and suppression of posttranscriptional gene silencing. J Virol 78(17):9487–9498

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van Wezel R, Dong X, Liu H, Tien P, Stanley J, Hong Y (2002) Mutation of three cysteine residues in Tomato yellow leaf curl virus—China C2 protein causes dysfunction in pathogenesis and posttranscriptional gene silencing suppression. Mol Plant Microbe Interact 15:203–208

    Article  Google Scholar 

  • Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20(7):759–771

    Article  CAS  PubMed  Google Scholar 

  • Vazquez F, Vaucheret H, Rajagopalan R, Lepers C, Gasciolli V, Mallory AC, Hilbert JL, Bartel DP, Crété P (2004) Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol Cell 16(1):69–79

    Article  CAS  PubMed  Google Scholar 

  • Vlugt RA, Ruiter RK, Goldbach R (1992) Evidence for sense RNA-mediated protection to PVYN in tobacco plants transformed with the viral coat protein cistron. Plant Mol Biol 20(4):631–639

    Article  PubMed  Google Scholar 

  • Voinnet O (2005) Induction and suppression of RNA silencing: insights from viral infections. Nat Rev Genet 6(3):206

    Article  CAS  PubMed  Google Scholar 

  • Voinnet O (2008) Use, tolerance and avoidance of amplified RNA silencing by plants. Trends Plant Sci 13(7):317–328

    Article  CAS  PubMed  Google Scholar 

  • Voinnet O, Lederer C, Baulcombe DC (2000) A viral movement protein prevents spread of the gene silencing signal in Nicotiana benthamiana. Cell 103(1):157–167

    Article  CAS  PubMed  Google Scholar 

  • Voinnet O, Pinto YM, Baulcombe DC (1999) Suppression of gene silencing: a general strategy used by diverse DNA and RNA viruses of plants. Proc Natl Acad Sci 96(24):14147–14152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Voinnet O, Rivas S, Mestre P, Baulcombe D (2003) Retracted: an enhanced transient expression system in plants based on suppression of gene silencing by the p19 protein of tomato bushy stunt virus. Plant J 33(5):949–956

    Article  CAS  PubMed  Google Scholar 

  • Wang H, Hao L, Shung CY, Sunter G, Bisaro DM (2003) Adenosine kinase is inactivated by geminivirus AL2 and L2 proteins. The Plant Cell 15(12):3020–3032

    Google Scholar 

  • Wang XB, Wu Q, Ito T, Cillo F, Li WX, Chen X, Yu JL, Ding SW (2010) RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci 107(1):484–489

    Article  CAS  PubMed  Google Scholar 

  • Worrall EA, Bravo-Cazar A, Nilon AT, Fletcher SJ, Robinson KE, Carr JP, Mitter N (2019) Exogenous Application of RNAi-Inducing Double-Stranded RNA Inhibits Aphid-Mediated Transmission of a Plant Virus. Front Plant Sci 10:265. https://doi.org/10.3389/fpls.2019.00265

    Article  PubMed  PubMed Central  Google Scholar 

  • Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen SE, Carrington JC (2004) Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2(5):e104

    Article  PubMed  PubMed Central  Google Scholar 

  • Xie M, Yu B (2015) siRNA-directed DNA methylation in plants. Curr Genomics 16:23–31. https://doi.org/10.2174/1389202915666141128002211

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang X, Xie Y, Raja P, Li S, Wolf JN, Shen Q, Bisaro DM, Zhou X (2011) Suppression of methylation-mediated transcriptional gene silencing by βC1-SAHH protein interaction during geminivirus-betasatellite infection. PLoS Pathog 7(10):e1002329

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ye K, Patel DJ (2005) RNA silencing suppressor p21 of Beet yellows virus forms an RNA binding octameric ring structure. Structure 13(9):1375–1384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yelina NE, Savenkov EI, Solovyev AG, Morozov SY, Valkonen JP (2002) Long-distance movement, virulence, and RNA silencing suppression controlled by a single protein in hordei- and potyviruses: complementary functions between virus families. J Virol 76:12981–12991

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang X, Yuan Y-R, Pei Y, Lin S-S, Tuschl T, Patel DJ, Chua N-H (2006) Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense. Genes Dev 20(23):3255–3268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zheng X, Zhu J, Kapoor A, Zhu JK (2007) Role of Arabidopsis AGO6 in siRNA accumulation, DNA methylation and transcriptional gene silencing. EMBO J 26(6):1691–1701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE (2004) Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 14(13):1214–1220

    Article  CAS  PubMed  Google Scholar 

  • Zvereva AS, Pooggin MM (2012) Silencing and innate immunity in plant defense against viral and non-viral pathogens. Viruses 4(11):2578–2597

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Plant RNAi Biology Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India

    Anurag Kumar Sahu & Neeti-Sanan Mishra

  2. Department of Biotechnology, Deen Dayal Upadhyaya University, Gorakhpur, UP, India

    Rajarshi Kumar Gaur

Authors
  1. Anurag Kumar Sahu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Neeti-Sanan Mishra
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Rajarshi Kumar Gaur
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Anurag Kumar Sahu or Rajarshi Kumar Gaur .

Editor information

Editors and Affiliations

  1. Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA

    Guiliang Tang

  2. Department of Biotechnology, Sharda University, Greater Noida, Uttar Pradesh, India

    Sachin Teotia

  3. Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA

    Xiaoqing Tang

  4. School of Biotechnology, Gautam Buddha University, Greater Noida, Uttar Pradesh, India

    Deepali Singh

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Sahu, A.K., Mishra, NS., Gaur, R.K. (2021). Suppressor to Survival: RNAi as a Molecular Weapon in Arms Race Between Virus and Host. In: Tang, G., Teotia, S., Tang, X., Singh, D. (eds) RNA-Based Technologies for Functional Genomics in Plants. Concepts and Strategies in Plant Sciences. Springer, Cham. https://doi.org/10.1007/978-3-030-64994-4_7

Download citation

Publish with us

Policies and ethics

Search

Navigation