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Development of Infectious Clone of Virus

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Abstract

An infectious clone is a full-length DNA clone from which infectious transcripts can be obtained in vitro or in vivo with a suitable promoter. An infectious clone is the basic need to study functional genomics, replication and expression of viral proteins and in understanding host–virus interactions. Infectious clones, considered as the pools of viral genes for designing antiviral strategies, are an essential source of material for the preparation of new viral vectors. In this chapter, production of in vitro and in vivo clones of viruses is discussed.

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References

  • Ahlquist P, Janda M (1984) cDNA cloning and in vitro transcription of the complete brome mosaic virus genome. Mol Cell Biol 4:2876–2882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Annamalai P, Rao ALN (2005) Replication-independent expression of genome components and capsid protein of brome mosaic virus in planta: a functional role for viral replicase in RNA packaging. Virology 338:96–111

    Article  CAS  PubMed  Google Scholar 

  • Bendahmane A, Querci M, Kanyuka K, Baulcombe DC (2000) Agrobacterium transient expression system as a tool for the isolation of disease resistance genes: application to the Rx2 locus in potato. Plant J 21:73–81

    Article  CAS  PubMed  Google Scholar 

  • Boyer JC, Haenni AL (1994) Infectious transcripts and cDNA clones of RNA viruses. Virology 198:415–426

    Article  CAS  PubMed  Google Scholar 

  • Chapman SN (2008) Construction of infectious clones for RNA viruses: TMV. Methods Mol Biol 451:477–490

    Article  CAS  PubMed  Google Scholar 

  • Chiang CH, Yeh SD (1997) Infectivity assays of in vitro and in vivo transcripts of papaya ring spot virus. Bot Bull Acad Sin 38:153–163

    CAS  Google Scholar 

  • Commandeur U, Martin R (1993) Investigations into the molecular biology of potato leaf roll luteovirus by means of agroinfection. Phytopathology 83:1426

    Google Scholar 

  • Dessens JT, Lomonossoff GP (1993) Cauliflower mosaic virus 35S promoter controlled DNA copies of cowpea mosaic virus RNAs are infectious on plants. J Gen Virol 74:889–892

    Article  CAS  PubMed  Google Scholar 

  • Ding XS, Schneider WL, Chaluvadi SR, Mian MA, 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 19:1229–1239

    Article  CAS  PubMed  Google Scholar 

  • Dore JM, Pinck L (1988) Plasmid DNA containing a copy of RNA 3 can substitute for RNA 3 in alfalfa mosaic virus RNA inocula. J Gen Virol 69:1331–1338

    Article  CAS  Google Scholar 

  • Dunn JJ, Studier FW (1983) Complete nucleotide-sequence of bacteriophage-T7 DNA and the locations of T7 genetic elements. J Mol Biol 166:477–535

    Article  CAS  PubMed  Google Scholar 

  • Fakhfakh H, Valaine F, Makni M, Robaglia C (1996) Cell-free cloning and biolistic inoculation of an infectious cDNA of potato virus Y. J Gen Virol 77:519–523

    Article  CAS  PubMed  Google Scholar 

  • Gal-On A, Meiri E, Huet H, Hua WJ, Raccah B, Gaba V (1995) Particle bombardment drastically increases the infectivity of cloned DNA of Zucchini yellow mosaic Potyvirus. J Gen Virol 76:3223–3227

    Article  CAS  PubMed  Google Scholar 

  • Govind K, Makinen K, Savithri HS (2012) Sesbania mosaic virus (SeMV) infectious clone: possible mechanism of 3′ and 5′ end repair and role of polyprotein processing in viral replication. PLoS One 7(2):e31190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gowda S, Satyanarayana T, Robertson CJ, Garnsey SM, Dawson WO (2005) Infection of citrus plants with virions generated in Nicotiana benthamiana plants agro-infiltrated with binary vector based Citrus tristeza virus. In: Hilf ME, Duran-Vila N, Rocha-Pena MA (eds) Proceedings of the 16th conference of the International Organization of Citrus Virologists. IOCV, Riverside, pp 23–33

    Google Scholar 

  • Grimsley N, Hohn B, Hohn T, Walden R (1986) ‘Agroinfection’, an alternative route for viral infection of plants by using the Ti plasmid. Proc Natl Acad Sci U S A 83:3282–3286

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grimsley N, Hohn T, Davies JW, Hohn B (1987) Agrobacterium-mediated delivery of infectious maize streak virus into maize plants. Nature 325:177–179

    Article  CAS  Google Scholar 

  • Hayes RJ, Buck KW (1990) Infectious cucumber mosaic virus RNA transcribed in vitro from clones obtained from cDNA amplified using the polymerase chain reaction. J Gen Virol 71:2503–2508

    Article  CAS  PubMed  Google Scholar 

  • Hearne PQ, Knorr DA, Hillman BI, Morris TJ (1990) The complete genome structure and synthesis of infectious RNA clones from Tomato bushy stunt virus. Virology 177:141–151

    Article  CAS  PubMed  Google Scholar 

  • Hemenway C, Weiss J, O’Connell K, Tumer NE (1990) Characterization of infectious transcripts from a potato virus X cDNA clone. Virology 175:365–371

    Article  CAS  PubMed  Google Scholar 

  • Holt CA, Beachy RN (1991) In vivo complementation of infectious transcripts from mutant tobacco mosaic virus cDNAs in transgenic plants. Virology 181:109–117

    Article  CAS  PubMed  Google Scholar 

  • Hull R (2002) Matthew’s plant virology, 4th edn. Academic Press, London

    Google Scholar 

  • Jones L, Hamilton AJ, Voinnet O, Thomas CL, Maule AJ, Baulcombe DC (1999) RNA–DNA interactions and DNA methylation in post-transcriptional gene silencing. Plant Cell 11:2291–2301

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kawchuk L, Jaag HM, Toohey K, Martin R, Rohde W, Prufer D (2002) In planta agroinfection by Canadian and German Potato leafroll virus full-length cDNAs. Can J Plant Pathol 24:239–243

    Article  CAS  Google Scholar 

  • Klump WM, Bergmann I, Muller BC, Ameis D, Kandolf R (1990) Complete nucleotide sequence of infectious cox sakie-virus B3 cDNA: two initial 5′ uridine residues are regained during plus-strand RNA synthesis. J Virol 64:1573–1583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kobayashi T, Antar AA, Boehme KW, Danthi P, Eby EA, Guglielmi KM, Holm GH, Johnson EM, Maginnis MS, Naik S, Skelton WB, Wetzel JD, Wilson GJ, Chappell JD, Dermody TS (2007) A plasmid-based reverse genetics system for animal double-stranded RNA viruses. Cell Host Microbe 1:147–157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kurth EG, Peremyslov VV, Prokhnevsky AI, Kasschau KD, Miller M, Carrington JC, Dolja VV (2012) Virus-derived gene expression and RNA interference vector for grapevine. J Virol 86:6002–6009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee L, Palukaitis P, Gray SM (2002) Host-dependent requirement for the Potato leaf roll virus 17-kda protein in virus movement. Mol Plant Microbe Interact 15:1086–1094

    Article  CAS  PubMed  Google Scholar 

  • Lee MY, Song YS, Ryu KH (2011) Development of infectious transcripts from full length and GFP-tagged cDNA clones of Pepper mottle virus and stable systemic expression of GFP in tobacco and pepper. Virus Res 155:487–494

    Article  CAS  PubMed  Google Scholar 

  • Leiser RM, Ziegler-Graff V, Reutenauer A, Herrbach E, Lemaire O, Guilley H, Richards K, Jonard G (1992) Agroinfection as an alternative to insects for infecting plants with Beet western yellows luteovirus. Proc Natl Acad Sci 89:9136–9140

    Article  CAS  PubMed  Google Scholar 

  • Liu L, Lomonossoff G (2002) Agro infection as a rapid method for propagating Cowpea mosaic virus-based constructs. J Virol Methods 105:343–348

    Article  CAS  PubMed  Google Scholar 

  • Maiss E, Timpe U, Brisske-Rode A, Lesemann DE, Casper R (1992) Infectious in vivo transcripts of a Plum pox potyvirus full length cDNA clone containing the Cauliflower mosaic virus 35S RNA promoter. J Gen Virol 73:709–713

    Article  CAS  PubMed  Google Scholar 

  • Melton DA, Krieg PA, Rebagliati MR, Maniatis T, Zinn K, Green MR (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res 12:7035–7056

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nagyova A, Subr Z (2007) Infectious full-length clones of plant viruses and their use for construction of viral vectors. Acta Virol 51:223–237

    CAS  PubMed  Google Scholar 

  • Nam M, Kim SM, Domier LL, Koh S, Moon JK, Choi HS, Kim HG, Moon JS, Lee SH (2009) Nucleotide sequence and genome organization of a newly identified member of the genus Carmovirus, Soybean yellow mottle mosaic virus from soybean. Arch Virol 154:1679–1684

    Article  CAS  PubMed  Google Scholar 

  • Nielsen DA, Shapiro DJ (1986) Preparation of capped RNA transcripts using T7 RNA polymerase. Nucleic Acids Res 14:5936

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nurkiyanova KM, Ryabov EV, Commandeur U, Duncan GH, Canto T, Gray SM, Mayo MA, Taliansky ME (2000) Tagging Potato leafroll virus with the jellyfish green fluorescent protein gene. J Gen Virol 81:617–626

    Article  CAS  PubMed  Google Scholar 

  • Prufer DC, Wipf-Scheibel C, Richards K, Guilley H, Lecoq H, Jonard G (1995) Synthesis of a full-length infectious cDNA clone of cucurbit aphid-borne yellows virus and its use in gene exchange experiments with structural proteins from other luteoviruses. Virology 214:150–158

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Scholthof HB (1999) Rapid delivery of foreign genes into plants by direct rub inoculation with intact plasmid DNA of a Tomato bushy stunt virus gene vector. J Virol 73:7823–7829

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scholthof HB, Gowda S, Wu F, Shepherd RJ (1992) The full-length transcript of a caulimovirus is a polycistronic mRNA whose genes are transactivated by the product of gene VI. J Virol 66:3131–3139

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stephan D, Maiss E (2006) Biological properties of Beet mild yellowing virus derived from a full-length cDNA clone. J Gen Virol 87:445–449

    Article  CAS  PubMed  Google Scholar 

  • Turpen TH, Turpen AM, Weinzettl N, Kumagai MH, Dawson WO (1993) Transfection of whole plants from wounds inoculated with Agrobacterium tumefaciens containing cDNA of Tobacco mosaic virus. J Virol Methods 42:227–239

    Article  CAS  PubMed  Google Scholar 

  • Van Bakoven H, Venver J, Wellinck J, Van Kammen A (1993) Protoplasts transiently expressing the 200K coding sequence of cowpea mosaic virus BRNA support replication of M-RNA. J Gen Virol 74:2233–2241

    Article  Google Scholar 

  • Vlot AC, Neeleman L, Linthorst HJ, Bol JF (2001) Role of the 3′-untranslated regions of alfalfa mosaic virus RNAs in the formation of a transiently expressed replicase in plants and in the assembly of virions. J Virol 75:6440–6449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Yamaya Y, Yoshioka M, Meshi T, Okada Y, Ohno T (1988) Expression of tobacco mosaic virus RNA in transgenic plants. Mol Gen Genet 211:520–525

    Article  CAS  PubMed  Google Scholar 

  • Zhang AP, Zhu HQ, Yu SQ, Yang L, Lou Y (2002) Cloning of complete carnation mottle virus cDNA and its infectivity. Acta Horticult 568(568):149–154

    Article  CAS  Google Scholar 

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Bhat, A.I., Rao, G.P. (2020). Development of Infectious Clone of Virus. In: Characterization of Plant Viruses . Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0334-5_46

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  • DOI: https://doi.org/10.1007/978-1-0716-0334-5_46

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0333-8

  • Online ISBN: 978-1-0716-0334-5

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