Virus infection cycle events coupled to RNA replication

Annual Review of Phytopathology

Volumn 52, Issue , 2014, Pages 197-212

  Saxena, Pooja ^a   Lomonossoff, George P ^a  

^a JOHN INNES CENTRE   (United Kingdom)

Author keywords

Coreplicational disassembly; Coreplicational movement; Cotranslational replication; Packaging specificity

Indexed keywords

VIRUS RNA;

BIOSYNTHESIS; GENETICS; PROTEIN SYNTHESIS; RNA VIRUS;

PROTEIN BIOSYNTHESIS; RNA VIRUSES; RNA, VIRAL;

EID: 84905498183     PISSN: 00664286     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev-phyto-102313-050205     Document Type: Article

References (82)

1. Ahlquist P, Noueiry AO, Lee WM, Kushner DB, Dye BT. 2003. Host factors in positive-strand RNA virus genome replication. J. Virol. 15:8181-86
2. Annamalai P, Rao AL. 2006. Packaging of Brome mosaic virus subgenomic RNA is functionally coupled to replication-dependent transcription and translation of coat protein. J. Virol. 80:10096-108
3. Annamalai P, Rofail F, Demason DA, Rao AL. 2008. Replication-coupled packaging mechanism in positive-strand RNA viruses: synchronized coexpression of functional multigenome RNA components of an animal and a plant virus in Nicotiana benthamiana cells by agroinfiltration. J. Virol. 82:1484-95
4. Barton DJ, O'Donell BJ, Flanegan JB. 2001. 5- cloverleaf in poliovirus RNA is a cis-acting replication element required for negative-strand synthesis. EMBO J. 20:1439-48
5. Brisco M, Hull R, Wilson TM. 1986. Swelling of isometric and of bacilliform plant virus nucleocapsids is required for virus-specific protein synthesis in vitro. Virology 148:210-17
6. Brisco MJ, Hull R, Wilson TMA. 1985. Southern bean mosaic virus-specific proteins are synthesized in an in vitro system supplemented with intact, treated virions. Virology 143:392-98
7. Bushell M, Sarnow P. 2002. Hijacking the translation apparatus by RNA viruses. J. Cell Biol. 158:395-99
8. Carette JE, Kujawa A, G uhl K, Verver J, Wellink J, van Kammen A. 2001. Mutational analysis of the genome-linked protein of Cowpea mosaic virus. Virology 290:21-29
9. Choi YG, Rao AL. 2003. Packaging of Brome mosaic virus RNA3 is mediated through a bipartite signal. J. Virol. 77:9750-57
10. Choi SK, Hema M, Gopinath K, Santos J, Kao C. 2004. Replicase-binding sites on plus- and minus-strand Brome mosaic virus RNAs and their roles in RNA replication in plant cells. J. Virol. 78:13420-29
11. Damayanti TA, Tsukaguchi S, Mise K, Okuno T. 2003. cis-acting elements required for efficient packaging of Brome mosaic virus RNA3 in barley protoplasts. J. Virol. 77:9979-86
12. Decroly E, Ferron F, Lescar J, Canard B. 2012. Conventional and unconventional mechanisms for capping viral mRNA. Nat. Rev. Microbiol. 10:51-65
13. de Groot RJ, van der Most RG, Spaan WJ. 1992. The fitness of defective interfering murine coronavirus DI-a and its derivatives is decreased by nonsense and frameshift mutations. J. Virol. 66:5898-905
14. de Varennes A, Lomonossoff GP, Shanks M, Maule AJ. 1986. The stability of Cowpea mosaic virus VPg in reticulocyte lysates. J. Gen. Virol. 67:2347-54
15. Diez J, Ishikawa M, Kaido M, Ahlquist P. 2000. Identification and characterization of a host protein required for efficient template selection in viral RNA replication. Proc. Natl. Acad. Sci. USA 97:3913-18
16. Drake JW. 1993. Rates of spontaneous mutation among RNA viruses. Proc. Natl. Acad. Sci. USA 90:4171-75
17. Dreher TW. 1999. Functions of the 3-untranslated regions of positive strand RNA viral genomes. Annu. Rev. Phytopathol. 37:151-74
18. Dunigan DD, Zaitlin M. 1990. Capping of Tobacco mosaic virus RNA: analysis of viral-coded guanylyltransferase-like activity. J. Biol. Chem. 265:7779-86
19. Dykeman EC, Stockley PG, Twarock R. 2013. Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome. J. Mol. Biol. 425:3235-49
20. Ferron F, Decroly E, Selisko B, Canard B. 2012. The viral RNA capping machinery as a target for antiviral drugs. Antivir. Res. 96:21-31
21. Goldbach R, Rezelman G, vanKammen A. 1980. Independent replication and expression of B-component RNA of cowpea mosaic virus. Nature 286:297-300
22. Goldbach R, van Kammen A. 1985. Structure, replication and expression of the bipartite genome of cowpea mosaic virus. Mol. Plant Virol. 2:83-120
23. Gopal R, Venter PA, Schneemann A. 2014. Differential segregation of nodaviral coat protein and RNA into progeny virions during mixed infection with FHV and NoV. Virology. 454:280-90
24. Gordon KHJ. 1995. Were RNA replication and translation directly coupled in the RNA world? J. Theor. Biol. 173:179-93
25. Herold J, Andino R. 2000. Poliovirus requires a precise 5- end for efficient positive-strand RNA synthesis. J. Virol. 74:6394-400
26. Hirashima K, Watanabe Y. 2001. Tobamovirus replicase coding region is involved in cell-to-cell movement. J. Virol. 75:8831-36
27. Hirashima K, Watanabe Y. 2003. RNA helicase domain of tobamovirus replicase executes cell-to-cell movement possibly through collaboration with its non-conserved region. J. Virol. 77:12357-62
28. Hiscox JA, Ball LA. 1997. Cotranslational disassembly of flock house virus in a cell-free system. J. Virol. 71:7974-77
29. Hull R. 2009. Comparative Plant Virology. London: Acad. Press. 2nd ed.
30. Ishikawa M, Diez J, Restrepo-Hartwig M, Ahlquist P. 1997. Yeastmutations in multiple complementation groups inhibit brome mosaic virus RNA replication and transcription and perturb regulated expression of the viral polymerase-like gene. Proc. Natl. Acad. Sci. USA 94:13810-15
31. Ivanov KI, Puustinen P, Merits A, Saarma M, Makinen K. 2001. Phosphorylation down-regulates the RNA binding function of the coat protein of potato virus A. J. Biol. Chem. 276:13530-40
32. Jakubiec A, Jupin I. 2007. Regulation of positive-strand RNA virus replication: the emerging role of phosphorylation. Virus Res. 129:73-79
33. Jakubiec A, Tournier V, Drugeon G, Pflieger S, Camborde L, et al. 2006. Phosphorylation of viral RNA-dependent RNA polymerase and its role in replication of a plus-strand RNA virus. J. Biol. Chem. 281:21236-49
34. Karpova OV, Rodionova NP, Ivanov KI, Kozlovsky SV, Dorokhov YL, Atabekov JG. 1999. Phosphorylation of tobacco mosaic virus movement protein abolishes its translation repressing ability. Virology 261:20-24
35. Kawakami S, Watanabe Y, Beachy RN. 2004. Tobacco mosaic virus infection spreads cell to cell as intact replication complexes. Proc. Natl. Acad. Sci. USA 101:6291-96
36. Khromykh AA, Varnavski AN, Sedlak PL, Westaway EG. 2001. Coupling between replication and packaging of flavivirus RNA: evidence derived from the use of DNA-based full-length cDNA clones of Kunjin virus. J. Virol. 75:4633-40
37. Kim SH, Palukaitis P, Park YI. 2002. Phosphorylation of cucumber mosaic virus RNA polymerase 2a protein inhibits formation of replicase complex. EMBO J. 21:2292-300
38. Langereis MA, Feng Q, Nelissen FH, Virgen-Slane R, van der Heden van Noort GJ, et al. 2013. Modification of picornavirus genomic RNA using "click" chemistry shows that unlinking of the VPg peptide is dispensable for translation and replication of the incoming viral RNA. Nucleic Acids Res. 42:2473-82
39. Latham JR, Wilson AK. 2008. Transcomplementation and synergism in plants: implications for viral transgenes? Mol. Plant Pathol. 9:85-103
40. Lee WM, Ishikawa M, Ahlquist P. 2001. Mutation of host-9 fatty acid desaturase inhibits brome mosaic virus RNA replication between template recognition and RNA synthesis. J. Virol. 75:2097-106
41. Lomonossoff GP, Shanks M, Evans D. 1985. The structure of cowpea mosaic virus replicative form RNA. Virology 144:351-62
42. Nomoto A, Kitamura N, Golini F, Wimmer E. 1977. The 5-terminal structures of poliovirion RNA and poliovirus mRNA differ only in the genome-linked protein VPg. Proc. Natl. Acad. Sci. USA 74:5345-49
43. Novak JE, Kirkegaard K. 1994. Coupling between genome translation and replication in an RNA virus. Genes Dev. 8:1726-37
44. Nugent CI, Johnson KL, Sarnow P, Kirkegaard K. 1999. Functional coupling between replication and packaging of poliovirus replicon RNA. J. Virol. 73:427-35
45. Osman TA, Buck KW. 1997. The tobacco mosaic virus RNA polymerase complex contains a plant protein related to the RNA-binding subunit of yeast eIF-3. J. Virol. 71:6075-82
46. Pilipenko EV, Poperechny KV, Maslova SV, Melchers WJ, Slot HJ, Agol VI. 1996. Cis-element, oriR, involved in the initiation of () strand poliovirus RNA: a quasi-globular multi-domain RNA structure maintained by tertiary interactions. EMBO J. 15:5428-36
47. Puustinen P, Makinen K. 2004. Uridylylation of the potyvirus VPg by viral replicase NIb correlates with the nucleotide binding capacity of VPg. J. Biol. Chem. 279:38103-10
48. Qu F, Morris TJ. 1997. Encapsidation of turnip crinkle virus is defined by a specific packaging signal and RNA size. J. Virol. 71:1428-35
49. Rajamaki ML, Maki-Valkama T, Makinen K, Valkonen J. 2004. Infection with potyviruses. In Plant- Pathogen Interactions, ed. NJ Talbot, pp. 68-91. Sheffield, UK: Blackwell Publ.
50. Reade R, Kakani K, Rochon D. 2010. A highly basic KGKKGK sequence in the RNA-binding domain of the Cucumber necrosis virus coat protein is associated with encapsidation of full-length CNV RNA during infection. Virology 403:181-88
51. Reider E, Paul AV, Kim DW, van Boom JH, Wimmer E. 2000. Genetic and biochemical studies of poliovirus cis-acting replication element cre in relation to VPg uridylylation. J. Virol. 74:10371-80
52. Rochon D, Siegel A. 1984. Chloroplast DNA transcripts are encapsidated by tobacco mosaic virus coat protein. Proc. Natl. Acad. Sci. USA 81:1719-23
53. Roenhorst JW, Verduin BJM, Goldbach RW. 1989. Virus ribosome complexes from cell-free translation systems supplemented with cowpea chlorotic mottle virus particles. Virology 168:138-46
54. Sadowy E, Milner M, Haenni AL. 2001. Proteins attached to viral genomes are multifunctional. Adv. Virus Res. 57:185-262
55. Saunders K, Sainsbury F, Lomonossoff GP. 2009. Efficient generation of Cowpea mosaic virus empty viruslike particles by the proteolytic processing of precursors in insect cells and plants. Virology 393:329-37
56. Schwartz M, Chen J, Lee WM, Janda M, Ahlquist P. 2004. Alternate, virus-induced membrane rearrangements support positive-strand RNA virus genome replication. Proc. Natl. Acad. Sci. USA 101:11263-68
57. Seo JK, Kwon SJ, Rao ALN. 2012. A physical interaction between viral replicase and capsid protein is required for genome-packaging specificity in an RNA virus. J. Virol. 86:6210-21
58. Serva S, Nagy PD. 2006. Proteomics analysis of the tombusvirus replicase: Hsp70 molecular chaperone is associated with the replicase and enhances viral RNA replication. J. Virol. 80:2162-69
59. Shapka N, Stork J, Nagy PD. 2005. Phosphorylation of the p33 replication protein of Cucumber necrosis tombusvirus adjacent to the RNA binding site affects viral RNA replication. Virology 343:65-78
60. Stork J, Panaviene Z, Nagy PD. 2005. Inhibition of in vitro RNA binding and replicase activity by phosphorylation of the p33 replication protein of Cucumber necrosis tombusvirus. Virology 343:79-92
61. Taylor DN, Carr JP. 2000. The GCD10 subunit of yeast eIF-3 binds the methyltransferase-like domain of the 126 and 183 kDa replicase proteins of tobacco mosaic virus in the yeast two-hybrid system. J. Gen. Virol. 81:1587-91
62. Tilsner J, Linnik O, Louveaux M, Roberts IM, Chapman SN, Oparka KJ. 2013. Replication and trafficking of a plant virus are coupled at the entrances of plasmodesmata. J. Cell Biol. 201:981-95
63. Tilsner J, Oparka KJ. 2012. Missing links? The connection between replication and movement of plant RNA viruses. Curr. Opin. Virol. 2:705-11
64. Turner DR, Joyce LE, Butler PJ. 1988. The tobacco mosaic virus assembly origin RNA. Functional characteristics defined by directed mutagenesis. J. Mol. Biol. 203:531-47
65. van Bokhoven H, Mulders M, Wellink J, Vlak JM, Goldbach R, van Kammen A. 1991. Evidence for dissimilar properties of comoviral and picornaviral RNA polymerases. J. Gen. Virol. 72:567-72
66. van Bokhoven H, Le Gall O, Kasteel D, Verver J, Wellink J, van Kammen AB. 1993. Cis- and trans-acting elements in cowpea mosaic virus RNA replication. Virology 195:377-86
67. van Bokhoven H, van Lent JW, Custers R, Vlak JM, Wellink J, van Kammen A. 1992. Synthesis of the complete 200K polyprotein encoded by cowpea mosaic virus B-RNA in insect cells. J. Gen. Virol. 73:2775-84
68. van Kammen A, Wellink J, Goldbach R, Eggen R, Vos P. 1987. The use of full-length DNA copies in the study of the expression and replication of the RNA genome of cowpea mosaic virus. In Plant Molecular Biology, ed. D von Wettstein, N-H Chua, pp. 433-42. New York: Plenum
69. Venter PA, Krishna NK, Schneemann A. 2005. Capsid protein synthesis from replicating RNA directs specific packaging of the genome of a multipartitite, positive-strand RNA virus. J. Virol. 79:6239-48
70. Volkova E, Gorchakov R, Frolov I. 2006. The efficient packaging of Venezuelan equine encephalitis virus-specific RNAs into viral particles is determined by nsP1-3 synthesis. Virology 344:315-27
71. Waigmann E, Chen MH, Bachmaier R, Ghoshroy S, Citovsky V. 2000. Regulation of plasmodesmal transport by phosphorylation of tobacco mosaic virus cell-to-cell movement protein. EMBO J. 19:4875-84
72. Weiland JJ, Dreher TW. 1993. Cis-preferential replication of the turnip yellowmosaic virusRNAgenome. Proc. Natl. Acad. Sci. USA 90:6095-99
73. Wellink J, van Bokhoven H, Le Gall O, Verver J, van Kammen A. 1994. Replication and translation of cowpea mosaic virus RNAs are tightly linked. Arch. Virol. Suppl. 9:381-92
74. White KA, Bancroft JB, Mackie GA. 1992. Coding capacity determines in vivo accumulation of a defective RNA of clover yellow mosaic virus. J. Virol. 66(5):3069-76
75. Wilson TMA. 1984. Cotranslational disassembly of tobacco mosaic virus in vitro. Virology 137:255-65
76. Wilson TMA. 1985. Nucleocapsid disassembly and early gene expression by positive-strand RNA viruses. J. Gen. Virol. 66:1201-7
77. Wimmer E. 1982. Genome-linked proteins of viruses. Cell 28:199-201
78. Wimmer E, Hellen CUT, Cao X. 1993. Genetics of poliovirus. Annu. Rev. Genet. 27:353-436
79. Wu X, Shaw JG. 1996. Bidirectional uncoating of the genomic RNA of a helical virus. Proc. Natl. Acad. Sci. USA 93:2981-84
80. Wu X, Shaw JG. 1997. Evidence that a viral replicase protein is involved in the disassembly of tobacco mosaic virus particles in vivo. Virology 239:426-34
81. Wu X, Xu Z, Shaw JG. 1994. Uncoating of tobacco mosaic virus RNA in protoplasts. Virology 200:256-62
82. Zimmern D. 1977. The nucleotide sequence at the origin for assembly on tobacco mosaic virus RNA. Cell 11:463-82