Subgenomic messenger RNA amplification in coronaviruses

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 27, 2010, Pages 12257-12262

  Wu, Hung Yi ^a,b   Brian, David A ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

^b NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

Author keywords

Bovine coronavirus; Discontinuous transcription; Negative strand RNA ligation; Negative strand RNA synthesis; Severe acute respiratory syndrome

Indexed keywords

GREEN FLUORESCENT PROTEIN; MESSENGER RNA; RNA DIRECTED RNA POLYMERASE;

3' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; CORONAVIRUS; CORONAVIRUS INFECTION; GENE AMPLIFICATION; GENE EXPRESSION; GENETIC TRANSFECTION; HOMOLOGOUS RECOMBINATION; MESSENGER RNA SYNTHESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA TRANSCRIPTION; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS SURVIVAL;

BLOTTING, NORTHERN; CELL LINE, TUMOR; CORONAVIRUS; GENE AMPLIFICATION; GENOME, VIRAL; HUMANS; MODELS, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, MESSENGER; RNA, VIRAL; TEMPLATES, GENETIC; VIRUS REPLICATION;

BOVINE CORONAVIRUS; CORONAVIRUS;

EID: 77955462625     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1000378107     Document Type: Article

References (51)

1. Masters PS (2006) The molecular biology of coronaviruses. Adv Virus Res 66:193-292.
2. Zúñiga S, Sola I, Alonso S, Enjuanes L (2004) Sequence motifs involved in the regulation of discontinuous coronavirus subgenomic RNA synthesis. J Virol 78:980-994. (Pubitemid 38067619)
3. Sawicki SG, Sawicki DL, Siddell SG (2007) A contemporary view of coronavirus transcription. J Virol 81:20-29.
4. Lai MM, Patton CD, Baric RS, Stohlman SA (1983) Presence of leader sequences in the mRNA of mouse hepatitis virus. J Virol 46:1027-1033.
5. Wu HY, Brian DA (2007) 5′-proximal hot spot for an inducible positive-to-negative strand template switch by coronavirus RNA-dependent RNA polymerase. J Virol 81:3206-3215.
6. Hofmann MA, Sethna PB, Brian DA (1990) Bovine coronavirus mRNA replication continues throughout persistent infection in cell culture. J Virol 64:4108-4114.
7. Kopecky-Bromberg SA, Martínez-Sobrido L, Frieman M, Baric RA, Palese P (2007) Severe acute respiratory syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as interferon antagonists. J Virol 81:548-557.
8. Cowley TJ, Long SY, Weiss SR (2010) The murine coronavirus nucleocapsid gene is a determinant of virulence. J Virol 84:1752-1763.
9. Sethna PB, Hung SL, Brian DA (1989) Coronavirus subgenomic minus-strand RNAs and the potential for mRNA replicons. Proc Natl Acad Sci USA 86:5626-5630.
10. Li X, Palese P (1992) Mutational analysis of the promoter required for influenza virus virion RNA synthesis. J Virol 66:4331-4338.
11. Levis R, Weiss BG, Tsiang M, Huang H, Schlesinger S (1986) Deletion mapping of Sindbis virus DI RNAs derived from cDNAs defines the sequences essential for replication and packaging. Cell 44:137-145.
12. Sawicki D, Wang T, Sawicki S (2001) The RNA structures engaged in replication and transcription of the A59 strain of mouse hepatitis virus. J Gen Virol 82:385-396.
13. Baric RS, Yount B (2000) Subgenomic negative-strand RNA function during mouse hepatitis virus infection. J Virol 74:4039-4046.
14. Sawicki SG, Sawicki DL (1990) Coronavirus transcription: Subgenomic mouse hepatitis virus replicative intermediates function in RNA synthesis. J Virol 64:1050-1056.
15. Lin YJ, Liao CL, Lai MM (1994) Identification of the cis-acting signal for minus-strand RNA synthesis of a murine coronavirus: Implications for the role of minus-strand RNA in RNA replication and transcription. J Virol 68:8131-8140.
16. Chang RY, Hofmann MA, Sethna PB, Brian DA (1994) A cis-acting function for the coronavirus leader in defective interfering RNA replication. J Virol 68:8223-8231.
17. Makino S, Joo M, Makino JK (1991) A system for study of coronavirus mRNA synthesis: A regulated, expressed subgenomic defective interfering RNA results from intergenic site insertion. J Virol 65:6031-6041.
18. Wu HY,Ozdarendeli A, Brian DA(2006) Bovine coronavirus 5′-proximal genomic acceptor hotspot for discontinuous transcription is 65 nucleotides wide. J Virol 80:2183-2193.
19. Goebel SJ, Miller TB, Bennett CJ, Bernard KA, Masters PS (2007) A hypervariable region within the 3′ cis-acting element of the murine coronavirus genome is nonessential for RNA synthesis but affects pathogenesis. J Virol 81:1274-1287.
20. Wu H-Y, et al. (2003) Common RNA replication signals exist among group 2 coronaviruses: Evidence for in vivo recombination between animal and human coronavirus molecules. Virology 315:174-183.
21. Peng D, Koetzner CA, McMahon T, Zhu Y, Masters PS (1995) Construction of murine coronavirus mutants containing interspecies chimeric nucleocapsid proteins. J Virol 69: 5475-5484.
22. Schenborn ET, Mierendorf RC, Jr (1985) A novel transcription property of SP6 and T7 RNA polymerases: Dependence on template structure. Nucleic Acids Res 13:6223-6236.
23. Nichols NM, Tabor S, McReynolds LA (2008) RNA ligases. Curr Protoc Mol Biol unit 3:15.
24. Szymkowiak C, et al. (2003) Rapid method for the characterization of 3′ and 5′ UTRs of influenza viruses. J Virol Methods 107:15-20.
25. Hofmann MA, Senanayake SD, Brian DA (1993) A translation-attenuating intraleader open reading frame is selected on coronavirus mRNAs during persistent infection. Proc Natl Acad Sci USA 90:11733-11737.
26. Lai MM (1992) Genetic recombination in RNA viruses. Curr Top Microbiol Immunol 176:21-32.
27. Baric RS, Fu K, Schaad MC, Stohlman SA (1990) Establishing a genetic recombination mapformurine coronavirus strain A59 complementation groups. Virology 177:646-656.
28. Fu K, Baric RS (1994) Map locations of mouse hepatitis virus temperature-sensitive mutants: Confirmation of variable rates of recombination. J Virol 68:7458-7466.
29. Koetzner CA, Parker MM, Ricard CS, Sturman LS, Masters PS (1992) Repair and mutagenesis of the genome of a deletion mutant of the coronavirus mouse hepatitis virus by targeted RNA recombination. J Virol 66:1841-1848.
30. Masters PS, Koetzner CA, Kerr CA, Heo Y (1994) Optimization of targeted RNA recombination and mapping of a novel nucleocapsid gene mutation in the coronavirus mouse hepatitis virus. J Virol 68:328-337.
31. Ozdarendeli A, et al. (2001) Downstream sequences influence the choice between a naturally occurring noncanonical and closely positioned upstream canonical heptameric fusion motif during bovine coronavirus subgenomic mRNA synthesis. J Virol 75:7362-7374.
32. Krishnan R, Chang RY, Brian DA (1996) Tandem placement of a coronavirus promoter results in enhanced mRNA synthesis from the downstream-most initiation site. Virology 218:400-405.
33. Züst R, Miller TB, Goebel SJ, Thiel V, Masters PS (2008) Genetic interactions between an essential 3′ cis-acting RNA pseudoknot, replicase gene products, and the extreme 3′ end of the mouse coronavirus genome. J Virol 82:1214-1228.
34. Cheng A, et al. (2005) Expression, purification, and characterization of SARS coronavirus RNA polymerase. Virology 335:165-176.
35. te Velthuis AJ, Arnold JJ, Cameron CE, van den Worm SH, Snijder EJ (2010) The RNA polymerase activity of SARS-coronavirus nsp12 is primer-dependent. Nucleic Acids Res 38:203-214.
36. Kao CC, Singh P, Ecker DJ (2001) De novo initiation of viral RNA-dependent RNA synthesis. Virology 287:251-260.
37. Imbert I, et al. (2006) A second, non-canonical RNA-dependent RNA polymerase in SARS coronavirus. EMBO J 25:4933-4942.
38. Ivanov KA, et al. (2004) Major genetic marker of nidoviruses encodes a replicative endoribonuclease. Proc Natl Acad Sci USA 101:12694-12699.
39. Bhardwaj K, Sun J, Holzenburg A, Guarino LA, Kao CC (2006) RNA recognition and cleavage by the SARS coronavirus endoribonuclease. J Mol Biol 361:243-256.
40. Wang RY, Nagy PD (2008) Tomato bushy stunt virus co-opts the RNA-binding function of a host metabolic enzyme for viral genomic RNA synthesis. Cell Host Microbe 3:178-187.
41. Wang X, Ahlquist P (2008) Filling a GAP(DH) in asymmetric viral RNA synthesis. Cell Host Microbe 3:124-125.
42. Eckerle LD, Albariño CG, Ball LA (2003) Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2. Virology 317:95-108.
43. Fischer F, Stegen CF, Koetzner CA, Masters PS (1997) Analysis of a recombinant mouse hepatitis virus expressing a foreign gene reveals a novel aspect of coronavirus transcription. J Virol 71:5148-5160.
44. Moreno JL, Zúñiga S, Enjuanes L, Sola I (2008) Identification of a coronavirus transcription enhancer. J Virol 82:3882-3893.
45. Sola I, Moreno JL, Zúñiga S, Alonso S, Enjuanes L (2005) Role of nucleotides immediately flanking the transcription-regulating sequence core in coronavirus subgenomic mRNA synthesis. J Virol 79:2506-2516.
46. Hsue B, Masters PS (1999) Insertion of a new transcriptional unit into the genome of mouse hepatitis virus. J Virol 73:6128-6135.
47. An S, Makino S (1998) Characterizations of coronavirus cis-acting RNA elements and the transcription step affecting its transcription efficiency. Virology 243:198-207.
48. Fu K, Baric RS (1992) Evidence for variable rates of recombination in the MHV genome. Virology 189:88-102.
49. García-Arriaza J, Ojosnegros S, Dávila M, Domingo E, Escarmís C (2006) Dynamics of mutation and recombination in a replicating population of complementing, defective viral genomes. J Mol Biol 360:558-572.
50. Eckerle LD, Lu X, Sperry SM, Choi L, Denison MR (2007) High fidelity of murine hepatitis virus replication is decreased in nsp14 exoribonuclease mutants. J Virol 81:12135-12144.
51. Yount B, Denison MR, Weiss SR, Baric RS (2002) Systematic assembly of a full-length infectious cDNA of mouse hepatitis virus strain A59. J Virol 76:11065-11078.