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Chapter 8 : RNA Signals Regulating Nidovirus RNA Synthesis

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Abstract:

Nidovirus RNA synthesis has now been studied at the molecular level for almost three decades, but the understanding of the molecular interplay between RNA signals and protein functions that is the basis for replication and transcription is still in its infancy. This chapter summarizes what is known about the primary and higher-order RNA structures, in particular for coronaviruses and arteriviruses, and addresses various other aspects of nidovirus replication and transcription. Coronavirus defective interfering (DI) genomes have been useful tools to investigate RNA signals and elements involved in replication. The recent development of reverse-genetic systems based on cloned full-length cDNA copies of coronavirus genomes has provided an alternative to the use of DI RNA systems and will further enhance the understanding of coronavirus replication signals. Coronaviruses exhibit the phenomenon of leader switching, which is presumably based on frequent RdRp template switching occurring near the 5’ end of the genome.

Citation: van den Born E, Snijder E. 2008. RNA Signals Regulating Nidovirus RNA Synthesis, p 115-131. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch8

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Figures

Image of Figure 1.
Figure 1.

Nidoviruses produce a 3’-coterminal nested set of mRNAs. The genome organization and expression strategies of the arterivirus EAV, the coronavirus MHV, bovine torovirus (BToV), WBV (tentative genus, and the ronivirus gill-associated virus (GAV) are summarized. Shown are structural relationships of the genome-length and subgenome-length mRNAs. The leader sequence and leader TRS found at the genomic 5’ ends of EAV, MHV, and WBV are indicated as black and white boxes, respectively. The same color coding is used for the genome and largest sg mRNA of BToV. The TREs found at the 5’ ends of all other BToV and GAV sg mRNAs are indicated as dark gray boxes. The ribosomal frameshifting element found in genome-length mRNA is indicated as a black circle. Only the translated ORFs are indicated for each mRNA. E, envelope protein; M, membrane protein; GP, glycoprotein; S, spike glycoprotein; HE, hemagglutinin-esterase protein; ns2, nonstructural protein 2; I, internal gene product. Adapted from reference .

Citation: van den Born E, Snijder E. 2008. RNA Signals Regulating Nidovirus RNA Synthesis, p 115-131. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch8
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Image of Figure 2.
Figure 2.

Secondary-structure elements in the 3’-proximal regions of different coronavirus genomes. The feline coronavirus (FCoV; feline infectious peritonitis virus WSU-79/1146 strain) structure was adapted from reference . The MHV (A59 strain) structure was combined and adapted from references and . The conserved octanucleotide motif (GGAAGAGC) is indicated. The BCoV (Mebus strain) and SARS-CoV (Urbani strain) RNA structures are adapted from references and , respectively. The IBV (strain Beaudette) and SARS-CoV s2m hairpins were taken from reference . The most 5’-positioned hairpin of the IBV structure and the pseudoknot were adapted from references and , respectively. The translation stop codon (UAA) of the N protein ORF is indicated in bold.

Citation: van den Born E, Snijder E. 2008. RNA Signals Regulating Nidovirus RNA Synthesis, p 115-131. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch8
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Image of Figure 3.
Figure 3.

Secondary-structure model of the BCoV 5’ UTR. The BCoV (Mebus strain) structure model was adapted from reference . The replicase translation initiation codon is indicated in bold and is marked with an arrow. The core sequence of the leader TRS is also indicated in bold. Nucleotide numbers refer to positions in the BCoV genome.

Citation: van den Born E, Snijder E. 2008. RNA Signals Regulating Nidovirus RNA Synthesis, p 115-131. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch8
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Image of Figure 4.
Figure 4.

Secondary-structure elements in arterivirus genomes. Depicted are the RNA structure models for the 5’-terminal 313 nt (A) and the 3’-terminal 300 nt (B) of the EAV genome (Bucyrus strain). Adapted from references and , respectively. The replicase translation initiation codon is indicated with an arrow. The leader TRS (UCAACU) and the translation stop codon of the N protein gene are indicated in bold. (C) Model of the kissing loop interaction identified in the 3’-proximal region of the PRRSV genome (Lelystad strain), adapted from reference .

Citation: van den Born E, Snijder E. 2008. RNA Signals Regulating Nidovirus RNA Synthesis, p 115-131. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch8
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Image of Figure 5.
Figure 5.

Models for nidovirus transcription, including (A) or lacking (B) a discontinuous step during minus-strand RNA synthesis. Plus- and minus-strand RNAs are represented by solid and dashed lines, respectively. See the text for details.

Citation: van den Born E, Snijder E. 2008. RNA Signals Regulating Nidovirus RNA Synthesis, p 115-131. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch8
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Image of Figure 6.
Figure 6.

Secondary-structure models of LTHs. Presented are the LTHs of the arteriviruses EAV (Bucyrus strain) and PRRSV (VR-2332 strain), adapted from reference . The LTH of a representative of each of the three coronavirus subgroups is shown: TGEV (Purdue strain), BCoV (Quebec strain), and IBV (Beaudette strain), adapted from reference . The core sequence of the leader TRS is indicated in bold. The arterivirus replicase translation initiation codon is marked with an arrow.

Citation: van den Born E, Snijder E. 2008. RNA Signals Regulating Nidovirus RNA Synthesis, p 115-131. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch8
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References

/content/book/10.1128/9781555815790.ch08
1. Almazan, F.,, C. Galan, and, L. Enjuanes. 2004. The nucleoprotein is required for efficient coronavirus genome replication. J. Virol. 78:1268312688.
2. Alonso, S.,, A. Izeta,, I. Sola, and, L. Enjuanes. 2002. Transcription regulatory sequences and mRNA expression levels in the coronavirus transmissible gastroenteritis virus. J. Virol. 76:12931308.
3. An, S. W., and, S. Makino. 1998. Characterizations of corona-virus cis-acting RNA elements and the transcription step affecting its transcription efficiency. Virology 243:198207.
4. Ayllon, M. A.,, S. Gowda,, T. Satyanarayana, and, W. O. Dawson. 2004. Cis-acting elements at opposite ends of the Citrus tristeza virus genome differ in initiation and termination of subgenomic RNAs. Virology 322:4150.
5. Baric, R. S.,, S. A. Stohlman, and, M. M. Lai. 1983. Characterization of replicative intermediate RNA of mouse hepatitis virus: presence of leader RNA sequences on nascent chains. J. Virol. 48:633640.
6. Baric, R. S., and, B. Yount. 2000. Subgenomic negative-strand RNA function during mouse hepatitis virus infection. J. Virol. 74:40394046.
7. Beerens, N., and, E. J. Snijder. 2006. RNA signals in the 3’ terminus of the genome of Equine arteritis virus are required for viral RNA synthesis. J. Gen. Virol. 87:19771983.
8. Brian, D. A., and, R. S. Baric. 2005. Coronavirus genome structure and replication. Curr. Top. Microbiol. Immunol. 287:130.
9. Brian, D. A., and, W. J. M. Spaan. 1997. Recombination and coronavirus defective interfering RNAs. Semin. Virol. 8:101111.
10. Casais, R.,, V. Thiel,, S. G. Siddell,, D. Cavanagh, and, P. Britton. 2001. Reverse genetics system for the avian coronavirus infectious bronchitis virus. J. Virol. 75:1235912369.
11. Chang, R. Y.,, M. A. Hofmann,, P. B. Sethna, and, D. A. Brian. 1994. A cis -acting function for the coronavirus leader in defective interfering RNA replication. J. Virol. 68:82238231.
12. Chang, R. Y.,, R. Krishnan, and, D. A. Brian. 1996. The UCUAAAC promoter motif is not required for high-frequency leader recombination in bovine coronavirus defective interfering RNA. J. Virol. 70:27202729.
13. Chen, H.,, A. Gill,, B. K. Dove,, S. R. Emmett,, C. F. Kemp,, M. A. Ritchie,, M. Dee, and, J. A. Hiscox. 2005. Mass spectroscopic characterization of the coronavirus infectious bronchitis virus nucleoprotein and elucidation of the role of phosphorylation in RNA binding by using surface plasmon resonance. J. Virol. 79:11641179.
14. Choi, K. S.,, P. Huang, and, M. M. Lai. 2002. Polypyrimidinetract-binding protein affects transcription but not translation of mouse hepatitis virus RNA. Virology 303:5868.
15. Cowley, J. A.,, C. M. Dimmock, and, P. J. Walker. 2002. Gillassociated nidovirus of Penaeus monodon prawns transcribes 3’-coterminal subgenomic mRNAs that do not possess 5’-leader sequences. J. Gen. Virol. 83:927935.
16. Curtis, K. M.,, B. Yount,, A. C. Sims, and, R. S. Baric. 2004. Reverse genetic analysis of the transcription regulatory sequence of the coronavirus transmissible gastroenteritis virus. J. Virol. 78:60616066.
17. Dalton, K.,, R. Casais,, K. Shaw,, K. Stirrups,, S. Evans,, P. Britton,, T. D. Brown, and, D. Cavanagh. 2001. cis -Acting sequences required for coronavirus infectious bronchitis virus defective-RNA replication and packaging. J. Virol. 75:125133.
18. de Groot, R. J.,, R. G. van der Most, and, W. J. M. Spaan. 1992. The fitness of defective interfering murine coronavirus DI-a and its derivatives is decreased by nonsense and frameshift mutations. J. Virol. 66:58985905.
19. de Haan, C. A. M.,, H. Volders,, C. A. Koetzner,, P. S. Masters, and, P. J. M. Rottier. 2002. Coronaviruses maintain viability despite dramatic rearrangements of the strictly conserved genome organization. J. Virol. 76:1249112502.
20. den Boon, J. A.,, M. F. Kleijnen,, W. J. M. Spaan, and, E. J. Snijder. 1996. Equine arteritis virus subgenomic mRNA synthesis: analysis of leader-body junctions and replicative-form RNAs. J. Virol. 70:42914298.
21. den Boon, J. A.,, E. J. Snijder,, E. D. Chirnside,, A. A. de Vries,, M. C. Horzinek, and, W. J. M. Spaan. 1991. Equine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily. J. Virol. 65:29102920.
22. de Vries, A. A.,, E. D. Chirnside,, P. J. Bredenbeek,, L. A. Gravestein,, M. C. Horzinek, and, W. J. M. Spaan. 1990. All subgenomic mRNAs of equine arteritis virus contain a common leader sequence. Nucleic Acids Res. 18:32413247.
23. Dye, C., and, S. G. Siddell. 2005. Genomic RNA sequence of Feline coronavirus strain FIPV WSU-79/1146. J. Gen. Virol. 86:22492253.
24. Escors, D.,, A. Izeta,, C. Capiscol, and, L. Enjuanes. 2003. Transmissible gastroenteritis coronavirus packaging signal is located at the 5’ end of the virus genome. J. Virol. 77:78907902.
25. Fischer, F.,, C. F. Stegen,, C. A. Koetzner, and, P. S. Masters. 1997. Analysis of a recombinant mouse hepatitis virus expressing a foreign gene reveals a novel aspect of coronavirus transcription. J. Virol. 71:51485160.
26. Fu, K., and, R. S. Baric. 1994. Map locations of mouse hepatitis virus temperature-sensitive mutants: confirmation of variable rates of recombination. J. Virol. 68:74587466.
27. Furuya, T., and, M. M. Lai. 1993. Three different cellular proteins bind to complementary sites on the 5’ -end-positive and 3’-end-negative strands of mouse hepatitis virus RNA. J. Virol. 67:72157222.
28. Goebel, S. J.,, B. Hsue,, T. F. Dombrowski, and, P. S. Masters. 2004. Characterization of the RNA components of a putative molecular switch in the 3’ untranslated region of the murine coronavirus genome. J. Virol. 78:669682.
29. Goebel, S. J.,, T. B. Miller,, C. J. Bennett,, K. A. Bernard, and, P. S. Masters. 2006. A hypervariable region within the 3’ cis -acting element of the murine coronavirus genome is nonessential for RNA synthesis but affects pathogenesis. J. Virol. 81:12741287.
30. Goebel, S. J.,, J. Taylor, and, P. S. Masters. 2004. The 3’ cis-acting genomic replication element of the severe acute respiratory syndrome coronavirus can function in the murine coronavirus genome. J. Virol. 78:78467851.
31. Gorbalenya, A. E.,, E. J. Snijder, and, W. J. M. Spaan. 2004. Severe acute respiratory syndrome coronavirus phylogeny: toward consensus. J. Virol. 78:78637866.
32. Hofmann, M. A.,, R. Y. Chang,, S. Ku, and, D. A. Brian. 1993. Leader-mRNA junction sequences are unique for each subgenomic mRNA species in the bovine coronavirus and remain so throughout persistent infection. Virology 196:163171.
33. Hsue, B.,, T. Hartshorne, and, P. S. Masters. 2000. Characterization of an essential RNA secondary structure in the 3 ’ untranslated region of the murine coronavirus genome. J. Virol. 74:69116921.
34. Hsue, B., and, P. S. Masters. 1997. A bulged stem-loop structure in the 3’ untranslated region of the genome of the coronavirus mouse hepatitis virus is essential for replication. J. Virol. 71:75677578.
35. Hsue, B., and, P. S. Masters. 1999. Insertion of a new transcriptional unit into the genome of mouse hepatitis virus. J. Virol. 73:61286135.
36. Huang, P., and, M. M. Lai. 1999. Polypyrimidine tract-binding protein binds to the complementary strand of the mouse hepatitis virus 3’ untranslated region, thereby altering RNA conformation. J. Virol. 73:91109116.
37. Huang, P., and, M. M. Lai. 2001. Heterogeneous nuclear ribonucleoprotein a1 binds to the 3’-untranslated region and mediates potential 5’-3’-end cross talks of mouse hepatitis virus RNA. J. Virol. 75:50095017.
38. Izeta, A.,, C. Smerdou,, S. Alonso,, Z. Penzes,, A. Mendez,, J. Plana-Duran, and, L. Enjuanes. 1999. Replication and packaging of transmissible gastroenteritis coronavirus-derived synthetic minigenomes. J. Virol. 73:15351545.
39. Jeong, Y. S.,, J. F. Repass,, Y. N. Kim,, S. M. Hwang, and, S. Makino. 1996. Coronavirus transcription mediated by sequences flanking the transcription consensus sequence. Virology 217:311322.
40. Johnson, R. F.,, M. Feng,, P. Liu,, J. J. Millership,, B. Yount,, R. S. Baric, and, J. L. Leibowitz. 2005. Effect of mutations in the mouse hepatitis virus 3’( + )42 protein binding element on RNA replication. J. Virol. 79:1457014585.
41. Jonassen, C. M.,, T. O. Jonassen, and, B. Grinde. 1998. A common RNA motif in the 3’ end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus. J. Gen. Virol. 79:715718.
42. Jonassen, C. M.,, T. Kofstad,, I. L. Larsen,, A. Lovland,, K. Handeland,, A. Follestad, and, A. Lillehaug. 2005. Molecular identification and characterization of novel coronaviruses infecting graylag geese (Anser anser), feral pigeons (Columbia livia) and mallards (Anas platyrhynchos). J. Gen. Virol. 86:15971607.
43. Joo, M., and, S. Makino. 1992. Mutagenic analysis of the coronavirus intergenic consensus sequence. J. Virol. 66:63306337.
44. Joo, M., and, S. Makino. 1995. The effect of two closely inserted transcription consensus sequences on coronavirus transcription. J. Virol. 69:272280.
45. Kang, H.,, M. Feng,, M. E. Schroeder,, D. P. Giedroc, and, J. L. Leibowitz. 2006. Putative cis-acting stem-loops in the 5’ untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts. J. Virol. 80:1060010614.
46. Kim, Y. N.,, Y. S. Jeong, and, S. Makino. 1993. Analysis of cis-acting sequences essential for coronavirus defective interfering RNA replication. Virology 197:5363.
47. Kim, Y. N., and, S. Makino. 1995. Characterization of a murine coronavirus defective interfering RNA internal cis-acting replication signal. J. Virol. 69:49634971.
48. Lai, M. M. 1998. Cellular factors in the transcription and replication of viral RNA genomes: a parallel to DNA-dependent RNA transcription. Virology 244:112.
49. Lai, M. M.,, R. S. Baric,, P. R. Brayton, and, S. A. Stohlman. 1984. Characterization of leader RNA sequences on the virion and mRNAs of mouse hepatitis virus, a cytoplasmic RNA virus. Proc. Natl. Acad. Sci. USA 81:36263630.
50. Lai, M. M. C. 1996. Recombination in large RNA viruses: coronaviruses. Semin. Virol. 7:381388.
51. Li, H. P.,, P. Huang,, S. Park, and, M. M. Lai. 1999. Polypyrimidine tract-binding protein binds to the leader RNA of mouse hepatitis virus and serves as a regulator of viral transcription. J. Virol. 73:772777.
52. Li, H. P.,, X. Zhang,, R. Duncan,, L. Comai, and, M. M. Lai. 1997. Heterogeneous nuclear ribonucleoprotein A1 binds to the transcription-regulatory region of mouse hepatitis virus RNA. Proc. Natl. Acad. Sci. USA 94:95449549.
53. Liao, C. L., and, M. M. Lai. 1994. Requirement of the 5’-end genomic sequence as an upstream cis -acting element for coronavirus subgenomic mRNA transcription. J. Virol. 68:47274737.
54. Lin, H. X., and, K. A. White. 2004. A complex network of RNA-RNA interactions controls subgenomic mRNA transcription in a tombusvirus. EMBO J. 23:33653374.
55. Lin, Y. J., and, M. M. Lai. 1993. Deletion mapping of a mouse hepatitis virus defective interfering RNA reveals the requirement of an internal and discontiguous sequence for replication. J. Virol. 67:61106118.
56. Lin, Y. J.,, C. L. Liao, and, M. M. Lai. 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. 68:81318140.
57. Liu, Q.,, R. F. Johnson, and, J. L. Leibowitz. 2001. Secondary structural elements within the 3’ untranslated region of mouse hepatitis virus strain JHM genomic RNA. J. Virol. 75:1210512113.
58. Liu, Q.,, W. Yu, and, J. L. Leibowitz. 1997. A specific host cellular protein binding element near the 3’ end of mouse hepatitis virus genomic RNA. Virology 232:7485.
59. Luytjes, W.,, H. Gerritsma, and, W. J. M. Spaan. 1996. Replication of synthetic defective interfering RNAs derived from coronavirus mouse hepatitis virus-A59. Virology 216:174183.
60. Makino, S., and, M. Joo. 1993. Effect of intergenic consensus sequence flanking sequences on coronavirus transcription. J. Virol. 67:33043311.
61. Makino, S.,, M. Joo, and, J. K. Makino. 1991. A system for study of coronavirus mRNA synthesis: a regulated, expressed subgenomic defective interfering RNA results from intergenic site insertion. J. Virol. 65:60316041.
62. Makino, S., and, M. M. Lai. 1989. High-frequency leader sequence switching during coronavirus defective interfering RNA replication. J. Virol. 63:52855292.
63. Makino, S.,, S. A. Stohlman, and, M. M. Lai. 1986. Leader sequences of murine coronavirus mRNAs can be freely reas-sorted: evidence for the role of free leader RNA in transcription. Proc. Natl. Acad. Sci. USA 83:42044208.
64. Masters, P. S. 2006. The molecular biology of coronaviruses. Adv. Virus Res. 66:193292.
65. Masters, P. S.,, C. A. Koetzner,, C. A. Kerr, and, Y. Heo. 1994. Optimization of targeted RNA recombination and mapping of a novel nucleocapsid gene mutation in the coronavirus mouse hepatitis virus. J. Virol. 68:328337.
66. Masters, P. S., and, P. J. Rottier. 2005. Coronavirus reverse genetics by targeted RNA recombination. Curr. Top. Microbiol. Immunol. 287:133159.
67. Meulenberg, J. J. M.,, J. N. A. Bos-De Ruijter,, R. van de Graaf,, G. Wensvoort, and, R. J. M. Moormann. 1998. Infectious transcripts from cloned genome-length cDNA of porcine reproductive and respiratory syndrome virus. J. Virol. 72:380387.
68. Miller, W. A.,, T. W. Dreher, and, T. C. Hall. 1985. Synthesis of brome mosaic virus subgenomic RNA in vitro by internal initiation on ( — )-sense genomic RNA. Nature 313:6870.
69. Miller, W. A., and, G. Koev. 2000. Synthesis of subgenomic RNAs by positive-strand RNA viruses. Virology 273:18.
70. Mizutani, T.,, J. F. Repass, and, S. Makino. 2000. Nascent synthesis of leader sequence-containing subgenomic mRNAs in coronavirus genome-length replicative intermediate RNA. Virology 275:238243.
71. Molenkamp, R.,, S. Greve,, W. J. M. Spaan, and, E. J. Snijder. 2000. Efficient homologous RNA recombination and requirement for an open reading frame during replication of equine arteritis virus defective interfering RNAs. J. Virol. 74:90629070.
72. Molenkamp, R.,, B. C. Rozier,, S. Greve,, W. J. M. Spaan, and, E. J. Snijder. 2000. Isolation and characterization of an arterivirus defective interfering RNA genome. J. Virol. 74:31563165.
73. Molenkamp, R.,, H. van Tol,, B. C. Rozier,, Y. van der Meer,, W. J. M. Spaan, and, E. J. Snijder. 2000. The arterivirus replicase is the only viral protein required for genome replication and subgenomic mRNA transcription. J. Gen. Virol. 81:24912496.
74. Nelson, G. W.,, S. A. Stohlman, and, S. M. Tahara. 2000. High affinity interaction between nucleocapsid protein and leader/ intergenic sequence of mouse hepatitis virus RNA. J. Gen. Virol. 81:181188.
75. Ozdarendeli, A.,, S. Ku,, S. Rochat,, G. D. Williams,, S. D. Senanayake, and, D. A. Brian. 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. 75:73627374.
76. Pasternak, A. O. 2003. Nidovirus Transcription-Regulating Sequences. Ph.D. thesis. Leiden University, Leiden, The Netherlands.
77. Pasternak, A. O.,, A. P. Gultyaev,, W. J. M. Spaan, and, E. J. Snijder. 2000. Genetic manipulation of arterivirus alternative mRNA leader-body junction sites reveals tight regulation of structural protein expression. J. Virol. 74:1164211653.
78. Pasternak, A. O.,, W. J. M. Spaan, and, E. J. Snijder. 2004. Regulation of relative abundance of arterivirus subgenomic mRNAs. J. Virol. 78:81028113.
79. Pasternak, A. O.,, W. J. M. Spaan, and, E. J. Snijder. 2006. Nidovirus transcription: how to make sense . . . ? J. Gen. Virol. 87:14031421.
80. Pasternak, A. O.,, E. van den Born,, W. J. M. Spaan, and, E. J. Snijder. 2001. Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis. EMBO J. 20:72207228.
81. Pasternak, A. O.,, E. van den Born,, W. J. M. Spaan, and, E. J. Snijder. 2003. The stability of the duplex between sense and antisense transcription-regulating sequences is a crucial factor in arterivirus subgenomic mRNA synthesis. J. Virol. 77:11751183.
82. Posthuma, C. C.,, D. D. Nedialkova,, J. C. Zevenhoven-Dobbe,, J. H. Blokhuis,, A. E. Gorbalenya, and, E. J. Snijder. 2006. Site-directed mutagenesis of the nidovirus replicative endoribonuclease NendoU exerts pleiotropic effects on the arterivirus life cycle. J. Virol. 80:16531661.
83. Raman, S.,, P. Bouma,, G. D. Williams, and, D. A. Brian. 2003. Stem-loop III in the 5’ untranslated region is a cis -acting element in bovine coronavirus defective interfering RNA replication. J. Virol. 77:67206730.
84. Raman, S., and, D. A. Brian. 2005. Stem-loop IV in the 5’ untranslated region is a cis -acting element in bovine coronavirus defective interfering RNA replication. J. Virol. 79:1243412446.
85. Repass, J. F., and, S. Makino. 1998. Importance of the positive-strand RNA secondary structure of a murine coronavirus defective interfering RNA internal replication signal in positive-strand RNA synthesis. J. Virol. 72:79267933.
86. Robertson, M. P.,, H. Igel,, R. Baertsch,, D. Haussler,, M. Ares, Jr., and, W. G. Scott. 2005. The structure of a rigorously conserved RNA element within the SARS virus genome. PLoS Biol. 3:e5.
87. Sawicki, D.,, T. Wang, and, S. Sawicki. 2001. The RNA structures engaged in replication and transcription of the A59 strain of mouse hepatitis virus. J. Gen. Virol. 82:385396.
88. Sawicki, S. G., and, D. L. Sawicki. 1990. Coronavirus transcription: subgenomic mouse hepatitis virus replicative intermediates function in RNA synthesis. J. Virol. 64:10501056.
89. Sawicki, S. G., and, D. L. Sawicki. 1995. Coronaviruses use discontinuous extension for synthesis of subgenome-length negative strands. Adv. Exp. Med. Biol. 380:499506.
90. Sawicki, S. G., and, D. L. Sawicki. 2005. Coronavirus transcription: a perspective. Curr. Top. Microbiol. Immunol. 287:3155.
91. Sawicki, S. G.,, D. L. Sawicki, and, S. G. Siddell. 2007. A contemporary view of coronavirus transcription. J. Virol. 81:2029.
92. Schelle, B.,, N. Karl,, B. Ludewig,, S. G. Siddell, and, V. Thiel. 2005. Selective replication of coronavirus genomes that express nucleocapsid protein. J. Virol. 79:66206630.
93. Schutze, H.,, R. Ulferts,, B. Schelle,, S. Bayer,, H. Granzow,, B. Hoffmann,, T. C. Mettenleiter, and, J. Ziebuhr. 2006. Characterization of white bream virus reveals a novel genetic cluster of nidoviruses. J. Virol. 80:1159811609.
94. Sethna, P. B.,, S. L. Hung, and, D. A. Brian. 1989. Coronavirus subgenomic minus-strand RNAs and the potential for mRNA replicons. Proc. Natl. Acad. Sci. USA 86:56265630.
95. Shen, X., and, P. S. Masters. 2001. Evaluation of the role of heterogeneous nuclear ribonucleoprotein A1 as a host factor in murine coronavirus discontinuous transcription and genome replication. Proc. Natl. Acad. Sci. USA 98:27172722.
96. Shi, S. T.,, P. Huang,, H. P. Li, and, M. M. Lai. 2000. Heterogeneous nuclear ribonucleoprotein A1 regulates RNA synthesis of a cytoplasmic virus. EMBO J. 19:47014711.
97. Shi, S. T., and, M. M. Lai. 2005. Viral and cellular proteins involved in coronavirus replication. Curr. Top. Microbiol. Immunol. 287:95131.
98. Siddell, S. G.,, J. Ziebuhr, and, E. J. Snijder. 2005. Coronaviruses, toroviruses, and arteriviruses, p. 823856. In B. W. J. Mahy and, V. ter Meulen (ed.), Topley and Wilson’s Microbiology and Microbial Infections, 10th ed. Virology. Hodder Arnold, London, United Kingdom.
99. Sit, T. L.,, A. A. Vaewhongs, and, S. A. Lommel. 1998. RNA-mediated trans-activation of transcription from a viral RNA. Science 281:829832.
100. Smits, S. L.,, A. L. W. van Vliet,, K. Segeren,, H. el Azzouzi,, M. van Essen, and, R. J. de Groot. 2005. Torovirus non-discontinuous transcription: mutational analysis of a subgenomic mRNA promoter. J. Virol. 79:82758281.
101. Snijder, E. J.,, J. A. den Boon,, M. C. Horzinek, and, W. J. M. Spaan. 1991. Characterization of defective interfering RNAs of Berne virus. J. Gen. Virol. 72:16351643.
102. Snijder, E. J.,, M. C. Horzinek, and, W. J. M. Spaan. 1990. A 3’-coterminal nested set of independently transcribed mRNAs is generated during Berne virus replication. J. Virol. 64:331338.
103. Sola, I.,, J. L. Moreno,, S. Zuniga,, S. Alonso, and, L. Enjuanes. 2005. Role of nucleotides immediately flanking the transcription-regulating sequence core in coronavirus subgenomic mRNA synthesis. J. Virol. 79:25062516.
104. Spaan, W. J. M.,, H. Delius,, M. Skinner,, J. Armstrong,, P. Rottier,, S. Smeekens,, B. A. van der Zeijst, and, S. G. Siddell. 1983. Coronavirus mRNA synthesis involves fusion of noncontiguous sequences. EMBO J. 2:18391844.
105. Spagnolo, J. F., and, B. G. Hogue. 2000. Host protein interactions with the 3’ end of bovine coronavirus RNA and the requirement of the poly(A) tail for coronavirus defective genome replication. J. Virol. 74:50535065.
106. Stirrups, K.,, K. Shaw,, S. Evans,, K. Dalton,, D. Cavanagh, and, P. Britton. 2000. Leader switching occurs during the rescue of defective RNAs by heterologous strains of the coronavirus infectious bronchitis virus. J. Gen. Virol. 81:791801.
107. Thiel, V.,, J. Herold,, B. Schelle, and, S. G. Siddell. 2001. Infectious RNA transcribed in vitro from a cDNA copy of the human coronavirus genome cloned in vaccinia virus. J. Gen. Virol. 82:12731281.
108. Thiel, V.,, J. Herold,, B. Schelle, and, S. G. Siddell. 2001. Viral replicase gene products suffice for coronavirus discontinuous transcription. J. Virol. 75:66766681.
109. Tijms, M. A.,, L. C. van Dinten,, A. E. Gorbalenya, and, E. J. Snijder. 2001. A zinc finger-containing papain-like protease couples subgenomic mRNA synthesis to genome translation in a positive-stranded RNA virus. Proc. Natl. Acad. Sci. USA 98:18891894.
110. van den Born, E.,, A. P. Gultyaev, and, E. J. Snijder. 2004. Secondary structure and function of the 5’-proximal region of the equine arteritis virus RNA genome. RNA 10:424437.
111. van den Born, E.,, C. C. Posthuma,, A. P. Gultyaev, and, E. J. Snijder. 2005. Discontinuous subgenomic RNA synthesis in arteriviruses is guided by an RNA hairpin structure located in the genomic leader region. J. Virol. 79:63126324.
112. van der Meer, Y.,, E. J. Snijder,, J. C. Dobbe,, S. Schleich,, M. R. Denison,, W. J. M. Spaan, and, J. Krijnse Locker. 1999. Localization of mouse hepatitis virus nonstructural proteins and RNA synthesis indicates a role for late endosomes in viral replication. J. Virol. 73:76417657.
113. van der Most, R. G.,, P. J. Bredenbeek, and, W. J. M. Spaan. 1991. A domain at the 3’ end of the polymerase gene is essential for encapsidation of coronavirus defective interfering RNAs. J. Virol. 65:32193226.
114. van der Most, R. G.,, R. J. de Groot, and, W. J. M. Spaan. 1994. Subgenomic RNA synthesis directed by a synthetic defective interfering RNA of mouse hepatitis virus: a study of coronavirus transcription initiation. J. Virol. 68:36563666.
115. van der Most, R. G.,, L. Heijnen,, W. J. M. Spaan, and, R. J. de Groot. 1992. Homologous RNA recombination allows efficient introduction of site-specific mutations into the genome of coronavirus MHV-A59 via synthetic co-replicating RNAs. Nucleic Acids Res. 20:33753381.
116. van der Most, R. G.,, W. Luytjes,, S. Rutjes, and, W. J. M. Spaan. 1995. Translation but not the encoded sequence is essential for the efficient propagation of the defective interfering RNAs of the coronavirus mouse hepatitis virus. J. Virol. 69:37443751.
117. van Dinten, L. C.,, J. A. den Boon,, A. L. M. Wassenaar,, W. J. M. Spaan, and, E. J. Snijder. 1997. An infectious arteri-virus cDNA clone: identification of a replicase point mutation that abolishes discontinuous mRNA transcription. Proc. Natl. Acad. Sci. USA 94:991996.
118. van Marle, G.,, J. C. Dobbe,, A. P. Gultyaev,, W. Luytjes,, W. J. M. Spaan, and, E. J. Snijder. 1999. Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences. Proc. Natl. Acad. Sci. USA 96:1205612061.
119. van Marle, G.,, W. Luytjes,, R. G. van der Most,, T. van der Straaten, and, W. J. Spaan. 1995. Regulation of coronavirus mRNA transcription. J. Virol. 69:78517856.
120. van Marle, G.,, L. C. van Dinten,, W. J. M. Spaan,, W. Luytjes, and, E. J. Snijder. 1999. Characterization of an equine arteritis virus replicase mutant defective in subgenomic mRNA synthesis. J. Virol. 73:52745281.
121. van Vliet, A. L.,, S. L. Smits,, P. J. Rottier, and, R. J. de Groot. 2002. Discontinuous and non-discontinuous subgenomic RNA transcription in a nidovirus. EMBO J. 21:65716580.
122. Verheije, M. H.,, R. C. L. Olsthoorn,, M. V. Kroese,, P. J. M. Rottier, and, J. J. M. Meulenberg. 2002. Kissing interaction between 3’ noncoding and coding sequences is essential for porcine arterivirus RNA replication. J. Virol. 76:15211526.
123. Wang, Y., and, X. Zhang. 2000. The leader RNA of coronavirus mouse hepatitis virus contains an enhancer-like element for subgenomic mRNA transcription. J. Virol. 74:1057110580.
124. White, K. A. 2002. The premature termination model: a possible third mechanism for subgenomic mRNA transcription in ( + )-strand RNA viruses. Virology 304:147154.
125. Williams, G. D.,, R. Y. Chang, and, D. A. Brian. 1995. Evidence for a pseudoknot in the 3’ untranslated region of the bovine coronavirus genome. Adv. Exp. Med. Biol. 380:511514.
126. Williams, G. D.,, R. Y. Chang, and, D. A. Brian. 1999. A phylogenetically conserved hairpin-type 3’ untranslated region pseudoknot functions in coronavirus RNA replication. J. Virol. 73:83498355.
127. Wu, H. Y., and, D. A. Brian. 2007. 5’-Proximal hotspot for an inducible positive-to-negative-strand template switch by coronavirus RNA-dependent RNA polymerase. J. Virol. 81:32063215.
128. Wu, H. Y.,, J. S. Guy,, D. Yoo,, R. Vlasak,, E. Urbach, and, D. A. Brian. 2003. Common RNA replication signals exist among group 2 coronaviruses: evidence for in vivo recombination between animal and human coronavirus molecules. Virology 315:174183.
129. Yount, B.,, M. R. Denison,, S. R. Weiss, and, R. S. Baric. 2002. Systematic assembly of a full-length infectious cDNA of mouse hepatitis virus strain A59. J. Virol. 76:1106511078.
130. Yu, W., and, J. L. Leibowitz. 1995. A conserved motif at the 3 ’ end of mouse hepatitis virus genomic RNA required for host protein binding and viral RNA replication. Virology 214:128138.
131. Zhang, X., and, M. M. Lai. 1994. Unusual heterogeneity of leader-mRNA fusion in a murine coronavirus: implications for the mechanism of RNA transcription and recombination. J. Virol. 68:66266633.
132. Zhang, X., and, M. M. Lai. 1995. Interactions between the cytoplasmic proteins and the intergenic (promoter) sequence of mouse hepatitis virus RNA: correlation with the amounts of subgenomic mRNA transcribed. J. Virol. 69:16371644.
133. Zhang, X., and, M. M. Lai. 1996. A 5’-proximal RNA sequence of murine coronavirus as a potential initiation site for genomic-length mRNA transcription. J. Virol. 70:705711.
134. Zhang, X.,, C. L. Liao, and, M. M. Lai. 1994. Coronavirus leader RNA regulates and initiates subgenomic mRNA transcription both in trans and in cis. J. Virol. 68:47384746.
135. Zhang, X., and, R. Liu. 2000. Identification of a noncanonical signal for transcription of a novel subgenomic mRNA of mouse hepatitis virus: implication for the mechanism of coronavirus RNA transcription. Virology 278:7585.
136. Zuniga, S.,, I. Sola,, S. Alonso, and, L. Enjuanes. 2004. Sequence motifs involved in the regulation of discontinuous coronavirus subgenomic RNA synthesis. J. Virol. 78:980994.

Tables

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Table 1.

Maximal -acting replication signals in nidovirus genomes

Citation: van den Born E, Snijder E. 2008. RNA Signals Regulating Nidovirus RNA Synthesis, p 115-131. In Perlman S, Gallagher T, Snijder E (ed), Nidoviruses. ASM Press, Washington, DC. doi: 10.1128/9781555815790.ch8

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