A stem-loop motif formed by the immediate 5' terminus of the bovine viral diarrhea virus genome modulates translation as well as replication of the viral RNA

Journal of Virology

Volumn 74, Issue 13, 2000, Pages 5825-5835

  Yu, Haiying ^a   Isken, Olaf ^a   Grassmann, Claus W ^a   Behrens, Sven Erik ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; VIRUS RNA;

ANIMAL CELL; ARTICLE; BOVINE DIARRHEA VIRUS; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; RNA REPLICATION; RNA STRUCTURE; RNA TRANSLATION; UNTRANSLATED REGION; VIRUS GENOME; VIRUS REPLICATION;

5' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CATTLE; CELL LINE; CRICETINAE; DIARRHEA VIRUSES, BOVINE VIRAL; GENOME, VIRAL; MOLECULAR SEQUENCE DATA; MUTAGENESIS; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; RNA, COMPLEMENTARY; RNA, VIRAL; VIRUS REPLICATION;

EID: 0034086727     PISSN: 0022538X     EISSN: None     Source Type: Journal    
DOI: 10.1128/JVI.74.13.5825-5835.2000     Document Type: Article

References (52)

1. Andino, R., G. E. Rieckhof, and D. Baltimore. 1990. A functional ribonucleoprotein complex forms around the 5′ end of poliovirus RNA. Cell 63: 369-380.
2. Andino, R., G. E. Rieckhof, P. L. Achacoso, and D. Baltimore. 1993. Poliovirus RNA synthesis utilizes an RNP complex formed around the 5′ end of viral RNA. EMBO J. 12:3587-3598.
3. Argos, P. 1988. A sequence motif in many polymerases. Nucleic Acids Res. 16:9909-9916.
4. Barton, D. J., and J. B. Flanegan. 1993. Coupled translation and replication of poliovirus RNA in vitro: synthesis of functional 3D polymerase and infectious virus. J. Virol. 67:822-831.
5. Becher, P., M. Orlich, and H.-J. Thiel. 1998. Complete genomic sequence of horder disease virus, a pestivirus from sheep. J. Virol. 72:5165-5173.
6. Behrens, S.-E., C. W. Grassmann, H.-J. Thiel, G. Meyers, and N. Tautz. 1998. Characterization of an autonomous subgenomic pestivirus RNA replicon. J. Virol. 72:2364-2372.
7. Borman, A. M., F. G. Deliat, and K. M. Kean. 1994. Sequences within the poliovirus internal ribosome entry segment control viral RNA synthesis. EMBO J. 13:3149-3157.
8. Brown, E. A., H. Zhang, L. Ping, and S. M. Lemon. 1992. Secondary structure of the 5′ nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. Nucleic Acids Res. 20:5041-5045.
9. Chon, S. K., D. R. Perez, and R. O. Donis. 1998. Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology 251: 370-382.
10. Christiansen, J., and R. Garrett. 1988. Enzymatic and chemical probing of rihosomal RNA-protein interactions. Methods Enzymol. 164:456-468.
11. Deng, R., and K. V. Brock. 1993. 5′ and 3′ untranslated regions of pestivirus genome: primary and secondary structure analyses. Nucleic Acids Res. 21: 1949-1957.
12. Francki, R. I., D. L. Fauquet, D. L. Knudson, and F. Brown. 1991. Classification and nomenclature of viruses. Arch. Virol. Suppl. 2:223-233.
13. Frolov, I., M. S. McBride, and C. M. Rice. 1998. Cis-acting RNA elements required for replication of bovine viral diarrhea virus-hepatitis C virus 5′ nontranslated region chimeras. RNA 4:1418-1435.
14. Fukushi, S., K. Katayama, C. Kurihara, N. Ishiyama, F. B. Hoshino, T. Ando, and A. Oya. 1994. Complete 5′ noncoding region is necessary for the efficient internal initiation of hepatitis C virus RNA. Biochem. Biophys. Res. Commun. 199:425-432.
15. Garmanik, A. V., and R. Andino. 1996. Replication of poliovirus in Xenopus oocytes requires two human factors. EMBO J. 15:5988-5998.
16. Garmanik, A. V., and R. Andino. 1997. Two functional complexes formed by KH domain containing proteins with the 5′ noncoding region of poliovirus RNA. RNA 3:882-892.
17. Grassmann, C. W., O. Isken, and S.-E. Behrens. 1999. Assignment of the multifunctional NS3 protein of bovine viral diarrhea virus during RNA replication: an in vivo and in vitro study. J. Virol. 73:9195-9205.
18. Hahn, C. S., Y. S. Hahn, C. M. Rice, E. Lee, L. Dalgarno, E. G. Strauss, and J. H. Strauss. 1987. Conserved elements in the 3′ untranslated region of flavivirus RNAs and potential cyclization sequences. J. Mol. Biol. 198:33-41.
19. Honda, M., L.-H. Ping, R. C. A. Rijnbrand, E. Amphlett, B. Clarke, D. Rowlands, and S. M. Lemon. 1996. Structural requirements for initiation of translaion by internal ribosome entry site within genome-length hepatitis C virus RNA. Virology 222:31-42.
20. Ito, T., and M. C. Lai. 1999. An internal polypyrimidine-tract binding protein-binding site in the hepatitis C virus RNA attenuates translation, which is relieved by the 3′-untranslated region. Virology 254:288-296.
21. Jang, S. K., T. V. Pestova, C. U. T. Hellen, G. W. Witherell, and E. Wimmer. 1990. Cap-independent translation of picornavirus RNAs: structure and function of the internal ribosomal entry site. Enzyme 44:292-309.
22. Kaminski, A., M. T. Howell, and R. J. Jackson. 1990. Initiation of encephalomyocarditis virus RNA translation: the authentic initiation site is not selected by a scanning mechanism. EMBO J. 9:3753-3759.
23. Mathews, D. H., J. Sabina, M. Zuker, and D. H. Turner. 1999. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol. 288:911-940.
24. Mendez, E., N. Ruggli, M. S. Collett, and C. M. Rice. 1998. Infectious bovine viral diarrhea virus (strain NADL) RNA from stable cDNA clones: a cellular insert determines NS3 production and viral cytopathogenicity. J. Virol. 72: 4737-4745.
25. Meyers, G., N. Tautz, P. Becher, H.-J. Thiel, and B. M. Kümmerer. 1996. Recovery of cytopathogenic and noncytopathogenic bovine viral diarrhea viruses from cDNA constructs. J. Virol. 70:8606-8613.
26. Molla, A., A. V. Paul, and E. Wimmer. 1991. Cell-free, de novo synthesis of poliovirus. Science 254:1647-1651.
27. Pelletier, J., and N. Sonenberg. 1988. Internal initiation of translation of eukaryotic mRNA directed from a sequence derived from poliovirus RNA. Nature 334:320-325.
28. Pestova, T. V., I. N. Shalsky, S. P. Fletcher, R. J. Jackson, and C. U. T. Hellen. 1998. A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal initiation of translation of hepatitis C virus and classical swine fever virus RNAs. Genes Dev. 12:67-83.
29. Poole, T. L., C. Wang, R. A. Popp, L. N. D. Potgieter, A. Siddiqui, and M. S. Collett. 1995. Pestivirus translation initiation occurs by internal ribosome entry. Virology 206:750-754.
30. Rice, C. M. 1996. Flaviviridae: the viruses and their replication, p. 931-959. In B. N. Fields, D. M. Knipe, and P. M. Howley (ed.), Fields virology. Raven Press, Philadelphia, Pa.
31. Rijnbrand, R., P. Bredenbeek, T. van der Straaten, L. Whetter, G. Inchauspe, S. Lemon, and W. Spaan. 1995. Almost the entire 5′ non-translated region of hepatitis C virus is required for cap-independent translation. FEBS Lett. 365:115-119.
32. Rijnbrand, R., T. van der Straaten, P. A. van Rijn, W. J. M. Spaan, and P. J. Bredenbeek. 1997. Internal entry of ribosomes is directed by the 5′ noncoding region of classical swine fever virus and is dependent on the presence of an RNA pseudoknot upstream of the initiation codon. J. Virol. 71:451-457.
33. Rohll, J. B., N. Percy, R. Ley, D. J. Evans, J. W. Almond, and W. S. Barclay. 1994. The 5′-untranslated regions of picornavirus RNAs contain independent functional domains essential for RNA replication and translation. J. Virol. 68:4384-4391.
34. Shiroki, K., T. Ishii, T. Aoki, M. Kobashi, S. Ohka, and A. Nomoto. 1995. A new cis-acting element for RNA replication within the 5′ noncoding region of poliovirus type 1 RNA. J. Virol. 69:6825-6832.
35. Simoes, E. A., and P. Sarnow. 1991. An RNA hairpin at the extreme 5′ end of the poliovirus RNA genome modulates viral translation in human cells. J. Virol. 65:913-921.
36. Steffens, S., H.-J. Thiel, and S.-E. Behrens. 1999. The RNA-dependent RNA polymerases of different members of the Flaviviridae family exhibit similar properties under in vitro conditions. J. Gen. Virol. 80:2583-2590.
37. Stern, S., D. Moazed, and H. F. Noller. 1988. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164:481-489.
38. Strauss, J. H., and E. G. Strauss. 1994. The alphaviruses: gene expression, replication, and evolution. Microbiol. Rev. 58:491-562.
39. Takamizawa, A., C. Mori, I. Fuke, S. Manabe, S. Murakami, J. Fujita, E. Onishi, T. Andoh, I. Yoshida, and H. Okayama. 1991. Structure and organization of the hepatitis C virus genome isolated from human carriers. J. Virol. 65:1105-1113.
40. Tamura, J. K., P. Warrener, and M. S. Collett. 1993. RNA-stimulated NTPase activity associated with the p80 protein of the pestivirus bovine viral diarrhea virus. Virology 193:1-10.
41. Tautz, N., H.-J. Thiel, E. J. Dubovi, and G. Meyers. 1994. Pathogenesis of mucosal disease: a cytopathogenic pestivirus generated by an internal deletion. J. Virol. 68:3289-3297.
42. Tautz, N., G. Meyers, R. Stark, E. J. Dubovi, and H.-J. Thiel. 1996. Cytopathogenicity of a pestivirus correlates with a 27-nucleotide insertion. J. Virol. 70:7851-7858.
43. Tautz, N., K. Elbers, D. Stoll, G. Meyers, and H.-J. Thiel. 1997. Serine protease of pestiviruses: determination of cleavage sites. J. Virol. 71:5415-5422.
44. Thiel, H.-J., P. G. W. Plagemann, and V. Moennig. 1996. Pestiviruses, p. 1059-1074. In B. N. Fields, D. M. Knipe, and P. M. Howley (ed.), Fields virology. Raven Press, Philadelphia, Pa.
45. Tsukiyama-Kohara, K., N. Iizuka, M. Kohara, and A. Nomoto. 1992. Internal ribosome entry site within hepatitis C virus RNA. J. Virol. 66:1476-1483.
46. Vassilev, V. B., M. S. Collett, and R. O. Donis. 1997. Authentic and chimeric full-length genomic cDNA clones of bovine viral diarrhea virus that yield infectious transcripts. J. Virol. 71:471-478.
47. Warrener, P., and M. S. Collett. 1995. Pestivirus NS3 (p80) protein possesses RNA helicase activity. J. Virol. 69:1720-1726.
48. Wimmer, E., C. U. T. Hellen, and X. Cao. 1993. Genetics of poliovirus. Annu. Rev. Genet. 27:353-436.
49. Wiskerchen, M., S. K. Belzer, and M. S. Collett. 1991. Pestivirus gene expression: the first protein product of the bovine viral diarrhea virus large open reading frame, p20, possesses proteolytic activity. J. Virol. 65:4508-4514.
50. Xu, J., E. Mendez, P. R. Caron, C. Lin, M. A. Murcko, M. S. Collett, and C. M. Rice. 1997. Bovine viral diarrhea virus NS3 serine protease: polyprotein cleavage sites, cofactor requirements, and molecular model of an enzyme essential for pestivirus replication. J. Virol. 71:5312-5322.
51. Yu, H., C. W. Grassmann, and S.-E. Behrens. 1999. Sequence and structural elements at the 3′ terminus of bovine viral diarrhea virus genomic RNA: functional role during RNA replication. J. Virol. 73:3638-3648.
52. Zhong, W., L. L. Gutshall, and A. M. Del Vecchio. 1998. Identification and characterization of an RNA-dependent RNA polymerase activity within the nonstructural protein 5B region of bovine viral diarrhea virus. J. Virol. 72: 9365-9369.