Virus-encoded proteinases of the Flaviviridae

Journal of General Virology

Volumn 79, Issue 5, 1998, Pages 947-959

  Ryan, Martin D ^a   Monaghan, Susan ^a   Flint, Mike ^b  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b UNIVERSITY OF READING   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEINASE; VIRUS ENZYME;

ENZYME ACTIVATION; ENZYME STRUCTURE; FLAVIVIRUS; PESTIVIRUS; PRIORITY JOURNAL; PROTEIN DEGRADATION; REVIEW;

FLAVIVIRIDAE; FLAVIVIRUS; PESTIVIRUS;

EID: 0031898959     PISSN: 00221317     EISSN: None     Source Type: Journal    
DOI: 10.1099/0022-1317-79-5-947     Document Type: Review

References (146)

1. Adams, A., Chamberlain, R. W., Taylor, L. A., Davidson, F., Lin, C. K., Simmonds, P. & Elliott, R. M. (1997). Complete coding sequence of hepatitis C virus genotype 6a. Biochemical and Biophysical Research Communications 234, 393-396.
2. Allaire, M., Cheraia, M. M., Malcolm, B. A. & James, M. N. G. (1994). Picornaviral 3C cysteine proteinases have a fold similar to chymotrypsin-like serine proteinases. Nature 369, 72-76.
3. Arias, C., Preugschat, F. & Strauss, J. H. (1993). Dengue 2 virus NS2B and NS3 form a stable complex that can cleave NS3 within the helicase domain. Virology 193, 888-899.
4. Bartenschlager, R. L., Ahlborn-Laake, L., Mous, J. & Jacobsen, H. (1993). Nonstructural protein 3 of the hepatitis C virus encodes a serine-type proteinase required for cleavage at the NS3/4 and NS4/5 junctions. Journal of Virology 67, 3835-3844.
5. Bartenschlager, R. L., Ahlborn-Laake, L., Mous, J. & Jacobsen, H. (1994). Kinetic and structural analysis of hepatitis C virus polyprotein processing. Journal of Virology 68, 5045-5055.
6. Bartenschlager, R. L., Lohmann, V., Wilkinson, T. & Koch, J. O. (1995). Complex formation between the NS3 serine-type proteinase of the hepatitis C virus and NS4A and its importance for polyprotein maturation. Journal of Virology 69, 7519-7528.
7. Bazan, J. F. & Fletterick, R. J. (1989). Detection of a trypsin-like serine protease domain in flaviviruses and pestiviruses. Virology 171, 637-639.
8. Bazan, J. F. & Fletterick, R. J. (1990). Structural and catalytic models of trypsin-like viral proteases. Seminars in Virology 1, 311-322.
9. Becher, P., Meyers, G., Shannon, A. D. & Thiel, H.-J. (1996). Cytopathogenicity of border disease virus is correlated with integration of cellular sequences into the viral genome. Journal of Virology 70, 2992-2998.
10. Bianchi, E., Steinkuhler, C., Taliani, M., Urbani, A., De Francesco, R. & Pessi, A. (1996). Synthetic depsipeptide substrates for the assay of human hepatitis C virus protease. Analytical Biochemistry 237, 239-244.
11. Biedrzycka, A., Cauchi, M. R., Bartholomeusz, A., Gorman, J. J. & Wright, P. J. (1987). Characterization of protease cleavage sites involved in the formation of the envelope glycoprotein and three non-structural proteins of dengue virus type 2, New Guinea C strain. Journal of General Virology 68, 1317-1326.
12. Bouffard, P., Bartenschlager, R., Ahlborn-Laake, L., Mous, J., Roberts, N. & Jacobsen, H. (1995). An in vitro assay for hepatitis C virus serine proteinase. Virology 209, 52-59.
13. Butkiewicz, N. J., Wendel, M., Zhang, R., Jubin, R., Pichardo, J., Smith, E. B., Hart, A. M., Ingram, R., Durkin, J., Mui, P. W., Murray, M. G., Ramanthan, L. & Dasmahapatra, B. (1996). Enhancement of hepatitis C virus NS3 proteinase activity by association with NS4A-specific synthetic peptides: Identification of sequence and critical residues of NS4A for the cofactor activity. Virology 225, 328-338.
14. Cahour, A., Falgout, B. & Lai, C.-J. (1992). Cleavage of the dengue virus polyprotein at the NS3/NS4A and NS4B/NS5 junctions is mediated by viral protease NS2B-NS3, whereas NS4A/NS4B may be processed by a cellular protease. Journal of Virology 66, 1535-1542.
15. Castle, E., Leidner, U., Nowak, T. & Wengler, G. (1986). Primary structure of the West Nile flavivirus genome region coding for all nonstructural proteins. Virology 149, 10-26.
16. Chamberlain, R. W., Adams, N., Saeed, A. A., Simmonds, P. & Elliott, R. M. (1997a). Complete nucleotide sequence of a type 4 hepatitis C virus variant, the predominant genotype in the Middle East. Journal of General Virology 78, 1341-1347.
17. Chamberlain, R. W., Adams, N. J., Taylor, L. A., Simmonds, P. & Elliott, R. M. (1997b). The complete coding sequence of hepatitis C virus genotype 5a, the predominant genotype in South Africa. Biochemical and Biophysical Research Communications 236, 44-49.
18. Chambers, T. J., McCourt, D. W. & Rice, C. M. (1989). Yellow fever virus proteins NS2a, NS2b and NS4b; identification and partial amino acid sequence analysis. Virology 169, 100-109.
19. Chambers, T. J., Grakoui, A. & Rice, C. M. (1990a). Flavivirus genome organization, expression and replication. Annual Review of Microbiology 44, 649-688.
20. Chambers, T. J., Wier, R. C., Grakoui, A., McCourt, D. W., Bazan, J. F., Fletterick, R. J. & Rice, C. M. (1990b). Evidence that the N-terminal domain of yellow fever virus NS3 is a serine protease responsible for site-specific cleavages in the viral polyprotein. Proceedings of the National Academy of Sciences, USA 87, 8898-8902.
21. Chambers, T. J., Grakoui, A. & Rice, C. M. (1991). Processing of the yellow fever virus nonstructural polyprotein: a catalytically active NS3 protease domain and NS2B are required for cleavages at dibasic sites. Journal of Virology 65, 6042-6050.
22. Chayama, K., Tsubota, A., Koida, I., Arase, Y., Saitoh, S., Ikeda, K. & Kumada, H. (1994). Nucleotide sequence of hepatitis C virus (type 3b) isolated from a Japanese patient with chronic hepatitis C. Journal of General Virology 75, 3623-3628.
23. Choo, Q. L., Richman, K., Han, J. H., Berger, K., Lee, C., Dong, C., Gallegos, C., Coit, D., Medina-Selby, A., Barr, P. J., Weiner, A., Bradley, D. W., Kuo, G. & Houghton, M. (1991). Genomic organization and diversity of the hepatitis C virus. Proceedings of the National Academy of Sciences, USA 88, 2451-2455.
24. Clarke, B. (1997). Molecular virology of hepatitis C virus. Journal of General Virology 78, 2397-2410.
25. Cleaves, G. R. (1985). Identification of dengue type 2 virus-specific high molecular weight proteins in virus-infected BHK cells. Journal of General Virology 66, 2767-2771.
26. Coia, G., Parker, M. D., Speight, G., Byrne, M. E. & Westaway, E. G. (1988). Nucleotide and complete amino acid sequences of Kunjin virus: definitive gene order and characteristics of the virus-specified proteins. Journal of General Virology 69, 1-21.
27. Collett, M. S., Larson, R., Belzer, S. K. & Retzel, E. (1988a). Pestivirus p80 (p125) may be a bifunctional protein with helicase and protease activity. Virology 165, 200-208.
28. Collet, M. S., Larson, R., Gold, C., Strick, D., Anderson, D. K. & Purchio, A. F. (1988b). Molecular cloning and nucleotide sequence of the pestivirus bovine viral diarrhea virus. Virology 165, 191-199.
29. Dalgarno, L., Trent, D. W., Strauss, J. H. & Rice, C. M. (1986). Partial nucleotide sequence of the Murray Valley encephalitis virus genome -comparison of the encoded polypeptides with yellow fever virus structural and non-structural proteins. Journal of Molecular Biology 187, 309-323.
30. De Moerlooze, L., Lecomte, C., Brown-Shimmer, S., Schmetz, D., Guiot, C., Vandenbergh, D., Allaer, D., Rossius, M., Chappuis, G., Dina, D., Renard, A. & Martial, J. A. (1993). Nucleotide sequence of the bovine viral diarrhoea virus Osloss strain: comparison with related viruses and identification of specific DNA probes in the 5′ untranslated region. Journal of General Virology 74, 1433-1438.
31. Deng, R. & Brock, K. V. (1992). Molecular cloning and nucleotide sequence of a pestivirus genome, noncytopathic bovine viral diarrhea virus strain SD-1. Virology 191, 867-869.
32. Devaney, M. A., Vakharia, V. N., Lloyd, R. E., Ehrenfeld, E. & Grubman, M. J. (1988). Leader protein of foot-and-mouth disease virus is required for cleavage of the p220 component of the cap-binding protein complex. Journal of Virology 62, 4407-4409.
33. Ding, J. Z., McGrath, W. J., Sweet, R. M. & Mangel, W. F. (1996). Crystal-structure of the human adenovirus proteinase with its 11-amino-acid cofactor. EMBO Journal 15, 1778-1783.
34. Dougherty, W. G. & Semler, B. L. (1993). Expression of virus-encoded proteinases: functional and structural similarities with cellular enzymes. Microbiological Reviews 57, 781-822.
35. D'Souza, E. D. A., Grace, K., Sangar, D. V., Rowlands, D. J. & Clarke, B. E. (1995). In vitro cleavage of hepatitis C virus polyprotein substrates by purified recombinant NS3 protease. Journal of Virology 76, 1729-1736.
36. Eckart, M. R., Selby, M., Masiarz, F., Lee, C., Berger, K., Crawford, K., Kuo, C., Kuo, G., Houghton, M. & Choo, Q.-L. (1993). The hepatitis C virus encodes a serine proteinase involved in processing of the putative nonstructural proteins from the viral polyprotein precursor. Biochemical and Biophysical Research Communications 192, 399-406.
37. Failla, C., Tomei, L. & De Francesco, R. (1994). Both NS3 and NS4A are required for proteolytic processing of hepatitis C virus nonstructural proteins. Journal of Virology 68, 3753-3760.
38. Failla, C., Tomei, L. & De Francesco, R. (1995). An amino-terminal domain of the hepatitis C virus NS3 protease is essential for interaction with NS4A. Journal of Virology 69, 1769-1777.
39. Falgout, B. & Markoff, L. (1995). Evidence that flavivirus NS1-NS2A cleavage is mediated by a membrane-bound host protease in the endoplasmic reticulum. Journal of Virology 69, 7232-7243.
40. Falgout, B., Channock, R. & Lai, C.-J. (1989). Proper processing of dengue virus nonstructural glycoprotein NS1 requires the N-terminal hydrophobic signal sequence and the downstream nonstructural protein NS2a. Journal of Virology 63, 1852-1860.
41. Falgout, B., Pethel, Y.-M. & Lai, C.-J. (1991). Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins. Journal of Virology 65, 2467-2475.
42. Falgout, B., Miller, R. H. & Lai, C.-J. (1993). Deletion analysis of dengue virus type 4 nonstructural protein NS2B: identification of a domain required for NS2B-NS3 protease activity. Journal of Virology 67, 2034-2042.
43. Felsenstein, J. (1991). PHYLIP manual, version 3.4, University Herbarium, University of California, Berkeley, California.
44. Filocamo, G., Pacini, L. & Migliaccio, G. (1997). Chimeric Sindbis viruses dependent on the NS3 protease of hepatitis C virus. Journal of Virology 71, 1417-1427.
45. Fu, J., Tan, B.-H., Yap, E.-H., Chan, Y.-C. & Tan, Y. H. (1992). Full-length cDNA sequence of dengue type 1 virus (Singapore strain S275/90). Virology 188, 953-958.
46. Gorbalenya, A. E., Donchenko, A. P., Blinov, V. M. & Koonin, E. V. (1989a). Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold. FEBS Letters 243, 103-114.
47. Gorbalenya, A. E., Donchenko, A. P., Blinov, V. M. & Koonin, E. V. (1989b). N-terminal domains of putative helicases of flavi-and pestiviruses may be serine proteases. Nucleic Acids Research 17, 3889-3897.
48. Gorbalenya, A. G., Koonin, E. V. & Lai, M. M.-C. (1991). Putative papain-related thiol proteases of positive strand RNA viruses. FEBS Letters 288, 201-205,
49. Grakoui, A., McCourt, D. W., Wychowski, C., Feinstone, S. M. & Rice, C. M. (1993a). Characterization of the hepatitis C virus-encoded serine proteinase: determination of proteinase-dependent polyprotein cleavage sites. Journal of Virology 67, 2832-2843.
50. Grakoui, A., McCourt, D. W., Wychowski, C., Feinstone, S. M. & Rice, C. M. (1993b). A second hepatitis C virus-encoded serine proteinase. Proceedings of the National Academy of Sciences, USA 90, 10583-10587.
51. Hahm, B., Han, D. S., Back, S. H., Song, O.-K., Cho, M.-J., Kim, C.-J., Shimotohno, K. & Jang, S. K. (1995). NS3-4A of hepatitis C virus is a chymotrypsin-like protease. Journal of Virology 69, 2534-2539.
52. Hahm, B., Back, S. H., Lee, T. G., Wimmer, E. & Jang, S. K. (1996). Generation of a novel poliovirus with a requirement of hepatitis C virus NS3 activity. Virology 226, 318-326.
53. Hahn, Y. S., Galler, R., Hunkapiller, T., Dalrymple, J. M., Strauss, J. H. & Strauss, E. G. (1988). Nucleotide sequence of dengue 2 RNA and comparison of the encoded proteins with those of other flaviviruses. Virology 162, 167-180.
54. Han, D. S., Hahm, B., Rho, H.-M. & Jang, S. K. (1995). Identification of the protease domain in NS3 of hepatitis C virus. Journal of General Virology 76, 985-993.
55. Higgins, D. E., Bleasby, A. J. & Fuchs, R. (1991). Improved software for multiple sequence alignment. Computer Applications in the BioSciences 8, 189-191.
56. Hijikata, M., Mizushima, H., Tanji, Y., Komoda, Y., Hirowatari, Y., Akagi, T., Kato, N., Kimura, K. & Shimotohno, K. (1993a). Two distinct proteinase activities required for the processing of a putative non-structural precursor protein of hepatitis C virus. Journal of Virology 67, 4665-4675.
57. Hijikata, M., Mizushima, H., Akagi, T., Mori, S., Kakiuchi, N., Kato, N., Tanaka, T., Kimura, K. & Shimotohno, K. (1993b). Proteolytic processing and membrane association of putative nonstructural proteins of hepatitis C virus. Proceedings of the National Academy of Sciences, USA 90, 10773-10777.
58. Kakiuchi, N., Hijikata, M., Komoda, Y., Tanji, Y., Hirowatari, Y. & Shimotohno, K. (1995). Bacterial expression and analysis of cleavage activity of HCV serine proteinase using recombinant and synthetic substrate. Biochemical and Biophysical Research Communications 210, 1059-1065.
59. Kato, N., Hijikata, M., Ootsuyama, Y., Nakagawa, M., Ohkoshi, S., Sugimura, T. & Shimotohno, K. (1990). Molecular cloning of the human hepatitis C virus genome from Japanese patients with non-A, non-B hepatitis. Proceedings of the National Academy of Sciences, USA 87, 9524-9528.
60. Kim, J. L., Morgenstern, K. A., Lin, C., Fox, T., Dwyer, M. D., Landro, J. A., Chambers, S. P., Markland, W., Lepre, C. A., O'Malley, E. T., Harbeson, S. L., Rice, C. M., Murcko, M. A., Caron, P. R. & Thomson, J. A. (1996). Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 87, 343-355.
61. Kim, D. W., Gwack, Y., Han, J. H. & Choe, J. (1997). Towards defining a minimal functional domain for NTPase and RNA helicase activities of the hepatitis C virus NS3 protein. Virus Research 49, 17-25.
62. Koch, J. O., Lohmann, V., Herian, U. & Bartenschlager, R. (1996). In vitro studies on the activation of the hepatitis C virus NS3 proteinase by the NS4 cofactor. Virology 221, 54-66.
63. Komoda, Y., Hijikata, M., Sato, S., Shin-Ichi, A., Kimura, K. & Shimotohno, K. (1994). Substrate requirements of hepatitis C virus serine proteinase for intermolecular polypeptide cleavage in Escherichia coli. Journal of Virology 68, 7351-7357.
64. Koonin, E. V. & Dolja, V. V. (1993). Evolution and taxonomy of positive strand RNA viruses: implications of comparative analysis of amino acid sequences. Critical Reviews in Biochemistry and Molecular Biology 28, 375-430.
65. Landro, J. A., Raybuck, S. A., Luong, Y. P. C., O'Malley, E. T., Harbeson, S. L., Morgenstern, K. A., Rao, G. & Livingston, D. J. (1997). Mechanistic role of an NS4A peptide cofactor with the truncated NS3 protease of hepatitis C virus: elucidation of the NS4A stimulatory effect via kinetic analysis and inhibitor mapping. Biochemistry 36, 9340-9348.
66. Leary, T. P., Muerhoff, A. S., Simons, J. N., Pilot-Matias, T. J., Erker, J. C., Chalmers, M. L., Schlauder, G. G., Dawson, G. J., Desai, S. M. & Mushahwar, I. K. (1995). Sequence and genomic organization of GBV-C: a novel member of the Flaviviridae associated with human non A-E hepatitis. Journal of Medical Virology 48, 60-67.
67. Liao, D.-I. & Remington, S. J. (1990). Structure of wheat serine carboxypeptidase II at 3. 5 Å resolution. Journal of Biological Chemistry 265, 6528-6531.
68. Lin, C. & Rice, C. M. (1995). The hepatitis C virus NS3 serine proteinase and NS4A protein cofactor: establishment of a cell-free trans-processing assay. Proceedings of the National Academy of Sciences, USA 92, 7622-7626.
69. Lin, C., Amberg, S. M., Chambers, T. J. & Rice, C. M. (1993). Cleavage at a novel site in the NS4A region by the yellow fever virus NS2B-3 proteinase is a prerequisite for processing at the downstream 4A/B signalase site. Journal of Virology 67, 2327-2335.
70. Lin, C., Thomson, J. A. & Rice, C. M. (1995). A central region in the hepatitis C virus NS4A protein allows formation of an active NS3-NS4A serine proteinase complex in vivo and in vitro. Journal of Virology 69, 4373-4380.
71. Lobigs, M. (1993). Flavivirus premembrane protein cleavage and spike heterodimer secretion require the function of the viral proteinase NS3. Proceedings of the National Academy of Sciences, USA 90, 6218-6222.
72. Love, R. A., Parge, H. E., Wickersham, J. A., Hostomsky, Z., Habuka, N., Moomaw, E. W., Adachi, T. & Hostomska, Z. (1996). The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Cell 87, 331-342.
73. Mackow, E. R., Makino, Y., Zhao, B., Zhang, Y.-M., Markoff, L., Buckler-White, A. J., Guiler, M., Chanock, R. M. & Lai, C.-J. (1987). The nucleotide sequence of dengue type 4 virus: analysis of genes coding for nonstructural proteins. Virology 159, 217-228.
74. Manabe, S., Fuke, I., Tanishita, O., Kaji, C., Gomi, Y., Yoshida, S., Mori, C., Takamizawa, A., Yosida, I. & Okayama, H. (1994). Production of nonstructural proteins of hepatitis C virus requires a putative viral protease encoded by NS3. Virology 198, 636-644.
75. Mangel, W. F., Toledo, D. L., Brown, M. T., Martin, J. H. & McGrath, W. J. (1996). Characterization of 3 components of human adenovirus proteinase activity in vitro. Journal of Biological Chemistry 271, 536-543.
76. Markland, W., Petrillo, R. A., Fitzgibbon, M., Fox, T., McCarrick, R., McQuaid, T., Fulghum, J. R., Chen, W., Fleming, M. A., Thomson, J. A. & Chambers, S. P. (1997). Purification and characterization of the NS3 serine protease domain of hepatitis C virus expressed in Saccharomyces cerevisiae. Journal of General Virology 78, 39-43.
77. Markoff, L. (1989). In vitro processing of dengue virus structural proteins: cleavage of the pre-membrane protein. Journal of Virology 63, 3345-3352.
78. Meyers, G. & Thiel, H.-J. (1996). Molecular characterization of pestiviruses. Advances in Virus Research 47, 53-118.
79. Meyers, G., Rumenapf, T. & Thiel, H.-J. (1989). Molecular cloning and nucleotide sequence of the hog cholera virus. Virology 171, 555-567.
80. Meyers, G., Tautz, N., Dubovi, E. J. & Thiel, H.-J. (1991). Viral cytopathogenicity correlated with integration of ubiquitin-coding sequences. Virology 180, 602-616.
81. Meyers, G., Tautz, N., Stark, R., Brownlie, J., Dubovi, E. J., Collet, M. S. & Thiel, H.-J. (1992). Rearrangement of viral sequences in cytopathogenic pestiviruses. Virology 191, 368-386.
82. Meyers, G., Tautz, N., Becher, P., Thiel, H.-J. & Kuemmerer, B. M. (1996). Recovery of cytopathogenic and noncytopathogenic bovine viral diarrhea viruses from cDNA constructs. Journal of Virology 70, 8606-8613.
83. Miller, R. H. & Purcell, R. H. (1990). Hepatitis C virus shares amino acid sequence similarity with pesti-and flaviviruses as well as members of two plant virus supergroups. Proceedings of the National Academy of Sciences, USA 87, 2057-2061.
84. Mills, J. S. (1996). Virus proteinase inhibitors - what next after HIV? Antiviral Chemistry & Chemotherapy 7, 281-293.
85. Moorman, R. J. M., Warmerdam, P. A. M., Van Der Meer, B., Schapper, W. M. M., Wensvoort, G. & Hulst, M. M. (1990). Molecular cloning and nucleotide sequence of hog cholera virus strain Brescia and mapping of the genomic region encoding envelope protein E1. Virology 177, 184-198.
86. Moormann, R. J. M., van Gennip, H. G. P., Miedema, G. K. W., Hulst, M. M. & van Rijn, P. A. (1996). Infectious RNA transcribed from an engineered full-length cDNA template of the genome of a pestivirus. Journal of Virology 70, 763-770.
87. Morgenstern, K. A., Landro, J. A., Hsiao, K., Lin, C., Gu, Y., Su, M. S.-S. & Thomson, J. A. (1997). Polynucleotide modulation of the protease, nucleoside triphosphatase and helicase activities of a hepatitis NS3-NS4A complex isolated from transfected COS cells. Journal of Virology 71, 3767-3775.
88. Muramatsu, S., Ishido, S., Fujita, T., Itoh, M. & Hotta, H. (1997). Nuclear localization of the NS3 protein of hepatitis C virus and factors affecting the localization. Journal of Virology 71, 4954-4961.
89. Muyldermans, G., SanGabriel, M. A. C., Hamers, R. & Wyns, L. (1997). Expression in E. coli and purification of the active autoprotease p20 of classical swine fever virus. Virus Genes 13, 135-142.
90. Nakao, H., Okamoto, H., Tokita, H., Inoue, T., Iizuka, H., Pozzato, G. & Mishiro, S. (1996). Full-length genomic sequence of a hepatitis C virus genotype 2c isolate (BEBE1) and the 2c-specific PCR primers. Archives of Virology 141, 701-704.
91. Nowak, T., Farber, P. M., Wengler, G. & Wengler, G. (1989). Analyses of the terminal sequences of West Nile virus structural proteins and of the in vitro translation of these proteins allow the proposal of a complete scheme of the proteolytic cleavages involved in their synthesis. Virology 169, 365-376.
92. Ohba, K.-I., Mizokami, M., Lau, J. Y. N., Orito, E., Ikeo, K. & Gojobori, T. (1996). Evolutionary relationship of hepatitis C, pesti-, flavi-, plant viruses and newly discovered GB hepatitis agents. FEBS Letters 378, 232-234.
93. Okamoto, H., Okada, S., Sugiyama, Y., Kurai, K., Iizuka, H., Machida, A., Miyakawa, Y. & Mayumi, M. (1991). Nucleotide sequences of the genomic RNA of hepatitis C virus isolated from a human carrier: comparison with reported isolates for conserved and divergent regions. Journal of General Virology 72, 2697-2704.
94. Okamoto, H., Kurai, K., Okada, S.-I., Yamamoto, K., Lizuka, H., Tanaka, T., Fukuda, S., Tsuda, F. & Mishiro, S. (1992). Full-length sequence of a hepatitis C virus genome having poor homology to reported isolates: comparative study of four distinct genotypes. Virology 188, 331-341.
95. Okamoto, H., Kojima, M., Sakamoto, M., Iizuka, H., Hadiwandowo, S., Suwignyo, S., Miyakawa, Y. & Mayumi, M. (1994). The entire nucleotide sequence and classification of a hepatitis C virus isolate of a novel genotype from an Indonesian patient with chronic liver disease. Journal of General Virology 75, 629-635.
96. Osatomi, K. & Sumiyoshi, H. (1990). Complete nucleotide sequence of dengue type 3 virus genome RNA. Virology 176, 643-647.
97. Overton, H., McMillan, D., Gillespie, F. & Mills, J. (1995). Recombinant baculovirus-expressed NS3 proteinase of hepatitis C virus shows activity in cell-based and in vitro assays. Journal of General Virology 76, 3009-3019.
98. Pieroni, L., Santolini, E., Fipaldini, C., Pacini, L., Migliaccio, G. & La Monica, N. (1997). In vitro study of the NS2-3 protease of hepatitis C virus. Journal of Virology 71, 6373-6380.
99. Pizzi, E., Tramontane, A., Tomei, L., La Monica, N., Failla, C., Sardana, M., Wood, T. & De Francesco, R. (1994). Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. Proceedings of the National Academy of Sciences, USA 91, 888-892.
100. Pletnev, A. G., Yamshchikov, V. F. & Blinov, V. M. (1990). Nucleotide sequence of the genome and complete amino acid sequence of the polyprotein of tick-borne encephalitis virus. Virology 174, 250-263.
101. Preugschat, F. & Strauss, J. H. (1991). Processing of nonstructural protein-NS4A and protein-NS4B of dengue-2 virus in vitro and in vivo. Virology 185, 689-697.
102. Preugschat, F., Yao, C.-W. & Strauss, J. H. (1990). In vitro processing of dengue virus type 2 nonstructural proteins NS2A, NS2B and NS3. Journal of Virology 64, 4364-4374.
103. Preugschat, F., Lenches, E. M. & Strauss, J. H. (1991). Flavivirus enzyme-substrate interactions studied with chimeric proteinases -identification of an intragenic locus important for substrate recognition. Journal of Virology 65, 4749-4758.
104. Pugachev, K. V., Nomokonova, N. Y., Dobrikova, E. Y. & Wolf, Y. I. (1993). Site-directed mutagenesis of the tick-borne encephalitis virus NS3 gene reveals the putative serine protease domain of the NS3 protein. FEBS Letters 328, 115-118.
105. Reed, K. E., Grakoui, A. & Rice, C. M. (1995). Hepatitis C virus-encoded NS2-3 protease: cleavage site mutagenesis and requirements for bimolecular cleavage. Journal of Virology 69, 4127-4136.
106. Renard, A., Dino, D. & Martial, J. (1987). Vaccines and diagnostics derived from bovine diarrhea virus. European Patent Application 86870095. 6. Publication no. 0208672 14 January 1987.
107. Rice, C. M. & Strauss, J. H. (1990). Production of flavi virus polypeptides by proteolytic processing. Seminars in Virology 1, 357-367.
108. Rice, C. M., Lenches, E. M., Eddy, S. R., Shin, S. J., Sheets, R. L. & Strauss, J. H. (1985). Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution. Science 229, 726-733.
109. Rice, C. M., Aebersold, R., Teplow, D. B., Pata, J., Bell, J. R., Vorndam, A. V., Trent, D. W., Brandriss, M. W., Schlesinger, J. J. & Strauss, J. H. (1986). Partial N-terminal amino acid sequences of three nonstructural proteins of two flaviviruses. Virology 151, 1-9.
110. Ridpath, J. F. & Bolin, S. R. (1995). The genomic sequence of a virulent bovine viral diarrhea virus (BVDV) from the type 2 genotype: detection of a large genomic insertion in a noncytopathic BVDV. Virology 212, 39-46.
111. Ridpath, J. F., Bolin, S. R., Evermann, J. F., Landgraf, J. G. & Frey, M. L. The complete genomic sequence of the pestivirus border disease virus: comparison to genomic sequences of other pestiviruses. Unpublished. Accession no. U70263.
112. Roath, P. D. & Berry, E. S. Nucleotide sequence of ILLC-bovine viral diarrhea virus. Unpublished. Acc. No. U86599.
113. Ruiz-Linares, A., Cahour, A., Despres, P., Girard, M. & Bouloy, M. (1989). Processing of yellow fever virus polyprotein: role of cellular proteases in maturation of the structural proteins. Journal of Virology 63, 4199-4209.
114. Ryan, M. D. & Flint, M. (1997). Virus-encoded proteinases of the picornavirus super-group. Journal of General Virology 78, 699-723.
115. Sakamoto, M., Akahane, Y., Tsuda, F., Tanaka, T., Woodfield, D. G. & Okamoto, H. (1994). Entire nucleotide sequence and characterization of a hepatitis C virus of genotype V/3a. Journal of General Virology 75, 1761-1768.
116. Satoh, S., Tanji, Y., Hijikata, M., Kimura, K. & Shimotohono, K. (1995). The N-terminal region of hepatitis C virus nonstructural protein 3 (NS3) is essential for stable complex formation with NS4A. Journal of Virology 69, 4255-4260.
117. Scarselli, E., Urbani, A., Sbardellati, A., Tomei, L., De Francesco, R. & Traboni, C. (1997). GB virus B and hepatitis C virus NS3 serine proteases share substrate specificity. Journal of Virology 71, 4985-4989.
118. Shimizu, Y., Yamaji, K., Masuho, Y., Yokota, T., Inoue, H., Sudo, K., Satoh, S. & Shimotohno, K. (1996). Identification of the sequence on NS4A required for enhanced cleavage of the NS4A/SB site by hepatitis C virus NS3 proteinase. Journal of Virology 70, 127-132.
119. Simons, J. N., Pilot-Matias, T. J., Leary, T. P., Dawson, G. J., Desai, S. M., Schlauder, G. G., Muerhoff, A. S., Erker, J. C., Buijk, S. L., Chalmers, M. L., van Sant, C. L. & Mushahwar, I. K. (1995). Identification of two flavivirus-like genomes in the GB hepatitis agent. Proceedings of the National Academy of Sciences, USA 92, 3401-3405.
120. Song, O.-K., Cho, O. H., Hahm, B. & Jang, S. K. (1996). Development of an in vitro assay system suitable for screening inhibitors of hepatitis C viral protease. Molecules and Cells 6, 183-189.
121. Speight, G., Coia, G., Parker, M. D. & Westaway, E. G. (1988). Gene mapping and positive identification of the non-structural proteins NS2A. NS2B, NS3, NS4B and NS5 of the flavivirus Kunjin and their cleavage sites. Journal of General Virology 69, 23-34.
122. Stark, R., Meyers, G., Rumenapf, T. & Thiel, H.-J. (1993). Processing of pestivirus polyprotein: cleavage site between autoprotease and nucleocapsid protein of classical swine fever virus. Journal of Virology 67, 7088-7095.
123. Steinkuhler, C., Tomei, L. & De Francesco, R. (1996a). In vitro activity of hepatitis C virus protease NS3 purified from recombinant bacutovirus-infected Sf9 cells. Journal of Biological Chemistry 271, 6367-6373.
124. Steinkuhler, C., Urbani, A., Tomei, L., Biasiol, G., Sardana, M., Bianchi, E., Pessi, A. & De Francesco, R. (19966). Activity of purified hepatitis C virus protease NS3 on peptide substrates. Journal of Virology 70, 6694-6700.
125. Sudo, K., Inoue, H., Shimizu, Y., Yamaji, K., Konno, K., Shigeta, S., Kaneko, T., Yokota, T. & Shimotohno, K. (1996). Establishment of an in vitro assay system for screening hepatitis C virus protease inhibitors using high performance liquid chromatography. Antiviral Research 32, 9-18.
126. Sumiyoshi, H., Mori, C., Fuke, I., Morita, K., Kuhara, S., Kondou, J., Kikuchi, Y., Nagamatu, H. & Igarishi, A. (1987). Complete nucleotide sequence of the Japanese encephalitis virus genome RNA. Virology 161, 497-510.
127. Suzich, J. A., Tamura, J. K., Palmer-Hill, F., Warrener, P., Grakoui, A., Rice, C. M., Feinstone, S. M. & Collett, M. S. (1993). Hepatitis C virus NS3 protein polynucleotide-stimulated nucleoside triphosphatase and comparison with the related pestivirus and flavivirus enzymes. Journal of Virology 67, 6152-6158.
128. Suzuki, T., Sato, M., Cheida, S., Shji, I., Harada, T., Yamakawa, Y., Watabe, S., Matsuura, Y. & Miyamura, T. (1995). In vitro and in vivo trans-cleavage activity of hepatitis C virus serine proteinase expressed by recombinant baculoviruses. Journal of General Virology 76, 3021-3029.
129. Tanji, Y., Hijikata, M., Satoh, S., Kaneko, T. & Shimitohno, K. (1995). Hepatitis C virus-encoded nonstructural protein NS4A has versatile functions in viral polyprotein processing. Journal of Virology 69, 1575-1581.
130. Tautz, N., Elbers, K., Stoll, D., Meyers, G. & Thiel, H.-J. (1997). Serine protease of pestiviruses: determination of cleavage sites. Journal of Virology 71, 5415-5422.
131. Teo, K. F. & Wright, P. J. (1997). Internal proteolysis of the NS3 protein specified by dengue virus 2. Journal of General Virology 78, 337-341.
132. Tomei, L., Failla, C., Santolini, E., De Francesco, R. & La Monica, N. (1993). NS3 is a serine protease required for processing of hepatitis C virus polyprotein. Journal of Virology 67, 4017-4026.
133. Tomei, L., Failla, C., Vitale, R. L., Bianchi, E. & De Francesco, R. (1996). A central hydrophobic domain of the hepatitis C virus NS4A protein is necessary and sufficient for the activation of the NS3 protease. Journal of General Virology 77, 1065-1070.
134. Warrerner, P. & Collet, M. S. (1995). Pestivirus NS3 (p80) protein possesses RNA helicase activity. Journal of Virology 69, 1720-1726.
135. Webster, A., Hay, R. T. & Kemp, G. (1993). The adenovirus protease is activated by a virus-coded disulphide-linked peptide. Cell 72, 97-104.
136. Wengler, G. & Wengler, G. (1991). The carboxy-terminal part of the NS3 protein of the West Nile flavivirus can be isolated as a soluble protein after proteolytic cleavage and represents an RNA-stimulated NTPase. Virology 184, 707-715.
137. Wengler, G. & Wengler, G. (1993). The NS3 nonstructural protein of flavivirus contains an RNA triphosphatase activity. Virology 197, 265-373.
138. Wengler, G., Czaya, G., Färber, P. M. & Hegemann, J. H. (1991). In vitro synthesis of West Nile virus proteins indicates that the amino-terminal segment of the NS3 protein contains the active centre of the protease which cleaves the viral polyprotein after multiple basic amino acids. Journal of General Virology 72, 851-858.
139. Wiskerchen, M. & Collett, M. S. (1991). Pestivirus gene-expression -protein p80 of bovine viral diarrhea virus is a proteinase involved in polyprotein processing. Virology 184, 341-350.
140. Wiskerchen, M., Beizer, S. K. & Collet, M. S. (1991). Pestivirus gene expression: the first protein product of the bovine viral diarrhea virus large open reading frame, p20, possesses proteolytic activity. Journal of Virology 65, 4508-4514.
141. Wright, P. S., Cauchi, M. R. & Ng, M. L. (1989). Definition of the carboxy termini of the three glycoproteins specified by dengue virus type 2. Virology 171, 61-67.
142. Xu, J. A., Mendez, E., Caron, P. R., Lin, C., Murcko, M. A., Collet, M. S. & Rice, C. M. (1997). Bovine viral diarrhea virus NS3 serine proteinase: polyprotein cleavage sites, cofactor requirements, and molecular model of an enzyme essential for pestivirus replication. Journal of Virology 71, 5312-5322.
143. Yamshchikov, V. F. & Compans, R. W. (1994). Processing of the intracellular form of the West Nile virus capsid protein by the viral NS2B-NS3 protease: an in vitro study. Journal of Virology 68, 5765-5771.
144. Yamshchikov, V. F. & Compans, R. W. (1995). Formation of the flavivirus envelope: role of the viral NS2B-NS3 protease. Journal of Virology 69, 1995-2003.
145. Yan, Y., Munshi, S., Li, Y., Sardana, V., Blue, J., Johns, B., Cole, J., Steinkuhler, C., Tomei, L., Francesco, R. D., Kuo, L. C. & Chen, Z. (1998). Three dimensional structure of BK strain hepatitis C virus (HCV) NS3-NS4A complex in a hexagonal crystal form at 2.2 Å resolution. Unpublished.
146. Zhang, R., Durkin, J., Windsor, W. T., McNemar, C., Ramanathan, L. & Le, H. V. (1997). Probing the substrate specificity of hepatitis C virus NS3 serine proteinase by using synthetic peptides. Journal of Virology 71, 6208-6213.