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Methods for the Study of Sequence-Specific Binding of Proteins to the HCV RNA Genome

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Hepatitis C Protocols

Part of the book series: Methods in Molecular Medicineā„¢ ((MIMM,volume 19))

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Abstract

The appropriate formation of specific RNA-protein complexes regulates the normal synthesis, trafficking, and metabolism of intracellular RNA. For RNA viruses, these interactions are essential for replication and translation of the viral genome, as well as packaging of progeny strands into mature virions. Sequence-specific RNA-protein interactions allow the replication and translation machinery to distinguish between viral and host-cell RNA species, thus insuring that the viral replicative apparatus acts on the appropriate RNA targets. Identifying these proteins and determining their biological activities provide important clues about the mechanisms of viral replication. Their physiological importance suggests that blocking these interactions may be effective means of inhibiting viral replication. Thus, the identification and characterization of sequence-specific RNA-binding proteins are valuable steps in the development of potent and selective antiviral agents.

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References

  1. Blackwell, J. L. and Brinton, M. A. (1995) BHK cell proteins that bind to the 3ā€² stem-loop structure of the West Nile vims genome RNA. J. Virol. 69, 5650ā€“5658.

    PubMedĀ  CASĀ  Google ScholarĀ 

  2. Del Angel, R. M., Papavassihou, A G., Fernandez-Tomas, C, Silverstein, S J., and Racaniello, V R. (1989) Cell proteins bind to multiple sites within the 5ā€² untranslated region of pohovirus RNA. Proc. Natl Acad Sci USA 86, 8299ā€“8303

    ArticleĀ  PubMedĀ  Google ScholarĀ 

  3. Haller, A A and Semler, B. L (1995) Stem-loop structure synergy in binding cellular proteins to the 5ā€² noncoding region of poliovirus RNA Virology 206, 923ā€“934

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  4. Leopardi, R., Hukkanen, V, Vainionpaa, R., and Salmi, A A. (1993) Cell proteins bind to sites within the 3ā€² noncoding region and the positive-strand leader sequence of measles virus RNA J. Virol. 67, 785ā€“790.

    PubMedĀ  CASĀ  Google ScholarĀ 

  5. Liu, Q., Yu, W., and Leibowitz, J L (1997) A specific host cellular protein binding element near the 3ā€² end of mouse hepatitis virus genomic RNA Virology 232, 74ā€“85

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  6. Nakhasi, H L, Cao, X-Q., Rouault, T. A, and Liu, T-Y. (1991) Specific binding of host cell proteins to the 3ā€²-terminal stem-loop structure of rubella virus negative-strand RNA J Virol 65, 5961ā€“5967

    PubMedĀ  CASĀ  Google ScholarĀ 

  7. Pardigon, N and Strauss, J H. (1992) Cellular proteins bind to the 3ā€² end of Sindbis virus minus-strand RNA J Virol. 66, 1007ā€“1015

    PubMedĀ  CASĀ  Google ScholarĀ 

  8. Pardigon, N., Lenches, E, and Strauss, J. H. (1993) Multiple binding sites for cellular proteins in the 3ā€² end of Sindbis alphavirus minus-sense RNA J Virol 67, 5003ā€“5011

    PubMedĀ  CASĀ  Google ScholarĀ 

  9. Quadt, R., Kao, C C, Browning, K S., Hershberger, R P., and Ahlquist, P (1993) Characterization of a host protein associated with brome mosaic virus RNA-dependent RNA polymerase. Proc. Natl Acad Set USA 90, 1498ā€“1502

    ArticleĀ  CASĀ  Google ScholarĀ 

  10. Todd, S., Nguyen, J H C, and Semler, B L. (1995) RNAā€”protein interactions directed by the 3ā€² end of human rhinovirus genomic RNA J Virol 69, 3605ā€“3614

    PubMedĀ  CASĀ  Google ScholarĀ 

  11. Major, M. E and Femstone, S. M. (1997) The molecular virology of hepatitis C Hepatology 25, 1527ā€“1538

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  12. Chang, K H, Brown, E. A, and Lemon, S M. (1993) Cell type-specific proteins which interact with the 5ā€² nontranslated region of hepatitis A virus RNA. J Virol 67, 6716ā€“6725.

    PubMedĀ  CASĀ  Google ScholarĀ 

  13. Hellen, C. U. T, Witherell, G. W, Schmid, M, Shin, S H, Pestova, T V., Gil, A. M., and Wimmer, E. (1993) A cytoplasmic 57-kD protein that is required for translation of picornavirus RNA by internal ribosomal entry is identical to the nuclear pynmidine tract-binding protein Proc Natl Acad Set USA 90, 7642ā€“7646.

    ArticleĀ  CASĀ  Google ScholarĀ 

  14. Hellen, C U. T., Pestova, T V, Litterst, M., and Wimmer, E (1994) The cellular polypeptide p57 (pyrimidine tract-binding protein) binds to multiple sites in the poliovirus 5ā€²nontranslated region J Virol 68, 941ā€“950.

    PubMedĀ  CASĀ  Google ScholarĀ 

  15. Niepmann, M (1996) Porcine polypyrimidine tract-binding protein stimulates translation initiation at the internal ribosome entry site of foot-and-mouth-disease virus FEBS Lett. 388, 39ā€“42

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  16. Witherell, G W and Wimmer, E. (1994) Encephalomyocarditis virus internal ribosomal entry site RNAā€”protein interactions J Virol 68, 3183ā€“3192

    PubMedĀ  CASĀ  Google ScholarĀ 

  17. Ali, N. and Siddiqui, A. (1995) Interaction of polypyrimidine tract-binding protein with the 5ā€² noncoding region of the hepatitis C virus RNA genome and its functional requirement in internal initiation of translation. J Virol 69, 6367ā€“6375.

    PubMedĀ  CASĀ  Google ScholarĀ 

  18. Ah, N. and Siddiqui, A. (1997) The La antigen binds 5ā€² noncoding region of the hepatitis C virus RNA in the context of the initiator AUG codon and stimulates internal ribosome entry site-mediated translation. Proc Natl Acad Sci USA 94, 2249ā€“2254

    ArticleĀ  Google ScholarĀ 

  19. Chung, R. T., Kawashima, T, and Kaplan, L M (1996) Expressed HCV NS5B polymerase catalyzes primer-dependent elongation. Gastroenterology 110, A1172.

    Google ScholarĀ 

  20. Lohmann, V, Korner, F, Herian, U, and Bartenschlager, R (1997) Biochemical properties of hepatitis C virus NS5B RNA-dependent RNA polymerase and identification of amino acid sequence motifs essential for enzymatic activity J Virol 71, 8416ā€“8428

    PubMedĀ  CASĀ  Google ScholarĀ 

  21. Behrens, S. E., Tomei, L, and De Francesco, R (1996) Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus EMBOJ 15, 12ā€“22

    CASĀ  Google ScholarĀ 

  22. Kolykhalov, A A, Feinstone, S M., and Rice, C. M. (1996) Identification of a highly conserved sequence element at the 3ā€² terminus of hepatitis C virus genome RNA J Virol 70, 3363ā€“3371

    PubMedĀ  CASĀ  Google ScholarĀ 

  23. Tanaka, T, Kato, N, Cho, M. J, and Shimotohno, K (1995) A novel sequence found at the 3ā€² terminus of hepatitis C virus genome. Biochem Biophys Res Commun 215, 744ā€“749

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  24. Tanaka, T., Kato, N., Cho, M J, Sugiyama, K, and Shimotohno, K. (1996) Structure of the 3ā€²terminus of hepatitis C virus genome J Virol 70, 3307ā€“3312

    PubMedĀ  CASĀ  Google ScholarĀ 

  25. Chung, R. T. and Kaplan, L M. (1998) Heterogeneous nuclear nbonucleoprotein I (hnRNP-I/PTB) selectively binds the conserved 3ā€² terminus of the hepatitis C virus genome Submitted for publication.

    Google ScholarĀ 

  26. Garcia-Blanco, M A, Jamison, S. F, and Sharp, P. A. (1989) Identification and purification of a 62,000-dalton protein that binds specifically to the polypyrimidine tract of introns Genes Dev 3, 1874ā€“1886

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  27. Ghetti, Z, Pinol-Roma, S, Michael, W M., Morandi, C, and Dreyfuss, G. (1992) hnRNP I, the polypyrimidine tract-binding protein: distinct nuclear localization with hnRNAs Nucleic Acids Res 20, 3671ā€“3678

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  28. Patton, J. G., Mayer, S. A., Tempst, P., and Nadal-Ginard, B. (1991) Characterization and cloning of polypyrimidine tract-binding protein, a component of a complex necessary for pre-mRNA splicing Genes Dev 5, 1237ā€“1251

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  29. Reynolds, J. E, Kaminski, A., Kettinen, H. J, Grace, K., Clarke, B. E., Carroll, A. R, Rowlands, D. J, and Jackson, R J (1995) Unique features of internal initiation of hepatitis C virus RNA translation. EMBOJ 14, 6010ā€“6020

    CASĀ  Google ScholarĀ 

  30. Ito, T. and Lai, M. M. (1997) Determination of the secondary structure of and cellular protein binding to the 3ā€²-untranslated region of the hepatitis C virus genome. J Virol 71, 8698ā€“8706.

    PubMedĀ  CASĀ  Google ScholarĀ 

  31. Yen, J-H., Chang, S. C, Hu, C-R, Chu, S-C, Lin, S.-S, Hsieh, S-S., and Chang, M.-F (1995) Cellular proteins specifically bind to the 5ā€² noncoding region of hepatitis C virus RNA. Virology 208, 723ā€“732

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

  32. Lin, C. H and Patton, J. G (1995) Regulation of alternative 3ā€² splice site selection by constitutive splicing factors. RNA 1, 234ā€“245.

    PubMedĀ  CASĀ  Google ScholarĀ 

  33. Konarska, M. M and Sharp, P A. (1986) Electrophoretic separation of complexes involved in the splicing of precursors to mRNAs Cell 46, 845ā€“855

    ArticleĀ  PubMedĀ  CASĀ  Google ScholarĀ 

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Ā© 1998 Humana Press Inc., Totowa, NJ

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Kaplan, L.M., Chung, R.T. (1998). Methods for the Study of Sequence-Specific Binding of Proteins to the HCV RNA Genome. In: Lau, J.YN. (eds) Hepatitis C Protocols. Methods in Molecular Medicineā„¢, vol 19. Humana Press. https://doi.org/10.1385/0-89603-521-2:385

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  • DOI: https://doi.org/10.1385/0-89603-521-2:385

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-521-8

  • Online ISBN: 978-1-59259-260-9

  • eBook Packages: Springer Protocols

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