1887

Abstract

Efficient internal initiation of translation from the hepatitis C virus (HCV) internal ribosome entry site (IRES) requires sequences of domain II, but the precise role of these sequences is still unknown. In this study, the formation of RNA–RNA complexes in the HCV IRES was evaluated. Using transcripts that contain the sequences of the structural HCV IRES domains II, IIIabcd, IIIabc, IV and IIIef-IV, specific long-range interactions between domains II and IV, as well as domains II and IIIabcd, have been found. These interactions were readily detected in a gel mobility-shift assay and required the presence of magnesium ions. A high concentration of nonspecific competitors, an 80 nt fragment of 18S rRNA or poly(I:C), did not interfere with the formation of RNA complexes. Interestingly, an RNA oligonucleotide bearing the sequence of stem–loop IIId interacted with domain II but not with domain IV or IIIef-IV, strongly suggesting that the interaction between domains II and IIIabcd was mediated by the IIId hairpin. Interaction between domains IIIabcd and IV was barely detected, consistent with the result that the apical part of domain III folds independently of the rest of the IRES. Moreover, the addition of stem–loop IIIef sequences to domain IV significantly reduced its ability to interact, which is in agreement with the formation of a compact RNA structure of domain IV with IIIef. The interactions observed in the absence of proteins between domains II and IV as well as stem–loop IIId and domain II may be transient, having a regulatory role in the translation efficiency of the HCV IRES.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/0022-1317-83-5-1113
2002-05-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/83/5/0831113a.html?itemId=/content/journal/jgv/10.1099/0022-1317-83-5-1113&mimeType=html&fmt=ahah

References

  1. Beales L. P., Rowlands D. J., Holzenburg A. 2001; The internal ribosome entry site (IRES) of hepatitis C virus visualized by electron microscopy. RNA 7:661–670
    [Google Scholar]
  2. Buratti E., Tisminetzky S., Zotti M., Baralle F. E. 1998; Functional analysis of the interaction between HCV 5′UTR and putative subunits of eukaryotic translation initiation factor eIF3. Nucleic Acids Research 26:3179–3187
    [Google Scholar]
  3. Fedor M. J., Uhlenbeck O. C. 1990; Substrate sequence effects on ‘hammerhead’ RNA catalytic efficiency. Proceedings of the National Academy of Sciences USA 87:1668–1672
    [Google Scholar]
  4. Ferrandon D., Koch I., Westhof E., Nusslein-Volhard C. 1997; RNA–RNA interaction is required for the formation of specific bicoid mRNA 3′ UTR-STAUFEN ribonucleoprotein particles. EMBO Journal 16:1751–1758
    [Google Scholar]
  5. Honda M., Brown E. A., Lemon S. M. 1996; Stability of a stem–loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA. RNA 2:955–968
    [Google Scholar]
  6. Honda M., Beard M. R., Ping L.-H., Lemon S. M. 1999; A phylogenetically conserved stem–loop structure at the 5′ border of the internal ribosome entry site of hepatitis C virus is required for cap-independent viral translation. Journal of Virology 73:1165–1174
    [Google Scholar]
  7. Jackson R. J. 2000; Comparative view of initiation site selection mechanism. In Translational Control of Gene Expression . pp 127–184 Edited by Sonenberg N., Hershey J. W. B., Mathews M. B. Cold Spring Habor, NY: Cold Spring Harbor Laboratories;
  8. Jubin R., Vantuno N. E., Kieft J. S., Murray M. G., Doudna J. A., Lau J. Y. N., Baroudy B. M. 2000; Hepatitis C virus internal ribosome entry site (IRES) stem loop IIId contains a phylogenetically conserved GGG triplet essential for translation and IRES folding. Journal of Virology 74:10430–10437
    [Google Scholar]
  9. Kanamori Y., Nakashima N. 2001; A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation. RNA 7:266–274
    [Google Scholar]
  10. Kieft J. S., Zhou K., Jubin R., Murray M. G., Lau J. Y., Doudna J. A. 1999; The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. Journal of Molecular Biology 292:513–529
    [Google Scholar]
  11. Kieft J. S., Zhou K., Jubin R., Doudna J. A. 2001; Mechanism of ribosome recruitment by hepatitis C IRES RNA. RNA 7:194–206
    [Google Scholar]
  12. Kolupaeva V. G., Pestova T. V., Hellen C. U. T. 2000; An enzymatic footprinting analysis of the interaction of 40S ribosomal subunits with the internal ribosomal entry site of hepatitis C virus. Journal of Virology 74:6242–6250
    [Google Scholar]
  13. López de Quinto S., Martínez-Salas E. 1997; Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation. Journal of Virology 71:4171–4175
    [Google Scholar]
  14. López de Quinto S., Martínez-Salas E. 1999; Involvement of the aphthovirus RNA region located between the two functional AUGs in start codon selection. Virology 255:324–336
    [Google Scholar]
  15. López de Quinto S., Martínez-Salas E. 2000; Interaction of the eIF4G initiation factor with the aphthovirus IRES is essential for internal translation initiation in vivo. RNA 61380–1392
    [Google Scholar]
  16. López de Quinto S., Lafuente E., Martínez-Salas E. 2001; IRES interaction with translation initiation factors: functional characterization of novel RNA contacts with eIF3, eIF4B, and eIF4GII. RNA 7:1213–1226
    [Google Scholar]
  17. Lyons A. J., Lytle J. R., Gómez J., Robertson H. D. 2001; Hepatitis C virus internal ribosome entry site RNA contains a tertiary structural element in a functional domain of stem–loop II. Nucleic Acids Research 29:2535–2541
    [Google Scholar]
  18. Lytle J. R., Wu L., Robertson H. D. 2001; The ribosome binding site of hepatitis C virus mRNA. Journal of Virology 75:7629–7636
    [Google Scholar]
  19. Martínez-Salas E., Ramos R., Lafuente E., López de Quinto S. 2001; Functional interactions in internal translation initiation directed by viral and cellular IRES elements. Journal of General Virology 82:973–984
    [Google Scholar]
  20. Paillart J. C., Skripkin E., Ehresmann B., Ehresmann C., Marquet R. 1996; A loop–loop ‘kissing’ complex is the essential part of the dimer linkage of genomic HIV-1 RNA. Proceedings of the National Academy of Sciences USA 93:5572–5577
    [Google Scholar]
  21. Pestova T. V., Shatsky I. N., Fletcher S. P., Jackson R. J., Hellen C. U. T. 1998; A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes & Development 12:67–83
    [Google Scholar]
  22. Pilipenko E. V., Pestova T. V., Kolupaeva V. G., Khitrina E. V., Poperechnaya A. N., Agol V. I., Hellen C. U. T. 2000; A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes & Development 14:2028–2045
    [Google Scholar]
  23. Ramos R., Martínez-Salas E. 1999; Long-range RNA interactions between structural domains of the aphthovirus internal ribosome entry site (IRES. RNA 5:1374–1383
    [Google Scholar]
  24. Robertson M. E., Seamons R. A., Belsham G. J. 1999; A selection system for functional internal ribosome entry site (IRES) elements: analysis of the requirement for a conserved GNRA tetraloop in the encephalomyocarditis virus IRES. RNA 5:1167–1179
    [Google Scholar]
  25. Sáiz J. C., López de Quinto S., Ibarrola N., López-Labrador F. X., Sánchez-Tapias J. M., Rodés J., Martínez-Salas E. 1999; Internal initiation of translation efficiency in different hepatitis C genotypes isolated from interferon treated patients. Archives of Virology 144:215–229
    [Google Scholar]
  26. Sizova D. V., Kolupaeva V. G., Pestova T. V., Shatsky I. N., Hellen C. U. T. 1998; Specific interaction of eukaryotic translation initiation factor 3 with the 5′ nontranslated regions of hepatitis C virus and classical swine fever virus RNAs. Journal of Virology 72:4775–4782
    [Google Scholar]
  27. Spahn C. M., Kieft J. S., Grassucci R. A., Penczek P. A., Zhou K., Doudna J. A., Frank J. 2001; Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science 291:1959–1962
    [Google Scholar]
  28. Tang S., Collier A. J., Elliott R. M. 1999; Alterations to both the primary and predicted secondary structure of stem–loop IIIc of the hepatitis C virus 1b 5′ untranslated region (5′UTR) lead to mutants severely defective in translation which cannot be complemented in trans by the wild-type 5′UTR sequence. Journal of Virology 73:2359–2364
    [Google Scholar]
  29. Wang C., Le S-Y., Ali N., Siddiqui A. 1995; An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5′ noncoding region. RNA 1:526–537
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/0022-1317-83-5-1113
Loading
/content/journal/jgv/10.1099/0022-1317-83-5-1113
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error