The pathway of hepatitis C virus mRNA recruitment to the human ribosome (original) (raw)

References

  1. Pestova, T.V., Lorsch, J.R. & Hellen, C.U.T. The mechanism of translation initiation in eukaryotes. in Translational Control in Biology and Medicine (eds. Mathews, M.B., Sonenberg, N. & Hershey, J.W.B.) 87–128 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2007).
    Google Scholar
  2. Fraser, C.S. & Doudna, J.A. Quantitative studies of ribosome conformational dynamics. Q. Rev. Biophys. 40, 163–189 (2007).
    Article CAS Google Scholar
  3. Doudna, J.A. & Sarnow, P. Translation initiation by viral internal ribosome entry sites. in Translational Control in Biology and Medicine (eds. Mathews, M.B., Sonenberg, N. & Hershey, J.W.B.) 129–153 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2007).
    Google Scholar
  4. Elroy-Stein, O. & Merrick, W.C. translation initiation via cellular internal ribosome entry sites. in Translational Control in Biology and Medicine (eds. Mathews, M.B., Sonenberg, N. & Hershey, J.W.B.) 155–172 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2007).
    Google Scholar
  5. Pisarev, A.V., Shirokikh, N.E. & Hellen, C.U. Translation initiation by factor-independent binding of eukaryotic ribosomes to internal ribosomal entry sites. C. R. Biol. 328, 589–605 (2005).
    Article CAS Google Scholar
  6. Fraser, C.S. & Doudna, J.A. Structural and mechanistic insights into hepatitis C viral translation initiation. Nat. Rev. Microbiol. 5, 29–38 (2007).
    Article CAS Google Scholar
  7. Pestova, T.V., Shatsky, I.N., Fletcher, S.P., Jackson, R.J. & Hellen, C.U. 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 Dev. 12, 67–83 (1998).
    Article CAS Google Scholar
  8. Trachsel, H., Erni, B., Schreier, M.H. & Staehelin, T. Initiation of mammalian protein synthesis. II. The assembly of the initiation complex with purified initiation factors. J. Mol. Biol. 116, 755–767 (1977).
    Article CAS Google Scholar
  9. Benne, R. & Hershey, J.W. The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes. J. Biol. Chem. 253, 3078–3087 (1978).
    CAS PubMed Google Scholar
  10. Ji, H., Fraser, C.S., Yu, Y., Leary, J. & Doudna, J.A. Coordinated assembly of human translation initiation complexes by the hepatitis C virus internal ribosome entry site RNA. Proc. Natl. Acad. Sci. USA 101, 16990–16995 (2004).
    Article CAS Google Scholar
  11. Spahn, C.M. et al. Structure of the 80S ribosome from _Saccharomyces cerevisiae_–tRNA-ribosome and subunit-subunit interactions. Cell 107, 373–386 (2001).
    Article CAS Google Scholar
  12. Taylor, D.J., Frank, J. & Kinzy, T.G. Structure and function of the eukaryotic ribosome and elongation fractors. in Translational Control in Biology and Medicine (eds. Mathews, M.B., Sonenberg, N. & Hershey, J.W.B.) pp. 59–85 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2007).
    Google Scholar
  13. Spahn, C.M. et al. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40S ribosomal subunit. Science 291, 1959–1962 (2001).
    Article CAS Google Scholar
  14. Passmore, L.A. et al. The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Mol. Cell 26, 41–50 (2007).
    Article CAS Google Scholar
  15. Kolupaeva, V.G., Pestova, T.V. & Hellen, C.U. An enzymatic footprinting analysis of the interaction of 40S ribosomal subunits with the internal ribosomal entry site of hepatitis C virus. J. Virol. 74, 6242–6250 (2000).
    Article CAS Google Scholar
  16. Otto, G.A. & Puglisi, J.D. The pathway of HCV IRES-mediated translation initiation. Cell 119, 369–380 (2004).
    Article CAS Google Scholar
  17. Spahn, C.M. et al. Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor. Cell 118, 465–475 (2004).
    Article CAS Google Scholar
  18. Unbehaun, A., Borukhov, S.I., Hellen, C.U. & Pestova, T.V. Release of initiation factors from 48S complexes during ribosomal subunit joining and the link between establishment of codon-anticodon base-pairing and hydrolysis of eIF2-bound GTP. Genes Dev. 18, 3078–3093 (2004).
    Article CAS Google Scholar
  19. Fraser, C.S., Berry, K.E., Hershey, J.W. & Doudna, J.A. eIF3j is located in the decoding center of the human 40S ribosomal subunit. Mol. Cell 26, 811–819 (2007).
    Article CAS Google Scholar
  20. Pisarev, A.V., Hellen, C.U. & Pestova, T.V. Recycling of eukaryotic posttermination ribosomal complexes. Cell 131, 286–299 (2007).
    Article CAS Google Scholar
  21. Hartz, D., McPheeters, D.S., Traut, R. & Gold, L. Extension inhibition analysis of translation initiation complexes. Methods Enzymol. 164, 419–425 (1988).
    Article CAS Google Scholar
  22. Anthony, D.D. & Merrick, W.C. Analysis of 40 S and 80 S complexes with mRNA as measured by sucrose density gradients and primer extension inhibition. J. Biol. Chem. 267, 1554–1562 (1992).
    CAS PubMed Google Scholar
  23. Kozak, M. Primer extension analysis of eukaryotic ribosome-mRNA complexes. Nucleic Acids Res. 26, 4853–4859 (1998).
    Article CAS Google Scholar
  24. Kieft, J.S., Zhou, K., Jubin, R. & Doudna, J.A. Mechanism of ribosome recruitment by hepatitis C IRES RNA. RNA 7, 194–206 (2001).
    Article CAS Google Scholar
  25. ElAntak, L., Tzakos, A.G., Locker, N. & Lukavsky, P.J. Structure of eIF3b RNA recognition motif and its interaction with eIF3j: structural insights into the recruitment of eIF3b to the 40 S ribosomal subunit. J. Biol. Chem. 282, 8165–8174 (2007).
    Article CAS Google Scholar
  26. Joseph, S. & Noller, H.F. Directed hydroxyl radical probing using iron(II) tethered to RNA. Methods Enzymol. 318, 175–190 (2000).
    Article CAS Google Scholar
  27. Reynolds, J.E. et al. Unique features of internal initiation of hepatitis C virus RNA translation. EMBO J. 14, 6010–6020 (1995).
    Article CAS Google Scholar
  28. Jivotovskaya, A.V., Valasek, L., Hinnebusch, A.G. & Nielsen, K.H. Eukaryotic translation initiation factor 3 (eIF3) and eIF2 can promote mRNA binding to 40S subunits independently of eIF4G in yeast. Mol. Cell. Biol. 26, 1355–1372 (2006).
    Article CAS Google Scholar
  29. Pisarev, A.V., Kolupaeva, V.G., Yusupov, M.M., Hellen, C.U. & Pestova, T.V. Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J. 27, 1609–1621 (2008).
    Article CAS Google Scholar
  30. Pestova, T.V. & Kolupaeva, V.G. The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection. Genes Dev. 16, 2906–2922 (2002).
    Article CAS Google Scholar
  31. Fraser, C.S. et al. The j-subunit of human translation initiation factor eIF3 is required for the stable binding of eIF3 and its subcomplexes to 40 S ribosomal subunits in vitro. J. Biol. Chem. 279, 8946–8956 (2004).
    Article CAS Google Scholar
  32. Pestova, T.V. & Hellen, C.U. Preparation and activity of synthetic unmodified mammalian tRNAi(Met) in initiation of translation in vitro. RNA 7, 1496–1505 (2001).
    Article CAS Google Scholar
  33. Spanggord, R.J., Siu, F., Ke, A. & Doudna, J.A. RNA-mediated interaction between the peptide-binding and GTPase domains of the signal recognition particle. Nat. Struct. Mol. Biol. 12, 1116–1122 (2005).
    Article CAS Google Scholar
  34. Kieft, J.S. et al. The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. J. Mol. Biol. 292, 513–529 (1999).
    Article CAS Google Scholar
  35. Lomakin, I.B., Kolupaeva, V.G., Marintchev, A., Wagner, G. & Pestova, T.V. Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes Dev. 17, 2786–2797 (2003).
    Article CAS Google Scholar
  36. Culver, G.M. & Noller, H.F. Directed hydroxyl radical probing of RNA from iron(II) tethered to proteins in ribonucleoprotein complexes. Methods Enzymol. 318, 461–475 (2000).
    Article CAS Google Scholar
  37. Pisarev, A.V., Unbehaun, A., Hellen, C.U. & Pestova, T.V. Assembly and analysis of eukaryotic translation initiation complexes. Methods Enzymol. 430, 147–177 (2007).
    Article CAS Google Scholar

Download references