HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation (original) (raw)
References
Tsukiyama-Kohara, K., Iizuka, N., Kohara, M. & Nomoto, A. Internal ribosome entry site within hepatitis C virus RNA. J. Virol.66, 1476–1483 (1992). CASPubMedPubMed Central Google Scholar
Bukh, J., Purcell, R.H. & Miller, R.H. Sequence analysis of the 5′ noncoding region of hepatitis C virus. Proc. Natl. Acad. Sci. USA89, 4942–4946 (1992). ArticleCASPubMedPubMed Central Google Scholar
Simmonds, P. et al. Sequence variability in the 5′ non-coding region of hepatitis C virus: identification of a new virus type and restrictions on sequence diversity. J. Gen. Virol.74, 661–668 (1993). ArticleCASPubMed Google Scholar
Fraser, C.S. & Doudna, J.A. Structural and mechanistic insights into hepatitis C viral translation initiation. Nat. Rev. Microbiol.5, 29–38 (2007). ArticleCASPubMed Google Scholar
Jackson, R.J., Hellen, C.U. & Pestova, T.V. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol.11, 113–127 (2010). ArticleCASPubMedPubMed Central Google Scholar
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). ArticleCASPubMedPubMed Central Google Scholar
Lytle, J.R., Wu, L. & Robertson, H.D. Domains on the hepatitis C virus internal ribosome entry site for 40s subunit binding. RNA8, 1045–1055 (2002). ArticleCASPubMedPubMed Central Google Scholar
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). ArticleCASPubMedPubMed Central Google Scholar
Otto, G.A. & Puglisi, J.D. The pathway of HCV IRES-mediated translation initiation. Cell119, 369–380 (2004). ArticleCASPubMed Google Scholar
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. USA101, 16990–16995 (2004). ArticleCASPubMedPubMed Central Google Scholar
Fraser, C.S., Hershey, J.W. & Doudna, J.A. The pathway of hepatitis C virus mRNA recruitment to the human ribosome. Nat. Struct. Mol. Biol.16, 397–404 (2009). ArticleCASPubMedPubMed Central Google Scholar
Locker, N., Easton, L.E. & Lukavsky, P.J. HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly. EMBO J.26, 795–805 (2007). ArticleCASPubMedPubMed Central Google Scholar
Terenin, I.M., Dmitriev, S.E., Andreev, D.E. & Shatsky, I.N. Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2. Nat. Struct. Mol. Biol.15, 836–841 (2008). ArticleCASPubMed Google Scholar
Kim, J.H., Park, S.M., Park, J.H., Keum, S.J. & Jang, S.K. eIF2A mediates translation of hepatitis C viral mRNA under stress conditions. EMBO J.30, 2454–2464 (2011). ArticleCASPubMedPubMed Central Google Scholar
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). ArticleCASPubMed Google Scholar
Sizova, D.V., Kolupaeva, V.G., Pestova, T.V., Shatsky, I.N. & Hellen, C.U. Specific interaction of eukaryotic translation initiation factor 3 with the 5′ nontranslated regions of hepatitis C virus and classical swine fever virus RNAs. J. Virol.72, 4775–4782 (1998). CASPubMedPubMed Central Google Scholar
Honda, M., Brown, E.A. & Lemon, S.M. Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA. RNA2, 955–968 (1996). CASPubMedPubMed Central Google Scholar
Berry, K.E., Waghray, S. & Doudna, J.A. The HCV IRES pseudoknot positions the initiation codon on the 40S ribosomal subunit. RNA16, 1559–1569 (2010). ArticleCASPubMedPubMed Central Google Scholar
Filbin, M.E. & Kieft, J.S. HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove. RNA17, 1258–1273 (2011). ArticleCASPubMedPubMed Central Google Scholar
Spahn, C.M. et al. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science291, 1959–1962 (2001). ArticleCASPubMed Google Scholar
Boehringer, D., Thermann, R., Ostareck-Lederer, A., Lewis, J.D. & Stark, H. Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES. Structure13, 1695–1706 (2005). ArticleCASPubMed Google Scholar
Fukushi, S. et al. Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus. J. Biol. Chem.276, 20824–20826 (2001). ArticleCASPubMed Google Scholar
Wower, J., Scheffer, P., Sylvers, L.A., Wintermeyer, W. & Zimmermann, R.A. Topography of the E site on the Escherichia coli ribosome. EMBO J.12, 617–623 (1993). ArticleCASPubMedPubMed Central Google Scholar
Yusupov, M.M. et al. Crystal structure of the ribosome at 5.5-Å resolution. Science292, 883–896 (2001). ArticleCASPubMed Google Scholar
Döring, T., Mitchell, P., Osswald, M., Bochkariov, D. & Brimacombe, R. The decoding region of 16S RNA; a cross-linking study of the ribosomal A, P and E sites using tRNA derivatized at position 32 in the anticodon loop. EMBO J.13, 2677–2685 (1994). ArticlePubMedPubMed Central Google Scholar
Odreman-Macchioli, F., Baralle, F.E. & Buratti, E. Mutational analysis of the different bulge regions of hepatitis C virus domain II and their influence on internal ribosome entry site translational ability. J. Biol. Chem.276, 41648–41655 (2001). ArticleCASPubMed Google Scholar
Kalliampakou, K.I., Psaridi-Linardaki, L. & Mavromara, P. Mutational analysis of the apical region of domain II of the HCV IRES. FEBS Lett.511, 79–84 (2002). ArticleCASPubMed Google Scholar
Passmore, L.A. et al. The eukaryotic translation initiation factors eIF1 and eIF1A induce an open conformation of the 40S ribosome. Mol. Cell26, 41–50 (2007). ArticleCASPubMed Google Scholar
Rabl, J., Leibundgut, M., Ataide, S.F., Haag, A. & Ban, N. Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science331, 730–736 (2011). ArticleCASPubMed Google Scholar
Lukavsky, P.J., Kim, I., Otto, G.A. & Puglisi, J.D. Structure of HCV IRES domain II determined by NMR. Nat. Struct. Biol.10, 1033–1038 (2003). ArticleCASPubMed Google Scholar
Pestova, T.V., Hellen, C.U. & Shatsky, I.N. Canonical eukaryotic initiation factors determine initiation of translation by internal ribosomal entry. Mol. Cell Biol.16, 6859–6869 (1996). ArticleCASPubMedPubMed Central Google Scholar
Wilson, J.E., Pestova, T.V., Hellen, C.U. & Sarnow, P. Initiation of protein synthesis from the A site of the ribosome. Cell102, 511–520 (2000). ArticleCASPubMed Google Scholar
Hartz, D., McPheeters, D.S., Traut, R. & Gold, L. Extension inhibition analysis of translation initiation complexes. Methods Enzymol.164, 419–425 (1988). ArticleCASPubMed Google Scholar
Devaraj, A., Shoji, S., Holbrook, E.D. & Fredrick, K. A role for the 30S subunit E site in maintenance of the translational reading frame. RNA15, 255–265 (2009). ArticleCASPubMedPubMed Central Google Scholar
Monro, R.E. & Marcker, K.A. Ribosome-catalysed reaction of puromycin with a formylmethionine-containing oligonucleotide. J. Mol. Biol.25, 347–350 (1967). ArticleCASPubMed Google Scholar
Peske, F., Savelsbergh, A., Katunin, V.I., Rodnina, M.V. & Wintermeyer, W. Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation. J. Mol. Biol.343, 1183–1194 (2004). ArticleCASPubMed Google Scholar
Dibrov, S.M. et al. Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches. Proc. Natl. Acad. Sci. USA109, 5223–5228 (2012). ArticleCASPubMedPubMed Central Google Scholar
Robert, F. & Brakier-Gingras, L. A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome. J. Biol. Chem.278, 44913–44920 (2003). ArticleCASPubMed Google Scholar
Galkin, O. et al. Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5. RNA13, 2116–2128 (2007). ArticleCASPubMedPubMed Central Google Scholar
Geigenmüller, U. & Nierhaus, K.H. Significance of the third tRNA binding site, the E site, on E. coli ribosomes for the accuracy of translation: an occupied E site prevents the binding of non-cognate aminoacyl-tRNA to the A site. EMBO J.9, 4527–4533 (1990). ArticlePubMedPubMed Central Google Scholar
Petropoulos, A.D. & Green, R. Further in vitro exploration fails to support the allosteric three-site model. J. Biol. Chem.287, 11642–11648 (2012). ArticleCASPubMedPubMed Central Google Scholar
Chen, C. et al. Allosteric vs. spontaneous exit-site (E-site) tRNA dissociation early in protein synthesis. Proc. Natl. Acad. Sci. USA108, 16980–16985 (2011). ArticleCASPubMedPubMed Central Google Scholar
Malygin, A.A., Yanshina, D.D. & Karpova, G.G. Interactions of human ribosomal proteins S16 and S5 with an 18S rRNA fragment containing their binding sites. Biochimie91, 1180–1186 (2009). ArticleCASPubMed Google Scholar
Ian'shina, D.D., Malygin, A.A. & Karpova, G.G. Binding of human ribosomal protein S5 with the 18S rRNA fragment 1203–1236/1521–1698 [in Russian]. Mol. Biol. (Mosk.)40, 460–467 (2006). CAS Google Scholar
Yu, Y. et al. Position of eukaryotic translation initiation factor eIF1A on the 40S ribosomal subunit mapped by directed hydroxyl radical probing. Nucleic Acids Res.37, 5167–5182 (2009). ArticleCASPubMedPubMed Central Google Scholar
Antúnez de Mayolo, P. & Woolford, J.L. Jr. Interactions of yeast ribosomal protein rpS14 with RNA. J. Mol. Biol.333, 697–709 (2003). ArticlePubMedCAS Google Scholar
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). ArticleCASPubMedPubMed Central Google Scholar
Acker, M.G. et al. Kinetic analysis of late steps of eukaryotic translation initiation. J. Mol. Biol.385, 491–506 (2009). ArticleCASPubMed Google Scholar
Fringer, J.M., Acker, M.G., Fekete, C.A., Lorsch, J.R. & Dever, T.E. Coupled release of eukaryotic translation initiation factors 5B and 1A from 80S ribosomes following subunit joining. Mol. Cell. Biol.27, 2384–2397 (2007). ArticleCASPubMedPubMed Central Google Scholar
van Heel, M., Harauz, G., Orlova, E.V., Schmidt, R. & Schatz, M. A new generation of the IMAGIC image processing system. J. Struct. Biol.116, 17–24 (1996). ArticleCASPubMed Google Scholar
Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science313, 1935–1942 (2006). ArticleCASPubMed Google Scholar
Ben-Shem, A. et al. The structure of the eukaryotic ribosome at 3.0-Å resolution. Science334, 1524–1529 (2011). ArticleCASPubMed Google Scholar
Stoneley, M., Paulin, F.E., Le Quesne, J.P., Chappell, S.A. & Willis, A.E. C-Myc 5′ untranslated region contains an internal ribosome entry segment. Oncogene16, 423–428 (1998). ArticleCASPubMed Google Scholar
Keel, A.Y., Easton, L.E., Lukavsky, P.J. & Kieft, J.S. Large-scale native preparation of in vitro transcribed RNA. Methods Enzymol.469, 3–25 (2009). ArticleCASPubMed Google Scholar
Ohi, M., Li, Y., Cheng, Y. & Walz, T. Negative Staining and Image Classification - Powerful Tools in Modern Electron Microscopy. Biol. Proced. Online6, 23–34 (2004). ArticleCASPubMedPubMed Central Google Scholar
Mindell, J.A. & Grigorieff, N. Accurate determination of local defocus and specimen tilt in electron microscopy. J. Struct. Biol.142, 334–347 (2003). ArticlePubMed Google Scholar
Grigorieff, N. FREALIGN: high-resolution refinement of single particle structures. J. Struct. Biol.157, 117–125 (2007). ArticleCASPubMed Google Scholar
Sousa, D. & Grigorieff, N. Ab initio resolution measurement for single particle structures. J. Struct. Biol.157, 201–210 (2007). ArticleCASPubMed Google Scholar
Kleywegt, G.J. & Jones, T.A. xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr. D Biol. Crystallogr.52, 826–828 (1996). ArticleCASPubMed Google Scholar
Pettersen, E.F. et al. UCSF Chimera–a visualization system for exploratory research and analysis. J. Comput. Chem.25, 1605–1612 (2004). ArticleCASPubMed Google Scholar