Structural aspects of messenger RNA reading frame maintenance by the ribosome (original) (raw)

• Kurland, C.G., Hughes, D. & Ehrenberg, M. Limitation of translation accuracy. in Escherichia coli and Salmonella. Cellular and Molecular Biology (ed. Neidhardt, F.C.) 979–1004 (American Society for Microbiology, Washington, DC, 1996).
• Jorgensen, F. & Kurland, C.G. Processivity errors of gene expression in Escherichia coli. J. Mol. Biol. 215, 511–521 (1990).
  Article CAS Google Scholar
• Bouadloun, F., Srichaiyo, T., Isaksson, L.A. & Bjork, G.R. Influence of modification next to the anticodon in tRNA on codon context sensitivity of translational suppression and accuracy. J. Bacteriol. 166, 1022–1027 (1986).
  Article CAS Google Scholar
• Konevega, A.L., Soboleva, N.G., Makhno, V.I., Peshekhonov, A.V. & Katunin, V.I. The effect of modification of tRNA nucleotide-37 on the tRNA interaction with the P- and A-site of the 70S ribosome Escherichia coli. Mol. Biol. (Mosk.) 40, 669–683 (2006).
  Article CAS Google Scholar
• Urbonavicius, J., Qian, Q., Durand, J.M., Hagervall, T.G. & Bjork, G.R. Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J. 20, 4863–4873 (2001).
  Article CAS Google Scholar
• Gustilo, E.M., Vendeix, F.A. & Agris, P.F. tRNA's modifications bring order to gene expression. Curr. Opin. Microbiol. 11, 134–140 (2008).
  Article CAS Google Scholar
• Rozenski, J., Crain, P.F. & McCloskey, J.A. The RNA modification database: 1999 update. Nucleic Acids Res. 27, 196–197 (1999).
  Article CAS Google Scholar
• Murphy, F.V. IV, Ramakrishnan, V., Malkiewicz, A. & Agris,, P.F. The role of modifications in codon discrimination by tRNA(Lys)UUU. Nat. Struct. Mol. Biol. 11, 1186–1191 (2004).
  Article CAS Google Scholar
• Weixlbaumer, A. et al. Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat. Struct. Mol. Biol. 14, 498–502 (2007).
  Article CAS Google Scholar
• Vacher, J., Grosjean, H., Houssier, C. & Buckingham, R.H. The effect of point mutations affecting Escherichia coli tryptophan tRNA on anticodon-anticodon interactions and on UGA suppression. J. Mol. Biol. 177, 329–342 (1984).
  Article CAS Google Scholar
• Yanofsky, C. Mutations affecting tRNATrp and its charging and their effect on regulation of transcription termination at the attenuator of the tryptophan operon. J. Mol. Biol. 113, 663–677 (1977).
  Article CAS Google Scholar
• Petrullo, L.A., Gallagher, P.J. & Elseviers, D. The role of 2-methylthio-N6-isopentenyladenosine in readthrough and suppression of nonsense codons in Escherichia coli. Mol. Gen. Genet. 190, 289–294 (1983).
  Article CAS Google Scholar
• Wilson, R.K. & Roe, B.A. Presence of the hypermodified nucleotide N6-(δ 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA. Proc. Natl. Acad. Sci. USA 86, 409–413 (1989).
  Article CAS Google Scholar
• Urbonavicius, J. et al. Transfer RNA modifications that alter +1 frameshifting in general fail to affect −1 frameshifting. RNA 9, 760–768 (2003).
  Article CAS Google Scholar
• Yusupov, M.M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883–896 (2001).
  Article CAS Google Scholar
• Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H.F. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065–1077 (2006).
  Article CAS Google Scholar
• Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006).
  Article CAS Google Scholar
• Ogle, J.M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897–902 (2001).
  Article CAS Google Scholar
• Yusupova, G.Z., Yusupov, M.M., Cate, J.H. & Noller, H.F. The path of messenger RNA through the ribosome. Cell 106, 233–241 (2001).
  Article CAS Google Scholar
• Jenner, L. et al. Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding. Science 308, 120–123 (2005).
  Article CAS Google Scholar
• Yusupova, G., Jenner, L., Rees, B., Moras, D. & Yusupov, M. Structural basis for messenger RNA movement on the ribosome. Nature 444, 391–394 (2006).
  Article CAS Google Scholar
• Gogia, Z.V., Yusupov, M.M. & Spirina, T.N. Structure of Thermus thermophilus ribosomes. Method of isolation and purification of the ribosomes. Molekul. Biol. 20, 519–526 (1986).
  Google Scholar
• Jukes, T.H. Possibilities for the evolution of the genetic code from a preceding form. Nature 246, 22–26 (1973).
  Article CAS Google Scholar
• Jenner, L., Rees, B., Yusupov, M. & Yusupova, G. Messenger RNA conformations in the ribosomal E site revealed by X-ray crystallography. EMBO Rep. 8, 846–850 (2007).
  Article CAS Google Scholar
• Lill, R. & Wintermeyer, W. Destabilization of codon-anticodon interaction in the ribosomal exit site. J. Mol. Biol. 196, 137–148 (1987).
  Article CAS Google Scholar
• Shine, J. & Dalgarno, L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. USA 71, 1342–1346 (1974).
  Article CAS Google Scholar
• Weixlbaumer, A. et al. Crystal structure of the ribosome recycling factor bound to the ribosome. Nat. Struct. Mol. Biol. 14, 733–737 (2007).
  Article CAS Google Scholar
• Weixlbaumer, A. et al. Insights into translational termination from the structure of RF2 bound to the ribosome. Science 322, 953–956 (2008).
  Article CAS Google Scholar
• Laurberg, M. et al. Structural basis for translation termination on the 70S ribosome. Nature 454, 852–857 (2008).
  Article CAS Google Scholar
• Korostelev, A. et al. Crystal structure of a translation termination complex formed with release factor RF2. Proc. Natl. Acad. Sci. USA 105, 19684–19689 (2008).
  Article CAS Google Scholar
• Schurr, T., Nadir, E. & Margalit, H. Identification and characterization of E. coli ribosomal binding sites by free energy computation. Nucleic Acids Res. 21, 4019–4023 (1993).
  Article CAS Google Scholar
• Geigenmuller, 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).
  Article CAS Google Scholar
• Menichi, B. & Heyman, T. Study of tyrosine transfer ribonucleic acid modification in relation to sporulation in Bacillus subtilis. J. Bacteriol. 127, 268–280 (1976).
  CAS PubMed PubMed Central Google Scholar
• Hoburg, A., Aschhoff, H.J., Kersten, H., Manderschied, U. & Gassen, H.G. Function of modified nucleosides 7-methylguanosine, ribothymidine, and 2-thiomethyl-N6-(isopentenyl)adenosine in procaryotic transfer ribonucleic acid. J. Bacteriol. 140, 408–414 (1979).
  CAS PubMed PubMed Central Google Scholar
• Klein, D.J., Moore, P.B. & Steitz, T.A. The contribution of metal ions to the structural stability of the large ribosomal subunit. RNA 10, 1366–1379 (2004).
  Article CAS Google Scholar
• Pyle, A.M. Metal ions in the structure and function of RNA. J. Biol. Inorg. Chem. 7, 679–690 (2002).
  Article CAS Google Scholar
• Ogle, J.M., Murphy, F.V., Tarry, M.J. & Ramakrishnan, V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111, 721–732 (2002).
  Article CAS Google Scholar
• Valle, M. et al. Locking and unlocking of ribosomal motions. Cell 114, 123–134 (2003).
  Article CAS Google Scholar
• Spahn, C.M. et al. Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J. 23, 1008–1019 (2004).
  Article CAS Google Scholar
• Zhang, W., Dunkle, J.A. & Cate, J.H. Structures of the ribosome in intermediate states of ratcheting. Science 325, 1014–1017 (2009).
  Article CAS Google Scholar
• Kabsch, W. Automatic indexing of rotation diffraction patterns. J. Appl. Crystallogr. 21, 67–72 (1988).
  Article CAS Google Scholar
• Kabsch, W. Evaluation of single-crystal X-ray diffraction data from a position-sensitive detector. J. Appl. Crystallogr. 21, 916–924 (1988).
  Article CAS Google Scholar
• Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
  Article Google Scholar
• Brunger, A.T. Version 1.2 of the Crystallography and NMR system. Nat. Protoc. 2, 2728–2733 (2007).
  Article CAS Google Scholar
• Brunger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998).
  Article CAS Google Scholar