Site-Specific Release of Nascent Chains from Ribosomes at a Sense Codon

REFERENCES

• Alkalaeva, E. Z., A. V. Pisarev, L. Y. Frolova, L. L. Kisselev, and T. V. Pestova. 2006. In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell 125:1125–1136.
   PubMed Web of Science ®Google Scholar
• Anthony, D. D., and W. C. Merrick. 1992. 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.
   PubMedGoogle Scholar
• Arava, Y., F. E. Boas, P. O. Brown, and D. Herschlag. 2005. Dissecting eukaryotic translation and its control by ribosome density mapping. Nucleic Acids Res. 33:2421–2432.
   PubMed Web of Science ®Google Scholar
• Atkins, J. F., N. M. Wills, G. Loughran, C. Y. Wu, K. Parsawar, M. D. Ryan, C. H. Wang, and C. C. Nelson. 2007. A case for “StopGo”: reprogramming translation to augment codon meaning of GGN by promoting unconventional termination (Stop) after addition of glycine and then allowing continued translation (Go). RNA 13:803–810.
   PubMed Web of Science ®Google Scholar
• Baranov, P. V., O. L. Gurvich, A. W. Hammer, R. F. Gesteland, and J. F. Atkins. 2003. RECODE 2003. Nucleic Acids Res. 31:87–89.
   PubMedGoogle Scholar
• Berisio, R., F. Schluenzen, J. Harms, A. Bashan, T. Auerbach, D. Baram, and A. Yonath. 2003. Structural insight into the role of the ribosomal tunnel in cellular regulation. Nat. Struct. Biol. 10:366–370.
   PubMedGoogle Scholar
• Bidou, L., G. Stahl, I. Hatin, O. Namy, J. P. Rousset, and P. J. Farabaugh. 2000. Nonsense-mediated decay mutants do not affect programmed −1 frameshifting. RNA 6:952–961.
   PubMedGoogle Scholar
• Bonetti, B., L. Fu, J. Moon, and D. M. Bedwell. 1995. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J. Mol. Biol. 251:334–345.
   PubMed Web of Science ®Google Scholar
• Chapman, R. E., and S. Munro. 1994. The functioning of the yeast Golgi apparatus requires an ER protein encoded by ANP1, a member of a new family of genes affecting the secretory pathway. EMBO J. 13:4896–4907.
   PubMedGoogle Scholar
• de Felipe, P., L. E. Hughes, M. D. Ryan, and J. D. Brown. 2003. Co-translational, intraribosomal cleavage of polypeptides by the foot-and-mouth disease virus 2A peptide. J. Biol. Chem. 278:11441–11448.
   PubMed Web of Science ®Google Scholar
• de Felipe, P., G. A. Luke, L. E. Hughes, D. Gani, C. Halpin, and M. D. Ryan. 2006. E unum pluribus: multiple proteins from a self-processing polyprotein. Trends Biotechnol. 24:68–75.
   PubMedGoogle Scholar
• Derkatch, I. L., Y. O. Chernoff, V. V. Kushnirov, S. G. Inge-Vechtomov, and S. W. Liebman. 1996. Genesis and variability of [PSI] prion factors in Saccharomyces cerevisiae. Genetics 144:1375–1386.
   PubMed Web of Science ®Google Scholar
• Dodding, M. P., M. Bock, M. W. Yap, and J. P. Stoye. 2005. Capsid processing requirements for abrogation of Fv1 and Ref1 restriction. J. Virol. 79:10571–10577.
   PubMed Web of Science ®Google Scholar
• Donnelly, M. L., D. Gani, M. Flint, S. Monaghan, and M. D. Ryan. 1997. The cleavage activities of aphthovirus and cardiovirus 2A proteins. J. Gen. Virol. 78:13–21.
   PubMed Web of Science ®Google Scholar
• Donnelly, M. L., L. E. Hughes, G. Luke, H. Mendoza, E. ten Dam, D. Gani, and M. D. Ryan. 2001. The ‘cleavage’ activities of foot-and-mouth disease virus 2A site-directed mutants and naturally occurring ‘2A-like’ sequences. J. Gen. Virol. 82:1027–1041.
   PubMed Web of Science ®Google Scholar
• Donnelly, M. L., G. Luke, A. Mehrotra, X. Li, L. E. Hughes, D. Gani, and M. D. Ryan. 2001. Analysis of the aphthovirus 2A/2B polyprotein ‘cleavage’ mechanism indicates not a proteolytic reaction, but a novel translational effect: a putative ribosomal ‘skip’. J. Gen. Virol. 82:1013–1025.
   PubMed Web of Science ®Google Scholar
• Fang, P., C. C. Spevak, C. Wu, and M. S. Sachs. 2004. A nascent polypeptide domain that can regulate translation elongation. Proc. Natl. Acad. Sci. USA 101:4059–4064.
   PubMedGoogle Scholar
• Gaba, A., Z. Wang, T. Krishnamoorthy, A. G. Hinnebusch, and M. S. Sachs. 2001. Physical evidence for distinct mechanisms of translational control by upstream open reading frames. EMBO J. 20:6453–6463.
   PubMedGoogle Scholar
• Gross, T., A. Siepmann, D. Sturm, M. Windgassen, J. J. Scarcelli, M. Seedorf, C. N. Cole, and H. Krebber. 2007. The DEAD-box RNA helicase Dbp5 functions in translation termination. Science 315:646–649.
   PubMed Web of Science ®Google Scholar
• Hahn, H., and A. C. Palmenberg. 1996. Mutational analysis of the encephalomyocarditis virus primary cleavage. J. Virol. 70:6870–6875.
   PubMed Web of Science ®Google Scholar
• Hansen, W., P. D. Garcia, and P. Walter. 1986. In vitro protein translocation across the yeast endoplasmic reticulum: ATP-dependent post-translational translocation of the prepro-α factor. Cell 45:397–406.
   PubMedGoogle Scholar
• Heras, S. R., M. C. Thomas, M. Garcia-Canadas, P. de Felipe, J. L. Garcia-Perez, M. D. Ryan, and M. C. Lopez. 2006. L1Tc non-LTR retrotransposons from Trypanosoma cruzi contain a functional viral-like self-cleaving 2A sequence in frame with the active proteins they encode. Cell. Mol. Life Sci. 63:1449–1460.
   PubMed Web of Science ®Google Scholar
• Janzen, D. M., L. Frolova, and A. P. Geballe. 2002. Inhibition of translation termination mediated by an interaction of eukaryotic release factor 1 with a nascent peptidyl-tRNA. Mol. Cell. Biol. 22:8562–8570.
   PubMedGoogle Scholar
• Jørgensen, F., F. M. Adamski, W. P. Tate, and C. G. Kurland. 1993. Release factor-dependent false stops are infrequent in Escherichia coli. J. Mol. Biol. 230:41–50.
   PubMedGoogle Scholar
• Keeling, K. M., J. Lanier, M. Du, J. Salas-Marco, L. Gao, A. Kaenjak-Angeletti, and D. M. Bedwell. 2004. Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae. RNA 10:691–703.
   PubMedGoogle Scholar
• Law, G. L., A. Raney, C. Heusner, and D. R. Morris. 2001. Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase. J. Biol. Chem. 276:38036–38043.
   PubMed Web of Science ®Google Scholar
• Luke, G. A., P. De Felipe, A. Lukashev, S. E. Kallioinen, E. A. Bruno, and M. D. Ryan. 2008. Occurrence, function and evolutionary origins of “2A-like” sequences in virus genomes. J. Gen. Virol. 89:1036–1042.
   PubMed Web of Science ®Google Scholar
• Muto, H., H. Nakatogawa, and K. Ito. 2006. Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall. Mol. Cell 22:545–552.
   PubMed Web of Science ®Google Scholar
• Namy, O., S. J. Moran, D. I. Stuart, R. J. Gilbert, and I. Brierley. 2006. A mechanical explanation of RNA pseudoknot function in programmed ribosomal frameshifting. Nature 441:244–247.
   PubMed Web of Science ®Google Scholar
• Ng, D. T. W., J. D. Brown, and P. Walter. 1996. Signal sequences specify the targeting route to the endoplasmic reticulum membrane. J. Cell Biol. 134:269–278.
   PubMed Web of Science ®Google Scholar
• Ogle, J. M., F. V. Murphy, M. J. Tarry, and V. Ramakrishnan. 2002. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111:721–732.
   PubMed Web of Science ®Google Scholar
• Palmenberg, A. C., G. D. Parks, D. J. Hall, R. H. Ingraham, T. W. Seng, and P. V. Pallai. 1992. Proteolytic processing of the cardioviral P2 region: primary 2A/2B cleavage in clone-derived precursors. Virology 190:754–762.
   PubMedGoogle Scholar
• Pestova, T. V., and C. U. Hellen. 2003. Translation elongation after assembly of ribosomes on the cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes Dev. 17:181–186.
   PubMedGoogle Scholar
• Pringle, F. M., K. H. Gordon, T. N. Hanzlik, J. Kalmakoff, P. D. Scotti, and V. K. Ward. 1999. A novel capsid expression strategy for Thosea asigna virus (Tetraviridae). J. Gen. Virol. 80:1855–1863.
   PubMedGoogle Scholar
• Rakwalska, M., and S. Rospert. 2004. The ribosome-bound chaperones RAC and Ssb1/2p are required for accurate translation in Saccharomyces cerevisiae. Mol. Cell. Biol. 24:9186–9197.
   PubMedGoogle Scholar
• Rigaut, G., A. Shevchenko, B. Rutz, M. Wilm, M. Mann, and B. Seraphin. 1999. A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 17:1030–1032.
   PubMed Web of Science ®Google Scholar
• Robertson, B. H., M. J. Grubman, G. N. Weddell, D. M. Moore, J. D. Welsh, T. Fischer, D. J. Dowbenko, D. G. Yansura, B. Small, and D. G. Kleid. 1985. Nucleotide and amino acid sequence coding for polypeptides of foot-and-mouth disease virus type A12. J. Virol. 54:651–660.
   PubMedGoogle Scholar
• Ryan, M. D., M. L. Donnelly, A. Lewis, A. P. Mehotra, J. Wilke, and D. Gani. 1999. A model for non-stoichiometric, co-translational protein scission in eukaryotic ribosomes. Bioorg. Chem. 27:55–79.
   Web of Science ®Google Scholar
• Ryan, M. D., and J. Drew. 1994. Foot-and-mouth disease virus 2A oligopeptide mediated cleavage of an artificial polyprotein. EMBO J. 13:928–933.
   PubMed Web of Science ®Google Scholar
• Ryan, M. D., A. M. King, and G. P. Thomas. 1991. Cleavage of foot-and-mouth disease virus polyprotein is mediated by residues located within a 19 amino acid sequence. J. Gen. Virol. 72:2727–2732.
   PubMed Web of Science ®Google Scholar
• Sachs, M. S., Z. Wang, A. Gaba, P. Fang, J. Belk, R. Ganesan, N. Amrani, and A. Jacobson. 2002. Toeprint analysis of the positioning of translation apparatus components at initiation and termination codons of fungal mRNAs. Methods 26:105–114.
   PubMedGoogle Scholar
• Salas-Marco, J., and D. M. Bedwell. 2004. GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination. Mol. Cell. Biol. 24:7769–7778.
   PubMed Web of Science ®Google Scholar
• Stansfield, I., L. Eurwilaichitr, Akhmaloka, and M. F. Tuite. 1996. Depletion in the levels of the release factor eRF1 causes a reduction in the efficiency of translation termination in yeast. Mol. Microbiol. 20:1135–1143.
   PubMed Web of Science ®Google Scholar
• Stansfield, I., V. V. Kushnirov, K. M. Jones, and M. F. Tuite. 1997. A conditional-lethal translation termination defect in a sup45 mutant of the yeast Saccharomyces cerevisiae. Eur. J. Biochem. 245:557–563.
   PubMedGoogle Scholar
• St. John, T. P., and R. W. Davis. 1981. The organization and transcription of the galactose gene cluster of Saccharomyces. J. Mol. Biol. 152:285–315.
   PubMedGoogle Scholar
• Tenson, T., and M. Ehrenberg. 2002. Regulatory nascent peptides in the ribosomal tunnel. Cell 108:591–594.
   PubMed Web of Science ®Google Scholar
• Wang, Z., A. Gaba, and M. S. Sachs. 1999. A highly conserved mechanism of regulated ribosome stalling mediated by fungal arginine attenuator peptides that appears independent of the charging status of arginyl-tRNAs. J. Biol. Chem. 274:37565–37574.
   PubMedGoogle Scholar
• Wang, Z., and M. S. Sachs. 1997. Ribosome stalling is responsible for arginine-specific translational attenuation in Neurospora crassa. Mol. Cell. Biol. 17:4904–4913.
   PubMedGoogle Scholar
• Wilson, J. E., T. V. Pestova, C. U. Hellen, and P. Sarnow. 2000. Initiation of protein synthesis from the A site of the ribosome. Cell 102:511–520.
   PubMed Web of Science ®Google Scholar
• Wu, C. Y., C. F. Lo, C. J. Huang, H. T. Yu, and C. H. Wang. 2002. The complete genome sequence of Perina nuda picorna-like virus, an insect-infecting RNA virus with a genome organization similar to that of the mammalian picornaviruses. Virology 294:312–323.
   PubMedGoogle Scholar
• Yen, K., P. Gitsham, J. Wishart, S. G. Oliver, and N. Zhang. 2003. An improved tetO promoter replacement system for regulating the expression of yeast genes. Yeast 20:1255–1262.
   PubMed Web of Science ®Google Scholar
• Zieler, H. A., M. Walberg, and P. Berg. 1995. Suppression of mutations in two Saccharomyces cerevisiae genes by the adenovirus E1A protein. Mol. Cell. Biol. 15:3227–3237.
   PubMed Web of Science ®Google Scholar