Maintenance of the correct open reading frame by the ribosome

EMBO Reports

Volumn 4, Issue 5, 2003, Pages 499-504

  Hansen, Thomas M ^a,b   Baranov, Pavel V ^a   Ivanov, Ivaylo P ^a   Gesteland, Raymond F ^a   Atkins, John F ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; TRANSFER RNA;

ANTICODON; ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BINDING SITE; CODON; CONTROLLED STUDY; ESCHERICHIA COLI; GENE INTERACTION; GENE SEQUENCE; GENETIC CODE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; RIBOSOMAL FRAMESHIFTING; RIBOSOME; RNA TRANSLATION; SEQUENCE ANALYSIS; TRANSPOSON; YEAST; BASE PAIRING; GENETIC STABILITY; GENETIC TRANSCRIPTION AND TRANSLATION; P SITE TRNA SLIPPAGE; PROTEIN ANALYSIS; RNA ANALYSIS; RNA BINDING; RNA SEQUENCE;

ANTICODON; BASE PAIRING; BINDING SITES; CODON; CODON, TERMINATOR; DNA TRANSPOSABLE ELEMENTS; ESCHERICHIA COLI; FRAMESHIFTING, RIBOSOMAL; OPEN READING FRAMES; PLASMIDS; RIBOSOMES; RNA, MESSENGER; RNA, TRANSFER;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; TRANSPOSONS;

EID: 0037821775     PISSN: 1469221X     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.embor.embor825     Document Type: Article

References (37)

1. Asakura, T. et al. (1998) Isolation and characterization of a novel actin filament binding protein from Saccharomyces cerevisiae. Oncogene, 16, 121-130.
2. Atkins, J.F. et al. (2001) Over-riding standard decoding: implications of recoding for ribosome function and enrichment of gene expression. Cold Spring Harb. Symp. Quant. Biol., 66, 217-232.
3. Ban, N., Nissen, P., Hansen, J., Moore, P.B. & Steitz, T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science, 289, 905-920.
4. Baranov, P.V., Gesteland, R.F. & Atkins, J.F. (2002a) Recoding: translational bifurcations in gene expression. Gene, 286, 187-201.
5. Baranov, P.V., Gesteland, R.F. & Atkins, J.F. (2002b) Release factor 2 frameshifting sites in different bacteria. EMBO Rep., 3, 373-377.
6. Baranov, P.V., Gurvich, O.L., Hammer, A.W., Gesteland, R.F. & Atkins, J.F. (2003) RECODE 2003. Nucleic Acids Res., 31, 87-89.
7. Belcourt, M.F. & Farabaugh, P.J. (1990) Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7-nucleotide minimal site. Cell, 62, 339-352.
8. Brierley, I. & Pennell, S. (2001) Structure and function of the stimulatory RNAs involved in programmed eukaryotic-1 ribosomal frameshifting. Cold Spring Harb. Symp. Quant. Biol., 66, 233-248.
9. Chakraburtty, K., Steinschneider, A., Case, R.V. & Mehler, A.H. (1975) Primary structure of tRNA-Lys of E. coli B. Nucleic Acids Res., 2, 2069-2075.
10. Craigen, W.J. & Caskey, C.T. (1986) Expression of peptide chain release factor 2 requires high-efficiency frameshift. Nature, 322, 273-275.
11. Craigen, W.J., Cook, R.G., Tate, W.P. & Caskey. C.T. (1985) Bacterial peptide chain release factors: conserved primary structure and possible frameshift regulation of release factor 2. Proc. Natl Acad. Sci. USA, 82, 3616-3620.
12. Curran, J.F. (1993) Analysis of effects of tRNA:message stability on frameshift frequency at the Escherichia coli RF2 programmed frameshift site. Nucleic Acids Res., 21, 1837-1843.
13. Curran, J.F. & Yarus, M. (1988) Use of tRNA suppressors to probe regulation of Escherichia coli release factor 2. J. Mol. Biol., 203, 75-83.
14. Farabaugh, P.J. & Björk, G.R. (1999) How translational accuracy influences reading frame maintenance. EMBOJ., 18, 1427-1434.
15. Farabaugh, P.J., Zhao, H. & Vimaladithan, A. (1993) A novel programmed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: frameshifting without tRNA slippage. Cell, 74, 93-103.
16. Herr, A.J., Nelson, C.C., Wills, N.M., Gesteland, R.F. & Atkins, J.F. (2001) Analysis of the roles of tRNA structure, ribosomal protein L9, and the bacteriophage T4 gene 60 bypassing signals during ribosome slippage on mRNA. J. Mol. Biol., 309, 1029-1048.
17. Ivanov, I.P., Gesteland, R.F., Matsufuji, S. & Atkins, J.F. (1998) Programmed frameshifting in the synthesis of mammalian antizyme is +1 in mammals, predominantly +1 in fission yeast, but -2 in budding yeast. RNA, 4, 1230-1238.
18. Ivanov, I.P., Gurvich, O.L., Gesteland, R.F. & Atkins, J.F. (2002) in Translation Mechanisms (eds Lapointe, J. & Braker-Gingras, L.) Landes Bioscience, Austin, Texas, USA (http://www.eurekah.com/ chapter.php?chapid=841&bookid=59&catid=54).
19. Li, Z., Stahl, G. & Farabaugh, P.J. (2001) Programmed +1 frameshifting stimulated by complementarity between a downstream mRNA sequence and an error-correcting region of rRNA. RNA, 7, 275-284.
20. Lynch, S.R., Gonzalez, R.L. & Puglisi, J.D. (2003) Comparison of X-ray crystal structure of the 30S subunit-antibiotic complex with NMR structure of decoding site oligonucleotide-paromomycin complex. Structure, 11, 43-53.
21. Matsufuji, S., Matsufuji, T., Miyazaki, Y., Murakami, Y., Atkins, J.F., Gesteland, R.F. & Hayashi, S. (1995) Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell, 80, 51-60.
22. Matsufuji, S., Matsufuji, T., Wills, N.M., Gesteland, R.F. & Atkins, J.F. (1996) Reading two bases twice: mammalian antizyme frameshifting in yeast. EMBO J., 15, 1360-1370.
23. Neidhardt, F.C., Bloch, P.L. & Smith, D.F. (1974) Culture medium for enterobacteria. J. Bacteriol., 119, 736-747.
24. Ogle, J.M., Brodersen, D.E., Clemons, W.M., Tarry, M.J., Carter, A.P. & Ramakrishnan,V. (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science, 292, 897-902.
25. Pande, S.,Vimaladithan, A., Zhao, H. & Farabaugh, P.J. (1995) Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA. Mol. Cell. Biol., 15, 298-304.
26. Ramakrishnan, V. (2002) Ribosome structure and the mechanism of translation. Cell, 108, 557-572.
27. Schluenzen, F. et al. (2000) Structure of functionally activated small ribosomal subunit at 3.3 Å resolution. Cell, 102, 615-623.
28. Stahl, G., Ben Salem, S., Li, Z., McCarty, G., Raman, A., Shah, M. & Farabough, P.J. (2001) Programmed +1 translational frameshift in the yeast Saccharomyces cerevisiae results from disruption of translational error correction. Cold Spring Harb. Symp. Quant. Biol., 66, 249-257.
29. Sundaram, M., Durant, P.C. & Davis, D.R. (2000) Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure. Biochemistry, 39, 12575-12584.
30. Sundararajan, A., Michaud, W.A., Qian, Q., Stahl, G. & Farabaugh, P.J. (1999) Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast. Mol. Cell, 4, 1005-1015.
31. Weiss, R.B., Dunn, D.M., Atkins, J.F. & Gesteland, R.F. (1987) Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5 and +6 ribosomal frameshifting. Cold Spring Harb. Symp. Quant. Biol., 52, 687-693.
32. Weiss, R.B., Dunn, D.M., Dahlberg, A.E., Atkins, J.F. & Gesteland, R.F. (1988) Reading frame switch caused by base-pair formation between the 3′ end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. EMBO J., 7, 1503-1507.
33. Wimberly, B.T., Brodersen, D.E., Clemons, W.M., Morgan-Warren, R.J., Carter, A.P., Vonrhein, C., Hartsch, T. & Ramakrishnan, V. (2000) Structure of the 30S ribosomal subunit. Nature, 407, 327-339.
34. Yaniv, M. & Barrell, B.G. (1971) Sequence relationship of three valine acceptor tRNAs from Escherichia coli. Nature New Biol., 233, 113-114.
35. Yokoyama, S., Watanabe, T., Murao, K., Ishikura, H., Yamaizumi, Z., Nishimura, S. & Miyazawa, T. (1985) Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proc. Natl Acad. Sci. USA, 82, 4905-4909.
36. Yusupov, M.M., Yusupova, G.Z., Baucom, A., Lieberman, K., Earnest, T.N., Cate, J.H. & Noller, H.F. (2001) Crystal structure of the ribosome at 5.5 Å resolution. Science, 292, 883-896.
37. Yusupova, G.Z., Yusupov, M.M., Cate, J.H. & Noller, H.F. (2001) The path of messenger RNA through the ribosome. Cell, 106, 233-241.