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Volumn 345, Issue 1, 2005, Pages 39-49

P-site pairing subtleties revealed by the effects of different tRNAs on programmed translational bypassing where anticodon re-pairing to mRNA is separated from dissociation

Author keywords

codon:anticodon interaction; frameshifting; P site; ribosome; translational bypassing

Indexed keywords

MESSENGER RNA; NUCLEOTIDE; TRANSFER RNA;

EID: 9644273984     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.10.037     Document Type: Article
Times cited : (15)

References (62)
  • 1
    • 0037184536 scopus 로고    scopus 로고
    • Selection of tRNA by the ribosome requires a transition from an open to a closed form
    • J.M. Ogle, F.V. Murphy, M.J. Tarry, and V. Ramakrishnan Selection of tRNA by the ribosome requires a transition from an open to a closed form Cell 111 2002 721 732
    • (2002) Cell , vol.111 , pp. 721-732
    • Ogle, J.M.1    Murphy, F.V.2    Tarry, M.J.3    Ramakrishnan, V.4
  • 2
    • 0034213889 scopus 로고    scopus 로고
    • One protein from two open reading frames: Mechanism of a 50 nt translational bypass
    • A.J. Herr, R.F. Gesteland, and J.F. Atkins One protein from two open reading frames: mechanism of a 50 nt translational bypass EMBO J. 19 2000 2671 2680
    • (2000) EMBO J. , vol.19 , pp. 2671-2680
    • Herr, A.J.1    Gesteland, R.F.2    Atkins, J.F.3
  • 3
    • 0023519951 scopus 로고
    • Slippery runs, shifty stops, backward steps and forward hops: -2, -1, +1, +2, +5 and +6 ribosomal frameshifting
    • R.B. Weiss, D.M. Dunn, J.F. Atkins, and R.F. Gesteland Slippery runs, shifty stops, backward steps and forward hops: -2, -1, +1, +2, +5 and +6 ribosomal frameshifting Cold Spring Harbor Symp. Quant. Biol. 52 1987 687 693
    • (1987) Cold Spring Harbor Symp. Quant. Biol. , vol.52 , pp. 687-693
    • Weiss, R.B.1    Dunn, D.M.2    Atkins, J.F.3    Gesteland, R.F.4
  • 5
    • 0024790054 scopus 로고
    • TRNA hopping: Enhancement by an expanded anticodon
    • M. O'Connor, R.F. Gesteland, and J.F. Atkins tRNA hopping: enhancement by an expanded anticodon EMBO J. 8 1989 4315 4323
    • (1989) EMBO J. , vol.8 , pp. 4315-4323
    • O'Connor, M.1    Gesteland, R.F.2    Atkins, J.F.3
  • 6
    • 0027078856 scopus 로고
    • Novel in-frame two codon translational hop during synthesis of bovine placental lactogen in a recombinant strain of Escherichia coli
    • J.F. Kane, B.N. Violand, D.F. Curran, N.R. Staten, K.L. Duffin, and G. Bogosian Novel in-frame two codon translational hop during synthesis of bovine placental lactogen in a recombinant strain of Escherichia coli Nucl. Acids Res. 20 1992 6707 6712
    • (1992) Nucl. Acids Res. , vol.20 , pp. 6707-6712
    • Kane, J.F.1    Violand, B.N.2    Curran, D.F.3    Staten, N.R.4    Duffin, K.L.5    Bogosian, G.6
  • 7
    • 0032506003 scopus 로고    scopus 로고
    • Ribosomes can slide over and beyond "hungry" codons, resuming protein chain elongation many nucleotides downstream
    • J.A. Gallant, and D. Lindsley Ribosomes can slide over and beyond "hungry" codons, resuming protein chain elongation many nucleotides downstream Proc. Natl Acad. Sci. USA 95 1998 13771 13776
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 13771-13776
    • Gallant, J.A.1    Lindsley, D.2
  • 8
    • 0034724561 scopus 로고    scopus 로고
    • Quadruplet codons: Implications for code expansion and the specification of translation step size
    • M.B. Moore, B.C. Persson, C.C. Nelson, R.F. Gesteland, and J.F. Atkins Quadruplet codons: implications for code expansion and the specification of translation step size J. Mol. Biol. 298 2000 195 209
    • (2000) J. Mol. Biol. , vol.298 , pp. 195-209
    • Moore, M.B.1    Persson, B.C.2    Nelson, C.C.3    Gesteland, R.F.4    Atkins, J.F.5
  • 9
    • 0035933316 scopus 로고    scopus 로고
    • Analysis of the roles of tRNA structure, ribosomal protein L9, and the phage T4 gene 60 bypassing signals during ribosome slippage on mRNA
    • A.J. Herr, R.F. Gesteland, and J.F. Atkins Analysis of the roles of tRNA structure, ribosomal protein L9, and the phage T4 gene 60 bypassing signals during ribosome slippage on mRNA J. Mol. Biol. 309 2001 1029 1048
    • (2001) J. Mol. Biol. , vol.309 , pp. 1029-1048
    • Herr, A.J.1    Gesteland, R.F.2    Atkins, J.F.3
  • 10
    • 4444346213 scopus 로고    scopus 로고
    • On the role of the starved codon and the takeoff site in ribosome bypassing in Escherichia coli
    • J. Gallant, P. Bonthuis, D. Lindsley, K. Heaton, B. Kelley-Clarke, and L. MacDonald On the role of the starved codon and the takeoff site in ribosome bypassing in Escherichia coli J. Mol. Biol. 342 2004 713 724
    • (2004) J. Mol. Biol. , vol.342 , pp. 713-724
    • Gallant, J.1    Bonthuis, P.2    Lindsley, D.3    Heaton, K.4    Kelley-Clarke, B.5    MacDonald, L.6
  • 12
    • 0345255236 scopus 로고    scopus 로고
    • Evidence that the bypassing ribosome travels through the coding gap
    • J. Gallant, P. Bonthuis, and D. Lindsley Evidence that the bypassing ribosome travels through the coding gap Proc. Natl Acad. Sci. USA 100 2003 13430 13435
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 13430-13435
    • Gallant, J.1    Bonthuis, P.2    Lindsley, D.3
  • 13
    • 0032483043 scopus 로고    scopus 로고
    • Rabbit β-globin is extended beyond its UGA stop codon by multiple suppressions and translational reading gaps
    • H.S. Chittum, W.S. Lane, B.A. Carlson, P.P. Roller, F.-D.T. Lung, B.J. Lee, and D.L. Hatfield Rabbit β-globin is extended beyond its UGA stop codon by multiple suppressions and translational reading gaps Biochemistry 37 1998 10866 10870
    • (1998) Biochemistry , vol.37 , pp. 10866-10870
    • Chittum, H.S.1    Lane, W.S.2    Carlson, B.A.3    Roller, P.P.4    Lung, F.-D.T.5    Lee, B.J.6    Hatfield, D.L.7
  • 14
    • 1642442581 scopus 로고    scopus 로고
    • Factors that influence selection of coding resumption sites in translational bypassing
    • A.J. Herr, N.M. Wills, C.C. Nelson, R.F. Gesteland, and J.F. Atkins Factors that influence selection of coding resumption sites in translational bypassing J. Biol. Chem. 279 2004 11081 11087
    • (2004) J. Biol. Chem. , vol.279 , pp. 11081-11087
    • Herr, A.J.1    Wills, N.M.2    Nelson, C.C.3    Gesteland, R.F.4    Atkins, J.F.5
  • 15
    • 0025312745 scopus 로고
    • A nascent peptide is required for ribosomal bypass of the coding gap in bacteriophage T4 gene 60
    • R.B. Weiss, W.M. Huang, and D.M. Dunn A nascent peptide is required for ribosomal bypass of the coding gap in bacteriophage T4 gene 60 Cell 62 1990 117 126
    • (1990) Cell , vol.62 , pp. 117-126
    • Weiss, R.B.1    Huang, W.M.2    Dunn, D.M.3
  • 16
    • 0023909946 scopus 로고
    • A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60
    • W.M. Huang, S.Z. Ao, S. Casjens, R. Orlandi, R. Zeikus, and R. Weiss A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60 Science 239 1988 1005 1012
    • (1988) Science , vol.239 , pp. 1005-1012
    • Huang, W.M.1    Ao, S.Z.2    Casjens, S.3    Orlandi, R.4    Zeikus, R.5    Weiss, R.6
  • 17
    • 0031947172 scopus 로고    scopus 로고
    • Efficiency of T4 gene 60 translational bypassing
    • R. Maldonado, and A.J. Herr Efficiency of T4 gene 60 translational bypassing J. Bacteriol. 180 1998 1822 1830
    • (1998) J. Bacteriol. , vol.180 , pp. 1822-1830
    • Maldonado, R.1    Herr, A.J.2
  • 18
    • 0033577756 scopus 로고    scopus 로고
    • Gly reduce T4 gene 60 translational bypassing efficiency
    • Gly reduce T4 gene 60 translational bypassing efficiency EMBO J. 18 1999 2886 2896
    • (1999) EMBO J. , vol.18 , pp. 2886-2896
    • Herr, A.J.1    Atkins, J.F.2    Gesteland, R.F.3
  • 19
    • 0028587369 scopus 로고
    • A mutation in ribosomal protein L9 affects ribosomal hopping during translation of gene 60 from bacteriophage T4
    • K.L. Herbst, L.M. Nichols, R.F. Gesteland, and R.B. Weiss A mutation in ribosomal protein L9 affects ribosomal hopping during translation of gene 60 from bacteriophage T4 Proc. Natl Acad. Sci. USA 91 1994 12525 12529
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 12525-12529
    • Herbst, K.L.1    Nichols, L.M.2    Gesteland, R.F.3    Weiss, R.B.4
  • 20
    • 0030598966 scopus 로고    scopus 로고
    • Ribosomal protein L9 interactions with 23S rRNA: The use of a translational bypass assay to study the effect of amino acid substitutions
    • F.M. Adamski, J.F. Atkins, and R.F. Gesteland Ribosomal protein L9 interactions with 23S rRNA: the use of a translational bypass assay to study the effect of amino acid substitutions J. Mol. Biol. 261 1996 357 371
    • (1996) J. Mol. Biol. , vol.261 , pp. 357-371
    • Adamski, F.M.1    Atkins, J.F.2    Gesteland, R.F.3
  • 23
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • H. Dong, L. Nilsson, and C.G. Kurland Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates J. Mol. Biol. 260 1996 649 663
    • (1996) J. Mol. Biol. , vol.260 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 26
    • 0032973714 scopus 로고    scopus 로고
    • A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell-free translation system
    • K. Takai, S. Okumura, K. Hosono, S. Yokoyama, and H. Takaku A single uridine modification at the wobble position of an artificial tRNA enhances wobbling in an Escherichia coli cell-free translation system FEBS Letters 447 1999 1 4
    • (1999) FEBS Letters , vol.447 , pp. 1-4
    • Takai, K.1    Okumura, S.2    Hosono, K.3    Yokoyama, S.4    Takaku, H.5
  • 27
    • 0002365884 scopus 로고
    • Modified nucleosides and codon recognition
    • D. Söll U.L. RajBhandary ASM Press Washington DC
    • S. Yokoyama, and S. Nishimura Modified nucleosides and codon recognition D. Söll U.L. RajBhandary tRNA Structure, Biosynthesis and Function 1995 ASM Press Washington DC 207 223
    • (1995) TRNA Structure, Biosynthesis and Function , pp. 207-223
    • Yokoyama, S.1    Nishimura, S.2
  • 28
    • 0028069147 scopus 로고
    • Analysis of action of wobble nucleoside modifications on codon-anticodon pairing within the ribosome
    • V.I. Lim Analysis of action of wobble nucleoside modifications on codon-anticodon pairing within the ribosome J. Mol. Biol. 240 1994 8 19
    • (1994) J. Mol. Biol. , vol.240 , pp. 8-19
    • Lim, V.I.1
  • 29
    • 0015242835 scopus 로고
    • Structure of serine tRNA from Escherichia coli. 1. Purification of serine tRNAs with different codon responses
    • H. Ishikura, Y. Yamada, and S. Nishimura Structure of serine tRNA from Escherichia coli. 1. Purification of serine tRNAs with different codon responses Biochim. Biophys. Acta 228 1971 471 481
    • (1971) Biochim. Biophys. Acta , vol.228 , pp. 471-481
    • Ishikura, H.1    Yamada, Y.2    Nishimura, S.3
  • 31
    • 0033600832 scopus 로고    scopus 로고
    • Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes
    • P. Auffinger, and E. Westhof Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes J. Mol. Biol. 292 1999 467 483
    • (1999) J. Mol. Biol. , vol.292 , pp. 467-483
    • Auffinger, P.1    Westhof, E.2
  • 34
    • 0035801515 scopus 로고    scopus 로고
    • Improvement of reading frame maintenance is a common function for several tRNA modifications
    • J. Urbonavičius, Q. Qian, J.M.B. Durand, T.G. Hagervall, and G.R. Björk Improvement of reading frame maintenance is a common function for several tRNA modifications EMBO J. 20 2001 4863 4873
    • (2001) EMBO J. , vol.20 , pp. 4863-4873
    • Urbonavičius, J.1    Qian, Q.2    Durand, J.M.B.3    Hagervall, T.G.4    Björk, G.R.5
  • 35
    • 0018127496 scopus 로고
    • The accumulation as peptidyl-transfer RNA of isoaccepting transfer RNA families in Escherichia coli with temperature-sensitive peptidyl-transfer RNA hydrolase
    • J.R. Menninger The accumulation as peptidyl-transfer RNA of isoaccepting transfer RNA families in Escherichia coli with temperature-sensitive peptidyl-transfer RNA hydrolase J. Biol. Chem. 253 1978 6808 6813
    • (1978) J. Biol. Chem. , vol.253 , pp. 6808-6813
    • Menninger, J.R.1
  • 37
    • 0034555130 scopus 로고    scopus 로고
    • Sequestration of specific tRNA species cognate to the last sense codon of an overproduced gratuitous protein
    • J. Menez, V. Heurgué-Hamard, and R.H. Buckingham Sequestration of specific tRNA species cognate to the last sense codon of an overproduced gratuitous protein Nucl. Acids Res. 28 2000 4725 4732
    • (2000) Nucl. Acids Res. , vol.28 , pp. 4725-4732
    • Menez, J.1    Heurgué-Hamard, V.2    Buckingham, R.H.3
  • 39
    • 0023722029 scopus 로고
    • Codon choice and gene expression: Synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro
    • L.K. Thomas, D.B. Dix, and R.C. Thompson Codon choice and gene expression: synonymous codons differ in their ability to direct aminoacylated-transfer RNA binding to ribosomes in vitro Proc. Natl Acad. Sci. USA 85 1988 4242 4246
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 4242-4246
    • Thomas, L.K.1    Dix, D.B.2    Thompson, R.C.3
  • 40
    • 0029923751 scopus 로고    scopus 로고
    • Structure of the C-terminal end of the nascent peptide influences translation termination
    • A. Björnsson, S. Mottagui-Tabar, and L.A. Isaksson Structure of the C-terminal end of the nascent peptide influences translation termination EMBO J. 15 1996 1696 1704
    • (1996) EMBO J. , vol.15 , pp. 1696-1704
    • Björnsson, A.1    Mottagui-Tabar, S.2    Isaksson, L.A.3
  • 41
    • 0037072794 scopus 로고    scopus 로고
    • Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination
    • C.S. Hayes, B. Bose, and R.T. Sauer Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination J. Biol. Chem. 277 2002 33825 33832
    • (2002) J. Biol. Chem. , vol.277 , pp. 33825-33832
    • Hayes, C.S.1    Bose, B.2    Sauer, R.T.3
  • 42
    • 0028821311 scopus 로고
    • The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli
    • E.S. Poole, C.M. Brown, and W.P. Tate The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli EMBO J. 14 1995 151 158
    • (1995) EMBO J. , vol.14 , pp. 151-158
    • Poole, E.S.1    Brown, C.M.2    Tate, W.P.3
  • 43
    • 0038369839 scopus 로고    scopus 로고
    • Comparative study of translation termination sites and release factors (RF1 and RF2) in prokaryotes
    • Y. Ozawa, R. Saito, T. Washio, and M. Tomita Comparative study of translation termination sites and release factors (RF1 and RF2) in prokaryotes J. Mol. Evol. 56 2003 665 672
    • (2003) J. Mol. Evol. , vol.56 , pp. 665-672
    • Ozawa, Y.1    Saito, R.2    Washio, T.3    Tomita, M.4
  • 44
    • 0037492900 scopus 로고    scopus 로고
    • The rate of peptidyl-tRNA dissociation from the ribosome during minigene expression depends on the nature of the last decoding interaction
    • L.R. Cruz-Vera, E. Hernández-Ramón, B. Pérez- Zamorano, and G. Guarneros The rate of peptidyl-tRNA dissociation from the ribosome during minigene expression depends on the nature of the last decoding interaction J. Biol. Chem. 278 2003 26065 26070
    • (2003) J. Biol. Chem. , vol.278 , pp. 26065-26070
    • Cruz-Vera, L.R.1    Hernández-Ramón, E.2    Pérez-Zamorano, B.3    Guarneros, G.4
  • 45
    • 0024766985 scopus 로고
    • E. coli ribosomes re-phase on retroviral shift signals at rates ranging from 2 to 50 percent
    • R.B. Weiss, D.M. Dunn, M. Shuh, J.F. Atkins, and R.F. Gesteland E. coli ribosomes re-phase on retroviral shift signals at rates ranging from 2 to 50 percent New Biol. 1 1989 159 169
    • (1989) New Biol. , vol.1 , pp. 159-169
    • Weiss, R.B.1    Dunn, D.M.2    Shuh, M.3    Atkins, J.F.4    Gesteland, R.F.5
  • 46
    • 0026594057 scopus 로고
    • Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA (Lys) and an AAG lysine codon
    • Z. Tsuchihashi, and P.O. Brown Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA (Lys) and an AAG lysine codon Genes. Dev. 6 1992 511 519
    • (1992) Genes. Dev. , vol.6 , pp. 511-519
    • Tsuchihashi, Z.1    Brown, P.O.2
  • 47
    • 0027477486 scopus 로고
    • Translational frameshifting in the control of transposition in bacteria
    • M. Chandler, and O. Fayet Translational frameshifting in the control of transposition in bacteria Mol. Microbiol. 7 1993 497 503
    • (1993) Mol. Microbiol. , vol.7 , pp. 497-503
    • Chandler, M.1    Fayet, O.2
  • 49
    • 0029976654 scopus 로고    scopus 로고
    • The growth defect in Escherichia coli deficient in peptidyl-tRNA hydrolase is due to starvation for Lys-tRNA(Lys)
    • V. Heurgué-Hamard, L. Mora, G. Guarneros, and R.H. Buckingham The growth defect in Escherichia coli deficient in peptidyl-tRNA hydrolase is due to starvation for Lys-tRNA(Lys) EMBO J. 15 1996 2826 2833
    • (1996) EMBO J. , vol.15 , pp. 2826-2833
    • Heurgué-Hamard, V.1    Mora, L.2    Guarneros, G.3    Buckingham, R.H.4
  • 52
    • 0028899217 scopus 로고
    • Decoding with the A:I wobble pair is inefficient
    • J.F. Curran Decoding with the A:I wobble pair is inefficient Nucl. Acids Res. 23 1995 683 688
    • (1995) Nucl. Acids Res. , vol.23 , pp. 683-688
    • Curran, J.F.1
  • 53
    • 0032947999 scopus 로고    scopus 로고
    • Ribosomal -1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG
    • N. Mejlhede, J.F. Atkins, and J. Neuhard Ribosomal -1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG J. Bacteriol. 181 1999 2930 2937
    • (1999) J. Bacteriol. , vol.181 , pp. 2930-2937
    • Mejlhede, N.1    Atkins, J.F.2    Neuhard, J.3
  • 54
    • 0141625262 scopus 로고    scopus 로고
    • Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs
    • P. Licznar, N. Mejlhede, M.-F. Prère, N. Wills, R.F. Gesteland, J.F. Atkins, and O. Fayet Programmed translational -1 frameshifting on hexanucleotide motifs and the wobble properties of tRNAs EMBO J. 22 2003 4770 4778
    • (2003) EMBO J. , vol.22 , pp. 4770-4778
    • Licznar, P.1    Mejlhede, N.2    Prère, M.-F.3    Wills, N.4    Gesteland, R.F.5    Atkins, J.F.6    Fayet, O.7
  • 58
    • 0002167901 scopus 로고    scopus 로고
    • Modulation role of modified nucleotides in RNA loop-loop interaction
    • H. Grosjean R. Benne ASM Press Washington, DC
    • H. Grosjean, C. Houssier, P. Romby, and R. Marquet Modulation role of modified nucleotides in RNA loop-loop interaction H. Grosjean R. Benne Modification and Editing of RNA 1998 ASM Press Washington, DC 113 133
    • (1998) Modification and Editing of RNA , pp. 113-133
    • Grosjean, H.1    Houssier, C.2    Romby, P.3    Marquet, R.4
  • 60
    • 0028804862 scopus 로고
    • Selection of aminoacyl-tRNAs at sense codons: The size of the tRNA variable loop determines whether the immediate 3′ nucleotide to the codon has a context effect
    • J.F. Curran, E.S. Poole, W.P. Tate, and B.L. Gross Selection of aminoacyl-tRNAs at sense codons: the size of the tRNA variable loop determines whether the immediate 3′ nucleotide to the codon has a context effect Nucl. Acids Res. 23 1995 4104 4108
    • (1995) Nucl. Acids Res. , vol.23 , pp. 4104-4108
    • Curran, J.F.1    Poole, E.S.2    Tate, W.P.3    Gross, B.L.4
  • 61
    • 0030847410 scopus 로고    scopus 로고
    • Reported translational bypass in a trpR-lacZ fusion is accounted for by unusual initiation and +1 frameshifting
    • N.M. Wills, J.A. Ingram, R.F. Gesteland, and J.F. Atkins Reported translational bypass in a trpR-lacZ fusion is accounted for by unusual initiation and +1 frameshifting J. Mol. Biol. 271 1997 491 498
    • (1997) J. Mol. Biol. , vol.271 , pp. 491-498
    • Wills, N.M.1    Ingram, J.A.2    Gesteland, R.F.3    Atkins, J.F.4


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