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Volumn 28, Issue 4, 2007, Pages 533-543

Stop Codon Recognition by Release Factors Induces Structural Rearrangement of the Ribosomal Decoding Center that Is Productive for Peptide Release

Author keywords

RNA

Indexed keywords

AMINOACYL TRANSFER RNA; AMINOGLYCOSIDE ANTIBIOTIC AGENT; PAROMOMYCIN; PEPTIDYLTRANSFERASE; STREPTOMYCIN;

EID: 36248994061     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2007.09.015     Document Type: Article
Times cited : (61)

References (49)
  • 1
    • 33745071762 scopus 로고    scopus 로고
    • Peptide bond formation does not involve acid-base catalysis by ribosomal residues
    • Bieling P., Beringer M., Adio S., and Rodnina M.V. Peptide bond formation does not involve acid-base catalysis by ribosomal residues. Nat. Struct. Mol. Biol. 13 (2006) 423-428
    • (2006) Nat. Struct. Mol. Biol. , vol.13 , pp. 423-428
    • Bieling, P.1    Beringer, M.2    Adio, S.3    Rodnina, M.V.4
  • 3
    • 0028559880 scopus 로고
    • Direct recognition of mRNA stop signals by Escherichia coli polypeptide chain release factor two
    • Brown C.M., and Tate W.P. Direct recognition of mRNA stop signals by Escherichia coli polypeptide chain release factor two. J. Biol. Chem. 269 (1994) 33164-33170
    • (1994) J. Biol. Chem. , vol.269 , pp. 33164-33170
    • Brown, C.M.1    Tate, W.P.2
  • 4
    • 0027176806 scopus 로고
    • Two regions of the Escherichia coli 16S ribosomal RNA are important for decoding stop signals in polypeptide chain termination
    • Brown C.M., McCaughan K.K., and Tate W.P. Two regions of the Escherichia coli 16S ribosomal RNA are important for decoding stop signals in polypeptide chain termination. Nucleic Acids Res. 21 (1993) 2109-2115
    • (1993) Nucleic Acids Res. , vol.21 , pp. 2109-2115
    • Brown, C.M.1    McCaughan, K.K.2    Tate, W.P.3
  • 5
    • 29844448116 scopus 로고    scopus 로고
    • The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity
    • Brunelle J.L., Youngman E.M., Sharma D., and Green R. The interaction between C75 of tRNA and the A loop of the ribosome stimulates peptidyl transferase activity. RNA 12 (2006) 33-39
    • (2006) RNA , vol.12 , pp. 33-39
    • Brunelle, J.L.1    Youngman, E.M.2    Sharma, D.3    Green, R.4
  • 6
    • 0034699519 scopus 로고    scopus 로고
    • Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
    • Carter A.P., Clemons W.M., Brodersen D.E., Morgan-Warren R.J., Wimberly B.T., and Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407 (2000) 340-348
    • (2000) Nature , vol.407 , pp. 340-348
    • Carter, A.P.1    Clemons, W.M.2    Brodersen, D.E.3    Morgan-Warren, R.J.4    Wimberly, B.T.5    Ramakrishnan, V.6
  • 7
    • 0043168057 scopus 로고    scopus 로고
    • Stop codons and UGG promote efficient binding of the polypeptide release factor eRF1 to the ribosomal A site
    • Chavatte L., Frolova L., Laugaa P., Kisselev L., and Favre A. Stop codons and UGG promote efficient binding of the polypeptide release factor eRF1 to the ribosomal A site. J. Mol. Biol. 331 (2003) 745-758
    • (2003) J. Mol. Biol. , vol.331 , pp. 745-758
    • Chavatte, L.1    Frolova, L.2    Laugaa, P.3    Kisselev, L.4    Favre, A.5
  • 8
    • 18844408328 scopus 로고    scopus 로고
    • An active role for tRNA in decoding beyond codon:anticodon pairing
    • Cochella L., and Green R. An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308 (2005) 1178-1180
    • (2005) Science , vol.308 , pp. 1178-1180
    • Cochella, L.1    Green, R.2
  • 9
    • 33846038387 scopus 로고    scopus 로고
    • Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome
    • Cochella L., Brunelle J.L., and Green R. Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome. Nat. Struct. Mol. Biol. 14 (2007) 30-36
    • (2007) Nat. Struct. Mol. Biol. , vol.14 , pp. 30-36
    • Cochella, L.1    Brunelle, J.L.2    Green, R.3
  • 10
  • 11
    • 29444458984 scopus 로고    scopus 로고
    • Quantitative analysis of deoxynucleotide substitutions in the codon-anticodon helix
    • Fahlman R.P., Olejniczak M., and Uhlenbeck O.C. Quantitative analysis of deoxynucleotide substitutions in the codon-anticodon helix. J. Mol. Biol. 355 (2006) 887-892
    • (2006) J. Mol. Biol. , vol.355 , pp. 887-892
    • Fahlman, R.P.1    Olejniczak, M.2    Uhlenbeck, O.C.3
  • 12
    • 0030949960 scopus 로고    scopus 로고
    • Release factor RF3 in E.coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner
    • Freistroffer D.V., Pavlov M.Y., MacDougall J., Buckingham R.H., and Ehrenberg M. Release factor RF3 in E.coli accelerates the dissociation of release factors RF1 and RF2 from the ribosome in a GTP-dependent manner. EMBO J. 16 (1997) 4126-4133
    • (1997) EMBO J. , vol.16 , pp. 4126-4133
    • Freistroffer, D.V.1    Pavlov, M.Y.2    MacDougall, J.3    Buckingham, R.H.4    Ehrenberg, M.5
  • 14
    • 0032840382 scopus 로고    scopus 로고
    • Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis
    • Frolova L.Y., Tsivkovskii R.Y., Sivolobova G.F., Oparina N.Y., Serpinsky O.I., Blinov V.M., Tatkov S.I., and Kisselev L.L. Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis. RNA 5 (1999) 1014-1020
    • (1999) RNA , vol.5 , pp. 1014-1020
    • Frolova, L.Y.1    Tsivkovskii, R.Y.2    Sivolobova, G.F.3    Oparina, N.Y.4    Serpinsky, O.I.5    Blinov, V.M.6    Tatkov, S.I.7    Kisselev, L.L.8
  • 16
    • 0842267211 scopus 로고    scopus 로고
    • Kinetic determinants of high-fidelity tRNA discrimination on the ribosome
    • Gromadski K.B., and Rodnina M.V. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13 (2004) 191-200
    • (2004) Mol. Cell , vol.13 , pp. 191-200
    • Gromadski, K.B.1    Rodnina, M.V.2
  • 17
    • 1842420639 scopus 로고    scopus 로고
    • Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome
    • Gromadski K.B., and Rodnina M.V. Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome. Nat. Struct. Mol. Biol. 11 (2004) 316-322
    • (2004) Nat. Struct. Mol. Biol. , vol.11 , pp. 316-322
    • Gromadski, K.B.1    Rodnina, M.V.2
  • 18
    • 0035830860 scopus 로고    scopus 로고
    • Principles for the buffering of genetic variation
    • Hartman IV J.L., Garvik B., and Hartwell L. Principles for the buffering of genetic variation. Science 291 (2001) 1001-1004
    • (2001) Science , vol.291 , pp. 1001-1004
    • Hartman IV, J.L.1    Garvik, B.2    Hartwell, L.3
  • 19
    • 0032493451 scopus 로고    scopus 로고
    • Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons
    • Ito K., Uno M., and Nakamura Y. Single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons. Proc. Natl. Acad. Sci. USA 95 (1998) 8165-8169
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 8165-8169
    • Ito, K.1    Uno, M.2    Nakamura, Y.3
  • 20
    • 0034628438 scopus 로고    scopus 로고
    • A tripeptide 'anticodon' deciphers stop codons in messenger RNA
    • Ito K., Uno M., and Nakamura Y. A tripeptide 'anticodon' deciphers stop codons in messenger RNA. Nature 403 (2000) 680-684
    • (2000) Nature , vol.403 , pp. 680-684
    • Ito, K.1    Uno, M.2    Nakamura, Y.3
  • 21
    • 0027464670 scopus 로고
    • Release factor-dependent false stops are infrequent in Escherichia coli
    • Jorgensen F., Adamski F.M., Tate W.P., and Kurland C.G. Release factor-dependent false stops are infrequent in Escherichia coli. J. Mol. Biol. 230 (1993) 41-50
    • (1993) J. Mol. Biol. , vol.230 , pp. 41-50
    • Jorgensen, F.1    Adamski, F.M.2    Tate, W.P.3    Kurland, C.G.4
  • 22
    • 0032721006 scopus 로고    scopus 로고
    • Correction of genetic disease by making sense from nonsense
    • Kaufman R.J. Correction of genetic disease by making sense from nonsense. J. Clin. Invest. 104 (1999) 367-368
    • (1999) J. Clin. Invest. , vol.104 , pp. 367-368
    • Kaufman, R.J.1
  • 24
    • 0013797741 scopus 로고
    • Denatured DNA as a direct template for in vitro protein synthesis
    • McCarthy B.J., and Holland J.J. Denatured DNA as a direct template for in vitro protein synthesis. Proc. Natl. Acad. Sci. USA 54 (1965) 880-886
    • (1965) Proc. Natl. Acad. Sci. USA , vol.54 , pp. 880-886
    • McCarthy, B.J.1    Holland, J.J.2
  • 25
    • 0003098935 scopus 로고    scopus 로고
    • Footprinting and modification-interference analysis of binding sites on RNA
    • Smith C.W.J. (Ed), Oxford University Press, Oxford
    • Merryman C., and Noller H.F. Footprinting and modification-interference analysis of binding sites on RNA. In: Smith C.W.J. (Ed). RNA-Protein Interactions: A Practical Approach (1998), Oxford University Press, Oxford 237-253
    • (1998) RNA-Protein Interactions: A Practical Approach , pp. 237-253
    • Merryman, C.1    Noller, H.F.2
  • 26
    • 0022916242 scopus 로고
    • Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes
    • Moazed D., and Noller H.F. Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47 (1986) 985-994
    • (1986) Cell , vol.47 , pp. 985-994
    • Moazed, D.1    Noller, H.F.2
  • 27
    • 0023238983 scopus 로고
    • Interaction of antibiotics with functional sites in 16S ribosomal RNA
    • Moazed D., and Noller H.F. Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature 327 (1987) 389-394
    • (1987) Nature , vol.327 , pp. 389-394
    • Moazed, D.1    Noller, H.F.2
  • 28
    • 0347517767 scopus 로고    scopus 로고
    • Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli
    • Mora L., Zavialov A., Ehrenberg M., and Buckingham R.H. Stop codon recognition and interactions with peptide release factor RF3 of truncated and chimeric RF1 and RF2 from Escherichia coli. Mol. Microbiol. 50 (2003) 1467-1476
    • (2003) Mol. Microbiol. , vol.50 , pp. 1467-1476
    • Mora, L.1    Zavialov, A.2    Ehrenberg, M.3    Buckingham, R.H.4
  • 29
    • 18844413446 scopus 로고    scopus 로고
    • Structural insights into translational fidelity
    • Ogle J.M., and Ramakrishnan V. Structural insights into translational fidelity. Annu. Rev. Biochem. 74 (2005) 129-177
    • (2005) Annu. Rev. Biochem. , vol.74 , pp. 129-177
    • Ogle, J.M.1    Ramakrishnan, V.2
  • 31
    • 0037184536 scopus 로고    scopus 로고
    • Selection of tRNA by the ribosome requires a transition from an open to a closed form
    • Ogle J.M., Murphy F.V., Tarry M.J., and Ramakrishnan V. 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
  • 32
    • 0033961143 scopus 로고    scopus 로고
    • Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome
    • Pape T., Wintermeyer W., and Rodnina M.V. Conformational switch in the decoding region of 16S rRNA during aminoacyl-tRNA selection on the ribosome. Nat. Struct. Biol. 7 (2000) 104-107
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 104-107
    • Pape, T.1    Wintermeyer, W.2    Rodnina, M.V.3
  • 34
    • 0029051827 scopus 로고
    • Ribosomal decoding processes at codons in the A or P sites depend differently on 2′-OH groups
    • Potapov A.P., Triana-Alonso F.J., and Nierhaus K.H. Ribosomal decoding processes at codons in the A or P sites depend differently on 2′-OH groups. J. Biol. Chem. 270 (1995) 17680-17684
    • (1995) J. Biol. Chem. , vol.270 , pp. 17680-17684
    • Potapov, A.P.1    Triana-Alonso, F.J.2    Nierhaus, K.H.3
  • 36
    • 0034923932 scopus 로고    scopus 로고
    • Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms
    • Rodnina M.V., and Wintermeyer W. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu. Rev. Biochem. 70 (2001) 415-435
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 415-435
    • Rodnina, M.V.1    Wintermeyer, W.2
  • 37
    • 17444384877 scopus 로고    scopus 로고
    • Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough
    • Salas-Marco J., and Bedwell D.M. Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough. J. Mol. Biol. 348 (2005) 801-815
    • (2005) J. Mol. Biol. , vol.348 , pp. 801-815
    • Salas-Marco, J.1    Bedwell, D.M.2
  • 38
    • 0038012848 scopus 로고    scopus 로고
    • Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2
    • Scarlett D.J., McCaughan K.K., Wilson D.N., and Tate W.P. Mapping functionally important motifs SPF and GGQ of the decoding release factor RF2 to the Escherichia coli ribosome by hydroxyl radical footprinting. Implications for macromolecular mimicry and structural changes in RF2. J. Biol. Chem. 278 (2003) 15095-15104
    • (2003) J. Biol. Chem. , vol.278 , pp. 15095-15104
    • Scarlett, D.J.1    McCaughan, K.K.2    Wilson, D.N.3    Tate, W.P.4
  • 39
    • 28544452248 scopus 로고    scopus 로고
    • An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA
    • Schmeing T.M., Huang K.S., Strobel S.A., and Steitz T.A. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 438 (2005) 520-524
    • (2005) Nature , vol.438 , pp. 520-524
    • Schmeing, T.M.1    Huang, K.S.2    Strobel, S.A.3    Steitz, T.A.4
  • 41
    • 0037133246 scopus 로고    scopus 로고
    • Polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational release factors
    • Uno M., Ito K., and Nakamura Y. Polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational release factors. Proc. Natl. Acad. Sci. USA 99 (2002) 1819-1824
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 1819-1824
    • Uno, M.1    Ito, K.2    Nakamura, Y.3
  • 43
    • 0033784538 scopus 로고    scopus 로고
    • Functional sites of interaction between release factor RF1 and the ribosome
    • Wilson K.S., Ito K., Noller H.F., and Nakamura Y. Functional sites of interaction between release factor RF1 and the ribosome. Nat. Struct. Biol. 7 (2000) 866-870
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 866-870
    • Wilson, K.S.1    Ito, K.2    Noller, H.F.3    Nakamura, Y.4
  • 45
    • 0033040888 scopus 로고    scopus 로고
    • Amber (UAG) suppressors affected in UGA/UAA-specific polypeptide release factor 2 of bacteria: genetic prediction of initial binding to ribosome preceding stop codon recognition
    • Yoshimura K., Ito K., and Nakamura Y. Amber (UAG) suppressors affected in UGA/UAA-specific polypeptide release factor 2 of bacteria: genetic prediction of initial binding to ribosome preceding stop codon recognition. Genes Cells 4 (1999) 253-266
    • (1999) Genes Cells , vol.4 , pp. 253-266
    • Yoshimura, K.1    Ito, K.2    Nakamura, Y.3
  • 46
    • 23044457405 scopus 로고    scopus 로고
    • Affinity purification of in vivo-assembled ribosomes for in vitro biochemical analysis
    • Youngman E.M., and Green R. Affinity purification of in vivo-assembled ribosomes for in vitro biochemical analysis. Methods 36 (2005) 305-312
    • (2005) Methods , vol.36 , pp. 305-312
    • Youngman, E.M.1    Green, R.2
  • 47
    • 2542470615 scopus 로고    scopus 로고
    • The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release
    • Youngman E.M., Brunelle J.L., Kochaniak A.B., and Green R. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117 (2004) 589-599
    • (2004) Cell , vol.117 , pp. 589-599
    • Youngman, E.M.1    Brunelle, J.L.2    Kochaniak, A.B.3    Green, R.4
  • 48
    • 34250648939 scopus 로고    scopus 로고
    • Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors
    • Youngman E.M., Cochella L., Brunelle J.L., He S., and Green R. Two distinct conformations of the conserved RNA-rich decoding center of the small ribosomal subunit are recognized by tRNAs and release factors. Cold Spring Harb. Symp. Quant. Biol. 71 (2006) 545-549
    • (2006) Cold Spring Harb. Symp. Quant. Biol. , vol.71 , pp. 545-549
    • Youngman, E.M.1    Cochella, L.2    Brunelle, J.L.3    He, S.4    Green, R.5
  • 49
    • 34047120718 scopus 로고    scopus 로고
    • Release factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies
    • Zoldak G., Redecke L., Svergun D.I., Konarev P.V., Voertler C.S., Dobbek H., Sedlak E., and Sprinzl M. Release factors 2 from Escherichia coli and Thermus thermophilus: structural, spectroscopic and microcalorimetric studies. Nucleic Acids Res. 35 (2007) 1343-1353
    • (2007) Nucleic Acids Res. , vol.35 , pp. 1343-1353
    • Zoldak, G.1    Redecke, L.2    Svergun, D.I.3    Konarev, P.V.4    Voertler, C.S.5    Dobbek, H.6    Sedlak, E.7    Sprinzl, M.8


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