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Volumn 13, Issue 5, 2007, Pages 713-722

Structure probing of tmRNA in distinct stages of trans-translation

Author keywords

Lead(II); SmpB; Structural probing; tmRNA; trans translation

Indexed keywords

ANTIBIOTIC AGENT; ELONGATION FACTOR TU; LEAD ACETATE; MESSENGER RNA; PROTEIN SMALL PROTEIN B; RNA BINDING PROTEIN; TRANSFER MESSENGER RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

EID: 34247338538     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.451507     Document Type: Article
Times cited : (18)

References (45)
  • 2
    • 0030026177 scopus 로고    scopus 로고
    • A case for trans- translation
    • Atkins, J.F. and Gesteland, R.F. 1996. A case for trans- translation. Nature 379: 769-771.
    • (1996) Nature , vol.379 , pp. 769-771
    • Atkins, J.F.1    Gesteland, R.F.2
  • 3
    • 0034646235 scopus 로고    scopus 로고
    • Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli
    • Barends, S., Wower, J., and Kraal, B. 2000. Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli. Biochemistry 39: 2652-2658.
    • (2000) Biochemistry , vol.39 , pp. 2652-2658
    • Barends, S.1    Wower, J.2    Kraal, B.3
  • 4
    • 0035900548 scopus 로고    scopus 로고
    • Simultaneous and functional binding of SmpB and EF-Tu·GTP to the alanyl acceptor arm of tmRNA
    • Barends, S., Karzai, A.W., Sauer, R.T., Wower, J., and Kraal, B. 2001. Simultaneous and functional binding of SmpB and EF-Tu·GTP to the alanyl acceptor arm of tmRNA. J. Mol. Biol. 314: 9-21.
    • (2001) J. Mol. Biol , vol.314 , pp. 9-21
    • Barends, S.1    Karzai, A.W.2    Sauer, R.T.3    Wower, J.4    Kraal, B.5
  • 5
    • 0025369028 scopus 로고
    • Control of replication of plasmid R1: The duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III
    • Blomberg, P., Wagner, E.G.H., and Nordström, K. 1990. Control of replication of plasmid R1: The duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III. EMBO J. 9: 2331-2340.
    • (1990) EMBO J , vol.9 , pp. 2331-2340
    • Blomberg, P.1    Wagner, E.G.H.2    Nordström, K.3
  • 6
    • 0036703022 scopus 로고    scopus 로고
    • Ribosomal protein S1 induces a conformational change of tmRNA; more than one protein S1 per molecule of tmRNA
    • Bordeau, V. and Felden, B. 2002. Ribosomal protein S1 induces a conformational change of tmRNA; more than one protein S1 per molecule of tmRNA. Biochimie 84: 723-729.
    • (2002) Biochimie , vol.84 , pp. 723-729
    • Bordeau, V.1    Felden, B.2
  • 8
    • 0035312250 scopus 로고    scopus 로고
    • Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature
    • Felden, B., Massire, C., Westhof, E., Atkins, J.F., and Gesteland, R.F. 2001. Phylogenetic analysis of tmRNA genes within a bacterial subgroup reveals a specific structural signature. Nucleic Acids Res. 29: 1602-1607.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1602-1607
    • Felden, B.1    Massire, C.2    Westhof, E.3    Atkins, J.F.4    Gesteland, R.F.5
  • 9
    • 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. 1997. 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: 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
  • 10
    • 0036566827 scopus 로고    scopus 로고
    • Two-piece tmRNA in cyanobacteria and its structural analysis
    • Gaudin, C., Zhou, X., Williams, K.P., and Felden, B. 2002. Two-piece tmRNA in cyanobacteria and its structural analysis. Nucleic Acids Res. 30: 2018-2024.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2018-2024
    • Gaudin, C.1    Zhou, X.2    Williams, K.P.3    Felden, B.4
  • 11
    • 0024564403 scopus 로고
    • Use of lead(II) to probe the structure of large RNA's. Conformation of the 39 terminal domain of E. coli 16S rRNA and its involvement in building the tRNA binding sites
    • Gornicki, P., Baudin, F., Romby, P., Wiewiorowski, M., Kryzosiak, W., Ebel, J.P., Ehresmann, C., and Ehresmann, B. 1989. Use of lead(II) to probe the structure of large RNA's. Conformation of the 39 terminal domain of E. coli 16S rRNA and its involvement in building the tRNA binding sites. J. Biomol. Struct. Dyn. 6: 971-984.
    • (1989) J. Biomol. Struct. Dyn , vol.6 , pp. 971-984
    • Gornicki, P.1    Baudin, F.2    Romby, P.3    Wiewiorowski, M.4    Kryzosiak, W.5    Ebel, J.P.6    Ehresmann, C.7    Ehresmann, B.8
  • 12
    • 0041737720 scopus 로고    scopus 로고
    • Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB
    • Gutmann, S., Haebel, P.W., Metzinger, L., Sutter, M., Felden, B., and Ban, N. 2003. Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB. Nature 424: 699-703.
    • (2003) Nature , vol.424 , pp. 699-703
    • Gutmann, S.1    Haebel, P.W.2    Metzinger, L.3    Sutter, M.4    Felden, B.5    Ban, N.6
  • 13
    • 2942755867 scopus 로고    scopus 로고
    • Pre-binding of small protein B to a stalled ribosome triggers trans-translation
    • Hallier, M., Ivanova, N., Rametti, A., Pavlov, M., Ehrenberg, M., and Felden, B. 2004. Pre-binding of small protein B to a stalled ribosome triggers trans-translation. J. Biol. Chem. 279: 25978-25985.
    • (2004) J. Biol. Chem , vol.279 , pp. 25978-25985
    • Hallier, M.1    Ivanova, N.2    Rametti, A.3    Pavlov, M.4    Ehrenberg, M.5    Felden, B.6
  • 14
    • 0035890475 scopus 로고    scopus 로고
    • Importance of the conserved nucleotides around the tRNA-like structure of Escherichia coli transfer-messenger RNA for protein tagging
    • Hanawa-Suetsugu, K., Bordeau, V., Himeno, H., Muto, A., and Felden, B. 2001. Importance of the conserved nucleotides around the tRNA-like structure of Escherichia coli transfer-messenger RNA for protein tagging. Nucleic Acids Res. 29: 4663-4673.
    • (2001) Nucleic Acids Res , vol.29 , pp. 4663-4673
    • Hanawa-Suetsugu, K.1    Bordeau, V.2    Himeno, H.3    Muto, A.4    Felden, B.5
  • 16
    • 0032511223 scopus 로고    scopus 로고
    • A nickel complex cleaves uridine in folded RNA structures: Application to E. coli tmRNA and related engineered molecules
    • Hickerson, R.P., Watkins-Sims, C.D., Burrows, C.J., Atkins, J.F., Gesteland, R.F., and Felden, B. 1998. A nickel complex cleaves uridine in folded RNA structures: Application to E. coli tmRNA and related engineered molecules. J. Mol. Biol. 279: 577-587.
    • (1998) J. Mol. Biol , vol.279 , pp. 577-587
    • Hickerson, R.P.1    Watkins-Sims, C.D.2    Burrows, C.J.3    Atkins, J.F.4    Gesteland, R.F.5    Felden, B.6
  • 18
  • 19
    • 21344471643 scopus 로고    scopus 로고
    • Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA
    • Ivanova, N., Pavlov, M.Y., Bouakaz, E., Ehrenberg, M., and Schiavone, L.H. 2005a. Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA. Nucleic Acids Res. 33: 3529-3539.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3529-3539
    • Ivanova, N.1    Pavlov, M.Y.2    Bouakaz, E.3    Ehrenberg, M.4    Schiavone, L.H.5
  • 20
    • 21744443970 scopus 로고    scopus 로고
    • tmRNA-induced release of messenger RNA from stalled ribosomes
    • Ivanova, N., Pavlov, M.Y., and Ehrenberg, M. 2005b. tmRNA-induced release of messenger RNA from stalled ribosomes. J. Mol. Biol. 350: 897-905.
    • (2005) J. Mol. Biol , vol.350 , pp. 897-905
    • Ivanova, N.1    Pavlov, M.Y.2    Ehrenberg, M.3
  • 21
    • 0018498843 scopus 로고
    • Nucleoside triphosphate regeneration decreases the frequency of translation errors
    • Jelenc, P.C. and Kurland, C.G. 1979. Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc. Natl. Acad. Sci. 76: 3174-3178.
    • (1979) Proc. Natl. Acad. Sci , vol.76 , pp. 3174-3178
    • Jelenc, P.C.1    Kurland, C.G.2
  • 22
    • 0345465673 scopus 로고    scopus 로고
    • SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA)
    • Karzai, A.W., Susskind, M.M., and Sauer, R.T. 1999. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J. 18: 3793-3799.
    • (1999) EMBO J , vol.18 , pp. 3793-3799
    • Karzai, A.W.1    Susskind, M.M.2    Sauer, R.T.3
  • 23
    • 33750838456 scopus 로고    scopus 로고
    • Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome
    • Kaur, S., Gillet, R., Li, W., Gursky, R., and Frank, J. 2006. Cryo-EM visualization of transfer messenger RNA with two SmpBs in a stalled ribosome. Proc. Natl. Acad. Sci. 103: 16484-16489.
    • (2006) Proc. Natl. Acad. Sci , vol.103 , pp. 16484-16489
    • Kaur, S.1    Gillet, R.2    Li, W.3    Gursky, R.4    Frank, J.5
  • 24
    • 0030063988 scopus 로고    scopus 로고
    • Sequence determinants of C-terminal substrate recognition by the Tsp protease
    • Keiler, K.C. and Sauer, R.T. 1996. Sequence determinants of C-terminal substrate recognition by the Tsp protease. J. Biol. Chem. 271: 2589-2593.
    • (1996) J. Biol. Chem , vol.271 , pp. 2589-2593
    • Keiler, K.C.1    Sauer, R.T.2
  • 25
    • 0034608854 scopus 로고    scopus 로고
    • tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter
    • Keiler, K.C., Shapiro, L., and Williams, K.P. 2000. tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter. Proc. Natl. Acad. Sci. 97: 7778-7783.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 7778-7783
    • Keiler, K.C.1    Shapiro, L.2    Williams, K.P.3
  • 27
    • 0028124122 scopus 로고
    • A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli
    • Komine, Y., Kitabatake, M., Yokogawa, T., Nishikawa, K., and Inokuchi, H. 1994. A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc. Natl. Acad. Sci. 91: 9223-9227.
    • (1994) Proc. Natl. Acad. Sci , vol.91 , pp. 9223-9227
    • Komine, Y.1    Kitabatake, M.2    Yokogawa, T.3    Nishikawa, K.4    Inokuchi, H.5
  • 28
    • 0036232115 scopus 로고    scopus 로고
    • Lead(II) as a probe for investigating RNA structure in vivo
    • Lindell, M., Romby, P., and Wagner, E.G.H. 2002. Lead(II) as a probe for investigating RNA structure in vivo. RNA 8: 534-541.
    • (2002) RNA , vol.8 , pp. 534-541
    • Lindell, M.1    Romby, P.2    Wagner, E.G.H.3
  • 29
    • 17844381357 scopus 로고    scopus 로고
    • Independent binding sites of small protein B onto transfer-messenger RNA during trans- translation
    • Metzinger, L., Hallier, M., and Felden, B. 2005. Independent binding sites of small protein B onto transfer-messenger RNA during trans- translation. Nucleic Acids Res. 33: 2384-2394.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2384-2394
    • Metzinger, L.1    Hallier, M.2    Felden, B.3
  • 30
    • 0033568555 scopus 로고    scopus 로고
    • An NMR and mutational analysis of an RNA pseudoknot of Escherichia coli tmRNA involved in trans-translation
    • Nameki, N., Chattopadhyay, P., Himeno, H., Muto, A., and Kawai, G. 1999. An NMR and mutational analysis of an RNA pseudoknot of Escherichia coli tmRNA involved in trans-translation. Nucleic Acids Res. 27: 3667-3675.
    • (1999) Nucleic Acids Res , vol.27 , pp. 3667-3675
    • Nameki, N.1    Chattopadhyay, P.2    Himeno, H.3    Muto, A.4    Kawai, G.5
  • 33
    • 0027991544 scopus 로고
    • In vitro transcription: Preparative RNA yields in analytical scale reactions
    • Pokrovskaya, I.D. and Gurevich, V.V. 1994. In vitro transcription: Preparative RNA yields in analytical scale reactions. Anal. Biochem. 220: 420-423.
    • (1994) Anal. Biochem , vol.220 , pp. 420-423
    • Pokrovskaya, I.D.1    Gurevich, V.V.2
  • 34
    • 0032840381 scopus 로고    scopus 로고
    • Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu
    • Rudinger-Thirion, J., Giege, R., and Felden, B. 1999. Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu. RNA 5: 989-992.
    • (1999) RNA , vol.5 , pp. 989-992
    • Rudinger-Thirion, J.1    Giege, R.2    Felden, B.3
  • 35
    • 0037029092 scopus 로고    scopus 로고
    • The role of SmpB protein in trans-translation
    • Shimizu, Y. and Ueda, T. 2002. The role of SmpB protein in trans-translation. FEBS Lett. 514: 74-77.
    • (2002) FEBS Lett , vol.514 , pp. 74-77
    • Shimizu, Y.1    Ueda, T.2
  • 37
    • 14044271596 scopus 로고    scopus 로고
    • A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation
    • Sundermeier, T.R., Dulebohn, D.P., Cho, H.J., and Karzai, A.W. 2005. A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation. Proc. Natl. Acad. Sci. 102: 2316-2321.
    • (2005) Proc. Natl. Acad. Sci , vol.102 , pp. 2316-2321
    • Sundermeier, T.R.1    Dulebohn, D.P.2    Cho, H.J.3    Karzai, A.W.4
  • 38
    • 0028170454 scopus 로고
    • tRNA-like structures in 10Sa RNAs of Mycoplasma capricolum and Bacillus subtilis
    • Ushida, C., Himeno, H., Watanabe, T., and Muto, A. 1994. tRNA-like structures in 10Sa RNAs of Mycoplasma capricolum and Bacillus subtilis. Nucleic Acids Res. 22: 3392-3396.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3392-3396
    • Ushida, C.1    Himeno, H.2    Watanabe, T.3    Muto, A.4
  • 40
    • 0029907105 scopus 로고    scopus 로고
    • Phylogenetic analysis of tmRNA secondary structure
    • Williams, K.P. and Bartel, D.P. 1996. Phylogenetic analysis of tmRNA secondary structure. RNA 2: 1306-1310.
    • (1996) RNA , vol.2 , pp. 1306-1310
    • Williams, K.P.1    Bartel, D.P.2
  • 41
    • 0345711467 scopus 로고    scopus 로고
    • The tmRNA database (tmRDB)
    • Wower, J. and Zwieb, C. 1999. The tmRNA database (tmRDB). Nucleic Acids Res. 27: 167.
    • (1999) Nucleic Acids Res , vol.27 , pp. 167
    • Wower, J.1    Zwieb, C.2
  • 42
    • 0037118708 scopus 로고    scopus 로고
    • SmpB: A protein that binds to double-stranded segments in tmRNA and tRNA
    • Wower, J., Zwieb, C.W., Hoffman, D.W., and Wower, I.K. 2002. SmpB: A protein that binds to double-stranded segments in tmRNA and tRNA. Biochemistry 41: 8826-8836.
    • (2002) Biochemistry , vol.41 , pp. 8826-8836
    • Wower, J.1    Zwieb, C.W.2    Hoffman, D.W.3    Wower, I.K.4
  • 43
    • 11144236530 scopus 로고    scopus 로고
    • Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans- translation
    • Wower, I.K., Zwieb, C., and Wower, J. 2004. Contributions of pseudoknots and protein SmpB to the structure and function of tmRNA in trans- translation. J. Biol. Chem. 279: 54202-54209.
    • (2004) J. Biol. Chem , vol.279 , pp. 54202-54209
    • Wower, I.K.1    Zwieb, C.2    Wower, J.3
  • 44
    • 17844398246 scopus 로고    scopus 로고
    • Transfer-messenger RNA unfolds as it transits the ribosome
    • Wower, I.K., Zwieb, C., and Wower, J. 2005. Transfer-messenger RNA unfolds as it transits the ribosome. RNA 11: 668-673.
    • (2005) RNA , vol.11 , pp. 668-673
    • Wower, I.K.1    Zwieb, C.2    Wower, J.3
  • 45
    • 0033562579 scopus 로고    scopus 로고
    • Comparative sequence analysis of tmRNA
    • Zwieb, C., Wower, I., and Wower, J. 1999. Comparative sequence analysis of tmRNA. Nucleic Acids Res. 27: 2063-2071.
    • (1999) Nucleic Acids Res , vol.27 , pp. 2063-2071
    • Zwieb, C.1    Wower, I.2    Wower, J.3


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