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Volumn 15, Issue 1, 2009, Pages 128-137

Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro

Author keywords

Protein tagging; Pseudoknot; SmpB; tmRNA; trans translation

Indexed keywords

BACTERIAL RNA; MESSENGER RNA; PROTEIN PSEUDOKNOT 1; PROTEIN PSEUDOKNOT 2; PROTEIN PSEUDOKNOT 3; PROTEIN PSEUDOKNOT 4; PROTEIN SMPB; PROTEIN TAG; SINGLE STRANDED RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

EID: 58149091374     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1192409     Document Type: Article
Times cited : (10)

References (44)
  • 2
    • 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
  • 3
    • 0035900548 scopus 로고    scopus 로고
    • Simultaneous and functional binding of SmpB and EF-Tu-TP 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-TP 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
  • 7
    • 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
  • 8
    • 0346494971 scopus 로고    scopus 로고
    • The tmRNA website: Reductive evolution of tmRNA in plastids and other endosymbionts
    • Gueneau de Novoa, P. and Williams, K.P. 2004. The tmRNA website: Reductive evolution of tmRNA in plastids and other endosymbionts. Nucleic Acids Res. 32: D104-D108.
    • (2004) Nucleic Acids Res , vol.32
    • Gueneau de Novoa, P.1    Williams, K.P.2
  • 9
    • 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
  • 10
    • 33645802168 scopus 로고    scopus 로고
    • Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation
    • Hallier, M., Desreac, J., and Felden, B. 2006. Small protein B interacts with the large and the small subunits of a stalled ribosome during trans-translation. Nucleic Acids Res. 34: 1935-1943.
    • (2006) Nucleic Acids Res , vol.34 , pp. 1935-1943
    • Hallier, M.1    Desreac, J.2    Felden, B.3
  • 11
    • 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. 2005. 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
  • 12
    • 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
  • 13
    • 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
  • 14
    • 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
  • 15
    • 0034852587 scopus 로고    scopus 로고
    • Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities
    • Kelley, S.T., Harris, J.K., and Pace, N.R. 2001. Evaluation and refinement of tmRNA structure using gene sequences from natural microbial communities. RNA 7: 1310-1316.
    • (2001) RNA , vol.7 , pp. 1310-1316
    • Kelley, S.T.1    Harris, J.K.2    Pace, N.R.3
  • 16
    • 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
  • 17
    • 34748881977 scopus 로고    scopus 로고
    • A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation
    • Konno, T., Kurita, D., Takada, K., Muto, A., and Himeno, H. 2007. A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation. RNA 13: 1723-1731.
    • (2007) RNA , vol.13 , pp. 1723-1731
    • Konno, T.1    Kurita, D.2    Takada, K.3    Muto, A.4    Himeno, H.5
  • 18
    • 0034951396 scopus 로고    scopus 로고
    • Determinants on tmRNA for initiating efficient and precise trans-translation: Some mutations upstream of the tag-encoding sequence of Escherichia coli tmRNA shift the initiation point of trans-translation in vitro
    • Lee, S., Ishii, M., Tadaki, T., Muto, A., and Himeno, H. 2001. Determinants on tmRNA for initiating efficient and precise trans-translation: Some mutations upstream of the tag-encoding sequence of Escherichia coli tmRNA shift the initiation point of trans-translation in vitro. RNA 7: 999-1012.
    • (2001) RNA , vol.7 , pp. 999-1012
    • Lee, S.1    Ishii, M.2    Tadaki, T.3    Muto, A.4    Himeno, H.5
  • 19
    • 0032539857 scopus 로고    scopus 로고
    • 39 Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli
    • Li, Z., Pandit, S., and Deutscher, M.P. 1998. 39 Exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc. Natl. Acad. Sci. 95: 2856-2861.
    • (1998) Proc. Natl. Acad. Sci , vol.95 , pp. 2856-2861
    • Li, Z.1    Pandit, S.2    Deutscher, M.P.3
  • 20
    • 4544289260 scopus 로고    scopus 로고
    • Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules
    • McGinness, K.E. and Sauer, R.T. 2004. Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules. Proc. Natl. Acad. Sci. 101: 13454-13459.
    • (2004) Proc. Natl. Acad. Sci , vol.101 , pp. 13454-13459
    • McGinness, K.E.1    Sauer, R.T.2
  • 21
    • 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
  • 22
    • 48249108321 scopus 로고    scopus 로고
    • The role of upstream sequences in selecting the reading frame on tmRNA
    • Miller, M.R., Heally, D.W., Robison, S.G., Dewey, J.D., and Buskirk, A.R. 2008. The role of upstream sequences in selecting the reading frame on tmRNA. BMC Biol. 6: 29-38.
    • (2008) BMC Biol , vol.6 , pp. 29-38
    • Miller, M.R.1    Heally, D.W.2    Robison, S.G.3    Dewey, J.D.4    Buskirk, A.R.5
  • 23
    • 34247103448 scopus 로고    scopus 로고
    • The tmRNA system for translational surveillance and ribosome rescue
    • Moore, S.D. and Sauer, R.T. 2007. The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76: 101-124.
    • (2007) Annu. Rev. Biochem , vol.76 , pp. 101-124
    • Moore, S.D.1    Sauer, R.T.2
  • 24
    • 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. 1999a. 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
  • 25
    • 0033605218 scopus 로고    scopus 로고
    • Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA
    • Nameki, N., Felden, B., Atkins, J.F., Gesteland, R.F., Himeno, H., and Muto, A. 1999b. Functional and structural analysis of a pseudoknot upstream of the tag-encoded sequence in E. coli tmRNA. J. Mol. Biol. 286: 733-744.
    • (1999) J. Mol. Biol , vol.286 , pp. 733-744
    • Nameki, N.1    Felden, B.2    Atkins, J.F.3    Gesteland, R.F.4    Himeno, H.5    Muto, A.6
  • 26
    • 0034737453 scopus 로고    scopus 로고
    • Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single-stranded RNAs
    • Nameki, N., Tadaki, T., Himeno, H., and Muto, A. 2000. Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single-stranded RNAs. FEBS Lett. 470: 345-349.
    • (2000) FEBS Lett , vol.470 , pp. 345-349
    • Nameki, N.1    Tadaki, T.2    Himeno, H.3    Muto, A.4
  • 27
    • 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
  • 28
    • 0023953676 scopus 로고
    • Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro
    • Sampson, J.R. and Uhlenbeck, O.C. 1988. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA transcribed in vitro. Proc. Natl. Acad. Sci. 85: 1033-1037.
    • (1988) Proc. Natl. Acad. Sci , vol.85 , pp. 1033-1037
    • Sampson, J.R.1    Uhlenbeck, O.C.2
  • 29
    • 4344705601 scopus 로고    scopus 로고
    • A third lineage with two-piece tmRNA
    • Sharkady, S.M. and Williams, K.P. 2004. A third lineage with two-piece tmRNA. Nucleic Acids Res. 32: 4531-4538.
    • (2004) Nucleic Acids Res , vol.32 , pp. 4531-4538
    • Sharkady, S.M.1    Williams, K.P.2
  • 30
    • 0024241761 scopus 로고
    • Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension
    • Stern, S., Moazed, D., and Noller, H.F. 1988. Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164: 481-489.
    • (1988) Methods Enzymol , vol.164 , pp. 481-489
    • Stern, S.1    Moazed, D.2    Noller, H.F.3
  • 31
    • 36849093840 scopus 로고    scopus 로고
    • Functional SmpB-ribosome interactions require tmRNA
    • Sundermeier, T.R. and Karzai, A.W. 2007. Functional SmpB-ribosome interactions require tmRNA. J. Biol. Chem. 282: 34779-34786.
    • (2007) J. Biol. Chem , vol.282 , pp. 34779-34786
    • Sundermeier, T.R.1    Karzai, A.W.2
  • 32
    • 33744505213 scopus 로고    scopus 로고
    • Genetic analysis of the structure and function of transfer-messenger RNA pseudoknot 1
    • Tanner, D.R., Dewey, J.D., Miller, M.R., and Buskirk, A.R. 2006. Genetic analysis of the structure and function of transfer-messenger RNA pseudoknot 1. J. Biol. Chem. 281: 10561-10566.
    • (2006) J. Biol. Chem , vol.281 , pp. 10561-10566
    • Tanner, D.R.1    Dewey, J.D.2    Miller, M.R.3    Buskirk, A.R.4
  • 33
    • 1942533456 scopus 로고    scopus 로고
    • tRNA slippage at the tmRNA resume codon
    • Trimble, M.J., Minnicus, A., and Williams, K.P. 2004. tRNA slippage at the tmRNA resume codon. RNA 10: 805-812.
    • (2004) RNA , vol.10 , pp. 805-812
    • Trimble, M.J.1    Minnicus, A.2    Williams, K.P.3
  • 35
    • 0026350896 scopus 로고
    • Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase
    • Varshney, U., Lee, C.P., and RajBhandary, U.L. 1991. Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J. Biol. Chem. 266: 24712-24718.
    • (1991) J. Biol. Chem , vol.266 , pp. 24712-24718
    • Varshney, U.1    Lee, C.P.2    RajBhandary, U.L.3
  • 36
    • 0036567510 scopus 로고    scopus 로고
    • Descent of a split RNA
    • Williams, K.P. 2002. Descent of a split RNA. Nucleic Acids Res. 30: 2025-2030.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2025-2030
    • Williams, K.P.1
  • 37
    • 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
  • 38
    • 0033215307 scopus 로고    scopus 로고
    • Resuming translation on tmRNA: A unique mode of determining a reading frame
    • Williams, K.P., Martindale, K.A., and Bartel, D.P. 1999. Resuming translation on tmRNA: A unique mode of determining a reading frame. EMBO J. 18: 5423-5433.
    • (1999) EMBO J , vol.18 , pp. 5423-5433
    • Williams, K.P.1    Martindale, K.A.2    Bartel, D.P.3
  • 39
    • 0034423519 scopus 로고    scopus 로고
    • Binding and cross-linking of tmRNA to ribosomal protein S1, on and off the Escherichia coli ribosome
    • Wower, I.K., Zwieb, C.W., Guven, S.A., and Wower, J. 2000. Binding and cross-linking of tmRNA to ribosomal protein S1, on and off the Escherichia coli ribosome. EMBO J. 19: 6612-6621.
    • (2000) EMBO J , vol.19 , pp. 6612-6621
    • Wower, I.K.1    Zwieb, C.W.2    Guven, S.A.3    Wower, J.4
  • 40
    • 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
  • 41
    • 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
  • 42
    • 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
  • 43
    • 0033983838 scopus 로고    scopus 로고
    • tmRDB (tmRNA database)
    • Zwieb, C. and Wower, J. 2000. tmRDB (tmRNA database). Nucleic Acids Res. 28: 169-170.
    • (2000) Nucleic Acids Res , vol.28 , pp. 169-170
    • Zwieb, C.1    Wower, J.2
  • 44
    • 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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