메뉴 건너뛰기




Volumn 35, Issue 21, 2007, Pages 7248-7255

Interaction of SmpB with ribosome from directed hydroxyl radical probing

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; FERROUS ION; HYDROXYL RADICAL; MESSENGER RNA; PROTEIN SMPB; RNA BINDING PROTEIN; SMALL PROTEIN B PROTEIN; TRANSFER RNA; UNCLASSIFIED DRUG;

EID: 37549063937     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm677     Document Type: Article
Times cited : (40)

References (51)
  • 1
    • 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
  • 3
    • 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
  • 6
    • 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. (1999) 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
  • 7
    • 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
  • 8
    • 0030024281 scopus 로고    scopus 로고
    • Role of a peptide tagging system in degradation of protein synthesized from messenger RNA
    • Keiler,K.C., Waller,P.R.H. and Sauer,R.T. (1996) Role of a peptide tagging system in degradation of protein synthesized from messenger RNA. Science, 271, 990-993.
    • (1996) Science , vol.271 , pp. 990-993
    • Keiler, K.C.1    Waller, P.R.H.2    Sauer, R.T.3
  • 10
    • 0031939779 scopus 로고    scopus 로고
    • A bacterial RNA that functions as both a tRNA and an mRNA
    • Muto,A., Ushida,C. and Himeno,H. (1998) A bacterial RNA that functions as both a tRNA and an mRNA. Trends Biochem. Sci., 23, 25-29.
    • (1998) Trends Biochem. Sci , vol.23 , pp. 25-29
    • Muto, A.1    Ushida, C.2    Himeno, H.3
  • 11
    • 0242523959 scopus 로고    scopus 로고
    • A salvage pathway for protein structures: TmRNA and trans-translation
    • Withey,J.H. and Friedman,D.I. (2003) A salvage pathway for protein structures: TmRNA and trans-translation. Annu. Rev. Microbiol. 57, 101-123.
    • (2003) Annu. Rev. Microbiol , vol.57 , pp. 101-123
    • Withey, J.H.1    Friedman, D.I.2
  • 12
    • 0034161440 scopus 로고    scopus 로고
    • Charged tmRNA but not tmRNA-mediated proteolysis is essential for Neisseria gonorrhoeae viability
    • Huang,C., Wolfgang,M.C., Withey,J., Koomey,M. and Friedman,D.I. (2000) Charged tmRNA but not tmRNA-mediated proteolysis is essential for Neisseria gonorrhoeae viability. EMBO J., 19, 1098-1107.
    • (2000) EMBO J , vol.19 , pp. 1098-1107
    • Huang, C.1    Wolfgang, M.C.2    Withey, J.3    Koomey, M.4    Friedman, D.I.5
  • 13
    • 0033873650 scopus 로고    scopus 로고
    • Requirement of transfer-messenger RNA (tmRNA) for the growth of Bacillus subtilis under stresses
    • Muto,A., Fujihara,A., Ito,K., Matsuno,J., Ushida,C. and Himeno,H. (2000) Requirement of transfer-messenger RNA (tmRNA) for the growth of Bacillus subtilis under stresses. Genes Cells, 5, 627-636.
    • (2000) Genes Cells , vol.5 , pp. 627-636
    • Muto, A.1    Fujihara, A.2    Ito, K.3    Matsuno, J.4    Ushida, C.5    Himeno, H.6
  • 14
    • 0343627965 scopus 로고    scopus 로고
    • SsrA-mediated tagging and proteolysis of LacI and its role in the regulation of lac operon
    • Abo,T., Inada,T., Ogawa,K. and Aiba,H. (2000) SsrA-mediated tagging and proteolysis of LacI and its role in the regulation of lac operon. EMBO J., 19, 3762-3769.
    • (2000) EMBO J , vol.19 , pp. 3762-3769
    • Abo, T.1    Inada, T.2    Ogawa, K.3    Aiba, H.4
  • 16
    • 0037336119 scopus 로고    scopus 로고
    • tmRNA in Caulobacter crescentus is cell cycle regulated by temporally controlled transcription and RNA degradation
    • Keiler,K.C. and Shapiro,L. (2003) tmRNA in Caulobacter crescentus is cell cycle regulated by temporally controlled transcription and RNA degradation. J. Bacteriol., 185, 1825-1830.
    • (2003) J. Bacteriol , vol.185 , pp. 1825-1830
    • Keiler, K.C.1    Shapiro, L.2
  • 17
    • 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
  • 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
    • 0032840381 scopus 로고    scopus 로고
    • Aminoacylated tmRNA from Escherichia coli interacts with procaryotic elongation factor Tu
    • Rudinger-Thirion,J., Giegé,R. and Felden,B. (1999) Aminoacylated tmRNA from Escherichia coli interacts with procaryotic elongation factor Tu. RNA, 5, 989-992.
    • (1999) RNA , vol.5 , pp. 989-992
    • Rudinger-Thirion, J.1    Giegé, R.2    Felden, B.3
  • 20
    • 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
  • 21
    • 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
  • 22
    • 0034423519 scopus 로고    scopus 로고
    • Binding and cross-linking of tmRNA to ribosomal protein S1, on and off the Escherichia coli ribosome
    • Wower,J., Zwieb,C., Guven,S.A. and Wower,I. (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, J.1    Zwieb, C.2    Guven, S.A.3    Wower, I.4
  • 24
    • 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
  • 25
    • 33947718697 scopus 로고    scopus 로고
    • In vitro trans-translation of Thermus thermophilus: Ribosomal protein S1 is not required for the early stage of trans translation
    • Takada,K., Takemoto,C., Kawazoe,M., Konno,T., Hanawa-Suetsugu,K., Lee,S., Shirouzu,M., Yokoyama,S., Muto,A. et al. (2007) In vitro trans-translation of Thermus thermophilus: Ribosomal protein S1 is not required for the early stage of trans translation. RNA, 13, 1-8.
    • (2007) RNA , vol.13 , pp. 1-8
    • Takada, K.1    Takemoto, C.2    Kawazoe, M.3    Konno, T.4    Hanawa-Suetsugu, K.5    Lee, S.6    Shirouzu, M.7    Yokoyama, S.8    Muto, A.9
  • 26
    • 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, 5503-5509.
    • (2003) Nature , vol.424 , pp. 5503-5509
    • Gutmann, S.1    Haebel, P.W.2    Metzinger, L.3    Sutter, M.4    Felden, B.5    Ban, N.6
  • 28
    • 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. USA, 103, 16484-16489.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 16484-16489
    • Kaur, S.1    Gillet, R.2    Li, W.3    Gursky, R.4    Frank, J.5
  • 29
    • 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
  • 30
    • 22144462503 scopus 로고    scopus 로고
    • Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB
    • Hong,S.J., Tran,Q.A. and Keiler,K. (2005) Cell cycle-regulated degradation of tmRNA is controlled by RNase R and SmpB. Mol. Microbiol., 57, 565-575.
    • (2005) Mol. Microbiol , vol.57 , pp. 565-575
    • Hong, S.J.1    Tran, Q.A.2    Keiler, K.3
  • 31
    • 0037007224 scopus 로고    scopus 로고
    • Structure of small protein B: The protein component of the tmRNA-SmpB system for ribosome rescue
    • Dong,G., Nowakowski,J. and Hoffman,D.W. (2002) Structure of small protein B: The protein component of the tmRNA-SmpB system for ribosome rescue. EMBO J., 21, 1845-1854.
    • (2002) EMBO J , vol.21 , pp. 1845-1854
    • Dong, G.1    Nowakowski, J.2    Hoffman, D.W.3
  • 33
    • 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. USA., 102, 2316-2321.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 2316-2321
    • Sundermeier, T.R.1    Dulebohn, D.P.2    Cho, H.J.3    Karzai, A.W.4
  • 34
    • 14044265657 scopus 로고    scopus 로고
    • Function of the SmpB tail in transfer-messenger RNA translation revealed by a nucleus-encoded form
    • Jacob,Y., Sharkady,S.M., Bhardwaj,K., Sanda,A.A. and Williams,K.P. (2005) Function of the SmpB tail in transfer-messenger RNA translation revealed by a nucleus-encoded form. J. Biol. Chem., 280, 5503-5509.
    • (2005) J. Biol. Chem , vol.280 , pp. 5503-5509
    • Jacob, Y.1    Sharkady, S.M.2    Bhardwaj, K.3    Sanda, A.A.4    Williams, K.P.5
  • 35
    • 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
  • 36
    • 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. (2000) Functional sites of interaction between release factor RF1 and the ribosome. Nat. Struct. Biol., 7, 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
  • 37
    • 0034759978 scopus 로고    scopus 로고
    • Interaction of translation initiation factor 3 with the 30S ribosomal subunit
    • Dallas,A. and Noller,H.F. (2001) Interaction of translation initiation factor 3 with the 30S ribosomal subunit. Mol. Cell, 8, 855-864.
    • (2001) Mol. Cell , vol.8 , pp. 855-864
    • Dallas, A.1    Noller, H.F.2
  • 38
    • 0033612218 scopus 로고    scopus 로고
    • Amino acid acceptor identity switch of Escherichia coli tmRNA from alanine to histidine in vitro
    • Nameki,N., Tadaki,T., Muto,A. and Himeno,H. (1999) Amino acid acceptor identity switch of Escherichia coli tmRNA from alanine to histidine in vitro. J. Mol. Biol., 289, 1-7.
    • (1999) J. Mol. Biol , vol.289 , pp. 1-7
    • Nameki, N.1    Tadaki, T.2    Muto, A.3    Himeno, H.4
  • 39
    • 0037020031 scopus 로고    scopus 로고
    • Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing
    • Lancaster,L., Kiel,M.C., Kaji,A. and Noller,H.F. (2002) Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing. Cell, 111, 129-140.
    • (2002) Cell , vol.111 , pp. 129-140
    • Lancaster, L.1    Kiel, M.C.2    Kaji, A.3    Noller, H.F.4
  • 40
    • 0042847384 scopus 로고    scopus 로고
    • Various effects of paromomycin on tmRNA-directed trans-translation
    • Takahashi,T., Konno,T., Muto,A. and Himeno,H. (2003) Various effects of paromomycin on tmRNA-directed trans-translation. J. Biol. Chem. 278, 27672-27680.
    • (2003) J. Biol. Chem , vol.278 , pp. 27672-27680
    • Takahashi, T.1    Konno, T.2    Muto, A.3    Himeno, H.4
  • 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
    • 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
  • 44
    • 34748881977 scopus 로고    scopus 로고
    • 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, doi:10.1261/rna.604907.
    • 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, doi:10.1261/rna.604907.
  • 45
    • 33749395736 scopus 로고    scopus 로고
    • Role of conserved surface amino acids in binding of SmpB protein to SsrA RNA
    • Dulebohn,D.P., Cho,H.J. and Karzai,A.W. (2006) Role of conserved surface amino acids in binding of SmpB protein to SsrA RNA. J. Biol. Chem. 281, 28536-28545.
    • (2006) J. Biol. Chem , vol.281 , pp. 28536-28545
    • Dulebohn, D.P.1    Cho, H.J.2    Karzai, A.W.3
  • 46
    • 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
  • 47
    • 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
  • 48
    • 34250380391 scopus 로고    scopus 로고
    • Scaffolding as an organizing principle in trans-translation: The roles of small protein B and ribosomal protein S1
    • Gillet,R., Kaur,S., Li,W., Hallier,M., Felden,B. and Frank,J. (2006) Scaffolding as an organizing principle in trans-translation: The roles of small protein B and ribosomal protein S1. J. Biol. Chem., 282, 6356-6363.
    • (2006) J. Biol. Chem , vol.282 , pp. 6356-6363
    • Gillet, R.1    Kaur, S.2    Li, W.3    Hallier, M.4    Felden, B.5    Frank, J.6
  • 50
    • 26944432029 scopus 로고    scopus 로고
    • Competition between trans-translation and termination or elongation of translation
    • Asano,K., Kurita,D., Takada,K., Konno,T., Muto,A. and Himeno,H. (2005) Competition between trans-translation and termination or elongation of translation. Nucleic Acids Res., 33, 5544-5552.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5544-5552
    • Asano, K.1    Kurita, D.2    Takada, K.3    Konno, T.4    Muto, A.5    Himeno, H.6
  • 51
    • 3442899924 scopus 로고    scopus 로고
    • A minimum structure of aminoglycosides that causes an initiation shift of trans-translation
    • Konno,T., Takahashi,T., Kurita,D., Muto,A. and Himeno,H. (2004) A minimum structure of aminoglycosides that causes an initiation shift of trans-translation. Nucleic Acids Res., 32, 4119-4126.
    • (2004) Nucleic Acids Res , vol.32 , pp. 4119-4126
    • Konno, T.1    Takahashi, T.2    Kurita, D.3    Muto, A.4    Himeno, H.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.