Interaction analysis between tmRNA and SmpB from Thermus thermophilus

Journal of Biochemistry

Volumn 138, Issue 6, 2005, Pages 729-739

  Nameki, Nobukazu ^a,b,h   Someya, Tatsuhiko ^a   Okano, Satoshi ^a   Suemasa, Reiko ^a   Kimoto, Michiko ^b   Hanawa Suetsugu, Kyoko ^b   Terada, Takaho ^b   Shirouzu, Mikako ^b   Hirao, Ichiro ^b,c   Takaku, Hiroshi ^a   Himeno, Hyouta ^d   Muto, Akira ^d   Kuramitsu, Seiki ^b,e,f   Yokoyama, Shigeyuki ^b,e,g   Kawai, Gota ^a  

^a CHIBA INSTITUTE OF TECHNOLOGY   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

^d HIROSAKI UNIVERSITY   (Japan)

^e RIKEN HARIMA INSTITUTE   (Japan)

^f OSAKA UNIVERSITY   (Japan)

^g UNIVERSITY OF TOKYO   (Japan)

^h GUNMA UNIVERSITY   (Japan)

Author keywords

Induced fit; Protein RNA interactions; SmpB; tmRNA; tRNA like domain

Indexed keywords

1 CYCLOHEXYL 3 (2 MORPHOLINOETHYL) CARBODIIMIDE METHO 4 TOLUENE SULFONATE; BINDING PROTEIN; DIMETHYL SULFATE; ELONGATION FACTOR; ELONGATION FACTOR TU; MESSENGER RNA; OLIGONUCLEOTIDE; SMALL PROTEIN B; SULFONIC ACID DERIVATIVE; TRANSFER RNA; UNCLASSIFIED DRUG;

AQUIFEX AEOLICUS; ARTICLE; GENE AMPLIFICATION; HYDROGEN BOND; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PROTEIN BINDING; PROTEIN INTERACTION; PROTEIN PURIFICATION; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; THERMUS THERMOPHILUS;

BACTERIAL PROTEINS; BINDING SITES; PROTEIN CONFORMATION; RNA, BACTERIAL; RNA-BINDING PROTEINS; THERMUS THERMOPHILUS;

AQUIFEX AEOLICUS; THERMUS THERMOPHILUS;

EID: 32944469826     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvi180     Document Type: Article

References (44)

1. 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
2. Zwieb, C., Gorodkin, J., Knudsen, B., Burks, J., and Wower, J. (2003) tmRDB (tmRNA database). Nucleic Acids Res. 31, 446-447
3. Withey, J.H. and Friedman, D.I. (2003) A salvage pathway for protein structures: tmRNA and trans-translation. Annu. Rev. Microbiol. 57, 101-123
4. Haebel, P.W., Gutmann, S., and Ban, N. (2004) Dial tm for rescue: tmRNA engages ribosomes stalled on defective mRNAs. Curr. Opin. Struct. Biol. 14, 58-65
5. Yamamoto, Y., Sunohara, T., Jojima, K., Inada, T., and Aiba, H. (2003) SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs. RNA 9, 408-418
6. 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
7. Muto, A., Fujihara, A., Ito, K.I., Matsuno, J., Ushida, C., and Himeno, H. (2000) Requirement of transfer-messenger RNA for the growth of Bacillus subtilis under stresses. Genes Cells 5, 627-335
8. 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
9. Keiler, K.C. and Shapiro, L. (2003) tmRNA is required for correct timing of DNA replication in Caulobacter crescentus. J. Bacteriol. 185, 573-580
10. 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
11. 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
12. Karzai, A.W., Roche, B.D., and Sauer, R.T. (2000) The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nat. Struct. Biol. 7, 449-455
13. Hanawa-Suetsugu, K., Takagi, M., Inokuchi, H., Himeno, H., and Muto, A. (2002) SmpB functions in various steps of trans-translation. Nucleic Acids Res. 30, 1620-1629
14. Karzai, A. W. and Sauer, R.T. (2001) Protein factors associated with the SsrA-SmpB tagging and ribosome rescue complex. Proc. Natl. Acad. Sci. USA 98, 3040-3044
15. 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
16. 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. USA 101, 13454-13459
17. Shimizu, Y. and Ueda, T. (2002) The role of SmpB protein in trans-translation. FEBS Lett. 514, 74-77
18. 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
19. Someya, T., Nameki, N., Hosoi, H., Suzuki, S., Hatanaka, H., Fujii, M., Terada, T., Shirouzu, M., Inoue, Y., Shibata, T., Kuramitsu, S., Yokoyama, S., and Kawai, G. (2003) Solution structure of a tmRNA-binding protein, SmpB, from Thermus thermophilus. FEBS Lett. 535, 94-100
20. Williams, K.P. and Bartel, D.P. (1996) Phylogenetic analysis of tmRNA secondary structure. RNA 2, 1306-1310
21. Felden, B., Himeno, H., Muto, A., McCutcheon, J.P., Atkins, J.F., and Gesteland, R.F. (1997) Probing the structure of the Escherichia coli 10Sa RNA (tmRNA). RNA 3, 89-103
22. Zwieb, C., Wower, I., and Wower, J. (1999) Comparative sequence analysis of tmRNA. Nucleic Acids Res. 27, 2063-2071
23. 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
24. 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
25. Gill, A., Leatherbarrow, R.J., Hoare, M., Pollard-Knight, D.V., Lowe, P.A., and Fortune, D.H. (1996) Analysis of kinetic data of antibody-antigen interaction from an optical biosensor by exponential curve fitting. J. Biotech. 48, 117-127
26. Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNK pipes. J. Biomol. NMR 6, 277-293
27. Goddard, T.D. and Kneller, D.G. SPARKY 3, University of California, San Francisco.
28. Koradi, R., Billeter, M., and Wuthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55
29. Cush, R., Cronin, J.M., Stewart, W.J., Maule, C.H., Molloy, J., and Goddard, N.J. (1993) The resonant mirror: a novel optical biosensor for direct sensing of biomolecular interactions. Part I: Principles of operation and associated instrumentation. Biosensors & Bioelectronics 8, 347-364
30. Canziani, G., Zhang, W., Cines, D., Rux, A., Willis, S., Cohen, G., Eisenberg, R., and Chaiken, I. (1999) Exploring biomolecular recognition using optical biosensors. Methods 19, 253-269
31. 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, 4663-1673
32. Barends, S., Björk, K., Gultyaev, A.P., de Smit, M.H., Pleij, C.W., and Kraal, B. (2002) Functional evidence for D- and T-loop interactions in tmRNA. FEBS Lett. 514, 78-83
33. Zwieb, C., Guven, S.A., Wower, I.K., and Wower, J. (2001) Three-dimensional folding of the tRNA-like domain of Escherichia coli tmRNA. Biochemistry 40, 9587-9595
34. Stagg, S.M., Frazer-Abel, A.A., Hagerman, P.J., and Harvey, S.C. (2001) Structural studies of the tRNA domain of tmRNA. J. Mol. Biol. 309, 727-735
35. Gaudin, C., Nonin-Lecomte, S., Tisne, C., Corvaisier, S., Bordeau, V., Dardel, F., and Felden, B. (2003) The tRNA-like domains of E. coli and A. aeolicus transfer-messenger RNA: structural and functional studies. J. Mol. Biol. 331, 457-471
36. 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
37. Felden, B., Hanawa, K., Atkins, J.F., Himeno, H., Muto, A., Gesteland, R.F., McCloskey, J.A., and Grain, F.F. (1998) Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches. EMBO J. 17, 3188-3196
38. Leulliot, N. and Varani, G. (2001) Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40, 7947-7956
39. Williamson, J.R. (2000) Induced fit in RNA-protein recognition. Nat. Struct. Biol. 7, 834-837
40. Valle, M., Gillet, R., Kaur, S., Henne, A., Ramakrishnan, V., and Frank, J. (2003) Visualizing tmRNA entry into a stalled ribosome. Science 300, 127-130
41. Theobald, D.L., Mitton-Fry, R.M., and Wuttke, D.S. (2003) Nucleic acid recognition by OB-fold proteins. Annu. Rev. Biophys. Biomol. Struct. 32, 115-133
42. Draper, D.E. and Reynaldo, L.P. (1999) RNA binding strategies of ribosomal proteins. Nucleic Acids Res. 27, 381-388
43. Jacob, Y., Sharkady, S.M., Bhardwaj, K., Sanda, 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
44. Bekke, A., Kiefmann, M., Kremerskothen, J., Vornlocher, H.P., Sprinzl, M., and Brosius, J. (1998) The 10Sa RNA gene of Thermus thermophilus. DNA Seq. 9, 31-35