SmpB Contributes to Reading Frame Selection in the Translation of Transfer-Messenger RNA

Journal of Molecular Biology

Volumn 391, Issue 2, 2009, Pages 275-281

  Watts, Talina ^a   Cazier, DeAnna ^a   Healey, David ^a   Buskirk, Allen ^a  

^a Brigham Young University   (United States)

Author keywords

reading frame; SmpB; tmRNA; trans translation

Indexed keywords

ALANINE; BINDING PROTEIN; MESSENGER RNA; NUCLEOTIDE; PEPTIDE; POLYPEPTIDE; SMALL PROTEIN B; TRANSFER MESSENGER RNA; TRANSFER RNA; UNCLASSIFIED DRUG;

AMINO ACID TRANSPORT; ARTICLE; CODON; CONTROLLED STUDY; ESCHERICHIA COLI; EUBACTERIUM; GENE ACTIVITY; GENE FUNCTION; GENETIC SELECTION; LOSS OF FUNCTION MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RIBOSOME; RNA SEQUENCE; RNA TRANSLATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 67650656654     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.06.037     Document Type: Article

References (34)

1. Moore S.D., and Sauer R.T. The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76 (2007) 101-124
2. Withey J.H., and Friedman D.I. A salvage pathway for protein synthesis: tmRNA and trans-translation. Annu. Rev. Microbiol. 57 (2003) 101-123
3. Dulebohn D., Choy J., Sundermeier T., Okan N., and Karzai A.W. Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay. Biochemistry 46 (2007) 4681-4693
4. Burks J., Zwieb C., Muller F., Wower I., and Wower J. Comparative 3-D modeling of tmRNA. BMC Mol. Biol. 6 (2005) 14
5. Tanner D.R., Dewey J.D., Miller M.R., and Buskirk A.R. Genetic analysis of the structure and function of transfer messenger RNA pseudoknot 1. J. Biol. Chem. 281 (2006) 10561-10566
6. Nameki N., Tadaki T., Himeno H., and Muto A. Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single-stranded RNAs. FEBS Lett. 470 (2000) 345-349
7. Wower I.K., Zwieb C., and Wower J. Escherichia coli tmRNA lacking pseudoknot 1 tags truncated proteins in vivo and in vitro. RNA 15 (2009) 128-137
8. Williams K.P., Martindale K.A., and Bartel D.P. Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO J. 18 (1999) 5423-5433
9. Lee S., Ishii M., Tadaki T., Muto A., and Himeno H. 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 (2001) 999-1012
10. Miller M.R., Healey D.W., Robison S.G., Dewey J.D., and Buskirk A.R. The role of upstream sequences in selecting the reading frame on tmRNA. BMC Biol. 6 (2008) 29
11. Lim V.I., and Garber M.B. Analysis of recognition of transfer-messenger RNA by the ribosomal decoding center. J. Mol. Biol. 346 (2005) 395-398
12. Wower I.K., Zwieb C.W., Guven S.A., and Wower J. Binding and cross-linking of tmRNA to ribosomal protein S1, on and off the Escherichia coli ribosome. EMBO J. 19 (2000) 6612-6621
13. Gillet R., Kaur S., Li W., Hallier M., Felden B., and Frank J. Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1. J. Biol. Chem. 282 (2007) 6356-6363
14. Saguy M., Gillet R., Skorski P., Hermann-Le Denmat S., and Felden B. Ribosomal protein S1 influences trans-translation in vitro and in vivo. Nucleic Acids Res. 35 (2007) 2368-2376
15. Qi H., Shimizu Y., and Ueda T. Ribosomal protein S1 is not essential for the trans-translation machinery. J. Mol. Biol. 368 (2007) 845-852
16. Takada K., Takemoto C., Kawazoe M., Konno T., Hanawa-Suetsugu K., Lee S., et al. In vitro trans-translation of Thermus thermophilus: ribosomal protein S1 is not required for the early stage of trans-translation. RNA 13 (2007) 503-510
17. McGinness K.E., and Sauer R.T. Ribosomal protein S1 binds mRNA and tmRNA similarly but plays distinct roles in translation of these molecules. Proc. Natl Acad. Sci. USA 101 (2004) 13454-13459
18. Bessho Y., Shibata R., Sekine S., Murayama K., Higashijima K., Hori-Takemoto C., et al. Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc. Natl Acad. Sci. USA 104 (2007) 8293-8298
19. Sundermeier T.R., Dulebohn D.P., Cho H.J., and Karzai A.W. A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation. Proc. Natl Acad. Sci. USA 102 (2005) 2316-2321
20. Shimizu Y., and Ueda T. SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans-translation initiation. J. Biol. Chem. 281 (2006) 15987-15996
21. Nonin-Lecomte S., Germain-Amiot N., Gillet R., Hallier M., Ponchon L., Dardel F., and Felden B. Ribosome hijacking: a role for small protein B during trans-translation. EMBO Rep. 10 (2009) 160-165
22. Metzinger L., Hallier M., and Felden B. Independent binding sites of small protein B onto transfer-messenger RNA during trans-translation. Nucleic Acids Res. 33 (2005) 2384-2394
23. Metzinger L., Hallier M., and Felden B. The highest affinity binding site of small protein B on transfer messenger RNA is outside the tRNA domain. RNA 14 (2008) 1761-1772
24. Konno T., Kurita D., Takada K., Muto A., and Himeno H. A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation. RNA 13 (2007) 1723-1731
25. Wower J., Zwieb C.W., Hoffman D.W., and Wower I.K. SmpB: a protein that binds to double-stranded segments in tmRNA and tRNA. Biochemistry 41 (2002) 8826-8836
26. Kurita D., Sasaki R., Muto A., and Himeno H. Interaction of SmpB with ribosome from directed hydroxyl radical probing. Nucleic Acids Res. 35 (2007) 7248-7255
27. Barends S., Karzai A.W., Sauer R.T., Wower J., and Kraal B. Simultaneous and functional binding of SmpB and EF-Tu-TP to the alanyl acceptor arm of tmRNA. J. Mol. Biol. 314 (2001) 9-21
28. Ivanova N., Lindell M., Pavlov M., Holmberg Schiavone L., Wagner E.G., and Ehrenberg M. Structure probing of tmRNA in distinct stages of trans-translation. RNA 13 (2007) 713-722
29. Cadwell R.C., and Joyce G.F. Mutagenic PCR. PCR Methods Appl. 3 (1994) S136-S140
30. Hallier M., Ivanova N., Rametti A., Pavlov M., Ehrenberg M., and Felden B. Pre-binding of small protein B to a stalled ribosome triggers trans-translation. J. Biol. Chem. 279 (2004) 25978-25985
31. Hayes C.S., Bose B., and Sauer R.T. Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination. J. Biol. Chem. 277 (2002) 33825-33832
32. Wang L., Brock A., Herberich B., and Schultz P.G. Expanding the genetic code of Escherichia coli. Science 292 (2001) 498-500
33. Bugaeva E.Y., Shpanchenko O.V., Felden B., Isaksson L.A., and Dontsova O.A. One SmpB molecule accompanies tmRNA during its passage through the ribosomes. FEBS Lett. 582 (2008) 1532-1536
34. Ivanova N., Pavlov M.Y., Bouakaz E., Ehrenberg M., and Schiavone L.H. Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA. Nucleic Acids Res. 33 (2005) 3529-3539