A Snapshot of the 30S Ribosomal Subunit Capturing mRNA via the Shine-Dalgarno Interaction

Structure

Volumn 15, Issue 3, 2007, Pages 289-297

  Kaminishi, Tatsuya ^a   Wilson, Daniel N ^b   Takemoto, Chie ^a   Harms, Joerg M ^b   Kawazoe, Masahito ^a   Schluenzen, Frank ^b   Hanawa Suetsugu, Kyoko ^a   Shirouzu, Mikako ^a   Fucini, Paola ^b   Yokoyama, Shigeyuki ^a,c  

^a RIKEN YOKOHAMA INSTITUTE   (Japan)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

RNA

Indexed keywords

MESSENGER RNA; RNA 16S;

ARTICLE; CONTROLLED STUDY; CROSS LINKING; CRYSTAL STRUCTURE; NONHUMAN; PRIORITY JOURNAL; RIBOSOME SUBUNIT; RNA BINDING; RNA TRANSLATION; THERMUS THERMOPHILUS; TRANSLATION INITIATION;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RIBOSOMES; RNA, BACTERIAL; RNA, MESSENGER; THERMUS THERMOPHILUS;

BACTERIA (MICROORGANISMS); THERMUS THERMOPHILUS;

EID: 33847670917     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2006.12.008     Document Type: Article

References (46)

1. Antoun A., Pavlov M.Y., Lovmar M., and Ehrenberg M. How initiation factors tune the rate of initiation of protein synthesis in bacteria. EMBO J. 25 (2006) 2539-2550
2. Antoun A., Pavlov M.Y., Lovmar M., and Ehrenberg M. How initiation factors maximize the accuracy of tRNA selection in initiation of bacterial protein synthesis. Mol. Cell 23 (2006) 183-193
3. Baranov P.V., Fayet O., Hendrix R.W., and Atkins J.F. Recoding in bacteriophages and bacterial IS elements. Trends Genet. 22 (2006) 174-181
4. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54 (1998) 905-921
5. Calogero R.A., Pon C.L., Canonaco M.A., and Gualerzi C.O. Selection of the mRNA translation initiation region by Escherichia coli ribosomes. Proc. Natl. Acad. Sci. USA 85 (1988) 6427-6431
6. Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'Souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Muller K.M., et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3 (2002) 2
7. Canonaco M.A., Gualerzi C.O., and Pon C.L. Alternative occupancy of a dual ribosomal binding site by mRNA affected by translation initiation factors. Eur. J. Biochem. 182 (1989) 501-506
8. Carter A.P., Clemons Jr. W.M., Brodersen D.E., Morgan-Warren R.J., Hartsch T., Wimberly B.T., and Ramakrishnan V. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 291 (2001) 498-501
9. CCP4 (Collaborative Computational Project, Number 4). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50 (1994) 760-763
10. de Smit M.H., and van Duin J. Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction. J. Mol. Biol. 235 (1994) 173-184
11. de Smit M.H., and van Duin J. Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA. J. Mol. Biol. 331 (2003) 737-743
12. Diaconu M., Kothe U., Schlunzen F., Fischer N., Harms J.M., Tonevitsky A.G., Stark H., Rodnina M.V., and Wahl M.C. Structural basis for the function of the ribosomal L7/12 stalk in factor binding and GTPase activation. Cell 121 (2005) 991-1004
13. Dontsova O., Kopylov A., and Brimacombe R. The location of mRNA in the ribosomal 30S initiation complex; site-directed cross-linking of mRNA analogues carrying several photo-reactive labels simultaneously on either side of the AUG start codon. EMBO J. 10 (1991) 2613-2620
14. Gold L., and Stormo G.D. High-level translation initiation. Methods Enzymol. 185 (1990) 89-93
15. Gualerzi C.O., and Pon C.L. Initiation of mRNA translation in prokaryotes. Biochemistry 29 (1990) 5881-5889
16. Gualerzi C.O., Brandi L., Caserta E., Garofalo C., Lammi M., La Teana A., Petrelli D., Spurio R., Tomsic J., and Pon C.L. Initiation factors in the early events of mRNA translation in bacteria. Cold Spring Harb. Symp. Quant. Biol. 66 (2001) 363-376
17. Hartmann R.K., and Erdmann V.A. Thermus thermophilus 16S rRNA is transcribed from an isolated transcription unit. J. Bacteriol. 171 (1989) 2933-2941
18. Hui A., and de Boer H.A. Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. Proc. Natl. Acad. Sci. USA 84 (1987) 4762-4766
19. Huttenhofer A., and Noller H.F. Footprinting mRNA-ribosome complexes with chemical probes. EMBO J. 13 (1994) 3892-3901
20. Jacob W.F., Santer M., and Dahlberg A.E. A single base change in the Shine-Dalgarno region of 16S rRNA of Escherichia coli affects translation of many proteins. Proc. Natl. Acad. Sci. USA 84 (1987) 4757-4761
21. Jenner L., Romby P., Rees B., Schulze-Briese C., Springer M., Ehresmann C., Ehresmann B., Moras D., Yusupova G., and Yusupov M. Translational operator of mRNA on the ribosome: how repressor proteins exclude ribosome binding. Science 308 (2005) 120-123
22. Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Cryst. 26 (1993) 795-800
23. Karimi R., Pavlov M.Y., Buckingham R.H., and Ehrenberg M. Novel roles for classical factors at the interface between translation termination and initiation. Mol. Cell 3 (1999) 601-609
24. Komarova A.V., Tchufistova L.S., Supina E.V., and Boni I.V. Protein S1 counteracts the inhibitory effect of the extended Shine-Dalgarno sequence on translation. RNA 8 (2002) 1137-1147
25. La Teana A., Gualerzi C.O., and Brimacombe R. From stand-by to decoding site. Adjustment of the mRNA on the 30S ribosomal subunit under the influence of the initiation factors. RNA 1 (1995) 772-782
26. Laursen B.S., Sorensen H.P., Mortensen K.K., and Sperling-Petersen H.U. Initiation of protein synthesis in bacteria. Microbiol. Mol. Biol. Rev. 69 (2005) 101-123
27. Macke T., and Case D.A. Modeling unusual nucleic acid structures. In: Leontis N.B., and Santa Lucia J.J. (Eds). Molecular Modeling of Nucleic Acids (1998), American Chemical Society, Washington, D.C. 379-393
28. McCarthy J.E., and Brimacombe R. Prokaryotic translation: the interactive pathway leading to initiation. Trends Genet. 10 (1994) 402-407
29. Ogle J.M., Carter A.P., and Ramakrishnan V. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem. Sci. 28 (2003) 259-266
30. Petrelli D., LaTeana A., Garofalo C., Spurio R., Pon C.L., and Gualerzi C.O. Translation initiation factor IF3: two domains, five functions, one mechanism?. EMBO J. 20 (2001) 4560-4569
31. Ringquist S., MacDonald M., Gibson T., and Gold L. Nature of the ribosomal mRNA track: analysis of ribosome-binding sites containing different sequences and secondary structures. Biochemistry 32 (1993) 10254-10262
32. Rudd K.E., and Schneider T.D. Compilation of E. coli ribosome binding sites. In: Miller J.H. (Ed). Laboratory Manual and Handbook for Escherichia coli and Related Bacteria (1992), Cold Spring Harbor Laboratory Press, New York 17.19-17.45
33. Schindelin H., Zhang M., Bald R., Furste J.P., Erdmann V.A., and Heinemann U. Crystal structure of an RNA dodecamer containing the Escherichia coli Shine-Dalgarno sequence. J. Mol. Biol. 249 (1995) 595-603
34. Schluenzen F., Tocilj A., Zarivach R., Harms J., Gluehmann M., Janell D., Bashan A., Bartels H., Agmon I., Franceschi F., et al. Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution. Cell 102 (2000) 615-623
35. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M., and Cate J.H. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310 (2005) 827-834
36. Selmer M., Dunham C.M., Murphy IV F.V., Weixlbaumer A., Petry S., Kelley A.C., Weir J.R., and Ramakrishnan V. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313 (2006) 1935-1942
37. Sharma M.R., Barat C., Wilson D.N., Booth T.M., Kawazoe M., Hori-Takemoto C., Shirouzu M., Yokoyama S., Fucini P., and Agrawal R.K. Interaction of Era with the 30S ribosomal subunit: implications for 30S subunit assembly. Mol. Cell 18 (2005) 319-329
38. Shine J., and Dalgarno L. The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc. Natl. Acad. Sci. USA 71 (1974) 1342-1346
39. Steitz J.A., and Jakes K. How ribosomes select initiator regions in mRNA: base pair formation between the 3′ terminus of 16S rRNA and the mRNA during initiation of protein synthesis in Escherichia coli. Proc. Natl. Acad. Sci. USA 72 (1975) 4734-4738
40. Studer S.M., and Joseph S. Unfolding of mRNA secondary structure by the bacterial translation initiation complex. Mol. Cell 22 (2006) 105-115
41. Voorma H.O. Control of Translation Initiation in Prokaryotes. In: Hershey J.W.B., Mathews M.B., and Sonenberg N. (Eds). Translational Control (1996), Cold Spring Harbor Laboratory Press, New York 759-777
42. Weiel J., and Hershey J.W. The binding of fluorescein-labeled protein synthesis initiation factor 2 to Escherichia coli 30 S ribosomal subunits determined by fluorescence polarization. J. Biol. Chem. 257 (1982) 1215-1220
43. Wimberly B.T., Brodersen D.E., Clemons Jr. W.M., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., and Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature 407 (2000) 327-339
44. Wintermeyer W., and Gualerzi C. Effect of Escherichia coli initiation factors on the kinetics of N-Acphe-tRNAPhe binding to 30S ribosomal subunits. A fluorescence stopped-flow study. Biochemistry 22 (1983) 690-694
45. Yusupova G.Z., Yusupov M.M., Cate J.H., and Noller H.F. The path of messenger RNA through the ribosome. Cell 106 (2001) 233-241
46. Yusupova G., Jenner L., Rees B., Moras D., and Yusupov M. Structural basis for messenger RNA movement on the ribosome. Nature 444 (2006) 391-394