Structural basis for the control of translation initiation during stress

Nature Structural and Molecular Biology

Volumn 11, Issue 11, 2004, Pages 1054-1059

  Vila Sanjurjo, Antón ^a   Schuwirth, Barbara S ^a   Hau, Cathy W ^a,b   Cate, Jamie H D ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HEAT SHOCK PROTEIN; INITIATION FACTOR 3; LIGANDIN; MESSENGER RNA; TRANSFER RNA;

ARTICLE; CONTROLLED STUDY; DISSOCIATION; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTEIN SYNTHESIS; RIBOSOME SUBUNIT; STRESS; STRUCTURE ANALYSIS; TEMPERATURE DEPENDENCE; TRANSLATION INITIATION; TRANSLATION REGULATION;

BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; PROTEIN BIOSYNTHESIS; RIBOSOMAL PROTEINS; RIBOSOMES; RNA, MESSENGER; RNA, TRANSFER; TEMPERATURE; X-RAYS;

ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 7544242316     PISSN: 15459993     EISSN: None     Source Type: Journal    
DOI: 10.1038/nsmb850     Document Type: Article

References (43)

1. Agafonov, D.E., Kolb, V.A. & Spirin, A.S. Ribosome-associated protein that inhibits translation at the aminoacyl-tRNA binding stage. EMBO Rep. 2, 399-402 (2001).
2. Maki, Y., Yoshida, H. & Wada, A. Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli. Genes Cells 5, 965-974 (2000).
3. Ye, K., Serganov, A., Hu, W., Garber, M. & Patel, D.J. Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold. Eur. J. Biochem. 269, 5182-5191 (2002).
4. Rak, A., Kalinin, A., Shcherbakov, D. & Bayer, P. Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli. Biochem. Biophys. Res. Commun. 299, 710-714 (2002).
5. Agafonov, D.E., Kolb, V.A., Nazimov, I.V. & Spirin, A.S. A protein residing at the subunit interface of the bacterial ribosome. Proc. Natl. Acad. Sci. USA 96, 12345-12349 (1999).
6. Agafonov, D.E. & Spirin, A.S. The ribosome-associated inhibitor A reduces translation errors. Biochem. Biophys. Res. Commun. 320, 354-358 (2004).
7. VanBogelen, R.A. & Neidhardt, F.C. Ribosomes as sensors of heat and cold shock in Escherichia coli. Proc. Natl. Acad. Sci. USA 87, 5589-5593 (1990).
8. Cashel, M., Gentry, D.R., Hernandez, V.J. & Vinella, D. The stringent response. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology Vol. 2 (eds. Neidhardt, F.C. et al.) 1458-1496 (ASM Press, Washington, DC, 1996).
9. Ashe, M.P., De Long, S.K. & Sachs, A.B. Glucose depletion rapidly inhibits translation initiation in yeast. Mol. Biol. Cell 11, 833-848 (2000).
10. Vila-Sanjurjo, A. et al. X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Proc. Natl. Acad. Sci. USA 100, 8682-8687 (2003).
11. Yusupov, M.M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883-896 (2001).
12. Maivali, U. & Remme, J. Definition of bases in 23S rRNA essential for ribosomal subunit association. RNA 10, 600-604 (2004).
13. Yusupova, G.Z., Yusupov, M.M., Cate, J.H. & Noller, H.F. The path of messenger RNA through the ribosome. Cell 106, 233-241 (2001).
14. Prince, J.B., Taylor, B.H., Thurlow, D.L., Ofengand, J. & Zimmermann, R.A. Covalent crosslinking of tRNA1Val to 16S RNA at the ribosomal P site: identification of crosslinked residues. Proc. Natl. Acad. Sci. USA 79, 5450-5454 (1982).
15. Moazed, D. & Noller, H.F. Intermediate states in the movement of transfer RNA in the ribosome. Nature 342, 142-148 (1989).
16. von Ahsen, U. & Noller, H.F. Identification of bases in 16S rRNA essential for tRNA binding at the 30S ribosomal P site. Science 267, 234-237 (1995).
17. Vila-Sanjurjo, A. & Dahlberg, A.E. Mutational analysis of the conserved bases C1402 and A1500 in the center of the decoding domain of Escherichia coli 16 S rRNA reveals an important tertiary interaction. J. Mol. Biol. 308, 457-463 (2001).
18. Wimberly, B.T. et al. Structure of the 30S ribosomal subunit. Nature 407, 327-339 (2000).
19. Jacob, W.F., Santer, M. & 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, 4757-4761 (1987).
20. Gualerzi, C.O., Giuliodori, A.M. & Pon, C.L. Transcriptional and post-transcriptional control of cold-shock genes. J. Mol. Biol. 331, 527-539 (2003).
21. Brock, S., Szkaradkiewicz, K. & Sprinzl, M. Initiation factors of protein biosynthesis in bacteria and their structural relationship to elongation and termination factors. Mol. Microbiol. 29, 409-417 (1998).
22. McCutcheon, J.P. et al. Location of translational initiation factor IF3 on the small ribosomal subunit. Proc. Natl. Acad. Sci. USA 96, 4301-4306 (1999).
23. Dallas, A. & Noller, H.F. Interaction of translation initiation factor 3 with the 30S ribosomal subunit. Mol. Cell 8, 855-864 (2001).
24. Carter, A.P. et al. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 291, 498-501 (2001).
25. Giuliodori, A.M., Brandi, A., Gualerzi, C.O. & Pon, C.L. Preferential translation of cold-shock mRNAs during cold adaptation. RNA 10, 265-276 (2004).
26. Thieringer, H.A., Jones, P.G. & Inouye, M. Cold shock and adaptation. Bioessays 20, 49-57 (1998).
27. Uchida, T., Abe, M., Matsuo, K. & Yoneda, M. Amounts of free 70S ribosomes and ribosomal subunits found in Escherichia coli at various temperatures. Biochem. Biophys. Res. Commun. 41, 1048-1054 (1970).
28. Broeze, R.J., Solomon, C.J. & Pope, D.H. Effects of low temperature on in vivo and in vitro protein synthesis in Escherichia coli and Pseudomonas fluorescens. J. Bacteriol. 134, 861-874 (1978).
29. Barbieri, M., Vittone, A. & Maraldi, N.M. Cell stress and ribosome crystallization. J. Submicrosc. Cytol. Pathol. 27, 199-207 (1995).
30. Ranu, R.S., Levin, D.H., Delaunay, J., Ernst, V. & London, I.M. Regulation of protein synthesis in rabbit reticulocyte lysates: characteristics of inhibition of protein synthesis by a translational inhibitor from heme-deficient lysates and its relationship to the initiation factor which binds Met-tRNAf. Proc. Natl. Acad. Sci. USA 73, 2720-2724 (1976).
31. Cooper, H.L., Berger, S.L. & Braverman, R. Free ribosomes in physiologically nondividing cells. Human peripheral lymphocytes. J. Biol. Chem. 251, 4891-4900 (1976).
32. Kyrpides, N.C. & Woese, C.R. Universally conserved translation initiation factors. Proc. Natl. Acad. Sci. USA 95, 224-228 (1998).
33. Lomakin, I.B., Kolupaeva, V.G., Marintchev, A., Wagner, G. & Pestova, T.V. Position of eukaryotic initiation factor elF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes Dev. 17, 2786-2797 (2003).
34. Johnson, C.H., Kruft, V. & Subramanian, A.R. Identification of a plastid-specific ribosomal protein in the 30S subunit of chloroplast ribosomes and isolation of the cDNA clone encoding its cytoplasmic precursor. J. Biol. Chem. 265, 12790-12795 (1990).
35. Bubunenko, M.G. & Subramanian, A.R. Recognition of novel and divergent higher plant chloroplast ribosomal proteins by Escherichia coli ribosome during in vivo assembly. J. Biol. Chem. 269, 18223-18231 (1994).
36. Tan, X., Varughese, M. & Widger, W.R. A light-repressed transcript found in Synechococcus PCC 7002 is similar to a chloroplast-specific small subunit ribosomal protein and to a transcription modulator protein associated with sigma 54. J. Biol. Chem. 269, 20905-20912 (1994).
37. Otwinowski, Z. & Minor, W. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 307-326 (1997).
38. Brünger, A.T. et al. Crystallography & NMR system: A new software suite for macro-molecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
39. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
40. Kleywegt, G.J. & Read, R.J. Not your average density. Structure 5, 1557-1569 (1997).
41. Yang, H. et al. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res. 31, 3450-3460 (2003).
42. Ramesh, V., Gite, S., Li, Y. & RajBhandary, U.L. Suppressor mutations in Escherichia coli methionyl-tRNA formyltransferase: role of a 16-amino acid insertion module in initiator tRNA recognition. Proc. Natl. Acad. Sci. USA 94, 13524-13529 (1997).
43. Jelenc, P.C. & Kurland, C.G. Nucleoside triphosphate regeneration decreases the frequency of translation errors. Proc. Natl. Acad. Sci. USA 76, 3174-3178 (1979).