Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing

Cell

Volumn 92, Issue 1, 1998, Pages 131-139

  Wilson, Kevin S ^a   Noller, Harry F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR; MUTANT PROTEIN;

ARTICLE; ESCHERICHIA COLI; GENE TARGETING; NONHUMAN; PRIORITY JOURNAL; PROTEIN INDUCTION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; RIBOSOME;

ESCHERICHIA COLI;

EID: 0032498266     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)80905-8     Document Type: Article

References (52)

1. Abel, K., and Jurnak, F. (1996). A complex profile of protein elongation: translating chemical energy into molecular movement. Structure 4, 229-238.
2. Ævarsson, A. (1995). Structure-based sequence alignment of elongation factors Tu and G with related GTPases involved in translation. J. Mol. Evol. 41, 1096-1104.
3. Ævarsson, A., Brazhnikov, E., Garber, M., Zheltonosova, J., Chirgadze, Y., al Karadaghi, S., Svensson, L.A., and Liljas, A. (1994). Three-dimensional structure of the ribosomal translocase: elongation factor G from Thermus thermophilus. Embo J. 13, 3669-3677.
4. Agrawal, R.K., Penczek, P., Grassucci, R.A., Li, Y., Leith, A., Nierhaus, K.H., and Frank, J. (1996). Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome. Science 271, 1000-1002.
5. Berchtold, H., Reshetnikova, L., Reiser, C.O., Schirmer, N.K., Sprinzl, M., and Hilgenfeld, R. (1993). Crystal structure of active elongation factor Tu reveals major domain rearrangements. Nature 365, 126-132.
6. Bodley, J.W., and Lin, L. (1970). Interaction of E. coli G factor with the 50S ribosomal subunit. Nature 227, 60-61.
7. Bourne, H.R., Sanders, D.A., and McCormick, F. (1991). The GTPase superfamily: conserved structure and molecular mechanism. Nature 349, 117-127.
8. Bretscher, M.S. (1968). Translocation in protein synthesis: a hybrid structure model. Nature 218, 675-677.
9. Brigotti, M., Rambelli, F., Zamboni, M., Montanaro, L., and Sperti, S. (1989). Effect of alpha-sarcin and ribosome-inactivating proteins on the interaction of elongation factors with ribosomes. Biochem. J. 257, 723-727.
10. Brimacombe, R., Atmadja, J., Stiege, W., and Schuler, D. (1988). A detailed model of the three-dimensional structure of Escherichia coli 16 S ribosomal RNA in situ in the 30 S subunit. J. Mol. Biol. 199, 115-136.
11. Capel, M.S., Engelman, D.M., Freeborn, B.R., Kjeldgaard, M., Langer, J.A., Ramakrishnan, V., Schindler, D.G., Schneider, D.K., Schoenborn, B.P., Sillers, I.Y., et al. (1987). A complete mapping of the proteins in the small ribosomal subunit of Escherichia coll. Science 238, 1403-1406.
12. Czworkowski, J., Wang, J., Steitz, T.A., and Moore, P.B. (1994). The crystal structure of elongation factor G complexed with GDP, at 2.7 A resolution. Embo J. 13, 3661-3668.
13. Döring, T., Mitchell, P., Osswald, M., Bochkariov, D., and Brimacombe, R. (1994). The decoding region of 16S RNA; a cross-linking study of the ribosomal A, P and E sites using tRNA derivatized at position 32 in the anticodon loop. Embo J. 13, 2677-2685.
14. 4 pentameric complex in the GTPase domain of 23 S ribosomal RNA from Escherichia coli. J. Mol. Biol. 213, 275-88.
15. Frank, J., Penczek, P., Grassucci, R., and Srivastava, S. (1991). Three-dimensional reconstruction of the 70S Escherichia coli ribosome in ice: the distribution of ribosomal RNA. J. Cell. Biol. 115, 597-605.
16. Gavrilova, L.P., Kostiashkina, O.E., Koteliansky, V.E., Rutkevitch, N.M., and Spirin, A.S. (1976). Factor-free ("non-enzymic")and factor-dependent systems of translation of polyuridylic acid by Escherichia coli ribosomes. J. Mol. Biol. 101, 537-552.
17. Gordon, J. (1969). Hydrolysis of guanosine 5′-triphosphate associated with binding of aminoacyl transfer ribonucleic acid to ribosomes. J. Biol. Chem. 244, 5680-5686.
18. Hausner, T.P., Atmadja, J., and Nierhaus, K.H. (1987). Evidence that the G2661 region of 23S rRNA is located at the ribosomal binding sites of both elongation factors. Biochimie 69, 911-923.
19. Heilek, G.M., and Noller, H.F. (1996). Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5. Science 272, 1659-1662.
20. Heilek, G.M., Marusak, R., Meares, C.F., and Noller, H.F. (1995). Directed hydroxyl radical probing of 16S rRNA using Fe(II) tethered to ribosomal protein S4. Proc. Natl. Acad. Sci. USA 92, 1113-1116.
21. Hochuli, E., Dobeli, H., and Schacher, A. (1987). New metal chelate adsorbent selective for proteins and peptides containing neighbouring histidine residues. J. Chromatogr. 411, 177-184.
22. Johansson, U., and Hughes, D. (1994). Fusidic acid-resistant mutants define three regions in elongation factor G of Salmonella typhimurium. Gene 143, 55-59.
23. Joseph, S., Weiser, B., and Noller, H.F. (1997). Mapping the inside of the ribosome with an RNA helical ruler. Science 278, 1093-1097.
24. Maassen, J.A., and Möller, W. (1981). Photochemical cross-linking of elongation factor G to 70-S ribosomes from Escherichia coli by 4-(6-formyl-3-azidophenoxy)butyrimidate. Eur. J. Biochem. 115, 279-285.
25. Mitchell, P., Osswald, M., and Brimacombe, R. (1992). Identification of intermolecular RNA cross-links at the subunit interface of the Escherichia coli ribosome. Biochemistry 31, 3004-3011.
26. Moazed, D., and Noller, H.F. (1986). Transfer RNA shields specific nucleotides in 16S ribosomal RNA from attack by chemical probes. Cell 47, 985-994.
27. Moazed, D., and Noller, H.F. (1989). Intermediate states in the movement of transfer RNA in the ribosome. Nature 342, 142-148.
28. Moazed, D., Robertson, J.M., and Noller, H.F. (1988). Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23S RNA. Nature 334, 362-364.
29. Mueller, F., and Brimacombe, R. (1997). A new model for the three-dimensional folding of Esherichia coli 16 S ribosomal RNA. 1. Fitting the RNA to a 3D electron microscopic map at 20 angstrom. J. Mol. Biol. 271, 524-544.
30. Phe, EF-Tu, and a GTP analog. Science 270, 1464-1472.
31. Noller, H.F., Moazed, D., Stern, S., Powers, T., Allen, P.N., Robertson, J.M., Weiser, B., and Triman, K. (1989). Structure of rRNA and its functional interactions in translation. In The Ribosome: Structure, Function, and Evolution, W.E. Hill, A. Dahlberg, R.A. Garrett, P.B. Moore, D. Schlessinger, and J.R. Warner, eds. (Washington, DC: American Society for Microbiology), pp. 73-92.
32. Oakes, M.I., Scheinman, A., Atha,T., Shankweiler, G., and Lake, J.A. (1989). Ribosome structure: three dimensional locations of rRNA and proteins. In The Ribosome: Structure, Function, and Evolution, W.E. Hill, A. Dahlberg, R.A. Garrett, P.B. Moore, D. Schlessinger, and J.R. Warner, eds. (Washington, DC: American Society for Microbiology), pp. 180-193.
33. Pestka, S. (1969). Studies on the formation of transfer ribonucleic acid-ribosome complexes. VI. Oligopeptide synthesis and translocation on ribosomes in the presence and absence of soluble transfer factors. J. Biol. Chem. 244, 1533-1539.
34. Powers, T., and Noller, H.F. (1993). Evidence for functional interaction between elongation factor Tu and 16S ribosomal RNA. Proc. Natl. Acad. Sci. USA 90, 1364-1368.
35. Powers, T., and Noller, H.F. (1995). Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA 1, 194-209.
36. Prince, J.B., Taylor, B.H., Thurlow, D.L., Ofengand, J., and Zimmermann, R.A. (1982). Covalent cross-linking of tRNA1 Val to 16S RNA at the ribosomal P site: identification of cross-linked residues. Proc. Natl. Acad. Sci. USA 79, 5450-5454.
37. Rana, T., and Meares, C. (1991). Iron chelate mediated proteolysis - protein structure dependence. J. Am. Chem. Soc. 112, 2457-2458.
38. Richman, N., and Bodley, J.W. (1972). Ribosomes cannot interact simultaneously with elongation factors EF Tu and EF G. Proc. Natl. Acad. Sci. USA 69, 686-689.
39. Rodnina, M.V., Savelsbergh, A., Katunin, V.I., and Wintermeyer, W. (1997). Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome. Nature 385, 37-41.
40. Rosset, R., and Gorini, L. (1969). A ribosomal ambiguity mutation. J. Mol. Biol. 39, 95-112.
41. Samaha, R.R., O'Brien, B., O'Brien, T.W., and Noller, H.F. (1994). Independent in vitro assembly of a ribonucleoprotein particle containing the 3′ domain of 16S rRNA. Proc. Natl. Acad. Sci. USA 91, 7884-7888.
42. Schilling, B.S., Bartetzko, A., and Nierhaus, K.H. (1992). Kinetic and thermodynamic parameters for tRNA binding to the ribosome and for the translocation reaction. J. Biol. Chem. 267, 4703-4712.
43. Serdyuk, I., Baranov, V., Tsalkova, T., Gulyamova, D., Pavlov, M., Spirin, A., and May, R. (1992). Structural dynamics of translating ribosomes. Biochimie 74, 299-306.
44. Sköld, S.E. (1983). Chemical cross-linking of elongation factor G to the 23S RNA in 70S ribosomes from Escherichia coli. Nucleic Acids Res. 11, 4923-4932.
45. Spirin, A.S. (1985). Ribosomal translocation: facts and models. Prog. Nucleic Acid Res. Mol. Biol. 32, 75-114.
46. Stark, H., Orlova, E.V., Rinke, A.J., Junke, N., Mueller, F., Rodnina, M., Wintermeyer, W., Brimacombe, R., and van Heel, H.M. (1997a). Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy. Cell 88, 19-28.
47. Stark, H., Rodnina, M.V., Rinke, A.J., Brimacombe, R., Wintermeyer, W., and van Heel, H.M. (1997b). Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature 389, 403-406.
48. Stern, S., Moazed, D., and Noller, H.F. (1988a). Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol. 164, 481-489.
49. Stern, S., Weiser, B., and Noller, H.F. (1988b). Model for the three-dimensional folding of 16 S ribosomal RNA. J. Mol. Biol. 204, 447-481.
50. Szewczak, A.A., Moore, P.B., Chang, Y.L., and Wool, I.G. (1993). The conformation of the sarcin/ricin loop from 28S ribosomal RNA. Proc. Natl. Acad. Sci. USA 90, 9581-9585.
51. Thompson, J., Schmidt, F., and Cundliffe, E. (1982). Site of action of a ribosomal RNA methylase conferring resistance to thiostrepton. J. Biol. Chem. 257, 7915-7917.
52. Phe derivatives containing azidoadenosine at the 3′ end of the acceptor arm: a model of the tRNA-ribosome complex. Proc. Natl. Acad. Sci. USA 86, 5232-5236.