Three-dimensional cryo-electron microscopy localization of EF2 in the Saccharomyces cerevisiae 80S ribosome at 17.5 Å resolution

EMBO Journal

Volumn 19, Issue 11, 2000, Pages 2710-2718

  Gomez Lorenzo, Maria G ^a   Spahn, Christian M T ^a   Agrawal, Rajendra K ^a   Grassucci, Robert A ^a   Penczek, Pawel ^a   Chakraburtty, Kalpana ^b   Ballesta, Juan P G ^d   Lavandera, Jose L ^c   Garcia Bustos, Jose F ^c   Frank, Joachim ^a,e  

^a STATE UNIVERSITY OF NEW YORK   (United States)

^b MEDICAL COLLEGE OF WISCONSIN   (United States)

^c GLAXOSMITHKLINE   (Spain)

^d CSIC   (Spain)

^e HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Elongation; GM193663; Sordarin; Translation; Yeast

Indexed keywords

ELONGATION FACTOR 2; SORDARIN DERIVATIVE;

ARTICLE; CRYOELECTRON MICROSCOPY; NONHUMAN; PRIORITY JOURNAL; RIBOSOME; RIBOSOME SUBUNIT; SACCHAROMYCES CEREVISIAE;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 18744420805     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/19.11.2710     Document Type: Article

References (59)

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., 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.
3. Agrawal, R.K., Penczek, P., Grassucci, R.A. and Frank, J. (1998) Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proc. Natl Acad. Sci. USA, 95, 6134-6138.
4. Agrawal, R.K., Heagle, A.B., Penczek, P., Grassucci, R.A. and Frank, J. (1999) EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nature Struct. Biol., 6, 643-647.
5. Agrawal, R.K., Heagle, A.B. and Frank, J. (2000) Studies of elongation factor G-dependent tRNA translocation by three-dimensional cryo-electron microscopy. In Garrett, R.A., Douthwaite, S.R., Liljas, A., Matheson, A.T., Moore, P.B. and Noller, H.F. (eds). The Ribosome: Structure, Function, Antibiotics and Cellular Interactions. ASM Press, Washington, DC, pp. 53-62.
6. Ban, N., Nissen, P., Hansen, J.C., Capel, M., Moore, P.B. and Steitz, T.A. (1999) Placement of protein and RNA structures into a 5 Å-resolution map of the 50S ribosomal subunit. Nature, 400, 841-847.
7. Beckmann, R., Bubeck, D., Grassucci, R., Penczek, P., Verschoor, A., Blobel, G. and Frank, J. (1997) Alignment of conduits for the nascent polypeptide chain in the ribosome-Sec61 complex. Science, 278, 2123-2126.
8. Bourne, H.R., Sanders, D.A. and McCormick, F. (1991) The GTPase superfamily: conserved structure and molecular mechanism. Nature, 349, 117-127.
9. Briones, E., Briones, C., Remacha, M. and Ballesta, J.P. (1998) The GTPase center protein L12 is required for correct ribosomal stalk assembly but not for Saccharomyces cerevisiae viability. J. Biol. Chem., 273, 31956-31961.
10. Capa, L., Mendoza, A., Lavandera, J.L., Gomez de las Heras, F. and Garcia-Bustos, J.F. (1998) Translation elongation factor 2 is part of the target for a new family of antifungals. Antimicrob. Agents Chemother., 42, 2694-2699.
11. Cate, J.H., Yusupov, M.M., Yusupova, G.Zh., Earnest, T.N. and Noller, H.F. (1999) X-ray crystal structures of 70S ribosome functional complexes. Science, 285, 2095-2104.
12. Clemons, W.M., Jr, May, J.L.C., Wimberly, B.T., McCutcheon, J.P., Capel, M. and Ramakrishnan, V. (1999) Structure of a bacterial 30S ribosomal subunit at 5.5 Å resolution. Nature, 400, 833-840.
13. 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 Å resolution. EMBO J., 13, 3661-3668.
14. Dasmahapatra, B. and Chakraburtty, K. (1981) Protein synthesis in yeast. I. Purification and properties of elongation factor 3 from Saccharomyces cerevisiae. J. Biol. Chem., 256, 9999-10004.
15. Dominguez, J.M. and Martin, J.J. (1998) Identification of elongation factor 2 as the essential protein targeted by sordarins in Candida albicans. Antimicrob. Agents Chemother., 42, 2279-2283.
16. Dominguez, J.M., Kelly, V.A., Kinsman, O.S., Marriott, M.S., Gomez de las Heras, F. and Martin, J.J. (1998) Sordarins: A new class of antifungals with selective inhibition of the protein synthesis elongation cycle in yeast. Antimicrob. Agents Chemother., 42, 2274-2278.
17. Dominguez, J.M., Gomez-Lorenzo, M.G. and Martin, J.J. (1999) Sordarin inhibits fungal protein synthesis by blocking translocation differently to fusidic acid. J. Biol. Chem., 274, 22423-22427.
18. Dube, P., Wieske, M., Stark, H., Schatz, M., Stahl, J., Zemlin, F., Lutsch, G. and van Heel, M. (1998a) The 80S rat liver ribosome at 25 Å resolution by electron cryomicroscopy and angular reconstruction. Structure, 6, 389-399.
19. Dube, P., Bacher, G., Stark, H., Mueller, F., Zemlin, F., van Heel, M. and Brimacombe, R. (1998b) Correlation of the expansion segments in mammalian rRNA with the fine structure of the 80 S ribosome; a cryoelectron microscopic reconstruction of the rabbit reticulocyte ribosome at 21 Å resolution. J. Mol. Biol., 279, 403-421.
20. Foley, B.T., Moehring, J.M. and Moehring, T.J. (1995) Mutations in the elongation factor 2 gene which confer resistance to diphtheria toxin and Pseudomonas exotoxin A. J. Biol. Chem., 270, 23218-23225.
21. Frank, J. et al. (1995a) A model of the translational apparatus based on a three-dimensional reconstruction of the Escherichia coli ribosome. Biochem. Cell Biol., 73, 757-765.
22. Frank, J., Zhu, J., Penczek, P., Li, Y., Srivastava, S., Verschoor, A., Radermacher, M., Grassucci, R., Lata, R.K. and Agrawal, R.K. (1995b) A model of protein synthesis based on cryo-electron microscopy of the E.coli ribosome. Nature, 376, 441-444.
23. Gabashvili, I.S., Agrawal, R.K., Spahn, C.M.T., Grassucci, R.A., Svergun, D.I., Frank, J. and Penczek, P. (2000) Solution structure of the E.coli 70S ribosome at 11.5 Å resolution. Cell, 100, 537-549.
24. Gomez-Lorenzo, M.G. and Garcia-Bustos, J.F. (1998) Ribosomal P-protein stalk function is targeted by sordarin antifungals. J. Biol. Chem., 273, 25041-25044.
25. 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.
26. Hershey, J.W.B., Mathews, M.B. and Sonenberg, N. (1996) Translational Control. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
27. Holmberg, L. and Nygard, O. (1994) Interaction sites of ribosome-bound eukaryotic elongation factor 2 in 18S and 28S rRNA. Biochemistry, 33, 15159-15167.
28. Justice, M.C., Hsu, M.J., Tse, B., Ku, T., Balkovec, J., Schmatz, D. and Nielsen, J. (1998) Elongation factor 2 as a novel target for selective inhibition of fungal protein synthesis. J. Biol. Chem., 273, 3148-3151.
29. Justice, M.C., Ku, T., Hsu, M.J., Carniol, K., Schmatz, D. and Nielsen, J. (1999) Mutations in ribosomal protein L10e confer resistance to the fungal-specific eukaryotic elongation factor 2 inhibitor sordarin. J. Biol. Chem., 274, 4869-4875.
30. Kinsman, O.S. et al. (1998) Isolation and characterisation of an antifungal antibiotic (GR 135402) with protein synthesis inhibition. J. Antibiot., 51, 41-49.
31. f and fitting of L1 protein. J. Mol. Biol., 280, 103-116.
32. Martemyanov, K.A. and Gudkov, A.T. (1999) Domain IV of elongation factor G from Thermus thermophilus is strictly required for translocation. FEBS Lett., 452, 155-159.
33. 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.
34. Möller, W. and Maassen, J.A. (1986) On the structure, function, and dynamics of L7/L12 from Escherichia coli ribosomes. In Hardesty, B. and Kramer, G. (eds), Structure, Function and Genetics of Ribosomes. Springer-Verlag, New York, NY, pp. 309-325.
35. Musters, W., Gonzalves, P.M., Boon, K., Raué, H.A., Heerikhuizen, H. and Planta, R.J. (1991) The conserved GTPase center and variable V9 from Saccharomyces cerevisiae 26S rRNA can be replaced by their equivalent from other prokaryotes or eukaryotes without detectable loss of ribosomal function. Proc. Natl Acad. Sci. USA, 88, 1469-1473.
36. Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B.F. and Nyborg, J. (1995) Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu and a GTP analog. Science, 270, 1464-1472.
37. Oppenheimer, N.J. and Bodley, J.W. (1981) Diphtheria toxin. Site and configuration of ADP-ribosylation of diphthamide in elongation factor 2. J. Biol. Chem., 256, 8579-8581.
38. Orlova, E.V., Dube, P., Harris, J.R., Beckman, E., Zemlin, F., Markl, J. and van Heel, M. (1997) Structure of keyhole limpet hemocyanin type 1 (KLH1) at 15 Å resolution by electron cryomicroscopy and angular reconstitution. J. Mol. Biol., 271, 417-437.
39. Penczek, P.A., Grassucci, R.A. and Frank, J. (1994) The ribosome at improved resolution: new techniques for merging and orientation refinement in 3D cryo-electron microscopy of biological particles. Ultramicroscopy, 53, 251-270.
40. Remacha, M., Jimenez-Diaz, A., Bermejo, B., Rodriguez-Gabriel, M.A., Guarinos, E. and Ballesta, J.P.G. (1995) Ribosomal acidic phosphoproteins P1 and P2 are not required for cell viability but regulate the pattern of protein expression in Saccharomyces cerevisiae. Mol. Cell. Biol., 15, 4754-4762.
41. 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.
42. Rodnina, M.V., Savelsbergh, A. and Wintermeyer, W. (1999) Dynamics of translation on the ribosome: molecular mechanics of translocation. FEMS Microbiol. Rev., 23, 317-333.
43. Saenz-Robles, M.T., Remacha, M., Vilella, M.D., Zinker, S. and Ballesta, J.P.G. (1990) The acidic ribosomal proteins as regulators of the eukaryotic ribosomal activity. Biochim. Biophys. Acta, 1050, 51-55.
44. Santos, C. and Ballesta, J.P.G. (1994) Ribosomal protein P0, contrary to phosphoproteins P1 and P2, is required for ribosome activity and Saccharomyces cerevisiae viability. J. Biol. Chem., 269, 15689-15696.
45. Skogerson, L. and Wakatama, E. (1976) A ribosome-dependent GTPase from yeast distinct from elongation factor 2. Proc. Natl Acad. Sci. USA, 73, 73-76.
46. Spahn, C.M.T., Grassucci, R.A., Penczek, P. and Frank, J. (1999) Direct three-dimensional localization and positive identification of RNA helices within the ribosome by means of genetic tagging and cryo-electron microscopy. Structure, 7, 1567-1573.
47. Stark, H., Rodnina, M.V., Rinke-Appel, J., Brimacombe, R., Wintermeyer, W. and van Heel, M. (1997) Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature, 389, 403-406.
48. Thompson, J., Musters, W., Cundliffe, E. and Dahlberg, A.E. (1993) Replacement of the L11 binding region within E.coli 23S ribosomal RNA with its homologue from yeast: in vivo and in vitro analysis of hybrid ribosomes altered in the GTPase centre. EMBO J., 12, 1499-1504.
49. Triana-Alonso, F.J., Chakraburtty, K. and Nierhaus, K.H. (1995) The elongation factor 3 unique in higher fungi and essential for protein biosynthesis is an E site factor. J. Biol. Chem., 270, 20473-20478.
50. Uchiumi, T. and Kominami, R. (1994) A functional site of the GTPase-associated center within 28S ribosomal RNA probed with an anti-RNA autoantibody. EMBO J., 13, 3389-3394.
51. Uchiumi, T., Kikuchi, M., Terao, K., Iwasaki, K. and Ogata, K. (1986) Cross-linking of elongation factor 2 to rat-liver ribosomal proteins by 2-iminothiolane. Eur. J. Biochem., 156, 37-48.
52. Uchiumi, T., Traut, R.R. and Kominami, R. (1990) Monoclonal antibodies against acidic phosphoproteins P0, P1 and P2 of eukaryotic ribosomes as functional probes. J. Biol. Chem., 265, 89-95.
53. Uchiumi, T., Hori, K., Nomura, T. and Hachimori, A. (1999) Replacement of L7/L12 L10 protein complex in Escherichia coli ribosomes with the eukaryotic counterpart changes the specificity of elongation factor binding. J. Biol. Chem., 274, 27578-27582.
54. van Agthoven, A.J., Maassen, J.A. and Möller, W. (1977) Structure and phosphorylation of an acidic protein from 60S ribosomes and its involvement in elongation factor-2 dependent GTP hydrolysis. Biochem. Biophys. Res. Commun., 77, 989-998.
55. Verschoor, A., Warner, J.R., Srivastava, S., Grassucci, R.A. and Frank, J. (1998) Three-dimensional structure of the yeast ribosome. Nucleic Acids Res., 26, 655-661.
56. Wagenknecht, T., Grassucci, R. and Frank, J. (1988) Electron microscopy and computer image averaging of ice-embedded large ribosomal subunits from Escherichia coli. J. Mol. Biol., 199, 137-147.
57. Warner, J.R. (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci., 24, 437-440.
58. Wilson, K.S. and Noller, H.F. (1998) Mapping the position of translational elongation factor EF-G in the ribosome by directed hydroxyl radical probing. Cell, 92, 131-139.
59. Wool, I.G., Gluck, A. and Endo, Y. (1992) Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation. Trends Biochem. Sci., 17, 266-269.