GTP-dependent formation of a ribonucleoprotein subcomplex required for ribosome biogenesis

Journal of Molecular Biology

Volumn 356, Issue 2, 2006, Pages 432-443

  Karbstein, Katrin ^a   Doudna, Jennifer A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

GTPase; Pre ribosome assembly; Ribosome; Ribosome biogenesis; RNA

Indexed keywords

ENDONUCLEASE; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATASE; PROTEIN; PROTEIN BMS 1; RIBONUCLEOPROTEIN; RIBOSOME RNA; SMALL NUCLEOLAR RNA; UNCLASSIFIED DRUG;

ARTICLE; BIOGENESIS; COMPLEX FORMATION; CONTROLLED STUDY; EUKARYOTE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ASSEMBLY; RIBOSOME SUBUNIT; THERMODYNAMICS;

EUKARYOTA;

EID: 30744437648     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.11.052     Document Type: Article

References (45)

1. M. Fromont-Racine, B. Senger, C. Saveanu, and F. Fasiolo Ribosome assembly in eukaryotes Gene 313 2003 17 42
2. F. Dragon, J.E. Gallagher, P.A. Compagnone-Post, B.M. Mitchell, K.A. Porwancher, and K.A. Wehner A large nucleolar U3 ribonucleoprotein required for 18 S ribosomal RNA biogenesis Nature 417 2002 967 970
3. P. Grandi, V. Rybin, J. Bassler, E. Petfalski, D. Strauss, and M. Marzioch 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40 S subunit processing factors but predominantly lack 60 S synthesis factors Mol. Cell 10 2002 105 115
4. D. Gelperin, L. Horton, J. Beckman, J. Hensold, and S.K. Lemmon Bms1p, a novel GTP-binding protein, and the related Tsr1p are required for distinct steps of 40 S ribosome biogenesis in yeast RNA 7 2001 1268 1283
5. T. Wegierski, E. Billy, F. Nasr, and W. Filipowicz Bms1p, a G-domain-containing protein, associates with Rcl1p and is required for 18 S rRNA biogenesis in yeast RNA 7 2001 1254 1267
6. N.J. Krogan, W.T. Peng, G. Cagney, M.D. Robinson, R. Haw, and G. Zhong High-definition macromolecular composition of yeast RNA-processing complexes Mol. Cell 13 2004 225 239
7. K. Karbstein, S. Jonas, and J.A. Doudna An essential GTPase promotes assembly of pre-ribosomal processing complexes Mol. Cell 20 2005 633 643
8. H.R. Bourne, D.A. Sanders, and F. McCormick The GTPase superfamily: conserved structure and molecular mechanism Nature 349 1991 117 127
9. A. Antoun, M.Y. Pavlov, K. Andersson, T. Tenson, and M. Ehrenberg The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis EMBO J. 22 2003 5593 5601
10. L.D. Kapp, and J.R. Lorsch GTP-dependent recognition of the methionine moiety on initiator tRNA by translation factor eIF2 J. Mol. Biol. 335 2004 923 936
11. K.B. Gromadski, H.J. Wieden, and M.V. Rodnina Kinetic mechanism of elongation factor Ts-catalyzed nucleotide exchange in elongation factor Tu Biochemistry 41 2002 162 169
12. A. Pingoud, W. Block, A. Wittinghofer, H. Wolf, and E. Fischer The elongation factor Tu binds aminoacyl-tRNA in the presence of GDP J. Biol. Chem. 257 1982 11261 11267
13. A. Pingoud, and C. Urbanke Aminoacyl transfer ribonucleic acid binding site of the bacterial elongation factor Tu Biochemistry 19 1980 2108 2112
14. A.V. Zavialov, R.H. Buckingham, and M. Ehrenberg A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3 Cell 107 2001 115 124
15. A.V. Zavialov, V.V. Hauryliuk, and M. Ehrenberg Guanine-nucleotide exchange on ribosome-bound elongation factor G initiates the translocation of tRNAs J. Biol. 4 2005 9
16. G. Romero, V. Chau, and R.L. Biltonen Kinetics and thermodynamics of the interaction of elongation factor Tu with elongation factor Ts, guanine nucleotides, and aminoacyl-tRNA J. Biol. Chem. 260 1985 6167 6174
17. D. Moazed, J.M. Robertson, and H.F. Noller Interaction of elongation factors EF-G and EF-Tu with a conserved loop in 23 S RNA Nature 334 1988 362 364
18. B.P. Klaholz, A.G. Myasnikov, and M. Van Heel Visualization of release factor 3 on the ribosome during termination of protein synthesis Nature 427 2004 862 865
19. G.S. Allen, A. Zavialov, R. Gursky, M. Ehrenberg, and J. Frank The cryo-EM structure of a translation initiation complex from Escherichia coli Cell 121 2005 703 712
20. M.V. Rodnina, A. Savelsbergh, V.I. Katunin, and W. Wintermeyer Hydrolysis of GTP by elongation factor G drives tRNA movement on the ribosome Nature 385 1997 37 41
21. T. Pape, W. Wintermeyer, and M.V. Rodnina Complete kinetic mechanism of elongation factor Tu-dependent binding of aminoacyl-tRNA to the A site of the E. coli ribosome EMBO J. 17 1998 7490 7497
22. A. Parmeggiani, and G. Sander Properties and regulation of the GTPase activities of elongation factors Tu and G, and of initiation factor 2 Mol. Cell. Biochem. 35 1981 129 158
23. J. Tomsic, L.A. Vitali, T. Daviter, A. Savelsbergh, R. Spurio, and P. Striebeck Late events of translation initiation in bacteria: a kinetic analysis EMBO J. 19 2000 2127 2136
24. S.O. Shan, and P. Walter Induced nucleotide specificity in a GTPase Proc. Natl Acad. Sci. USA 100 2003 4480 4485
25. S. Shan, A.V. Kravchuk, J.A. Piccirilli, and D. Herschlag Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction Biochemistry 40 2001 5161 5171
26. S.O. Shan, G.J. Narlikar, and D. Herschlag Protonated 2′-aminoguanosine as a probe of the electrostatic environment of the active site of the Tetrahymena group I ribozyme Biochemistry 38 1999 10976 10988
27. L. Ortoleva-Donnelly, M. Kronman, and S.A. Strobel Identifying RNA minor groove tertiary contacts by nucleotide analogue interference mapping with N-2-methylguanosine Biochemistry 37 1998 12933 12942
28. A.A. Szewczak, L. Ortolevadonnelly, S.P. Ryder, E. Moncoeur, and S.A. Strobel A minor-groove RNA triple-helix within the catalytic core of a group I intron Nature Struct. Biol. 5 1998 1037 1042
29. K. Karbstein, K.H. Tang, and D. Herschlag A base triple in the Tetrahymena group I core affects the reaction equilibrium via a threshold effect RNA 10 2004 1730 1739
30. D.S. Knitt, G.J. Narlikar, and D. Herschlag Dissection of the role of the conserved G.U pair in group I RNA self-splicing Biochemistry 33 1994 13864 13879
31. P. Peluso, D. Herschlag, S. Nock, D.M. Freymann, A.E. Johnson, and P. Walter Role of 4.5 S RNA in assembly of the bacterial signal recognition particle with its receptor Science 288 2000 1640 1643
32. S.O. Shan, and P. Walter Molecular crosstalk between the nucleotide specificity determinant of the SRP GTPase and the SRP receptor Biochemistry 44 2005 6214 6222
33. D. Maag, and J.R. Lorsch Communication between eukaryotic translation initiation factors 1 and 1A on the yeast small ribosomal subunit J. Mol. Biol. 330 2003 917 924
34. I.R. Vetter, and A. Wittinghofer The guanine nucleotide-binding switch in three dimensions Science 294 2001 1299 1304
35. K. Karbstein, K.S. Carroll, and D. Herschlag Probing the Tetrahymena group I ribozyme reaction in both directions Biochemistry 41 2002 11171 11183
36. J.R. Lorsch, and D. Herschlag The DEAD box protein eIF4A 1. A minimal kinetic and thermodynamic framework reveals coupled binding of RNA and nucleotide Biochemistry 37 1998 2180 2193
37. S. Ghaemmaghami, W.K. Huh, K. Bower, R.W. Howson, A. Belle, and N. Dephoure Global analysis of protein expression in yeast Nature 425 2003 737 741
38. A. Fersht Enzyme Structure and Mechanism 1984 W.H. Freeman & Company New York
39. R. Sanchez, and A. Sali Large-scale protein structure modeling of the Saccharomyces cerevisiae genome Proc. Natl Acad. Sci. USA 95 1998 13597 13602
40. P. Peluso, S.O. Shan, S. Nock, D. Herschlag, and P. Walter Role of SRP RNA in the GTPase cycles of Ffh and FtsY Biochemistry 40 2001 15224 15233
41. J. Venema, and D. Tollervey Ribosome synthesis in Saccharomyces cerevisiae Annu. Rev. Genet. 33 1999 261 311
42. E. Billy, T. Wegierski, F. Nasr, and W. Filipowicz Rcl1p, the yeast protein similar to the RNA 3′-phosphate cyclase, associates with U3 snoRNP and is required for 18 S rRNA biogenesis EMBO J. 19 2000 2115 2126
43. A. van Hoof, P. Lennertz, and R. Parker Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5 S, 5.8 S, U4, U5, RNase MRP and RNase P RNAs in yeast EMBO J. 19 2000 1357 1365
44. S.E. Neal, J.F. Eccleston, A. Hall, and M.R. Webb Kinetic analysis of the hydrolysis of GTP by p21N-ras. The basal GTPase mechanism J. Biol. Chem. 263 1988 19718 19722
45. A.K. Kabcenell, B. Goud, J.K. Northup, and P.J. Novick Binding and hydrolysis of guanine nucleotides by Sec4p, a yeast protein involved in the regulation of vesicular traffic J. Biol. Chem. 265 1990 9366 9372