The Translational Apparatus Structure, Function, Regulation, Evolution The Translational Apparatus Structure, Function, Regulation, Evolution Edited by Knud H. Nierhaus Franceschi Fran~ois Alap R. Subramanian Max-Planck-Institut fiir Molekulare Genetik Berlin, Germany Volker A. Erdmann Freie Universităt Berlin Berlin, Gennany and Brigitte Wittmann-Liebold Max-Delbriick-Centrum ffir Molekulare Medizin Berlin, Germany Springer Science+Business Media, LLC Llb~a~y af Cang~ass Catalaglng-ln-Publlcatlan Data The Translatlanal appa~atus , structura, functlon, regulatlon, evolutlon I edlted by Knud H. Nlarhaus ..• [et al.1. p. cm. "Proceadlngs of an InternatIonal conference an the translatlonal apparatus, held October 31-Novuber 5, 1992, In Berlin, Geruny" -Copr. p. Includes blbllographlcal references and Index. ISBN 978-1-4613-6021-6 ISBN 978-1-4615-2407-6 (eBook) DOI 10.1007/978-1-4615-2407-6 1. Genetic translatlon--Congresses. 2. Genetic translatlon -Ragulatlon--Congrasses. I. Nlerhaus, Knud H. QH450.5.T723 1993 574.B7'3223--dc20 93-37131 CIP Proceedings of an International Conference on The Translational Apparatus, held October 31- November 5, 1992, in Berlin, Germany ISBN 978-1-4613-6021-6 @ 1993 Springer Science+Business Media New York Origina11y published by Plenurn Press, New York in 1993 Softcover reprint of the hardcover 1s t edition 1993 AlI rights reserved No part of this book may be reproduced, stored in retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher PREFACE The conference entitled "The Translational Apparatus" was held in Berlin from October 31 to November 5, 1992, in honorem et memoriam of H. G. Wittmann. The presentations of the rewarding, enjoyable and scientifically exciting week in Berlin were a fitting appreciation of this great man, and all participants and speakers contributed to the success of the meeting. The second reason for holding the Berlin meeting was to convene a group of scientists for a state-of-the-art presentation on ribosomes and related subjects; the outcome is this book. We have broadened the spectrum of topics to cover activities preceding and following pure ribosomal functions, such as "Synthetases" and "Protein Sorting", respectively, and we took the liberty of ordering the contributions in a way which does not always reflect the order of speakers. We are grateful to the authors who patiently tolerated our organization and our regulations for manuscripts. K.H. Nierhaus F. Franceschi A.R. Subramanian v CONTENTS I. tRNA and Aminoaeyl-tRNA Synthetases 1. The Crystal Structure of SeryI-tRNA Synthetase and its Complexes with A TP and tRNASer................................................................................................................. 1 S. Cusack, C. Berthet-Colominas, V. Biou, F. Borel, M. Fujinaga, M. Hartlein, I. Krikliviy, N. Nassar, S. Price, M.A. Tukalo, A.D. Yaremchuk, and R.Leberman 2. Charging of RNA Microhelices and Decoding Genetic Information: Evaluation of Functional Coupling between Distal Parts of a tRNA Structure ........................... 13 P. Schimmel 3. Identity of a Prokaryotic Initiator tRNA ....................................................................... 23 M.R. Dyson, c.P. Lee, N. Mandai, B.L. Seong, U. Varshney, and U.L. RajBhandary 4. Genetic Systems in Yeast for Analysis of InitiatorlElongator tRNA Speci ficity ......... 3 S A.S. Bystrom, U. von Pawel-Rammingen, and S.U. Astrom S. Specificity in RNA:Protein Interactions; the Recognition of Escherichia coli GlutaInine tRNA .................................................................................................... 47 M.J. Rogers, I. Weygand-Durasevic, E. Schwob, J.M. Sherman, K.C. Rogers, H.-U. Thomann, L.A. Sylvers, M. Jahn, H. Inokuchi, E. Ohtsuka, and D. SolI 6. Conformational Change oftRNA Upon Interaction of the Identity-Determinant Set with Aminoacyl-tRNA Synthetase......................................................................... S9 O. Nureki, T. Niimi, Y. Muto, H. Kanno, T. Kohno, T. Muramatsu, G. Kawai, T. Miyazawa, R. Giege, C. Florentz, and S. Yokoyama 7. Functional Aspects of Three Modified Nucleosides, 'If, ms2io6A, and mIG, Present in the Anticodon Loop oftRNA ............................................................................ 67 T.G. Hagervall, B. Esberg, J.-N. Li, T.M.F. Tuohy, J.F. Atkins, J.F. Curran, and G.R. Bjork 8. The Determination ofPosttranscriptional Modification in RNA ................................. 79 J.A. Kowalak and J.A. McCloskey vii II. rRNA and mRNA: Regulation, Processing, Assembly 9. RNA Polymerase I, the Nucleolus and Synthesis of35S rRNA in the Yeast Saccharomyces cerevisiae ..... .............................. .... ............... ............... .... ............. 89 M. Nomura, Y. Nogi, R. Yano, M. Oakes, D.A. Keys, L. Vu, and J.A. Dodd 10. DNA Elements and Protein Factors Involved in the Regulation of Transcription of the Ribosomal RNA Genes in yeast...................................................................... 101 R.J. Planta and T. Kulkens 11. Genetic Approaches to the Study of Eukaryotic Ribosomes... ............................. ........ 109 J.R. Warner, J. Vilardell, B.E. Morrow, Q.D. Ju, F.J. Eng, M.D. Dabeva, and L.B. Alksne 12. Regulation of Ribosomal RNA Synthesis and Control of Ribosome Formation in E. coli ..................................................................................................................... 119 R. Wagner, G. TheiSen, and M. Zacharias 13. Regulation of the Eleven Gene S 10 Ribosomal Protein Operon by the 50S Subunit Protein IA...... ......................... ........ ..................... .... ............................. .................. 131 J.M. Zengel and L. Lindahl 14. Fis-Dependent Trans-Activation of8table RNA Operons and Bacterial Growth........ 139 L. Bosch, L. Nilsson, E. Vijgenboom, and H. Verbeek 15. Ribosomal RNA Processing in Saccharomyces cerevisiae .......................................... 151 R.W. van Nues, J. Venema, R.J. Planta, and H.A. Raue 16. Analysis of Mutations in the 238 rRNA ....................................................................... 163 U. Samma, B.T.U. Lewicki, T. Margus, S. Nigul, and J. Remme 17. Extrinsic Factors in Ribosome Assembly ..................................................................... 173 J.-H. Alix 18. Non-Ribosomal Proteins Affecting the Assembly of Ribosomes in Escherichia coli........ 185 H. Nashimoto III. Translational Initiation and Termination 19. Mechanisms of Translational Initiation and Repression in Prokaryotes ...................... 197 D.E. Draper 20. The Central Pseudoknot Connecting the Three Major Domains in 168 rRNA is Required for Translational Initiation...................................................................... 209 M.F. Brink, M.Ph. Verbeet, and H.A. de Boer 21. RNA Helicase Activity in Translation Initiation in Eukaryotes ................................... 221 A. Pause and N. 80nenberg viii 22. Translation Initiation by Internal Ribosome Binding of Eukaryotic mRNA ............... 229 Molecules Ch.-Y. Chen, D.G. Macejak, S.-K. Oh, and P. Samow 23. Novel Structural and Functional Aspects of Translational Initiation Factor IF2 ......... 241 R. Spurio, M. Severini, A. La Teana, M.A. Canonaco, R.T. Pawlik, C.O. Gualerzi, and c.L. Pon 24. Translational Stop Signals: Evolution, Decoding for Protein Synthesis and Recoding for Alternative Events ............................................................................................ 253 W.P. Tate, F.M. Adamski, C.M. Brown, M.E. Dalphin, J.P. Gray, J.A. Horsfield, K.K. McCaughan, J.G. Moffat, R.J. Powell, K.M. Timms, and C.N.A. Trotman IV. The Elongation Process: Sites, Factors, Nascent Chain 25. The Allosteric Three-Site Model and the Mechanism of Action of Both Elongation Factors EF-Tu and EF-G ........................................................................................ 263 K.H. Nierhaus, R. Adlung, T.-P. Hausner, S. Schilling-Bartetzko, T. Twardowski, and F. Triana 26. Elongation Factor Tu from Thermus thermophilus, Structure, Domains and Interactions ............................................................................................................. 273 M. Sprinzl and R. Hilgenfeld 27. Topography of the Ternary EF-TulGTPlPhe-tRNAPhe Complex as Studied by Crosslinking and Limited Proteolysis .................................................................... 285 1. Reinbolt, M.-H. Metz, P. Romby, B. Ehresmann, and C. Ehresmann 28. Specific Functions of Elongation Factor Tu, a Molecular Switch in Protein Biosynthesis, as Studied by Site-Directed Mutagenesis ........................................ 295 A. Weijland, K. Harmark, P.H Anborgh, and A. Parmeggiani 29. EF-Tu Stoichiometries in Code Translation ................................................................. 305 M. Ehrenberg, N. Bilgin, and J. ScobIe 30. Kinetic Fluorescence Study on EF-Tu-Dependent Binding ofPhe-tRNAPhe to the Ribosomal A Site ................................................................................................... 317 M.V. Rodnina, R. Fricke, and W. Wintermeyer 31. Defining the Function ofEF-3, a Unique Elongation Factor in Low Fungi................. 327 F.J. Triana, K.H. Nierhaus, 1. Ziehler, and K. Chakraburtty 32. Antibiotic and Protein Interactions with the GTPase and Peptidyl Transferase Regions in 23S rRNA ............................................................................................ 339 S. Douthwaite, B. Vester, C. Aagaard, and G. Rosendahl ix 33. Extension and Folding of Nascent Peptides on Ribosomes.......................................... 347 B. Hardesty, O.W. Odom, W. Kudlicki, and G. Kramer 34. Protein Synthesis and Secretion as Seen by the Nascent Protein Chain....................... 359 AE. Johnson, K.S. Crowley, S.K. Shore, and G.D. Reinhart V. Accuracy in Translation 35. Mutants oftRNA, Ribosomes and mRNA Affecting Frameshifting, Hopping or Stop Codon Read-11rrough............................................................................................. 371 J.F. Atkins, K. Herbst, M. O'Connor, T.M.F. Tuohy, R.B. Weiss, N.M. Wills and R.F. Gesteland 36. Use of Ribosomal Accuracy Mutants to Probe Mechanisms of Programmed Translational Frameshifts in Escherichia coli ....................................................... 375 J. Sipley and E. Goldman 37. 23S rRNA Tunes Ribosomal Accuracy ........................................................................ 385 N. Bilgin and M. Ehrenberg VI. Quaternary Structure, Functional Centers and Domains in the Ribosome 38. Towards Atomic Resolution of Prokaryotic Ribosomes: Crystallographic, Genetic and Biochemical Studies........................................................................................ 397 F. Franceschi, S. Weinstein, U. Evers, E. Arndt, W. Jahn, H.A.S. Hansen, K. von Bohlen, Z. Berkovitch-Yellin, M. Eisenstein, I. Agmon, J. Thygesen, N. Volkmann, H. Bartels, F. Schlilnzen, A Zaytzev-Bashan, R. Sharon, I. Levin, A Drlbin, I. Sagi, T. Choli-Papadopoulou, P. Tsiboli, G. Kryger, W.S. Bennett, and A Yonath 39. Functional Site Determinations in Three Dimensions on Eukaryotic and Eubacterial Ribosomes .............................................................................................................. 411 A Verschoor, S. Srivastava, M. Radermacher, J. Frank, R.R. Traut, M. Stofller Meilicke, and D. Glitz 40. Messenger RNA Path Through the Procaryotic Ribosome .......................................... 421 AA Bogdanov, O.A Dontsova, and R. Brimacombe 41. Mapping the Functional Centre of the Escherichia coli Ribosome.............................. 433 R. Brimacombe, T. Doring, B. Greuer, N. Jiinke, P. Mitchell, F. MUller, M. Osswald, J. Rinke-Appel, and K. Stade 42. The Arrangement of tRNA in the Ribosome ................................................................ 445 AS. Spirin, V.1. Lim, and R. Brimacombe 43. A Model of the tRNA Binding Sites on the Escherichia coli Ribosome ..................... 455 J. Wower, L.A. Sylvers, K.V. Rosen, S.S. Hixson, and R.A. Zimmermann x 44. Photolabile Oligodeoxyribonucleotide Probes of E. coli Ribosome Structure............. 465 B.S Cooperman, P. Muralikrishna, and R.W. Alexander 45. The Simplicity Behind the Elucidation of Complex Structure in Ribosomal RNA ..... 477 R.R. Gutell 46. The Functional Role of Conserved Sequences of 16S Ribosomal RNA in Protein Synthesis ......................... .................. ............. ........ ..... .... .... ... .... .... ............... ......... 489 J. Ofe nga nd, A Bakin, and K. Nurse 47. Crystallization and Diffraction Studies of Thermus flavus 5S rRNA and Synthetic Fragments of the 5S rRNA ..................................................................................... 501 V.A Erdmann, S. Lorenz, E. Raderschall, J.P. Fiirste, R. Bald, M. Zhang, Ch. Betzel, and K.S. Wilson 48. Towards Ribosomal Structure at Peptide Level: Use of Crossl inking, Antipeptide Antibodies and Limited Proteolysis. ......... ..... .... ......................... .... .... .... ... .... .... .... 509 V. Kroft, O. Bischof, U. Bergmann, E. Herfurth, and B. Wittmann-Liebold 49. Structure and Function of Escherichia coli Ribosomal Protein L71L12: Effect of Cross-Links and Deletions ..................................................................................... 521 R.R. Traut, AV. Oleinikov, E. Makarov, G. Jokhadze, B. Perroud, and B. Wang 50. Structural Studies on Prokaryotic Ribosomal Proteins................................................. 533 V. Ramakrishnan, S.E. Gerchman, B.L. Golden, D.W. Hoffman, J.H. Kycia, S.J. Porter, and S.W. White VII. Translation in Cell Organelles 51. Molecular Genetics of Chloroplast Ribosomes in Chlamydomonas reinhardtii .......... 545 C.R. Hauser, B.L. Randolph-Anderson, T.M. Hohl, E.H. Harris, J.E. Boynton, and N.W. Gillham 52. The Nuclear Genes for Chloroplast Ribosomal Proteins LIt and LI2 in Higher Plants ...................................................................................................................... 555 J. Schmidt, W. Wegiohner, andAR. Subramanian 53. The Spinach Plastid Ribosome: Protein Properties and Aspects of Ribosome Biosynthesis. .... .... ... .... .... .... ..... ... .... ..... ......... ......... ......... ........... .... .... .... .... .... ... ..... 565 R. Mache, D.-X. Zhou, B. Franzetti, T. Lagrange, S. Lerbs-Mache, and C. Bisanz Seyer 54. Structure and Function of Mammalian Mitochondrial Ribosome ................................ 575 T.W. O'Brien, N.D. Denslow, W.H. Faunce, J.C. Anders, J. Liu, and BJ. O'Brien 55. Essential Features of the Peptidyl Transferase Center in the Yeast Mitochondrial Ribosome ............................................................................................................... 587 C. Pan, K. Sirum-Connolly, and T.L. Mason xi 56. Genes for Mitochondrial Ribosomal Proteins in Plants ............................................... 599 L. Grohmann, A Brennicke, and W. Schuster 57. Editing Creates the Initiator Codon of the rpl2 Transcript from Maize Chloroplasts ................................................................................................... .... .... 609 H. Kossel, B. Hoch, G.L. Igloi, R.M. Maier, and S. Ruf 58. The Plant Mitochondrial Transfer RNA Population: A Mosaic of Species with Different Genetic Origins....................................................................................... 617 A Dietrich, I. Small, T. Desprez, J. Masson, F. Weber, D. Ramamonjisoa, G. Souciet, A Cosset, G. Green, P. Guillemaut, G. Pelletier, J.-H. Wei!, and L. Marechal-Drouard VIn. Post-Translation: Protein Sorting 59. Assembly ofSRP from Single Polypeptides and 7S RNA ........................................... 627 H. Liitcke, and B. Dobberstein 60. The Alu-Domain of the Signal Recognition Particle.................................................... 635 K. Strub, N. Wolff, and S. Oertle IX. The Translational Apparatus and Evolution 61. Molecular Mechanism of the Genetic Code Variations Found in Candida Species and its Implications in Evolution of the Genetic Code .......................................... 647 K. Watanabe, T. Veda, T. Yokogawa, T. Suzuki, K. Nishikawa, M. Mori, T. Ohama, H. Nakabayashi, T. Nakase, and S. Osawa 62. The Aminoacyl-tRNA Synthetase Family: An Evolutionary View of Their Structural Organization .......................................................................................... 657 M. Mirande, M. Lazard, P. KeIjan, G. Bec, F. Agou, S. Quevillon, and J.-P. Waller 63. Evolution of the EF-Tu Family.................................................................................... 669 W.C. Merrick, J. Cavallius, T. Goss Kinzy, and W.L. Zoll 64. The Evolution of Ribosomal Protein and Ribosomal RNA Operons: Coding Sequences, Regulatory Mechanisms and Processing Pathways ............................ 679 P. Durovic, D. Liao, S. Mylvaganam, and P.P. Dennis 65. The Ribosomal Proteins: Compilation of Protein Species Equivalents from Various Organisms, Based on Evolutionary Analyses ........ .................................. .............. 689 E. Otaka, T. Hashimoto, K. Mizuta, and K. Suzuki 66. Expression and Assembly of Chloroplast Ribosomal Proteins in E. coli..................... 701 W. WeglOhner, 1. Schmidt, K. Giese, and AR. Subramanian xii