The Ribosome

Symposium Participants v Foreword xvii

Ribosome Structure

RNA Structure and the Roots of Protein Synthesis A. Ric 1 Atomic Structures of the 30S Subunit and Its Complexes with Ligands and Antibiotics D.E. Brodersen, A.P. Carter, W.M. Clemons, Jr., R.J. Morgan-Warren, F.V. Murphy IV, J.M. Ogle, M.J. Tarry, B.T. Wimberly, and V. Ramakrishnan 17 Progress toward an Understanding of the Structure and Enzymatic Mechanism of the Large Ribosomal Subunit J.L. Hansen, T.M. Schmeing, D.J. Klein, J.A. Ippolito, N. Ban, P. Nissen, B. Freeborn, P.B. Moore, and T.A. Steitz 33 High-resolution Structures of Ribosomal Subunits: Initiation, Inhibition, and Conformational Variability A. Bashan, I. Agmon, R. Zarivach, F. Schluenzen, J. Harms, M. Pioletti, H. Bartels, M. Gluehmann, H. Hansen, T. Auerbach, F. Franceschi, and A. Yonath 43 Structure of the Ribosome at 5.5 Å Resolution and Its Interactions with Functional Ligands H.F. Noller, M.M. Yusupov, G.Z. Yusupova, A. Baucom, K. Lieberman, L. Lancaster, A. Dallas, K. Fredrick, T.N. Earnest, and J.H.D. Cate 57 Ratchet-like Movements between the Two Ribosomal Subunits: Their Implications in Elongation Factor Recognition and tRNA Translocation J.Frank and R.K. Agrawal 67 Do Single (Ribosome) Molecules Phase Themselves? M. van Heel 77

Ribosome Biochemistry

Correlating the X-ray Structures for Halo- and Thermophilic Ribosomal Subunits with Biochemical Data for the Escherichia coli Ribosome P. Sergiev, A. Leonov, S. Dokudovskaya, O. Shpanchenko, O. Dontsova, A. Bogdanov, J. Rinke-Appel, F. Mueller, M. Osswald, K. von Knoblauch, and R. Brimacombe 87 Probing Ribosome Structure and Function by Mutagenesis S.T. Gregory, M.A. Bayfield, M. O'Connor, J. Thompson, and A.E. Dahlberg 101 Exploring the Mechanism of the Peptidyl Transfer Reaction by Chemical Footprinting S.A. Strobel, G.W. Muth, and L. Chen 109 Analysis of the Active Site of the Ribosome by Site-directed Mutagenesis D.F. Kim, K. Semrad, and R. Green 119 Codon Recognition and Decoding: The Transorientation Hypothesis A.B. Simonson and J.A. Lake 127 Features and Functions of the Ribosomal E Site G. Blaha and K.H. Nierhaus 135 Pseudouridines and Pseudouridine Synthases of the Ribosome J. Ofengand, A. Malhotra, J. Remme, N.S. Gutgsell, M. Del Campo, S. Jean-Charles, L. Peil, and Y. Kaya 147

The Genetic Code

Formation of Two Classes of tRNA Synthetases in Relation to Editing Functions and Genetic Code P. Schimmel and L. Ribas de Pouplana 161 Structural Basis for Amino Acid and tRNA Recognition by Class I Aminoacyl-tRNA Synthetases O. Nureki, S. Fukai, S. Sekine, A. Shimada, T. Terada, T. Nakama, M. Shirouzu, D.G. Vassylyev, and S. Yokoyama 167 Aminoacyl-tRNA Synthesis: A Postgenomic Perspective C. Stathopoulos, I. Ahel, K. Ali, A. Ambrogelly, H. Becker, S. Bunjun, L. Feng, S. Herring, C. Jacquin-Becker, H. Kobayashi, D. Korencvicv , B. Krett, N. Mejlhede, B. Min, H. Nakano, S. Namgoong, C. Polycarpo, G. Raczniak, J. Rinehart, G. Rosas-Sandoval, B. Ruan, J. Sabina, A. Sauerwald, H. Toogood, D. Tumbula-Hansen, M. Ibba, and D. Söll 175 tRNA Conformity A.D. Wolfson, F.J. LaRiviere, J.A. Pleiss, T. Dale, H. Asahara, and O.C. Uhlenbeck 85 Initiator tRNA and Its Role in Initiation of Protein Synthesis C. Mayer, A. Stortchevoi, C. Köhrer, U. Varshney, and U.L. RajBhandary 195 On Translation by RNAs Alone M. Yarus 207

Frameshifting, Recoding, Shunting, IRES

Overriding Standard Decoding: Implications of Recoding for Ribosome Function and Enrichment of Gene Expression J.F. Atkins, P.V. Baranov, O. Fayet, A.J. Herr, M.T. Howard, I.P. Ivanov, S. Matsufuji, W.A. Miller, B. Moore, M.F. Prère, N.M. Wills, J. Zhou, and R.F. Gesteland 217 Structure and Function of the Stimulatory RNAs Involved in Programmed Eukaryotic -1 Ribosomal Frameshifting I. Brierley and S. Pennell 233 Programmed +1 Translational Frameshifting in the Yeast Saccharomyces cerevisiae Results from Disruption of Translational Error Correction G. Stahl, S. Ben Salem, Z. Li, G. McCarty, A. Raman, M. Shah, and P.J. Farabaugh 249 Preferential Translation of Adenovirus mRNAs in Infected Cells R. Cuesta, Q. Xi, and R.J. Schneider 259 Shunting and Controlled Reinitiation: The Encounter of Cauliflower Mosaic Virus with the Translational Machinery T. Hohn, H.-S. Park, O. Guerra-Peraza, L. Stavolone, M.M. Pooggin, K. Kobayashi, and L.A. Ryabova 269 Mechanisms of Internal Ribosome Entry in Translation Initiation J.S. Kieft, A. Grech, P. Adams, and J.A. Doudna 277 Initiator Met-tRNA-independent Translation Mediated by an Internal Ribosome Entry Site Element in Cricket Paralysis Virus-like Insect Viruses E. Jan, S.R. Thompson, J.E. Wilson, T.V. Pestova, C.U.T. Hellen, and P. Sarnow 285

Messenger RNA and Translational Control

The mRNA Closed-loop Model: The Function of PABP and PABP-interacting Proteins in mRNA Translation A. Kahvejian, G. Roy, and N. Sonenberg 293 The mRNA Capping Apparatus as Drug Target and Guide to Eukaryotic Phylogeny S. Shuman 301 Nonsense-mediated mRNA Decay: Insights into Mechanism from the Cellular Abundance of Human Upf1, Upf2, Upf3, and Upf3X Proteins L.E. Maquat and G. Serin 313 Nonsense-mediated mRNA Decay in Saccharomyces cerevisiae: A Quality Control Mechanism That Degrades Transcripts Harboring Premature Termination Codons C.I. González, W. Wang, and S.W. Peltz 321 Translational Control of 15-Lipoxygenase and msl-2 mRNAs: Single Regulators or Corepressor Assemblies? F. Gebauer, D.H. OOstareck, A. Ostareck-Lederer M. Grskovic, and M.W. Hentze 329 PUF Proteins and 3´UTR Regulation in the Caenorhabditis elegans Germ Line M. Wickens, D. Bernstein, S. Crittenden, C. Luitjens, and J. Kimble 337 Translational Control of Embryonic Cell Division by CPEB and Maskin I. Groisman, Y.-S. Huang, R. Mendez, Q. Cao, and J.D. Richter 345 Small RNA Regulators of Translation: Mechanisms of Action and Approaches for Identifying New Small RNAs S. Gottesman, G. Storz, C. Rosenow, N. Majdalani, F. Repoila, and K.M. Wassarman 353

Initiation

Initiation Factors in the Early Events of mRNA Translation in Bacteria C.O. Gualerzi, L. Brandi, E. Caserta, C. Garofalo, M. Lammi, A. La Teana, D. Petrelli, R. Spurio, J. Tomsic, and C.L. Pon 363 The Translation of Capped mRNAs Has an Absolute Requirement for the Central Domain of eIF4G but Not for the Cap-binding Initiation Factor eIF4E I.K. Ali and R.J. Jackson 377 Functions of Eukaryotic Factors in Initiation of Translation T.V. Pestova and C.U.T. Hellen 389 Interactions of the Eukaryotic Translation Initiation Factor eIF4E J.D. Gross, H. Matsuo, M. Fletcher, A.B. Sachs, and G. Wagner 397 A Multifactor Complex of eIF1, eIF2, eIF3, eIF5, and tRNAiMet Promotes Initiation Complex Assembly and Couples GTP Hydrolysis to AUG Recognition K. Asano, L. Phan, L. Valásek, L.W. Schoenfeld, A. Shalev, J. Clayton, K. Nielsen, T.F. Donahue, and A.G. Hinnebusch 403 Universal Translation Initiation Factor IF2/eIF5B T.E. Dever, A. Roll-Mecak, S.K. Choi, J.H. Lee, C. Cao, B.-S. Shin, and S.K. Burley 417

Elongation and Termination

Structural Studies of Eukaryotic Elongation Factors G.R. Andersen and J. Nyborg 425 Translation Elongation Factor 1 Functions in the Yeast Saccharomyces cerevisiae M. Anand, L. Valente, A. Carr-Schmid, R. Munshi, O. Olarewaju, P.A. Ortiz, and T.G. Kinzy 439 Mechanism of Elongation Factor G Function in tRNA Translocation on the Ribosome W. Wintermeyer, A. Savelsbergh, Y.P. Semenkov, V.I. Katunin, and M.V. Rodnina 449 Modulation of Translation Termination Mechanisms by cis- and trans-Acting Factors D.M. Janzen and A.P. Geballe 459 Protein tRNA Mimicry in Translation Termination Y. Nakamura, M. Uno, T. Toyoda, T. Fujiwara, and K. Ito 469

Regulation of Protein Synthesis

Mitogenic and Nutritional Signals Are Transduced into Translational Efficiency of TOP mRNAs E. Hornstein, H. Tang, and O. Meyuhas 477 Double-stranded RNA-binding Proteins and the Control of Protein Synthesis and Cell Growth L.M. Parker, I. Fierro-Monti, T.W. Reichman, S. Gunnery, and M.B. Mathews 485 Translational Regulation in the Cellular Response to Biosynthetic Load on the Endoplasmic Reticulum H.P. Harding, I. Novoa, A. Bertolotti, H. Zeng, Y. Zhang, F. Urano, C. Jousse, and D. Ron 499 A Novel Stress-response Protein That Binds at the Ribosomal Subunit Interface and Arrests Translation D.E. Agafonov, V.A. Kolb, and A.S. Spirin 509 The Fourth Step of Protein Synthesis: Disassembly of the Posttermination Complex Is Catalyzed by Elongation Factor G and Ribosome Recycling Factor, a Near-perfect Mimic of tRNA A. Kaji, M.C. Kiel, G. Hirokawa, A.R. Muto, Y. Inokuchi, and H. Kaji 515 Structure, Function, and Regulation of Free and Membrane-bound Ribosomes: The View from Their Substrates and Products A.E. Johnson, J.-C. Chen, J.J. Flanagan, Y. Miao, Y. Shao, J. Lin, and P.E. Bock 531 The Active 80S Ribosome-Sec61 Complex R. Beckmann, C.M.T. Spahn, J. Frank, and G. Blobel 543

Ribosome Biogenesis

Ribosomal RNA Genes, RNA Polymerases, Nucleolar Structures, and Synthesis of rRNA in the Yeast Saccharomyces cerevisiae M. Nomura 555 Economics of Ribosome Biosynthesis J.R. Warner, J. Vilardell, and J.H. Sohn 567 Ribosome Biogenesis: Role of Small Nucleolar RNA in Maturation of Eukaryotic rRNA S.A. Gerbi, A.V. Borovjagin, M. Ezrokhi, and T.S. Lange 575 Thermodynamics and Kinetics of Central Domain Assembly M.I. Recht and J.R. Williamson 591 Nuclear Export of the Large Ribosomal Subunit A.W. Johnson, J.H.-N. Ho, G. Kallstrom, C. Trotta, E. Lund, L. Kahan, J. Dahlberg, and J. Hedges 599 Summary: The Ribosome in the 21st Century: The Post-structural Era P.B. Moore 607