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The Symposia, 1933 — 2003

2001:   The Ribosome, Vol. LXVI

Organizer: Bruce Stillman


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Symposium Participants    v

Foreword    xvii
Ribosome StructureRNA Structure and the Roots of Protein Synthesis A. Ric    1Atomic 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    17Progress 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    33High-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    43Structure 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    57Ratchet-like Movements between the Two Ribosomal Subunits: Their Implications in Elongation Factor Recognition and tRNA Translocation J.Frank and R.K. Agrawal    67Do Single (Ribosome) Molecules Phase Themselves? M. van Heel    77Ribosome BiochemistryCorrelating 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    87Probing Ribosome Structure and Function by Mutagenesis S.T. Gregory, M.A. Bayfield, M. O'Connor, J. Thompson, and A.E. Dahlberg    101Exploring the Mechanism of the Peptidyl Transfer Reaction by Chemical Footprinting S.A. Strobel, G.W. Muth, and L. Chen    109Analysis of the Active Site of the Ribosome by Site-directed Mutagenesis D.F. Kim, K. Semrad, and R. Green    119Codon Recognition and Decoding: The Transorientation Hypothesis A.B. Simonson and J.A. Lake    127Features and Functions of the Ribosomal E Site G. Blaha and K.H. Nierhaus    135Pseudouridines 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    147The Genetic CodeFormation of Two Classes of tRNA Synthetases in Relation to Editing Functions and Genetic Code P. Schimmel and L. Ribas de Pouplana    161Structural 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    167Aminoacyl-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    175tRNA Conformity A.D. Wolfson, F.J. LaRiviere, J.A. Pleiss, T. Dale, H. Asahara, and O.C. Uhlenbeck    85Initiator tRNA and Its Role in Initiation of Protein Synthesis C. Mayer, A. Stortchevoi,C. Köhrer, U. Varshney, and U.L. RajBhandary    195On Translation by RNAs Alone M. Yarus    207Frameshifting, Recoding, Shunting, IRESOverriding 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    217Structure and Function of the Stimulatory RNAs Involved in Programmed Eukaryotic -1 Ribosomal Frameshifting I. Brierley and S. Pennell    233Programmed +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    249Preferential Translation of Adenovirus mRNAs in Infected Cells R. Cuesta, Q. Xi, and R.J. Schneider    259Shunting 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    269Mechanisms of Internal Ribosome Entry in Translation Initiation J.S. Kieft, A. Grech, P. Adams, and J.A. Doudna    277Initiator 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    285Messenger RNA and Translational ControlThe mRNA Closed-loop Model: The Function of PABP and PABP-interacting Proteins in mRNA Translation A. Kahvejian, G. Roy, and N. Sonenberg    293The mRNA Capping Apparatus as Drug Target and Guide to Eukaryotic Phylogeny S. Shuman    301Nonsense-mediated mRNA Decay: Insights into Mechanism from the Cellular Abundance of Human Upf1, Upf2, Upf3, and Upf3X Proteins L.E. Maquat and G. Serin    313Nonsense-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    321Translational 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 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