About the Book
This is the first book to contain the newly published findings on the structure of the ribosome and discuss their meaning for our understanding of how proteins are made and processed inside the cell. With over 60 contributions from the world's most innovative ribosome biology laboratories, this is the latest volume in the annual series that for over 60 years has provided analysis and interpretation of the most interesting problems in biology.
Table of Contents:
Symposium Participants Foreword Ribosome Structure RNA Structure and the Roots of Protein Synthesis (A. Rich) 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) 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) 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) Structure of the Ribosome at 5.5 c5; 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) Ratchet-like Movements between the Two Ribosomal Subunits: Their Implications in Elongation Factor Recognition and tRNATranslocation (J. Frank and R.K. Agrawal) Do Single (Ribosome) Molecules Phase Themselves? (M. van Heel) 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) Probing Ribosome Structure and Function by Mutagenesis (S.T. Gregory, M.A. Bayfield, M. O'Connor, J. Thompson, and A.E. Dahlberg) Exploring the Mechanism of the Peptidyl Transfer Reaction by Chemical Footprinting (S.A. Strobel, G.W. Muth, and L. Chen) Analysis of the Active Site of the Ribosome by Site-directed Mutagenesis (D.F. Kim, K. Semrad, and R. Green) Codon Recognition and Decoding: The Transorientation Hypothesis (A.B. Simonson and J.A. Lake) Features and Functions of the Ribosomal E Site (G. Blaha and K.H. Nierhaus) Pseudouridines and Pseudouridine Synthases of the Ribosome (J. Ofengand, A. Malhotra, J. Remme, N. Gutgsell, M. Del Campo, S. Jean-Charles, L. Peil, and Y. Kaya) 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) Structural Basis for the Amino Acid and tRNA Recognition by Class-I Aminoacyl-tRNA Synthetases (O. Nureki, S. Fukai, S.-I. Sekine, A. Shimada, T. Terada, T. Nakama, M. Shirouzu, D.G. Vassylyev, and S. Yokoyama) Aminoacyl-tRNA Synthesis: A Post-genomic Perspective (C. Stathopoulos, I. Ahel, K. Ali, A. Ambrogelly, H. Becker, S. Bunjun, K. Doerr, L. Feng, S. Herring, C. Jacquin-Becker, H. Kobayashi, D. Korencic, 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. S f6;ll) tRNA Conformity (A.D. Wolfson, F.J. LaRiviere, J.A. Pleiss, T. Dale, H. Asahara, and O.C. Uhlenbeck) Initiator tRNA and Its Role in Initiation of Protein Synthesis (C. Mayer, A. Stortchevoi, C. K f6;hrer, U. Varshney, and U.L. RajBhandary) On Translation by RNAs Alone (M. Yarus) 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, I.P. Ivanov, S. Matsufuji, W.A. Miller, B. Moore, M.F. Pr e8;re, N.M. Wills, J. Zhou, and R.F. Gesteland) Structure and Function of the Stimulatory RNAs Involved in Programmed Eukaryotic -1 Ribosomal Frameshifting (I. Brierley and S. Pennell) 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) Preferential Translation of Adenovirus mRNAs in Infected Cells (R. Cuesta, Q. Xi, and R.J. Schneider) 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) Mechanisms of Internal Ribosome Entry in Translation Initiation (J.S. Kieft, A. Grech, P. Adams, and J.A. Doudna) 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. Pestova, C.U.T. Hellen, and P. Sarnow) 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) The mRNA Capping Apparatus as Drug Target and Guide to Eukaryotic Phylogeny (S. Shuman) 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) Nonsense-mediated mRNA Decay in Saccharomyces cerevisiae: A Quality Control Mechanism That Degrades Transcripts Harboring Premature Termination Codons (C.I. Gonz e1;lez, W. Wang, and S.W. Peltz) Translational Control of 15-Lipoxygenase and msl-2 mRNAs: Single Regulators or Co-repressor Assemblies? (F. Gebauer, D.H. Ostareck, A. Ostareck-Lederer, M. Grskovic, and M.W. Hentze) PUF Proteins and 3'UTR Regulation in the Caenorhabditis elegans Germ Line (M. Wickens, D. Bernstein, S. Crittenden, C. Luitjens, and J. Kimble) Translational Control of Embryonic Cell Division by CPEB and Maskin (I. Groisman, Y.-S. Huang, R. Mendez, Q. Cao, and J.D. Richter) 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) Initiation Role of the 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) 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) Functions of Eukaryotic Factors in Initiation of Translation (T.V. Pestova and C.U.T. Hellen) Interactions of the Eukaryotic Translation Initiation Factor eIF4E (J.D. Gross, H. Matsuo, M. Fletcher, A.B. Sachs, and G. Wagner) 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. Val e1;sek, L.W. Schoenfeld, A. Shalev, J. Clayton, K. Nielsen, T.F. Donahue, and A.G. Hinnebusch) The 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) Elongation and Termination Structural Studies of Eukaryotic Elongation Factors (G.R. Andersen and J. Nyborg) Translation Elongation Factor 1 Functions in the Yeast Saccharomyces cerevisiae (M. Anand, L. Valente, A. Carr-Schmid, R. Munshi, O. Olarewaju, P. Ortiz, and T.G. Kinzy) 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) Modulation of Translation Termination by cis- and trans-acting Factors (D.M. Janzen and A.P. Geballe) Protein tRNA Mimicry in Translation Termination (Y. Nakamura, M. Uno, T. Toyoda, T. Fujiwara, and K. Ito) Regulation of Protein Synthesis Mitogenic and Nutritional Signals Are Transduced into Translational Efficiency of TOP mRNAs (E. Hornstein, H. Tang, and O. Meyuhas) 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) Translational Regulation in the Cellular Response to Biosynthetic Load on the Endoplasmic Reticulum (H. Harding, I. Novoa, A. Bertolotti, H. Zeng, Y. Zhang, F. Urano, C. Jousse, and D. Ron) 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) The Fourth Step of Protein Synthesis: Disassembly of the Posttermination Complex Is Catalyzed by Elongation Factor G and Ribosome Recycling Factor, RRF, a Near-perfect Mimic of tRNA (A. Kaji, M.C. Kiel, G. Hirokawa, A. Muto, Y. Inokuchi, and H. Kaji) 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) The Active 80S Ribosome-Sec61 Complex (R. Beckmann, C.M.T. Spahn, J. Frank, and G. Blobel) Ribosome Biogenesis Ribosomal RNA Genes, RNA Polymerases, Nucleolar Structures, and Synthesis of rRNA in the Yeast Saccharomyces cerevisiae (M. Nomura) The Economics of Ribosome Biosynthesis (J.R. Warner, J. Vilardell, and J.H. Sohn) Ribosome Biogenesis: Role of Small Nucleolar RNA in Maturation of Eukaryotic rRNA (S.A. Gerbi, A.V. Borovjagin, M. Ezrokhi, and T.S. Lange) Thermodynamics and Kinetics of Central Domain Assembly (M.I. Recht and J.R. Williamson) 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) Summary: The Ribosome in the 21st Century: The Post-structural Era (P.B. Moore) Author Index Subject Index
