Protein synthesis and ribosome structure

Preface XV 1 A History of Protein Biosynthesis and Ribosome Research 1 Hans-Jörg Rheinberger 1.1 Introduction 1 1.2 The Archaeology of Protein Synthesis – The 1940s: Forgotten Paradigms 2 1.3 Basic Mechanisms – The 1950s 5 1.3.1 Steps toward an in vitro Protein Synthesis System 5 1.3.2 Amino Acid Activation and the Emergence of Soluble RNA 7 1.3.3 From Microsomes to Ribosomes 13 1.3.4 Models 17 1.4 The Golden Age of Translation – The 1960s 21 1.4.1 From Enzymatic Adaptation to Gene Regulation: Messenger RNA 21 1.4.2 A Bacterial in vitro System of Protein Synthesis and the Cracking of the Genetic Code 25 1.4.3 The Functional Dissection of Translation 28 1.4.4 The Structural Dissection of the Ribosome 33 1.5 1970–1990s: A Brief Synopsis 35 References 38 2 Structure of the Ribosome 53 Gregor Blaha and Pavel Ivanov 2.1 General Features of the Ribosome and Ribosomal Subunits 53 2.2 A Special Feature of the 50S Subunit: The Tunnel 54 2.3 Features of the Ribosomal Subunits at Atomic Resolution 59 2.4 The Domain Structure of the Ribosomal Subunits 62 2.5 Interactions of RNA with RNA or Struts and Bolts in the Threedimensional Fold of rRNA: Coaxial Stacking and A-minor Motifs 65 2.5.1 Coaxial Stacking 66 2.5.2 A-minor Motifs 69 2.5.3 Ribose Zippers and Patches of A-minor Motifs 71 2.5.3.1 Canonical Ribose Zipper 71 2.5.3.2 Single-base Ribose Zipper 71 VI Contents 2.6 Progress and New Developments in Understanding rRNA Structures 72 2.6.1 K-turn 73 2.6.2 Lonepair Triloop 73 2.6.2.1 Classification of Lonepair Triloops 75 2.6.3 Systemizing Base Pairs 76 2.6.4 Systemizing RNA Structural Elements 78 2.7 RNA–protein Interactions 79 2.7.1 Problem of RNA Recognition 79 2.7.2 Chemistry of RNA–protein Interactions 80 2.7.3 rRNA–protein Interaction 81 References 82 3 Ribosome Assembly 85 3.1 Assembly Of The Prokaryotic Ribosome 85 Knud H. Nierhaus 3.1.1 Introduction 85 3.1.2 Processing of rRNAs 86 3.1.3 Precursor Particles and Reconstitution Intermediates 90 3.1.4 Assembly-initiator Proteins 91 3.1.5 Proteins Essential for the Early Assembly: The Assembly Gradient 95 3.1.6 Late-assembly Components 96 3.1.7 Proteins Solely Involved in Assembly 97 3.1.8 Assembly Maps 99 References 104 3.2 Eukaryotic Ribosome Synthesis 107 Denis L.J. Lafontaine 3.2.1 Introduction 107 3.1.1 Prelude 107 3.2.2 Why so many RRPs? 109 3.2.3 (Pre-)ribosome Assembly, the Proteomic Era 110 3.2.4 Ribosomal RNA Processing, Getting there… 113 3.2.5 Ribosomal RNA Modification: A Solved Issue? 118 3.2.5.1 Ribose Methylation, Pseudouridines formation and the snoRNAs 119 3.2.5.2 The Emergence of the snoRNAs 121 3.2.5.3 Non-ribosomal RNA Substrates for the snoRNAs 122 3.2.5.4 Possible function(s) of RNA modifications 123 3.2.5.5 Base methylation 123 3.2.5.6 U3 snoRNP, the ‘SSU Processome’, and the Central Pseudoknot 124 3.2.6 SnoRNA Synthesis and Intranuclear Trafficking 125 3.2.6.1 SnoRNAs Synthesis 125 Contents VII 3.2.6.2 Non-core snoRNP Proteins required for snoRNA Accumulation 126 3.2.6.3 Interactions between Cleavage Factors and Core snoRNP Proteins 128 3.2.6.4 SnoRNAs Trafficking 128 3.2.6.5 CB/NB are Conserved Sites of Small RNP Synthesis 130 3.2.7 Ribosome Intranuclear Movements and Ribosome Export 130 3.2.8 The Cytoplasmic Phase of Ribosome Maturation 132 3.2.9 Regulatory Mechanisms, all along 134 3.2.10 And Now … What’s Next? 134 3.2.11 Epilogue 135 3.3.12 Useful WWW links 135 References 136 4 tRNA and Synthetases 145 4.1 tRNA: Structure and Function 145 Viter Marquéz and Knud H. Nierhaus 4.1.1 Introduction 145 4.1.2 Secondary Structure 146 4.1.3 Tertiary Structure 149 4.1.4 tRNA Modifications 154 4.1.5 Recognition of tRNA by tRNA synthetase: Identity Elements 154 4.1.6 Is the tRNA Cloverleaf Structure a Pre-requisite for the L-shape? 160 4.1.7 Other Functions of tRNA outside the Ribosomal Elongation Cycle 161 4.1.8 Human Neurodegenerative Disorders Associated with Mitochondrial tRNAs 162 References 166 4.2 Aminoacylations of tRNAs: Record-keepers for the Genetic Code 169 Lluís Ribas de Pouplana and Paul Schimmel 4.2.1 Introduction 169 4.2.2 The Operational RNA Code 170 4.2.3 Extant Aminoacyl-tRNA Synthetases 172 4.2.4 The Origin of Aminoacyl-tRNA Synthetase Classes: Two Proteins bound to one tRNA 174 4.2.5 A Common Genetic Origin for all Aminoacyl-tRNA Synthetases? 177 4.2.5.1 Evolution of Extant Enzymes prior to LUCA 179 4.2.5.2 Changes in Acceptor Stem Identity Elements Correlate with Changes in the Code 180 References 183 5 mRNA Decay and RNA-degrading Machines in Prokaryotes and Eukaryotes 185 Agamemnon J. Carpousis and Marc Dreyfus 5.1 Summary 185 VIII Contents 5.2 Introduction 185 5.3 mRNA Decay in E. coli 186 5.4 mRNA Decay in S. cerevisiae 188 5.5 A Comparison of mRNA Decay in E. coli and S. cerevisiae 188 5.6 RNase E Specificity: A Role in Translation Arrest? 189 5.7 The E. coli RNA degradosome 192 5.8 The Autoregulation of RNase E and PNPase Synthesis: A Link between Bulk Translation and mRNA Stability 195 5.9 RNA-degrading Machines in other Organisms 197 5.10 DEAD-box ATPases 201 5.11 Perspective 202 References 204 6 tRNA Locations on the Ribosome 207 Knud H. Nierhaus 6.1 tRNAs Move through Functional Sites on the Ribosome 207 6.2 Visualization of tRNAs on the Ribosome 209 6.3 tRNA–ribosome Contacts 215 References 216 7 Initiation of Protein Synthesis 219 7.1 Initiation of Protein Synthesis in Eubacteria 219 Daniel N. Wilson 7.1.1 Overview of Initiation in Eubacteria 219 7.1.2 Specialized initiation events: translational coupling, 70S initiation and leaderless mRNAs 222 7.1.3 Initiation Factor 1 Binds to the Ribosomal A-site 224 7.1.4 The Domain Structure of Bacterial IF2 227 7.1.5 Interaction Partners of IF2 230 7.1.6 The Role of the IF2-dependent GTPase Activity 232 7.1.7 The Mystery of the IF3-binding Site on the 30S Subunit 233 References 236 7.2 Mechanism and Regulation of Protein Synthesis Initiation in Eukaryotes 241 Alan G. Hinnebusch, Thomas E. Dever, and Nahum Sonenberg 7.2.1 Introduction 241 7.2.1.1 Overview of Translation-initiation Pathways in Eukaryotes and Prokaryotes 241 7.2.1.2 Conservation and diversity of translation-initiation factors among bacteria, archaea and eukaryotes 244 7.2.1.3 Genetic assays for in vivo functions of eIF2 248 7.2.2 Generation of Free 40S Subunits and 40S Binding of Met-tRNA 251 Contents IX 7.2.2.1 Dissociation of Idle 80S Ribosomes 251 7.2.2.2 Components of the eIF2/GTP/Met-tRNA Ternary Complex 252 7.2.2.3 The GEF eIF2B regulates ternary complex formation 263 7.2.2.4 Binding of Ternary Complex and mRNA to the 40S Ribosome is Stimulated by eIF3 269 7.2.2.5 eIF1A Stimulates Ternary Complex Binding to 40S Subunits and Participates in AUG Selection During Scanning 275 7.2.3 Binding of Ribosomes to mRNA 279 7.2.3.1 The Ends of Eukaryotic mRNAs Contain Distinctive Conserved Structures 279 7.2.3.2 Ribosome Binding to mRNA is Stimulated by the eIF4 Factors 279 7.2.3.3 Circularization of mRNA via eIF4G–PABP Interaction 290 7.2.4 Translational Control by mRNA Circularization 291 7.2.5 Regulation of eIF4 Function by Phosphorylation 292 7.2.5.1 eIF4E Phosphorylation 292 7.2.5.2 eIF4E-4E-BPs 292 7.2.5.3 eIF4G Phosphorylation 294 7.2.5.4 eIF4B Phosphorylation 295 7.2.6 Translational Control by Paips – PABP Interacting Proteins 295 7.2.7 AUG Recognition during Scanning 296 7.2.7.1 AUG is the Predominant Signal for Initiation and is Selected by Proximity to the 5
-end by the Scanning Mechanism 296 7.2.7.2 The Anticodon of tRNA , eIF2 Subunits, eIF1, and eIF5 are Determinants of AUG Selection during Scanning 299 7.2.7.3 eIF1 plays a role in TC binding, scanning, and AUG selection 299 7.2.7.4 eIF5 Functions as a GTPase Activating Protein for eIF2 in AUG Selection and Subunit Joining 300 7.2.8 Joining of 60S Subunits to 40S Ribosomal Complexes 302 7.2.8.1 eIF5B Catalyzes a Second GTP-dependent Step in Translation Initiation 303 7.2.8.2 GTPase Switch Regulates Ribosome Affinity of eIF5B and Governs Translational Efficiency 304 7.2.9 IRES-mediated Translation Initiation 308 7.2.10 Future Prospects 310 References 313 8 The Elongation Cycle 323 Knud H. Nierhaus 8.1 Models of the Elongation Cycle 326 8.1.1 The Hybrid-site Model for Elongation 326 8.1.2 The Allosteric Three-site Model (????–???? Model; Reciprocal Coupling between the A- and E-sites) 329 Met i Met i X Contents 8.2 Decoding and A-site Occupation 333 8.2.1 Some General Remarks about Proofreading 333 8.2.2 Discrimination against Noncognate aa-tRNAs 333 8.2.3 Decoding of an aa-tRNA (Cognate versus Near-cognate aa-tRNAs) 337 8.2.4 Roles of EF-Tu 341 8.2.5 Mimicry at the Ribosomal A-site 341 8.2.5 Translational Errors 342 8.3 The PTF Reaction 345 8.3.1 A Short Intermission: Two Enzymatic Principles of PTF Activity 348 8.3.1.1 Chemical Concept: A Transient Covalent Bond between Active Center and Substrate(s) 348 8.3.1.2 Physical Concept: The Template Model 350 8.3.2 Data from the Crystal Structures 352 8.3.3 Why both the Physical and Chemical Concepts for Peptide-bond Formation? 355 8.4 The Translocation Reaction 355 8.4.1 Conservation in the Elongation Factor-G Binding Site 356 8.4.2 Dynamics within the Ribosome 359 References 363 9 Termination and Ribosome Recycling 367 Daniel N. Wilson 9.1 Introduction 367 9.2 Stop Codon Recognition and Release of the Nascent Polypeptide Chain 368 9.3 The Bacterial Class I Decoding Release Factors 369 9.3.1 The Structure of RF2 and Translational Mimicry 369 9.3.2 The Two-domain Functional Model for RF2 371 9.3.3 Identifying Functional Important Regions within the Decoding RFs 371 9.3.4 Codon Recognition Domain of Bacterial RFs: the Termination Signal 374 9.3.5 Codon Recognition Domain of Bacterial RFs: the “Tripeptide Motif” 375 9.3.6 Peptidyl-tRNA hydrolase function of bacterial RFs: domain III and the GGQ motif 376 9.3.7 Large Conformational Changes Associated with RF2 Binding to the Ribosome 379 9.3.8 The Trigger for RF-mediated Release of the Nascent Chain and the Outcome 383 9.4 Eukaryotic Class I Termination Factors 384 9.4.1 Stop-codon Recognition is Associated with Domain I of eRF1 386 Contents XI 9.4.2 eRF1-mediated Polypeptide Release 388 9.5 Dissociation of the Post-termination Complex 388 9.5.1 Eubacterial RF3 Dissociates the Class I Termination Factors 388 9.5.2 Eukaryotic RF3: Dissociation versus Delivery of eRF1 390 9.6 Ribosome Recycling 391 9.6.1 RRF Mediates Ribosome Recycling in Eubacteria 391 References 392 10 The Mechanism of Recoding in Pro- and Eukaryotes 397 Elizabeth S. Poole, Louise L. Major, Andrew G. Cridge, and Warren P. Tate 10.1 Introduction 397 10.2 Maintaining Decoding Accuracy and the Reading Frame 398 10.3 The Use of a Stop Signal for both Elongation and Termination of Protein Synthesis 399 10.4 The Mechanism for Sec Incorporation at UGA Sites in Bacterial mRNAs 399 10.4.1 The Gene Products 400 10.4.2 The Mechanism of Sec Incorporation 401 10.4.3 The Competition between Sec Incorporation and Canonical Decoding of UGA by RF2 401 10.5 Mechanism for Sec Incorporation at UGA Sites in Eukaryotic and Archaeal mRNAs 403 10.5.1 The Gene Products 403 10.5.2 The Mechanism of Sec Incorporation at Specific UGA Stop Codons 404 10.6 Why does Recoding Occur at Stop Signals? 404 10.6.1 The Stop Signal of Prokaryotic Genomes – Engineered for High Efficiency Decoding? 406 10.6.2 The Stop Signal of Eukaryotic Genomes – Diversity Contributes to Recoding 411 10.7 Readthrough of a Stop Signal: Decoding Stop as Sense 413 10.8 Bypassing of a Stop Codon: ‘Free-wheeling’ on the mRNA 415 10.9 Frameshifting Around Stop or Sense Codons 417 10.9.1 Forward Frameshifting: the +1 Event 418 10.9.2 Programed –1 Frameshifting: A Common Mechanism used by Many Viruses During Gene Expression 420 10.10 Conclusion 424 References 426 11 Regulation of Ribosome Biosynthesis in Escherichia coli 429 Madina Iskakova, Sean R. Connell, and Knud H. Nierhaus Overview of Ribosome Biosynthesis Regulation 429 XII Contents 11.1 Regulation of rRNA Synthesis 430 11.1.1 Organization of rRNA Operons and Elements of rRNA Promoters 430 11.1.2 Models for rRNA Regulation 434 11.1.3 Stringent Response 435 11.2 Regulation of r-protein Synthesis 438 11.2.1 Some General Remarks 438 11.2.2 Various Models for r-protein Regulation 441 11.2.2.1 spc operon 441 11.2.2.2 S10 operon 441 11.2.2.3 α operon 443 11.2.2.4 str operon 443 11.2.2.5 IF3 operon 444 11.3 Conclusion 445 References 446 12 Antibiotics and the Inhibition of Ribosome Function 449 Daniel N. Wilson 12.1 Introduction 449 12.1.1 The Inhibition of Protein Synthesis in Bacteria 449 12.2 Inhibitors of Initiation 453 12.2.1 Kasugamycin 456 12.2.2 Edeine 457 12.2.3 Pactamycin 459 12.2.4 Evernimicin and Avilamycin 460 12.2.5 Antibiotic Inhibitors of Ribosome Assembly 462 12.3 Inhibitors of the Elongation Cycle 464 12.3.1 Antibiotic Action and A-site Occupation 465 12.3.1.1 Tetracycline: An Inhibitor of A-site Occupation 465 12.3.1.2 Antibiotics Affecting the Fidelity of Translation 468 12.3.1.3 Inhibitors of EF-Tu-mediated Reactions 475 12.3.2 Inhibitors of Peptide-bond Formation and Nascent Chain Progression 480 12.3.2.1 Puromycin and Blasticidin S mimic the CCA end of tRNAs 480 12.3.2.2 Sparsomycin Prevents A-site Binding and Stimulates P-site Binding 483 12.3.2.3 Antibiotic Overlap in the PTF Center: chloramphenicol, Anisomycin and the Lincosamides 484 12.3.2.4 Blocking the Progression of the Nascent Chain by the Macrolide Antibiotics 488 12.3.2.5 Streptogramins 494 12.3.2.6 New Classes of Translation Inhibitors; the Oxazolidinones and Novel Ribosome Inhibitors 496 Contents XIII 12.3.3 Translocation Inhibitors 499 12.3.3.1 Thiostrepton and Micrococcin 499 12.3.3.2 Viomycin Blocks Coupled GTPase Activity 502 12.3.3.3 Spectinomycin Interferes with EF-G Binding 503 12.3.3.4 Fusidic Acid is the Counterpart of Kirromycin 504 12.4 Inhibitors of Termination, Recycling and trans-Translation 506 12.4.1 Termination 507 12.4.2 Recycling 507 12.4.3 Trans-translation 508 12.5 Mechanisms Causing Drug Resistance 508 12.5.1 Modification of the Antibiotic 509 12.5.2 Blockage of Transport (without Modification of the Drug) 509 12.5.3 Overproduction of the Inhibited Substrate (Target Dilution) 509 12.5.4 Bypassing or Replacement of the Inhibited Reaction 510 12.5.5 Alteration of the Target Site 510 12.5.6 Active Protection of the Target by a Third Component 511 12.6 Future Perspectives 512 References 513 13 The Work of Chaperones 529 Jean–Hervé Alix 13.1 From The Levinthal Paradox To The Anfinsen Cage 529 13.2 The Folding Machines 532 13.2.1 The Trigger Factor (TF) 532 13.2.2 The DnaK/DnaJ/GrpE System 532 13.2.3 The GroEL/GroES System 535 13.2.4 Other Chaperones 539 13.2.4.1 HSP90 539 13.2.4.2 Clp/HSP100 Family 539 13.2.4.3 DegP 540 13.2.4.4 Periplasmic Chaperones 540 13.2.4.5 Pili Chaperones 541 13.2.4.6 Small HSPs 541 13.2.4.7 Endoplasmic Reticulum (ER) Chaperones 543 13.2.4.8 Intramolecular Chaperones 543 13.3 Chaperone Networks 543 13.3.1 De novo Protein Folding 543 13.3.2 Protein Disaggregation 545 13.3.3 Posttranslational Quality Control 545 13.4 Chaperones and Stress 547 13.4.1 The Heat-shock Response and its Regulation 547 XIV Contents 13.4.2 Thermotolerance 548 13.4.3 Who Detects Stress? 548 13.5 Assembly and Disassembly of Macromolecular Complexes 549 13.6 Protein Translocation Across Membranes 550 13.7 New Horizons in Chaperone Research 551 13.7.1 HSP90 and the Pandora’s Box of Hidden Mutations 551 13.7.2 Chaperones and Prions 551 13.7.3 Chaperones and Ribosome Biogenesis 552 13.7.4 RNA Chaperones 553 13.7.5 Chemical Chaperones 553 13.7.6 Medical implications 553 13.7.7 Chaperoning the chaperones 553 References 554 Index 563