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RNA Polymerases as Molecular Motors [Kietas viršelis]

Edited by (Institut Pasteur, France), Contributions by , Contributions by , Edited by (Institut Jacques Monod, France), Series edited by (The National Institute of Diabetes and Digestive and Kidney Diseases, USA), Contributions by (Jacobs University), Contributions by (University of Cambridge), Series edited by (University of Dun), Series edited by , Series edited by (University of London, UK)
  • Formatas: Hardback, 331 pages, aukštis x plotis: 234x156 mm, weight: 665 g, No
  • Serija: RSC Biomolecular Sciences Volume 16
  • Išleidimo metai: 10-Mar-2009
  • Leidėjas: Royal Society of Chemistry
  • ISBN-10: 0854041346
  • ISBN-13: 9780854041343
Kitos knygos pagal šią temą:
  • Formatas: Hardback, 331 pages, aukštis x plotis: 234x156 mm, weight: 665 g, No
  • Serija: RSC Biomolecular Sciences Volume 16
  • Išleidimo metai: 10-Mar-2009
  • Leidėjas: Royal Society of Chemistry
  • ISBN-10: 0854041346
  • ISBN-13: 9780854041343
Kitos knygos pagal šią temą:
The cell can be viewed as a 'collection of protein machines' and understanding these molecular machines requires sophisticated cooperation between cell biologists, geneticists, enzymologists, crystallographers, chemists and physicists. To observe these machines in action, researchers have developed entirely new methodologies for the detection and the nanomanipulation of single molecules. This book, written by expert scientists in the field, analyses how these diverse fields of research interact on a specific example - RNA polymerase. The book concentrates on RNA polymerases because they play a central role among all the other machines operating in the cell and are the target of a wide range of regulatory mechanisms. They have also been the subject of spectacular advances in their structural understanding in recent years, as testified by the attribution of the Nobel prize in chemistry in 2006 to Roger Kornberg. The book focuses on two aspects of the transcription cycle that have been more intensively studied thanks to this increased scientific cooperation - the recognition of the promoter by the enzyme, and the achievement of consecutive translocation steps during elongation of the RNA product. Each of these two topics is introduced by an overview, and is then presented by worldwide experts in the field, taking the viewpoint of their speciality. The overview chapters focus on the mechanism-structure interface and the structure-machine interface while the individual chapters within each section concentrate more specifically on particular processes-kinetic analysis, single-molecule spectroscopy, and termination of transcription, amongst others. Specific attention has been paid to the newcomers in the field, with careful descriptions of new emerging techniques and the constitution of an atlas of three-dimensional pictures of the enzymes involved. For more than thirty years, the study of RNA polymerases has benefited from intense cooperation between the scientific partners involved in the various fields listed above. It is hoped that a collection of essays from outstanding scientists on this subject will catalyse the convergence of scientific efforts in this field, as well as contribute to better teaching at advanced levels in Universities.

This book, written by expert scientists in the field, analyses how diverse fields of scientific research interact on a specific example - RNA polymerases.
There and Back Again: A Structural Atlas of RNAP 1
Seth Darst
Part I From Promoter Recognition to Promoter Escape
Chapter 1 Where it all Begins: An Overview of Promoter Recognition and Open Complex Formation
Stephen Busby, Annie Kolb and Henri Buc
1.1 Gene Expression as a Driver of Life
13
1.2 Escherichia coli RNA Polymerase
14
1.3 Promoters and Core Promoter Elements
17
1.4 Biochemistry: It Works with RNA Polymerase!
19
1.5 Biochemistry of Promoter Regulation
22
1.6 A Word about the Intracellular Environment
26
1.7 Coupling Transcription to Changes in a Complex Environment
27
1.8 A Global View of the RNA Polymerase Economy
30
1.9 The Real World, Emergency Procedures and RNA Polymerase
32
1.10 This is just the Beginning!
33
References
34
Chapter 2 Opening the DNA at the Promoter; The Energetic Challenge
Bianca Sclavi
2.1 Introduction
38
2.2 Structural Characterization
42
2.2.1 Crystal Structure of the Holoenzyme
42
2.2.2 Crystal Structure of the Holoenzyme with Fork junction DNA
43
2.2.3 Structural Model of the Open Complex
45
2.3 Physical Characterization and Structure of the Intermediates
47
2.4 Finding the Promoter. Induced fit and Indirect Sequence Recognition
48
2.5 Formation of the Closed Complex
49
2.5.1 On a Unique Structure of the Closed Complex
49
2.5.2 Role of Upstream Contacts for the Stability of the Closed Complex and in Leading the Complex Towards Subsequent Isomerization
50
2.6 The First Isomerization Step. The role of Sigma, Formation of Specific Interactions
51
2.6.1 Upstream Contacts
51
2.6.2 Nucleation of the Single Stranded Region and its Propagation
52
2.6.3 Phasing of –10 and –35 Regions, the Role of the Spacer
54
2.6.4 Probing Possible Sequential Linear Pathways by the use of Temperature
54
2.6.5 Specific Protein Domains Destabilize the Intermediates in the Pathway
57
2.6.6 Overstabilization is sometimes used as a Regulatory Mechanism
59
2.7 Formation of Transcriptionally Active Open Complex and the Rate-limiting Step: Protein Conformational Changes or DNA Melting?
60
2.8 A Rugged Energy Landscape
61
2.9 Summary and Conclusions
62
Acknowledgements
63
References
63
Chapter 3 Intrinsic In vivo Modulators: Negative Supercoiling and the Constituents of the Bacterial Nucleoid
Georgi Muskhelishvili and Andrew Travers
3.1 Introduction
69
3.2 DNA Superhelicity – Structures and Implications
69
3.3 Structure of the Bacterial Nucleoid
72
3.4 Supercoiling Utilization
75
3.5 Promoter Structure and DNA Supercoiling
78
3.6 Role of RNA Polymerase Composition
80
3.6.1 Exchange of σ Factors
81
3.6.2 Auxiliary Subunits
82
3.6.3 Role of ppGpp
82
3.7 Model and Implications
82
3.8 Causality
85
3.9 Cooperation with Nucleoid Associated Proteins
86
3.10 Conversion of Supercoil Energy into Genomic Transcript Patterns
87
3.11 Conclusions
88
References
88
Chapter 4 Transcription by RNA Polymerases: From Initiation to Elongation, Translocation and Strand Separation
Thomas A Steitz
4.1 Introduction
96
4.2 Transition from the Initiation to the Elongation Phase
98
4.2.1 T7 RNA Polymerase
98
4.2.2 Multi-subunit RNA Polymerases
103
4.3 Translocation and Strand Separation
103
4.3.1 T7 RNA Polymerase
103
4.3.2 Multi-subunit Cellular RNAPs
108
4.4 Additional Similarities between Single and Multi-subunit Polymerases
112
Acknowledgements
113
References
113
Chapter 5 Single-molecule FRET Analysis of the Path from Transcription Initiation to Elongation
Achillefs N. Kapanidis and Shimon Weiss
5.1 Introduction
115
5.2 Methodology: FRET and ALEX Spectroscopy
117
5.3 Transcription Mechanisms Addressed using Single-molecule FRET and ALEX
124
5.4 Fate of Initiation Factor 670 in Elongation
126
5.5 Mechanism of Initial Transcription
133
5.6 Kinetic Analysis of Initial Transcription and Promoter Escape
141
5.7 Comparison of FRET Approaches with Magnetic-trap Approaches
142
5.8 Future Prospects
145
5.9 Summary
147
Acknowledgements
148
References
148
Chapter 6 Real-time Detection of DNA Unwinding by Escherichia coli RNAP: From Transcription Initiation to Termination
Terence R. Strick and Andrey Revyakin
6.1 Introduction
157
6.2 Twist Deformations at the Promoter
158
6.3 Magnetic Trapping and Supercoiling of a Single DNA Molecule
159
6.3.1 General Features of the Magnetic Trap
159
6.3.2 Calibrating the DNA Sensor
161
6.4 Characterization of RPo at two Canonical Promoters
166
6.4.1 Structural Characterization of RPo
167
6.4.2 Kinetic Analysis of RPo
168
6.4.3 Effect of Environmental Variables on Kinetics of RPo
171
6.5 Promoter Escape by DNA Scrunching
172
6.5.1 Characterization of DNA Scrunching during Abortive Initiation
173
6.5.2 Characterization of DNA Scrunching during Promoter Escape
176
6.6 Future Directions
182
References
183
Part II Transcription Elongation and Termination
Interlude: The Engine and the Brake
Henri Buc and Terence Strick
I.1 Introduction
191
I.2 The Engine
193
I.2.1 Mechano-chemical Coupling at the Catalytic Site
194
I.2.2 Coupling between Translocation and Topology
200
I.3 The Brake
201
I.4 Conclusions
202
References
204
Chapter 7 Substrate Loading, Nucleotide Addition, and Translocation by RNA Polymerase
Jinwei Zhang and Robert Landick
7.1 Basic Mechanisms of Transcript Elongation by RNA Polymerase
206
7.1.1 Active-site Features of an Elongation Complex
207
7.1.2 The Nucleotide Addition Cycle
207
7.1.3 Pyrophosphorolysis and Transcript Cleavage
208
7.1.4 Regulation of Transcript Elongation by Pauses
211
7.2 Structural Basis of NTP Loading and Nucleotide Addition
212
7.2.1 Bridge-helix-centric Models of Nucleotide Addition and Translocation
213
7.2.2 Central Role of the Trigger Loop in Nucleotide Addition and Pausing
216
7.2.3 A Trigger-loop Centric Mechanism for Substrate Loading and Catalysis
217
7.3 Models of Translocation: Power-stroke versus Brownian Ratchet
219
7.3.1 Key Distinctions between Power-stroke and Brownian Ratchet Models
220
7.3.2 Power-stroke Models
221
7.3.3 Brownian Ratchet Models
221
7.3.4 Technical Outlook in Detecting the Precise Translocation Register
222
7.4 Kinetic Models of Nucleotide Addition
223
7.4.1 Allosteric NTP Binding Model
223
7.4.2 NTP-driven Translocation Model
226
7.4.3 Two-pawl Ratchet Model
226
7.4.4 Biophysical Models for Transcript Elongation
227
7.5 Technological Advances in Studies of Transcript Elongation
228
7.6 Concluding Remarks
228
References
229
Chapter 8 Regulation of RNA Polymerase through its Active Center
Sergei Nechaev, Nikolay Zenkin and Konstantin Severinov
8.1 Introduction
236
8.2 Regulatory Checkpoints of the RNAP Active Center
237
8.2.1 Versatility of the Active Center. How many Metals are Enough?
237
8.2.2 Delivery of NTPs to the Active Center. How many Channels are Enough?
238
8.2.3 Nucleotide Selection. How many Steps are Enough?
241
8.3 Regulators that Target the RNAP Active Center
244
8.3.1 Small-molecule Effectors of RNAP
244
8.3.2 Regulation of RNAP by Proteins that Bind in the Secondary Channel
250
8.4 Transcript Proofreading
254
8.4.1 Transcriptional Proofreading through Pyrophosphorolysis
255
8.4.2 Proofreading by Transcript Cleavage Factors
256
8.4.3 Transcript-assisted Proofreading. A New Class of Ribozymes?
257
8.5 Conclusions
258
Acknowledgements
259
References
259
Chapter 9 Kinetic Modeling of Transcription Elongation
Lu Bai, Alla Shundrovsky and Michelle D. Wang
9.1 Introduction
263
9.2 Background
265
9.3 Mechano-chemical Coupling of Transcription
266
9.3.1 NTP Incorporation Cycle
266
9.3.2 NTP Incorporation Pathway in a Simple Brownian Ratchet Model
266
9.3.3 NTP Incorporation Pathways in more Elaborate Brownian Ratchet Models
267
9.3.4 NTP Incorporation Pathway in a Power-stroke Model
269
9.3.5 Elongation Kinetics
270
9.3.6 Force-dependent Elongation Kinetics
271
9.4 Sequence-dependent RNAP Kinetics
274
9.4.1 Thermodynamic Analysis of the TEC
274
9.4.2 Sequence-dependent NTP Incorporation Kinetics in Brownian Ratchet Models
275
9.4.3 Model Predictions of Pause Locations, Kinetics and Mechanisms
277
Acknowledgements
278
References
278
Chapter 10 Mechanics of Transcription Termination
Evgeny Nudler
10.1 Introduction
281
10.2 Structure/Function Overview of the Elongation Complex (EC)
282
10.3 Mechanism of Intrinsic Termination
283
10.3.1 The Pausing Phase
285
10.3.2 The Termination Phase
287
10.4 Mechanism of Rho Termination
294
10.5 Summary
295
10.6 Concluding Remarks
296
References
296
Conclusion Past, Present, and Future of Single-molecule Studies of Transcription
Carlos Bustamante and Jeffrey R. Moffitt
C.1 Introduction
302
C.2 RNA Polymerase as a Molecular Machine: Past and Present
303
C.3 Technical Developments in Optical Tweezers
307
C.4 A Look into the Future
309
References
312
Subject Index 315
Professor Henri C Buc, Institut Pasteur, Paris, France has a special interest in the enzymology of nucleic acid polymerases. Terence R Strick, Centre National de la Recherche Scientifique, Paris, France has a special interest in single-molecule enzymology.