Rna Polymerases As Molecular Motors (Rsc Biomolecular Sciences),Used

Excerpt. Reprinted by permission. All rights reserved.RNA Polymerases as Molecular MotorsBy Henri Buc, Terence Strick The Royal Society of ChemistryCopyright 2009 The Royal Society of ChemistryAll rights reserved.ISBN: 9780854041343ContentsThere and Back Again: A Structural Atlas of RNAP Seth Darst, 1,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,Chapter 2 Opening the DNA at the Promoter; The Energetic Challenge Bianca Sclavi,Chapter 3 Intrinsic In vivo Modulators: Negative Supercoiling and the Constituents of the Bacterial Nucleoid Georgi Muskhelishvili and Andrew Travers,Chapter 4 Transcription by RNA Polymerases: From Initiation to Elongation, Translocation and Strand Separation Thomas A Steitz,Chapter 5 Singlemolecule FRET Analysis of the Path from Transcription Initiation to Elongation Achillefs N. Kapanidis and Shimon Weiss,Chapter 6 Realtime Detection of DNA Unwinding by Escherichia coli RNAP: From Transcription Initiation to Termination Terence R. Strick and Andrey Revyakin,Part II Transcription Elongation and Termination,Interlude The Engine and the Brake Henri Buc and Terence Strick,Chapter 7 Substrate Loading, Nucleotide Addition, and Translocation by RNA Polymerase Jinwei Zhang and Robert Landick,Chapter 8 Regulation of RNA Polymerase through its Active Center Sergei Nechaev, Nikolay Zenkin and Konstantin Severinov,Chapter 9 Kinetic Modeling of Transcription Elongation Lu Bai, Alla Shundrovsky and Michelle D. Wang,Chapter 10 Mechanics of Transcription Termination Evgeny Nudler,Conclusion Past, Present, and Future of Singlemolecule Studies of Transcription Carlos Bustamante and Jeffrey R. Moffitt,Subject Index, 315,CHAPTER 1Where it all Begins: An Overview of Promoter Recognition and Open Complex FormationSTEPHEN BUSBY, ANNIE KOLB AND HENRI BUC1.1 Gene Expression as a Driver of LifeThe importance of transcription, the process by which information encoded in DNA is copied into RNA, cannot be overstated. As soon as the dogma that DNA makes RNA makes protein was established, the hunt was on for the machinery that orchestrates transcription. Thus, in the late 1950s and early 1960s, classical methods of protein fractionation were used to identify DNAdependent RNA polymerase activity. Remarkably, in parallel, primarily using Escherichia coli genetics, Jacob, Monod and their colleagues were discovering gene regulatory proteins and establishing the paradigm that gene transcription was the key point at which gene regulation is effected. Thus, right from the start, Escherichia coli K12 was established as the model system to use and, with the benefit of hindsight, it is easy to see now how 40 years of amazing progress was sparked by the fusion of two very different worlds, one populated by the biochemists and the other by the bacterial geneticists. Put very simply, the stories in this book expand on how the biochemistry explains the genetics and how the genetics gives reason to the biochemistry. The crucial discoveries that set the scene for these stories were made in the late 1960s: the characterization of the single multisubunit RNA polymerase in E. coli, the discovery of promoters and terminators, and the realization that different genes are transcribed at widely differing frequencies. The pace accelerated with the arrival of cloning and DNA sequencing in the 1970s and indepth studies of how different promoters are regulated exploiting increasingly sophisticated methodologies. The arrival of whole genome sequences in the late 1990s led to the complete catalogue of the different players and attempts to integrate our knowledge with systems biology approaches. And finally, the structural biologists have provided us with models of many of the major players, including the multisubunit RNA polymerases, the principal topic of this book.1.2 Esche