Download or read book Studies of Key Regions of Escherichia Coli RNA Polymerase and Promoter DNA in Transcription Initiation written by and published by . This book was released on 2015 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Key Conformational Changes of Escherichia Coli RNA Polymerase and Promoter DNA in Transcription Initiation written by and published by . This book was released on 2012 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial RNA polymerase (RNAP) is a multi-subunit (α2, β, β', ω, and σ) enzyme that synthesizes RNA from a DNA template. My research has focused on the mechanism of formation of transcriptionally-competent open promoter complexes by E. coli RNAP, using the λPR promoter as a model system. Using chemical footprinting and filter binding techniques, I have tested our mechanistic proposals that RNAP bends duplex promoter DNA into the active site cleft, opens 13 DNA base pairs in the cleft and loads the +1 base of the template strand into the active site, and then assembles and tightens several mobile protein elements on downstream duplex DNA as the discriminator region ( -6 to -2) of the nontemplate strand rearranges. My fast permanganate and hydroxyl radical footprinting data demonstrate that the first kinetically significant intermediate I1 is unambiguously a closed complex in which the downstream duplex has been inserted in and is periodically protected by the RNAP cleft; further, the nontemplate strand of the I2 intermediate is globally less protected than in the final open complexes. Two RNAP variants (one a partial deletion of the β' jaw (∆JAW), and the other a deletion of region 1.1 of σ70 (∆1.1)) are found to associate with λPR promoter DNA slower than wild-type (WT) RNAP complexes. My hydroxyl radical footprints and dissociation kinetic studies on ∆JAW at full length or downstream-truncated promoter DNA indicate that the jaw forms an interface with the far-downstream duplex (+10 to +20) after DNA opening. Urea-dependence dissociation kinetic studies show that folding/assembly of the jaw contributes to stabilization of the late steps of open complex formation, likely in the conversion of I3 to RPo. Kinetic dissociation studies indicate that the lifetime of the ∆1.1 open complex is greatly extended relative to WT RNAP. Heparin increases the dissociation rate of ∆1.1 but not WT open complexes. Furthermore, at high heparin concentrations the dissociation rate of ∆1.1 exceeds that of WT open complexes, suggesting that region 1.1 of σ70 is required to displace one or both strands of the initiation bubble in the cleft in dissociation of WT open complexes.
Download or read book The Lac 45 Region CAP and RNA Polymerase written by Richard J. Noel and published by . This book was released on 1998 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cryo EM Part A Sample Preparation and Data Collection written by and published by Academic Press. This book was released on 2010-09-30 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Cryo-EM Part A: Sample Preparation and Data Collection is dedicated to a description of the instruments, samples, protocols, and analyses that belong to cryo-EM. It emphasizes the relatedness of the ideas, instrumentation, and methods underlying all cryo-EM approaches, which allow practitioners to easily move between them. Within each section, the articles are ordered according to the most common symmetry of the sample to which their methods are applied. - Includes time-tested core methods and new innovations applicable to any researcher - Methods included are useful to both established researchers and newcomers to the field - Relevant background and reference information given for procedures can be used as a guide
Download or read book Regulation of Gene Expression in Escherichia coli written by E. C. C. Lin and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 1010 pages. Available in PDF, EPUB and Kindle. Book excerpt: This up-to-date guide focuses on the understanding of key regulatory mechanisms governing gene expression in Escherichia coli. Studies of E. coli not only provide the first models of gene regulation, but research continues to yield different control mechanisms.
Download or read book In Vitro Studies of the Transcript Initiation Process by E Coli RNA Polymerase written by Nam Viet Vo and published by . This book was released on 1998 with total page 658 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book An Immunological Approach to Studying Transcription Initiation in E Coli written by Scott Allan Lesley and published by . This book was released on 1989 with total page 442 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Regulation of Transcription of the Gene for the Sigma Subunit of E Coli RNA Polymerase by a Heat Shock Promoter written by Wayne Emery Taylor and published by . This book was released on 1983 with total page 450 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Fluorescence detected Intermediates in Open Complex Formation by E coli RNA Polymerase written by Munish Chhabra and published by . This book was released on 2019 with total page 254 pages. Available in PDF, EPUB and Kindle. Book excerpt: In transcription, the key first steps of gene expression, the enzyme RNA polymerase (RNAP) catalyzes the synthesis of RNA (ribonucleic acid) complementary to one strand of a DNA (deoxyribonucleic acid) template. All steps of transcription, and particularly those of initiation at the start site region of promoter DNA, are highly regulated by promoter sequences, transcription factors, and other environmental conditions. In initiation, RNA polymerase binds specifically to double-stranded promoter DNA and operates on it as a biophysical machine to open 13-14 bp including the transcription start site, place the template strand of the DNA in its active site, and initiate the synthesis of RNA transcripts when provided with nucleotide triphosphates (NTP). There is a plethora of structural information available about RNAP and the open promoter complex (OC), but the mechanism of OC formation is not yet understood. In my thesis research, I have developed and applied several novel real-time biophysical fluorescence assays that use DNA-DNA FRET (energy transfer) between cyanine (Cy3 and Cy5) dyes located at far upstream (-100 bp from the start site) and downstream (+14 bp from the start site) positions, and RNAP-DNA PIFE (enhanced fluorescence of these individual dyes) to determine the kinetics and mechanism of OC formation by bacterial E.coli RNAP and [lowercase lambda]PR promoter DNA. First, using equilibrium FRET, another lab member and I showed that the upstream region of promoter DNA bends and wraps around RNAP in the OC and in an ensemble of closed complexes (CC) stabilized by low temperature (2oC). Then I used fast kinetic (stopped-flow) studies on this system to discover the mechanism by which bending and wrapping of far-upstream promoter DNA facilitate bending the downstream promoter region into the active site cleft of RNAP (Figure) prior to DNA opening. This research can be translated to understand the action of different broad-spectrum antibiotics targeting the different intermediates formed in the process. In the third part of the thesis, I describe kinetic-mechanistic experiments with Lipiarmycin (LpM), an active ingredient of Fidaxomicin antibiotic (FDA-approved for recurrent Clostridium difficile associated diarrhea infection in adults), using FRET and PIFE kinetic assays. I find that LpM acts on a relatively late CC intermediate in which the clamp is open (I1M) forming an off-pathway intermediate (I1M-LpM) in the mechanism of OC formation. My findings regarding the mechanism of OC formation and LpM inhibition forms a basis to understand the sites of action and effects of transcriptional activators and repressors that modulate the kinetics of transcription initiation to achieve gene regulation.
Download or read book Studies on the Regulation of Ribosomal RNA Transcription in Escherichia Coli written by Cathleen Ann Josaitis and published by . This book was released on 1995 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Characterization by DNA Footprinting of Intermediates Involved in Transcription Initiation by Escherichia Coli E Sigma70 RNA Polymerase at the Lambda PR Promoter written by Marni Raffaelle and published by . This book was released on 2003 with total page 242 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book An Analysis of the sigma core Interface in E Coli written by Meghan M. Sharp and published by . This book was released on 2001 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biology for AP Courses written by Julianne Zedalis and published by . This book was released on 2017-10-16 with total page 1923 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology for AP® courses covers the scope and sequence requirements of a typical two-semester Advanced Placement® biology course. The text provides comprehensive coverage of foundational research and core biology concepts through an evolutionary lens. Biology for AP® Courses was designed to meet and exceed the requirements of the College Board’s AP® Biology framework while allowing significant flexibility for instructors. Each section of the book includes an introduction based on the AP® curriculum and includes rich features that engage students in scientific practice and AP® test preparation; it also highlights careers and research opportunities in biological sciences.
Download or read book Characterization by DNA Footprinting of Intermediates in Transcription Initiation by Escherichia Coli E sigma 70 RNA Polymerase at the lambdal PR Promoter written by Maria Lee Craig and published by . This book was released on 1996 with total page 356 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Transcription Initiation at the Escherichia Coli Galactose Operon Promoter Region written by Sreenivasan Ponnambalam and published by . This book was released on 1988 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Interaction of E Coli RNA Polymerase with Lambda Phage PR Promoter written by Won-Chul Suh and published by . This book was released on 1993 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Mechanism of Interaction of E Coli RNA Polymerase with Bacteriophage and Bacterial Promoters written by Sigrid Leirmo and published by . This book was released on 1989 with total page 324 pages. Available in PDF, EPUB and Kindle. Book excerpt:
