The Mechanism of NusG-Mediated Transcription-Translation Coupling and The Role of RacR in Transcription Regulation in Escherichia Coli PDF Download
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Author: Elizabeth Jean Bailey
Publisher:
ISBN:
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Languages : en
Pages :
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Book Description
Transcription and translation are essential cellular processes that are coupled in bacteria. Though it was well-known that the rate of translation matches the rate of transcription, only in 2010 did evidence suggest direct physical coupling between the transcribing RNA polymerase (RNAP) and the translating ribosome. Nuclear magnetic resonance spectroscopy data showed that the RNAP-binding, transcription factor NusG could bind to the small ribosomal subunit protein, S10, through its C-terminal domain, thus, suggesting a model in which NusG simultaneously binds the transcription and translation machineries. In Chapter Two, I describe my investigations of the mechanism through which NusG-mediated transcription-translation coupling is established in bacteria, and how this coupling is regulated during gene expression. Specifically, I employed cell extract-based luciferase assays and purified C-terminal NusG mutants to show that the NusG N-terminal domain (NTD) and NusG F165A both inhibit transcription.
Author: Elizabeth Jean Bailey
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Transcription and translation are essential cellular processes that are coupled in bacteria. Though it was well-known that the rate of translation matches the rate of transcription, only in 2010 did evidence suggest direct physical coupling between the transcribing RNA polymerase (RNAP) and the translating ribosome. Nuclear magnetic resonance spectroscopy data showed that the RNAP-binding, transcription factor NusG could bind to the small ribosomal subunit protein, S10, through its C-terminal domain, thus, suggesting a model in which NusG simultaneously binds the transcription and translation machineries. In Chapter Two, I describe my investigations of the mechanism through which NusG-mediated transcription-translation coupling is established in bacteria, and how this coupling is regulated during gene expression. Specifically, I employed cell extract-based luciferase assays and purified C-terminal NusG mutants to show that the NusG N-terminal domain (NTD) and NusG F165A both inhibit transcription.
Author: Expery O. Omollo
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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RNA polymerase (RNAP) often pauses during transcription to regulate gene expressionacross all life forms. This pausing behavior is regulated by specific DNA sequences, RNA structures, and transcription factors. This work investigates the bacterial RNAP pausing mechanism, particularly at hairpin-stabilized pauses, and how NusG and NusA proteins modulate RNAP pausing. Additionally, this study also examines the mechanism of intrinsic transcription termination in bacteria and how it's modulated by NusG and NusA. Both hairpin-stabilized pausing and intrinsic termination begin when RNAP pauses momentarily to enable the nascent RNA to fold inside the exit channel. However, these processes differ in the proximity and base composition of the hairpin structure to the RNA 3' end. Pause hairpins are positioned 11 or 12 bases away from the RNA 3' end, with non-specific bases in between whereas terminator hairpins form 7 or 8 bases away, with a U-tract in the RNA of the RNA-DNA hybrid. Using biochemical approaches, and cryo-electron microscopy, this study demonstrates that the RNA exit channel widens to accommodate RNA hairpin formation. This expansion causes a mobile portion of RNAP to rotate relative to its static portion, adopting an inactive "swiveled state" that halts nucleotide incorporation. Although certain transcription factors can rescue swiveled and paused RNAP, this work reveals that NusA stabilizes RNAP in its swiveled and paused state. In contrast, NusG shows species-specific effects: in Mycobacterium tuberculosis, it stabilizes the swiveled and paused state, whereas in Escherichia coli, it reverses the swivel, promoting RNAP elongation. For RNAP paused at intrinsic terminators, this study shows that RNAP must rewind the transcription bubble to allow the terminator hairpin to fully form. A complete terminator hairpin triggers the release of RNA and then DNA. These findings define a fundamental structural mechanism of bacterial RNAP during hairpin-stabilized pausing and intrinsic termination, providing a broader understanding of transcription regulation.
Author: Marcel Geertz
Publisher:
ISBN:
Category :
Languages : en
Pages : 172
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Book Description
For understanding the concerted molecular interactions aiding into the assembly of cellular transcription programs it is essential to reveal a general mechanism which directs the transcription machinery to particular sets of gene promoters in a spatially and temporally ordered way. A global regulatory network involving nucleoid-associated proteins (NAPs), DNA topoisomerases and the components of RNA polymerase (RNAP) is implicated in this mechanism. While DNA supercoiling is a global regulator of gene transcription, in Escherichia coli the reorganisation of cellular transcription is associated with concerted alterations of two principal parameters: the composition of RNAP and the structural organisation of the nucleoid DNA, both of which change with growth. The mechanism of coupling between compositional alterations of NAPs, RNAP and topological changes of DNA remains unclear. Different facets of transcriptional regulation were studied to reveal this coupling mechanism. This work shows a determinative role of RNAP composition for the overall supercoiling level and reveals structural coupling between RNAP and the NAPs as a mechanism coordinating global transcription. This work further shows that the NAPs regulate the genomic distributions of DNA supercoils, whereas the sensing and utilization of the supercoils is in turn dependent on the composition of RNAP. For one of the NAPs, H-NS, the binding site consensus has been identified and the genomic transcript profiles were investigated to elucidate, how the genomic distributions of these sites can regulate supercoil dynamics. This work distinguishes the transcriptional regulatory network of functionally related genes from the network of spatially neighboring genes and shows their tight interdependence in organizing global transcription. In summary, this work provides novel insights in the organizational principles and understanding of molecular mechanisms underlying the coordination of bacterial gene expression.
Author: Smarajit Mondal
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Transcription in bacteria is regulated at the level of initiation, elongation and termination. Although the regulation of transcriptional initiation is well studied, the regulation of elongation and termination are not well understood. This thesis focuses on understanding the role of NusA on intrinsic termination and the role of NusG on RNA polymerase pausing using genomic, biochemical and computational analyses. Tight regulation of transcription termination is required to maintain proper levels of gene expression in bacteria, because termination failure abolishes operon boundaries, leading to misregulation of downstream genes. NusA is a negative transcription elongation factor that was known to cause a slight stimulation of termination at intrinsic terminators in vitro, but its impact on termination and global gene expression in vivo was not known. In this thesis, I describe the mapping of intrinsic terminators genome wide in B subtilis and measure the effect of NusA on the efficiency of these terminators in vivo using a novel high resolution 3' end-mapping technique coupled with mRNA profiling. Based on these studies, I report the existence of a subclass of previously unidentified pseudo-intrinsic terminators that are dependent on NusA for termination. Sequence comparison of different terminators reveals that weak hairpins and/or distal U-tract interruptions favors NusA-dependent termination, supporting a model in which NusA assists hairpin folding and slows down RNA polymerase near the termination window. These studies also revealed that readthrough of NusA-dependent terminators increases transcription of genes related to replication and DNA metabolism, suggesting a role of NusA in maintaining genome stability. I further show that nusA is autoregulated by a transcription attenuation mechanism that does not rely on antiterminator structures to prevent termination. Instead, NusA-stimulated termination in its 5'UTR dictates the extent of transcription into the operon. Another major focus of this thesis is to understand the regulation of transcription elongation by NusG-stimulated pausing of RNA polymerase. NusG is a positive elongation factor in E. coli that accelerates transcription by reducing the dwell time of RNA polymerase at pause sites. In B. subtilis, NusG stimulates pausing at positions U107 and U144 in the trp-leader transcript. NusG-stimulated pausing at U144 requires a short sequence in the non-template DNA strand and participates in the TRAP-dependent translation repression mechanism. In this thesis, I report the characterization of the NusG-stimulated U107 pause signal and show that disruption of the NusG recognition motif dramatically reduces pausing. These results suggest a mechanism in which RNA polymerase pausing at this site participates in the transcription attenuation mechanism by increasing additional time for TRAP binding to the nascent transcript.
Author: Benjamin Lewin
Publisher: Jones & Bartlett Publishers
ISBN: 1449655831
Category : Science
Languages : en
Pages : 832
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Book Description
The Second Edition of Lewin's Essential GENES continues to provide students with the latest findings in the field of molecular biology and molecular genetics. An exceptional new pedagogy enhances student learning and helps readers understand and retain key material like never before. New Concept and Reasoning Checks at the end of each chapter section, End of Chapter Questions and Further Readings for each chapter, and several categories of special topics boxes within each chapter expand and reinforce important concepts. The reorganization of topics in this edition allows students to focus more sharply on the key material at hand and improves the natural flow of course material. New end-of-chapter questions reviews major points in the chapter and allow students to test themselves on important course material. Important Notice: The digital edition of this book is missing some of the images or content found in the physical edition.
Author: Vishvanath Nene
Publisher: Springer Science & Business Media
ISBN: 3540740422
Category : Science
Languages : en
Pages : 253
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Book Description
Achievements and progress in genome mapping and the genomics of microbes supersede by far those for higher plants and animals, in part due to their enormous economic implication but also smaller genome size. In the post-genomic era, whole genome sequences of animal-associated microbes are providing clues to depicting the genetic basis of the complex host-pathogen relationships and the evolution of parasitism; and to improving methods of controlling pathogens. This volume focuses on a globally important group of intracellular prokaryotic pathogens which affect livestock animals. These include Brucella, Mycobacterium, Anaplasma and Ehrlichia, as well as the protozoan pathogens Cryptosporidium and Theileria, for which genome sequence data is available. Insights from comparative genomics of the microbes described provide clues to the adaptation involved in host-microbe interactions, as well as resources potentially useful for application in future research and product development.
Author: Kim Sneppen
Publisher: Cambridge University Press
ISBN: 1107061903
Category : Science
Languages : en
Pages : 353
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Book Description
An overview of current models of biological systems, reflecting the major advances that have been made over the past decade.
Author: Tilman Heise
Publisher:
ISBN: 9781071602317
Category : Human genetics
Languages : en
Pages : 314
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Book Description
This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones. Chapter 3 is available Open Access under a CC-BY 4.0 license via link.springer.com.
Author: Robert M Blumenthal
Publisher: World Scientific
ISBN: 9814494976
Category : Science
Languages : en
Pages : 419
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Book Description
This invaluable volume, written by an international group of scientists, presents an overview of the AdoMet-dependent methyltransferases, with special emphasis on structure-function relationships.S-adenosyl-L-methionine (AdoMet) is the second most commonly used enzyme cofactor after ATP. The AdoMet-dependent methyltransferases act on a wide variety of target molecules, including DNA, RNA, protein, polysaccharides, lipids and a range of small molecules.The well-conserved architecture of these enzymes, and the implications of this conservation for their evolutionary history, are major themes of this book. The thirteen chapters describe in detail the structures, enzyme kinetics and biological roles of the AdoMet-dependent methyltransferases from a wide range of cell types: plant, animal, bacterial and archaeal.
Author: Matthew Schneider-Mayerson
Publisher: U of Minnesota Press
ISBN: 1452961522
Category : Science
Languages : en
Pages : 475
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Book Description
Presents thirty novel terms that do not yet exist in English to envision ways of responding to the environmental challenges of our generation As the scale and gravity of climate change becomes undeniable, a cultural revolution must ultimately match progress in the realms of policy, infrastructure, and technology. Proceeding from the notion that dominant Western cultures lack the terms and concepts to describe or respond to our environmental crisis, An Ecotopian Lexicon is a collaborative volume of short, engaging essays that offer ecologically productive terms—drawn from other languages, science fiction, and subcultures of resistance—to envision and inspire responses and alternatives to fossil-fueled neoliberal capitalism. Each of the thirty suggested “loanwords” helps us imagine how to adapt and even flourish in the face of the socioecological adversity that characterizes the present moment and the future that awaits. From “Apocalypso” to “Qi,” “ ~*~ “ to “Total Liberation,” thirty authors from a range of disciplines and backgrounds assemble a grounded yet dizzying lexicon, expanding the limited European and North American conceptual lexicon that many activists, educators, scholars, students, and citizens have inherited. Fourteen artists from eleven countries respond to these chapters with original artwork that illustrates the contours of the possible better worlds and worldviews. Contributors: Sofia Ahlberg, Uppsala U; Randall Amster, Georgetown U; Cherice Bock, Antioch U; Charis Boke, Cornell U; Natasha Bowdoin, Rice U; Kira Bre Clingen, Harvard U; Caledonia Curry (SWOON); Lori Damiano, Pacific Northwest College of Art; Nicolás De Jesús; Jonathan Dyck; John Esposito, Chukyo U; Rebecca Evans, Winston-Salem State U; Allison Ford, U of Oregon; Carolyn Fornoff, U of Illinois at Urbana-Champaign; Michelle Kuen Suet Fung; Andrew Hageman, Luther College; Michael Horka, George Washington U; Yellena James; Andrew Alan Johnson, Princeton U; Jennifer Lee Johnson, Purdue U; Melody Jue, U of California, Santa Barbara; Jenny Kendler; Daehyun Kim (Moonassi); Yifei Li, NYU Shanghai; Nikki Lindt; Anthony Lioi, Juilliard School of New York; Maryanto; Janet Tamalik McGrath; Pierre-Héli Monot, Ludwig Maximilian U of Munich; Kari Marie Norgaard, U of Oregon; Karen O’Brien, U of Oslo, Norway; Evelyn O’Malley, U of Exeter; Robert Savino Oventile, Pasadena City College; Chris Pak; David N. Pellow, U of California, Santa Barbara; Andrew Pendakis, Brock U; Kimberly Skye Richards, U of California, Berkeley; Ann Kristin Schorre, U of Oslo, Norway; Malcolm Sen, U of Massachusetts Amherst; Kate Shaw; Sam Solnick, U of Liverpool; Rirkrit Tiravanija, Columbia U; Miriam Tola, Northeastern U; Sheena Wilson, U of Alberta; Daniel Worden, Rochester Institute of Technology.
