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Author: Rebecca Sophia Natalie Krupp
Publisher:
ISBN:
Category :
Languages : en
Pages : 360
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Book Description
Author: Rebecca Sophia Natalie Krupp
Publisher:
ISBN:
Category :
Languages : en
Pages : 360
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Book Description
Author: E. C. C. Lin
Publisher: Springer Science & Business Media
ISBN: 1468486012
Category : Medical
Languages : en
Pages : 1010
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Book Description
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.
Author: Hemali Bharat Patel
Publisher:
ISBN:
Category :
Languages : en
Pages : 392
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Book Description
Abstract: The stringent response is a response network in bacteria that is triggered by nutrient limitation and involves a global reprogramming of gene transcription, orchestrated largely by a signaling molecule guanosine tetraphosphate (ppGpp). Despite decades of studies on individual genes perturbed during the stringent response in Escherichia coli, the characteristic transcriptional profile and the role of ppGpp in affecting global transcriptional changes during the stringent response had remained to be determined systematically. We provoked the stringent response, in the strain E. coli K-12, by multiple induction pathways and identified the core transcriptional profile that is characteristic of the cellular response to ppGpp accumulation. By comparison of wild type and ppGpp-deficient E. coli mutant strains, we identified the gene expression changes that are specifically dependent upon ppGpp. We found six transcriptional regulators that are recruited in the core stringent response. We show the regulatory targets of one of these six regulators, RpoS. Over 80% of transcriptional regulation was directly or indirectly dependent upon the general stress response sigma factor, RpoS, even in presence of ppGpp. Our findings suggest that ppGpp alone is not capable of mounting a global stringent response, and it relies heavily on transcriptional regulators such as RpoS. Existing regulatory models for ppGpp-mediated regulation suggest a global redistribution of RNA polymerase (RNAP), upon binding with ppGpp, during stringent response. We have shown evidence for such redistribution of RNAP in presence of ppGpp by conducting ChIP-chip analysis of ppGpp-rich and ppGpp-deficient cells with an antibody specific to the alpha-subunit of RNAP. We also correlated transcriptional changes with a phenotype of increased viability in acidic medium, and demonstrated that it was dependent upon both ppGpp and RpoS. We have shown that ppGpp enhances long-term survival, up to two hours, in acid. Our results reveal the significance of stringent response in development of phenotypes that facilitate adaptation in acidic host environments for E. coli.
Author: Thomas Edward Kuhlman
Publisher:
ISBN: 9781109953855
Category :
Languages : en
Pages : 200
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Book Description
In Chapter 4, Quantitative Characteristics of Gene Regulation by Small RNA, we study quantitatively two classes of bacterial small RNAs (sRNA) in Escherichia coli. We demonstrate that sRNA provide a novel mode of gene regulation with characteristics distinct from those of protein-mediated gene regulation. These include a threshold-linear response with a tuneable threshold and a built-in capability for hierarchical cross talk.
Author: Shuang-En Chuang
Publisher:
ISBN:
Category :
Languages : en
Pages : 310
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Author: Tara Jean Palmer
Publisher:
ISBN:
Category :
Languages : en
Pages : 254
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Author: Dean Alexander Tolla
Publisher:
ISBN: 9781124509402
Category :
Languages : en
Pages :
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Book Description
This work examines the role of a cyclic genetic regulatory circuit acting as an environmental sensor. As a representative of this class of systems, we focus on the FNR regulatory circuit of Escherichia coli for which a large body of experimental evidence describing its molecular components and their individual interactions exists. However, until recently this information had never been integrated into a coherent model of the intact system. The FNR protein is an oxygen sensor that acts as a global transcription factor and when active modifies gene expression to adapt the cell to anaerobic growth. Our study provides strong support for an integrated model of FNR regulation that demonstrates self-consistency of a large body of experimental work, makes predictions of additional mutant behavior that are validated by experimental data, predicts the dynamics of the aerobic-to-anaerobic transition, provides estimates of active FNR in vivo, and makes it possible to predict in situ the dimerization rate of the transcription factor. We provide an original definition of what is meant by phenotype at the molecular level that is based on the concept of a "system design space". This definition allows us to rigorously characterize the regulatory phenotypes exhibited by the master transcription factor FNR. We identify 15 qualitatively-distinct phenotypes, analyze the alternatives, and compare their relative fitness. Our analysis reveals desirable and undesirable phenotypes as well as an optimal band of operation corresponding to the transition between aerobic and anaerobic environments. We analyze specific mutations and predict their associated phenotypic changes. By identifying the phenotypic repertoire our design space analysis provides a means to evaluate the evolutionary pressures that have shaped this system. Our application of the design space approach to the FNR network provides a detailed framework for characterizing other environmental sensing regulatory networks, and this approach is sufficiently general that it can be used to analyze the distinct behaviors presented by essentially any biochemical network. By examining a family of FNR models each with different cycling speeds but mathematically constrained to be otherwise equivalent, we are able to elucidate the relationship between the cycling rate and response time of the FNR circuit. We identify an optimum cycling rate for the FNR system. Our analysis of a currently uncharacterized double mutant argues in favor of these predicted results and provides a means to test our predictions in the laboratory. We examine the phenotype of increasing the number of fnr gene copies and show that the copy-number mutant exaggerates the predicted dynamics of active FNR induction. We provide an experimental method capable of capturing the dynamics of active FNR induction and repression, and predict its results for the wild-type, double mutant, and copy-number mutant.
Author: Ross S. Rabin
Publisher:
ISBN:
Category :
Languages : en
Pages : 418
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Author: Tassia Kolesnikow
Publisher:
ISBN:
Category :
Languages : en
Pages : 428
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Book Description
Author: Frans J. de Bruijn
Publisher: John Wiley & Sons
ISBN: 1119004896
Category : Science
Languages : en
Pages : 1472
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Book Description
Bacteria in various habitats are subject to continuously changing environmental conditions, such as nutrient deprivation, heat and cold stress, UV radiation, oxidative stress, dessication, acid stress, nitrosative stress, cell envelope stress, heavy metal exposure, osmotic stress, and others. In order to survive, they have to respond to these conditions by adapting their physiology through sometimes drastic changes in gene expression. In addition they may adapt by changing their morphology, forming biofilms, fruiting bodies or spores, filaments, Viable But Not Culturable (VBNC) cells or moving away from stress compounds via chemotaxis. Changes in gene expression constitute the main component of the bacterial response to stress and environmental changes, and involve a myriad of different mechanisms, including (alternative) sigma factors, bi- or tri-component regulatory systems, small non-coding RNA’s, chaperones, CHRIS-Cas systems, DNA repair, toxin-antitoxin systems, the stringent response, efflux pumps, alarmones, and modulation of the cell envelope or membranes, to name a few. Many regulatory elements are conserved in different bacteria; however there are endless variations on the theme and novel elements of gene regulation in bacteria inhabiting particular environments are constantly being discovered. Especially in (pathogenic) bacteria colonizing the human body a plethora of bacterial responses to innate stresses such as pH, reactive nitrogen and oxygen species and antibiotic stress are being described. An attempt is made to not only cover model systems but give a broad overview of the stress-responsive regulatory systems in a variety of bacteria, including medically important bacteria, where elucidation of certain aspects of these systems could lead to treatment strategies of the pathogens. Many of the regulatory systems being uncovered are specific, but there is also considerable “cross-talk” between different circuits. Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria is a comprehensive two-volume work bringing together both review and original research articles on key topics in stress and environmental control of gene expression in bacteria. Volume One contains key overview chapters, as well as content on one/two/three component regulatory systems and stress responses, sigma factors and stress responses, small non-coding RNAs and stress responses, toxin-antitoxin systems and stress responses, stringent response to stress, responses to UV irradiation, SOS and double stranded systems repair systems and stress, adaptation to both oxidative and osmotic stress, and desiccation tolerance and drought stress. Volume Two covers heat shock responses, chaperonins and stress, cold shock responses, adaptation to acid stress, nitrosative stress, and envelope stress, as well as iron homeostasis, metal resistance, quorum sensing, chemotaxis and biofilm formation, and viable but not culturable (VBNC) cells. Covering the full breadth of current stress and environmental control of gene expression studies and expanding it towards future advances in the field, these two volumes are a one-stop reference for (non) medical molecular geneticists interested in gene regulation under stress.
