Role of PpGpp in Regulating Global Gene Expression in Escherichia Coli PDF Download
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Author: Matthew F. Traxler
Publisher:
ISBN:
Category : Bacterial genomes
Languages : en
Pages : 392
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Author: Matthew F. Traxler
Publisher:
ISBN:
Category : Bacterial genomes
Languages : en
Pages : 392
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Author: Lisa Magnusson
Publisher:
ISBN: 9789162871550
Category : Escherichia coli
Languages : en
Pages : 49
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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: Mingzhu Liu
Publisher:
ISBN:
Category :
Languages : en
Pages : 186
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Author: Patricia Sánchez-Vázquez
Publisher:
ISBN:
Category :
Languages : en
Pages : 313
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Upon amino acid starvation of Escherichia coli, the second messenger nucleotide ppGpp dramatically alters gene expression in order to adjust cellular metabolism to the nutritional conditions. ppGpp specifically regulates transcription by interacting directly with RNA polymerase (RNAP) at two sites identified in vitro. I created strains with chromosomal mutations in the residues identified in vitro, coding for residues needed for ppGpp binding to RNAP. I used recombineering combined with CRISPR-Cas9 selection followed by whole genome sequencing to clone and verify the binding site mutant strains created. The strains were used first to evaluate the physiological significance of ppGpp binding sites 1 and 2, and second as tools for separating the transcriptional effects of ppGpp binding to RNAP vs other potential targets. To study the direct genome-wide transcriptional effects of ppGpp, I performed RNA-seq analysis on cells in which ppGpp was induced without introducing a nutrient starvation, and we compared effects of ppGpp induction in cells lacking the ppGpp binding sites on RNAP rather than by eliminating the regulators themselves. The results identify a much larger number of ppGpp-responsive targets than previous studies and show that all transcriptional responses result from binding of ppGpp to RNAP rather than to other proteins. In vitro transcription analysis of more than 100 promoters from the in vivo dataset unequivocally identified a large collection of directly regulated promoters, facilitating comparison of the sequences from directly inhibited, activated, and unaffected promoters. This analysis suggests DNA sequence features that contribute to promoter specificity and to the mechanism of the stringent response. Together, the results presented here expand on the knowledge of regulatory targets and the mechanism of ppGpp action.
Author: Kristian Kvint
Publisher:
ISBN: 9789162852368
Category :
Languages : en
Pages : 46
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Author: Rachel Isabelle Salemi
Publisher:
ISBN:
Category :
Languages : en
Pages : 0
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Bacteria must respond quickly to stressful environmental stimuli and nutrient deprivation in order to survive. Conserved across the bacterial domain are the intracellular stress signaling molecules ppGpp and pppGpp, referred to here as (p)ppGpp for brevity. In Escherichia coli and other gammaproteobacteria, (p)ppGpp binds directly to RNA polymerase (RNAP) to affect the transcription of hundreds of genes. Depending on the intrinsic promoter kinetics, transcription from promoters will be inhibited, activated, or unaffected by (p)ppGpp. Because (p)ppGpp affects the kinetics of transcription during the isomerization steps of open complex formation, determining promoter sequences that result in regulation by (p)ppGpp is extremely challenging as there are many sequences that can result in the same kinetic profile. To address this issue, we compiled a promoter dataset of over 1000 promoters and compared promoters that were inhibited, unaffected, or activated by (p)ppGpp to determine sequences that may be responsible for regulation. We find that promoters with specific bases at the -9 and -8 positions, -5 position, and three bases upstream of the transcription start site correlate with regulation via (p)ppGpp. In addition to better understanding the promoter sequences for regulation by (p)ppGpp, we explored the purpose of the two (p)ppGpp binding sites on RNAP. (p)ppGpp binds to two sites on RNAP: site 1 at the interface of [omega] and [beta]' subunits, and site 2 at the interface of DksA and [beta]'. Large phenotypic effects are associated with site 2 both in vitro and in vivo, but the function of site 1 has remained a mystery. Despite the lack of obvious function, site 1 is well-conserved throughout gammaproteobacteria and binds with similar affinity to (p)ppGpp as site 2. Using RNA-sequencing before and after (p)ppGpp induction in strains lacking either site 1 or site 2, we confirm that site 1 is capable only of inhibition and not of activation, and that site 2 performs the majority of gene regulation on a short time scale after induction of (p)ppGpp. We also find that in the conditions we tested, during steady state growth strains lacking site 1 are unable to properly express genes from the [sigma]S regulon and exhibit decreased [sigma]S protein levels compared to strains containing site 1. Additionally, strains lacking site 1 were sensitive to low pH, while strains containing site 1 regardless of the presence of site 2 survived exposure to low pH. Together, this work provides a new perspective on both promoter analysis for promoters regulated by (p)ppGpp and the function of site 1 through implementing genome-wide approaches.
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.
Author: Ryutaro Utsumi
Publisher: Springer Science & Business Media
ISBN: 0387788859
Category : Medical
Languages : en
Pages : 257
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Book Description
This fascinating book encourages many microbiologists and students to enter the new world of signal transduction in microbiology. Over the past decade, a vast amount of exciting new information on the signal transduction pathway in bacteria has been unearthed.
Author: Antony Bacic
Publisher: Academic Press
ISBN: 0080920543
Category : Medical
Languages : en
Pages : 713
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Book Description
Chemistry, Biochemistry, and Biology of 1-3 Beta Glucans and Related Polysaccharides presents a comprehensive, systematic and authoritative survey of information about a family of chemically related, but functionally diverse, naturally occurring polysaccharides--the (1-3)-glucans. International contributors describe the chemical and physicochemical properties of these glucans and their derivatives and the molecular biological and structural aspects of the enzymes involved in their formation and breakdown. A detailed analysis of their physiological roles in the various biological situations in which they are found will be provided. Additionally, evolutionary relationships among the family of these glucans will be described. - Topics of medical relevance include detailing the glucans' interactions with the immune system and research for cancer therapy applications - Web resource links allow scientists to explore additional beta glucan research - Separate indexes divided into Species and Subject for enhanced searchability
