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 Gene Regulation in Escherichia Coli Beyond the 0 rate0 Approximation written by Lok-hang So and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The blueprint of a living cell is inscribed in its DNA. A region of DNA encoding a protein is called a gene. The cell reads the DNA and makes molecular machines made up of proteins to carry out all cellular functions required for survival. All cells live in ever-changing environments, and have different needs at different times. The control of when and how often each protein is produced from a gene is called gene regulation. Transcription, the copying of a DNA sequence into a complementary mRNA molecule, is the first step in the information flow from DNA to proteins, and most regulation is already done at the transcription level to avoid the production of superfluous intermediates. A living cell takes environmental stimuli as input, and regulates the activity of genes through DNA-binding proteins called transcription factors. The activity of a gene is described by its time-series of discrete mRNA production events. The events constituting this transcriptional time-series are stochastic and exhibit intermittent, bursty behavior, in bacteria as well as higher organisms. Thus the transcriptional time-series cannot be fully described by a simple chemical 0́−rate0́+0́4the probability per unit time of transcribing an mRNA molecule. An important consequence of this temporal complexity is that gene expression level can be tuned by varying different features of the time-series. It is then natural to ask: What modulation scheme is used by the cell to change expression levels of genes? Furthermore, if we look at the transcriptional time-series of multiple genes, would we see different modulation schemes for different genes, or a common modulation scheme shared by all genes? Last but not least, what is the molecular mechanism leading to bursty transcriptional time-series? What are the biophysical states that correspond to the active and inactive periods in a bursty transcriptional time-series? To answer these questions, I characterized the mRNA copy-number statistics from multiple promoters in the model organism Escherichia coli under various growth conditions using single-molecule fluorescence in situ hybridization. The kinetics of the underlying transcriptional time-series was then inferred using the two-state model, a simple stochastic mathematical model that describes bursty transcription time-series. I found that the degree of burstiness depends only on the gene expression level, while being independent of the details of gene regulation. The observed behavior is explained by the underlying variation in the duration of bursting events. At this stage, there is no mechanistic, molecular-level understanding of what gives rise to the bursty behavior of gene activity in bacteria. However, my finding here, that the properties of the transcriptional time-series are gene-independent rather than gene-specific, is contrary to the most common theoretical model used to explain bursty transcriptional time-series in bacteria, which involves the binding and unbinding of transcription factors at the promoter. My data suggests that the observed bursty kinetics arises from gene-nonspecific mechanisms such as DNA topology modulation, RNA polymerase dynamics, or regulation by broad-target DNA-binding proteins. Further investigation would narrow down the source of bursty transcriptional time-series.

Download or read book Higher Levels of Gene Regulation in Escherichia Coli written by Karen Cooke and published by . This book was released on 2019 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: "Epigenetic" mechanisms result in information being carried by DNA, independent of its base sequence. These are widely studied in eukaryotic cells, but less so in bacterial contexts. DNA methylases, such as DNA adenine methyltransferase (DAM), methylate DNA at '5-GATC-3' sequences. This is known to impact upon DNA replication, DNA repair, and transcriptional regulation at some virulence promoters. Investigations in to cell methylation were achieved by digestion of plasmid pBR322 with DpnI restriction enzyme; this showed nutrient-dependent differences in methylation levels. DNA topology in wild-type and ∆dam cells was investigated by chloroquine gel electrophoresis, and this revealed a higher degree of supercoiling in ∆dam cells in the exponential phase of growth. To investigate global effects of DAM on transcription in Escherichia coli K-12, a lac28::egfp fusion was inserted at different chromosomal loci, and expression was measured using flow cytometry. Differences in gene expression between wild-type and ∆dam cells were found at these loci, with some differences depending on growth medium. At many loci, ∆dam cell populations exhibited increased fluorescence and, occasionally, less variation than wild-type cells. In further experiments, interactions between DAM and CRP (the catabolite-repression global transcription regulator protein) were explored, and found that DAM methylation could affect the action of CRP at a model promoter. My work implicates DAM methylase as a potent regulator of gene expression in Escherichia coli and an agent of cell-to-cell heterogeneity. The mechanisms by which DAM methylase affected gene regulation were probed, bioinformatically. These studies revealed that while the absolute number of GATC motifs in the locality of the lac28 promoter did not seem to correlate to overall increases in gene expression, the number of GATC sites upstream of the same promoter may correlate with changes in the variability of GFP expression. This study also highlighted that DAM regulation of some loci may be protein-dependent. Lastly, the effect of genetic position on the expression of antibiotic resistance genes was investigated in both the chromosomal and plasmid contexts. This work highlighted that chromosomal resistance cassettes may express differently, depending on their location. This in turn, yields different resistance phenotypes within the "same" bacterial strain. This concept was addditionally explored within a plasmid, whereby a transposon encoding a resistance gene was inserted randomly in to different locations in the plasmid genome. Thence, different levels of antibiotic resistance where seen that were location dependent. In sum, this work aims to further traverse the existence of so-called "higher levels" of genetic regulation within Escherichia coli.

Download or read book Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria written by Frans J. de Bruijn and published by John Wiley & Sons. This book was released on 2016-07-13 with total page 1472 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book Integrative Approaches to Molecular Biology written by Julio Collado-Vides and published by MIT Press. This book was released on 1996 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: It charts the course of the emerging discipline of integrative molecular biology from macromolecular sequences to a biological (and theoretical) perspective, showing that novel integrative methodologies and paradigms are emerging at the confluence of such disciplines as computer science, logic, linguistics, and mathematics.

Download or read book A Quantitative Analysis of Genetic Transcriptional and Post transcriptional Regulation in Escherichia Coli written by Thomas Edward Kuhlman and published by . This book was released on 2007 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.

Download or read book ModE mediated gene regulation in Escherichia coli written by Lisa Ann Anderson and published by . This book was released on 1998 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Global Regulation of Gene Expression in Escherichia Coli written by Shuang-En Chuang and published by . This book was released on 1992 with total page 310 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book The Operon written by Jeffrey H. Miller and published by . This book was released on 1980 with total page 488 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Maximizing Gene Expression written by William Reznikoff and published by Elsevier. This book was released on 2014-05-20 with total page 390 pages. Available in PDF, EPUB and Kindle. Book excerpt: Maximizing Gene Expression focuses on prokaryotic and eukaryotic gene expression. The book first discusses E. coli promoters. Topics include structure analysis, steps in transcription initiation, structure-function correlation, and regulation of transcription initiation. The text also highlights yeast promoters, including elements that select initiation sites, transcription regulation, regulatory proteins, and upstream promoter elements. The text also describes protein coding genes of higher eukaryotes; instability of messenger RNA in bacteria; and replication control of the ColE1-type plasmids. The text then describes translation initiation, including the translation of prokaryotes and eukaryotes. The book puts emphasis on the selective degradation of abnormal proteins in bacteria. Topics include proteins rapidly hydrolyzed in E. coli; intracellular aggregates of abnormal polypeptides; energy requirement and pathway for proteins; proteolytic enzymes in E. coli; and regulation of ion expression. The text also highlights the detection of proteins produced by recombinant DNA techniques and mechanism and practice. The book is a good source of information for readers wanting to study gene expression.

Download or read book Transcriptional Regulation in Escherichia Coli written by Markus Willard Covert and published by . This book was released on 2003 with total page 434 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Gene Function written by Robert E. Glass and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 496 pages. Available in PDF, EPUB and Kindle. Book excerpt: My aim in writing Gene Function has been to present an up-to-date picture ofthe molecular biology of Escherichia coli. I have not attempted a chronological description, believing that a mechanistic account is more useful for such a highly developed field. I have divided the book into four parts. Part I is a general introduction to bacterial systems, their genetic material, structure, composition and growth. It has seemed desirable to include herein a brief preview of the remaining text, to introduce the nomenclature and to help place subsequent chapters in perspective. The expression of genetic material and its perturbation through mutation is considered in Part II. Part III discusses how the transfer of prokaryotic genetic material can be mediated by plasmids and bacteriophages. It describes the DNA transactions involved (replication, recombination and repair) and ends with a description of the genetic and biochemical techniques employed in the study of gene organisation. Finally, Part IV considers the control of expression of bacterial, plasmid and phage genes. Key reviews are listed at the end of each chapter.

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 Gene Regulation in Enteropathogenic Escherichia Coli written by Nhi My Van and published by . This book was released on 2018 with total page 80 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Regulation of Gene Expression by Small RNAs written by Rajesh K. Gaur and published by CRC Press. This book was released on 2009-04-27 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: New Findings Revolutionize Concepts of Gene FunctionEndogenous small RNAs have been found in various organisms, including humans, mice, flies, worms, fungi, and bacteria. Furthermore, it's been shown that microRNAs acting as cellular rheostats have the ability to modulate gene expression. In higher eukaryotes, microRNAs may regulate as much as 50 p

Download or read book Gene Regulation and Metabolism written by Julio Collado-Vides and published by MIT Press. This book was released on 2002 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: An overview of current computational approaches to metabolism and gene regulation.

Download or read book Metal Ions in Gene Regulation written by Simon Silver and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 479 pages. Available in PDF, EPUB and Kindle. Book excerpt: This is the first volume on the role of metal ions in regulating genes to focus not only on toxicity effects of metals but also on the role of metal ions in normal metabolisms, in both prokaryotes and in eukaryotes. This book is a comprehensive treatment of the role of metal ions in gene regulation, and it will be of great utility for those doing basic biological and biomedical research.