Download or read book Integrating Genome wide Analyses to Investigate the Regulatory Role of FNR and IscR in Response to Anaerobiosis in Escherichia Coli written by and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Escherichia coli contains multiple O2-sensing transcription factors, including FNR and IscR. FNR is predominantly active under anaerobic conditions, where it ligates an O20́3labile [4Fe0́34S] cluster for dimerization and DNA binding. Ligation of a [2Fe0́32S] cluster by IscR broadens its DNA binding specificity from binding only a Type 2 site to binding both Type 1 and Type 2 sites. Fe0́3S occupancy of IscR is regulated by O2 availability and a complex pattern of gene expression results under aerobic and anaerobic conditions. We studied the FNR and IscR regulons on a genome0́3scale and found little overlap between the two regulons. FNR occupancy at many sites was strongly influenced by nucleoid0́3associated proteins (NAPs). While only a subset of predicted FNR binding sites were bound in vivo, many sites appeared to be masked by the NAPs H0́3NS, IHF, and Fis. Cells lacking H0́3NS and its paralog StpA showed increased FNR occupancy at sites normally bound by H0́3NS, indicating that the genome is not readily accessible for FNR binding. Correlation of FNR ChIP0́3seq peaks with transcriptomic data showed that less than half of the FNR regulated operons could be attributed to direct FNR binding. FNR bound some promoters without regulating expression, presumably requiring additional condition specific transcription factors. ChIP0́3chip analysis of IscR binding revealed that IscR primarily binds Type 2 sites under aerobic and anaerobic conditions. Correlation of IscR binding regions containing a Type 1 or Type 2 site with the transcriptomic data revealed 33 operons directly regulated by IscR under aerobic or anaerobic conditions. The four previously reported promoters containing Type 1 sites and both known and novel promoters containing Type 2 sites were identified. The previous finding that promoters with Type 2 sites are also regulated by IscR primarily under aerobic conditions extended to newly identified operons. Further analyses suggested that multiple mechanisms prevent IscR regulation of Type 2 sites under anaerobic conditions including action of other global transcription factors FNR, ArcA, and Fur. In summary, this work expands our knowledge of the FNR and IscR regulons and the role of combinatorial regulation in the E. coli response to changes in O2 concentration.
Download or read book Exploring the Regulatory Network and Physiological Significance of the Dipeptide Transport System During Anaerobic Adaptation in Escherichia Coli written by Xiang Gao and published by . This book was released on 2017-01-26 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: This dissertation, "Exploring the Regulatory Network and Physiological Significance of the Dipeptide Transport System During Anaerobic Adaptation in Escherichia Coli" by Xiang, Gao, 高翔, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Abstract of thesis entitled "EXPLORING THE REGULATORY NETWORK AND PHYSIOLOGICAL SIGNIFICANCE OF THE DIPEPTIDE TRANSPORT SYSTEM DURING ANAEROBIC ADAPTATION IN ESCHERICHIA COLI" Submitted by Gao Xiang for the Degree of Doctor of Philosophy at The University of Hong Kong in August 2014 Escherichia coli (E. coli) and other facultative anaerobes are genetically programmed to adapt to both aerobic and anaerobic growth conditions. Among the various genes which expression is altered during the transition from aerobic to anaerobic growth, those involved in the nutrients uptake and waste product extrusion is of particular essential to the physiology of E. coli. Genome-wide studies have suggested that the dipeptide transporter system Dpp which can also transport heme and its precursor ALA (δ-aminolevulinic acid) is one of the anaerobically repressed transporters during anaerobiosis. To understand the mechanisms of this regulation, the roles of the anaerobic global regulators FNR, the two-component system ArcAB, and the sRNA GcvB on the expression of the dpp operon were investigated. Results of translational fusion of Pdpp-lacZ, RT-qPCR, and Western blot analysis showed that FNR repressed the expression of dpp since Δfnr caused increased expression of Dpp under anaerobic conditions in LB medium. However, mutation of the FNR putative binding site on Pdpp did not cause de-repression and no direct binding of FNR to Pdpp was observed in EMSA, suggesting that FNR may not directly regulate dpp expression. Interestingly, deletion of arcA or gcvB caused increased expression of Dpp and ΔgcvB ΔarcA double deletion led to a further increase of Dpp protein level, indicating the simultaneous repression of Dpp by both ArcA and GcvB. EMSA demonstrated direct binding of the phosphorylated ArcA (ArcA P) to Pdpp and PgcvB, and ΔarcA caused decreased level of GcvB under anaerobic conditions, suggesting that ArcA can both directly repress dpp expression and through its activation of GcvB. These results together indicated a "coherent feed-forward regulatory loop" on the expression of Dpp in which ArcA and GcvB co-repress dpp, and ArcA also activates GcvB. To investigate the physiological significance of the repression of the Dpp expression under anaerobic condition, the Dpp system was overexpressed and examined on the growth and viability of E. coli under various anaerobic growth conditions. It was found that overexpression of the system in ΔtolC E. coli background strain caused accumulation of red fluorescent substances and photosensitivity to near-UV irradiation (366 nm) in the presence of 3 μg/ml ALA. Deletion of fnr, arcA, gcvB, and both gcvB and arcA caused similarly decreased viability to photo-irradiation. However, under aerobic conditions, except for the ΔgcvB ΔtolC strain, none of these strains displayed increased photosensitivity even in the presence of 10 μg/ml ALA, suggesting that E. coli cells were more tolerant to near-UV irradiation under anaerobic conditions and the importance of repressing the dpp expression under this condition. Consistent with the viability assay, the concentration of intracellular coproporphyrin was highest in E. coli ΔtolC background containing ΔgcvB ΔarcA (24.9 μM), followed by ΔgcvB, ΔarcA, and Δfnr (17, 16.7, and 14.8 μM) respectively, suggesting that the increas
Download or read book Oxygen Sensing in Escherichia Coli and the Role of Cyclic Regulation written by Dean Alexander Tolla and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Systematic Mutagenesis of Escherichia Coli Genome and Genome wide Expression Analysis Indicates that FNR of E Coli K12 Regulates a Large Number of Genes of Unknown Function written by Yisheng Kang and published by . This book was released on 2005 with total page 144 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Bacterial Signaling written by Reinhard Krämer and published by John Wiley & Sons. This book was released on 2009-12-09 with total page 513 pages. Available in PDF, EPUB and Kindle. Book excerpt: Providing a comprehensive insight into cellular signaling processes in bacteria with a special focus on biotechnological implications, this is the first book to cover intercellular as well as intracellular signaling and its relevance for biofilm formation, host pathogen interactions, symbiotic relationships, and photo- and chemotaxis. In addition, it deals in detail with principal bacterial signaling mechanisms -- making this a valuable resource for all advanced students in microbiology. Dr. Krämer is a world-renowned expert in intracellular signaling and its implications for biotechnology processes, while Dr. Jung is an expert on intercellular signaling and its relevance for biomedicine and agriculture.
Download or read book Bayesian Networks in R written by Radhakrishnan Nagarajan and published by Springer Science & Business Media. This book was released on 2014-07-08 with total page 168 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bayesian Networks in R with Applications in Systems Biology is unique as it introduces the reader to the essential concepts in Bayesian network modeling and inference in conjunction with examples in the open-source statistical environment R. The level of sophistication is also gradually increased across the chapters with exercises and solutions for enhanced understanding for hands-on experimentation of the theory and concepts. The application focuses on systems biology with emphasis on modeling pathways and signaling mechanisms from high-throughput molecular data. Bayesian networks have proven to be especially useful abstractions in this regard. Their usefulness is especially exemplified by their ability to discover new associations in addition to validating known ones across the molecules of interest. It is also expected that the prevalence of publicly available high-throughput biological data sets may encourage the audience to explore investigating novel paradigms using the approaches presented in the book.
Download or read book The Prokaryotes written by Edward F. DeLong and published by Springer. This book was released on 2014-10-13 with total page 567 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Prokaryotes is a comprehensive, multi-authored, peer reviewed reference work on Bacteria and Achaea. This fourth edition of The Prokaryotes is organized to cover all taxonomic diversity, using the family level to delineate chapters. Different from other resources, this new Springer product includes not only taxonomy, but also prokaryotic biology and technology of taxa in a broad context. Technological aspects highlight the usefulness of prokaryotes in processes and products, including biocontrol agents and as genetics tools. The content of the expanded fourth edition is divided into two parts: Part 1 contains review chapters dealing with the most important general concepts in molecular, applied and general prokaryote biology; Part 2 describes the known properties of specific taxonomic groups. Two completely new sections have been added to Part 1: bacterial communities and human bacteriology. The bacterial communities section reflects the growing realization that studies on pure cultures of bacteria have led to an incomplete picture of the microbial world for two fundamental reasons: the vast majority of bacteria in soil, water and associated with biological tissues are currently not culturable, and that an understanding of microbial ecology requires knowledge on how different bacterial species interact with each other in their natural environment. The new section on human microbiology deals with bacteria associated with healthy humans and bacterial pathogenesis. Each of the major human diseases caused by bacteria is reviewed, from identifying the pathogens by classical clinical and non-culturing techniques to the biochemical mechanisms of the disease process. The 4th edition of The Prokaryotes is the most complete resource on the biology of prokaryotes. The following volumes are published consecutively within the 4th Edition: Prokaryotic Biology and Symbiotic Associations Prokaryotic Communities and Ecophysiology Prokaryotic Physiology and Biochemistry Applied Bacteriology and Biotechnology Human Microbiology Actinobacteria Firmicutes Alphaproteobacteria and Betaproteobacteria Gammaproteobacteria Deltaproteobacteria and Epsilonproteobacteria Other Major Lineages of Bacteria and the Archaea
Download or read book Metallomics and the Cell written by Lucia Banci and published by Springer Science & Business Media. This book was released on 2013-04-18 with total page 642 pages. Available in PDF, EPUB and Kindle. Book excerpt: Metallomics and the Cell provides in an authoritative and timely manner in 16 stimulating chapters, written by 37 internationally recognized experts from 9 nations, and supported by more than 3000 references, several tables, and 110 illustrations, mostly in color, a most up-to-date view of the "metallomes" which, as defined in the "omics" world, describe the entire set of biomolecules that interact with or are affected by each metal ion. The most relevant tools for visualizing metal ions in the cell and the most suitable bioinformatic tools for browsing genomes to identify metal-binding proteins are also presented. Thus, MILS-12 is of relevance for structural and systems biology, inorganic biological chemistry, genetics, medicine, diagnostics, as well as teaching, etc.
Download or read book Regulation of Bacterial Virulence written by Michael L. Vasil and published by American Society for Microbiology Press. This book was released on 2012-12-05 with total page 1189 pages. Available in PDF, EPUB and Kindle. Book excerpt: A comprehensive compendium of scholarly contributions relating to bacterial virulence gene regulation. • Provides insights into global control and the switch between distinct infectious states (e.g., acute vs. chronic). • Considers key issues about the mechanisms of gene regulation relating to: surface factors, exported toxins and export mechanisms. • Reflects on how the regulation of intracellular lifestyles and the response to stress can ultimately have an impact on the outcome of an infection. • Highlights and examines some emerging regulatory mechanisms of special significance. • Serves as an ideal compendium of valuable topics for students, researchers and faculty with interests in how the mechanisms of gene regulation ultimately affect the outcome of an array of bacterial infectious diseases.
Download or read book Flavins written by Eduardo Silva and published by Royal Society of Chemistry. This book was released on 2006 with total page 335 pages. Available in PDF, EPUB and Kindle. Book excerpt: Flavins and flavoproteins are a widely investigated and highly versatile group of compounds. Participation of these compounds in photochemistry and photobiology processes are of particular importance in the fields of biology, chemistry and medicine. Written by leading experts in the field each section of the book includes a historical overview of the subject, state of the art developments and future perspectives. Flavins: Photochemistry and Photobiology begins with the properties and applications of flavins, including their photochemistry in aqueous and organic solutions. Subsequent sections discuss riboflavin as a visible light sensitizer in the photo degradation of drugs, antiviral and antibacterial effects, the role of flavins in light induced toxicity and blue light initiated DNA repair by photolyase. Finally there are sections on the flavin based photoreceptors in plants, bacteria and eukaryotic photosynthetic flagelettes. This book brings together leading experts with a unique interdisciplinary emphasis, to provide an authoritative resource on flavins and their role in photochemistry and photobiology.
Download or read book Biotechnology for Biofuels A Sustainable Green Energy Solution written by Nitish Kumar and published by Springer Nature. This book was released on 2020-05-16 with total page 291 pages. Available in PDF, EPUB and Kindle. Book excerpt: The depletion of petroleum-derived fuel and environmental concerns have prompted many millennials to consider biofuels as alternative fuel sources. But completely replacing petroleum-derived fuels with biofuels is currently impossible in terms of production capacity and engine compatibility. Nevertheless, the marginal replacement of diesel with biofuel could delay the depletion of petroleum resources and abate the radical climate change caused by automotive pollutants. Energy security and climate change are the two major driving forces for worldwide biofuel development, and also have the potential to stimulate the agro-industry. The development of biofuels as alternative and renewable sources of energy has become critical in national efforts towards maximum self-reliance, the cornerstone of our energy security strategy. At the same time, the production of biofuels from various types of biomass such as plants, microbes, algae and fungi is now an ecologically viable and sustainable option. This book describes the biotechnological advances in biofuel production from various sources, while also providing essential information on the genetic improvement of biofuel sources at both the conventional and genomic level. These innovations and the corresponding methodologies are explained in detail.
Download or read book Bacterial Genomics written by Aswin Sai Narain Seshasayee and published by Cambridge University Press. This book was released on 2015-03-05 with total page 227 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents the application of genomic tools to examine bacterial adaptation. The emphasis is on data analysis and interpretation.
Download or read book Computational Systems Biology written by Andres Kriete and published by Academic Press. This book was released on 2013-11-26 with total page 549 pages. Available in PDF, EPUB and Kindle. Book excerpt: This comprehensively revised second edition of Computational Systems Biology discusses the experimental and theoretical foundations of the function of biological systems at the molecular, cellular or organismal level over temporal and spatial scales, as systems biology advances to provide clinical solutions to complex medical problems. In particular the work focuses on the engineering of biological systems and network modeling. - Logical information flow aids understanding of basic building blocks of life through disease phenotypes - Evolved principles gives insight into underlying organizational principles of biological organizations, and systems processes, governing functions such as adaptation or response patterns - Coverage of technical tools and systems helps researchers to understand and resolve specific systems biology problems using advanced computation - Multi-scale modeling on disparate scales aids researchers understanding of dependencies and constraints of spatio-temporal relationships fundamental to biological organization and function.
Download or read book Fe S Proteins written by Patricia C. dos Santos and published by . This book was released on 2021 with total page 351 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume explores current technologies used to investigate the formation, insertion, and function of metalloclusters associated with proteins. Chapters describe relevant topics about Fe-S cluster metabolism are explored through genetic, biochemical, spectroscopic methods. Written in the highly successful Methods in Molecular Biology series format, 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 cutting-edge, Fe-S Proteins: Methods and Protocols aims to be a useful practical guide to researchers to help further their study in this field.
Download or read book Methods in Methane Metabolism written by Amy Claire Rosenzweig and published by Academic Press. This book was released on 2011 with total page 421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Produced by microbes on a large scale, methane is an important alternative fuel as well as a potent greenhouse gas. This volume focuses on microbial methane metabolism, which is central to the global carbon cycle. Both methanotrophy and methanogenesis are covered in detail. Topics include isolation and classification of microorganisms, metagenomics approaches, biochemistry of key metabolic enzymes, gene regulation and genetic systems, and field measurements. The state of the art techniques described here will both guide researchers in specific pursuits and educate the wider scientific community about this exciting and rapidly developing field. Topics include isolation and classification of microorganisms, metagenomics approaches, biochemistry of key metabolic enzymes, gene regulation and genetic systems, and field measurements. The state of the art techniques described here will both guide researchers in specific pursuits and educate the wider scientific community about this exciting and rapidly developing field.
Download or read book Photosynthesis Research Protocols written by Robert Carpentier and published by Springer Science & Business Media. This book was released on 2008-02-04 with total page 341 pages. Available in PDF, EPUB and Kindle. Book excerpt: Photosynthesis is one of the most important biological phenomena on earth. The conversion of sunlight by photosynthetic organisms supplies most of the energy required to develop and sustain life on the planet. Photosynthesis is not only at the heart of plant bioenergetics, it is also fundamental to plant prod- tivity and biomass. Photosynthetic carbon fixation and oxygen evolution - rectly intervene in many environmental, including the global atmospheric CO 2 level and global climate. Therefore, it is not surprising that a large effort is devoted to photosynthesis research. Several biochemical methods of isolation, treatment, and analysis have been developed to fulfill the needs of photosynthesis research. Photosynthesis Research Protocols contains a broad range of general and fundamental me- ods that are commonly used by plant biochemists, physiologists, and mole- lar biologists. This book is thus intended as a source of information for scientists working on any of the multiple aspects of photosynthesis, and should be of great interest to a multidisciplinary field of research involving agric- ture, biochemistry, biotechnology, botany, cell biology, environmental s- ences, forestry, plant genetics, plant molecular biology, photobiology, photophysics, photoprotection, plant physiology, plant stress, etc.
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.
