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Regulation Of Bacterial Chromosome Replication Origins Through Binding Of Response Regulator Transcription Factors And Regulated Proteolysis
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Book Synopsis Regulation of Bacterial Chromosome Replication Origins Through Binding of 'response Regulator' Transcription Factors and Regulated Proteolysis by : Donald Patrick Bastedo
Download or read book Regulation of Bacterial Chromosome Replication Origins Through Binding of 'response Regulator' Transcription Factors and Regulated Proteolysis written by Donald Patrick Bastedo and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Bacterial Transcription Factors and the Cell Cycle, 2nd edition by : Morigen Morigen
Download or read book Bacterial Transcription Factors and the Cell Cycle, 2nd edition written by Morigen Morigen and published by Frontiers Media SA. This book was released on 2022-10-10 with total page 181 pages. Available in PDF, EPUB and Kindle. Book excerpt: Analogous to the eukaryotic G1, S and M phase of the cell cycle, the bacterial cell cycle can be classified into independent stages. Slowly growing bacterial cells undergo three different stages, B-, C- and D-phase, respectively, while the cell cycle of fast-growing bacteria involves at least two independent cycles: the chromosome replication and the cell division. The oscillation in gene expression regulated by transcription factors, and proteolysis mediated by ClpXP, are closely correlated with progression of the cell cycle. Indeed, it has been shown that DnaA couples DNA replication initiation with the expression of the two oscillating regulators GcrA and CtrA, and the DnaA/GcrA/CtrA regulatory cascade drives the forward progression of the Caulobacter cell cycle. Furthermore, it has been found that: the DnaA oscillation in Eschericha coli and Caulobacter crescentus plays an important role in the cell cycle coordination; RpoS in Coxiella regulates the gene expression involved in the developmental cycle; the SigB and SinR transcription factors control whether cells remain in or leave a biofilm responding to metabolic conditions in Bacillus subtilis; similarly, BolA in most Gram-negative bacteria turns off motility and turns on biofilm development as a transcription factor; CtrA regulates cell division and outer membrane composition of the pathogen Brucella abortus; an essential transcription factor SciP enhances robustness of Caulobacter cell cycle regulation. Interestingly, transcription factors mediated metabolism fluctuations are also related to progression of the cell cycle. It has been shown that: CggR and Cra factors are involved in the flux-signaling metabolite fructose-1,6-bisphosphate; IclR mediates para-hydroxybenzoate catabolism in Streptomyces coelicolor; CceR and AkgR regulate central carbon and energy metabolism in alphaproteobacteria; and these metabolism changes affect cell growth. In line with the argument, AspC-mediated aspartate metabolism coordinates the E. coli cell cycle. However, the molecular mechanisms of maintaining the proper cell cycle progression through coordination of transcription factors mediated gene transcription oscillation, cellular metabolism with the cell cycle are not yet well-established. This Research Topic is intended to cover the spectrum of cell cycle regulatory mechanisms, in particular the coordination of transcription factor mediated gene transcription oscillations, and the cellular metabolisms associated with the cell cycle. We welcome all types of articles including Original Research, Review, and Mini Review. The subject areas of interest include but are not limited to: 1. Cell cycle coordination through gene expression and expression oscillation mediated by transcription factors. 2. Regulation of the cell cycle by proteolysis oscillation. 3. Coordination of the cell cycle with metabolism fluctuation. 4. DNA methylation fluctuation and the cell cycle. 5. Novel transcription factors and gene expression patterns associated with the cell cycle.
Book Synopsis Bacterial Transcription Factors and the Cell Cycle by : Morigen Morigen
Download or read book Bacterial Transcription Factors and the Cell Cycle written by Morigen Morigen and published by Frontiers Media SA. This book was released on 2022-02-10 with total page 193 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis New Mechanisms in Transcription Regulation and Chromosome Organization in Caulobacter Crescentus by : Diane Laure Haakonsen
Download or read book New Mechanisms in Transcription Regulation and Chromosome Organization in Caulobacter Crescentus written by Diane Laure Haakonsen and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria use a variety of mechanisms to control transcription in response to environmental cues or growth conditions. Activation or repression of transcription is often carried out by proteins, called transcription factors, that interact with DNA or RNA polymerase (RNAP) or both, and can change the preference of RNAP for target promoters. Additionally, DNA is tightly compacted and organized inside cells. In bacteria, nucleoid-associated proteins (NAPs) play critical roles in shaping and compacting the chromosome by bending, wrapping and bridging the DNA. The binding of these proteins can also profoundly affect gene expression regulation. In this work, I have characterized two DNA-binding proteins from the bacterium Caulobacter crescentus; one transcription factor, GcrA, and one NAP, CnpA. First, I found that GcrA, an essential cell-cycle regulator in Caulobacter, activates transcription by a new mechanism. Unlike most transcription factors that bind to promoters independently of RNAP, GcrA constitutively associates with RNAP via an interaction with Domain 2 of Y70, the primary sigma factor. I showed that GcrA recognizes a subset of methylation sites and can promote binding of RNAP and increase the rate of open complex formation at promoters harboring such sites. Understanding the mechanism by which GcrA activates transcription enabled the identification of its direct regulon and provided important insights into its essential cell-cycle function. For my second project, I identified a new nucleoid-associated protein (NAP), CnpA, in Caulobacter, via mass-spectrometry analysis of its nucleoid content. I showed that CnpA associates with AT-rich DNA but unlike other NAPs, likely does not repress transcription at these loci. We propose a model in which CnpA impacts global supercoiling levels. In sum, these two projects have contributed to expanding our views of how gene expression and chromosome organization are regulated in bacteria.
Book Synopsis Transcription Factors and DNA Replication by : David Scott Pederson
Download or read book Transcription Factors and DNA Replication written by David Scott Pederson and published by R. G. Landes. This book was released on 1994 with total page 132 pages. Available in PDF, EPUB and Kindle. Book excerpt: Initiation of DNA synthesis: a general model from studies with prokaryotes. Regulatory transcription factors and the initiation of transcription in eucaryotic cells. Replication origins and the initiation of DNA synthesis in mammalian cells and the viruses. DNA replication in yeast. Transcription factors and control of DNA replication.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis A Novel Adapter Mechanism Regulates the Caulobacter Cell Cycle by Promoting the Degradation of the Transcriptional Regulator CtrA. by : Stephen Carl Smith
Download or read book A Novel Adapter Mechanism Regulates the Caulobacter Cell Cycle by Promoting the Degradation of the Transcriptional Regulator CtrA. written by Stephen Carl Smith and published by . This book was released on 2013 with total page 102 pages. Available in PDF, EPUB and Kindle. Book excerpt: Caulobacter crescentus is a powerful model organism for understanding cellular differentiation, cell polarity and cell cycle regulation in bacteria. An elaborate network of two-component signaling proteins works to orchestrate the developmental program that characterizes the Caulobacter cell cycle. The essential DNA-binding response regulator CtrA is at the center of this regulatory scheme and acts to control the transcription of>100 genes that are required for cell cycle progression, motility, DNA methylation, morphology and other processes. Because CtrA also inhibits chromosome replication at specific stages of the Caulobacter cell cycle, its activity must be temporarily eliminated in order for DNA replication to occur. Inactivation of CtrA is achieved though dephosphorylation and regulated degradation by the broadly conserved energy-dependent protease ClpXP. In this dissertation, I analyze the roles of three proteins that are required for CtrA degradation in living cells. These are a single domain response regulator CpdR, a protein with no predicted function, RcdA, and a cyclic diguanylate (cdG)-binding protein, PopA. Structure-directed mutagenesis of RcdA was used to probe RcdA function. Results from these studies undermine the prevailing model for RcdA function, which suggest that RcdA does not participate directly in delivering CtrA to ClpXP, but instead acts simply as a localization factor increasing the concentration of CtrA at the cell pole where the protease is located. Additionally, I reconstituted the regulated proteolytic reaction in vitro and probed the role of all three accessory proteins and the small molecule cdG in promoting CtrA degradation. Although ClpXP alone is known to degrade CtrA in vitro, I observed a dramatic acceleration of proteolysis in the presence of the accessory proteins and cdG. This accelerated proteolysis was characterized by a nearly 10-fold reduction in the KM of the reaction, which is consistent with predictions for an adaptor mediated mechanism. I began to characterize protein-protein interactions within the proteolytic complex using in vivo and in vitro techniques. These experiments demonstrate that CtrA interacts directly with PopA in a cdG-dependent fashion. CtrA also interacts directly with RcdA and with ClpX. The CtrA-PopA(cdG) and CtrA-RcdA interactions are weakened or abolished by mutations in the receiver domain of CtrA that slow its proteolysis in vivo. We propose a mechanism in which CtrA forms a ternary complex with PopA and RcdA in response to rising cdG concentrations in the cell. In this complex, PopA and RcdA act as a multi-protein adaptor complex to enhance the delivery of CtrA to the catalytic pore of ClpX. CpdR is required for accelerated CtrA proteolysis, but its precise role is still unknown. The accessory proteins were able to stimulate CtrA degradation even in the presence of a DNA fragment containing a CtrA binding site, which is known to inhibit CtrA proteolysis. Future work will determine if the accessory factors prevent the formation of inhibitory CtrA-DNA complexes or actively disassemble them. This dissertation alters the concept of proteolytic adaptors to include multi-protein complexes and expands the range of mechanisms by which proteolytic adaptors are controlled to include direct regulation by the small molecule cdG.
Book Synopsis DNA Replication Origins in Microbial Genomes by : Feng Gao
Download or read book DNA Replication Origins in Microbial Genomes written by Feng Gao and published by Frontiers Media SA. This book was released on 2016-03-11 with total page 117 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA replication, a central event for cell proliferation, is the basis of biological inheritance. Complete and accurate DNA replication is integral to the maintenance of the genetic integrity of organisms. In all three domains of life, DNA replication begins at replication origins. In bacteria, replication typically initiates from a single replication origin (oriC), which contains several DnaA boxes and the AT-rich DNA unwinding element (DUE). In eukaryotic genomes, replication initiates from significantly more replication origins, activated simultaneously at a specific time. For eukaryotic organisms, replication origins are best characterized in the unicellular eukaryote budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. The budding yeast origins contain an essential sequence element called the ARS (autonomously replicating sequence), while the fission yeast origins consist of AT-rich sequences. Within the archaeal domain, the multiple replication origins have been identified by a predict-and-verify approach in the hyperthermophilic archaeon Sulfolobus. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several short repetitive DNA sequences, known as origin recognition boxes (ORBs). It appears that archaea have a simplified version of the eukaryotic replication apparatus, which has led to considerable interest in the archaeal machinery as a model of that in eukaryotes. The research on replication origins is important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. Therefore, intensive studies have been carried out in the last two decades. The pioneer work to identify bacterial oriCs in silico is the GC-skew analysis. Later, a method of cumulative GC skew without sliding windows was proposed to give better resolution. Meanwhile, an oligomer-skew method was also proposed to predict oriC regions in bacterial genomes. As a unique representation of a DNA sequence, the Z-curve method has been proved to be an accurate and effective approach to predict bacterial and archaeal replication origins. Budding yeast origins have been predicted by Oriscan using similarity to the characterized ones, while the fission yeast origins have been identified initially from AT content calculation. In comparison with the in silico analysis, the experimental methods are time-consuming and labor-intensive, but convincing and reliable. To identify microbial replication origins in vivo or in vitro, a number of experimental methods have been used including construction of replicative oriC plasmids, microarray-based or high-throughput sequencing-based marker frequency analysis, two-dimensional gel electrophoresis analysis and replication initiation point mapping (RIP mapping). The recent genome-wide approaches to identify and characterize replication origin locations have boosted the number of mapped yeast replication origins. In addition, the availability of increasing complete microbial genomes and emerging approaches has created challenges and opportunities for identification of their replication origins in silico, as well as in vivo and in vitro. The Frontiers in Microbiology Research Topic on DNA replication origins in microbial genomes is devoted to address the issues mentioned above, and aims to provide a comprehensive overview of current research in this field.
Book Synopsis Bacterial Chromosomes Under Changing Environmental Conditions by : Leise Riber
Download or read book Bacterial Chromosomes Under Changing Environmental Conditions written by Leise Riber and published by Frontiers Media SA. This book was released on 2021-04-30 with total page 123 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Regulation of Gene Expression by Small RNAs by : Rajesh K. Gaur
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
Book Synopsis Proceedings of the National Academy of Sciences of the United States of America by :
Download or read book Proceedings of the National Academy of Sciences of the United States of America written by and published by . This book was released on 1998 with total page 1428 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis DNA Replication and Human Disease by : Melvin L. DePamphilis
Download or read book DNA Replication and Human Disease written by Melvin L. DePamphilis and published by CSHL Press. This book was released on 2006 with total page 814 pages. Available in PDF, EPUB and Kindle. Book excerpt: At least 5 trillion cell divisions are required for a fertilized egg to develop into an adult human, resulting in the production of more than 20 trillion meters of DNA! And yet, with only two exceptions, the genome is replicated once and only once each time a cell divides. How is this feat accomplished? What happens when errors occur? This book addresses these questions by presenting a thorough analysis of the molecular events that govern DNA replication in eukaryotic cells. The association between genome replication and cell proliferation, disease pathogenesis, and the development of targeted therapeutics is also addressed. At least 160 proteins are involved in replicating the human genome, and at least 40 diseases are caused by aberrant DNA replication, 35 by mutations in genes required for DNA replication or repair, 7 by mutations generated during mitochondrial DNA replication, and more than 40 by DNA viruses. Consequently, a growing number of therapeutic drugs are targeted to DNA replication proteins. This authoritative volume provides a rich source of information for researchers, physicians, and teachers, and will stimulate thinking about the relevance of DNA replication to human disease.
Book Synopsis Prokaryotic Cytoskeletons by : Jan Löwe
Download or read book Prokaryotic Cytoskeletons written by Jan Löwe and published by Springer. This book was released on 2017-05-11 with total page 457 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book describes the structures and functions of active protein filaments, found in bacteria and archaea, and now known to perform crucial roles in cell division and intra-cellular motility, as well as being essential for controlling cell shape and growth. These roles are possible because the cytoskeletal and cytomotive filaments provide long range order from small subunits. Studies of these filaments are therefore of central importance to understanding prokaryotic cell biology. The wide variation in subunit and polymer structure and its relationship with the range of functions also provide important insights into cell evolution, including the emergence of eukaryotic cells. Individual chapters, written by leading researchers, review the great advances made in the past 20-25 years, and still ongoing, to discover the architectures, dynamics and roles of filaments found in relevant model organisms. Others describe one of the families of dynamic filaments found in many species. The most common types of filament are deeply related to eukaryotic cytoskeletal proteins, notably actin and tubulin that polymerise and depolymerise under the control of nucleotide hydrolysis. Related systems are found to perform a variety of roles, depending on the organisms. Surprisingly, prokaryotes all lack the molecular motors associated with eukaryotic F-actin and microtubules. Archaea, but not bacteria, also have active filaments related to the eukaryotic ESCRT system. Non-dynamic fibres, including intermediate filament-like structures, are known to occur in some bacteria.. Details of known filament structures are discussed and related to what has been established about their molecular mechanisms, including current controversies. The final chapter covers the use of some of these dynamic filaments in Systems Biology research. The level of information in all chapters is suitable both for active researchers and for advanced students in courses involving bacterial or archaeal physiology, molecular microbiology, structural cell biology, molecular motility or evolution. Chapter 3 of this book is open access under a CC BY 4.0 license.
Book Synopsis The Cell Cycle and Development by : Gregory R. Bock
Download or read book The Cell Cycle and Development written by Gregory R. Bock and published by John Wiley and Sons. This book was released on 2001-06-29 with total page 274 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book brings together scientists working at the interface between the cell cycle, cell growth and development in a variety of model systems and research paradigms. The focus is on understanding how such diverse developmental inputs can modulate cell cycle regulation and, reciprocally, how a common way of regulating cell cycle progression can participate in different developmental strategies.
Book Synopsis Transcriptional Regulation and Nucleoid Binding Proteins in the Caulobacter Crescentus Swarmer Cell by : Jennifer Christine England
Download or read book Transcriptional Regulation and Nucleoid Binding Proteins in the Caulobacter Crescentus Swarmer Cell written by Jennifer Christine England and published by . This book was released on 2003 with total page 430 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Cumulated Index Medicus written by and published by . This book was released on 2000 with total page 1828 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Control of Macromolecular Synthesis by : Ole Maaløe
Download or read book Control of Macromolecular Synthesis written by Ole Maaløe and published by . This book was released on 1966 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt:
