Download or read book Transcriptional Regulation of a Stress Inducible Gene of Saccharomyces Cerevisiae written by Naoko Kobayashi and published by . This book was released on 1990 with total page 422 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Regulation of Stress Induced Gene Expression in Saccharomyces Cerevisiae written by Vasudha Bharatula and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Transcription initiation is complex process involving transcription factors(TF), co-activators, nucleosome remodelers and the pre-initiation complex (PIC);general transcription factors (GTF) and RNA polymerase II (RNAP2). The spatiotemporalorganization of these different proteins and their role in regulatingplasticity and selectivity of transcriptional reprogramming in various stressesremains unknown. I describe the role of Multicopy Suppressor of Snf1 mutation(Msn2); a stress responsive transcription factor, Mediator (coactivator) andnucleosome remodeling in fine-tuning gene expression in response to stress inyeast.Msn2 exhibits distinct patterns of nucleo-cytoplasmic oscillations indifferent stresses. I determined that Msn2 target genes exhibited fast or slowinduction kinetics in response to transient and persistent Msn2 nuclearoccupancy respectively. Chromatin immunoprecipitation studies revealed thatMsn2 binds promoters of common stress genes as well as condition specificgenes in nutrient and oxidative stresses, suggesting that TF dynamics could playa role in selective gene regulation in different stresses. Additionally, Msn2binding to ~30 oxidative genes was dependent on Yap1. However, deleting Msn2did not lead to a significant decrease in expression of oxidative stress responsegenes as did the absence of Yap1. These results suggest that indirectcooperativity between Msn2 and Yap1 could lead to selective promoter bindingbut the effects of such interactions on gene expression remain unclear.I studied the role of Mediator in native conditions, where its function has not been adequately addressed. Mediator occupies chromosomal interacting domains (CID), which mark boundaries between interacting genomic regions, suggesting that Mediator could play a significant role in higher-order genome organization along with functioning as a coactivator.Finally, I assessed the combined effect of Msn2, Mediator and nucleosome remodeling on gene expression upon nutrient deprivation. Both Msn2 and Mediator are selectively recruited to promoters of genes activated and repressed in nutrient stress. Genes activated by Msn2 exhibited rapid loss of nucleosomes, in an Msn2 dependent manner. In contrast, repression of genes was not accompanied by a significant gain in nucleosomes, suggesting additional mechanisms of repression could exist. The absence of Msn2, significantly decreased Mediator recruitment at promoters of target genes, indicating that Mediator- TF interactions are crucial for gene expression changes in stress. Interestingly, both RNAP2 and Mediator remained poised at promoters of repressed genes, possibly to re-initiate transcription once the stress has passed.These findings offer novel insights on how Msn2 regulates expression of specific genes depending on the environment by modulating its dynamics and genomic binding. The binding of Msn2 helps recruit Mediator and facilitate nucleosome loss at genes induced in stress. Whereas, repressed genes seems to possess Mediator and RNAP2 in an inactive form which could be the mechanism of repression and a way to activate these genes immediate after stress.
Download or read book Yeast Stress Responses written by Stefan Hohmann and published by Springer Science & Business Media. This book was released on 2007-10-23 with total page 398 pages. Available in PDF, EPUB and Kindle. Book excerpt: Every cell has developed mechanisms to respond to changes in its environment and to adapt its growth and metabolism to unfavorable conditions. The unicellular eukaryote yeast has long proven as a particularly useful model system for the analysis of cellular stress responses, and the completion of the yeast genome sequence has only added to its power This volume comprehensively reviews both the basic features of the yeast genral stress response and the specific adapations to different stress types (nutrient depletion, osmotic and heat shock as well as salt and oxidative stress). It includes the latest findings in the field and discusses the implications for the analysis of stress response mechanisms in higher eukaryotes as well.
Download or read book Mechanisms Involved in Transcriptional Regulation of the GPD1 Gene During Hyper osmotic Stress in Saccharomyces Cerevisiae written by Homan Alipour and published by . This book was released on 2002 with total page 100 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Mechanisms of Post Transcriptional Regulation in S Cerevisiae written by Vince Harjono and published by . This book was released on 2022 with total page 111 pages. Available in PDF, EPUB and Kindle. Book excerpt: Post-transcriptional regulation represents a powerful and versatile mechanism to fine-tune gene expression to meet cellular and environmental demands. One important aspect of post-transcriptional regulation involves regulation of protein translation, the process of building proteins from a messenger RNA. In this dissertation, I use biochemical and molecular biology techniques to study how translation is mechanistically regulated by both mRNA and protein factors. In chapter 2, I discuss the development of a quantitative method in eukaryotes to measure ribosomal stalls of cis-mRNA factors on protein elongation. We find that different distributions of nonoptimal codons trigger different surveillance and rescue pathways despite similar levels of elongation delay. In chapter 3, I explore the relationship between translatability and mRNA localization during glucose starvation and investigate potential factors that influence this relationship. We find that a complex made from Rvb1 and Rvb2 is involved in promoter-directed cytoplasmic fate in a subset of stress response genes in glucose starvation. Furthermore, we use carefully designed reporters to interrogate how translatability determines cytoplasmic localization and find that active translation is linked to exclusion from stress-induced cytoplasmic granules. Finally in chapter 4, I discuss improvements on the method we have developed, possible future directions for the work described in this dissertation, and my concluding remarks.
Download or read book Post transcriptional Regulation of Gene Expression by the PSI Prion of Saccharomyces Cerevisiae written by Jonathan Paul Richardson and published by . This book was released on 2001 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Transcriptional Regulation of Oxygen responsive Genes in Saccharomyces Cerevisiae written by Johanna Josephina Maria ter Linde and published by . This book was released on 2003 with total page 131 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Aspects of the Stress Response Chaperones Membranes and Networks written by Peter Csermely and published by Springer Science & Business Media. This book was released on 2007-08-09 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book makes a novel synthesis of the molecular aspects of the stress response and long term adaptation processes with the system biology approach of biological networks. Authored by an exciting mixture of top experts and young rising stars, it provides a comprehensive summary of the field and identifies future trends.
Download or read book Synthetic Biology written by Christina Smolke and published by John Wiley & Sons. This book was released on 2018-02-28 with total page 532 pages. Available in PDF, EPUB and Kindle. Book excerpt: A review of the interdisciplinary field of synthetic biology, from genome design to spatial engineering. Written by an international panel of experts, Synthetic Biology draws from various areas of research in biology and engineering and explores the current applications to provide an authoritative overview of this burgeoning field. The text reviews the synthesis of DNA and genome engineering and offers a discussion of the parts and devices that control protein expression and activity. The authors include information on the devices that support spatial engineering, RNA switches and explore the early applications of synthetic biology in protein synthesis, generation of pathway libraries, and immunotherapy. Filled with the most recent research, compelling discussions, and unique perspectives, Synthetic Biology offers an important resource for understanding how this new branch of science can improve on applications for industry or biological research.
Download or read book Stress Activated Protein Kinases written by Francesc Posas and published by Springer Science & Business Media. This book was released on 2008-01-24 with total page 322 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this book leading researchers in the field discuss the state-of-the-art of many aspects of SAPK signaling in various systems from yeast to mammals. These include various chapters on regulatory mechanisms as well as the contribution of the SAPK signaling pathways to processes such as gene expression, metabolism, cell cycle regulation, immune responses and tumorigenesis. Written by international experts, the book will appeal to cell biologists and biochemists.
Download or read book Stress Inducible Cellular Responses written by U. Feige and published by Birkhäuser. This book was released on 2013-03-11 with total page 487 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book will deal with heat shock proteins and more generally with stress-related inducible gene expression as a pleiotropic adaptive response to stress. It presents a textbook-like overview of the field not only to heat shock experts, but to physiologists, pharmacologists, physicians, neuropsychologists and others as well. It is intended to be a state-of-the-art and perspective book rather than an up-to-date presentation of recent data. It should provide a basis for new experimetal approaches to fields at the edge of the classical heat shock field. Drugs, UV irradiation and environmental toxics will be considered as important modulators of the stress response. Radical scavengers such as superoxide dismutases and inducible regulatory proteins of metallic ion status such as ferritin as well as immunophilins and protein disulfide isomerases will be considered within the frame of stress proteins. The potential practical applications of heat shock proteins in toxicology and medicine for the diagnosis, prognosis and eventually therapy of clinical conditions associated with an increased oxidative burden will be outlined. The role of heat shock proteins in the modulation of immune responses will also be included. The book considers heat shock from a broad perspective including fields for which heat-shock may become of importance in the very near future such as cellular responses to environmental stresses and complex stress responses under specific conditions. It was also felt timely to incorporate a whole section on medical and technological applications of stress proteins. The book will be invaluable for all those working on stress and is intended for every "stress laboratory" as a source of knowledge and perspectives.
Download or read book In VIVO Footprinting written by I.L. Cartwright and published by Elsevier Science. This book was released on 1997-08-22 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The revolution in biological research initiated by the demonstration that particular DNA molecules could be isolated, recombined in novel ways, and conveniently replicated to high copy number in vivo for further study, that is, the recombinant DNA era, has spawned many additional advances, both methodological and intellectual, that have enhanced our understanding of cellular processes to an astonishing degree. As part of the subsequent outpouring of information, research exploring the mechanisms of gene regulation, both in prokaryotes and eukaryotes (but particularly the latter), has been particularly well represented. Although no one technical approach can be said to have brought the filed to its current level of sophistication, the ability to map the interactions of trans-acting factors with their DNA recognition sequences to a high level of precision has certainly been one of the more important advances. This "footprinting" approach has become almost ubiquitous in gene regulatory studies; however, it is in its "in vivo" application that ambiguities, confusions, and inconsistencies that may arise from a purely "in vitro"-based approach can often be resolved and placed in their proper perspective. Put more simply, that an interaction can be demonstrated to occur between purified factors and a particular piece of DNA in a test tube does not, of course, say anything regarding whether such interactions are occurring in vivo. The ability to probe for such interactions as they occur inside cells, with due attention paid to the relevant developmental stage, or to the tissue specificity of the interaction being probed, has made in vivo footprinting approach an invaluable adjunct to the "gene jockey's" arsenal of weapons.
Download or read book RNA Exosome written by Torben Heick Jensen and published by Springer Science & Business Media. This book was released on 2011-06-29 with total page 161 pages. Available in PDF, EPUB and Kindle. Book excerpt: The diversity of RNAs inside living cells is amazing. We have known of the more “classic” RNA species: mRNA, tRNA, rRNA, snRNA and snoRNA for some time now, but in a steady stream new types of molecules are being described as it is becoming clear that most of the genomic information of cells ends up in RNA. To deal with the enormous load of resulting RNA processing and degradation reactions, cells need adequate and efficient molecular machines. The RNA exosome is arising as a major facilitator to this effect. Structural and functional data gathered over the last decade have illustrated the biochemical importance of this multimeric complex and its many co-factors, revealing its enormous regulatory power. By gathering some of the most prominent researchers in the exosome field, it is the aim of this volume to introduce this fascinating protein complex as well as to give a timely and rich account of its many functions. The exosome was discovered more than a decade ago by Phil Mitchell and David Tollervey by its ability to trim the 3’end of yeast, S. cerevisiae, 5. 8S rRNA. In a historic account they laid out the events surrounding this identification and the subsequent birth of the research field. In the chapter by Kurt Januszyk and Christopher Lima the structural organization of eukaryotic exosomes and their evolutionary counterparts in bacteria and archaea are discussed in large part through presentation of structures.
Download or read book Translational Control of Gene Expression written by Nahum Sonenberg and published by CSHL Press. This book was released on 2001 with total page 1034 pages. Available in PDF, EPUB and Kindle. Book excerpt: Since the 1996 publication of Translational Control, there has been fresh interest in protein synthesis and recognition of the key role of translation control mechanisms in regulating gene expression. This new monograph updates and expands the scope of the earlier book but it also takes a fresh look at the field. In a new format, the first eight chapters provide broad overviews, while each of the additional twenty-eight has a focus on a research topic of more specific interest. The result is a thoroughly up-to-date account of initiation, elongation, and termination of translation, control mechanisms in development in response to extracellular stimuli, and the effects on the translation machinery of virus infection and disease. This book is essential reading for students entering the field and an invaluable resource for investigators of gene expression and its control.
Download or read book Yeast Systems Biology written by Juan I. Castrillo and published by Humana Press. This book was released on 2011-08-23 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Systems Biology aims at deciphering the genotype-phenotype relationships at the levels of genes, transcripts (RNAs), peptides, proteins, metabolites, and environmental factors participating in complex cellular networks in order to reveal the mechanisms and principles governing the behavior of complex biological systems. Yeast Systems Biology: Methods and Protocols presents an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote, perspective on the latest experimental and computational techniques for systems biology studies, most of which were first designed for and validated in yeast, and selected examples of yeast systems biology studies and their applications in biotechnology and medicine. These experiments under controlled conditions can uncover the complexity and interplay of biological networks with their dynamics, basic principles of internal organization, and balanced orchestrated functions between organelles in direct interaction with the environment as well as the characterization of short and long-term effects of perturbations and dysregulation of networks that may illuminate the origin of complex human diseases. Written for the highly successful Methods in Molecular BiologyTM series, this volume contains the kind of detailed description and implementation advice that is crucial for getting optimal results. Practical and cutting-edge, Yeast Systems Biology: Methods and Protocols serves researchers interested in comprehensive systems biology strategies in well-defined model systems with specific objectives as well as a better knowledge of the latest post-genomic strategies at all ‘omic levels and computational approaches towards analysis, integration, and modeling of biological systems, from single-celled organisms to higher eukaryotes.
Download or read book Molecular Mechanisms in Yeast Carbon Metabolism written by Jure Piškur and published by Springer. This book was released on 2014-05-06 with total page 328 pages. Available in PDF, EPUB and Kindle. Book excerpt: Yeast is one of the most studied laboratory organisms and represents one of the most central models to understand how any eukaryote cell works. On the other hand, yeast fermentations have for millennia provided us with a variety of biotech products, like wine, beer, vitamins, and recently also with pharmaceutically active heterologous products and biofuels. A central biochemical activity in the yeast cell is the metabolism of carbon compounds, providing energy for the whole cell, and precursors for any of the final fermentation products. A complex set of genes and regulatory pathways controls the metabolism of carbon compounds, from nutrient sensing, signal transduction, transcription regulation and post-transcriptional events. Recent advances in comparative genomics and development of post-genomic tools have provided further insights into the network of genes and enzymes, and molecular mechanisms which are responsible for a balanced metabolism of carbon compounds in the yeast cell, and which could be manipulated in the laboratory to increase the yield and quality of yeast biotech products. This book provides a dozen of most comprehensive reviews on the recent developments and achievements in the field of yeast carbon metabolism, from academic studies on gene expression to biotechnology relevant topics.
Download or read book Yeast Functional Genomics written by Frédéric Devaux and published by Humana. This book was released on 2015-10-20 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a collection of protocols for the study of DNA-DNA contact maps, replication profiles, transcription rates, RNA secondary structures, protein-RNA interactions, ribosome profiling and quantitative proteomes and metabolomes. Written for the Methods in Molecular Biology series, 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 practical, Yeast Functional Genomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.
