Download or read book Gene Regulation During Stress Response Transcription in Saccharomyces Cerevisiae written by Christian Miller and published by . This book was released on 2013 with total page 282 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 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 Dynamic Signaling and Adaptation in Saccharomyces Cerevisiae Stress Response Pathways written by Zohreh AkhavanAghdam and published by . This book was released on 2017 with total page 155 pages. Available in PDF, EPUB and Kindle. Book excerpt: Living cells respond to environmental cues through complex signaling and gene regulatory networks. A common theme throughout this thesis will be exploring design principles in biological networks and how they operate dynamically to process information and make decisions. In Chapter 1, we tackle how different types of stresses induce distinct nuclear translocation dynamics of Msn2, an outstanding question in the field. In the absence of stress, PKA phosphorylates Msn2, causing it to be exported out of the nucleus. In response to stress, PKA activity is inhibited, Msn2 is dephosphorylated and translocated into the nucleus. In response to glucose limitation, Msn2 exhibits an initial homogenous pulse of nuclear translocation followed by sporadic nuclear pulses with dose-dependent frequency, but in response to osmotic stress Msn2 undergoes a single translocation pulse with dose-dependent duration. We hypothesized that the difference between glucose limitation and osmotic stress-induced Msn2 dynamics might be a result of glucose limitation-dependent Snf1 activation, since previous studies suggest that Snf1 and PKA mutually inhibit each other. We use modeling and experiments to demonstrate that these different upstream network structures could, in fact, be responsible for the differences we see in Msn2 translocation dynamics. In Chapter 2, we study a recurring scheme in gene regulatory networks, which is combinatorial gene regulation by seemingly redundant transcription factors (TFs), using time-lapse microscopy and microfluidics. We use the seemingly redundant yeast homologous stress responsive TFs Msn2 and Msn4 as a model to quantitatively study the functional relevance of closely related TFs in the same single cells and find that Msn2 and Msn4 have non-redundant and distinct functions in combinatorial gene regulation. In response to a transient input, either Msn2 or Msn4 alone is sufficient to induce the expression of target genes with fast kinetics promoters. Target genes with slow kinetics promoters, however, require activation of both Msn2 and Msn4 in these conditions. Importantly, slow kinetic promoter activation is dependent on duration of the upstream signal because in response to a prolonged input, slow kinetic promoter activation no longer requires both Msn2 and Msn4. Thus, in Chapter 2, we determine that coordinated gene regulation by seemingly redundant TFs is not fixed, but rather dependent on the dynamics of upstream signals. In Chapter 3, we demonstrate that cells retain a memory of many of upstream signaling events that occur in response to stress, which primes the cells to respond to future severe stress events. We use microfluidics and time-lapse microscopy to modulate the amplitude and duration of priming stimulus and also increase the break time in between the priming stimulus and severe stress. Using this system, we have determined that cells acquire an amplitude-dependent short-term memory of priming stimulus, which is induced and lost rapidly, and a duration-dependent long-term memory which is stable for a long period of time before finally declining after 100 minutes. We use this information about the dynamical specificity of different types of cellular memory and their stability to determine the cellular pathways responsible for the observed memory.

Download or read book Mechanism and Regulation of the Stress Response in Saccharomyces Cerevisiae written by Eric Edward Powers and published by . This book was released on 1998 with total page 356 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 Differential Activation of Homologous Transcription Factors Diversifies Stress Mediated Gene Expression Programs in S Cerevisiae written by Joydeb Sinha and published by . This book was released on 2016 with total page 38 pages. Available in PDF, EPUB and Kindle. Book excerpt: Homolog transcription factors have emerged from genome duplication events in evolutionary history, resulting in the co-existence of many similar proteomic pairs in eukaryotic cells. Although a large number of homologs have diversified over time to obtain unique roles from their partners, others have remained relatively conserved, limiting their downstream interactions to identical target genes. The functional advantages arising from the retention of such redundancy in the proteome have remained elusive in the context of biological design. Here, using quantitative single-cell imaging and microfluidics, we find that the yeast general stress response transcription factor Msn2 and its seemingly redundant homolog Msn4 play distinct roles in mediating the gene expression in response to environmental stressors, which is contrary to previous belief. We observe at the single cell level, that although Msn4 exhibits identical translocation dynamics to Msn2, the level of its nuclear translocation during stress is significantly more heterogeneous than that of Msn2. As a result, while target genes with fast kinetics are expressed in most of the cells, slower target genes are induced only in the fraction of cells with high Msn4 activity. We further show that this Msn4-dependent diversification in the gene expression program in single cells is important for the adaptive response to environmental stresses.

Download or read book Relating Stress to Strain at the Level of Gene Expression written by Stephen J. Callister and published by . This book was released on 2004 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book A Handbook of Statistical Analyses using R Third Edition written by Torsten Hothorn and published by CRC Press. This book was released on 2014-06-25 with total page 454 pages. Available in PDF, EPUB and Kindle. Book excerpt: Like the best-selling first two editions, A Handbook of Statistical Analyses using R, Third Edition provides an up-to-date guide to data analysis using the R system for statistical computing. The book explains how to conduct a range of statistical analyses, from simple inference to recursive partitioning to cluster analysis. New to the Third Edition Three new chapters on quantile regression, missing values, and Bayesian inference Extra material in the logistic regression chapter that describes a regression model for ordered categorical response variables Additional exercises More detailed explanations of R code New section in each chapter summarizing the results of the analyses Updated version of the HSAUR package (HSAUR3), which includes some slides that can be used in introductory statistics courses Whether you’re a data analyst, scientist, or student, this handbook shows you how to easily use R to effectively evaluate your data. With numerous real-world examples, it emphasizes the practical application and interpretation of results.

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 Distinct Binding Sites and Signaling Pathways Regulate the Saccharomyces Cerevisiae Heat Shock Transcription Factor written by Nicholas Santoro and published by . This book was released on 2000 with total page 478 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Download or read book Demystifying the Role of the Cap Binding Complex CBC Within the Gene Expression Network in Saccharomyces Cerevisiae written by Julia McBride Claggett and published by . This book was released on 2011 with total page 239 pages. Available in PDF, EPUB and Kindle. Book excerpt: The highly conserved Cap Binding Complex (CBC) is comprised of two subunits, Cbp20 and Cbp80, and binds to the 5' end of pre-mRNA as it emerges from the transcribing RNA polymerase (Pol II). Evidence suggesting a role for the CBC in multiple reactions during gene expression, including transcription, splicing, 3' end processing, and RNA export, prompted us to hypothesize that the CBC is involved in coupling these reactions, and that this coordinated regulation facilitates the ability of a cell to respond to stress. The research presented in this dissertation specifically dissects the roles of the CBC in splicing and in transcription and provides insight into a mechanism by which the CBC might contribute to the coupling of these two reactions in Saccharomyces cerevisiae. We have demonstrated that the CBC is specifically required for the splicing of two intron-containing genes with a particular non-consensus 5' splice site, SUS1 and GCR1. Through its effects on splicing, we found that the CBC contributes to the regulation of a histone modification and the acitivity of a key glycolytic transcription factor, resulting in genome-wide changes to gene expression when the CBC is deleted. We discovered that the CBC is down-regulated at multiple levels in response to nutrient stress, suggesting that the coordinated activities of the CBC are particularly important under these conditions. One of these levels of regulation appears to be proteolysis by the proteasome. Furthermore, a role for the CBC in repressing expression of Rpn4, a critical regulator of proteasome levels, suggests that the CBC is involved in a feedback loop in which its targeting to the proteasome is determined by its ability to influence gene expression. Directed mutagenesis of evolutionarily-conserved domains of Cbp80 allowed us to uncouple the functions of the CBC in gene expression revealing a role for the CBC in transcription that is independent of its ability to act in splicing. In sum, the findings presented here demystify the role of the CBC in gene expression by enhancing our understanding of the CBC's role in splicing, demonstrating novel functions for the CBC in transcription, identifying multiple mechanisms by which the CBC is regulated, and illustrating a requirement for the CBC in the cellular stress response.

Download or read book Stress Regulation of Heat Shock Transcription Factors written by Xiao-Dong Liu and published by . This book was released on 1999 with total page 394 pages. Available in PDF, EPUB and Kindle. Book excerpt:

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 Cellular Memory of a Prior Stress Response in Saccharomyces Cerevisiae written by and published by . This book was released on 2012 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: Precise optimal conditions are necessary for the growth and survival of organisms. Maintaining these conditions in the face of a fluctuating environment is crucial. In free-living microbes, this is uniquely challenging since they have neither a multicellular body for protection, nor the ability to "walk away". Much of the adaptation to changing environments comes from cellular responses. It has been observed that pretreatment with mild stress can confer resistance to what otherwise be a lethal dose of stress in various organisms. In fact, a cellular memory of past stress experiences has been observed in several organisms and across a variety of experiences, including bacteria 'remembering' prior nutritional status and amoeba `learning' to anticipate future environmental conditions. Here, we show that Saccharomyces cerevisiae maintains a multifaceted memory of prior stress exposure. We previously demonstrated that yeast cells exposed to a mild dose of salt acquire subsequent tolerance to severe doses of hydrogen peroxide. We set out to characterize the retention of acquired tolerance and in the process uncovered two distinct aspects of cellular memory. First, we found that hydrogen peroxide resistance persisted for 4-5 generations after cells were removed from the prior salt treatment and was transmitted to daughter cells that never directly experienced the pretreatment. Maintenance of this memory did not require nascent protein synthesis after the initial salt pretreatment, but rather required long-lived cytosolic catalase Ctt1p that was synthesized during salt exposure and then distributed to daughter cells during subsequent cell divisions. In addition to and separable from the memory of hydrogen peroxide resistance, these cells also displayed a faster gene expression response to subsequent stress at over a thousand genes, representing transcriptional memory. The faster gene expression response requires the nuclear pore component Nup42p and serves an important function by facilitating faster re-acquisition of hydrogen peroxide tolerance after a second cycle of salt exposure. Memory of prior stress exposure and the ability for a faster response to stress likely provides a significant advantage to microbial populations living in ever-changing environments.

Download or read book The Molecular Biology of Schizosaccharomyces pombe written by Richard Egel and published by Springer Science & Business Media. This book was released on 2013-03-14 with total page 464 pages. Available in PDF, EPUB and Kindle. Book excerpt: The fission yeast Schizosaccharomyces pombe is the favoured tool of many productive research groups throughout the world, serving as a useful model for fundamental principles and mechanisms, such as genome organization, differential gene regulation, cell-cycle control, signal transduction, or cellular morphogenesis. This book collates the current state of knowledge derived from molecular studies in this simple eukaryotic microorganism. The entire sequence of its genome has been completed, emphasizing the comparative value and model status of this yeast. The individual chapters, highlighting up-to-date views on prominent aspects of molecular organization, were written by active research scientists, presenting the results of their investigations to other workers in neighbouring fields. This book intends to serve the fission yeast community as a handy source of reference for years to come. It will also be of particular value to the ever-increasing number of researchers starting to look into fission yeast affairs for comparative reasons from other platforms of molecular genetics and cell biology.

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.