Proteomic and Transcriptomic Analyses Reveal Novel Aspects of Post-transcriptional Regulation in Saccharomyces Cerevisiae PDF Download
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Author: Gregory A. Cary
Publisher:
ISBN:
Category :
Languages : en
Pages : 129
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Book Description
Although gene expression begins with transcription, there are a variety of mechanisms that cells use to control and tune expression post-transcriptionally. Many post-transcriptional regulatory functions including translational regulation, transcript surveillance, intracellular RNA localization, and RNA decay occur in organelles known as RNA granules. RNA granules, such as processing (P)-bodies, are cytoplasmic accumulations of translationally repressed mRNA and associated proteins that are ubiquitous among eukaryotes. Much of what is known about RNA granule biology has been observed through genetic and cytological experimentation and very few biochemical enrichments of these structures have been reported. In this work I present an affinity enrichment strategy for Dhh1, a conserved core component of P-bodies, from the budding yeast Saccharomyces cerevisiae. We identify proteins co-enriching with Dhh1 using tandem mass spectrometry and show that many known RNA granule proteins are enriched by this approach. We go on to compare the association of proteins with the complex across two environmental conditions to examine the effect of stress induction on RNA granule assemblies. We find that metabolic enzymes and molecular chaperones are typically more abundant in the stress-induced P-body complex and demonstrate that one chaperone, YDJ1, is involved in the stress-induced aggregation of several P-body proteins into cytoplasmic foci. We also identify RNA co-enriching with Dhh1 and detect several classes of catalytic RNA as well as a strong enrichment for the mRNA encoding the P-body protein PAT1. Finally, I present and discuss the characterization of a yeast strain that exhibits sensitivity to the drug puromycin. The puromycin-sensitive strain incorporates the drug into nascent proteins in vivo and I discuss how this is a unique and useful approach for the detection of protein biosynthesis. The techniques developed and employed in this dissertation provide novel perspectives on post-transcriptional regulatory processes and enable further investigations into how these regulatory programs are executed within the cell.
Author: Gregory A. Cary
Publisher:
ISBN:
Category :
Languages : en
Pages : 129
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Book Description
Although gene expression begins with transcription, there are a variety of mechanisms that cells use to control and tune expression post-transcriptionally. Many post-transcriptional regulatory functions including translational regulation, transcript surveillance, intracellular RNA localization, and RNA decay occur in organelles known as RNA granules. RNA granules, such as processing (P)-bodies, are cytoplasmic accumulations of translationally repressed mRNA and associated proteins that are ubiquitous among eukaryotes. Much of what is known about RNA granule biology has been observed through genetic and cytological experimentation and very few biochemical enrichments of these structures have been reported. In this work I present an affinity enrichment strategy for Dhh1, a conserved core component of P-bodies, from the budding yeast Saccharomyces cerevisiae. We identify proteins co-enriching with Dhh1 using tandem mass spectrometry and show that many known RNA granule proteins are enriched by this approach. We go on to compare the association of proteins with the complex across two environmental conditions to examine the effect of stress induction on RNA granule assemblies. We find that metabolic enzymes and molecular chaperones are typically more abundant in the stress-induced P-body complex and demonstrate that one chaperone, YDJ1, is involved in the stress-induced aggregation of several P-body proteins into cytoplasmic foci. We also identify RNA co-enriching with Dhh1 and detect several classes of catalytic RNA as well as a strong enrichment for the mRNA encoding the P-body protein PAT1. Finally, I present and discuss the characterization of a yeast strain that exhibits sensitivity to the drug puromycin. The puromycin-sensitive strain incorporates the drug into nascent proteins in vivo and I discuss how this is a unique and useful approach for the detection of protein biosynthesis. The techniques developed and employed in this dissertation provide novel perspectives on post-transcriptional regulatory processes and enable further investigations into how these regulatory programs are executed within the cell.
Author: Attila Becskei
Publisher: Humana Press
ISBN: 9781617790850
Category : Science
Languages : en
Pages : 0
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Book Description
Regulation of gene expression, a major determinant of gene activity, occupies a central place in molecular biology. Yeast Genetic Networks: Methods and Protocols covers approaches to the systems biological analysis of small-scale gene networks in yeast. Divided into four convenient sections, this detailed volume discusses the methods used to analyze gene expression quantitatively, presents a collection of mathematical and computational tools to analyze stochasticity, adaptation, sensitivity in signal transmission, and oscillations in gene expression, provides instructional methods on how to utilize the tools of quantitative genetics to identify genes that regulate stochasticity and oscillations in gene expression, and concludes with a section devoted to the analysis of conserved gene expression systems and networks in different fungal species. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Yeast Genetic Networks: Methods and Protocols serves as an ideal and valuable resource for both novices and experienced researchers.
Author: Jacqueline Boultwood
Publisher: Springer Science & Business Media
ISBN: 1592591353
Category : Medical
Languages : en
Pages : 302
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Book Description
Over the past 20 years, technological advances in molecular biology have proven invaluable to the understanding of the pathogenesis of human cancer. The application of molecular technology to the study of cancer has not only led to advances in tumor diagnosis, but has also provided markers for the assessment of prognosis and disease progression. The aim of Molecular Ana- sis of Cancer is to provide a comprehensive collection of the most up-to-date techniques for the detection of molecular changes in human cancer. Leading researchers in the field have contributed chapters detailing practical pro- dures for a wide range of state-of-the-art techniques. Molecular Analysis of Cancer includes chapters describing techniques for the identification of chromosomal abnormalities and comprising: fluor- cent in situ hybridization (FISH), spectral karyotyping (SKY), comparative genomic hybridization (CGH), and microsatellite analysis. FISH has a pro- nent role in the molecular analysis of cancer and can be used for the detection of numerical and structural chromosomal abnormalities. The recently described SKY, in which all human metaphase chromosomes are visualized in specific colors, allows for the definition of all chromosomal rearrangements and marker chromosomes in a tumor cell. Protocols for the detection of chromosomal re- rangements by PCR and RT-PCR are described, as well as the technique of DNA fingerprinting, a powerful tool for studying somatic genetic alterations in tumorigenesis.
Author: Peter Csermely
Publisher: Springer Science & Business Media
ISBN: 0387399755
Category : Science
Languages : en
Pages : 218
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Book Description
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.
Author: Stefan Hohmann
Publisher: Springer Science & Business Media
ISBN: 3540456112
Category : Science
Languages : en
Pages : 398
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Book Description
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.
Author: Richard I. Morimoto
Publisher:
ISBN: 9781936113064
Category : Biological transport
Languages : en
Pages : 0
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Book Description
Proper folding of proteins is crucial for cell function. Chaperones and enzymes that post-translationally modify newly synthesized proteins help ensure that proteins fold correctly, and the unfolded protein response functions as a homeostatic mechanism that removes misfolded proteins when cells are stressed. This book covers the entire spectrum of proteostasis in healthy cells and the diseases that result when control of protein production, protein folding, and protein degradation goes awry.
Author: Helmut F van Emden
Publisher: CABI
ISBN: 1780647093
Category : Technology & Engineering
Languages : en
Pages : 716
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Book Description
Aphids are among the major global pest groups, causing serious economic damage to many food and commodity crops in most parts of the world. This revision and update of the well-received first edition published ten years ago reflects the expansion of research in genomics, endosymbionts and semiochemicals, as well as the shift from control of aphids with insecticides to a more integrated approach imposed by increasing resistance in the aphids and government restrictions on pesticides. The book remains a comprehensive and up-to-date reference work on the biology of aphids, the various methods of controlling them and the progress of integrated pest management as illustrated by ten case histories.
Author: Francesc Posas
Publisher: Springer Science & Business Media
ISBN: 3540755691
Category : Science
Languages : en
Pages : 322
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Book Description
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.
Author: Carsten Carlberg
Publisher: Springer
ISBN: 9401777411
Category : Medical
Languages : en
Pages : 219
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Book Description
This textbook aims to describe the fascinating area of eukaryotic gene regulation for graduate students in all areas of the biomedical sciences. Gene expression is essential in shaping the various phenotypes of cells and tissues and as such, regulation of gene expression is a fundamental aspect of nearly all processes in physiology, both in healthy and in diseased states. This pivotal role for the regulation of gene expression makes this textbook essential reading for students of all the biomedical sciences, in order to be better prepared for their specialized disciplines. A complete understanding of transcription factors and the processes that alter their activity is a major goal of modern life science research. The availability of the whole human genome sequence (and that of other eukaryotic genomes) and the consequent development of next-generation sequencing technologies have significantly changed nearly all areas of the biological sciences. For example, the genome-wide location of histone modifications and transcription factor binding sites, such as provided by the ENCODE consortium, has greatly improved our understanding of gene regulation. Therefore, the focus of this book is the description of the post-genome understanding of gene regulation. The purpose of this book is to provide, in a condensed form, an overview on the present understanding of the mechanisms of gene regulation. The authors are not aiming to compete with comprehensive treatises, but rather focus on the essentials. Therefore, the authors have favored a high figure-to-text ratio following the rule stating that “a picture tells more than thousand words”. The content of the book is based on the lecture course, which is given by Prof. Carlberg since 2001 at the University of Eastern Finland in Kuopio. The book is subdivided into 4 sections and 13 chapters. Following the Introduction there are three sections, which take a view on gene regulation from the perspective of transcription factors, chromatin and non-coding RNA, respectively. Besides its value as a textbook, Mechanisms of Gene Regulation will be a useful reference for individuals working in biomedical laboratories.
Author: Herbert Weissbach
Publisher: Elsevier
ISBN: 0323141706
Category : Science
Languages : en
Pages : 739
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Book Description
Molecular Mechanisms of Protein Biosynthesis is a collection of papers dealing with cell-free systems at the molecular level, including transfer RNA; the initiation, elongation, and termination processes; ribosome structure and function; mRNA translation; and DNA-directed in vitro protein synthesis. A couple of papers review tRNA, aminoacyl-tRNA synthetases, and aspects of ribosome structure. One paper discusses affinity labeling in the study of binding and catalytic sites of large complex and heterogeneous systems such as the ribosome. The investigator should be aware of the chemically reactive or photoactivatible analogue reacting specifically with one or more ribosomal components. This reaction should be determined if it is dependent on the correct binding of the affinity label at the functional site. Another paper describes the series of reactions in protein synthesis as the process by which the ribosome moves relative to the messenger RNA. Other papers discuss messenger RNA and its translation, DNA-dependent cell-free protein synthesis, as well as the genetics of the translational apparatus. The collection will benefit microbiologists, biotechnologists, and academicians connected with the biological sciences.
