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Characterization Of Novel Rna Protein Regulatory Interactions In Saccharomyces Cerevisiae
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Book Synopsis Characterization of Novel RNA-protein Regulatory Interactions in Saccharomyces Cerevisiae by : Nikoleta Georgieva Tsvetanova
Download or read book Characterization of Novel RNA-protein Regulatory Interactions in Saccharomyces Cerevisiae written by Nikoleta Georgieva Tsvetanova and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The dynamic processes of a living cell depend on the coordinated temporal and spatial regulation of the many steps of gene expression. Transcription regulation is one control point of gene expression, and a gene can also be regulated post-transcriptionally, by RNA-binding proteins (RBPs). The biological significance of post-transcriptional regulation is especially evident in cases, where RBP binding controls the temporal precision of suppression and activation of important cellular stress responses. We developed a proteome-wide experimental approach for in vitro identification of novel RBPs and RNA-protein interactions in Saccharomyces cerevisiae. We found 12 novel RNA-binding proteins, the majority of which, surprisingly, are currently annotated as enzymes with roles in metabolic processes. We next used this proteomic approach to screen for proteins specifically interacting with the HAC1 RNA, which mediates activation of the yeast unfolded protein response (UPR). We found that HAC1 associated reproducibly with four small yeast GTPases, three of which are of the Ypt family of ras-GTPases. We further characterized one of them, the yeast Rab1 homolog Ypt1, and showed that Ypt1 interacted with unspliced HAC1 RNA only in the absence of ER stress. Selective Ypt1 depletion increased HAC1 RNA stability and expression, and also affected timely recovery from UPR. By developing and applying a novel proteomic approach for studying RNA-protein interactions, we established Ypt1 as an important regulator of HAC1 expression and UPR signaling. This unexpected protein-RNA interaction provides a biochemical mechanism for coordinating the key cellular processes of vesicle trafficking and ER homeostasis.
Book Synopsis RNA-protein Interactions by : Kiyoshi Nagai
Download or read book RNA-protein Interactions written by Kiyoshi Nagai and published by Oxford University Press, USA. This book was released on 1994 with total page 302 pages. Available in PDF, EPUB and Kindle. Book excerpt: The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Book Synopsis Identification of RNA Regulatory Information in the Saccharomyces Cerevisiae Transcriptome by : Daniel Patrick Riordan
Download or read book Identification of RNA Regulatory Information in the Saccharomyces Cerevisiae Transcriptome written by Daniel Patrick Riordan and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The unique post-transcriptional behavior of each mRNA is thought to be largely determined by features present in its molecular sequence, representing a type of RNA regulatory code. However, the details by which distinct regulatory outcomes are programmed into the sequences of different transcripts are mostly unknown. We set out to identify features of yeast mRNAs that influence their post-transcriptional fates. Using bioinformatic and in vitro selection approaches, we characterized several RNA recognition elements involved in mediating specific interactions with individual yeast RNA-binding proteins (RBPs). Most of the RNA elements we uncovered were associated with significant mRNA expression changes and were phylogenetically conserved in related yeasts, providing insights into the function and evolution of the corresponding interactions. We also analyzed RNA-protein interaction sites for the yeast Puf3 RBP by high-throughput sequencing under different growth conditions. These results provided high-resolution experimental evidence for Puf3 binding at consensus RNA elements in the transcriptome, and enabled detailed comparisons of individual interaction sites. Finally, we developed complementary methods for transcriptome-wide mapping of potential sites of RNA 2'-O-methylation. Application of these methods to the yeast transcriptome successfully recovered known sites of RNA modification and suggested that ribose methylation of functionally-related transcripts may occur and influence the regulation of endogenous yeast mRNAs. Overall, these results contribute to understanding of how RNA sequence features help to specify global differences in gene expression characteristics.
Book Synopsis Mapping RNA Protein Interactions in Saccharomyces Cerevisiae by : Daniel Michael Klass
Download or read book Mapping RNA Protein Interactions in Saccharomyces Cerevisiae written by Daniel Michael Klass and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: We are on the threshold of a new era in our understanding of that fantastic feat of regulation at the core of life itself--gene expression. The rapid pace of new developments in genome-wide, high-throughput technologies has allowed us unprecedented access to observe multiple stages of the gene expression program for nearly the entire genome. This has revealed a widespread discordance between mRNA abundance and protein abundance for many genes whose expression changes in response to environmental stimuli, and a significant coordination of post-transcriptional regulation for specific sets of related mRNAs at the levels localization, translation, decay, and the noise in gene expression. Despite this evidence suggesting the existence of a coordinated regulatory framework that potentially affects the fate of every mRNA in the cell, our efforts to discern the underlying structure and regulatory themes are hindered by an incomplete understanding of RNA-protein interactions. To advance our comprehension of post-transcriptional regulation, we developed new tools to identify which proteins bind to RNA, which of those bind concurrently, which RNAs are bound by a given protein, and where each protein binds on each RNA. Using our proteomic tools we discovered hundreds unexpected RNA binding proteins, uncovered new RNA binding domains, identified widespread, concurrent binding with several RNA binding proteins, and inferred functional information from the simultaneous binding partners of several RNA binding proteins. We used our genomic, sequencing-based tools to systematically interrogate a large set of diverse RNA binding proteins and we discerned new themes from the resulting data. This revealed significant differences in function, localization, and regulation among the proteins encoded by the targets of a given RNA binding protein based on binding position. These results suggest that the functional consequences of the RBP-RNA interaction are determined not only by whether an mRNA is bound by an RBP but also by the position of the binding site within the mRNA and its relation to the other RBPs that bind the same mRNA. Overall, we found evidence of an extensive regulatory framework involving hundreds of RNA binding proteins, encompassing nearly the entire transcriptome, and extending our understanding of the RNA-protein interactions at the heart of post-transcriptional regulation.
Book Synopsis Characterization of Elements Regulating Transcription of the Enolase Genes of Saccharomyces Cerevisiae and the Mechanism of GCR1 Control by : Catherine Elizabeth Willett
Download or read book Characterization of Elements Regulating Transcription of the Enolase Genes of Saccharomyces Cerevisiae and the Mechanism of GCR1 Control written by Catherine Elizabeth Willett and published by . This book was released on 1992 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Characterization of Post-translational Modification and Protein-protein Interaction of RNA-binding Protein 1, Rbp1p, in Saccharomyces Cerevisiae by : 方瓊瑩
Download or read book Characterization of Post-translational Modification and Protein-protein Interaction of RNA-binding Protein 1, Rbp1p, in Saccharomyces Cerevisiae written by 方瓊瑩 and published by . This book was released on 2007 with total page 156 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Identification and Characterization of Novel Proteins and Pathways for MRNA Degradation and Quality Control in Saccharomyces Cerevisiae by :
Download or read book Identification and Characterization of Novel Proteins and Pathways for MRNA Degradation and Quality Control in Saccharomyces Cerevisiae written by and published by . This book was released on 2006 with total page 270 pages. Available in PDF, EPUB and Kindle. Book excerpt: In eukaryotes, mRNA decay pathways are important for cellular response to various physiological conditions and also function in co-translational quality control systems that target translationally aberrant mRNAs for degradation. My work on identification and characterization of novel components and pathways of mRNA degradation and quality control in Saccharomyces cerevisiae is summarized below. I have identified Edc3p as a novel protein important for mRNA decay. Deletion of Edc3p leads to a defect in mRNA decay in strains deficient in decapping enzymes and, in combination with a block to the 3' to 5' decay pathway, causes exaggerated growth defects and synthetic lethality. An Edc3p-GFP fusion protein localizes in processing bodies, which are specialized cytoplasmic foci containing decapping proteins. Together, these observations indicate that Edc3p directly interacts with the decapping complex to stimulate the mRNA decapping rate. Quality control during mRNA translation is critical for regulation of gene expression. My work shows that yeast mRNAs with defects in translation elongation, due to strong translational pauses, are recognized and targeted for degradation via an endonucleolytic cleavage in a novel process referred to as No-Go Decay (NGD). The cellular mRNA decay machinery degrades the 5' and 3' cleavage products produced by NGD. NGD is translation-dependent, occurs in a range of mRNAs and can be induced by a variety of elongation pauses. These results indicate NGD may occur at some rate inresponse to any stalled ribosome. I also show that two highly conserved proteins, Dom34p and Hbs1p, homologous to the eukaryotic release factors eRF1 and eRF3 respectively, are required for NGD. Further characterization of the No-Go decay pathway indicates that Dom34p function during NGD is conserved across species. Identification of RPS30, a small ribosomal protein as a trans-acting factor during NGD suggests that the ribosome may have a novel role during NGD. Other experiments indicate that the No-Go decay pathway may cross talk with the unfolded protein response pathway. The identification of No-Go decay as a novel quality control pathway during translation elongation supports the existence of a global cellular mechanism for maintenance of translational quality control.
Book Synopsis Functional Characterization of RNA-binding Protein Rbp1p and Its Interacting Proteins in Saccharomyces Cerevisiae by : 張翎君
Download or read book Functional Characterization of RNA-binding Protein Rbp1p and Its Interacting Proteins in Saccharomyces Cerevisiae written by 張翎君 and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Genomic and Precision Medicine by : Geoffrey S. Ginsburg
Download or read book Genomic and Precision Medicine written by Geoffrey S. Ginsburg and published by Academic Press. This book was released on 2022-04-09 with total page 379 pages. Available in PDF, EPUB and Kindle. Book excerpt: Genomic and Precision Medicine: Oncology, Third Edition focuses on the applications of genome discovery as research points to personalized cancer therapies. Each chapter is organized to cover the application of genomics and personalized medicine tools and technologies to a) Risk Assessment and Susceptibility, b) Diagnosis and Prognosis, c) Pharmacogenomics and Precision Therapeutics, and d) Emerging and Future Opportunities in the field. Provides a comprehensive volume written and edited by oncology genomic specialists for oncology health providers Includes succinct commentary and key learning points that will assist providers with their local needs for implementation of genomic and personalized medicine into practice Presents an up-to-date overview on major opportunities for genomic and personalized medicine in practice Covers case studies that highlight the practical use of genomics in the management of patients
Book Synopsis RNA-RNA Interactions by : Frank J. Schmidt
Download or read book RNA-RNA Interactions written by Frank J. Schmidt and published by Humana Press. This book was released on 2014-10-29 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this volume expert researchers in the field detail many of the methods which are now commonly used to study RNA. These methods are presented as a guidebook to scientists who are experienced with RNA research and want to brush up on a new technique. 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 key tips on troubleshooting and avoiding known pitfalls. Thorough and intuitive, RNA-RNA Interactions: Methods and Protocols guides scientists investigating biological systems and studying RNA.
Book Synopsis Serotonin Receptors in Neurobiology by : Amitabha Chattopadhyay
Download or read book Serotonin Receptors in Neurobiology written by Amitabha Chattopadhyay and published by CRC Press. This book was released on 2007-05-17 with total page 230 pages. Available in PDF, EPUB and Kindle. Book excerpt: A number of developments spanning a multitude of techniques makes this an exciting time for research in serotonin receptors. A comprehensive review of the subject from a multidisciplinary perspective, Serotonin Receptors in Neurobiology is among the first books to include information on serotonin receptor knockout studies. With contributions from l
Book Synopsis Genetics and Biotechnology by : Ulrich Kück
Download or read book Genetics and Biotechnology written by Ulrich Kück and published by Springer Science & Business Media. This book was released on 2013-03-09 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Mycology, the study of fungi, originated as a subdiscipline of botany and was a descriptive discipline, largely neglected as an experimental science until the early years of this century. A seminal paper by Blakeslee in 1904 provided evidence for self incompatibility, termed "heterothallism", and stimulated interest in studies related to the control of sexual reproduction in fungi by mating-type specificities. Soon to follow was the demonstration that sexually reproducing fungi exhibit Mendelian inheritance and that it was possible to conduct formal genetic analysis with fungi. The names Burgeff, Kniep and Lindegren are all associated with this early period of fungal genetics research. These studies and the discovery of penicillin by Fleming, who shared a Nobel Prize in 1945, provided further impetus for experimental research with fungi. Thus began a period of interest in mutation induction and analysis of mutants for bio chemical traits. Such fundamental research, conducted largely with Neurospora crassa, led to the one gene: one enzyme hypothesis and to a second Nobel Prize for fungal research awarded to Beadle and Tatum in 1958. Fundamental research in biochemical genetics was extended to other fungi, especially to Saccharomyces cere visiae, and by the mid-1960s fungal systems were much favored for studies in eukaryotic molecular biology and were soon able to compete with bacterial systems in the molecular arena.
Book Synopsis Stress-Activated Protein Kinases by : Francesc Posas
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.
Book Synopsis Biomolecular Networks by : Luonan Chen
Download or read book Biomolecular Networks written by Luonan Chen and published by John Wiley & Sons. This book was released on 2009-06-29 with total page 416 pages. Available in PDF, EPUB and Kindle. Book excerpt: Alternative techniques and tools for analyzing biomolecular networks With the recent rapid advances in molecular biology, high-throughput experimental methods have resulted in enormous amounts of data that can be used to study biomolecular networks in living organisms. With this development has come recognition of the fact that a complicated living organism cannot be fully understood by merely analyzing individual components. Rather, it is the interactions of components or biomolecular networks that are ultimately responsible for an organism's form and function. This book addresses the important need for a new set of computational tools to reveal essential biological mechanisms from a systems biology approach. Readers will get comprehensive coverage of analyzing biomolecular networks in cellular systems based on available experimental data with an emphasis on the aspects of network, system, integration, and engineering. Each topic is treated in depth with specific biological problems and novel computational methods: GENE NETWORKS—Transcriptional regulation; reconstruction of gene regulatory networks; and inference of transcriptional regulatory networks PROTEIN INTERACTION NETWORKS—Prediction of protein-protein interactions; topological structure of biomolecular networks; alignment of biomolecular networks; and network-based prediction of protein function METABOLIC NETWORKS AND SIGNALING NETWORKS—Analysis, reconstruction, and applications of metabolic networks; modeling and inference of signaling networks; and other topics and new trends In addition to theoretical results and methods, many computational software tools are referenced and available from the authors' Web sites. Biomolecular Networks is an indispensable reference for researchers and graduate students in bioinformatics, computational biology, systems biology, computer science, and applied mathematics.
Book Synopsis Synthetic Biology by : Christina Smolke
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.
Book Synopsis Molecular Biology of The Cell by : Bruce Alberts
Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Exosome by : Torben Heick Jensen
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.
