Download or read book Structural and Biochemical Characterisation of the Yeast Exosome Component Rrp40 written by Anna Oddone and published by . This book was released on 2007 with total page 131 pages. Available in PDF, EPUB and Kindle. Book excerpt: In eukaryotes, mRNA turnover, RNA quality control and 3'-end processing of several RNAs require the exosome, a multi-subunit protein complex that is conserved from yeast to human, and of which some archaeal counterparts have recently been described. The exosome core consists of six proteins homologous to bacterial RNase PH nucleases and of three S1-domain containing subunits, predicted to be involved in RNA substrate binding. Although the functional characterisation had considerably progressed since exosome first description, no structural information was available for the complex or its subunits, at the onset of this thesis. This thesis presents the first structure of a component of the eukaryotic exosome core, Rrp40 from Saccharomyces cerevisiae. The crystal structure of the N-terminal deletion construct of Rrp40 reveals that an S1 and an unusual KH domain are tightly packed against each other. The interface between the S1 and the KH domain is stabilised by a GxNG sequence, which is uniquely conserved in exosome KH domains. NMR data reveal the presence of a manganese-binding site at the interface of the two domains. Isothermal titration calorimetry shows that yeast Rrp40 and its archaeal counterpart Rrp4 have alone very low affinity for RNA, despite the fact that both S1 and KH domains are known nucleic acid-binding modules. The affinity of an archaeal core exosome for RNA, however, is significantly increased in the presence of Rrp4, indicating that multiple subunits may contribute to cooperative binding of RNA substrates by the exosome.

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 Molecular Biology of RNA Processing and Decay in Prokaryotes written by and published by Academic Press. This book was released on 2009-03-10 with total page 519 pages. Available in PDF, EPUB and Kindle. Book excerpt: Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences, including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume. - This series provides a forum for discussion of new discoveries, approaches, and ideas - Contributions from leading scholars and industry experts - Reference guide for researchers involved in molecular biology and related fields

Download or read book Ribonucleases written by Allen W. Nicholson and published by Springer Science & Business Media. This book was released on 2011-10-06 with total page 412 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribonucleases are a ubiquitous and functionally diverse group of enzymes that have a common ability to cleave RNA. Either through scission of internal phosphodiesters, or removal of nucleotides from RNA 5’ or 3’ ends, ribonucleases perform essential roles in gene expression and regulation, genome replication and maintenance, host defense, stress response, and viral strategies of infection. Ribonucleases have also served as highly informative models to understand virtually every aspect of biomolecular structure and function. The fifteen chapters in this volume are written by recognized researchers in the field, and provide in-depth analyses of the major ribonuclease families. Particular focus is given to the relation of ribonuclease structure and mechanism to biological function, as well as ribonuclease dysfunction in certain disease states. Other topics include the evolutionary genetics and functional diversification of ribonucleases, engineered ribonucleases as anti-cancer agents, the mechanisms of action of artificial ribonucleases, and ribonucleases as models to understand protein folding and stability. This volume should serve as an essential reference for a broad range of researchers and educators with interests in RNA metabolism, enzymology, and gene regulation.

Download or read book Eukaryotic RNases and their Partners in RNA Degradation and Biogenesis written by and published by Academic Press. This book was released on 2012-12-31 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This special issue of The Enzymes is targeted towards researchers in biochemistry, molecular and cell biology, pharmacology, and cancer. This volume discusses Eukaryotic RNases and their partners in RNA degradation and biogenesis. Contributions from leading authorities Informs and updates on all the latest developments in the field

Download or read book The Eukaryotic RNA Exosome written by John LaCava and published by Springer Nature. This book was released on 2019-11-25 with total page 514 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume provides a cross-section of RNA exosome research protocols, applied to a diversity of model organisms. Chapters guide readers through methods that e.g. delineate eukaryotic exosomes’ origins in prokaryotes, probe its RNA substrates, adapter complexes and macromolecular interaction of networks, and establish critical structural-function relationships. 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 tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, The Eukaryotic RNA Exosome: Methods and Protocols aims to ensure successful results in the further study of this vital field.

Download or read book RNA Turnover in Bacteria Archaea and Organelles written by Lynne E. Maquat and published by Academic Press. This book was released on 2008-12-23 with total page 621 pages. Available in PDF, EPUB and Kindle. Book excerpt: Specific complexes of protein and RNA carry out many essential biological functions, including RNA processing, RNA turnover, RNA folding, as well as the translation of genetic information from mRNA into protein sequences. Messenger RNA (mRNA) decay is now emerging as an important control point and a major contributor to gene expression. Continuing identification of the protein factors and cofactors, and mRNA instability elements, responsible for mRNA decay allow researchers to build a comprehensive picture of the highly orchestrated processes involved in mRNA decay and its regulation. Covers the difference in processing of mRNA between eukaryotes, bacteria and archea. Benefit: Processing of mRNA differs greatly between eukaryotes, bacteria and archea and this affords researchers readily reproducible techniques to understand and study the molecular pathogenesis of disease Expert researchers introduce the most advanced technologies and techniques to identify mRNA processing, transport, localization and turnover which are central to the process of gene expression. Benefit: Keeps MIE buyers and online subscribers up-to-date with the latest research Offers step by step lab instructions including necessary equipment and reagents. Benefit: Provides tried and tested techniques which eliminate searching through many different sources. Tested techniques are trustworthy and avoid pitfalls so the same mistakes are not made over and over

Download or read book RNA Metabolism in Neurodegenerative Diseases written by Rita Sattler and published by Springer. This book was released on 2018-06-18 with total page 321 pages. Available in PDF, EPUB and Kindle. Book excerpt: It has become evident over the last years that abnormalities in RNA processing play a fundamental part in the pathogenesis of neurodegenerative diseases. Cellular viability depends on proper regulation of RNA metabolism and subsequent protein synthesis, which requires the interplay of many processes including transcription, pre--‐mRNA splicing, mRNA editing as well as mRNA stability, transport and translation. Dysfunction in any of these processes, often caused by mutations in the coding and non--‐ coding RNAs, can be very destructive to the cellular environment and consequently impair neural viability. The result of this RNA toxicity can lead to a toxic gain of function or a loss of function, depending on the nature of the mutation. For example, in repeat expansion disorders, such as the newly discovered hexanucleotide repeat expansion in theC9orf72 gene found in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), a toxic gain of function leads to the formation of RNA foci and the sequestration of RNA binding proteins (RBPs). This in return leads to a loss of function of those RBPs, which is hypothesized to play a significant part in the disease progression of ALS and FTD. Other toxicities arising from repeat expansions are the formation of RNA foci, bi--‐directional transcription and production of repeat associated non--‐ATG (RAN) translation products. This book will touch upon most of these disease mechanisms triggered by aberrant RNA metabolism and will therefore provide a broad perspective of the role of RNA processing and its dysfunction in a variety of neurodegenerative disorders, including ALS, FTD, Alzheimer’s disease, Huntington’s disease, spinal muscular atrophy, myotonic dystrophy and ataxias. The proposed authors are leading scientists in the field and are expected to not only discuss their own work, but to be inclusive of historic as well as late breaking discoveries. The compiled chapters will therefore provide a unique collection of novel studies and hypotheses aimed to describe the consequences of altered RNA processing events and its newest molecular players and pathways.

Download or read book RNA Damage and Repair written by Ioly Kotta-Loizou and published by Springer Nature. This book was released on 2021-07-04 with total page 180 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribonucleic acid (RNA) is a macromolecule that plays a central role in cell physiology: RNA molecules act as intermediates between the deoxyribonucleic acid (DNA), where genetic information is stored, and proteins, which perform the necessary functions within the cell. Traditionally, the structural and functional properties of RNA are closely linked to gene expression. However, RNA-based enzymes, called ribozymes, are also involved in catalysis and small RNAs regulate key cellular processes, such as cell growth, division, differentiation, aging and death. RNA is a sensitive macromolecule that can be easily damaged by environmental conditions (ultraviolet radiation, oxidative stress) and biological factors (ribonucleases, ribotoxins, CRISPR-Cas systems). Therefore, cells have developed mechanisms to protect and/or repair RNA molecules. This book presents an overview of the biology of RNA damage, protection and repair in prokaryotes and eukaryotes. Individual chapters cover the expression regulation, enzymology and physiological role of such systems, and link them to important human diseases such as cancer and degenerative diseases.

Download or read book Fungal RNA Biology written by Ane Sesma and published by Springer Science & Business Media. This book was released on 2014-04-15 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents an overview of the RNA networks controlling gene expression in fungi highlighting the remaining questions and future challenges in this area. It covers several aspects of the RNA-mediated mechanisms that regulate gene expression in model yeasts and filamentous fungi, organisms of great importance for industry, medicine and agriculture. It is estimated that there are more than one million fungal species on the Earth. Despite their diversity (saprophytic, parasitic and mutualistic), fungi share common features distinctive from plants and animals and have been grouped taxonomically as an independent eukaryotic kingdom. In this book, 15 chapters written by experts in their fields cover the RNA-dependent processes that take place in a fungal cell ranging from formation of coding and non-coding RNAs to mRNA translation, ribosomal RNA biogenesis, gene silencing, RNA editing and epigenetic regulation.

Download or read book Biophysics of RNA Protein Interactions written by Chirlmin Joo and published by Springer Nature. This book was released on 2019-09-19 with total page 249 pages. Available in PDF, EPUB and Kindle. Book excerpt: RNA molecules play key roles in all aspects of cellular life, but to do so efficiently, they must work in synergism with proteins. This book addresses how proteins and RNA interact to carry out biological functions such as protein synthesis, regulation of gene expression, genome defense, liquid phase separation and more. The topics addressed in this volume will appeal to researchers in biophysics, biochemistry and structural biology. The book is a useful resource for anybody interested in elucidating the molecular mechanisms and discrete properties of RNA-protein complexes. Included are reviews of key systems such as microRNA and CRISPR/Cas that exemplify how RNA and proteins work together to perform their biological function. Also covered are techniques ranging from single molecule fluorescence and force spectroscopy to crystallography, cryo-EM microscopy, and kinetic modeling.

Download or read book Recent Progresses in Amebiasis written by Anjan Debnath and published by Frontiers Media SA. This book was released on 2019-10-14 with total page 415 pages. Available in PDF, EPUB and Kindle. Book excerpt: Amebiasis, a parasitic disease transmitted by the unicellular protozoan parasite Entamoeba histolytica, is the cause of at least 100,000 deaths each year. The disease is mostly prevalent in developing countries and is one of the three common causes of death from parasitic diseases. The parasite has two stages in its life cycle in the host: the infective cyst and the invasive trophozoite. In the large intestine, the parasite feeds on bacteria and on cellular debris. No vaccine against amebiasis currently exists. Although metronidazole is the drug of choice for treating amebiasis, adverse effects in patients and potential resistance to metronidazole in other protozoa exist. About nine out of 10 people who are infected with E. histolytica are asymptomatic and in those individuals who develop symptoms, bloody diarrhea (amebic colitis) and liver abscess are the most common symptoms. One possible explanation for this observation is the difference in the gut microbiota between individuals that may significantly influence the host’s immune response in amebiasis and E. histolytica's virulence. Amebiasis is characterized by acute inflammation of the intestine with release of pro-inflammatory cytokines, reactive oxygen species and reactive nitrogen species from activated cells of the host's immune system. In recent years, significant advances on the cell biology of Entamoeba infection have been achieved through the development of new genetic tools to manipulate gene expression in the parasite and through the application of Omics tools. In this Research Topic, we welcome high quality original research articles, as well as review, opinion or method articles, on amebiasis including but not limited to the regulation of gene expression, cell biology and signaling, adaptation and resistance to environmental stresses, metabolism, pathogenesis and immunity, pathogenesis and microbiome, drug discovery and drug resistance.

Download or read book Ribonucleases Part B Artificial and Engineered Ribonucleases and Speicifc Applications written by and published by Elsevier. This book was released on 2001-09-28 with total page 555 pages. Available in PDF, EPUB and Kindle. Book excerpt: This second volume on ribonucleases provides up-to-date, methods-related information on these enzymes. Of particular interest to researchers will be the discussion of artificial and engineered ribonucleases, as well as the application of ribonucleases in medicine and biotechnology.The critically acclaimed laboratory standard for more than forty years, Methods in Enzymology is one of the most highly respected publications in the field of biochemistry. Since 1955, each volume has been eagerly awaited, frequently consulted, and praised by researchers and reviewers alike. Now with more than 300 volumes (all of them still in print), the series contains much material still relevant today--truly an essential publication for researchers in all fields of life sciences.

Download or read book Practical Bioinformatics written by Janusz M. Bujnicki and published by Springer. This book was released on 2007-09-12 with total page 275 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book presents applications of bioinformatics tools that experimental research scientists use in "daily practice." Its interdisciplinary approach combines computational and experimental methods to solve scientific problems. The book begins with reviews of computational methods for protein sequence-structure-function analysis, followed by methods that use experimental data obtained in the laboratory to improve functional predictions.

Download or read book Guide to Yeast Genetics and Molecular Biology written by Christine Guthrie and published by . This book was released on 1991-01-28 with total page 933 pages. Available in PDF, EPUB and Kindle. Book excerpt: Guide to Yeast Genetics and Molecular Biology presents, for the first time, a comprehensive compilation of the protocols and procedures that have made Saccharomyces cerevisiae such a facile system for all researchers in molecular and cell biology. Whether you are an established yeast biologist or a newcomer to the field, this volume contains all the up-to-date methods you will need to study "Your Favorite Gene" in yeast. Basic Methods in Yeast Genetics**Physical and genetic mapping**Making and recovering mutants**Cloning and Recombinant DNA Methods**High-efficiency transformation**Preparation of yeast artificial chromosome vectors**Basic Methods of Cell Biology**Immunomicroscopy**Protein targeting assays**Biochemistry of Gene Expression**Vectors for regulated expression**Isolation of labeled and unlabeled DNA, RNA, and protein

Download or read book The Insect Viruses written by Lois K. Miller and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: There are over a million different species of insects, and individually they 8 outnumber humans by more than 10 to 1. Moreover, some insects live in close association with both plants and higher animals and naturally exchange viruses with them. It has even been speculated that viruses in general may have radiated through the plant and animal kingdoms from common insect origins. Be that as it may, since insects play pivotal roles in the biosphere, both to the benefit and detriment of mankind, they and the viruses that infect them are important subjects for study. Insects are infected by a diverse medley of viruses, and this volume focuses on those insect virus families that are found primarily or exclusively in insects. All major families of insect-selective viruses are covered except for the baculo viruses, which were described in a separate volume of The Viruses series. Included in this volume are the established families of insect viruses, the newly recognized ascovirus family, and the nudiviruses, which probably represent a separate family but currently remain unclassified. The coverage of arboviruses is limited to a single chapter that focuses on their potential utility as vectors and in insect control. Omitted for practical reasons are several individual insect viruses that have been described sporadically in the literature and probably represent novel virus families.

Download or read book The Cell Biology of Stem Cells written by Eran Meshorer and published by Springer Science & Business Media. This book was released on 2011-01-11 with total page 246 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stem cells have been gaining a lot of attention in recent years. Their unique potential to self-renew and differentiate has turned them into an attractive model for the study of basic biological questions such as cell division, replication, transcription, cell fate decisions, and more. With embryonic stem (ES) cells that can generate each cell type in the mammalian body and adult stem cells that are able to give rise to the cells within a given lineage, basic questions at different developmental stages can be addressed. Importantly, both adult and embryonic stem cells provide an excellent tool for cell therapy, making stem cell research ever more pertinent to regenerative medicine. As the title The Cell Biology of Stem Cells suggests, our book deals with multiple aspects of stem cell biology, ranging from their basic molecular characteristics to the in vivo stem cell trafficking of adult stem cells and the adult stem-cell niche, and ends with a visit to regeneration and cell fate reprogramming. In the first chapter, “Early embryonic cell fate decisions in the mouse”, Amy Ralson and Yojiro Yamanaka describe the mechanisms that support early developmental decisions in the mouse pre-implantation embryo and the current understanding of the source of the most immature stem cell types, which includes ES cells, trophoblast stem (TS) cells and extraembryonic endoderm stem (XEN) cells.