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Ribonuclease P
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Download or read book Ribonuclease P written by Fenyong Liu and published by Springer Science & Business Media. This book was released on 2009-12-03 with total page 293 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Discovery of Ribonuclease P and Enzymatic Activity of Its RNA Subunit Sydney Brenner and Francis H. C. Crick had a specific project in mind when they offered Sidney Altman a position in their group in 1969 to conduct postdoctoral research at the Medical Research Council Laboratory of Molecular Biology (LMB) in Cambridge, England. At the time, an intense international competition was on- ing in as many as a dozen labs to determine the three-dimensional structure of tRNA. At the LMB, Aaron Klug was attacking the structure by crystallographic analysis with Brian F. C. Clark providing large amounts of purified phenylalanine tRNA. (Eventually, Aaron announced his empirically determined 3-D structure of yeast phenylalanine tRNA, a structure that is generally common to tRNAs, due in part to several conserved, novel three-way nucleotide interactions. ) Concurrently, Michael Levitt, a Ph. D. student of Francis, was visually scrutinizing the cloverleaf secondary structure of the 14 tRNA sequences known at the time. Levitt was searching for nucleotide covariation in different parts of the molecules that were conserved in the 14 sequences known at the time. He identified a possible covariation of an apparent Watson-Crick pairing type between the residues at position 15 from the 5’ end of the tRNA and residue 48. This association implied these parts of the tRNA, namely the D loop containing residue 15 and the 5’ end of the T stem-adjoining residue 48, folded on one another in a tertiary structure shared by different tRNAs.
Book Synopsis Evolutionary Biology—A Transdisciplinary Approach by : Pierre Pontarotti
Download or read book Evolutionary Biology—A Transdisciplinary Approach written by Pierre Pontarotti and published by Springer Nature. This book was released on 2020-10-29 with total page 389 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book includes 16 selected contributions presented at the 23rd Evolutionary Biology Meeting, which took place in Marseille in September 2019. The annual Evolutionary Biology Meetings in Marseille serve to gather leading evolutionary biologists and other scientists using evolutionary biology concepts, e.g. for medical research. The aim of these meetings is to promote the exchange of ideas to encourage interdisciplinary collaborations. Offering an up-to-date overview of recent findings in the field of evolutionary biology, this book is an invaluable source of information for scientists, teachers and advanced students.
Download or read book Ribozymes written by Sabine Müller and published by John Wiley & Sons. This book was released on 2021-07-09 with total page 81 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ribozymes Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world’s top professionals in the field Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject. Ribozymes is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts. The first reference to tie together all aspects of the multi-faceted field of ribozymes Features more than 30 comprehensive chapters in two volumes Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.
Download or read book Ribonuclease P written by Fenyong Liu and published by Springer. This book was released on 2010-05-06 with total page 283 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Discovery of Ribonuclease P and Enzymatic Activity of Its RNA Subunit Sydney Brenner and Francis H. C. Crick had a specific project in mind when they offered Sidney Altman a position in their group in 1969 to conduct postdoctoral research at the Medical Research Council Laboratory of Molecular Biology (LMB) in Cambridge, England. At the time, an intense international competition was on- ing in as many as a dozen labs to determine the three-dimensional structure of tRNA. At the LMB, Aaron Klug was attacking the structure by crystallographic analysis with Brian F. C. Clark providing large amounts of purified phenylalanine tRNA. (Eventually, Aaron announced his empirically determined 3-D structure of yeast phenylalanine tRNA, a structure that is generally common to tRNAs, due in part to several conserved, novel three-way nucleotide interactions. ) Concurrently, Michael Levitt, a Ph. D. student of Francis, was visually scrutinizing the cloverleaf secondary structure of the 14 tRNA sequences known at the time. Levitt was searching for nucleotide covariation in different parts of the molecules that were conserved in the 14 sequences known at the time. He identified a possible covariation of an apparent Watson-Crick pairing type between the residues at position 15 from the 5’ end of the tRNA and residue 48. This association implied these parts of the tRNA, namely the D loop containing residue 15 and the 5’ end of the T stem-adjoining residue 48, folded on one another in a tertiary structure shared by different tRNAs.
Book Synopsis The Study of Nuclear Ribonuclease P in S. Cerevisiae Using Novel RNA Affinity Tags by : Chatchawan Srisawat
Download or read book The Study of Nuclear Ribonuclease P in S. Cerevisiae Using Novel RNA Affinity Tags written by Chatchawan Srisawat and published by . This book was released on 2002 with total page 266 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Many Faces of RNA by : D. S. Eggleston
Download or read book The Many Faces of RNA written by D. S. Eggleston and published by Elsevier. This book was released on 1997-12-19 with total page 261 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Many Faces of RNA is the subject for the eighth SmithKline Beecham Pharmaceuticals Research Symposia. It highlights a rapidly developing area of scientific investigation. The style and format are deliberately designed to promote in-depth presentations and discussions and to facilitate the forging of collaborations between academic and industrial partners.This symposium focuses on several of the many fundamental, advancing strategies for exploring RNA and its functions. It emphasizes the interplay between biology, chemistry, genomics, and molecular biology which is leading to exciting new insights and avenues of investigation. The book explores RNA as a therapeutic target, RNA as a tool, RNA and its interactions, along with chemical, computational, and structural investigations.
Book Synopsis Ribonucleases, Part B: Artificial and Engineered Ribonucleases and Speicifc Applications by :
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.
Book Synopsis Structure and Function of Bacterial Ribonuclease P by : Alexei V. Kazantsev
Download or read book Structure and Function of Bacterial Ribonuclease P written by Alexei V. Kazantsev and published by . This book was released on 2001 with total page 446 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis RNA Metabolism and Gene Expression in Archaea by : Béatrice Clouet-d'Orval
Download or read book RNA Metabolism and Gene Expression in Archaea written by Béatrice Clouet-d'Orval and published by Springer. This book was released on 2017-10-28 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book focuses on the regulation of transcription and translation in Archaea and arising insights into the evolution of RNA processing pathways. From synthesis to degradation and the implications of gene expression, it presents the current state of knowledge on archaeal RNA biology in 13 chapters. Topics covered include the modification and maturation of RNAs, the function of small non-coding RNAs and the CRISPR-Cas defense system. While Archaea have long been considered exotic microbial extremophiles, they are now increasingly being recognized as important model microorganisms for the study of molecular mechanisms conserved across the three domains of life, and with regard to the relevance of similarities and differences to eukaryotes and bacteria. This unique book offers a valuable resource for all readers interested in the regulation of gene expression in Archaea and RNA metabolism in general.
Book Synopsis Plant Resistance to Viruses by : David Evered
Download or read book Plant Resistance to Viruses written by David Evered and published by John Wiley & Sons. This book was released on 2008-04-30 with total page 226 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concern about the environmental consequences of the widespread use of pesticides has increased, and evidence of pesticide-resistant virus vectors have continued to emerge. This volume presents a timely survey of the mechanisms of plant resistance and examines current developments in breeding for resistance, with particular emphasis on advances in genetic engineering which allow for the incorporation of viral genetic material into plants. Discusses the mechanisms of innate resistance in strains of tobacco, tomato, and cowpea; various aspects of induced resistance, including the characterization and roles of the pathogenesis-related proteins; antiviral substances and their comparison with interferon; and cross-protection between plant virus strains. Also presents several papers which evaluate the status of genetic engineering as it relates to breeding resistant plants. Among these are discussions of the potential use of plant viruses as gene vectors, gene coding for viral coat protein, satellite RNA, and antisense RNA, and practical issues such as the durability of resistant crop plants in the field.
Book Synopsis Composition and Characterization of Nuclear Ribonuclease P from Saccharomyces Cerevisiae by : Joel Ranier Chamberlain
Download or read book Composition and Characterization of Nuclear Ribonuclease P from Saccharomyces Cerevisiae written by Joel Ranier Chamberlain and published by . This book was released on 1997 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Specificity Landscape of Ribonuclease P Processing of Pre-tRNA Substrates by High-throughput Enzymology by : Coutrney Nicole Niland
Download or read book Specificity Landscape of Ribonuclease P Processing of Pre-tRNA Substrates by High-throughput Enzymology written by Coutrney Nicole Niland and published by . This book was released on 2017 with total page 163 pages. Available in PDF, EPUB and Kindle. Book excerpt: To fully understand the roles of RNA processing enzymes in cellular processes and human health, it is essential to dissect their substrate specificity. Using Ribonuclease P (RNase P) as a model system, this body of work seeks to better understand multiple substrate recognition by RNA processing enzymes. The ubiquitous endonuclease RNase P removes the 5' leader from all pre-tRNAs in the cell. To understand how variation in the 5' leader is accommodated by the active site of RNase P, we comprehensively determined the processing rates of pre-tRNA substrates with all possible sequence combinations in the 5' leader. This quantification involved Illumina(R) sequencing of the residual substrate population at different reaction times to monitor substrate depletion and calculate relative rate constants, a technique termed HTS-Kin. Additionally, the 5' leader of pre-tRNA is recognized by both the catalytic RNA subunit (P RNA) and smaller protein subunit of RNase P, C5. We therefore hypothesized that variation in substrate sequence contacting one enzyme subunit may alter the recognition or energetic contribution of contacts to the other enzyme subunit. Upon comprehensive determination of RNase P specificity for 5' leader sequences, we have determined that this enzyme is tuned for specificity at association as the catalytic rate constant is unaffected by substrate variation. We have also performed mechanistic analysis to identify the key sources of error in the HTS-Kin technique: experimental error and Illumina sequencing error. Finally, we ascertained that the sequence identity of 5' leader nucleotides contacting P RNA does not alter C5 protein specificity but rather modulates its energetic contribution to the processing rate.
Book Synopsis Characterization of the Ribonuclease P RNA of Sulfolobus Acidocaldarius by : Thomas Edward LaGrandeur
Download or read book Characterization of the Ribonuclease P RNA of Sulfolobus Acidocaldarius written by Thomas Edward LaGrandeur and published by . This book was released on 1994 with total page 294 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Multiple Substrate Kinetics of Ribonuclease P by : Lindsay E. Yandek
Download or read book Multiple Substrate Kinetics of Ribonuclease P written by Lindsay E. Yandek and published by . This book was released on 2013 with total page 128 pages. Available in PDF, EPUB and Kindle. Book excerpt: A single enzyme, ribonuclease P (RNase P), processes all precursor tRNA (pre-tRNA) in cells and organelles that carry out tRNA biosynthesis. This substrate population includes over 80 different competing pre-tRNAs in Escherichia coli. While the reaction kinetics and molecular recognition of a few individual model substrates of bacterial RNase P have been well described, the competitive substrate kinetics of the enzyme are comparatively unexplored. To understand the factors that determine how different pre-tRNA substrates compete for processing by E. coli RNase P, we compared the steady state reaction kinetics of two pre-tRNAs that differ at sequences that are contacted by the enzyme. For both pre-tRNAs, we demonstrated that substrate cleavage is fast relative to dissociation such that there is a large commitment to catalysis. As a consequence, V/K, the rate constant for the reaction at limiting substrate concentrations, reflects the substrate association step for both pre-tRNAs. Reactions containing two or more pre-tRNAs follow simple competitive alternative substrate kinetics in which the relative rates of processing are determined by pre-tRNA concentration and their relative V/K values. The relative V/K values for eight different pre-tRNAs, that were selected to represent the range of structure variation at sites contacted by RNase P, were determined by internal competition in reactions in which all eight substrates are present simultaneously. The results reveal a relatively narrow range of V/K values suggesting rates of pre-tRNA processing by RNase P are tuned for uniform specificity and consequently optimal coupling to precursor biosynthesis. To evaluate this further, we developed a new, scalable method in order to study larger and more complex populations of pre-tRNAs. We examined all sequence variants in the cognate site of the RNA substrate for the C5 protein subunit of E. coli RNase P, which binds pre-tRNA leaders non-specifically. A high-throughput sequencing kinetics approach (HITS-KIN) reveals pronounced discrimination of C5 between sequence variants, determinants for discrimination that cannot be delineated by analysis of cellular substrates, and a distribution of substrate affinities of C5 that is very similar to specific DNA binding proteins.
Book Synopsis Handbook of RNA Biochemistry by : Roland K. Hartmann
Download or read book Handbook of RNA Biochemistry written by Roland K. Hartmann and published by John Wiley & Sons. This book was released on 2015-06-22 with total page 1370 pages. Available in PDF, EPUB and Kindle. Book excerpt: The second edition of a highly acclaimed handbook and ready reference. Unmatched in its breadth and quality, around 100 specialists from all over the world share their up-to-date expertise and experiences, including hundreds of protocols, complete with explanations, and hitherto unpublished troubleshooting hints. They cover all modern techniques for the handling, analysis and modification of RNAs and their complexes with proteins. Throughout, they bear the practising bench scientist in mind, providing quick and reliable access to a plethora of solutions for practical questions of RNA research, ranging from simple to highly complex. This broad scope allows the treatment of specialized methods side by side with basic biochemical techniques, making the book a real treasure trove for every researcher experimenting with RNA.
Book Synopsis RNA-protein Interactions in Prokaryotic and Eukaryotic Ribonuclease P. by : Jeremy J. Day
Download or read book RNA-protein Interactions in Prokaryotic and Eukaryotic Ribonuclease P. written by Jeremy J. Day and published by . This book was released on 2004 with total page 486 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis Structure-function Relationships in the Protein Subunit of Bacterial Ribonuclease P by :
Download or read book Structure-function Relationships in the Protein Subunit of Bacterial Ribonuclease P written by and published by . This book was released on 2004 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Ribonuclease P (RNase P) is a ribonucleoprotein involved in tRNA biosynthesis in all living organisms. Bacterial RNase P is comprised of a catalytic RNA subunit and a lone protein cofactor which plays a supporting, albeit essential, role in the tRNA processing reaction in vivo. In this study, we have searched various databases to identify homologs of the protein subunit of RNase P from diverse bacteria and generated an alignment of their primary sequences to determine the most highly conserved residues. Such an approach has helped us to extend earlier predictions of which residues might play an important role in RNase P catalysis. The amino acid residues identified as important for RNase P catalysis could be categorized in three groups: (i) the RNR motif in helix alpha 2, (ii) the substrate binding cleft, and (iii) amino acid residues involved in the overall stability of the bacterial RNase P protein subunit. By employing site-directed mutagenesis and a genetic complementation assay, we have also gained insights into structure-function relationships in the protein subunit of bacterial RNase P. Specifically, we were able to demonstrate that the bacterial RNase P protein uses one domain to recognize its cognate catalytic RNA subunit and another domain to recognize the 5' leader sequences of its precursor tRNA substrates. The plasticity of the substrate-binding cleft has also been demonstrated by both chemical and genetic rescue experiments. These results, taken together with earlier kinetic studies, have enabled us to understand how the bacterial RNase P protein subunit is able to enhance the rate of chemical cleavage 10-fold and enhance substrate binding 10,000-fold over the RNA alone ptRNA-processing reaction. Finally, we report an interesting study that demonstrates how the Escherichia coli RNase P protein subunit lacking a metal affinity tag can be purified under denaturing conditions using immobilized metal affinity chromatography (IMAC). We are not aware of a precedent in this regard and report these results as a potential new method for the purification of a protein lacking metal affinity tags under denaturing conditions using IMAC.
