Download or read book Involvement of Ribosomal RNA in Translational Accuracy written by Patrick Nikita Allen and published by . This book was released on 1991 with total page 250 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Ribosome written by Aleksandr S. Spirin and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 173 pages. Available in PDF, EPUB and Kindle. Book excerpt: This monograph is neither a historical outline of the development of the concepts of protein biosynthesis and the structure and functions of the ribosomes, nor an exhaustive survey of the literature on these questions. The monograph is based upon an analysis of the modern trends in this field. The purpose of the monograph was to formulate more or less generalized representations of the structure and" function of the ribosome, as we envision it at the present day. It may be that this attempt is premature for a number of reasons, and the concepts outlined here will very soon be revised. Nonetheless, despite this risk, we believe it to be advisable to undertake this attempt for the following reasons: firstly, the undertaken analysis could aid in the comprehension of the substantial mass of extremely scattered experimental data on the ribosomes presently available; secondly, in any event, even if most of the concepts outlined rapidly become obselete, they can still serve as a stimulus for a whole series of experiments; and thirdly, we hope that some of the concepts outlined will still remain essentially correct and relatively stable. In view of the aforementioned, we should make the following reservations. First of all, we made no attempt to cite all the literature on the problems discussed, but considered it sufficient to illustrate the various premises with one or several sample references.
Download or read book An Investigation Into the Effects of Alterations in Ribosomal Proteins S4 and S5 on Translational Accuracy Ribosomal RNA Processing and Ribosome Assembly written by Divya Kamath and published by . This book was released on 2016 with total page 196 pages. Available in PDF, EPUB and Kindle. Book excerpt: Accurate translation of genetic message is an essential step in gene expression and is carried out by the ribosome. Ribosomal proteins S4 and S5 are critical for the decoding and the assembly processes on the ribosome. The interaction between residues in the S4-S5 interface region is crucial for the large scale conformational changes occurring on the ribosome during decoding. Earlier studies predominantly isolated S4 and S5 mutations located near the S4-S5 interface. However, recent studies show that ribosomal proteins S4 and S5 affect translational accuracy to a larger extent than previously realized. To understand the diverse ways by which mutation in S4 and S5 can affect translational accuracy, we generated and studied a wide array of S4 and S5 mutants with altered accuracy phenotypes, that were located not only at the interface but also distributed throughout the protein. We also generated a collection of mutants with alteration in the loop 2 region of S5 protein. As the loop 2 region is away from the interface, it modulates accuracy by mechanisms different than disruption of the S4-S5 interface. The C-terminal region of S4 protein interacts extensively with the S5 protein and C-terminal truncated mutants are temperature sensitive, have a ribosome assembly defect and are error-prone. We obtained temperature insensitive S4 mutants with restored C-termini that partially rescued miscoding but almost completely rescued the ribosome assembly defect at 42 ̊C. Finally, in the process of exploring interactions of S4 and S5 with other regions in the ribosome, we discovered that accuracy can be altered indirectly by affecting amino acid pools or tRNA modification.
Download or read book The Aminoacyl tRNA Synthetases written by Michael Ibba and published by CRC Press. This book was released on 2005-04-01 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: By virtue of their role as catalysts of the aminoacylation reaction, the aminoacyl-tRNA synthetases ensure that the first step of translation is performed quickly and accurately. In this volume of 36 separate chapters, the many facets of this ancient and ubiquitous family are reviewed, including their surprising structural diversity, enzymology, tRNA interaction properties, and curious alternative functions. These chapters illustrate the degree to which the aminoacyl-tRNA synthetases employ a variety of mechanisms to carry out both the standard functions related to the synthesis of aminoacylated tRNA for protein synthesis, as well as the surprising functions associated with amino acid biosynthesis, cytokine function, and even the processivity of DNA replication. Other chapters explore the regulation of their synthesis, their role in disease, and their prospects as targets for antibacterial therapeutics. This monograph will be a valuable resource for all scientists interested in the fundamentals of protein synthesis from both a basic research and clinical perspective, as well as the relation of translational components to the evolution of the genetic code.
Download or read book Ribosomes Structure Function and Dynamics written by Marina V. Rodnina and published by Springer Science & Business Media. This book was released on 2011-12-10 with total page 428 pages. Available in PDF, EPUB and Kindle. Book excerpt: The ribosome is a macromolecular machine that synthesizes proteins with a high degree of speed and accuracy. Our present understanding of its structure, function and dynamics is the result of six decades of research. This book collects over 40 articles based on the talks presented at the 2010 Ribosome Meeting, held in Orvieto, Italy, covering all facets of the structure and function of the ribosome. New high-resolution crystal structures of functional ribosome complexes and cryo-EM structures of translating ribosomes are presented, while partial reactions of translation are examined in structural and mechanistic detail, featuring translocation as a most dynamic process. Mechanisms of initiation, both in bacterial and eukaryotic systems, translation termination, and novel details of the functions of the respective factors are described. Structure and interactions of the nascent peptide within, and emerging from, the ribosomal peptide exit tunnel are addressed in several articles. Structural and single-molecule studies reveal a picture of the ribosome exhibiting the energy landscape of a processive Brownian machine. The collection provides up-to-date reviews which will serve as a source of essential information for years to come.
Download or read book Recoding Expansion of Decoding Rules Enriches Gene Expression written by John F. Atkins and published by Springer Science & Business Media. This book was released on 2010-03-10 with total page 473 pages. Available in PDF, EPUB and Kindle. Book excerpt: The literature on recoding is scattered, so this superb book ?lls a need by prov- ing up-to-date, comprehensive, authoritative reviews of the many kinds of recoding phenomena. Between 1961 and 1966 my colleagues and I deciphered the genetic code in Escherichia coli and showed that the genetic code is the same in E. coli, Xenopus laevis, and guinea pig tissues. These results showed that the code has been c- served during evolution and strongly suggested that the code appeared very early during biological evolution, that all forms of life on earth descended from a c- mon ancestor, and thus that all forms of life on this planet are related to one another. The problem of biological time was solved by encoding information in DNA and retrieving the information for each new generation, for it is easier to make a new organism than it is to repair an aging, malfunctioning one. Subsequently, small modi?cations of the standard genetic code were found in certain organisms and in mitochondria. Mitochondrial DNA only encodes about 10–13 proteins, so some modi?cations of the genetic code are tolerated that pr- ably would be lethal if applied to the thousands of kinds of proteins encoded by genomic DNA.
Download or read book Cell Biology by the Numbers written by Ron Milo and published by Garland Science. This book was released on 2015-12-07 with total page 400 pages. Available in PDF, EPUB and Kindle. Book excerpt: A Top 25 CHOICE 2016 Title, and recipient of the CHOICE Outstanding Academic Title (OAT) Award. How much energy is released in ATP hydrolysis? How many mRNAs are in a cell? How genetically similar are two random people? What is faster, transcription or translation?Cell Biology by the Numbers explores these questions and dozens of others provid
Download or read book Characterization of Mutations in Ribosomal RNA that Alter the Accuracy of Translational Decoding in Yeast written by Irina V. Velichutina and published by . This book was released on 2000 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Studies of the Fidelity of Translation Elongation written by Aishwarya Devaraj and published by . This book was released on 2011 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Abstract: Protein synthesis occurs in ribosomes, megadalton RNA-protein machines that use aminoacyl-tRNA (aa-tRNA) molecules to translate messenger RNA (mRNA) with high fidelity. During translation elongation, the ribosome orchestrates 3 major events: decoding, peptidyl transfer and translocation. The process of proteins synthesis is also one of the major targets of antibiotics and hence understanding the basics of ribosome function should provide insight for the development of novel drugs. Genomes are maintained and expressed with remarkable fidelity and the accuracy of each process involved represents a compromise that optimizes the evolutionary fitness of the organism. The process of translation elongation is a complex one, and therefore there are potentially many ways the process can go awry. Chapter 1 introduces translation elongation errors and discusses the differences between missense, nonsense and frameshift errors. Mutations in the ribosome and other translation factors that affect the fidelity of translation elongation are also discussed. Chapter 2 is focused on the ribosomal exit (E) site and its role in maintaining the translational reading frame. It has been proposed that a critical role for the E site is in maintenance of translational reading frame, dependent on codon-anticodon pairing (191). Though several studies support the idea that codon-anticodon interaction in the E site contributes to frame maintenance (167), direct in vivo evidence for this hypothesis has been scant. In chapter 2, we investigated this fundamental question and found that the E site helps to maintain the reading frame, but does not contribute to the accuracy of decoding, as has been suggested (chapter 2, 204). We also showed that the mutation of the 30S E site does not inhibit EF-G-catalyzed translocation, in sharp contrast to the effects of mutations in 50S E site. These data provided evidence that the function of the E site in translocation is largely confined to the 50S subunit. One of the earliest identified examples of translational frameshifting occurs in the prfB gene of E. coli, encoding the peptide release factor 2 (RF2). While the genetic studies have identified the determinants of prfB programmed frameshifting and their relative importance, how these determinants act to promote frameshifting has remained unclear. In chapter 3, we compared ribosomal complexes with various spacer lengths between the SD sequence and P codon. We found that a close juxtaposition of the SD-ASD helix and P codon strongly destabilized P-site tRNA but had little or no effect on RF2-dependent termination or EF-Tu-dependent decoding. These data suggested that the intragenic SD of prfB destabilizes pairing of peptidyl-tRNALeu to the zero-frame CUU and promotes directional movement of the mRNA template with respect to the bound tRNA. In chapter 4, we have isolated 16S rRNA mutations that could suppress a +1 frameshift mutation in E. coli. In one of the screens (where the slippery sequence in the frameshift window had a stop codon), 31 independent mutations were identified and mapped to four different positions, of which C1054U was isolated 28 times. The C1054U mutation has also been isolated previously as a nonsense suppressor. Purine substitutions at this position also increased UGA readthrough and miscoding. While the C1054U mutation significantly increased nonsense readthrough and frameshift errors, the mutation had a hyperaccurate phenotype with respect to decoding (i.e., reduced misreading). Other substitutions at this position also had differential effects on the three reporters (missense, nonsense and frameshift). These interesting observations prompted us to characterize these A-site mutations as well as others in 16S rRNA (C1200U, G1491A and G299A) in vitro to get a better understanding of how the ribosome maintains its high fidelity (chapter 5). We investigated the effect of these mutations on RF2 function and found that all of the mutations tested had a defect in RF2-dependent termination. We directly tested the effect of these mutations on decoding by measuring the rate of GTP hydrolysis in both cognate and near-cognate mRNA. We found that all of the mutations tested (C1200U, G1491A, C1054U, C1054A, and G299A) had a substantial defect in initial selection, increasing the rate of GTP hydrolysis particularly on near-cognate mRNA. We also investigated the effect of these mutations on the stability of various tRNAs in the A site. Of the mutations analyzed, C1054U and G1491A seemed to differentially affect tRNA stability, suggesting that these mutations may stimulate GTP hydrolysis in a different way than the others.
Download or read book Protein Synthesis and Ribosome Structure written by Knud H. Nierhaus and published by John Wiley & Sons. This book was released on 2004-10-15 with total page 608 pages. Available in PDF, EPUB and Kindle. Book excerpt: Knud Nierhaus, who has studied the ribosome for more than 30 years, has assembled here the combined efforts of several scientific disciplines into a uniform picture of the largest enzyme complex found in living cells, finally resolving many decades-old questions in molecular biology. In so doing he considers virtually all aspects of ribosome structure and function -- from the molecular mechanism of different ribosomal ribozyme activities to their selective inhibition by antibiotics, from assembly of the core particle to the regulation of ribosome component synthesis. The result is a premier resource for anyone with an interest in ribosomal protein synthesis, whether in the context of molecular biology, biotechnology, pharmacology or molecular medicine.
Download or read book Role of Post transcriptional Modifications of Transfer RNA and Post translational Modification of Ribosomal Protein in Regulating Translational Accuracy in Saccharomyces Cerevisiae written by Kartikeya Joshi and published by . This book was released on 2017 with total page 632 pages. Available in PDF, EPUB and Kindle. Book excerpt: Misreading errors are a frequent source of error during translation that result in incorporation of a wrong amino acid in the growing polypeptide chain and can potentially generate a misfolded protein. Studies have estimated misreading errors to occur with a frequency of 10−3 - 10−4 errors per codon. However, recent studies in E. coli have determined that the frequency of misreading errors is in fact 100-fold lower (10−6 errors per codon) for most near-cognate codons. I developed a novel reporter based assay that can be used to quantify errors by a single tRNA(Glu UUC) in Saccharomyces cerevisiae. Using this reporter I find that the rate of misreading errors in yeast can vary from 10-6 - 10-4 errors per codon. I also find that the rate of errors in yeast is about 3-fold lower than that in bacteria. Another important conclusion made from this study is the occurrences of errors at the wobble position in yeast. Using the Beta-galactosidase reporter system developed in this study and the dual luciferase reporter system previously developed in our lab, I characterized the function of post-transcriptional modifications present in the anticodon stem loop of tRNA(Glu UUC) and tRNA(Lys UUU). I find that both mcm5s2U34 and t6A3-- modification regulate decoding accuracy during translation in a codon context dependent manner. mcm5s2U34 was found to promote errors for A- ending codons, while restricting errors for G- ending codons. Similarly, t6A3-- is found to restrict U·U mismatch at the first codon anticodon position but promotes the same error at the wobble position. Using genetic studies and our reporter system I established that Ctk1-dependent phosphorylation at serine 176 on ribosomal protein uS5 is critical in maintaining accuracy during translation. I show that loss of this phosphorylation site can increase misreading errors, while the presence of a phosphomimetic mutation at position 176 on uS5 can make a yeast strain hyper accurate. This study elucidates the important role played by modifications of the translational apparatus during decoding.
Download or read book Chemical Biology of Nucleic Acids written by Volker A. Erdmann and published by Springer Science & Business. This book was released on 2014-04-22 with total page 599 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume contains 29 engrossing chapters contributed by worldwide, leading research groups in the field of chemical biology. Topics include pre-biology; the establishment of the genetic code; isomerization of RNA; damage of nucleobases in RNA; the dynamic structure of nucleic acids and their analogs in DNA replication, extra- and intra-cellular transport; molecular crowding by the use of ionic liquids; new technologies enabling the modification of gene expression via editing of therapeutic genes; the use of riboswitches; the modification of mRNA cap regions; new approaches to detect appropriately modified RNAs with EPR spectroscopy and the use of parallel and high-throughput techniques for the analysis of the structure and new functions of nucleic acids. This volume discusses how chemistry can add new frontiers to the field of nucleic acids in molecular medicine, biotechnology and nanotechnology and is not only an invaluable source of information to chemists, biochemists and life scientists but will also stimulate future research.
Download or read book Water in Biological and Chemical Processes written by Biman Bagchi and published by Cambridge University Press. This book was released on 2013-11-14 with total page 383 pages. Available in PDF, EPUB and Kindle. Book excerpt: A unified overview of the dynamical properties of water and its unique and diverse role in biological and chemical processes.
Download or read book Physical Biochemistry written by David Freifelder and published by Macmillan. This book was released on 1982-08-15 with total page 786 pages. Available in PDF, EPUB and Kindle. Book excerpt: Suitable for advanced undergraduate and graduate students in biochemistry, this book provides clear, concise, well-exampled descriptions of the physical methods that biochemists and molecular biologists use.
Download or read book The Eukaryotic Ribosome written by Heinz Bielka and published by Walter de Gruyter GmbH & Co KG. This book was released on 1982-12-31 with total page 340 pages. Available in PDF, EPUB and Kindle. Book excerpt: No detailed description available for "The Eukaryotic Ribosome".
Download or read book Metagenomics for Microbiology written by Jacques Izard and published by Academic Press. This book was released on 2014-11-07 with total page 188 pages. Available in PDF, EPUB and Kindle. Book excerpt: Concisely discussing the application of high throughput analysis to move forward our understanding of microbial principles, Metagenomics for Microbiology provides a solid base for the design and analysis of omics studies for the characterization of microbial consortia. The intended audience includes clinical and environmental microbiologists, molecular biologists, infectious disease experts, statisticians, biostatisticians, and public health scientists. This book focuses on the technological underpinnings of metagenomic approaches and their conceptual and practical applications. With the next-generation genomic sequencing revolution increasingly permitting researchers to decipher the coding information of the microbes living with us, we now have a unique capacity to compare multiple sites within individuals and at higher resolution and greater throughput than hitherto possible. The recent articulation of this paradigm points to unique possibilities for investigation of our dynamic relationship with these cellular communities, and excitingly the probing of their therapeutic potential in disease prevention or treatment of the future. - Expertly describes the latest metagenomic methodologies and best-practices, from sample collection to data analysis for taxonomic, whole shotgun metagenomic, and metatranscriptomic studies - Includes clear-headed pointers and quick starts to direct research efforts and increase study efficacy, eschewing ponderous prose - Presented topics include sample collection and preparation, data generation and quality control, third generation sequencing, advances in computational analyses of shotgun metagenomic sequence data, taxonomic profiling of shotgun data, hypothesis testing, and mathematical and computational analysis of longitudinal data and time series. Past-examples and prospects are provided to contextualize the applications.
