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Author: Zhili Xu
Publisher:
ISBN:
Category :
Languages : en
Pages : 402
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Book Description
"Ribonucleic acids (RNAs) perform widely different biological functions ranging from regulation of gene expression to catalysis. Their functions are often tightly correlated with their structure. To explore the relationship between RNA structure and function, Escherichia coli (E. coli) small ribosomal subunit was used as a model system and its biogenesis was investigated using two different approaches. Firstly, we studied a RNA modification system which involves dimethylation of two universally conserved adjacent adenosines in the ultimate helix of the small subunit ribosomal RNAs (rRNA) and the KsgA (E. coli) methyltransferase family, enzyme responsible for these two dimethylations, which also appears to be universally conserved. We localized the position of KsgA relative to 30S subunits using directed hydroxyl radical probing and demonstrated that binding of KsgA and translation initiation factor 3 (IF3) are generally mutually exclusive. Our work strongly suggested that this modification system plays a critical role in differentiating fully assembled, functional subunits from those that are still involved in the biogenesis pathway. Secondly, we devised a modification interference approach to investigate nucleotides within 16S rRNA that are potentially important for the assembly of functional 30S subunits. We found that the majority of these nucleotides are located in the head and interdomain junction of the 30S subunit indicating that the different domains of the 30S subunit assemble differentially and that the assembly of the 3' domain and interdomain junction are more restricted than assembly of the other domains. Further in vivo investigation of individual residues identified in vitro delineated the importance of these residues in ribosome biogenesis. Overall, this dissertation has demonstrated the impact of 16S rRNA structural changes on biogenesis of the small ribosomal subunit and has enabled deeper understanding of ribosome assembly."--Leaves v-vi.
Author: Zhili Xu
Publisher:
ISBN:
Category :
Languages : en
Pages : 402
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Book Description
"Ribonucleic acids (RNAs) perform widely different biological functions ranging from regulation of gene expression to catalysis. Their functions are often tightly correlated with their structure. To explore the relationship between RNA structure and function, Escherichia coli (E. coli) small ribosomal subunit was used as a model system and its biogenesis was investigated using two different approaches. Firstly, we studied a RNA modification system which involves dimethylation of two universally conserved adjacent adenosines in the ultimate helix of the small subunit ribosomal RNAs (rRNA) and the KsgA (E. coli) methyltransferase family, enzyme responsible for these two dimethylations, which also appears to be universally conserved. We localized the position of KsgA relative to 30S subunits using directed hydroxyl radical probing and demonstrated that binding of KsgA and translation initiation factor 3 (IF3) are generally mutually exclusive. Our work strongly suggested that this modification system plays a critical role in differentiating fully assembled, functional subunits from those that are still involved in the biogenesis pathway. Secondly, we devised a modification interference approach to investigate nucleotides within 16S rRNA that are potentially important for the assembly of functional 30S subunits. We found that the majority of these nucleotides are located in the head and interdomain junction of the 30S subunit indicating that the different domains of the 30S subunit assemble differentially and that the assembly of the 3' domain and interdomain junction are more restricted than assembly of the other domains. Further in vivo investigation of individual residues identified in vitro delineated the importance of these residues in ribosome biogenesis. Overall, this dissertation has demonstrated the impact of 16S rRNA structural changes on biogenesis of the small ribosomal subunit and has enabled deeper understanding of ribosome assembly."--Leaves v-vi.
Author: Mirza A. Almehdi
Publisher:
ISBN:
Category : Ribosomes
Languages : en
Pages : 320
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Book Description
Ribosomes are multicomponent macromolecular particles and are essential for the survival of cells in all organisms. The ribosome's universal function is to catalyze polypeptide synthesis through translation of mRNA transcripts. Ribosomes from Escherichia coli, eubacterial organisms, have a sedimentation coefficient of 70S and are composed of 30S and 50S ribonucleoprotein subunits. The small ribosomal subunit is an assembly of 21 different proteins and a 16S ribosomal RNA. Within the 16S rRNA there are a few short stretches of universally conserved sequences spanning positions 517-533, 1394-1408, and 1492-1506. Clear functions for these sequence zones have not yet been assigned. Here I report a kinetic analysis of these highly conserved regions in the 16S rRNA and within the 30S ribosomal subunits. Binding affinity was measured in experiments that were based on protection from nuclease 51 digestion of short oligodeoxynucleotides hybridized to the designated regions. DNAs hybridized to regions 1400 and 1500 show significant differences in the apparent dissociation constants when measured in 30S particles as opposed to those found for 16S rRNA. Region 525 showed no difference in kinetic behavior. To further elucidate the functional and structural role played by the region centered about C1400 in 16S rRNA, a four nucleotide deletion was constructed within this region. The deletion was introduced by direct RNA manipulation using DNA/RNA hybridization, RNase H digestions, and ligation of the correct RNA fragments with T4 RNA ligase. I improved ligation efficiency of large RNA molecules by including a connector looped short DNA oligomer. Recycling products through phenyl boronate agarose (PBA-30) column also improved the efficiency of ligation. The mutagenized 16S rRNA fully reassembles into 30 particles and the altered 30S subunit possesses all of the normal ribosomal proteins. Altered ribosomes were functional in in vitro translation of MS2 mRNA. The altered ribosomes have lower translational activity relative to controls. Here I present indirect evidence suggesting that the decrease in the synthesis of MS2 coat proteins is the result of premature termination. The altered 16S RNA in ribosomes had an apparent dissociation constants with DNA probes comparable to those found for normal 16S rRNA. This suggest that the RNA is less flexible in the particle relative to normal 30S subunits. The deletion at 1400 did not have any effect on the physical properties of the 1500 region, as measured by DNA hybridization. A minor, but significant, effect on the 525 region was observed. A possible RNA/RNA interaction within the 30S particle is proposed to account for this observation.
Author: Heinz Bielka
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3112729757
Category : Science
Languages : en
Pages : 340
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Book Description
No detailed description available for "The Eukaryotic Ribosome".
Author:
Publisher: Academic Press
ISBN: 0128171944
Category : Medical
Languages : en
Pages : 444
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Book Description
RNA-based Regulation in Human Health and Disease offers an in-depth exploration of RNA mediated genome regulation at different hierarchies. Beginning with multitude of canonical and non-canonical RNA populations, especially noncoding RNA in human physiology and evolution, further sections examine the various classes of RNAs (from small to large noncoding and extracellular RNAs), functional categories of RNA regulation (RNA-binding proteins, alternative splicing, RNA editing, antisense transcripts and RNA G-quadruplexes), dynamic aspects of RNA regulation modulating physiological homeostasis (aging), role of RNA beyond humans, tools and technologies for RNA research (wet lab and computational) and future prospects for RNA-based diagnostics and therapeutics. One of the core strengths of the book includes spectrum of disease-specific chapters from experts in the field highlighting RNA-based regulation in metabolic & neurodegenerative disorders, cancer, inflammatory disease, viral and bacterial infections. We hope the book helps researchers, students and clinicians appreciate the role of RNA-based regulation in genome regulation, aiding the development of useful biomarkers for prognosis, diagnosis, and novel RNA-based therapeutics. Comprehensive information of non-canonical RNA-based genome regulation modulating human health and disease Defines RNA classes with special emphasis on unexplored world of noncoding RNA at different hierarchies Disease specific role of RNA - causal, prognostic, diagnostic and therapeutic Features contributions from leading experts in the field
Author: Sabine Müller
Publisher: John Wiley & Sons
ISBN: 3527814531
Category : Science
Languages : en
Pages : 81
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Book Description
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.
Author: Tilman Heise
Publisher:
ISBN: 9781071602317
Category : Human genetics
Languages : en
Pages : 314
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Book Description
This book provides a wide spectrum of methods to study RNA chaperones in vitro, at the single molecule level, and protocols useful for cell-based assays. Beginning with a section on a number of bacterial proteins for study, the volume also explores proteins from eukaryotic cells and how to delve into the complex interactions between RNA chaperones and the folding and unfolding of proteins. Written for the highly successful Methods in Molecular Biology series, 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 practical, RNA Chaperones: Methods and Protocols serves as an ideal guide for scientists and students interested in RNA biology and RNA chaperones. Chapter 3 is available Open Access under a CC-BY 4.0 license via link.springer.com.
Author: J. Michael Lord
Publisher: Springer Science & Business Media
ISBN: 3642121764
Category : Science
Languages : en
Pages : 275
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Book Description
Many plants produce enzymes collectively known as ribosome-inactivating proteins (RIPs). RIPs catalyze the removal of an adenine residue from a conserved loop in the large ribosomal RNA. The adenine residue removed by this depurination is crucial for the binding of elongation factors. Ribosomes modified in this way are no longer able to carry out protein synthesis. Most RIPs exist as single polypeptides (Type 1 RIPs) which are largely non-toxic to mammalian cells because they are unable to enter them and thus cannot reach their ribosomal substrate. In some instances, however, the RIP forms part of a heterodimer where its partner polypeptide is a lectin (Type 2 RIPs). These heterodimeric RIPs are able to bind to and enter mammalian cells. Their ability to reach and modify ribosomes in target cells means these proteins are some of the most potently cytotoxic poisons found in nature, and are widely assumed to play a protective role as part of the host plant’s defenses. RIPs are able to further damage target cells by inducing apoptosis. In addition, certain plants produce lectins lacking an RIP component but which are also cytotoxic. This book focuses on the structure/function and some potential applications of these toxic plant proteins.
Author: Béatrice Clouet-d'Orval
Publisher: Springer
ISBN: 331965795X
Category : Science
Languages : en
Pages : 276
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Book Description
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.
Author: Rob Phillips
Publisher: Garland Science
ISBN: 1134111584
Category : Science
Languages : en
Pages : 1089
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Book Description
Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that
Author: Neocles Leontis
Publisher: Springer Science & Business Media
ISBN: 3642257402
Category : Science
Languages : en
Pages : 402
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Book Description
With the dramatic increase in RNA 3D structure determination in recent years, we now know that RNA molecules are highly structured. Moreover, knowledge of RNA 3D structures has proven crucial for understanding in atomic detail how they carry out their biological functions. Because of the huge number of potentially important RNA molecules in biology, many more than can be studied experimentally, we need theoretical approaches for predicting 3D structures on the basis of sequences alone. This volume provides a comprehensive overview of current progress in the field by leading practitioners employing a variety of methods to model RNA 3D structures by homology, by fragment assembly, and by de novo energy and knowledge-based approaches.
