Understanding the Role in Translation of a Universally Conserved Structural Element in 16S Ribosomal RNA PDF Download
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Author: Albert Theodore Powers
Publisher:
ISBN:
Category : RNA.
Languages : en
Pages : 334
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Author: Albert Theodore Powers
Publisher:
ISBN:
Category : RNA.
Languages : en
Pages : 334
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Author: Matthew A. Firpo
Publisher:
ISBN:
Category :
Languages : en
Pages : 246
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Author: Jacques Lapointe
Publisher: Springer Science & Business Media
ISBN: 9780306478390
Category : Science
Languages : en
Pages : 476
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Book Description
Translation Mechanisms provides investigators and graduate students with overviews of recent developments in the field of protein biosynthesis that are fuelled by the explosive and synergic growth of structural biology, genomics, and bioinformatics. The outstanding progress in our understanding of the structure, dynamics, and evolution of the prokaryotic and eukaryotic translation machinery, as well as applications in medicine and biotechnology, are described in 26 chapters covering recent discoveries on: -the subtleties of tRNA aminoacylation with natural and unnatural amino acids. -the control of mRNA stability, a key step of gene regulation. -ribosome structure and function, in the era of the atomic-crystal resolution of the ribosome. -the regulation of the biosynthesis of the translational machinery components. -the action of a variety of inhibitors of translation and the prospect for clinical studies.
Author: Zhili Xu
Publisher:
ISBN:
Category :
Languages : en
Pages : 402
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"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: Heinz Bielka
Publisher: Walter de Gruyter GmbH & Co KG
ISBN: 3112729757
Category : Science
Languages : en
Pages : 340
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No detailed description available for "The Eukaryotic Ribosome".
Author: John Eargle
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Book Description
Translation, the process of reading genetic information and synthesizing the corresponding proteins, is universal and found throughout the three domains of life. The flow of information in translation involves a series of distinct but highly conserved RNA·protein complexes with the ribosome being the largest ribonucleoprotein complex in the cell. As the molecular instantiation of the genetic code, tRNA plays a central role in the translational machinery where it interacts with several proteins and other RNAs during the course of protein synthesis. We use molecular dynamics (MD) simulations informed by evolutionary analysis to investigate the dynamics of several RNA·protein complexes involved in translation. Many analysis methods and tools were developed during the course of this study. We present the evolutionary analysis environment MultiSeq, dynamical network analysis and visualization, and a protocol for the preparation of RNA·protein MD simulations. For several Class I aminoacyl-tRNA synthetases (aaRSs), the rate determining step in aminoacylation is the dissociation of the charged tRNA from the enzyme. Through molecular modeling, internal pKa calculations, and MD simulations, distinct, mechanistically relevant post-transfer states with the charged tRNA (Glu-tRNA(Glu)) bound to glutamyl-tRNA synthetase are considered. The behavior of these nonequilibrium states is characterized as a function of time using dynamical network analysis, local energetics, and changes in free energies to estimate transitions that occur during the release of the tRNA. Dynamical network analysis reveals that there are a large number of suboptimal paths through the protein·RNA complex that can be used for communication between the identity elements on the tRNAs and the catalytic site in the aaRS·tRNA complexes. Residues and nucleotides in the majority of pathways bridging communities, local substructures that are highly intraconnected but loosely interconnected, are evolutionarily conserved and are predicted to be important for allosteric signaling. The same monomers are also found in a majority of the suboptimal paths. Modifying these residues or nucleotides has a large effect on the communication pathways in the protein·RNA complex consistent with kinetic data. The highly conserved general base Glu41 is proposed to be a part of a proton relay system for destabilizing the bound charging amino acid following aminoacylation. Addition of elongation factor Tu (EF-Tu) to the aaRS·tRNA complex stimulates the dissociation of the tRNA core and acceptor stem. We use MD simulations to investigate the dynamics of the EF-Tu·GTP·aa-tRNA(Cys) complex and the roles played by Mg2+ ions and modified nucleosides on the free energy of RNA·protein binding. Combined energetic and evolutionary analyses identify the coevolution of residues in EF-Tu and aa-tRNAs at the binding interface. Highly conserved EF-Tu residues are responsible for both attracting aa-tRNAs as well as providing nearby nonbonded repulsive energies which help fine-tune molecular attraction at the binding interface. The trend in EF-Tu·Cys-tRNA(Cys) binding energies observed as the result of mutating the tRNA agrees with experimental observation. We also predict variations in binding free energies upon misacylation of tRNA(Cys) with D-cysteine or O-phosphoserine and upon changing the protonation state of L-cysteine. Finally, ongoing work is presented on the role of ribosomal signatures in the first steps of ribosomal assembly. Ribosomal signatures are features that are completely conserved within one domain of life but absent from the other domains. Correlations between rRNA signatures and signatures in the ribosomal proteins (r-proteins) show that the rRNA signatures coevolved with both domain specific r-proteins and inserts in universal r-proteins. The largest bacterial structural rRNA signature with such a coevolutionary protein partner is found in the five-way junction of the 16S rRNA 5' domain, which is held together by the universal r-protein S4. We characterize the dynamics and flexibility of the free S4 structural signature and rRNA signature helix 16 (h16) as well as the S4·h16 complex. Investigation into the folding and binding of these components will be carried out using Go-like potentials to bias the complex structure towards its native state.
Author: Béatrice Clouet-d'Orval
Publisher: Springer
ISBN: 331965795X
Category : Science
Languages : en
Pages : 276
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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: Marina V. Rodnina
Publisher: Springer Science & Business Media
ISBN: 3709102154
Category : Medical
Languages : en
Pages : 428
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Book Description
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.
Author: Gun Woo Byeon
Publisher:
ISBN:
Category :
Languages : en
Pages :
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Translation can be critically and pervasively regulated in a transcript-specific manner to modulate protein synthesis. However, it is poorly understood which and how cis-regulatory features of the messenger ribonucleic acid (mRNA) encode variable transcript-specific translation rates to impact spatiotemporal gene expression patterns. Here, I address the role of 5' untranslated (5' UTR) in regulating mRNA translation in vertebrate species. In the first part of the dissertation, I explore the phenomenon of extreme non-coding sequence conservation in vertebrate genomes at the level of RNA function in 5' UTRs. Extreme conservation is a fascinating mystery in comparative genomics in which sequence conservation, at levels often greater than coding regions with invariant polypeptide sequences, stretches on for hundreds of nucleotides in the non-coding regions of the genome. While extreme conservation has been extensively studied for its role in transcriptional regulation, its RNA-level function in translational regulation remains largely unknown. This work reveals the role of extremely conserved 5' UTRs in translational regulation of genes linked to the emergence of essential developmental features in vertebrate species. Extremely conserved 5' UTRs are found to contain cis-elements that promote cell-type specific non-canonical translation initiation. As these elements function as RNA molecules, an understanding of their structures is essential. To this end, I develop in-cell mutate-and-map (icM2), a methodology that maps RNA structure using high-throughput mutational analysis inside cells. icM2 maps the ensemble of multiple conformations in an extremely conserved 5' UTR which is found to be important for its translational regulatory function. I find that active RNA structural remodeling inside cells by RNA helicase activity maintains the relative balance of the conformations. Furthermore, cellular structural remodeling occurs frequently in the most conserved regions of the 5' UTRs. I propose a structural explanation for extreme conservation at the level of RNA and highlight the importance of comparative genomics and of RNA structure in understanding 5' UTR function and evolution. In the second part of the dissertation, I explore the genome-wide role of mammalian ribosome expansion segments (ES) in interacting with 5' UTRs to regulate mRNA translation. ESs are eukaryote-specific insertions to the ribosomal ribonucleic acid (rRNA). They are positioned mostly at the exterior surface of the ribosome structure, extending from the core of the ribosome like flexible tentacles. It has been recently shown that the mammalian ES9S in 18S rRNA directly interacts with a Hox gene 5' UTR element to promote its translation. Direct rRNA-mRNA interaction is not a widely recognized paradigm for translation initiation in eukaryotes. However, addressing the potential genome-wide significance of such a mechanism mediated by ribosome ESs and mRNA 5' UTRs is challenging. Since rRNAs are transcribed from tandem repeats of ribosomal DNA units that can range up to hundreds of thousands of copies, it has not been possible to directly manipulate ESs in most species. To solve this problem, I develop VELCRO-IP RNA-seq: variable expansion segment-ligand chimeric ribosome immunoprecipitation RNA sequencing. VELCRO-IP RNA-seq interrogates the interaction of a ribosome ES with mRNA elements genome-wide by combining yeast genetics, in vitro biochemical pull-down and high-throughput sequencing. By applying VELCRO-IP RNA-seq on mammalian ES9S, hundreds of mRNA regions that interact with the ribosome via specific interaction with the ES are identified. Furthermore, the 5' UTR targets of ES9S are found to promote non-canonical translation. A number of short k-mers that have Watson-Crick complementary to ES9S subsequences are overrepresented in its targets, suggesting potential importance of canonical base-pairing. These results provide evidence for the usage of direct mRNA-rRNA interaction as a mechanism of translation initiation on a wider scale than previously imagined for vertebrate species. Finally, in the last chapter, I discuss how my findings can shape future investigations into the remaining unanswered questions on 5' UTR regulation of translation. Altogether, this dissertation takes us a step closer to the ultimate goal of deciphering the code for translational regulation.
Author:
Publisher:
ISBN:
Category : Dissertations, Academic
Languages : en
Pages : 708
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