Download or read book Regulation of Aminoacyl tRNA Synthetase Genes in Bacillus Subtilis written by Rebecca N. Williams-Wagner and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial cells regulate gene expression in response to a variety of signals. Regulation can occur at each level of gene expression including, but not limited to, transcription initiation, transcription attenuation and translation initiation. T box riboswitches are found in 5’ untranslated leader regions upstream of amino acid related genes in Gram-positive bacteria. T box leader RNAs form several conserved structural elements including three stem-loops (Stem I, II and III), a Stem IIA/B pseudoknot, and mutually exclusive terminator and antiterminator helicies. T box riboswitches regulate gene expression at the level of transcription attenuation by interacting directly with a specific tRNA; uncharged tRNA promotes antitermination. This mechanism was identified through genetic analysis of the Bacillus subtilis tyrS gene, which encodes tyrosyl-tRNA synthetase and is expressed during normal growth. TyrS mischarges tRNATyr with D-tyrosine (D-Tyr), which inhibits growth and biofilm formation due to misincorporation of D-Tyr into proteins. B. subtilis produces D-Tyr and lacks known mechanisms to prevent mischarging. The B. subtilis genome has a second gene that encodes tyrosyl-tRNA synthetase, tyrZ, which is expressed when tyrS is mutated. The tyrZ gene is preceded by the dtrR gene, which encodes a MarR-like transcriptional regulator, and a T box riboswitch. We sought to determine how tyrZ gene expression is regulated and the role of TyrZ. We showed that DtrR represses transcription initiation of the dtrR-tyrZ operon by binding to an operator sequence within the promoter. The T box riboswitch also regulates tyrZ expression. We demonstrated that TyrZ is more selective against D-Tyr compared to TyrS, and that tyrZ expression permits growth and biofilm formation in the presence of D-Tyr. We concluded that tyrZ, which we showed is expressed during biofilm formation, may protect cells against D-Tyr during growth and biofilm formation. During analysis of tyrS in vitro, tRNATyr was unable to promote antitermination. However, tRNAGly-dependent antitermination of the glyQS gene, which encodes glycyl-tRNA synthetase, was observed in vitro. The glyQS leader RNA lacks Stem II and the Stem IIA/B pseudoknot, which are required for antitermination of tyrS in vivo. Antitermination of the thrS gene, which encodes threonyl-tRNA synthetase, was reported to require cell extract and fully modified tRNAThr. The thrS leader RNA contains Stem II and the Stem IIA/B pseudoknot. Another goal of this study was to establish conditions for in vitro analysis of T box riboswitch RNAs that contain the structural elements missing in glyQS to determine their role in antitermination. We analyzed the valS gene, which contains all of the conserved structural elements, and showed that the valS leader RNA bound specifically to tRNAVal. We observed tRNAVal-dependent antitermination in vitro, but antitermination was inefficient. We also analyzed the thrS gene, and demonstrated tRNAThr-dependent antitermination in the absence of cellular factors. We conclude that the thrS gene may be a suitable system to study the role of conserved structures in T box antitermination. Because T box riboswitches regulate essential genes in Gram-positive bacteria, this system is an excellent target for the development of antimicrobials. The effectiveness of the antibiotics may be tested using the thrS leader RNA.
Download or read book Characterizing the Landscape of Aminoacyl tRNA Synthetase Protein Production in Bacillus Subtilis written by Darren John Parker and published by . This book was released on 2020 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt: The phenotype of a cell is a consequence of both the identity of the genes in the genome and the magnitude of their expression into proteins. While the biochemical function of many proteins has been uncovered, for most it is unclear how important native protein abundances are for cell fitness. Furthermore, linking changes in abundances with downstream effects on enzymatic output, pathway function, and ultimately cell fitness is unexplored in nearly all cases. Here I use a model enzyme family, the aminoacyl tRNA synthetases (aaRS), to explore how sensitive Bacillus subtilis are to changes in aaRS production from the molecular to phenotypic level. This culmination of protein levels, functional output, and fitness, leads to a complete “fitness landscape” for the aaRS proteins and provides a framework for future study in quantitative biology. In Chapter I, I outline the conceptual questions explored in this thesis, review the current understandings of bacterial translation and aaRS function, and note the various regulatory strategies bacteria utilize to adapt to perturbations. In Chapter II, I find that the aaRS proteins are produced to optimize the growth rate of cells despite the presence of uncharged tRNAs. These native levels are positioned near a ‘fitness cliff’ as the underlying molecular processes of tRNA charging, translation, and regulation, are sensitive to reductions but not increases in synthetase production. In Chapter III, I complete the characterization of the aaRS fitness landscapes by exploring the source of the fitness defects of aaRS overproduction. In Chapter IV, I present a novel protocol for RNA-seq library preparation to reduce the cost and time associated with generating transcriptomic datasets. In Chapter V, using the aforementioned protocol, I characterize the transcriptomes of over 70 strains within the Escherichia coli single gene knockout collection. With the help of a colleague we find that strong selective pressures to induce genes involved in motility leads to a large amount of transcriptome heterogeneity within the collection. Finally, in Chapter VI, I discuss the results of my work, setting up future directions within the context of gene expression, bacterial physiology, and beyond.
Download or read book A Study of the Regulation of Aminoacyl TRNA Synthetase Gene Expression in Bacillus by T box Regulatory Elements written by Niall Foy and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Biology of Aminoacyl tRNA Synthetases written by and published by Academic Press. This book was released on 2020-10-23 with total page 440 pages. Available in PDF, EPUB and Kindle. Book excerpt: Biology of Aminoacyl-tRNA Synthetases, Volume 48 in The Enzymes series, highlights new advances in the field, with this new volume presenting interesting chapters on A narrative about our work on the endless frontier of editing, The puzzling evolution of aminoacyl-tRNA synthetases, Structural basis of the tRNA recognition by aminoacyl-tRNA synthetases, Catalytic strategies of aminoacyl-tRNA synthetases, Trans-editing by aminoacyl-tRNA synthetase-like editing domains, Adaptive and maladaptive mistranslation arising from aminoacyl-tRNA synthetases, Non-canonical inputs and outputs of tRNA aminoacylation, Structure and function of multi-tRNA synthetase complexes, Mitochondrial aminoacyl-tRNA synthetases, Non-canonical functions of human cytoplasmic tyrosyl-, tryptophanyl- and other aminoacyl-tRNA synthetases, and much more. - Provides the authority and expertise of leading contributors from an international board of authors - Presents the latest release in The Enzymes series
Download or read book A Mutation in the Leucyl tRNA Synthetase Gene Affects Expression of the Ilv leu Biosynthetic Operon of Bacillus Subtilis written by Peter Bradley Vander Horn and published by . This book was released on 1991 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt:
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 Reverend Samuel Barnes D D written by and published by . This book was released on 1912 with total page 47 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book The Regulation of Stable RNA in Bacteria written by Marshal Taylor Swanton and published by . This book was released on 1973 with total page 218 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Prokaryotic Metabolism and Physiology written by Byung Hong Kim and published by Cambridge University Press. This book was released on 2019-05-16 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Extensive and up-to-date review of key metabolic processes in bacteria and archaea and how metabolism is regulated under various conditions.
Download or read book Isolation and Characterization of the Trptophanyl trna Synthetase Gene trps from Bacillus Subtilis written by KING CHUEN. CHOW and published by . This book was released on 1988 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Determining the Fidelity of Protein Synthesis in Vivo Utlilizing Bacillus Subtilis ComX Pheromone written by Nicole Seu Fun Yu and published by . This book was released on 2012 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Cells maintain fidelity in protein synthesis through various mechanisms including aminoacyl-tRNA synthetases (aaRSs) that are able to discriminate tRNAs and their cognate amino acids. Substrate specificity along with editing functions of aaRSs act to prevent or remove incorrect amino acids charged onto tRNAs. Editing domains are highly conserved and found in both prokaryotes and eukaryotes; knocking out the editing function of an aaRS does not seem to affect cell viability. To determine the biological relevance of the editing domains found on aaRSs, it is essential to determine the contribution of editing to protein fidelity in vivo. Bacillus subtilis serves as an ideal model to study this phenomenon because it possesses a small gene-enocoded, 10 amino acid pheromone peptide, ComX. ComX is processed, modified, and secreted by B. subtilis as a signaling molecule that can easily be purified. The amino acid sequence of ComX can be altered to some degree while maintaining cellular activity enabling different strains that produce variants of ComX pheromone to be compared for levels of mistranslation. Ultimately future experiments will reveal the impact that editing by an aaRS has on the fidelity of protein synthesis in vivo by quantifying the rates of mistranslation in strains of B. subtilis that express an editing-defective tRNA synthetase and comparing it to levels of mistranslation to wild type strains.
Download or read book Translation Mechanisms written by Jacques Lapointe and published by Springer Science & Business Media. This book was released on 2003-07-31 with total page 476 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Download or read book Aminoacyl tRNA Synthetases in Biology and Medicine written by Sunghoon Kim and published by Springer. This book was released on 2014-04-28 with total page 355 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book will focus on new molecular interactions and novel activities and the associated diseases that have been recently discovered from the studies of eukaryotic and mammalian aminoacyl-tRNA synthetases. In addition, the potential applications of ARS researches in biotechnology and medicine will be addressed.
Download or read book TRNA written by Dieter Söll and published by . This book was released on 1995 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Desk Encyclopedia of Microbiology written by Moselio Schaechter and published by Academic Press. This book was released on 2010-04-19 with total page 1277 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Desk Encyclopedia of Microbiology, Second Edition is a single-volume comprehensive guide to microbiology for the advanced reader. Derived from the six volume e-only Encyclopedia of Microbiology, Third Edition, it bridges the gap between introductory texts and specialized reviews. Covering topics ranging from the basic science of microbiology to the current "hot" topics in the field, it will be invaluable for obtaining background information on a broad range of microbiological topics, preparing lectures and preparing grant applications and reports. - The most comprehensive single-volume source providing an overview of microbiology to non-specialists - Bridges the gap between introductory texts and specialized reviews - Provides concise and general overviews of important topics within the field making it a helpful resource when preparing for lectures, writing reports, or drafting grant applications
Download or read book Research Awards Index written by and published by . This book was released on 1985 with total page 1588 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Microbial Megaplasmids written by Edward Schwartz and published by Springer Science & Business Media. This book was released on 2009-01-29 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside. Microbial Megaplasmids reviews our knowledge of the extensively studied representatives, such as the catabolic plasmids of the pseudomonads, the rhizobial Sym plasmids, the Ti plasmids of the genus Agrobacterium and the giant enterobacterial virulence plasmids. It also presents snapshots of more recently discovered megaplasmids. The contribution of megaplasmids to the biology of their hosts is described, highlighting the interactions between megaplasmid and chromosomal genes.
