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Riboswitch OR Riboswitches

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https://www.readbyqxmd.com/read/27876054/engineering-an-inducible-gene-expression-system-for-bacillus-subtilis-from-a-strong-constitutive-promoter-and-a-theophylline-activated-synthetic-riboswitch
#1
Wenjing Cui, Laichuang Han, Jintao Cheng, Zhongmei Liu, Li Zhou, Junling Guo, Zhemin Zhou
BACKGROUND: Synthetic riboswitches have been increasingly used to control and tune gene expression in diverse organisms. Although a set of theophylline-responsive riboswitches have been developed for bacteria, fully functional expression elements mediated by synthetic riboswitches in Bacillus subtilis are rarely used because of the host-dependent compatibility between the promoters and riboswitches. RESULTS: A novel genetic element composed of the promoter P43 and a theophylline-riboswitch was developed and characterized in B...
November 22, 2016: Microbial Cell Factories
https://www.readbyqxmd.com/read/27873255/reporter-gene-based-screening-for-tpp-riboswitch-activators
#2
Christina E Lünse, Günter Mayer
With the rise of multidrug resistant bacteria and a growing number of nosocomial infections, there has been an increased interest in finding new antibacterial drugs and drug targets. Riboswitches represent attractive new antibacterial drug targets, because they not only inherently recognize a specific metabolite or ion with their RNA aptamer domain, but also often regulate essential metabolic pathways. Here, we describe a reporter gene-based screen to identify compounds that activate the thiamine pyrophosphate (TPP) riboswitch in bacteria...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27863061/how-to-understand-atomistic-molecular-dynamics-simulations-of-rna-and-protein-rna-complexes
#3
REVIEW
Jiří Šponer, Miroslav Krepl, Pavel Banáš, Petra Kührová, Marie Zgarbová, Petr Jurečka, Marek Havrila, Michal Otyepka
We provide a critical assessment of explicit-solvent atomistic molecular dynamics (MD) simulations of RNA and protein/RNA complexes, written primarily for non-specialists with an emphasis to explain the limitations of MD. MD simulations can be likened to hypothetical single-molecule experiments starting from single atomistic conformations and investigating genuine thermal sampling of the biomolecules. The main advantage of MD is the unlimited temporal and spatial resolution of positions of all atoms in the simulated systems...
November 10, 2016: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/27856567/transcriptional-and-translational-regulation-by-rna-thermometers-riboswitches-and-the-srna-dsra-in-escherichia-coli-o157-h7-sakai-under-combined-cold-and-osmotic-stress-adaptation
#4
Sarah Maria Hücker, Svenja Simon, Siegfried Scherer, Klaus Neuhaus
The enteric pathogen Escherichia coli O157:H7 Sakai (EHEC) is able to grow at lower temperatures compared to commensal E. coli Growth at environmental conditions displays complex challenges different to those in a host. EHEC was grown at 37°C (control) and at 14°C with 4% NaCl, a combination of cold and osmotic stress as present in the food chain. Comparison of RNAseq and RIBOseq data provided a snap shot of ongoing transcription and translation, differentiating transcriptional and post-transcriptional gene regulation, respectively...
November 16, 2016: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/27834404/small-regulatory-rnas-of-rickettsia-conorii
#5
Hema P Narra, Casey L C Schroeder, Abha Sahni, Mark Rojas, Kamil Khanipov, Yuriy Fofanov, Sanjeev K Sahni
Small regulatory RNAs comprise critically important modulators of gene expression in bacteria, yet very little is known about their prevalence and functions in Rickettsia species. R. conorii, the causative agent of Mediterranean spotted fever, is a tick-borne pathogen that primarily infects microvascular endothelium in humans. We have determined the transcriptional landscape of R. conorii during infection of Human Microvascular Endothelial Cells (HMECs) by strand-specific RNA sequencing to identify 4 riboswitches, 13 trans-acting (intergenic), and 22 cis-acting (antisense) small RNAs (termed 'Rc_sR's)...
November 11, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27822545/proteome-remodeling-in-response-to-sulfur-limitation-in-candidatus-pelagibacter-ubique
#6
Daniel P Smith, Carrie D Nicora, Paul Carini, Mary S Lipton, Angela D Norbeck, Richard D Smith, Stephen J Giovannoni
The alphaproteobacterium "Candidatus Pelagibacter ubique" strain HTCC1062 and most other members of the SAR11 clade lack genes for assimilatory sulfate reduction, making them dependent on organosulfur compounds that occur naturally in seawater. To investigate how these cells adapt to sulfur limitation, batch cultures were grown in defined medium containing either limiting or nonlimiting amounts of dimethylsulfoniopropionate (DMSP) as the sole sulfur source. Protein and mRNA expression were measured before, during, and after the transition from exponential growth to stationary phase...
July 2016: MSystems
https://www.readbyqxmd.com/read/27819065/characterization-of-mg-2-distributions-around-rna-in-solution
#7
Justin A Lemkul, Sirish Kaushik Lakkaraju, Alexander D MacKerell
Binding of metal ions is an important factor governing the folding and dynamics of RNA. Shielding of charges in the polyanionic backbone allows RNA to adopt a diverse range of folded structures that give rise to their many functions within the cell. Some RNA sequences fold only in the presence of Mg(2+), which may be bound via direct interactions or occupy the more diffuse "ion atmosphere" around the RNA. To understand the driving forces for RNA folding, it is important to be able to fully characterize the distribution of metal ions around the RNA...
October 31, 2016: ACS Omega
https://www.readbyqxmd.com/read/27813001/computer-aided-design-of-rna-origami-structures
#8
Steffen L Sparvath, Cody W Geary, Ebbe S Andersen
RNA nanostructures can be used as scaffolds to organize, combine, and control molecular functionalities, with great potential for applications in nanomedicine and synthetic biology. The single-stranded RNA origami method allows RNA nanostructures to be folded as they are transcribed by the RNA polymerase. RNA origami structures provide a stable framework that can be decorated with functional RNA elements such as riboswitches, ribozymes, interaction sites, and aptamers for binding small molecules or protein targets...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27805569/rational-design-of-aptazyme-riboswitches-for-efficient-control-of-gene-expression-in-mammalian-cells
#9
Guocai Zhong, Haimin Wang, Charles C Bailey, Guangping Gao, Michael Farzan
Efforts to control mammalian gene expression with ligand-responsive riboswitches have been hindered by lack of a general method for generating efficient switches in mammalian systems. Here we describe a rational-design approach that enables rapid development of efficient cis-acting aptazyme riboswitches. We identified communication-module characteristics associated with aptazyme functionality through analysis of a 32-aptazyme test panel. We then developed a scoring system that predicts an aptazymes's activity by integrating three characteristics of communication-module bases: hydrogen bonding, base stacking, and distance to the enzymatic core...
November 2, 2016: ELife
https://www.readbyqxmd.com/read/27802301/the-conserved-dcw-gene-cluster-of-r-sphaeroides-is-preceded-by-an-uncommonly-extended-5-leader-featuring-the-srna-upsm
#10
Lennart Weber, Clemens Thoelken, Marcel Volk, Bernhard Remes, Marcus Lechner, Gabriele Klug
Cell division and cell wall synthesis mechanisms are similarly conserved among bacteria. Consequently some bacterial species have comparable sets of genes organized in the dcw (division and cell wall) gene cluster. Dcw genes, their regulation and their relative order within the cluster are outstandingly conserved among rod shaped and gram negative bacteria to ensure an efficient coordination of growth and division. A well studied representative is the dcw gene cluster of E. coli. The first promoter of the gene cluster (mraZ1p) gives rise to polycistronic transcripts containing a 38 nt long 5' UTR followed by the first gene mraZ...
2016: PloS One
https://www.readbyqxmd.com/read/27798597/cotranscriptional-folding-of-a-riboswitch-at-nucleotide-resolution
#11
Kyle E Watters, Eric J Strobel, Angela M Yu, John T Lis, Julius B Lucks
RNAs can begin to fold immediately as they emerge from RNA polymerase. During cotranscriptional folding, interactions between nascent RNAs and ligands are able to direct the formation of alternative RNA structures, a feature exploited by noncoding RNAs called riboswitches to make gene-regulatory decisions. Despite their importance, cotranscriptional folding pathways have yet to be uncovered with sufficient resolution to reveal how cotranscriptional folding governs RNA structure and function. To access cotranscriptional folding at nucleotide resolution, we extended selective 2'-hydroxyl acylation analyzed by primer-extension sequencing (SHAPE-seq) to measure structural information of nascent RNAs during transcription...
October 31, 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27790856/a-family-of-genus-specific-rnas-in-tandem-with-dna-binding-proteins-control-expression-of-the-bada-major-virulence-factor-gene-in-bartonella-henselae
#12
Nhan Tu, Ronan K Carroll, Andy Weiss, Lindsey N Shaw, Gael Nicolas, Sarah Thomas, Amorce Lima, Udoka Okaro, Burt Anderson
Bartonella henselae is a gram-negative zoonotic bacterium that causes infections in humans including endocarditis and bacillary angiomatosis. B. henselae has been shown to grow as large aggregates and form biofilms in vitro. The aggregative growth and the angiogenic host response requires the trimeric autotransporter adhesin BadA. We examined the transcriptome of the Houston-1 strain of B. henselae using RNA-seq revealing nine novel, highly-expressed intergenic transcripts (Bartonella regulatory transcript, Brt1-9)...
October 28, 2016: MicrobiologyOpen
https://www.readbyqxmd.com/read/27771480/identification-of-a-guaay-pentaloop-sequence-involved-in-a-novel-rna-loop-helix-interaction
#13
Russell T Chan, Kevin S Keating, Michaela C Go, Navtej Toor
Large RNAs often utilize GNRA tetraloops as structural elements to stabilize the overall tertiary fold. These tetraloop-receptor (TR) interactions have a conserved geometry in which the tetraloop docks into the receptor at an angle of ~15° from the helix containing the receptor. Here, we show that the conserved GUAAY pentaloop found in domain III of group IIB1 introns participates in a novel class of RNA tertiary interaction with a geometry and mode of binding that are significantly different from that found in GNRA TR interactions...
October 19, 2016: Journal of Molecular Biology
https://www.readbyqxmd.com/read/27754501/regulation-of-map4k4-gene-expression-by-rna-interference-through-an-engineered-theophylline-dependent-hepatitis-delta-virus-ribozyme-switch
#14
Hui Cheng, Yuanyuan Zhang, Hongyan Wang, Na Sun, Min Liu, Hongxia Chen, Renjun Pei
Riboswitches are functional non-coding RNA regulatory components that play an important role in the regulation of gene expression in diverse organisms. In particular, using riboswitches to modulate RNA interference (RNAi) enables temporal and spatial control of gene expression in mammalian cells. Herein, a ribozyme gene switch to activate RNAi was fabricated for the artificial regulation of versatile gene silencing through the interaction of an RNA aptamer with small molecules. The device comprised an allosteric HDV ribozyme with an embedded theophylline aptamer and a primary miRNA (pri-miRNA) to silence the MAP4K4 gene in hepatic (HepG2) cells, aiming to achieve dose-dependent control of the activation of RNAi, and then the regulation of the MAP4K4 gene by theophylline...
October 18, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27729470/carotenogenesis-is-regulated-by-5-utr-mediated-translation-of-phytoene-synthase-splice-variants
#15
Daniel Álvarez, Björn Voß, Dirk Maass, Florian Wüst, Patrick Schaub, Peter Beyer, Ralf Welsch
Phytoene synthase (PSY) catalyzes the highly regulated, frequently rate-limiting synthesis of the first biosynthetically formed carotene. While PSY constitutes a small gene family in most plant taxa, the Brassicaceae, including Arabidopsis (Arabidopsis thaliana), predominantly possess a single PSY gene. This monogenic situation is compensated by the differential expression of two alternative splice variants (ASV), which differ in length and in the exon/intron retention of their 5'UTRs. ASV1 contains a long 5'UTR (untranslated region) and is involved in developmentally regulated carotenoid formation, such as during deetiolation...
December 2016: Plant Physiology
https://www.readbyqxmd.com/read/27690736/the-3-untranslated-region-of-mrnas-as-a-site-for-ribozyme-cleavage-dependent-processing-and-control-in-bacteria
#16
Michele Felletti, Anna Bieber, Jörg S Hartig
Besides its primary informational role, the sequence of the messenger RNA (mRNA) including its 5'- and 3'- untranslated regions (UTRs), contains important features that are relevant for post-transcriptional and translational regulation of gene expression. In this work a number of bacterial twister motifs are characterized both in vitro and in vivo. The analysis of their genetic contexts shows that these motifs have the potential of being transcribed as part of polycistronic mRNAs, thus we suggest the involvement of bacterial twister motifs in the processing of mRNA...
October 3, 2016: RNA Biology
https://www.readbyqxmd.com/read/27672192/uptake-and-metabolism-of-antibiotics-roseoflavin-and-8-demethyl-8-aminoriboflavin-in-riboflavin-auxotrophic-listeria-monocytogenes
#17
Andreas Matern, Danielle Pedrolli, Stephanie Großhennig, Jörgen Johansson, Matthias Mack
The riboflavin analogs roseoflavin (RoF) and 8-demethyl-8-aminoriboflavin (AF) are produced by the bacteria Streptomyces davawensis and Streptomyces cinnabarinus Riboflavin analogs have the potential to be used as broad-spectrum antibiotics, and we therefore studied the metabolism of riboflavin (vitamin B2), RoF, and AF in the human pathogen Listeria monocytogenes, a bacterium which is a riboflavin auxotroph. We show that the L. monocytogenes protein Lmo1945 is responsible for the uptake of riboflavin, RoF, and AF...
December 1, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27672149/trigger-phosphodiesterases-as-a-novel-class-of-c-di-gmp-effector-proteins
#18
REVIEW
Regine Hengge
The bacterial second messenger c-di-GMP controls bacterial biofilm formation, motility, cell cycle progression, development and virulence. It is synthesized by diguanylate cyclases (with GGDEF domains), degraded by specific phosphodiesterases (PDEs, with EAL of HD-GYP domains) and sensed by a wide variety of c-di-GMP-binding effectors that control diverse targets. c-di-GMP-binding effectors can be riboswitches as well as proteins with highly diverse structures and functions. The latter include 'degenerate' GGDEF/EAL domain proteins that are enzymatically inactive but still able to bind c-di-GMP...
November 5, 2016: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27670347/twister-ribozymes-as-highly-versatile-expression-platforms-for-artificial-riboswitches
#19
Michele Felletti, Julia Stifel, Lena A Wurmthaler, Sophie Geiger, Jörg S Hartig
The utilization of ribozyme-based synthetic switches in biotechnology has many advantages such as an increased robustness due to in cis regulation, small coding space and a high degree of modularity. The report of small endonucleolytic twister ribozymes provides new opportunities for the development of advanced tools for engineering synthetic genetic switches. Here we show that the twister ribozyme is distinguished as an outstandingly flexible expression platform, which in conjugation with three different aptamer domains, enables the construction of many different one- and two-input regulators of gene expression in both bacteria and yeast...
2016: Nature Communications
https://www.readbyqxmd.com/read/27665605/the-quick-and-the-dead-a-guide-to-fast-phasing-of-small-ribozyme-and-riboswitch-crystal-structures
#20
Jermaine L Jenkins, Joseph E Wedekind
Ribozymes and riboswitches are examples of non-protein-coding (nc)RNA molecules that achieve biological activity by adopting complex three-dimensional folds. Visualization of such molecules at near-atomic resolution can enhance our understanding of how chemical groups are organized spatially, thereby providing novel insight into function. This approach has its challenges, which mainly entail sample crystallization followed by the application of empirical, structure-determination methods that often include experimental "phasing" of X-ray diffraction data...
2016: Methods in Molecular Biology
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