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Riboswitch OR Riboswitches

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https://www.readbyqxmd.com/read/28431495/iron-regulated-small-rna-expression-as-neisseria-gonorrhoeae-fa-1090-transitions-into-stationary-phase-growth
#1
Lydgia A Jackson, Michael Day, Jennie Allen, Edgar Scott, David W Dyer
BACKGROUND: For most pathogens, iron (Fe) homeostasis is crucial for maintenance within the host and the ability to cause disease. The primary transcriptional regulator that controls intracellular Fe levels is the Fur (ferric uptake regulator) protein, which exerts its action on transcription by binding to a promoter-proximal sequence termed the Fur box. Fur-regulated transcriptional responses are often fine-tuned at the post-transcriptional level through the action of small regulatory RNAs (sRNAs)...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28430408/amplifying-riboswitch-signal-output-using-cellular-wiring
#2
Michael S Goodson, Annastacia C Bennett, Brenton R Jennewine, Emily Briskin, Svetlana V Harbaugh, Nancy Kelley-Loughnane
If fieldable riboswitch-based biological sensors are to fulfil their potential, it is necessary to increase their signal output. Here we report a novel modular amplification system using a riboswitch to initiate signaling between a sensing strain and a reporter strain of E. coli. A quorum sensing signaling molecule biologically wires the sensing and reporter strains together. The amplification circuit increased the amount of fluorescence generated on ligand binding compared to when the riboswitch controlled fluorescence expression directly...
April 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28427920/genome-improvement-of-the-acarbose-producer-actinoplanes-sp-se50-110-and-annotation-refinement-based-on-rna-seq-analysis
#3
Timo Wolf, Susanne Schneiker-Bekel, Armin Neshat, Vera Ortseifen, Daniel Wibberg, Till Zemke, Alfred Pühler, Jörn Kalinowski
Actinoplanes sp. SE50/110 is the natural producer of acarbose, which is used in the treatment of diabetes mellitus type II. However, until now the transcriptional organization and regulation of the acarbose biosynthesis is only understood rudimentarily. The genome sequence of Actinoplanes sp. SE50/110 was known before, but was resequenced in this study to remove assembly artifacts and incorrect base callings. The annotation of the genome was refined in a multi-step approach, including modern bioinformatic pipelines, transcriptome and proteome data...
April 17, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28420751/control-of-potassium-homeostasis-is-an-essential-function-of-the-second-messenger-cyclic-di-amp-in-bacillus-subtilis
#4
Jan Gundlach, Christina Herzberg, Volkhard Kaever, Katrin Gunka, Tamara Hoffmann, Martin Weiß, Johannes Gibhardt, Andrea Thürmer, Dietrich Hertel, Rolf Daniel, Erhard Bremer, Fabian M Commichau, Jörg Stülke
The second messenger cyclic di-adenosine monophosphate (c-di-AMP) is essential in the Gram-positive model organism Bacillus subtilis and in related pathogenic bacteria. It controls the activity of the conserved ydaO riboswitch and of several proteins involved in potassium (K(+)) uptake. We found that the YdaO protein was conserved among several different bacteria and provide evidence that YdaO functions as a K(+) transporter. Thus, we renamed the gene and protein KimA (K(+) importer A). Reporter activity assays indicated that expression beyond the c-di-AMP-responsive riboswitch of the kimA upstream regulatory region occurred only in bacteria grown in medium containing low K(+) concentrations...
April 18, 2017: Science Signaling
https://www.readbyqxmd.com/read/28403796/riboswitches-as-potential-targets-for-the-development-of-anti-biofilm-drugs
#5
José A Reyes-Darias, Tino Krell
In nature, bacteria can exist as single motile cells or as sessile cellular community, known as microbial biofilms. Bacteria within biofilms are embedded in a self-produced extracellular matrix that makes them more resistant to antibiotic treatment and responses of the host immune system. Microbial biofilms are very important in medicine since they are associated with several human diseases such as dental caries, periodontitis, otitis media, infective endocarditis, infectious kidney stones, osteomyelitis or prostatitis...
April 7, 2017: Current Topics in Medicinal Chemistry
https://www.readbyqxmd.com/read/28402873/saxs-oriented-ensemble-refinement-of-flexible-biomolecules
#6
Peng Cheng, Junhui Peng, Zhiyong Zhang
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28398719/deep-sequencing-analysis-of-aptazyme-variants-based-on-a-pistol-ribozyme
#7
Shungo Kobori, Kei Takahashi, Yohei Yokobayashi
Chemically regulated self-cleaving ribozymes, or aptazymes, are emerging as a promising class of genetic devices that allow dynamic control of gene expression in synthetic biology. However, further expansion of the limited repertoire of ribozymes and aptamers, and development of new strategies to couple the RNA elements to engineer functional aptazymes are highly desirable for synthetic biology applications. Here, we report aptazymes based on the recently identified self-cleaving pistol ribozyme class using a guanine aptamer as the molecular sensing element...
April 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28398514/distributed-biotin-streptavidin-transcription-roadblocks-for-mapping-cotranscriptional-rna-folding
#8
Eric J Strobel, Kyle E Watters, Yuri Nedialkov, Irina Artsimovitch, Julius B Lucks
RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks...
April 8, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28396576/riboswitch-diversity-and-distribution
#9
Phillip J McCown, Keith A Corbino, Shira Stav, Madeline E Sherlock, Ronald R Breaker
Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands. The research findings produced since the first riboswitch validation reports in 2002 reveal that these noncoding RNA domains exploit many different structural features to create binding pockets that are extremely selective for their target ligands...
April 10, 2017: RNA
https://www.readbyqxmd.com/read/28377919/tb-3-cleavage-assays-reveal-specific-mg-2-binding-sites-necessary-to-pre-fold-the-btub-riboswitch-for-adocbl-binding
#10
Pallavi K Choudhary, Sofia Gallo, Roland K O Sigel
Riboswitches are RNA elements that bind specific metabolites in order to regulate the gene expression involved in controlling the cellular concentration of the respective molecule or ion. Ligand recognition is mostly facilitated by Mg(2+) mediated pre-organization of the riboswitch to an active tertiary fold. To predict these specific Mg(2+) induced tertiary interactions of the btuB riboswitch from E. coli, we here report Mg(2+) binding pockets in its aptameric part in both, the ligand-free and the ligand-bound form...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28375743/engineering-and-in-vivo-applications-of-riboswitches
#11
Zachary F Hallberg, Yichi Su, Rebekah Z Kitto, Ming C Hammond
Riboswitches are common gene regulatory units mostly found in bacteria that are capable of altering gene expression in response to a small molecule. These structured RNA elements consist of two modular subunits: an aptamer domain that binds with high specificity and affinity to a target ligand and an expression platform that transduces ligand binding to a gene expression output. Significant progress has been made in engineering novel aptamer domains for new small molecule inducers of gene expression. Modified expression platforms have also been optimized to function when fused with both natural and synthetic aptamer domains...
March 30, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28375729/long-range-interactions-in-riboswitch-control-of-gene-expression
#12
Christopher P Jones, Adrian R Ferré-D'Amaré
Riboswitches are widespread RNA motifs that regulate gene expression in response to fluctuating metabolite concentrations. Known primarily from bacteria, riboswitches couple specific ligand binding and changes in RNA structure to mRNA expression in cis. Crystal structures of the ligand binding domains of most of the phylogenetically widespread classes of riboswitches, each specific to a particular metabolite or ion, are now available. Thus, the bound states-one end point-have been thoroughly characterized, but the unbound states have been more elusive...
March 30, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28345904/ligand-selectivity-mechanism-and-conformational-changes-in-guanine-riboswitch-by-molecular-dynamics-simulations-and-free-energy-calculations
#13
Guodong Hu, Aijing Ma, Jihua Wang
Riboswitches regulate gene expression through direct and specific interactions with small metabolite molecules. Binding of a ligand to its RNA target is high selectivity and affinity and induces conformational changes of the RNA's secondary and tertiary structure. The structural difference of two purine riboswitches aptamers is caused by only one single mutation, where cytosine 74 in the guanine riboswitch is corresponding to a uracil 74 in adenine riboswitch. Here we employed molecular dynamics (MD) simulation, molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and thermodynamic integration computational methodologies to evaluate the energetic and conformational changes of ligands binding to purine riboswitches...
April 6, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28333103/the-genetic-code-and-rna-amino-acid-affinities
#14
REVIEW
Michael Yarus
A significant part of the genetic code likely originated via a chemical interaction, which should be experimentally verifiable. One possible verification relates bound amino acids (or perhaps their activated congeners) and ribonucleotide sequences within cognate RNA binding sites. To introduce this interaction, I first summarize how amino acids function as targets for RNA binding. Then the experimental method for selecting relevant RNA binding sites is characterized. The selection method's characteristics are related to the investigation of the RNA binding site model treated at the outset...
March 23, 2017: Life
https://www.readbyqxmd.com/read/28265071/bioinformatic-analysis-of-riboswitch-structures-uncovers-variant-classes-with-altered-ligand-specificity
#15
Zasha Weinberg, James W Nelson, Christina E Lünse, Madeline E Sherlock, Ronald R Breaker
Riboswitches are RNAs that form complex, folded structures that selectively bind small molecules or ions. As with certain groups of protein enzymes and receptors, some riboswitch classes have evolved to change their ligand specificity. We developed a procedure to systematically analyze known riboswitch classes to find additional variants that have altered their ligand specificity. This approach uses multiple-sequence alignments, atomic-resolution structural information, and riboswitch gene associations. Among the discoveries are unique variants of the guanine riboswitch class that most tightly bind the nucleoside 2'-deoxyguanosine...
March 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28248966/a-magnesium-induced-triplex-pre-organizes-the-sam-ii-riboswitch
#16
Susmita Roy, Heiko Lammert, Ryan L Hayes, Bin Chen, Regan LeBlanc, T Kwaku Dayie, José N Onuchic, Karissa Y Sanbonmatsu
Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28239422/differential-regulation-of-riboflavin-supply-genes-in-vibrio-cholerae
#17
Ignacio Sepúlveda Cisternas, Alexia Torres, Andrés Fuentes Flores, Víctor Antonio García Angulo
BACKGROUND: Riboflavin is the precursor of important redox cofactors such as flavin mononucleotide (FMN) and flavin adenine dinucleotide, required for several biological processes. Vibrio cholerae, a pathogenic bacterium responsible for the cholera disease, possesses the ability to biosynthesize de novo as well as to uptake riboflavin through the riboflavin biosynthetic pathway (RBP) and the RibN importer, respectively. The intra-organism relationship between riboflavin biosynthesis and uptake functions has not been studied...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28225108/an-integrated-perspective-on-rna-aptamer-ligand-recognition-models-clearing-muddy-waters
#18
K McCluskey, J Carlos Penedo
Riboswitches are short RNA motifs that sensitively and selectively bind cognate ligands to modulate gene expression. Like protein receptor-ligand pairs, their binding dynamics are traditionally categorized as following one of two paradigmatic mechanisms: conformational selection and induced fit. In conformational selection, ligand binding stabilizes a particular state already present in the receptor's dynamic ensemble. In induced fit, ligand-receptor interactions enable the system to overcome the energetic barrier into a previously inaccessible state...
February 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28214735/rna-based-control-mechanisms-of-clostridium-difficile
#19
REVIEW
Olga Soutourina
Clostridium difficile (CD)-associated diarrhoea is currently the most prevalent nosocomial diarrhoea worldwide. Many characteristics of CD pathogenicity remain poorly understood. Recent data strongly indicate the importance of an RNA network for the control of gene expression in CD. More than 200 regulatory RNAs have been identified by deep sequencing and targeted approaches, including Hfq-dependent trans riboregulators, cis-antisense RNAs, CRISPR RNAs, and c-di-GMP-responsive riboswitches. These regulatory RNAs are involved in the control of major processes in the CD infection cycle, for example motility, biofilm formation, adhesion, sporulation, stress response, and defence against bacteriophages...
February 16, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28212758/the-guanidine-riboswitch-a-poor-orphan-no-longer
#20
David M J Lilley
Riboswitches are widespread in the bacterial kingdom, where they regulate gene expression in response to different small molecules and ions. However, some remain orphans with no known endogenous ligand. Three recently published papers (Battaglia et al., 2017; Nelson et al., 2017; and Reiss et al., 2017) de-orphanize a widespread ykkC element, showing that it responds to guanidine and elaborating on how that response is mediated.
February 16, 2017: Cell Chemical Biology
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