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https://www.readbyqxmd.com/read/29446752/allosteric-mechanism-of-the-v-vulnificus-adenine-riboswitch-resolved-by-four-dimensional-chemical-mapping
#1
Siqi Tian, Wipapat Kladwang, Rhiju Das
The structural interconversions that mediate the gene regulatory functions of RNA molecules may be different from classic models of allostery, but the relevant structural correlations have remained elusive in even intensively studied systems. Here, we present a four-dimensional expansion of chemical mapping called lock-mutate-map-rescue (LM 2 R), which integrates multiple layers of mutation with nucleotide-resolution chemical mapping. This technique resolves the core mechanism of the adenine-responsive V. vulnificus add riboswitch, a paradigmatic system for which both Monod-Wyman-Changeux (MWC) conformational selection models and non-MWC alternatives have been proposed...
February 15, 2018: ELife
https://www.readbyqxmd.com/read/29440394/structure-function-analysis-of-manganese-exporter-proteins-across-bacteria
#2
Rilee Zeinert, Eli Martinez, Jennifer Schmitz, Katherine Senn, Bakhtawar Usman, Vivek Anantharaman, L Aravind, Lauren S Waters
Manganese is an essential trace nutrient for organisms, because of its role in cofactoring enzymes and providing protection against reactive oxygen species (ROS). Many bacteria require manganese to form pathogenic or symbiotic interactions with eukaryotic host cells. However, excess manganese is toxic, requiring cells to have manganese export mechanisms. Bacteria are currently known to possess two widely-distributed classes of manganese export proteins, MntP and MntE, but other types of transporters likely exist...
February 13, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29420816/a-small-portable-rna-device-for-the-control-of-exon-skipping-in-mammalian-cells
#3
Marc Vogel, Julia E Weigand, Britta Kluge, Manuel Grez, Beatrix Suess
Splicing is an essential and highly regulated process in mammalian cells. We developed a synthetic riboswitch that efficiently controls alternative splicing of a cassette exon in response to the small molecule ligand tetracycline. The riboswitch was designed to control the accessibility of the 3' splice site by placing the latter inside the closing stem of a conformationally controlled tetracycline aptamer. In the presence of tetracycline, the cassette exon is skipped, whereas it is included in the ligand's absence...
February 6, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29413520/rna-based-fluorescent-biosensors-for-detecting-metabolites-in-vitro-and-in-living-cells
#4
Samie R Jaffrey
Genetically encoded sensors are important tools for measuring metabolites and other small molecules in vitro and in live cells. Until recently, genetically encoded sensors exclusively comprised fluorescent proteins that undergo changes in Förster resonance energy transfer upon binding a target analyte. However, recently a new class of fluorescent sensor has been developed composed of RNA. These RNA-based sensors rely on Spinach and other RNA mimics of green fluorescent protein. In each case, the RNA-based sensors contain an analyte-binding aptamer domain which transduces binding of the analyte into a conformational change in Spinach...
2018: Advances in Pharmacology
https://www.readbyqxmd.com/read/29412640/discovery-of-selective-rna-binding-small-molecules-by-affinity-selection-mass-spectrometry
#5
Noreen F Rizvi, John A Howe, Ali Nahvi, Daniel J Klein, Thierry O Fischmann, Hai-Young Kim, Mark A McCoy, Scott S Walker, Alan Hruza, Matthew P Richards, Chad Chamberlin, Peter Saradjian, Margaret T Butko, Gabriel Mercado, Julja Burchard, Corey Strickland, Peter J Dandliker, Graham F Smith, Elliott B Nickbarg
Recent advances in understanding the relevance of non-coding RNA (ncRNA) to disease have increased interest in drugging ncRNA with small molecules. The recent discovery of ribocil, a structurally distinct synthetic mimic of the natural ligand of the flavin mononucleotide (FMN) riboswitch, has revealed the potential chemical diversity of small molecules that target ncRNA. Affinity-selection mass spectrometry (AS-MS) is theoretically applicable to high-throughput screening (HTS) of small molecules binding to ncRNA...
February 7, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29378935/rna-force-field-with-accuracy-comparable-to-state-of-the-art-protein-force-fields
#6
Dazhi Tan, Stefano Piana, Robert M Dirks, David E Shaw
Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins. The application of such simulations to RNA structures, however, has proven more challenging, due in large part to the fact that the physical models ("force fields") available for MD simulations of RNA molecules are substantially less accurate in many respects than those currently available for proteins. Here, we introduce an extensive revision of a widely used RNA force field in which the parameters have been modified, based on quantum mechanical calculations and existing experimental information, to more accurately reflect the fundamental forces that stabilize RNA structures...
January 29, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29367662/comprehensive-profiling-of-the-ligand-binding-landscapes-of-duplexed-aptamer-families-reveals-widespread-induced-fit
#7
Jeffrey D Munzar, Andy Ng, David Juncker
Duplexed aptamers (DAs) are ligand-responsive constructs engineered by hybridizing an aptamer with an aptamer-complementary element (ACE, e.g., a DNA oligonucleotide). Although DAs are commonly deployed, the binding dynamics of ternary ACE-aptamer-ligand systems remain underexplored, having been conventionally described by a conformational selection framework. Here we introduce aptamer-complementary element scanning (ACE-Scan) as a method to generate comprehensive hybridization, spontaneous off-rate, and induced fit ligand-binding landscapes for entire DA families...
January 24, 2018: Nature Communications
https://www.readbyqxmd.com/read/29358079/bacterial-rna-biology-on-a-genome-scale
#8
REVIEW
Jens Hör, Stanislaw A Gorski, Jörg Vogel
Bacteria are an exceedingly diverse group of organisms whose molecular exploration is experiencing a renaissance. While the classical view of bacterial gene expression was relatively simple, the emerging view is more complex, encompassing extensive post-transcriptional control involving riboswitches, RNA thermometers, and regulatory small RNAs (sRNAs) associated with the RNA-binding proteins CsrA, Hfq, and ProQ, as well as CRISPR/Cas systems that are programmed by RNAs. Moreover, increasing interest in members of the human microbiota and environmental microbial communities has highlighted the importance of understudied bacterial species with largely unknown transcriptome structures and RNA-based control mechanisms...
January 16, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29352088/an-archaeal-fluoride-responsive-riboswitch-provides-an-inducible-expression-system-for-hyperthermophiles
#9
Michael Clayton Speed, Brett W Burkhart, Jonathan W Picking, Thomas J Santangelo
Robust genetic systems for the hyperthermophilic Thermococcales have facilitated overexpression of native genes, allowed for the addition of sequences encoding secretion signals, epitope, and affinity tags to coding regions, and permitted the introduction of sequences encoding new proteins in these fast growing fermentative heterotrophs. Tightly controlled and easily manipulated systems permitting regulated gene expression are however limited for these hosts. Here we describe an alternative method for regulatory control reliant on a cis-encoded functional riboswitch in the model archaeon Thermococcus kodakarensis Despite the hyperthermophilic growth temperatures, the proposed structure of the riboswitch conforms to a fluoride-responsive riboswitch encoded in many bacteria, and similarly functions to regulate a component conserved fluoride export pathway...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29346617/riboswitching-with-ciprofloxacin-development-and-characterization-of-a-novel-rna-regulator
#10
Florian Groher, Cristina Bofill-Bosch, Christopher Schneider, Johannes Braun, Sven Jager, Katharina Geißler, Kay Hamacher, Beatrix Suess
RNA molecules play important and diverse regulatory roles in the cell. Inspired by this natural versatility, RNA devices are increasingly important for many synthetic biology applications, e.g. optimizing engineered metabolic pathways, gene therapeutics or building up complex logical units. A major advantage of RNA is the possibility of de novo design of RNA-based sensing domains via an in vitro selection process (SELEX). Here, we describe development of a novel ciprofloxacin-responsive riboswitch by in vitro selection and next-generation sequencing-guided cellular screening...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29341438/natural-antisense-transcripts-in-diseases-from-modes-of-action-to-targeted-therapies
#11
REVIEW
Elżbieta Wanowska, Magdalena Regina Kubiak, Wojciech Rosikiewicz, Izabela Makałowska, Michał Wojciech Szcześniak
Antisense transcription is a widespread phenomenon in mammalian genomes, leading to production of RNAs molecules referred to as natural antisense transcripts (NATs). NATs apply diverse transcriptional and post-transcriptional regulatory mechanisms to carry out a wide variety of biological roles that are important for the normal functioning of living cells, but their dysfunctions can be associated with human diseases. In this review, we attempt to provide a molecular basis for the involvement of NATs in the etiology of human disorders such as cancers and neurodegenerative and cardiovascular diseases...
January 17, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29311281/cyclic-di-gmp-regulates-tfoy-in-vibrio-cholerae-to-control-motility-by-both-transcriptional-and-posttranscriptional-mechanisms
#12
Benjamin R Pursley, Michael M Maiden, Meng-Lun Hsieh, Nicolas Fernandez, Geoffrey B Severin, Christopher M Waters
Cyclic di-GMP (c-di-GMP) is a bacterial second messenger molecule that is a key global regulator in Vibrio cholerae, but the molecular mechanisms by which this molecule regulates downstream phenotypes have not been fully characterized. One such regulatory factor that may respond to c-di-GMP is the Vc2 c-di-GMP-binding riboswitch that is hypothesized to control the expression of the downstream putative transcription factor TfoY. Although much is known about the physical and structural properties of the Vc2 riboswitch aptamer, the nature of its expression and function in V...
January 8, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29297679/rna-structural-dynamics-as-captured-by-molecular-simulations-a-comprehensive-overview
#13
Jiří Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Richard A Cunha, Alejandro Gil-Ley, Giovanni Pinamonti, Simón Poblete, Petr Jurečka, Nils G Walter, Michal Otyepka
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods...
January 3, 2018: Chemical Reviews
https://www.readbyqxmd.com/read/29279370/single-molecule-fret-studies-on-the-cotranscriptional-folding-of-a-thiamine-pyrophosphate-riboswitch
#14
Heesoo Uhm, Wooyoung Kang, Kook Sun Ha, Changwon Kang, Sungchul Hohng
Because RNAs fold as they are being synthesized, their transcription rate can affect their folding. Here, we report the results of single-molecule fluorescence studies that characterize the ligand-dependent cotranscriptional folding of the Escherichia coli thiM riboswitch that regulates translation. We found that the riboswitch aptamer folds into the "off" conformation independent of its ligand, but switches to the "on" conformation during transcriptional pausing near the translational start codon. Ligand binding maintains the riboswitch in the off conformation during transcriptional pauses...
December 26, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29235474/engineering-cell-signaling-using-tunable-crispr-cpf1-based-transcription-factors
#15
Yuchen Liu, Jinghong Han, Zhicong Chen, Hanwei Wu, Hongsong Dong, Guohui Nie
The catalytically dead Cpf1 endonuclease from Acidaminococcus sp. BV3L6 (dAsCpf1) has been used to construct effective transcriptional repressors in bacteria and plants. However, it is still unclear if dAsCpf1 can function in human cells as a transcriptional regulator or a signal conductor. Here, we repurpose the dAsCpf1 system in human cells for a variety of functions, including the activation or repression of gene transcription. Moreover, we construct programmable ligand-controlled dAsCpf1 systems either by coupling crRNAs with engineered riboswitches or by fusing dAsCpf1 proteins with G protein-coupled receptors...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29227220/taxonomic-analyses-of-members-of-the-streptomyces-cinnabarinus-cluster-description-of-streptomyces-cinnabarigriseus-sp-nov-and-streptomyces-davaonensis-sp-nov
#16
Wiebke Landwehr, Peter Kämpfer, Stefanie P Glaeser, Christian Rückert, Jörn Kalinowski, Jochen Blom, Alexander Goesmann, Matthias Mack, Peter Schumann, Ewelina Atasayar, Richard L Hahnke, Manfred Rohde, Karin Martin, Marc Stadler, Joachim Wink
Roseoflavin is the only known riboflavin (vitamin B2) analog with antibiotic properties. It is actively taken up by many micro-organisms and targets flavinmononucleotide riboswitches and flavoproteins. It is described as the product of the tentatively named 'Streptomyces davawensis' JCM 4913. Taxonomic analysis of this strain with a polyphasic approach showed that it is very closely related to Streptomyces cinnabarinus (DSM 40467). The two Streptomyces isolates were obtained from different geographical locations (the Philippines and the Kamchatka Peninsula, respectively), their genomes have been sequenced and the question was whether or not the two isolates were representatives of the same species...
December 11, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29223402/genetic-regulation-mechanism-of-the-yjdf-riboswitch
#17
Sha Gong, Yanli Wang, Zhen Wang, Yujie Wang, Wenbing Zhang
The yjdF riboswitch resides in potential 5' UTRs of homologues of protein-coding gene yjdF in Firmicutes. Unlike other 30 riboswitch classes previously validated, this riboswitch class, can sense and bind to a broad collection of azaaromatic ligands. Among these compounds, some do activate production of yjdF protein driven by the riboswitch, while others are out of riboswitch-mediated modulation possibly because of the toxicity at high ligand concentrations. By incorporating the structures with pseudoknots and ligand binding kinetics into the co-transcriptional folding theory, we theoretically studied the co-transcriptional folding behaviors of the yjdF riboswitch from Bacillus subtilis at different transcription conditions...
December 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29220796/purine-analogs-targeting-the-guanine-riboswitch-as-potential-antibiotics-against-clostridioides-difficile
#18
Lok-Hang Yan, Antoine Le Roux, Kumaraswamy Boyapelly, Anne-Marie Lamontagne, Marie-Ann Archambault, Frédéric Picard-Jean, David Lalonde-Seguin, Emilie St-Pierre, Rafael J Najmanovich, Louis-Charles Fortier, Daniel Lafontaine, Éric Marsault
Riboswitches recently emerged as possible targets for the development of alternative antimicrobial approaches. Guanine-sensing riboswitches in the bacterial pathogen Clostridioides difficile (formerly known as Clostridium difficile) constitute potential targets based on their involvement in the regulation of basal metabolic control of purine compounds. In this study, we deciphered the structure-activity relationship of several guanine derivatives on the guanine riboswitch and determined their antimicrobial activity...
December 2, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29211762/ribofacseq-a-new-method-for-investigating-metabolic-and-transport-pathways-in-bacterial-cells-by-combining-a-riboswitch-based-sensor-fluorescence-activated-cell-sorting-and-next-generation-sequencing
#19
Zohaib Ghazi, Shahrzad Jahanshahi, Yingfu Li
The elucidation of the cellular processes involved in vitamin and cofactor biosynthesis is a challenging task. The conventional approaches to these investigations rely on the discovery and purification of the products (i.e proteins and metabolites) of a particular transport or biosynthetic pathway, prior to their subsequent analysis. However, the purification of low-abundance proteins or metabolites is a formidable undertaking that presents considerable technical challenges. As a solution, we present an alternative approach to such studies that circumvents the purification step...
2017: PloS One
https://www.readbyqxmd.com/read/29191010/design-of-a-temperature-responsive-transcription-terminator
#20
Johanna Roßmanith, Mareen Weskamp, Franz Narberhaus
RNA structures regulate various steps in gene expression. Transcription in bacteria is typically terminated by stable hairpin structures. Translation initiation can be modulated by metabolite- or temperature-sensitive RNA structures, called riboswitches or RNA thermometers (RNATs), respectively. RNATs control translation initiation by occlusion of the ribosome binding site at low temperatures. Increasing temperatures destabilize the RNA structure and facilitate ribosome access. In this study, we exploited temperature-responsive RNAT structures to design regulatory elements that control transcription termination instead of translation initiation in Escherichia coli...
November 30, 2017: ACS Synthetic Biology
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