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https://www.readbyqxmd.com/read/28543037/naringenin-responsive-riboswitch-based-fluorescent-biosensor-module-for-escherichia-coli-co-cultures
#1
Yu Xiu, Sungho Jang, J Andrew Jones, Nicholas A Zill, Robert J Linhardt, Qipeng Yuan, Gyoo Yeol Jung, Mattheos A G Koffas
The ability to design and construct combinatorial synthetic metabolic pathways has far exceeded our capacity for efficient screening and selection of the resulting microbial strains. The need for high-throughput rapid screening techniques is of upmost importance for the future of synthetic biology and metabolic engineering. Here we describe the development of a RNA riboswitch-based biosensor module with dual fluorescent reporters, and demonstrate a high-throughput flow cytometry-based screening method for identification of naringenin over producing Escherichia coli strains in co-culture...
May 20, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28541183/pausing-guides-rna-folding-to-populate-transiently-stable-rna-structures-for-riboswitch-based-transcription-regulation
#2
Hannah Steinert, Florian Sochor, Anna Wacker, Janina Buck, Christina Helmling, Fabian Hiller, Sara Keyhani, Jonas Noeske, Steffen Kaspar Grimm, Martin M Rudolph, Heiko Keller, Rachel Anne Mooney, Robert Landick, Beatrix Suess, Boris Fürtig, Jens Wöhnert, Harald Schwalbe
In bacteria, the regulation of gene expression by cis-acting transcriptional riboswitches located in the 5'-untranslated regions of messenger RNA requires the temporal synchronization of RNA synthesis and ligand binding-dependent conformational refolding. Ligand binding to the aptamer domain of the riboswitch induces premature termination of the mRNA synthesis of ligand-associated genes due to the coupled formation of 3'-structural elements acting as terminators. To date, there has been no high resolution structural description of the concerted process of synthesis and ligand-induced restructuring of the regulatory RNA element...
May 25, 2017: ELife
https://www.readbyqxmd.com/read/28531275/molecular-envelope-and-atomic-model-of-an-anti-terminated-glyqs-t-box-regulator-in-complex-with-trnagly
#3
Bhaskar Chetnani, Alfonso Mondragón
A T-box regulator or riboswitch actively monitors the levels of charged/uncharged tRNA and participates in amino acid homeostasis by regulating genes involved in their utilization or biosynthesis. It has an aptamer domain for cognate tRNA recognition and an expression platform to sense the charge state and modulate gene expression. These two conserved domains are connected by a variable linker that harbors additional secondary structural elements, such as Stem III. The structural basis for specific tRNA binding is known, but the structural basis for charge sensing and the role of other elements remains elusive...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28529506/roles-of-regulatory-rnas-for-antibiotic-resistance-in-bacteria-and-their-potential-value-as-novel-drug-targets
#4
REVIEW
Petra Dersch, Muna A Khan, Sabrina Mühlen, Boris Görke
The emergence of antibiotic resistance mechanisms among bacterial pathogens increases the demand for novel treatment strategies. Lately, the contribution of non-coding RNAs to antibiotic resistance and their potential value as drug targets became evident. RNA attenuator elements in mRNA leader regions couple expression of resistance genes to the presence of the cognate antibiotic. Trans-encoded small RNAs (sRNAs) modulate antibiotic tolerance by base-pairing with mRNAs encoding functions important for resistance such as metabolic enzymes, drug efflux pumps, or transport proteins...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28529131/the-structure-of-the-guanidine-ii-riboswitch
#5
Lin Huang, Jia Wang, David M J Lilley
The guanidine-II (mini-ykkC) riboswitch is the smallest of the guanidine-responsive riboswitches, comprising two stem loops of similar sequence. We have solved high-resolution crystal structures of both stem loops for the riboswitch from Gloeobacter violaceus. The stem loops have a strong propensity to dimerize by intimate loop-loop interaction. The dimerization creates specific binding pockets for two guanidine molecules, explaining their cooperative binding. Within the binding pockets the ligands are hydrogen bonded to a guanine at O6 and N7, and to successive backbone phosphates...
May 18, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28525764/two-are-better-than-one-dual-targeting-of-riboswitches-by-metabolite-analogs
#6
Stefanie Sandra Krajewski, Dmitry Ignatov, Jörgen Johansson
In this issue of Cell Chemical Biology, Wang et al. (2017) examine the effect of the novel synthetic molecule ribocil-C and the natural compound roseoflavin in Gram-positive pathogens. In methicillin-resistant Staphylococcus aureus (MRSA), ribocil-C and roseoflavin target two autonomous riboswitches simultaneously, thereby inhibiting de novo synthesis and uptake of riboflavin.
May 18, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28520932/translational-control-and-rho-dependent-transcription-termination-are-intimately-linked-in-riboswitch-regulation
#7
Laurène Bastet, Adrien Chauvier, Navjot Singh, Antony Lussier, Anne-Marie Lamontagne, Karine Prévost, Eric Massé, Joseph T Wade, Daniel A Lafontaine
Riboswitches are regulatory elements that control gene expression by altering RNA structure upon the binding of specific metabolites. Although Bacillus subtilis riboswitches have been shown to control premature transcription termination, less is known about regulatory mechanisms employed by Escherichia coli riboswitches, which are predicted to regulate mostly at the level of translation initiation. Here, we present experimental evidence suggesting that the majority of known E. coli riboswitches control transcription termination by using the Rho transcription factor...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28504865/real-time-crystallographic-studies-of-the-adenine-riboswitch-using-an-x-ray-free-electron-laser
#8
REVIEW
J R Stagno, Y R Bhandari, C E Conrad, Y Liu, Y-X Wang
Structures of the four reaction states of the adenine riboswitch aptamer domain, including a transient intermediate state were solved by serial femtosecond crystallography. The structures not only demonstrate the use of X-ray free electron lasers for RNA crystallography but have also proven that transient states can be determined in real time by mix-and-inject crystallography. These results illustrate the structural basis for the ligand-induced conformational changes associated with the molecular "switch". This article is protected by copyright...
May 15, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28500543/impact-of-spin-label-rigidity-on-extent-and-accuracy-of-distance-information-from-pre-data
#9
K A Schnorr, D B Gophane, C Helmling, E Cetiner, K Pasemann, B Fürtig, A Wacker, N S Qureshi, M Gränz, D Barthelmes, H R A Jonker, E Stirnal, S Th Sigurdsson, H Schwalbe
Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of short spin-labeled oligomer fragments. As an example of a flexible spin label, (Ureido)U-TEMPO was incorporated into the 3' terminal end of helix P1 while, the recently developed rigid spin-label Çm was incorporated in the 5' terminal end of helix P1...
May 12, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28483920/cobalamin-riboswitches-exhibit-a-broad-range-of-ability-to-discriminate-between-methylcobalamin-and-adenosylcobalamin
#10
Jacob T Polaski, Samantha M Webster, James E Johnson, Robert T Batey
Riboswitches are a widely distributed class of regulatory RNAs in bacteria that modulate gene expression via small molecule induced conforma- tional changes. Generally, these RNA elements are grouped into classes based upon conserved primary and secondary structure and their cognate effector molecule. While this approach has been very suc- cessful at identifying new riboswitch families and defining their distributions, small sequence differ- ences between structurally related RNAs can al- ter their ligand selectivity and regulatory behav- ior...
May 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28455443/metalloriboswitches-rna-based-inorganic-ion-sensors-that-regulate-genes
#11
Joseph E Wedekind, Debapratim Dutta, Ivan A Belashov, Jermaine L Jenkins
Divalent ions fulfill essential cellular roles and are required for virulence by certain bacteria. Free intracellular Mg(2+) can approach 5 mM, but at this level, Mn(2+), Ni(2+), or Co(2+) can be growth-inhibitory, and Mg(2+)-fluoride is toxic. To maintain ion homeostasis, many bacteria have evolved ion sensors embedded in the 5'-leader sequences of mRNAs encoding ion uptake or efflux channels. Here, we review current insights into these "metalloriboswitches," emphasizing ion-specific binding by structured RNA aptamers and associated conformational changes in downstream signal sequences...
April 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28434876/dual-targeting-small-molecule-inhibitors-of-the-staphylococcus-aureus-fmn-riboswitch-disrupt-riboflavin-homeostasis-in-an-infectious-setting
#12
Hao Wang, Paul A Mann, Li Xiao, Charles Gill, Andrew M Galgoci, John A Howe, Artjohn Villafania, Christopher M Barbieri, Juliana C Malinverni, Xinwei Sher, Todd Mayhood, Megan D McCurry, Nicholas Murgolo, Amy Flattery, Matthias Mack, Terry Roemer
Riboswitches are bacterial-specific, broadly conserved, non-coding RNA structural elements that control gene expression of numerous metabolic pathways and transport functions essential for cell growth. As such, riboswitch inhibitors represent a new class of potential antibacterial agents. Recently, we identified ribocil-C, a highly selective inhibitor of the flavin mononucleotide (FMN) riboswitch that controls expression of de novo riboflavin (RF, vitamin B2) biosynthesis in Escherichia coli. Here, we provide a mechanistic characterization of the antibacterial effects of ribocil-C as well as of roseoflavin (RoF), an antimetabolite analog of RF, among medically significant Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecalis...
May 18, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28431495/iron-regulated-small-rna-expression-as-neisseria-gonorrhoeae-fa-1090-transitions-into-stationary-phase-growth
#13
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
#14
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
#15
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 are 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
#16
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
#17
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
#18
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
#19
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
#20
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
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