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Riboswitch AND Sensor

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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
#1
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/29136199/site-specific-dual-color-labeling-of-long-rnas-for-single-molecule-spectroscopy
#2
Meng Zhao, Fabio D Steffen, Richard Börner, Michelle F Schaffer, Roland K O Sigel, Eva Freisinger
Labeling of long RNA molecules in a site-specific yet generally applicable manner is integral to many spectroscopic applications. Here we present a novel covalent labeling approach that is site-specific and scalable to long intricately folded RNAs. In this approach, a custom-designed DNA strand that hybridizes to the RNA guides a reactive group to target a preselected adenine residue. The functionalized nucleotide along with the concomitantly oxidized 3'-terminus can subsequently be conjugated to two different fluorophores via bio-orthogonal chemistry...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28956387/-structure-and-function-of-c-di-gmp-riboswitches
#3
Xinfeng Li, Fang Chen, Jinfeng Xiao, Jin He
Cyclic diguanosine monophosphate (c-di-GMP) is a ubiquitous nucleotide second messenger present in a wide variety of bacteria. It regulates many important bacterial physiological functions such as biofilm formation, motility, adhesion, virulence and extracellular polysaccharide synthesis. It binds with many different proteins or RNA receptors, one of which is called riboswitch that is usually located at the 5'-untranslational region (5'-UTR) in some mRNA. Riboswitch usually comprises a specific ligand-binding (sensor) domain (named aptamer domain, AD), as well as a variable domain, termed expression platform (EP), to regulate expression of downstream coding sequences...
September 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28892124/systematic-optimization-of-l-tryptophan-riboswitches-for-efficient-monitoring-of-the-metabolite-in-escherichia-coli
#4
Sungho Jang, Gyoo Yeol Jung
Riboswitches form a class of genetically encoded sensor-regulators and are considered as promising tools for monitoring various metabolites. Functional parameters of a riboswitch, like dynamic or operational range, should be optimized before the riboswitch is implemented in a specific application for monitoring the target molecule efficiently. However, optimization of a riboswitch was not straightforward and required detailed studies owing to its complex sequence-function relationship. Here, we present three approaches for tuning and optimization of functional parameters of a riboswitch using an artificial L-tryptophan riboswitch as an example...
September 11, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28867802/design-of-artificial-riboswitches-as-biosensors
#5
REVIEW
Sven Findeiß, Maja Etzel, Sebastian Will, Mario Mörl, Peter F Stadler
RNA aptamers readily recognize small organic molecules, polypeptides, as well as other nucleic acids in a highly specific manner. Many such aptamers have evolved as parts of regulatory systems in nature. Experimental selection techniques such as SELEX have been very successful in finding artificial aptamers for a wide variety of natural and synthetic ligands. Changes in structure and/or stability of aptamers upon ligand binding can propagate through larger RNA constructs and cause specific structural changes at distal positions...
August 30, 2017: Sensors
https://www.readbyqxmd.com/read/28749656/development-of-artificial-riboswitches-for-monitoring-of-naringenin-in-vivo
#6
Sungho Jang, Sungyeon Jang, Yu Xiu, Taek Jin Kang, Sang-Hyeup Lee, Mattheos A G Koffas, Gyoo Yeol Jung
Microbial strains are considered promising hosts for production of flavonoids because of their rapid growth rate and suitability for large-scale manufacturing. However, productivity and titer of current recombinant strains still do not meet the requirements of industrial processes. Genetically encoded biosensors have been applied for high-throughput screening or dynamic regulation of biosynthetic pathways for enhancing the performance of microbial strains that produce valuable chemicals. Currently, few protein sensor-regulators for flavonoids exist...
August 10, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28552565/production-of-amino-acids-genetic-and-metabolic-engineering-approaches
#7
REVIEW
Jin-Ho Lee, Volker F Wendisch
The biotechnological production of amino acids occurs at the million-ton scale and annually about 6milliontons of l-glutamate and l-lysine are produced by Escherichia coli and Corynebacterium glutamicum strains. l-glutamate and l-lysine production from starch hydrolysates and molasses is very efficient and access to alternative carbon sources and new products has been enabled by metabolic engineering. This review focusses on genetic and metabolic engineering of amino acid producing strains. In particular, rational approaches involving modulation of transcriptional regulators, regulons, and attenuators will be discussed...
May 15, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28543037/naringenin-responsive-riboswitch-based-fluorescent-biosensor-module-for-escherichia-coli-co-cultures
#8
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 an 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...
October 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28455443/metalloriboswitches-rna-based-inorganic-ion-sensors-that-regulate-genes
#9
REVIEW
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 magnesium 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...
June 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28430408/amplifying-riboswitch-signal-output-using-cellular-wiring
#10
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 fulfill 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 25, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28206750/synthetic-riboswitches-from-plug-and-pray-toward-plug-and-play
#11
REVIEW
Maja Etzel, Mario Mörl
In synthetic biology, metabolic engineering, and gene therapy, there is a strong demand for orthogonal or externally controlled regulation of gene expression. Here, RNA-based regulatory devices represent a promising emerging alternative to proteins, allowing a fast and direct control of gene expression, as no synthesis of regulatory proteins is required. Besides programmable ribozyme elements controlling mRNA stability, regulatory RNA structures in untranslated regions are highly interesting for engineering approaches...
March 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28121427/riboswitch-based-reversible-dual-color-sensor
#12
Svetlana V Harbaugh, Michael S Goodson, Kateri Dillon, Sarah Zabarnick, Nancy Kelley-Loughnane
Riboswitches are RNA-based "sensors" that utilize chemically induced structural changes in the 5'-untranslated region of mRNA to regulate expression of downstream genes. Coupling a specific riboswitch with a reporter gene system translates chemical detection by the cell into a quantifiable reporter protein signal. For the majority of reporter gene systems, the readout signal is only expressed in the presence of the target analyte. This makes it difficult to determine the viability and localization of the uninduced biosensor when it is used for "real-word" applications...
May 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28024528/tpp-riboswitch-characterization-in-alishewanella-tabrizica-and-alishewanella-aestuarii-and-comparison-with-other-tpp-riboswitches
#13
COMPARATIVE STUDY
Elnaz Mehdizadeh Aghdam, Malte Sinn, Vahideh Tarhriz, Abolfazl Barzegar, Jörg S Hartig, Mohammad Saeid Hejazi
Riboswitches are located in non-coding areas of mRNAs and act as sensors of cellular small molecules, regulating gene expression in response to ligand binding. The TPP riboswitch is the most widespread riboswitch occurring in all three domains of life. However, it has been rarely characterized in environmental bacteria other than Escherichia coli and Bacillus subtilis. In this study, TPP riboswitches located in the 5' UTR of thiC operon from Alishewanella tabrizica and Alishewanella aestuarii were identified and characterized...
January 2017: Microbiological Research
https://www.readbyqxmd.com/read/27729470/carotenogenesis-is-regulated-by-5-utr-mediated-translation-of-phytoene-synthase-splice-variants
#14
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/27672149/trigger-phosphodiesterases-as-a-novel-class-of-c-di-gmp-effector-proteins
#15
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/27541358/deciphering-the-transcriptional-response-mediated-by-the-redox-sensing-system-hbps-sens-senr-from-streptomycetes
#16
Tobias Busche, Anika Winkler, Ina Wedderhoff, Christian Rückert, Jörn Kalinowski, Darío Ortiz de Orué Lucana
The secreted protein HbpS, the membrane-embedded sensor kinase SenS and the cytoplasmic response regulator SenR from streptomycetes have been shown to form a novel type of signaling pathway. Based on structural biology as well as different biochemical and biophysical approaches, redox stress-based post-translational modifications in the three proteins were shown to modulate the activity of this signaling pathway. In this study, we show that the homologous system, named here HbpSc-SenSc-SenRc, from the model species Streptomyces coelicolor A3(2) provides this bacterium with an efficient defense mechanism under conditions of oxidative stress...
2016: PloS One
https://www.readbyqxmd.com/read/27269119/discriminating-self-and-non-self-by-rna-roles-for-rna-structure-misfolding-and-modification-in-regulating-the-innate-immune-sensor-pkr
#17
REVIEW
Chelsea M Hull, Philip C Bevilacqua
Pathogens are recognized by the innate immune system in part via their unique and complex RNA signatures. A key sensor in human innate immunity is the RNA-activated protein kinase, protein kinase R (PKR), which has two double-stranded RNA (dsRNA) binding motifs (dsRBMs) at its N-terminus. Early studies described PKR as being activated potently by long stretches of perfect dsRNA, a signature typical of viruses. More recently, we and others have found that PKR is also activated by RNAs having structural defects such as bulges and internal loops...
June 21, 2016: Accounts of Chemical Research
https://www.readbyqxmd.com/read/27241761/developing-fluorogenic-riboswitches-for-imaging-metabolite-concentration-dynamics-in-bacterial-cells
#18
J L Litke, M You, S R Jaffrey
Genetically encoded small-molecule sensors are important tools for revealing the dynamics of metabolites and other small molecules in live cells over time. We recently developed RNA-based sensors that exhibit fluorescence in proportion to a small-molecule ligand. One class of these RNA-based sensors are termed Spinach riboswitches. These are RNAs that are based on naturally occurring riboswitches, but have been fused to the Spinach aptamer. The resulting RNA is a fluorogenic riboswitch, producing fluorescence upon binding the cognate small-molecule analyte...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27220466/engineering-and-characterization-of-fluorogenic-glycine-riboswitches
#19
Simon Ketterer, Lukas Gladis, Adnan Kozica, Matthias Meier
A set of 12 fluorogenic glycine riboswitches with different thermodynamic and kinetic response properties was engineered. For the design of functional riboswitches, a three-part RNA approach was applied based on the idea of linking a RNA sensor, transmitter and actuator part together. For the RNA sensor and actuator part, we used the tandem glycine aptamer structure from Bacillus subtillis, and fluorogenic aptamer Spinach, respectively. To achieve optimal signal transduction from the sensor to the actuator, a riboswitch library with variable transmitter was screened with a microfluidic large-scale integration chip...
July 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27138234/molecular-buffers-permit-sensitivity-tuning-and-inversion-of-riboswitch-signals
#20
Peter Rugbjerg, Hans Jasper Genee, Kristian Jensen, Kira Sarup-Lytzen, Morten Otto Alexander Sommer
Predictable integration of foreign biological signals and parts remains a key challenge in the systematic engineering of synthetic cellular actuations, and general methods to improve signal transduction and sensitivity are needed. To address this problem we modeled and built a molecular signal buffer network in Saccharomyces cerevisiae inspired by chemical pH buffer systems. The molecular buffer system context-insulates a riboswitch enabling synthetic control of colony formation and modular signal manipulations...
July 15, 2016: ACS Synthetic Biology
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