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Riboswitch AND Sensor

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https://www.readbyqxmd.com/read/27729470/carotenogenesis-is-regulated-by-5-utr-mediated-translation-of-phytoene-synthase-splice-variants
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/27011290/bacterial-riboswitches-and-ribozymes-potently-activate-the-human-innate-immune-sensor-pkr
#8
Chelsea M Hull, Ananya Anmangandla, Philip C Bevilacqua
The innate immune system provides the first line of defense against pathogens through the recognition of nonspecific patterns in RNA to protect the cell in a generalized way. The human RNA-activated protein kinase, PKR, is a dsRNA binding protein and an essential sensor in the innate immune response, which recognizes viral and bacterial pathogens through their RNAs. Upon activation via RNA-dependent autophosphorylation, PKR phosphorylates the eukaryotic initiation factor eIF2α, leading to termination of translation...
April 15, 2016: ACS Chemical Biology
https://www.readbyqxmd.com/read/26968125/optimization-of-rna-based-c-di-gmp-fluorescent-sensors-through-tuning-their-structural-modules
#9
Saki Inuzuka, Shigeyoshi Matsumura, Yoshiya Ikawa
Cyclic diguanylate (c-di-GMP) is a second messenger of bacteria and its detection is an important issue in basic and applied microbiology. As c-di-GMP riboswitch ligand-binding domains (aptamer domains) capture c-di-GMP with high affinity and selectivity, they are promising platforms for the development of RNA-based c-di-GMP sensors. We analyzed two previously reported c-di-GMP sensor RNAs derived from the Vc2 riboswitch. We also designed and tested their variants, some of which showed improved properties as RNA-based c-di-GMP sensors...
August 2016: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/26739090/cyclic-dinucleotide-detection-with-riboswitch-g-quadruplex-hybrid
#10
Genichiro Tsuji, Herman O Sintim
A cyclic dinucleotide riboswitch has been fused with a G-quadruplex motif to produce a conditional riboswitch-peroxidase-mimicking sensor that oxidizes both colorimetric and fluorogenic substrates in the presence of c-di-GMP. We find that signal-to-noise ratio could be improved by using a two-, not three-, floor split G-quadruplex for this conditional peroxidase-mimicking riboswitch.
March 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/26621913/automated-physics-based-design-of-synthetic-riboswitches-from-diverse-rna-aptamers
#11
Amin Espah Borujeni, Dennis M Mishler, Jingzhi Wang, Walker Huso, Howard M Salis
Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it remains unclear how their sequence controls the physics of riboswitch switching and activation, particularly when changing the ligand-binding aptamer domain. We report the development of a statistical thermodynamic model that predicts the sequence-structure-function relationship for translation-regulating riboswitches that activate gene expression, characterized inside cells and within cell-free transcription-translation assays...
January 8, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/26539634/therapeutic-applications-of-aptamer-based-riboswitches
#12
REVIEW
Chang Ho Lee, Seung Ryul Han, Seong-Wook Lee
Aptamers bind to their targets with high affinity and specificity through structure-based complementarity, instead of sequence complementarity that is used by most of the oligonucleotide-based therapeutics. This property has been exploited in using aptamers as multifunctional therapeutic units, by attaching them to therapeutic drugs, nanoparticles, or imaging agents, or as direct molecular decoys for inducing loss-of-function or gain-of-function of targets. One of the most interesting fields of aptamer application is their development as molecular sensors to regulate artificial riboswitches...
February 2016: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/26493133/rethinking-metabolic-control
#13
REVIEW
Piero Morandini
Modulation of metabolic fluxes in plants is usually not a successful business. The main reason is our limited understanding of metabolic plasticity and metabolic control, with the latter still largely influenced by the idea that each pathway has a rate limiting step controlling the flux. Not only is experimental evidence for such steps lacking for most pathways, despite intensive search, but there are also theoretical arguments against the idea that highly regulated enzymes catalyzing reactions far from equilibrium must be considered a priori rate limiting...
April 2009: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/26227035/preparation-and-crystallization-of-riboswitches
#14
Alla Peselis, Ang Gao, Alexander Serganov
Recent studies have revealed that the majority of biological processes are controlled by noncoding RNAs. Among many classes of noncoding RNAs, metabolite-sensing segments of mRNAs called riboswitches are unique. Discovered over a decade ago in all three kingdoms of life, riboswitches specifically and directly interact with various metabolites and regulate expression of multiple genes, often associated with metabolism and transport of small molecules. Thus, riboswitches do not depend on proteins for binding to small molecules and play a role as both metabolite sensors and effectors of gene control...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/26201745/optimization-of-a-whole-cell-biocatalyst-by-employing-genetically-encoded-product-sensors-inside-nanolitre-reactors
#15
Andreas Meyer, René Pellaux, Sébastien Potot, Katja Becker, Hans-Peter Hohmann, Sven Panke, Martin Held
Microcompartmentalization offers a high-throughput method for screening large numbers of biocatalysts generated from genetic libraries. Here we present a microcompartmentalization protocol for benchmarking the performance of whole-cell biocatalysts. Gel capsules served as nanolitre reactors (nLRs) for the cultivation and analysis of a library of Bacillus subtilis biocatalysts. The B. subtilis cells, which were co-confined with E. coli sensor cells inside the nLRs, converted the starting material cellobiose into the industrial product vitamin B2...
August 2015: Nature Chemistry
https://www.readbyqxmd.com/read/26026708/mechanistic-analysis-of-activation-of-the-innate-immune-sensor-pkr-by-bacterial-rna
#16
Chelsea M Hull, Philip C Bevilacqua
The protein kinase PKR (protein kinase R) is a sensor in innate immunity. PKR autophosphorylates in the presence of double-stranded RNA enabling it to phosphorylate its substrate, eIF2α (eukaryotic initiation factor 2α), halting cellular translation. Classical activators of PKR are long viral double-stranded RNAs, but recently, PKR has been found to be activated by bacterial RNA. However, the features of bacterial RNA that activate PKR are unknown. We studied the Bacillus subtilis trp 5'-UTR (untranslated region), which is an indirect riboswitch with secondary and tertiary RNA structures that regulate gene function...
November 6, 2015: Journal of Molecular Biology
https://www.readbyqxmd.com/read/26005949/control-of-alphavirus-based-gene-expression-using-engineered-riboswitches
#17
Christie L Bell, Dong Yu, Christina D Smolke, Andrew J Geall, Clayton W Beard, Peter W Mason
Alphavirus-based replicons are a promising nucleic acid vaccine platform characterized by robust gene expression and immune responses. To further explore their use in vaccination, replicons were engineered to allow conditional control over their gene expression. Riboswitches, comprising a ribozyme actuator and RNA aptamer sensor, were engineered into the replicon 3' UTR. Binding of ligand to aptamer modulates ribozyme activity and, therefore, gene expression. Expression from DNA-launched and VRP-packaged replicons containing riboswitches was successfully regulated, achieving a 47-fold change in expression and modulation of the resulting type I interferon response...
September 2015: Virology
https://www.readbyqxmd.com/read/25978303/in-vitro-selection-for-small-molecule-triggered-strand-displacement-and-riboswitch-activity
#18
Laura Martini, Adam J Meyer, Jared W Ellefson, John N Milligan, Michele Forlin, Andrew D Ellington, Sheref S Mansy
An in vitro selection method for ligand-responsive RNA sensors was developed that exploited strand displacement reactions. The RNA library was based on the thiamine pyrophosphate (TPP) riboswitch, and RNA sequences capable of hybridizing to a target duplex DNA in a TPP regulated manner were identified. After three rounds of selection, RNA molecules that mediated a strand exchange reaction upon TPP binding were enriched. The enriched sequences also showed riboswitch activity. Our results demonstrated that small-molecule-responsive nucleic acid sensors can be selected to control the activity of target nucleic acid circuitry...
October 16, 2015: ACS Synthetic Biology
https://www.readbyqxmd.com/read/25964329/imaging-metabolite-dynamics-in-living-cells-using-a-spinach-based-riboswitch
#19
Mingxu You, Jacob L Litke, Samie R Jaffrey
Riboswitches are natural ligand-sensing RNAs typically that are found in the 5' UTRs of mRNA. Numerous classes of riboswitches have been discovered, enabling mRNA to be regulated by diverse and physiologically important cellular metabolites and small molecules. Here we describe Spinach riboswitches, a new class of genetically encoded metabolite sensor derived from naturally occurring riboswitches. Drawing upon the structural switching mechanism of natural riboswitches, we show that Spinach can be swapped for the expression platform of various riboswitches, allowing metabolite binding to induce Spinach fluorescence directly...
May 26, 2015: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/25938715/synthesis-and-applications-of-rnas-with-position-selective-labelling-and-mosaic-composition
#20
Yu Liu, Erik Holmstrom, Jinwei Zhang, Ping Yu, Jinbu Wang, Marzena A Dyba, De Chen, Jinfa Ying, Stephen Lockett, David J Nesbitt, Adrian R Ferré-D'Amaré, Rui Sousa, Jason R Stagno, Yun-Xing Wang
Knowledge of the structure and dynamics of RNA molecules is critical to understanding their many biological functions. Furthermore, synthetic RNAs have applications as therapeutics and molecular sensors. Both research and technological applications of RNA would be dramatically enhanced by methods that enable incorporation of modified or labelled nucleotides into specifically designated positions or regions of RNA. However, the synthesis of tens of milligrams of such RNAs using existing methods has been impossible...
June 18, 2015: Nature
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