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Riboswitch AND Sensor

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https://www.readbyqxmd.com/read/29751749/engineering-a-vitamin-b-12-high-throughput-screening-system-by-riboswitch-sensor-in-sinorhizobium-meliloti
#1
Yingying Cai, Miaomiao Xia, Huina Dong, Yuan Qian, Tongcun Zhang, Beiwei Zhu, Jinchuan Wu, Dawei Zhang
BACKGROUND: As a very important coenzyme in the cell metabolism, Vitamin B12 (cobalamin, VB12 ) has been widely used in food and medicine fields. The complete biosynthesis of VB12 requires approximately 30 genes, but overexpression of these genes did not result in expected increase of VB12 production. High-yield VB12 -producing strains are usually obtained by mutagenesis treatments, thus developing an efficient screening approach is urgently needed. RESULT: By the help of engineered strains with varied capacities of VB12 production, a riboswitch library was constructed and screened, and the btuB element from Salmonella typhimurium was identified as the best regulatory device...
May 11, 2018: BMC Biotechnology
https://www.readbyqxmd.com/read/29697203/guanidine-sensing-riboswitches-how-do-they-work-and-what-do-they-regulate
#2
REVIEW
Robert A Battaglia, Ailong Ke
After remaining an orphan for over a decade, the ykkC riboswitch family (ykkC, mini-ykkC, and ykkC-III) was recently characterized as guanidine-specific genetic regulatory elements (guanidine-I, II, and III). They respond to increased levels of intracellular guanidine by turning on genes involved in guanidine export and breakdown. Their existence suggests that regulation of intracellular guanidine levels could be an important piece of bacterial physiology which was not appreciated previously. Structural biologists moved exceptionally fast to reveal the guanidine-sensing mechanisms of these riboswitches at the atomic level...
April 26, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29522378/the-yebn-leader-rna-acts-as-a-mn2-sensor-required-for-the-interaction-of-xanthomonas-oryzae-and-rice
#3
Chunxia Li, Shiyao Liu, Peiyi Liu, Yaxin Wang, Chunli Xu, Jun Tao, Chaozu He
Riboswitches are RNA elements that sense metabolites and control gene expression. Recently, the yybP-ykoY riboswitches were found to sense manganese (Mn2+) and regulate the expression of diverse genes. Here, we show that the leader RNA (a yybP-ykoY RNA) of yebN in Xanthomonas oryzae pv. oryzae (Xoo) also functions as a sensor of Mn2+. This leader RNA detects Mn2+ levels in plants and is essential to Xoo virulence. Our data also indicate that Mn2+ is not only required as a microelement for plant growth but also acts as a defense molecule to inhibit pathogen growth...
March 9, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29518463/sensitive-and-specific-detection-of-ligands-using-engineered-riboswitches
#4
Daniel P Morse, Colin E Nevins, Joana Aggrey-Fynn, Rick J Bravo, Herman O I Pfaeffle, Jess E Laney
Riboswitches are RNA elements found in non-coding regions of messenger RNAs that regulate gene expression through a ligand-triggered conformational change. Riboswitches typically bind tightly and specifically to their ligands, so they have the potential to serve as highly effective sensors in vitro. In B. subtilis and other gram-positive bacteria, purine nucleotide synthesis is regulated by riboswitches that bind to guanine. We modified the xpt-pbuX guanine riboswitch for use in a fluorescence quenching assay that allowed us to specifically detect and quantify guanine in vitro...
April 20, 2018: Journal of Biotechnology
https://www.readbyqxmd.com/read/29413520/rna-based-fluorescent-biosensors-for-detecting-metabolites-in-vitro-and-in-living-cells
#5
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/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
#6
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
#7
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...
February 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/28956387/-structure-and-function-of-c-di-gmp-riboswitches
#8
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
#9
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
#10
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
#11
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...
November 17, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28552565/production-of-amino-acids-genetic-and-metabolic-engineering-approaches
#12
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
#13
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
#14
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 Mg2+ can approach 5 mm, but at this level Mn2+ , Ni2+ , or Co2+ 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
#15
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...
August 18, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28206750/synthetic-riboswitches-from-plug-and-pray-toward-plug-and-play
#16
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
#17
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
#18
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
#19
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
#20
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
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