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https://www.readbyqxmd.com/read/29235474/engineering-cell-signaling-using-tunable-crispr-cpf1-based-transcription-factors
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
https://www.readbyqxmd.com/read/29180020/aptamers-in-bordeaux-2017-an-exceptional-mill%C3%A3-sime
#7
Jean-Jacques Toulmé, Laurent Azéma, Fabien Darfeuille, Eric Dausse, Guillaume Durand, Olivier Paurelle
About 150 participants attended the symposium organised at the Palais de la Bourse in Bordeaux, France on September 22-23, 2017. Thirty speakers from all over the world delivered lectures covering selection processes, aptamer chemistry and innovative applications of these powerful tools that display major advantages over antibodies. Beyond the remarkable science presented, lively discussion and fruitful exchange between participants made this meeting a great success. A series of lectures were focused on synthetic biology (riboswitches, new synthetic base pairs, mutated polymerases)...
November 24, 2017: Biochimie
https://www.readbyqxmd.com/read/29170966/a-capture-selex-strategy-for-multiplexed-selection-of-rna-aptamers-against-small-molecules
#8
Lasse H Lauridsen, Holger B Doessing, Katherine S Long, Alex T Nielsen
In vitro selection of aptamers that recognize small organic molecules has proven difficult, in part due to the challenge of immobilizing small molecules on solid supports for SELEX (Systematic Evolution of Ligands by Exponential Enrichment). This study describes the implementation of RNA Capture-SELEX, a selection strategy that uses an RNA library to yield ligand-responsive RNA aptamers targeting small organic molecules in solution. To demonstrate the power of this method we selected several aptamers with specificity towards either the natural sweetener rebaudioside A or the food-coloring agent carminic acid...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29149090/computational-methods-for-modeling-aptamers-and-designing-riboswitches
#9
REVIEW
Sha Gong, Yanli Wang, Zhen Wang, Wenbing Zhang
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29138309/loss-of-popz-at-activity-in-agrobacterium-tumefaciens-by-deletion-or-depletion-leads-to-multiple-growth-poles-minicells-and-growth-defects
#10
Romain Grangeon, John Zupan, Yeonji Jeon, Patricia C Zambryski
Agrobacterium tumefaciens grows by addition of peptidoglycan (PG) at one pole of the bacterium. During the cell cycle, the cell needs to maintain two different developmental programs, one at the growth pole and another at the inert old pole. Proteins involved in this process are not yet well characterized. To further characterize the role of pole-organizing protein A. tumefaciens PopZ (PopZ At ), we created deletions of the five PopZ At domains and assayed their localization. In addition, we created a popZAt deletion strain (ΔpopZAt ) that exhibited growth and cell division defects with ectopic growth poles and minicells, but the strain is unstable...
November 14, 2017: MBio
https://www.readbyqxmd.com/read/29136199/site-specific-dual-color-labeling-of-long-rnas-for-single-molecule-spectroscopy
#11
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/29135333/challenges-of-ligand-identification-for-the-second-wave-of-orphan-riboswitch-candidates
#12
Etienne B Greenlee, Shira Stav, Ruben M Atilho, Kenneth I Brewer, Kimberly A Harris, Sarah N Malkowski, Gayan Mirihana Arachchilage, Kevin R Perkins, Madeline E Sherlock, Ronald R Breaker
Orphan riboswitch candidates are noncoding RNA motifs whose representatives are believed to function as genetic regulatory elements, but whose target ligands have yet to be identified. The study of certain orphans, particularly classes that have resisted experimental validation for many years, has led to the discovery of important biological pathways and processes once their ligands were identified. Previously, we highlighted details for four of the most common and intriguing orphan riboswitch candidates. This facilitated the validation of riboswitches for the signaling molecules c-di-AMP, ZTP, and ppGpp, the metal ion Mn(2+), and the metabolites guanidine and PRPP...
November 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/29132120/rna-based-dynamic-genetic-controllers-development-strategies-and-applications
#13
REVIEW
Sungho Jang, Sungyeon Jang, Jina Yang, Sang Woo Seo, Gyoo Yeol Jung
Dynamic regulation of gene expression in response to various molecules is crucial for both basic science and practical applications. RNA is considered an attractive material for creating dynamic genetic controllers because of its specific binding to ligands, structural flexibility, programmability, and small size. Here, we review recent advances in strategies for developing RNA-based dynamic controllers and applications. First, we describe studies that re-engineered natural riboswitches to generate new dynamic controllers...
November 10, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29106607/rnomics-of-thermus-themophilus-hb8-by-dna-microarray-and-next-generation-sequencing
#14
Gota Kawai, Yuri Aoki, Maina Otsu, Naomi Koike, Gen-Ichi Sampei
By using the data obtained by the DNA microarray analysis for the intergenic regions applied to RNA samples extracted from Thermus thermophilus HB8, seven small non-coding RNAs, TtR-1 to TtR-7, were found to be expressed in the cells growing in rich and/or minimal media. By analysing the time course of the expression for the cell growth in combination with the sequence comparison to the known RNAs, two RNAs, TtR-1 and TtR-2, are suggested to be riboswitches. The existence of the seven RNAs and the exact sequence and length, ranging 77-284 nt, were confirmed by the next-generation sequencing...
July 4, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29106323/sam-vi-rnas-selectively-bind-s-adenosylmethionine-and-exhibit-similarities-to-sam-iii-riboswitches
#15
Gayan Mirihana Arachchilage, Madeline E Sherlock, Zasha Weinberg, Ronald R Breaker
Five distinct riboswitch classes that regulate gene expression in response to the cofactor S-adenosylmethionine (SAM) or its metabolic breakdown product S-adenosylhomocysteine (SAH) have been reported previously. Collectively, these SAM- or SAH-sensing RNAs constitute the most abundant collection of riboswitches, and are found in nearly every major bacterial lineage. Here, we report a potential sixth member of this pervasive riboswitch family, called SAM-VI, which is predominantly found in Bifidobacterium species...
November 6, 2017: RNA Biology
https://www.readbyqxmd.com/read/29101204/effects-of-lowered-and-enhanced-glycogen-pools-on-salt-induced-sucrose-production-in-a-sucrose-secreting-strain-of-synechococcus-elongatus-pcc-7942
#16
Cuncun Qiao, Yangkai Duan, Mingyi Zhang, Martin Hagemann, Quan Luo, Xuefeng Lu
Sucrose and glycogen syntheses in cyanobacteria share the common precursor glucose-1-phosphate. It is generally assumed that lowering glycogen synthesis could drive more carbon towards sucrose synthesis that can be induced by salt stress among cyanobacteria. By using a theophyllin-dependent riboswitch system, the expression of glgC, a key gene in glycogen synthesis, was down-regulated in a quantitative manner in a sucrose-secreting strain of Synechococcus elongatus PCC 7942. We observed that the stepwise suppression of glycogen synthesis limited rather than stimulated sucrose production in the salt stressed cells, suggesting that glycogen could serve as a carbon pool for the synthesis of sucrose...
November 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29100491/detailed-transcriptome-analysis-of-the-plant-growth-promoting-paenibacillus-riograndensis-sbr5-by-using-rna-seq-technology
#17
Luciana Fernandes Brito, Marta Irla, Jörn Kalinowski, Volker F Wendisch
BACKGROUND: The plant growth promoting rhizobacterium Paenibacillus riograndensis SBR5 is a promising candidate to serve as crop inoculant. Despite its potential in providing environmental and economic benefits, the species P. riograndensis is poorly characterized. Here, we performed for the first time a detailed transcriptome analysis of P. riograndensis SBR5 using RNA-seq technology. RESULTS: RNA was isolated from P. riograndensis SBR5 cultivated under 15 different growth conditions and combined together in order to analyze an RNA pool representing a large set of expressed genes...
November 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29089431/in-vivo-behavior-of-the-tandem-glycine-riboswitch-in-bacillus-subtilis
#18
Arianne M Babina, Nicholas E Lea, Michelle M Meyer
In many bacterial species, the glycine riboswitch is composed of two homologous ligand-binding domains (aptamers) that each bind glycine and act together to regulate the expression of glycine metabolic and transport genes. While the structure and molecular dynamics of the tandem glycine riboswitch have been the subject of numerous in vitro studies, the in vivo behavior of the riboswitch remains largely uncharacterized. To examine the proposed models of tandem glycine riboswitch function in a biologically relevant context, we characterized the regulatory activity of mutations to the riboswitch structure in Bacillus subtilis using β-galactosidase assays...
October 31, 2017: MBio
https://www.readbyqxmd.com/read/29076719/structural-insight-into-the-unbound-state-of-the-dna-analogue-of-the-preq1-riboswitch-a-thermodynamic-approach
#19
Calliste Reiling-Steffensmeier, Luis A Marky
The preQ1 riboswitch aptamer domain is very dynamic in its unbound state with the ability to form multiple structures: a hairpin, kissing hairpins, and pseudoknot-like structure. The aim of this study is to determine whether the DNA analogue (PreQ1) is able to form structures similar to that of the reported RNA aptamer. Using a thermodynamic approach, we report on structural determination using differential scanning calorimetry under different salt conditions. Further analysis of the primary sequence allowed us to design modified molecules to determine what potential structures are forming in this single-stranded DNA analogue...
November 9, 2017: Biochemistry
https://www.readbyqxmd.com/read/29072147/tractable-rna-ligand-interaction-kinetics
#20
Felix Kühnl, Peter F Stadler, Sebastian Will
BACKGROUND: The binding of small ligands to RNA elements can cause substantial changes in the RNA structure. This constitutes an important, fast-acting mechanism of ligand-controlled transcriptional and translational gene regulation implemented by a wide variety of riboswitches. The associated refolding processes often cannot be explained by thermodynamic effects alone. Instead, they are governed by the kinetics of RNA folding. While the computational analysis of RNA folding can make use of well-established models of the thermodynamics of RNA structures formation, RNA-RNA interaction, and RNA-ligand interaction, kinetic effects pose fundamentally more challenging problems due to the enormous size of the conformation space...
October 16, 2017: BMC Bioinformatics
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