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Riboswitch OR Riboswitches

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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
#1
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
#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/29135333/challenges-of-ligand-identification-for-the-second-wave-of-orphan-riboswitch-candidates
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/29056046/synthesis-of-all-possible-canonical-3-5-linked-cyclic-dinucleotides-and-evaluation-of-riboswitch-interactions-and-immune-stimulatory-effects
#12
Changhao Wang, Malte Sinn, Julia Stifel, Anna C Heiler, Annette Sommershof, Jörg S Hartig
The cyclic dinucleotides (CDNs) c-di-GMP, c-di-AMP, and c-AMP-GMP are widely utilized as second messengers in bacteria, where they signal lifestyle changes such as motility and biofilm formation, cell wall and membrane homeostasis, virulence, and exo-electrogenesis. For all known bacterial CDNs, specific riboswitches have been identified that alter gene expression in response to the second messengers. In addition, bacterial CDNs trigger potent immune responses, making them attractive as adjuvants in immune therapies...
November 2, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29050666/the-contribution-of-bacteriophages-to-the-biology-and-virulence-of-pathogenic-clostridia
#13
Louis-Charles Fortier
Bacteriophages are key players in the evolution of most bacteria. Temperate phages have been associated with virulence of some of the deadliest pathogenic bacteria. Among the most notorious cases, the genes encoding the botulinum neurotoxin produced by Clostridium botulinum types C and D and the α-toxin (TcnA) produced by Clostridium novyi are both encoded within prophage genomes. Clostridium difficile is another important human pathogen and the recent identification of a complete binary toxin locus (CdtLoc) carried on a C...
2017: Advances in Applied Microbiology
https://www.readbyqxmd.com/read/29040738/nf90-nf45-is-a-selective-rna-chaperone-that-rearranges-viral-and-cellular-riboswitches-biochemical-analysis-of-a-virus-host-factor-activity
#14
Tobias Schmidt, Susann Friedrich, Ralph Peter Golbik, Sven-Erik Behrens
The heterodimer NF90-NF45 is an RNA-binding protein complex that modulates the expression of various cellular mRNAs on the post-transcriptional level. Furthermore, it acts as a host factor that supports the replication of several RNA viruses. The molecular mechanisms underlying these activities have yet to be elucidated. Recently, we showed that the RNA-binding capabilities and binding specificity of NF90 considerably improves when it forms a complex with NF45. Here, we demonstrate that NF90 has a substrate-selective RNA chaperone activity (RCA) involving RNA annealing and strand displacement activities...
October 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29019403/tertiary-interactions-in-the-unbound-guanine-sensing-riboswitch-focus-functional-conformational-variability-on-the-binding-site
#15
Christian Hanke, Holger Gohlke
Riboswitches are genetic regulatory elements mainly found in bacteria, which regulate gene expression based on the availability of a ligand. Purine-sensing riboswitches, including the guanine-sensing riboswitch (Gsw), possess tertiary interactions connecting the L2 and L3 loops. These interactions are important for ligand binding to the aptamer. However, atomic-level structural knowledge about the unbound state and how the tertiary interactions influence the conformational heterogeneity of the aptamer is still scarce...
October 11, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28988949/structure-of-the-guanidine-iii-riboswitch
#16
Lin Huang, Jia Wang, Timothy J Wilson, David M J Lilley
Riboswitches are structural elements found in mRNA molecules that couple small-molecule binding to regulation of gene expression, usually by controlling transcription or translation. We have determined high-resolution crystal structures of the ykkC guanidine III riboswitch from Thermobifida fusca. The riboswitch forms a classic H-type pseudoknot that includes a triple helix that is continuous with a central core of conserved nucleotides. These form a left-handed helical ramp of inter-nucleotide interactions, generating the guanidinium cation binding site...
September 28, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28986779/predicting-rna-structure-with-vfold
#17
Chenhan Zhao, Xiaojun Xu, Shi-Jie Chen
In order to carry out biological functions, RNA molecules must fold into specific three-dimensional (3D) structures. Current experimental methods to determine RNA 3D structures are expensive and time consuming. With the recent advances in computational biology, RNA structure prediction is becoming increasingly reliable. This chapter describes a recently developed RNA structure prediction software, Vfold, a virtual bond-based RNA folding model. The main features of Vfold are the physics-based loop free energy calculations for various RNA structure motifs and a template-based assembly method for RNA 3D structure prediction...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28978701/processing-of-potato-spindle-tuber-viroid-pstvd-rnas-in-yeast-a-nonconventional-host
#18
Dillon Friday, Priyadarshini Mukkara, Robert A Owens, Tilman Baumstark, Michael F Bruist
Potato spindle tuber viroid (PSTVd) is a circular, single-stranded, noncoding RNA plant pathogen that is a useful model for the processing of noncoding RNA in eukaryotes. Infective PSTVd circles are replicated via an asymmetric rolling circle mechanism to form linear multimeric RNAs. An endonuclease cleaves these into monomers; a ligase seals these into mature circles. All eukaryotes may have such enzymes for processing noncoding RNA. As a test, we investigated the processing of three PSTVd RNA constructs in the yeast Saccharomyces cerevisiae...
October 4, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28973457/direct-modulation-of-t-box-riboswitch-controlled-transcription-by-protein-synthesis-inhibitors
#19
Vassiliki Stamatopoulou, Maria Apostolidi, Shuang Li, Katerina Lamprinou, Athanasios Papakyriakou, Jinwei Zhang, Constantinos Stathopoulos
Recently, it was discovered that exposure to mainstream antibiotics activate numerous bacterial riboregulators that control antibiotic resistance genes including metabolite-binding riboswitches and other transcription attenuators. However, the effects of commonly used antibiotics, many of which exhibit RNA-binding properties, on the widespread T-box riboswitches, remain unknown. In Staphylococcus aureus, a species-specific glyS T-box controls the supply of glycine for both ribosomal translation and cell wall synthesis, making it a promising target for next-generation antimicrobials...
September 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28956757/sequence-determinants-of-the-folding-properties-of-box-c-d-kink-turns-in-rna
#20
Saira Ashraf, Lin Huang, David Lilley
Folding properties differ markedly between kink-turns (k-turns) that have different biological function. While ribosomal and riboswitch k-turns generally fold into their kinked conformation on addition of metal ions, box C/D snoRNP k-turns remain completely unfolded under these conditions, although they fold on addition of L7Ae protein. Sequence elements have been systematically exchanged between a standard ribosomal k-turn (Kt-7) that folds on addition of metal ions, and a box C/D k-turn. Folding was studied using fluorescence resonance energy transfer and gel electrophoresis...
September 27, 2017: RNA
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