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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28956389/-identification-of-cyclic-di-gmp-protein-receptors-high-throughput-screening-strategies-and-experimental-verification
#8
Shouting Cheng, Fangfang Wang, Wei Qian
cyclic di-GMP (c-di-GMP) is a universal second messenger in bacterial cells. It regulates various biological processes such as biofilm development, pathogenicity, motility, exopolysaccharide (EPS) production and cell cycle. The second messenger exerts its function by binding to effectors, such as riboswitches and proteins. However, due to the diverse conformations of c-di-GMP, its effectors are hardly to be predicted by homology search. Identification of c-di-GMP effectors is the initial step to investigate its regulatory function in bacterial signal transduction, however, it remains to be a technically difficult task...
September 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28956387/-structure-and-function-of-c-di-gmp-riboswitches
#9
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/28925284/ligand-design-for-riboswitches-an-emerging-target-class-for-novel-antibiotics
#10
Illimar Hugo Rek, Ruth Brenk
Riboswitches are cis-acting gene regulatory elements and constitute potential targets for new antibiotics. Recent studies in this field have started to explore these targets for drug discovery. New ligands found by fragment screening, design of analogs of the natural ligands or serendipitously by phenotypic screening have shown antibacterial effects in cell assays against a range of bacteria strains and in animal models. In this review, we highlight the most advanced drug design work of riboswitch ligands and discuss the challenges in the field with respect to the development of antibiotics with a new mechanism of action...
September 19, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28920931/single-molecule-fret-reveals-the-energy-landscape-of-the-full-length-sam-i-riboswitch
#11
Christoph Manz, Andrei Yu Kobitski, Ayan Samanta, Bettina G Keller, Andres Jäschke, G Ulrich Nienhaus
S-adenosyl-L-methionine (SAM) ligand binding induces major structural changes in SAM-I riboswitches, through which gene expression is regulated via transcription termination. Little is known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg(2+) and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling analysis...
September 18, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28918092/growth-rate-dependent-regulation-of-trna-level-and-charging-in-bacillus-licheniformis
#12
Iolanda Ferro, Klaus Liebeton, Zoya Ignatova
Cellular growth crucially depends on protein synthesis and the abundance of translational components. Among them, aminoacyl-tRNAs play a central role in biosynthesis and shape the kinetics of mRNA translation, thus influencing protein production. Here, we used microarray-based approaches to determine the charging levels and tRNA abundance of Bacillus licheniformis. We observed an interesting cross-talk among tRNA expression, charging pattern, and growth rate. For a large subset of tRNAs, we found a co-regulated and augmented expression at high growth rate...
October 13, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28892124/systematic-optimization-of-l-tryptophan-riboswitches-for-efficient-monitoring-of-the-metabolite-in-escherichia-coli
#13
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/28889309/identification-of-c-di-gmp-responsive-riboswitches
#14
Johann Peltier, Olga Soutourina
Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important signaling molecule for community behavior control, cell morphogenesis, and virulence in bacteria. In addition to protein effectors, this second messenger binds RNA molecules that act as riboswitches to control target gene expression. In this chapter, we describe a method for experimental validation of the functionality of c-di-GMP-responsive riboswitches and the analysis of c-di-GMP control of target gene expression by qRT-PCR and Northern blot...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28889282/enzymatic-production-of-c-di-gmp-using-a-thermophilic-diguanylate-cyclase
#15
Prabhadevi Venkataramani, Zhao-Xun Liang
C-di-GMP has emerged as a prevalent bacterial messenger that controls a multitude of bacterial behaviors. Having access to milligram or gram quantities of c-di-GMP is essential for the biochemical and structural characterization of enzymes and effectors involved in c-di-GMP signaling. Although c-di-GMP can be synthesized using chemical methods, diguanylate cyclases (DGC)-based enzymatic synthesis is the most efficient method of preparing c-di-GMP today. Many DGCs are not suitable for c-di-GMP production because of poor protein stability and the presence of a c-di-GMP-binding inhibitory site (I-site) in most DGCs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28886688/regulating-bacterial-virulence-with-rna
#16
Juan J Quereda, Pascale Cossart
Noncoding RNAs (ncRNAs) regulating virulence have been identified in most pathogens. This review discusses RNA-mediated mechanisms exploited by bacterial pathogens to successfully infect and colonize their hosts. It discusses the most representative RNA-mediated regulatory mechanisms employed by two intracellular [Listeria monocytogenes and Salmonella enterica serovar Typhimurium (S. Typhimurium)] and two extracellular (Vibrio cholerae and Staphylococcus aureus) bacterial pathogens. We review the RNA-mediated regulators (e...
September 8, 2017: Annual Review of Microbiology
https://www.readbyqxmd.com/read/28882001/efficient-approximations-of-rna-kinetics-landscape-using-non-redundant-sampling
#17
Juraj Michálik, Hélène Touzet, Yann Ponty
Motivation: Kinetics is key to understand many phenomena involving RNAs, such as co-transcriptional folding and riboswitches. Exact out-of-equilibrium studies induce extreme computational demands, leading state-of-the-art methods to rely on approximated kinetics landscapes, obtained using sampling strategies that strive to generate the key landmarks of the landscape topology. However, such methods are impeded by a large level of redundancy within sampled sets. Such a redundancy is uninformative, and obfuscates important intermediate states, leading to an incomplete vision of RNA dynamics...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28873470/comparative-genomics-and-phylogenomic-analyses-of-lysine-riboswitch-distributions-in-bacteria
#18
COMPARATIVE STUDY
Sumit Mukherjee, Danny Barash, Supratim Sengupta
Riboswitches are cis-regulatory elements that regulate the expression of genes involved in biosynthesis or transport of a ligand that binds to them. Among the nearly 40 classes of riboswitches discovered so far, three are known to regulate the concentration of biologically encoded amino acids glycine, lysine, and glutamine. While some comparative genomics studies of riboswitches focusing on their gross distribution across different bacterial taxa have been carried out recently, systematic functional annotation and analysis of lysine riboswitches and the genes they regulate are still lacking...
2017: PloS One
https://www.readbyqxmd.com/read/28871084/engineering-a-riboswitch-based-genetic-platform-for-the-self-directed-evolution-of-acid-tolerant-phenotypes
#19
Hoang Long Pham, Adison Wong, Niying Chua, Wei Suong Teo, Wen Shan Yew, Matthew Wook Chang
Environmental pH is a fundamental signal continuously directing the metabolism and behavior of living cells. Programming the precise cellular response toward environmental pH is, therefore, crucial for engineering cells for increasingly sophisticated functions. Herein, we engineer a set of riboswitch-based pH-sensing genetic devices to enable the control of gene expression according to differential environmental pH. We next develop a digital pH-sensing system to utilize the analogue-sensing behavior of these devices for high-resolution recording of host cell exposure to discrete external pH levels...
September 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/28867802/design-of-artificial-riboswitches-as-biosensors
#20
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
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