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Riboswitch OR Riboswitches

Russell T Chan, Kevin S Keating, Michaela C Go, Navtej Toor
Large RNAs often utilize GNRA tetraloops as structural elements to stabilize the overall tertiary fold. These tetraloop-receptor (TR) interactions have a conserved geometry in which the tetraloop docks into the receptor at an angle of ~15° from the helix containing the receptor. Here, we show that the conserved GUAAY pentaloop found in domain III of group IIB1 introns participates in a novel class of RNA tertiary interaction with a geometry and mode of binding that are significantly different from that found in GNRA TR interactions...
October 19, 2016: Journal of Molecular Biology
Hui Cheng, Yuanyuan Zhang, Hongyan Wang, Na Sun, Min Liu, Hongxia Chen, Renjun Pei
Riboswitches are functional non-coding RNA regulatory components that play an important role in the regulation of gene expression in diverse organisms. In particular, using riboswitches to modulate RNA interference (RNAi) enables temporal and spatial control of gene expression in mammalian cells. Herein, a ribozyme gene switch to activate RNAi was fabricated for the artificial regulation of versatile gene silencing through the interaction of an RNA aptamer with small molecules. The device comprised an allosteric HDV ribozyme with an embedded theophylline aptamer and a primary miRNA (pri-miRNA) to silence the MAP4K4 gene in hepatic (HepG2) cells, aiming to achieve dose-dependent control of the activation of RNAi, and then the regulation of the MAP4K4 gene by theophylline...
October 18, 2016: Molecular BioSystems
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, 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 and is involved in developmentally-regulated carotenoid formation, such as during deetiolation...
October 11, 2016: Plant Physiology
Michele Felletti, Anna Bieber, Jörg S Hartig
Besides its primary informational role, the sequence of the messenger RNA (mRNA) including its 5'- and 3'- untranslated regions (UTRs), contains important features that are relevant for post-transcriptional and translational regulation of gene expression. In this work a number of bacterial twister motifs are characterized both in vitro and in vivo. The analysis of their genetic contexts shows that these motifs have the potential of being transcribed as part of polycistronic mRNAs, thus we suggest the involvement of bacterial twister motifs in the processing of mRNA...
October 3, 2016: RNA Biology
Andreas Matern, Danielle Pedrolli, Stephanie Großhennig, Jörgen Johansson, Matthias Mack
The riboflavin analogs roseoflavin (RoF) and 8-demethyl-8-aminoriboflavin (AF) are produced by the bacteria Streptomyces davawensis and Streptomyces cinnabarinus Riboflavin analogs have the potential to be used as broad-spectrum antibiotics and we therefore studied the metabolism of riboflavin (vitamin B2), RoF and AF in the human pathogen Listeria monocytogenes, a bacterium which is a riboflavin auxotroph. We show that the L. monocytogenes protein Lmo1945 is responsible for uptake of riboflavin, RoF and AF...
September 26, 2016: Journal of Bacteriology
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
Michele Felletti, Julia Stifel, Lena A Wurmthaler, Sophie Geiger, Jörg S Hartig
The utilization of ribozyme-based synthetic switches in biotechnology has many advantages such as an increased robustness due to in cis regulation, small coding space and a high degree of modularity. The report of small endonucleolytic twister ribozymes provides new opportunities for the development of advanced tools for engineering synthetic genetic switches. Here we show that the twister ribozyme is distinguished as an outstandingly flexible expression platform, which in conjugation with three different aptamer domains, enables the construction of many different one- and two-input regulators of gene expression in both bacteria and yeast...
2016: Nature Communications
Jermaine L Jenkins, Joseph E Wedekind
Ribozymes and riboswitches are examples of non-protein-coding (nc)RNA molecules that achieve biological activity by adopting complex three-dimensional folds. Visualization of such molecules at near-atomic resolution can enhance our understanding of how chemical groups are organized spatially, thereby providing novel insight into function. This approach has its challenges, which mainly entail sample crystallization followed by the application of empirical, structure-determination methods that often include experimental "phasing" of X-ray diffraction data...
2016: Methods in Molecular Biology
Karen M Ruff, Ayesha Muhammad, Phillip J McCown, Ronald R Breaker, Scott A Strobel
The glycine riboswitch often occurs in a tandem architecture, with two ligand-binding domains (aptamers) followed by a single expression platform. Based on previous observations, we hypothesized that "singlet" versions of the glycine riboswitch, which contain only one aptamer domain, are able to bind glycine if appropriate structural contacts are maintained. An initial alignment of 17 putative singlet riboswitches indicated that the single consensus aptamer domain is flanked by a conserved peripheral stem-loop structure...
September 22, 2016: RNA
Akiyoshi Higo, Atsuko Isu, Yuki Fukaya, Toru Hisabori
In recent years, studies on the development of gene regulation tools in cyanobacteria have been extensively conducted towards efficient production of valuable chemicals. However, there is considerable scope for improving the economic feasibility of production. To improve a recently reported gene induction system using anhydrotetracycline (aTc)-TetR and an endogenous gene repression system using small antisense RNA in the filamentous nitrogen-fixing cyanobacterium Anabaena sp. PCC 7120 (Anabaena), we constructed a positive feedback loop, in which gfp and a small antisense RNA for tetR are controlled by an aTc-inducible promoter...
September 16, 2016: ACS Synthetic Biology
Adam M Saunders, Victoria J DeRose
It is well-known that RNA structure and function depend heavily on cations, and the ability of Mg(2+) to stabilize RNA structures has been emphasized. Recent studies, however, highlight the importance of transition metals in RNA function. Riboswitches that selectively bind Ni(2+), Co(2+), and Mn(2+) have been discovered with specific RNA-metal sites that influence metal-related gene expression. Exogenous metals such as Pt(II) from therapeutics also bind and may inhibit cellular RNA function. Novel reports that RNA can host Fe(II) in catalytic sites are relevant to early life in pre-oxygenic atmospheres...
September 5, 2016: Current Opinion in Chemical Biology
Anna V Sherwood, Tina M Henkin
Riboswitches are RNA elements that act on the mRNA with which they are cotranscribed to modulate expression of that mRNA. These elements are widely found in bacteria, where they have a broad impact on gene expression. The defining feature of riboswitches is that they directly recognize a physiological signal, and the resulting shift in RNA structure affects gene regulation. The majority of riboswitches respond to cellular metabolites, often in a feedback loop to repress synthesis of the enzymes used to produce the metabolite...
September 8, 2016: Annual Review of Microbiology
Ahmet Yildirim, Jin Zhang, Sergio Manzetti, David van der Spoel
A number of cases around the world have been reported where animals were found dead or dying with symptoms resembling a thiamine (vitamin B) deficiency, and for some of these, a link to pollutants has been suggested. Here, we investigate whether biomolecules involved in thiamin binding and transport could be blocked by a range of different pollutants. We used in silico docking of five compound classes (25 compounds in total) to each of five targets (prion protein, ECF-type ABC transporter, thi-box riboswitch receptor, thiamin pyrophosphokinase, and YKoF protein) and subsequently performed molecular dynamics (MD) simulations to assess the stability of the complexes...
October 17, 2016: Chemical Research in Toxicology
Yuchen Liu, Yonghao Zhan, Zhicong Chen, Anbang He, Jianfa Li, Hanwei Wu, Li Liu, Chengle Zhuang, Junhao Lin, Xiaoqiang Guo, Qiaoxia Zhang, Weiren Huang, Zhiming Cai
The complex phenotypes of eukaryotic cells are controlled by decision-making circuits and signaling pathways. A key obstacle to implementing artificial connections in signaling networks has been the lack of synthetic devices for efficient sensing, processing and control of biological signals. By extending sgRNAs to include modified riboswitches that recognize specific signals, we can create CRISPR-Cas9-based 'signal conductors' that regulate transcription of endogenous genes in response to external or internal signals of interest...
September 5, 2016: Nature Methods
Adi Millman, Daniel Dar, Maya Shamir, Rotem Sorek
A common strategy for regulation of gene expression in bacteria is conditional transcription termination. This strategy is frequently employed by 5'UTR cis-acting RNA elements (riboregulators), including riboswitches and attenuators. Such riboregulators can assume two mutually exclusive RNA structures, one of which forms a transcriptional terminator and results in premature termination, and the other forms an antiterminator that allows read-through into the coding sequence to produce a full-length mRNA. We developed a machine-learning based approach, which, given a 5'UTR of a gene, predicts whether it can form the two alternative structures typical to riboregulators employing conditional termination...
August 29, 2016: Nucleic Acids Research
Peter McPhie, Patrick Brown, Bin Chen, Theodore K Dayie, Allen P Minton
The dependence of the conformation of the S-adenosylmethionine (SAM) II riboswitch on the concentration of added Mg(2+) ions and SAM, individually and in mixtures, was monitored by circular dichroism (CD) spectroscopy and by measurement of the diffusion coefficient. The results are analyzed in the context of two complementary quantitative models, both of which are consistent with a single underlying physical model. Magnesium binding sites in the open state have an affinity on average higher than the affinity of those in the compact state, but formation of the compact state is accompanied by an increase in the number of binding sites...
September 13, 2016: Biochemistry
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
Ya-Hui Lin, Kung-Yao Chang
Metabolite-responsive RNA pseudoknots derived from prokaryotic riboswitches have been shown to stimulate -1 programmed ribosomal frameshifting (PRF), suggesting -1 PRF as a promising gene expression platform to extend riboswitch applications in higher eukaryotes. However, its general application has been hampered by difficulty in identifying a specific ligand-responsive pseudoknot that also functions as a ligand-dependent -1 PRF stimulator. We addressed this problem by using the -1 PRF stimulation pseudoknot of SARS-CoV (SARS-PK) to build a ligand-dependent -1 PRF stimulator...
October 14, 2016: Nucleic Acids Research
John A Howe, Li Xiao, Thierry O Fischmann, Hao Wang, Haifeng Tang, Artjohn Villafania, Rumin Zhang, Christopher M Barbieri, Terry Roemer
Bacterial riboswitches are non-coding RNA structural elements that direct gene expression in numerous metabolic pathways. The key regulatory roles of riboswitches, and the urgent need for new classes of antibiotics to treat multi-drug resistant bacteria, has led to efforts to develop small-molecules that mimic natural riboswitch ligands to inhibit metabolic pathways and bacterial growth. Recently, we reported the results of a phenotypic screen targeting the riboflavin biosynthesis pathway in the Gram-negative bacteria Escherichia coli that led to the identification of ribocil, a small molecule inhibitor of the flavin mononucleotide (FMN) riboswitch controlling expression of this biosynthetic pathway...
August 2, 2016: RNA Biology
Wei Wang, Cheng Jiang, Jinmai Zhang, Wei Ye, Ray Luo, Hai-Feng Chen
Riboswitches are a class of metabolism control elements mostly found in bacteria. Due to their fundamental importance in bacteria gene regulation, riboswitches have been proposed as antibacterial drug targets. Prequeuosine (preQ1) is the last free precursor in the biosynthetic pathway of queuosine that is crucial for translation efficiency and fidelity. However, the regulation mechanism for the preQ1 riboswitch remains unclear. Here we constructed fluctuation correlation network based on all-atom molecular dynamics simulations to reveal the regulation mechanism...
2016: Scientific Reports
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