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Ambadas Rode, Tamaki Endoh, Naoki Sugimoto
In bacteria, the binding between riboswitch aptamer domain and ligand is regulated by environmental cues, such as low Mg2+ in macrophages during pathogenesis to ensure spatiotemporal expression of virulence genes. We investigated binding between the flavin mononucleotide (FMN) riboswitch aptamer and its anionic ligand in the presence of molecular crowding agent without Mg2+ ion, which mimics pathogenic conditions. Structural, kinetic, and thermodynamic analyses under the crowding revealed more dynamic conformational rearrangements of the FMN riboswitch aptamer compared to dilute Mg2+-containing solution...
April 16, 2018: Angewandte Chemie
Sven Findeiß, Stefan Hammer, Michael T Wolfinger, Felix Kühnl, Christoph Flamm, Ivo L Hofacker
This contribution sketches a work flow to design an RNA switch that is able to adapt two structural conformations in a ligand-dependent way. A well characterized RNA aptamer, i.,e., knowing its Kd and adaptive structural features, is an essential ingredient of the described design process. We exemplify the principles using the well-known theophylline aptamer throughout this work. The aptamer in its ligand-binding competent structure represents one structural conformation of the switch while an alternative fold that disrupts the binding-competent structure forms the other conformation...
April 13, 2018: Methods: a Companion to Methods in Enzymology
Pruthvi Raj Bejugam, Shailza Singh
Post-transcriptional gene regulation is a vital process to regulate expression of the key genes in the eukaryotic cell. Such processes are essential for pathogens which reside inside the host cell. One such pathogen is Leishmania major, which causes cutaneous leishmaniasis. The parasite lives inside the macrophages of mammalian host (mostly human). Inside the macrophage, Leishmania genes show complex host-pathogen interaction regulating a plethora of gene expression. Till date, most of the studies have shown this kind of regulation with respect to the host macrophages...
April 12, 2018: International Journal of Biological Macromolecules
Stefan Schwenk, Alexandra Moores, Irene Nobeli, Timothy D McHugh, Kristine B Arnvig
The success of Mycobacterium tuberculosis relies on the ability to switch between active growth and non-replicating persistence, associated with latent TB infection. Resuscitation promoting factors (Rpfs) are essential for the transition between these states. Rpf expression is tightly regulated as these enzymes are able to degrade the cell wall, and hence potentially lethal to the bacterium itself. We have identified a regulatory element in the 5' untranslated region (UTR) of rpfB. We demonstrate that this element is a transcriptionally regulated RNA switch/riboswitch candidate, which appears to be restricted to pathogenic mycobacteria, suggesting a role in virulence...
March 29, 2018: Nucleic Acids Research
Sumit Mukherjee, Matan Drory Retwitzer, Danny Barash, Supratim Sengupta
Riboswitches are metabolite or ion sensing cis-regulatory elements that regulate the expression of the associated genes involved in biosynthesis or transport of the corresponding metabolite. Among the nearly 40 different classes of riboswitches discovered in bacteria so far, only the TPP riboswitch has also been found in algae, plants, and in fungi where their presence has been experimentally validated in a few instances. We analyzed all the available complete fungal and related genomes and identified TPP riboswitch-based regulation systems in 138 fungi and 15 oomycetes...
April 3, 2018: Scientific Reports
Christoph Manz, Andrei Yu Kobitski, Ayan Samanta, Andres Jäschke, G Ulrich Nienhaus
RNA (ribonucleic acid) molecules are highly flexible biopolymers fluctuating at physiological temperatures among many different conformations that are represented by minima in a hierarchical conformational free energy landscape. Here we have employed single-molecule FRET (smFRET) to explore the energy landscape of the B. subtilis yitJ SAM-I riboswitch (RS). In this small RNA molecule, specific binding of an S-adenosyl-L-methionine (SAM) ligand in the aptamer domain regulates gene expression by inducing structural changes in another domain, the expression platform, causing transcription termination by the RNA polymerase...
March 28, 2018: Journal of Chemical Physics
Anna V Sherwood, Jane K Frandsen, Frank J Grundy, Tina M Henkin
T box riboswitches are RNA regulatory elements widely used by organisms in the phyla Firmicutes and Actinobacteria to regulate expression of amino acid-related genes. Expression of T box family genes is down-regulated by transcription attenuation or inhibition of translation initiation in response to increased charging of the cognate tRNA. Three direct contacts with tRNA have been described; however, one of these contacts is absent in a subclass of T box RNAs and the roles of several structural domains conserved in most T box RNAs are unknown...
March 26, 2018: Proceedings of the National Academy of Sciences of the United States of America
Keunsub Lee, Kan Wang
During the last decade, small noncoding RNAs (ncRNAs) have emerged as essential post-transcriptional regulators in bacteria. Nearly all important physiological and stress responses are modulated by ncRNA regulators, such as riboswitches, trans-acting small RNAs (sRNAs), and cis-antisense RNAs. Recently, three RNA-seq studies identified a total of 1534 candidate ncRNAs from Agrobacterium tumefaciens, a pathogen and biotechnology tool for plants. Only a few ncRNAs have been functionally characterized in A. tumefaciens, and some of them appear to be involved in virulence...
March 20, 2018: Current Topics in Microbiology and Immunology
Mikhail A Moldovan, Svetlana A Petrova, Mikhail S Gelfand
Riboswitches are conserved RNA structures located in non-coding regions of mRNA and able to bind small molecules (e.g. metabolites) changing conformation upon binding. This feature enables them to function as regulators of gene expression. The thiamin pyrophosphate (TPP) riboswitch is the only type of riboswitches found not only in bacteria, but also in eukaryotes - in plants, green algae, protists, and fungi. Two main mechanisms of fungal TPP riboswitch action, involving alternative splicing, have been established so far...
March 13, 2018: Fungal Genetics and Biology: FG & B
Laurène Bastet, Pierre Turcotte, Joseph T Wade, Daniel A Lafontaine
Riboswitches are RNA regulators that control gene expression by modulating their structure in response to metabolite binding. The study of mechanisms by which riboswitches modulate gene expression is crucial to understand how riboswitches are involved in maintaining cellular homeostasis. Previous reports indicate that riboswitches can control gene expression at the level of translation, transcription or mRNA decay. However, there are very few described examples where riboswitches regulate multiple steps in gene expression...
March 14, 2018: RNA Biology
Ping Ge, Shahidul Islam, Cuncong Zhong, Shaojie Zhang
As functional components in three-dimensional (3D) conformation of an RNA, the RNA structural motifs provide an easy way to associate the molecular architectures with their biological mechanisms. In the past years, many computational tools have been developed to search motif instances by using the existing knowledge of well-studied families. Recently, with the rapidly increasing number of resolved RNA 3D structures, there is an urgent need to discover novel motifs with the newly presented information. In this work, we classify all the loops in non-redundant RNA 3D structures to detect plausible RNA structural motif families by using a clustering pipeline...
March 9, 2018: Nucleic Acids Research
Afsaneh Khani, Nicole Popp, Bernd Kreikemeyer, Nadja Patenge
Regulatory RNAs play important roles in the control of bacterial gene expression. In this study, we investigated gene expression regulation by a putative glycine riboswitch located in the 5'-untranslated region of a sodium:alanine symporter family (SAF) protein gene in the group A Streptococcus pyogenes serotype M49 strain 591. Glycine-dependent gene expression mediated by riboswitch activity was studied using a luciferase reporter gene system. Maximal reporter gene expression was observed in the absence of glycine and in the presence of low glycine concentrations...
2018: Frontiers in Microbiology
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
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...
March 5, 2018: Journal of Biotechnology
Ji Heon Noh, Kyoung Mi Kim, Waverly G McClusky, Kotb Abdelmohsen, Myriam Gorospe
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides found throughout the cell that lack protein-coding function. Their functions are closely linked to their interaction with RNA-binding proteins (RBPs) and nucleic acids. Nuclear lncRNAs have been studied extensively, revealing complexes with structural and regulatory roles that enable gene organization and control transcription. Cytoplasmic lncRNAs are less well understood, but accumulating evidence indicates that they also form complexes with diverse structural and regulatory functions...
March 8, 2018: Wiley Interdisciplinary Reviews. RNA
Payal Singh, Nilesh Kumar, Minesh Jethva, Saurabh Yadav, Pragati Kumari, Archana Thakur, Hemant Ritturaj Kushwaha
Cyanobacteria are one of the ancient bacterial species occupying a variety of habitats with diverse metabolic preferences. RNA regulators like riboswitches play significant role in controlling the gene expression in prokaryotes. The taxonomic distribution of riboswitches suggests that they might be one of the oldest mechanisms of gene control system. In this paper, we analyzed the distribution of different riboswitch families in various cyanobacterial genomes. It was observed that only four riboswitch classes were abundant in cyanobacteria, B12 -element (Cob)/AdoCbl/AdoCbl-variant riboswitch being the most abundant...
March 2018: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
Katherine D Launer-Felty, Scott A Strobel
Cyclic dinucleotides are second messenger molecules produced by both prokaryotes and eukaryotes in response to external stimuli. In bacteria, these molecules bind to RNA riboswitches and several protein receptors ultimately leading to phenotypic changes such as biofilm formation, ion transport and secretion of virulence factors. Some cyclic dinucleotide analogs bind differentially to biological receptors and can therefore be used to better understand cyclic dinucleotide mechanisms in vitro and in vivo. However, production of some of these analogs involves lengthy, multistep syntheses...
March 5, 2018: Nucleic Acids Research
Christina Helmling, Dean-Paulos Klötzner, Florian Sochor, Rachel Anne Mooney, Anna Wacker, Robert Landick, Boris Fürtig, Alexander Heckel, Harald Schwalbe
Transcriptional riboswitches modulate downstream gene expression by a tight coupling of ligand-dependent RNA folding kinetics with the rate of transcription. RNA folding pathways leading to functional ON and OFF regulation involve the formation of metastable states within well-defined sequence intervals during transcription. The kinetic requirements for the formation and preservation of these metastable states in the context of transcription remain unresolved. Here, we reversibly trap the previously defined regulatory relevant metastable intermediate of the Mesoplasma florum 2'-deoxyguanosine (2'dG)-sensing riboswitch using a photocaging-ligation approach, and monitor folding to its native state by real-time NMR in both presence and absence of ligand...
March 5, 2018: Nature Communications
Madeline E Sherlock, Narasimhan Sudarsan, Shira Stav, Ronald R Breaker
Gene control systems sometimes interpret multiple signals to set the expression levels of the genes they regulate. In rare instances, ligand-binding riboswitch aptamers form tandem arrangements to approximate the function of specific two-input Boolean logic gates. Here we report the discovery of riboswitch aptamers for phosphoribosyl pyrophosphate (PRPP) that naturally exist either in singlet arrangements, or occur in tandem with guanine aptamers. Tandem guanine-PRPP aptamers can bind the target ligands, either independently or in combination, to approximate the function expected for an IMPLY Boolean logic gate to regulate transcription of messenger RNAs for de novo purine biosynthesis in bacteria...
March 5, 2018: ELife
Xia Zou, Zhenxing Ren, Na Wang, Yin Cheng, Yuanyuan Jiang, Yan Wang, Chenggang Xu
Background: Anaerobic, mesophilic, and cellulolytic Clostridium papyrosolvens produces an efficient cellulolytic extracellular complex named cellulosome that hydrolyzes plant cell wall polysaccharides into simple sugars. Its genome harbors two long cellulosomal clusters: cip - cel operon encoding major cellulosome components (including scaffolding) and xyl - doc gene cluster encoding hemicellulases. Compared with works on cip - cel operon, there are much fewer studies on xyl - doc mainly due to its rare location in cellulolytic clostridia...
2018: Biotechnology for Biofuels
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