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Riboswitch OR Riboswitches

Madeline E Sherlock, Narasimhan Sudarsan, Ronald R Breaker
Riboswitches are noncoding portions of certain mRNAs that bind metabolite, coenzyme, signaling molecule, or inorganic ion ligands and regulate gene expression. Most known riboswitches sense derivatives of RNA monomers. This bias in ligand chemical composition is consistent with the hypothesis that widespread riboswitch classes first emerged during the RNA World, which is proposed to have existed before proteins were present. Here we report the discovery and biochemical validation of a natural riboswitch class that selectively binds guanosine tetraphosphate (ppGpp), a widespread signaling molecule and bacterial "alarmone" derived from the ribonucleotide GTP...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
Svetlana V Harbaugh, Jennifer Martin, Jenna Weinstein, Grant Ingram, Nancy Kelley-Loughnane
Synthetic riboswitches are engineered to regulate gene expression in response to a variety of non-endogenous small molecules, and a challenge to select this engineered response requires robust screening tools. A new synthetic riboswitch can be created by linking an in vitro-selected aptamer library with a randomized expression platform followed by in vivo selection and screening. In order to determine response to analyte, we developed a dual-color reporter comprising elements of the E. coli fimbriae phase variation system: recombinase FimE controlled by a synthetic riboswitch and an invertible DNA segment (fimS) containing a constitutively active promoter placed between two fluorescent protein genes...
May 17, 2018: Methods: a Companion to Methods in Enzymology
Cristopher Segovia, Raul Arias-Carrasco, Alejandro J Yañez, Vinicius Maracaja-Coutinho, Javier Santander
Piscirickettsia salmonis, a fastidious Gram-negative intracellular facultative bacterium, is the causative agent o Piscirickettsiosis. P. salmonis has broad host range with a nearly worldwide distribution, causing significant mortality. The molecular regulatory mechanisms of P. salmonis pathogenesis are relatively unknown, mainly due to its difficult in vitro culture and genomic differences between genogroups. Bacterial non-coding RNAs (ncRNAs) are important post-transcriptional regulators of bacterial physiology and virulence that are predominantly transcribed from intergenic regions (trans-acting) or antisense strand of open reading frames (cis-acting)...
2018: PloS One
Krishna C Suddala, Javier Cabello-Villegas, Malgorzata Michnicka, Collin Marshall, Edward P Nikonowicz, Nils G Walter
In Gram-positive bacteria, T-box riboswitches control gene expression to maintain the cellular pools of aminoacylated tRNAs essential for protein biosynthesis. Co-transcriptional binding of an uncharged tRNA to the riboswitch stabilizes an antiterminator, allowing transcription read-through, whereas an aminoacylated tRNA does not. Recent structural studies have resolved two contact points between tRNA and Stem-I in the 5' half of the T-box riboswitch, but little is known about the mechanism empowering transcriptional control by a small, distal aminoacyl modification...
May 14, 2018: Nature Communications
John C H Spence
Recent advances in the application of X-ray lasers to structural biology are providing time-resolved high-resolution imaging of many processes, from enzyme kinetics to the riboswitch in action, drug action, and light-sensitive proteins.
May 1, 2018: IUCrJ
Guohui Xiao, Liangliang Kong, Rongbo Che, Yusi Yi, Qinchao Zhang, Jie Yan, Xu'ai Lin
Leptospirosis is a widespread zoonotic disease caused by pathogenic Leptospira species. The most common species, Leptospira interrogans , can transfer from contaminated soil or water to the human body. It is able to survive these changing environments through sensing and responding to the changes of environmental cues. Cyclic di-GMP (c-di-GMP) is a special secondary messenger in bacteria, which can respond to the environment and regulate diverse bacterial behaviors. The c-di-GMP levels in bacterial cells are regulated by diguanylatecyclases (DGC) and phosphodiesterases (PDE), which are responsible for synthesizing or hydrolyzing c-di-GMP, respectively...
2018: Frontiers in Microbiology
Yingying Cai, Miaomiao Xia, Huina Dong, Yuan Qian, Tongcun Zhang, Beiwei Zhu, Jinchuan Wu, Dawei Zhang
BACKGROUND: As a very important coenzyme in the cell metabolism, Vitamin B12 (cobalamin, VB12 ) has been widely used in food and medicine fields. The complete biosynthesis of VB12 requires approximately 30 genes, but overexpression of these genes did not result in expected increase of VB12 production. High-yield VB12 -producing strains are usually obtained by mutagenesis treatments, thus developing an efficient screening approach is urgently needed. RESULT: By the help of engineered strains with varied capacities of VB12 production, a riboswitch library was constructed and screened, and the btuB element from Salmonella typhimurium was identified as the best regulatory device...
May 11, 2018: BMC Biotechnology
Carl J Balibar, Artjohn Villafania, Christopher M Barbieri, Nick Murgolo, Terry Roemer, Hao Wang, John A Howe
A riboflavin biosynthesis pathway-specific phenotypic screen using a library of compounds, all with unspecified antibiotic activity, identified one small molecule later named ribocil, for which intrinsic antibacterial activity against Escherichia coli was completely suppressed by addition of exogenous riboflavin to the bacterial growth medium. The ability of riboflavin to suppress the activity of ribocil, and further demonstration that ribocil inhibited riboflavin synthesis (IC50  = 0.3 μM), supported that a component of the riboflavin synthesis pathway was the molecular target...
2018: Methods in Molecular Biology
Michael T Wolfinger, Christoph Flamm, Ivo L Hofacker
Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics...
May 3, 2018: Methods: a Companion to Methods in Enzymology
Tao Sun, Shubin Li, Xinyu Song, Jinjin Diao, Lei Chen, Weiwen Zhang
Photosynthetic cyanobacteria are important primary producers and model organisms for studying photosynthesis and elements cycling on earth. Due to the ability to absorb sunlight and utilize carbon dioxide, cyanobacteria have also been proposed as renewable chassis for carbon-neutral "microbial cell factories". Recent progresses on cyanobacterial synthetic biology have led to the successful production of more than two dozen of fuels and fine chemicals directly from CO2 , demonstrating their potential for scale-up application in the future...
May 2, 2018: Biotechnology Advances
Mark Kerzhner, Hideto Matsuoka, Christine Wuebben, Michael Famulok, Olav Schiemann
Site-directed spin labeling is a powerful tool for investigating the conformation and dynamics of biomacromolecules such as RNA. Here we introduce a spin labeling strategy based on click-chemistry in solution that, in combination with enzymatic ligation, allows highly efficient labeling of complex and long RNAs with short reaction times and suppressed RNA degradation. With this approach a 34 nucleotides long aptamer domain of the preQ1 riboswitch and a 81 nucleotides long TPP riboswitch aptamer could be labeled with two labels in several positions...
May 1, 2018: Biochemistry
Faegheh Golabi, Mousa Shamsi, Mohammad Hosein Sedaaghi, Abolfazl Barzegar, Mohammad Saeid Hejazi
Introduction: Some non-coding RNAs have an important role in the regulation of gene expression and consequently cellular function. Riboswitches are examples of these regulatory RNAs. Riboswitches are classified into various families according to sequential and structural similarities. Methods: In this study, a block finder algorithm for identification of frequently appearing sequential blocks in five families of riboswitches from Rfam 12.0 database, without the use of alignment methods, was developed. Results: The developed program identified 21 frequently appearing blocks in five families of riboswitches...
2018: BioImpacts: BI
Robert A Battaglia, Ailong Ke
After remaining an orphan for over a decade, the ykkC riboswitch family (ykkC, mini-ykkC, and ykkC-III) was recently characterized as guanidine-specific genetic regulatory elements (guanidine-I, II, and III). They respond to increased levels of intracellular guanidine by turning on genes involved in guanidine export and breakdown. Their existence suggests that regulation of intracellular guanidine levels could be an important piece of bacterial physiology which was not appreciated previously. Structural biologists moved exceptionally fast to reveal the guanidine-sensing mechanisms of these riboswitches at the atomic level...
April 26, 2018: Wiley Interdisciplinary Reviews. RNA
Tom Hayon Eyles, Natalia Miguel Vior, Andrew W Truman
Heterologous expression of biosynthetic gene clusters (BGCs) represents an attractive route to the production of new natural products, but is often hampered by poor yields. It is therefore important to develop tools that enable rapid refactoring, gene insertion/deletion and targeted mutations in BGCs. Ideally, these tools should be highly efficient, affordable, accessible, marker free, and flexible for use with a wide range of BGCs. Here, we present a one-step yeast-based method that enables efficient, cheap and flexible modifications to BGCs...
April 25, 2018: ACS Synthetic Biology
Saki Inuzuka, Hitoshi Kakizawa, Kei-Ichiro Nishimura, Takuto Naito, Katsushi Miyazaki, Hiroyuki Furuta, Shigeyoshi Matsumura, Yoshiya Ikawa
The riboswitch is a class of RNA-based gene regulatory machinery that is dependent on recognition of its target ligand by RNA tertiary structures. Ligand recognition is achieved by the aptamer domain, and ligand-dependent structural changes of the expression platform then usually mediate termination of transcription or translational initiation. Ligand-dependent structural changes of the aptamer domain and expression platform have been reported for several riboswitches with short (<40 nucleotides) expression platforms...
April 25, 2018: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
Taejun Chin, Yukiko Okuda, Masahiko Ikeuchi
Biochemicals production is a major theme in the application of photosynthesis to address global warming and organic-resource problems. Among biochemicals, sugar alcohols have attracted research attention because they are directly derived from two photosynthetic products, sugars and reductants. Here, we produced sorbitol photosynthetically by using cyanobacteria and modified the supply of its substrates through genetic engineering. Expression of an NADPH-dependent enzyme that generates sorbitol-6-phosphate, S6PDH, was highly toxic to cyanobacteria likely due to the sorbitol production, whereas expression of an NADH-dependent enzyme, SrlD2, yielded no sorbitol...
April 20, 2018: Journal of Biotechnology
Robert A Battaglia, Ailong Ke
RNA structures called tandem riboswitches allow bacteria to employ complex logical operations in response to nutrient starvation.
April 23, 2018: ELife
Fabian Amman, Alexandre D'Halluin, Rudy Antoine, Ludovic Huot, Ilona Bibova, Kristina Keidel, Stéphanie Slupek, Peggy Bouquet, Loïc Coutte, Ségolène Caboche, Camille Locht, Branislav Vecerek, David Hot
Bordetella pertussis is the causative agent of whooping cough, a respiratory disease still considered as a major public health threat and for which recent re-emergence has been observed. Constant reshuffling of Bordetella pertussis genome organization was observed during evolution. These rearrangements are essentially mediated by Insertion Sequences (IS), a mobile genetic elements present in more than 230 copies in the genome, which are supposed to be one of the driving forces enabling the pathogen to escape from vaccine-induced immunity...
April 23, 2018: RNA Biology
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
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