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  • biosynthesis
  • The FMN riboswitch (also known as RFN element) is a highly conserved RNA element that is found frequently in the 5'-untranslated regions of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. (wikipedia.org)
  • aptamers
  • Natural ribozymes and riboswitches are examples of Nature's prowess at creating exceedingly good catalysts and ligand-sensing aptamers. (springer.com)
  • SAM-V features a similar consensus sequence and secondary structure as the binding site of SAM-II riboswitch, but bioinformatics scans cluster the two aptamers independently. (wikipedia.org)
  • It is thought that when glycine is in excess it will bind to both aptamers to activate these genes and facilitate glycine degradation. (wikipedia.org)
  • Although PreQ1-II riboswitch also works as queuosine biosynthetic intermediate, the structural and molecular recognition characteristics are distinct from preQ1-I riboswitch, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. (wikipedia.org)
  • bind
  • SAM-V riboswitch is the fifth known riboswitch to bind S-adenosyl methionine (SAM). (wikipedia.org)
  • Riboswitch elements located within noncoding regions of mRNA bind metabolites with high selectivity and specificity to mediate control of transcription, translation, or RNA processing ( 1 , 2 ). (pnas.org)
  • The discovery of the fluoride riboswitch was surprising as both fluoride ions and the crcB RNA phosphate groups are negatively charged and should not be able to bind to one another. (wikipedia.org)
  • The bacterial glycine riboswitch is an RNA element that can bind the amino acid glycine. (wikipedia.org)
  • The combination of these effects facilitates a more controlled translation of the add gene at lower temperatures: taking a portion of the unbound riboswitch and rendering it unable to bind adenine increases the sensitivity of the remaining portion to magnesium. (wikipedia.org)
  • Structural
  • Like most riboswitch domains, structural information pertaining to the ligand-free TPP riboswitch is relatively lacking. (pnas.org)
  • 2009. Analysis of the RNA backbone: Structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension (SHAPE). (umd.edu)
  • Recent structural studies of PilZ domains from two bacterial species have demonstrated that PilZ domains change conformation drastically upon binding to cyclic di-GMP. (wikipedia.org)
  • Glycine
  • The originally discovered, truncated version of the glycine riboswitch exhibits sigmoidal binding curves with Hill coefficients greater than one, which led to the idea of positive cooperativity between the two aptamer domains. (wikipedia.org)
  • Atomic resolution structures of portions of glycine riboswitches have been obtained by X-ray crystallography. (wikipedia.org)
  • Three of these were later experimentally confirmed as the glmS, glycine and PreQ1-I riboswitches (see below). (wikipedia.org)
  • secondary structure
  • The TPP riboswitch, also known as the THI element and Thi-box riboswitch, is a highly conserved RNA secondary structure. (wikipedia.org)
  • The THI element is an extension of a previously detected thiamin-regulatory element, the thi box, there is considerable variability in the predicted length and structures of the additional and facultative stem loops represented in dark blue in the secondary structure diagram Analysis of operon structures has identified a large number of new candidate thiamin-regulated genes, mostly transporters, in various prokaryotic organisms. (wikipedia.org)
  • Given the relative complexity of their secondary structure, and their hypothesized cis-regulatory role, they might be riboswitches. (wikipedia.org)
  • Its secondary structure and gene associations were predicted by bioinformatics. (wikipedia.org)
  • metal ions
  • The riboswitch is thought to be a part of a system that responds to toxic levels of these metal ions, although the riboswitch might also participate in dealing with the situation where insufficient levels of these trace elements are present in the cell. (wikipedia.org)
  • proteins
  • Thus, riboswitches do not depend on proteins for binding to small molecules and play a role as both metabolite sensors and effectors of gene control. (springer.com)
  • This review focuses on natural ribozymes and riboswitches and attempts to highlight how RNA can rival proteins when it comes to show off its capabilities. (springer.com)
  • These downstream genes transcribe fluoride sensitive enzymes such as enolase, pyrophosphatase, the presumed fluoride exporter CrcB and a superfamily of CLC membrane proteins called Eric^F proteins. (wikipedia.org)
  • ligand specificity
  • Although we were unable to demonstrate evolution of new riboswitch ligand specificity using PACE, we recommend careful design of recombinant M13 phage to avoid evolution of "cheaters" that short circuit the intended selection pressure. (springer.com)
  • The crystal structure of ydaO , a c‐di‐AMP binding riboswitch, illustrates the basis for ligand specificity. (embopress.org)
  • Listeria
  • Correspondingly, several bacterial species found within the GI tract encode the machinery necessary for ethanolamine catabolism, including, but not limited to, E. faecalis , Streptococcus sanguinis , Escherichia coli , and Salmonella , Listeria , and Clostridium species. (pnas.org)
  • transcription
  • We demonstrate that association of AdoCbl to this riboswitch prevents formation of an intrinsic transcription terminator element located within the intercistronic region. (pnas.org)
  • organism
  • Through in-line probing and mutational studies the fluoride riboswitch of the organism Thermotoga petrophila is recognized to have two helical stems adjoined by a helical loop with the capacity to become a pseudoknot. (wikipedia.org)
  • Further supporting a possible role as a cis-regulatory element in control of nitrogen metabolism, the Prochlorococcus marinus gene designed as PMT1479 was more repressed than another other gene in this organism when it was growth without a sufficient supply of nitrogen. (wikipedia.org)
  • glmS
  • This cleavage leads to the degradation of the mRNA that contains the ribozyme, and ultimately lowers production of the GlmS enzyme, encoded by the glmS gene. (wikipedia.org)
  • cofactor
  • Breakdown of ethanolamine requires adenosylcobalamin (AdoCbl) as a cofactor, and, intriguingly, we also identify an intercistronic AdoCbl riboswitch that has a predicted structure different from previously established AdoCbl riboswitches. (pnas.org)
  • motifs
  • It was proposed that both motifs represent riboswitches involved in nitrogen metabolism. (wikipedia.org)
  • Many of the earliest riboswitches to be discovered corresponded to conserved sequence "motifs" (patterns) in 5' UTRs that appeared to correspond to a structured RNA. (wikipedia.org)
  • abundant
  • Ethanolamine is a product of the catabolism of phosphatidylethanolamine, an abundant phospholipid in both mammalian and bacterial membranes ( 3 , 4 ). (pnas.org)
  • We cloned and characterized the most abundant riboswitch mutants and discovered three variants that produce different levels of translational output while retaining their theophylline specificity. (springer.com)
  • Fluoride
  • Many genes are presumed to be regulated by these fluoride riboswitches. (wikipedia.org)
  • The three-dimensional structure of a fluoride riboswitch has been solved at atomic resolution by X-ray crystallography. (wikipedia.org)
  • The identity of fluoride as the riboswitch ligand was accidentally discovered when a compound contaminated with fluoride caused significant conformational changes to the non-coding crcB RNA motif during an in-line probing experiment. (wikipedia.org)
  • organisms
  • Potential regulatory 5′UTRs were identified and filtered based on length, gene function, relative gene counts, and conservation in other organisms. (frontiersin.org)
  • This mechanistic uniqueness of the add adenine riboswitch may serve as a benefit for organisms like Vibrio vulnificus, whose varied habitats require a particularly nuanced metabolic sensitivity to a wide variety of environmental conditions. (wikipedia.org)