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Small-Molecule-Binding Riboswitches

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  • Authors: Thea S. Lotz1, Beatrix Suess2
  • Editors: Gisela Storz3, Kai Papenfort4
    Affiliations: 1: Synthetic Genetic Circuits, Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; 2: Synthetic Genetic Circuits, Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany; 3: Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD; 4: Department of Biology I, Microbiology, LMU Munich, Martinsried, Germany
  • Source: microbiolspec August 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0025-2018
  • Received 11 February 2018 Accepted 11 May 2018 Published 03 August 2018
  • Beatrix Suess, [email protected]
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  • Abstract:

    RNA is a versatile biomolecule capable of transferring information, taking on distinct three-dimensional shapes, and reacting to ambient conditions. RNA molecules utilize a wide range of mechanisms to control gene expression. An example of such regulation is riboswitches. Consisting exclusively of RNA, they are able to control important metabolic processes, thus providing an elegant and efficient RNA-only regulation system. Existing across all domains of life, riboswitches appear to represent one of the most highly conserved mechanisms for the regulation of a broad range of biochemical pathways. Through binding of a wide range of small-molecule ligands to their so-called aptamer domain, riboswitches undergo a conformational change in their downstream “expression platform.” In consequence, the pattern of gene expression changes, which in turn results in increased or decreased protein production. Riboswitches unite the sensing and transduction of a signal that can directly be coupled to the metabolism of the cell; thus they constitute a very potent regulatory mechanism for many organisms. Highly specific RNA-binding domains not only occur but can also be evolved by means of the SELEX (systematic evolution of ligands by exponential enrichment) method, which allows selection of aptamers against almost any ligand. Coupling of these aptamers with an expression platform has led to the development of synthetic riboswitches, a highly active research field of great relevance and immense potential. The aim of this review is to summarize developments in the riboswitch field over the last decade and address key questions of recent research.

  • Citation: Lotz T, Suess B. 2018. Small-Molecule-Binding Riboswitches. Microbiol Spectrum 6(4):RWR-0025-2018. doi:10.1128/microbiolspec.RWR-0025-2018.


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RNA is a versatile biomolecule capable of transferring information, taking on distinct three-dimensional shapes, and reacting to ambient conditions. RNA molecules utilize a wide range of mechanisms to control gene expression. An example of such regulation is riboswitches. Consisting exclusively of RNA, they are able to control important metabolic processes, thus providing an elegant and efficient RNA-only regulation system. Existing across all domains of life, riboswitches appear to represent one of the most highly conserved mechanisms for the regulation of a broad range of biochemical pathways. Through binding of a wide range of small-molecule ligands to their so-called aptamer domain, riboswitches undergo a conformational change in their downstream “expression platform.” In consequence, the pattern of gene expression changes, which in turn results in increased or decreased protein production. Riboswitches unite the sensing and transduction of a signal that can directly be coupled to the metabolism of the cell; thus they constitute a very potent regulatory mechanism for many organisms. Highly specific RNA-binding domains not only occur but can also be evolved by means of the SELEX (systematic evolution of ligands by exponential enrichment) method, which allows selection of aptamers against almost any ligand. Coupling of these aptamers with an expression platform has led to the development of synthetic riboswitches, a highly active research field of great relevance and immense potential. The aim of this review is to summarize developments in the riboswitch field over the last decade and address key questions of recent research.

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Image of FIGURE 1

Common mechanism of riboswitches in bacteria. (A) Regulation of translation initiation: In the absence of the ligand, a stem-loop structure is formed between the aptamer domain and a sequence complementary to the Shine-Dalgarno (SD) sequence. Thus, the SD sequence is accessible for 30S binding, and translation initiation occurs. As a consequence of ligand binding (pentagon) and the folding of the aptamer domain, an alternative stem-loop is formed, which sequesters the SD sequence, and the binding of the 30S ribosomal subunit is blocked. (B) Regulation of transcription termination: The aptamer domain is followed by a sequence complementary to the 3′ part of the aptamer and a U stretch. In the absence of the ligand, the complementary 3′ part is base-paired with the aptamer, forming a terminator structure. Thus, RNA polymerase (RNAP) dissociates and transcription is blocked. Upon ligand binding, terminator structure formation is inhibited and transcription can proceed, resulting in expression of the reporter gene.

Source: microbiolspec August 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0025-2018
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Image of FIGURE 2

Structure of the TPP riboswitch. (A) Schematic depiction of the secondary structure of the riboswitch with and without TPP (marked in pink). TPP stabilizes the P1-P1′ helix, which leads to secondary structure changes. The formation of the expression platform follows as a consequence, so that the Shine-Dalgarno (SD) sequence is sequestered in another stem, inhibiting any further gene expression. (B) The X-ray crystal structure of the aptamer bound to TPP (black sticks, center) and Mg ions (black spheres). PDB ID 2GDI ( 31 ); annotations on the structures refer to helices (P) and junctions (J). Adapted from reference 85 with permission.

Source: microbiolspec August 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0025-2018
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Naturally occurring riboswitches

Source: microbiolspec August 2018 vol. 6 no. 4 doi:10.1128/microbiolspec.RWR-0025-2018

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