Amino acid recognition and gene regulation by riboswitches

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
Biochimica et Biophysica Acta (Impact Factor: 4.66). 08/2009; 1789(9-10):592-611. DOI: 10.1016/j.bbagrm.2009.07.002
Source: PubMed


Riboswitches specifically control expression of genes predominantly involved in biosynthesis, catabolism and transport of various cellular metabolites in organisms from all three kingdoms of life. Among many classes of identified riboswitches, two riboswitches respond to amino acids lysine and glycine to date. Though these riboswitches recognize small compounds, they both belong to the largest riboswitches and have unique structural and functional characteristics. In this review, we attempt to characterize molecular recognition principles employed by amino acid-responsive riboswitches to selectively bind their cognate ligands and to effectively perform a gene regulation function. We summarize up-to-date biochemical and genetic data available for the lysine and glycine riboswitches and correlate these results with recent high-resolution structural information obtained for the lysine riboswitch. We also discuss the contribution of lysine riboswitches to antibiotic resistance and outline potential applications of riboswitches in biotechnology and medicine.

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    • "The D-ribose selection in the primordial ribonucleotides structures would have been decisive for the L-amino acids preponderance in life (Erives, 2011). Indeed, glutamine, a chiral amino acid, L-isomer has much higher binding affinities than D-glutamine to the RNA motifs (Serganov and Patel, 2009; Ames and Breaker, 2011). Only achiral glycine is independent of this factor. "
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    ABSTRACT: Some amino acids and their formal derivatives, currently riboswitch-binding species, could have interacted with polyribonucletides in prebiotic environments, leading to the peptide formation. If the resulting compounds had led to a sustainable polymerization of amino acids and the new structures had catalytic activity, such would have been an important contribution to the transition from the RNA world to the RNA/Protein world. Copyright © 2014. Published by Elsevier Ltd.
    Journal of Theoretical Biology 01/2015; 370. DOI:10.1016/j.jtbi.2014.12.013 · 2.12 Impact Factor
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    • "While nucleotides 84–86 (Region 3, Figure 1c) are known to form contacts to the ε-amine of the lysine side chain, nucleotides 148–149 (Region 2) hydrogen-bond to the acid functionality and the α-amine. Upon binding, the pocket obtains further stabilization, which can be seen from the reduced cleavage of nucleotides 170–174 (Region 1) (33,34). "
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    ABSTRACT: Chemical probing is a common method for the structural characterization of RNA. Typically, RNA is radioactively end-labelled, subjected to probing conditions, and the cleavage fragment pattern is analysed by gel electrophoresis. In recent years, many chemical modifications, like fluorophores, were introduced into RNA, but methods are lacking that detect the influence of the modification on the RNA structure with single-nucleotide resolution. Here, we first demonstrate that a 5'-terminal (32)P label can be replaced by a dye label for in-line probing of riboswitch RNAs. Next, we show that small, highly structured FRET-labelled Diels-Alderase ribozymes can be directly probed, using the internal or terminal FRET dyes as reporters. The probing patterns indeed reveal whether or not the attachment of the dyes influences the structure. The existence of two dye labels in typical FRET constructs is found to be beneficial, as 'duplexing' allows observation of the complete RNA on a single gel. Structural information can be derived from the probing gels by deconvolution of the superimposed band patterns. Finally, we use fluorescent in-line probing to experimentally validate the structural consequences of photocaging, unambiguously demonstrating the intentional destruction of selected elements of secondary or tertiary structure.
    Nucleic Acids Research 09/2011; 40(2):861-70. DOI:10.1093/nar/gkr733 · 9.11 Impact Factor
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    • "Riboswitches respond to a variety of cofactors used by protein enzymes, purines and their derivatives , magnesium cations, and amino acids (Roth and Breaker 2009). The importance of amino acids in protein biosynthesis and their catabolic use as an alternative energy source in bacteria make it necessary to control the level of amino acids in response to environmental and cellular changes (Serganov and Patel 2009). Three riboswitches have been identified to date that control amino acid concentrations in bacteria: the lysine, glycine, and S-adenosylmethionine (SAM)-responsive riboswitches (Grundy et al. 2003; Sudarsan et al. 2003; Winkler et al. 2003; Mandal et al. 2004). "
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    ABSTRACT: The glycine riboswitch has a tandem dual aptamer configuration, where each aptamer is a separate ligand-binding domain, but the aptamers function together to bind glycine cooperatively. We sought to understand the molecular basis of glycine riboswitch cooperativity by comparing sites of tertiary contacts in a series of cooperative and noncooperative glycine riboswitch mutants using hydroxyl radical footprinting, in-line probing, and native gel-shift studies. The results illustrate the importance of a direct or indirect interaction between the P3b hairpin of aptamer 2 and the P1 helix of aptamer 1 in cooperative glycine binding. Furthermore, our data support a model in which glycine binding is sequential; where the binding of glycine to the second aptamer allows tertiary interactions to be made that facilitate binding of a second glycine molecule to the first aptamer. These results provide insight into cooperative ligand binding in RNA macromolecules.
    RNA 01/2011; 17(1):74-84. DOI:10.1261/rna.2271511 · 4.94 Impact Factor
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