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

ABSTRACT 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.

    • "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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    • "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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