Amino acid recognition and gene regulation by riboswitches
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.
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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. "
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 · 2.30 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). "
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 · 4.62 Impact Factor
Conference Paper: Parallel symbolic processing-can it be done?[Show abstract] [Hide abstract]
ABSTRACT: My principle answer is: yes, but it depends. Parallelization of symbolic applications is possible, but only for certain classes of applications. Distributed memory may prevent parallelization in some cases where the relation of computation and communication overhead becomes too high, but also may be an advantage when applications require much garbage collection, which can then be done in a distributed way. There are also some applications which have a higher degree of parallelism than can be supported by shared memory, and so are candidates for profiting by massively parallel architecturesProgramming Models for Massively Parallel Computers, 1993. Proceedings; 10/1993