Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain

Gilbert, S.D.; Stoddard, C.D.; Wise, Sarah; Batey, Robert T.

doi:10.1016/j.jmb.2006.04.003

Cited by 254 publications

(319 citation statements)

References 53 publications

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“…In previous studies, a number of other well-characterized purine riboswitches have also been identified. However, these function through modulation of transcription, by a more complex mechanism (22)(23)(24)(25), which may be more organism-specific (26). From the x-ray crystal structures of the add A-riboswitch (18), it is clear that the aptamer domain entirely encapsulates adenine with four nucleotides (U22, U47, U51, and U74) making specific H-bonding contacts ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Reengineering orthogonally selective riboswitches

Dixon

Duncan²,

Geerlings³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

151

163

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The ability to independently control the expression of multiple genes by addition of distinct small-molecule modulators has many applications from synthetic biology, functional genomics, pharmaceutical target validation, through to gene therapy. Riboswitches are relatively simple, small-molecule-dependent, protein-free, mRNA genetic switches that are attractive targets for reengineering in this context. Using a combination of chemical genetics and genetic selection, we have developed riboswitches that are selective for synthetic "nonnatural" small molecules and no longer respond to the natural intracellular ligands. The orthogonal selectivity of the riboswitches is also demonstrated in vitro using isothermal titration calorimetry and x-ray crystallography. The riboswitches allow highly responsive, dose-dependent, orthogonally selective, and dynamic control of gene expression in vivo. It is possible that this approach may be further developed to reengineer other natural riboswitches for application as small-molecule responsive genetic switches in both prokaryotes and eukaryotes.

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Section: Resultsmentioning

confidence: 99%

Reengineering orthogonally selective riboswitches

Dixon

Duncan²,

Geerlings³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

151

163

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“…58 These results are in contrast to those obtained for the guanine riboswitch for which it was proposed that ligand recognition is performed through an induced-fit mechanism. 21 Indeed, Gilbert et al proposed that the core region of the ligand-free riboswitch is largely disorganized and that only ligand binding may promote the folding of the native state of the RNA. 21 Thus, riboswitches seem to employ various folding pathways to perform ligand recognition and gene regulation.…”

Section: Discussionmentioning

confidence: 99%

“…21 Indeed, Gilbert et al proposed that the core region of the ligand-free riboswitch is largely disorganized and that only ligand binding may promote the folding of the native state of the RNA. 21 Thus, riboswitches seem to employ various folding pathways to perform ligand recognition and gene regulation.…”

Section: Discussionmentioning

confidence: 99%

Folding of the SAM-I riboswitch

et al. 2012

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“…Riboswitches binding guanine and adenine have been found to use canonical Watson-Crick base pairs for selective ligand binding (Batey et al 2004;Mandal and Breaker 2004a;Serganov et al 2004;Noeske et al 2005;Gilbert et al 2006). A single point mutation of the purine riboswitch aptamer is sufficient to switch aptamer specificity between guanine and adenine (Mandal and Breaker 2004a).…”

Section: Watson-crick Base Pairing Is Unlikely To Account For Ligand mentioning

confidence: 99%

Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria

Meyer¹,

Roth²,

Chervin³

et al. 2008

RNA

109

155

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Bioinformatics searches of eubacterial genomes have yielded many riboswitch candidates where the identity of the ligand is not immediately obvious on examination of associated genes. One of these motifs is found exclusively in the family Streptococcaceae within the 59 untranslated regions (UTRs) of genes encoding the hypothetical membrane protein classified as COG4708 or DUF988. While the function of this protein class is unproven, a riboswitch binding the queuosine biosynthetic intermediate pre-queuosine 1 (preQ 1 ) has been identified in the 59 UTR of homologous genes in many Firmicute species of bacteria outside of Streptococcaceae. Here we show that a representative of the COG4708 RNA motif from Streptococcus pneumoniae R6 also binds preQ 1 . Furthermore, representatives of this RNA have structural and molecular recognition characteristics that are distinct from those of the previously described preQ 1 riboswitch class. PreQ 1 is the second metabolite for which two or more distinct classes of natural aptamers exist, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. Additionally, the association of preQ 1 binding RNAs with most genes encoding proteins classified as COG4708 strongly suggests that these proteins function as transporters for preQ 1 or another queuosine biosynthetic intermediate.

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Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain

Cited by 254 publications

References 53 publications

Reengineering orthogonally selective riboswitches

Reengineering orthogonally selective riboswitches

Folding of the SAM-I riboswitch

Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria

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Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain

Cited by 254 publications

References 53 publications

Reengineering orthogonally selective riboswitches

Reengineering orthogonally selective riboswitches

Folding of the SAM-I riboswitch

Confirmation of a second natural preQ1 aptamer class in Streptococcaceae bacteria

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Confirmation of a second natural preQ₁ aptamer class in Streptococcaceae bacteria