Erratum to “Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain” [J. Mol. Biol. 359 (2006) 754–768]

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

doi:10.1016/j.jmb.2006.04.075

Cited by 24 publications

(57 citation statements)

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“…Because of limitations in the signal-tonoise ratio and because some signals are unaffected by ligand binding, we were able to analyze the kinetic rates for 11 of these signals. The observed time constants, in general, are in agreement with the time constants derived from fluorescence techniques (25,26). The site-and time-resolved NMR methodology presented here can delineate the global folding behavior of the RNA molecule as a sequential model, detailing the different aspects of structure formation involved (Fig.…”

Section: Discussionsupporting

confidence: 83%

“…The mode of molecular recognition for both ligands is the same (22,23). To date, kinetic and thermodynamic studies concerning the ligand-induced structural rearrangement within the aptamer domain of the adenine-sensing riboswitch have revealed a folding event that operates on a slow time course over a period of seconds in the presence of Mg 2ϩ ions (25)(26)(27).…”

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confidence: 99%

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Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Buck

Fürtig²,

Noeske³

et al. 2007

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

132

140

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spectroscopy ͉ riboswitches ͉ dynamics ͉ purine ͉ caged compound S tructural transitions of proteins and RNA constitute an important aspect of cellular function and information transfer. In proteins, the kinetics of these structural transitions, mainly from an unfolded ensemble to a single unique folded state, can be investigated by hydrogen exchange experiments monitored by NMR spectroscopy (1). Such studies have profoundly influenced our understanding of protein-folding pathways. In hydrogen exchange experiments, labile hydrogen atoms become protected against exchange with the bulk solvent during folding. This acquired exchange protection indicates formation of a persistent structure at atomic resolution. Incorporation of structural information derived from exchange experiments into molecular dynamics (MD) simulations (2), including data from methods exhibiting time and atomic resolution together with -value analysis (3) derived from mutational work, has provided detailed structural information of intermediates populated during folding.RNA molecules can adopt a variety of secondary and tertiary conformations (4, 5). In general, the energetic difference between alternate RNA conformations is very small, and the equilibrium distribution is strongly affected through the binding of proteins (6), ions (7), or small metabolites (8-10), or by structural modifications (11). Alternate RNA structures are stabilized by different Watson-Crick base-pairing interactions (12). To date, RNA folding has been investigated by using x-ray footprinting (13), oligonucleotide hybridization, and classical biochemical methods in conjunction with mutational data (14). Although hydrogen exchange rates can be used as reporters of RNA ground-state dynamics and stability (15-17), RNA hydrogen exchange experiments conducted in a pulse-chase manner fail in most cases because of the high intrinsic exchange rates observed even in folded RNA structures.Here, we report on ligand-induced conformational changes of an RNA at atomic resolution by using real-time NMR methods. We investigated the hypoxanthine-induced folding of the guanine-sensing riboswitch aptamer domain (GSR apt ) of the Bacillus subtilis xpt-pbuX operon (18). Riboswitch RNAs have emerged as an important example of macromolecular structural transitions that lead to transcriptional or translational regulation of protein expression induced through the specific binding of a metabolite (reviewed in refs. 19 and 20). Riboswitches are located in the 5Ј-untranslated region (5Ј-UTR) of bacterial mRNA and consist of a highly specific metabolite receptor region (aptamer domain) coupled to a 3Ј-downstream sequence (expression platform). Gene expression is thought to be modulated in response to conformational differences between the ligand-bound and ligand-free conformations of the aptamer domain (21). Crystal structures of the ligand-bound aptamer domains belonging to the class of purine riboswitches (guanineand adenine-sensing riboswitches) have revealed the presence of complex tertiary stru...

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Section: Discussionsupporting

confidence: 83%

mentioning

confidence: 99%

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Buck

Fürtig²,

Noeske³

et al. 2007

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

132

140

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“…It has been reported that some riboswitches function as kinetically driven, rather than thermodynamically driven, gene-control elements (28,49,50). For example, to yield half-maximal modulation of transcription termination, kinetically driven riboswitches require a concentration of ligand much higher than the apparent K d of the aptamer for the metabolite.…”

Section: Transcription Of Rnas Carrying I-a and Iii-b Aptamers Revealmentioning

confidence: 99%

Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine

Kim

Roth

Breaker

2007

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

130

146

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Several mRNA aptamers have been identified in Mesoplasma florum that have sequence and structural features resembling those of guanine and adenine riboswitches. Two features distinguish these RNAs from established purine-sensing riboswitches. All possess shortened hairpin-loop sequences expected to alter tertiary contacts known to be critical for aptamer folding. The RNAs also carry nucleotide changes in the core of each aptamer that otherwise is strictly conserved in guanine and adenine riboswitches. Some aptamers retain the ability to selectively bind guanine or adenine despite these mutations. However, one variant type exhibits selective and highaffinity binding of 2-deoxyguanosine, which is consistent with its occurrence in the 5 untranslated region of an operon containing ribonucleotide reductase genes. The identification of riboswitch variants that bind nucleosides and reject nucleobases reveals that natural metabolite-sensing RNA motifs can accrue mutations that expand the diversity of ligand detection in bacteria.allosteric RNA ͉ aptamer ͉ metabolite ͉ ribonucleotide reductase ͉ transcription termination G ene-control elements called riboswitches (1) are mRNA motifs typically found in the 5Ј untranslated regions of bacterial mRNAs. Riboswitches selectively bind small molecules, and structural changes within the 5Ј untranslated regions are usually harnessed to control the expression of the adjoining ORF. The architectures of these RNAs are commonly formed from a metabolite-binding aptamer domain and an expression platform (2-5), although more diverse assemblies of aptamers and expression platforms have been found that yield more complex gene-control characteristics (6 -9).Each aptamer adopts a complex secondary-and tertiarystructured fold to form a conserved receptor for the ligand (10-17). This demand for precise structure formation and specific molecular recognition causes the aptamer domains to be highly conserved even among distantly related species. In contrast, the expression platform can adopt a variety of different structures provided it maintains its responsiveness to the occupation state of the aptamer domain.Computer-aided searches based on conserved RNA sequences and structures have been used to identify representatives of numerous riboswitch classes (18-24). However, these bioinformatics algorithms can fail to identify variants of known riboswitch classes that differ substantially from the established aptamer consensus. Furthermore, there could be exceedingly rare classes of riboswitch aptamers or exceptionally small aptamers that will be missed by existing bioinformatics algorithms because there are too few representatives for comparison or they have too few conserved features. Given these limitations, many new riboswitch classes might remain undiscovered, and the true number of metabolite-sensing aptamer folds could greatly exceed the many types published to date (25).Indications that there are many variant, small, or rare riboswitch classes to be discovered come from several recent reports...

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“…[8][9][10] This implies that there is a complex folding pathway that remains to be elucidated. Evidence has been collected by other research groups that suggests that in the unliganded state, the purine aptamer is organized globally, but that the binding pocket is disordered locally.…”

Section: Introductionmentioning

confidence: 99%

Ligand‐Induced Folding of the Adenosine Deaminase A‐Riboswitch and Implications on Riboswitch Translational Control

et al. 2007

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By using a structure-based fluorescence spectroscopic approach, we have examined the folding of an adenine-responsive riboswitch that regulates translation initiation. We observed adaptive recognition of the ligand for the aptamer domain of adenosine deaminase (add) mRNA from Vibrio vulnificus, and revealed pronounced conformational changes even in the preorganized loop-loop region that is distant from the binding site. Importantly, the full-length riboswitch domain, which has a potential translational repressor stem is able to form a binary complex with adenine, and does not act as a folding trap to inhibit binding. The aptamer that is extended by the expression platform therefore remains fully responsive to its ligand; this is in contrast to the previously investigated pbuE A-riboswitch, which becomes trapped in a nonresponsive terminator fold. Consequently, the latter must employ complex response mechanisms, such as operating in kinetic-control mode or using transcriptional pausing, to provide time for the aptamer portion to fold and to bind. The different behavior of the riboswitches can be rationalized by their distinct sequence interface between the aptamer and expression platform. For the add A-riboswitch, our data suggest a thermodynamically driven response mechanism.

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Erratum to “Thermodynamic and Kinetic Characterization of Ligand Binding to the Purine Riboswitch Aptamer Domain” [J. Mol. Biol. 359 (2006) 754–768]

Cited by 24 publications

References 0 publications

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine

Ligand‐Induced Folding of the Adenosine Deaminase A‐Riboswitch and Implications on Riboswitch Translational Control

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