Key Points
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Riboswitches are structured domains within the non-coding portions of some mRNAs, where they serve as metabolite-sensing genetic switches. Metabolite binding causes allosteric changes in the mRNA that bring about changes in gene-expression processes such as transcription termination and translation initiation.
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Riboswitches comprise two domains: an aptamer and an expression platform. The aptamer is highly conserved even in distantly related organisms, and serves as a precise sensor for its target metabolite. The expression platform is far more variable in sequence and in structure as it can function by assuming one of many structural forms to control gene expression.
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Experimental data that are now known to correspond to riboswitch function date back at least 30 years. Recent studies have confirmed that a variety of gene-control 'mysteries' described in the literature over the past decades can be explained by the presence of seven distinct classes of riboswitches.
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The aptamer domains of riboswitches exhibit surprising selectivity and specificity that compares favourably with protein receptors. These findings, along with the possibility that modern riboswitches might be evolutionary hold outs of an ancient form of gene-control system, indicate that the performance characteristics of riboswitches are competitive with those that are exhibited by proteins.
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The mechanisms of gene control by bacterial riboswitches are largely based on transcription termination and translation initiation. However, the discovery of a riboswitch that has ribozyme function, and evidence which indicates that eukaryotes might use riboswitches for splicing control, hint at the potential for far greater diversity for riboswitch function in ancient and modern organisms.
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New studies indicate that bacteria express numerous new RNA motifs and small non-coding RNAs. These findings suggest that more riboswitches will be identified, and so riboswitches seem to be a significant form of genetic control in bacteria.
Abstract
Riboswitches are complex folded RNA domains that serve as receptors for specific metabolites. These domains are found in the non-coding portions of various mRNAs, where they control gene expression by harnessing allosteric structural changes that are brought about by metabolite binding. New findings indicate that riboswitches are robust genetic elements that are involved in regulating fundamental metabolic processes in many organisms.
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Glossary
- ALLOSTERIC ENZYME
-
An enzyme that is triggered to alter its function in response to the binding of a target compound at a site that is distal from the active site of the enzyme.
- RNA WORLD
-
A hypothetical time in early evolution, before the emergence of DNA and proteins, when biological processes were guided entirely by RNA molecules.
- RIBOZYME
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A nucleic-acid molecule that folds to form an active site and catalyzes a chemical reaction.
- APTAMER
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An RNA domain, either engineered or natural, that forms a precise three-dimensional structure and selectively binds a target molecule.
- IN VITRO EVOLUTION
-
The use of various separation and amplification techniques that serve to mimic Darwinian evolution and create variants of proteins or nucleic acids that have new or improved functions.
- UTR
-
(Untranslated region). Stretches of untranslated sequences located upstream and downstream of the coding region of an mRNA.
- IN-LINE PROBING
-
An RNA-structure probing method that can be used to examine secondary-structure models and to determine whether RNAs undergo substantive structural rearrangements under different incubation conditions.
- DISSOCIATION CONSTANT
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The equilibrium constant for a ligand binding to its receptor, which, in the case of riboswitches, represents the concentration of ligand that is required to convert half of the aptamers that are present in a mixture to their ligand-bound form.
- EXPRESSION PLATFORM
-
The part of a riboswitch that interacts with an aptamer to transduce metabolite binding into a change in gene expression.
- INTRINSIC TERMINATOR
-
A hairpin structure followed by a run of U residues in a nascent RNA transcript that stalls the RNA polymerase and induces transcription termination.
- ANTI-TERMINATOR
-
A hairpin structure that, on formation, precludes the formation of an intrinsic terminator and thereby permits transcription to proceed.
- RIBOSOME-BINDING SITE
-
Also known as the Shine–Dalgarno sequence, it is a short stretch of conserved nucleotides that is situated several nucleotides upstream of the start codon in prokaryotic mRNAs. This sequence is recognized by the ribosome during translation initiation.
- TRANSCRIPTIONAL UNIT
-
An RNA transcript, such as mRNA, that is transcribed separately. In the case of operons, one transcriptional unit can encode several proteins.
- REGULON
-
A collection of separate genes, the expression of which is controlled as a unit by a specific signalling compound or factor.
- SELF-CLEAVING RIBOZYME
-
Five of the nine known natural ribozymes catalyze self-cleavage using an internal phosphoester transfer reaction.
- INTRON
-
A non-coding segment of mRNA that is removed by splicing processes before translation by ribosomes.
- ROSE ELEMENT
-
An RNA sequence in certain bacteria that responds to changes in temperature and controls expression of adjacent heat-shock genes.
- AMINOACYL-tRNA SYNTHETASE
-
An enzyme that recognizes a specific tRNA and selectively loads each with its cognate amino acid.
- LEADER PEPTIDE
-
A peptide that is encoded upstream of a larger open reading frame, the translation of which is used as a sensor for adequate levels of a particular aminoacylated tRNA.
- TRAP
-
A complex formed by the trp RNA-binding attenuation protein from B. subtilis. TRAP binds tryptophan and serves as a protein factor for regulating the trp operon.
- TRANSCRIPTIONAL PAUSING
-
The temporary stalling of RNA polymerase during transcription that is typically caused by hairpin structures or other sequence elements within the nascent mRNA.
- RNase P
-
A ribonucleoprotein-enzyme complex wherein the RNA component serves as a ribozyme that processes precursor RNAs such as pre-tRNA transcripts.
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Mandal, M., Breaker, R. Gene regulation by riboswitches. Nat Rev Mol Cell Biol 5, 451–463 (2004). https://doi.org/10.1038/nrm1403
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DOI: https://doi.org/10.1038/nrm1403
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