Mechanisms of Riboswitches
Riboswitches are often conceptually divided into two parts: an aptamer and an expression platform. The aptamer directly binds the small molecule, and the expression platform undergoes structural changes in response to the changes in the aptamer. The expression platform is what regulates gene expression.
Expression platforms typically turn off gene expression in response to the small molecule, but some turn it on. The following riboswitch mechanisms have been experimentally demonstrated.
- Riboswitch-controlled formation of rho-independent transcription termination hairpins leads to premature transcription termination.
- Riboswitch-mediated folding sequesters the ribosome-binding site, thereby inhibiting translation.
- The riboswitch is a ribozyme that cleaves itself in the presence of sufficient concentrations of its metabolite.
- Riboswitch alternate structures affect the splicing of the pre-mRNA.
- A TPP riboswitch in Neurospora crassa (a fungus) controls alternative splicing to conditionally produce an Upstream Open Reading Frame (uORF), thereby affecting the expression of downstream genes
- A TPP riboswitch in plants modifies splicing and alternative 3'-end processing
- A riboswitch in Clostridium acetobutylicum regulates an adjacent gene that is not part of the same mRNA transcript. In this regulation, the riboswitch interferes with transcription of the gene. The mechanism is uncertain but may be caused by clashes between two RNA polymerase units as they simultaneously transcribe the same DNA.
- A riboswitch in Listeria monocytogenes regulates the expression of its downstream gene. However, riboswitch transcripts subsequently modulate the expression of a gene located elsewhere in the genome. This trans regulation occurs via base-pairing to the mRNA of the distal gene.
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