Riboswitch RNAs: using RNA to sense cellular metabolism

Abstract

Riboswitches are RNA elements that undergo a shift in structure in response to binding of a regulatory molecule. These elements are encoded within the transcript they regulate, and act in cis to control expression of the coding sequence(s) within that transcript; their function is therefore distinct from that of small regulatory RNAs (sRNAs) that act in trans to regulate the activity of other RNA transcripts. Riboswitch RNAs control a broad range of genes in bacterial species, including those involved in metabolism or uptake of amino acids, cofactors, nucleotides, and metal ions. Regulation occurs as a consequence of direct binding of an effector molecule, or through sensing of a physical parameter such as temperature. Here we review the global role of riboswitch RNAs in bacterial cell metabolism.

Figure 1.

RNA thermosensors. (Left) At low temperature, the helical structure is stable, resulting in sequestration of the SD sequence by pairing with the ASD sequence (SD); this results in inhibition of translation initiation. (Right) At higher temperature, the ASD–SD helix is disrupted and the SD sequence is available for translation initiation.

Figure 2.

Basic model of a standard metabolite-binding riboswitch RNA. (Left) In the absence of the effector, the ligand-binding domain (L) is unoccupied, and the RNA is in a conformation that allows expression of the downstream coding sequence, either through formation of an antiterminator element (AT) that prevents formation of the terminator helix and therefore allows transcription to continue (top), or through capture of the ASD into a structure that liberates the SD sequence and allows translation to initiate (bottom). (Right) In the presence of the effector (*), the ligand-binding domain is occupied, resulting in a structural shift in the downstream region of the RNA. This allows the terminator (T) to form, which results in premature termination of transcription (top) or sequestration of the SD sequence in an ASD–SD helix that prevents translation initiation (bottom). Variations from this basic model are discussed in the text.

Figure 3.

The T-box mechanism. (Left) When a high proportion of a tRNA with a specific anti-codon is charged with the cognate amino acid, the tRNA anti-codon loop can interact with the matching codon (the Specifier Sequence, S) in an internal loop in the RNA. The presence of the amino acid at the 3′ end of the tRNA blocks interaction with the antiterminator element (AT). In the absence of this second interaction, the more stable terminator helix (T) will form, and transcription terminates. (Right) When the tRNA is poorly charged, the uncharged tRNA interacts both at the Specifier Sequence and at the antiterminator bulge. This second interaction stabilizes the antiterminator and prevents formation of the terminator helix, which results in readthrough of the termination site and transcription of the full-length mRNA. Each gene in the T-box family responds specifically to the cognate tRNA, with specificity determined primarily by the Specifier Sequence–anti-codon pairing. Discrimination between charged and uncharged tRNA occurs at the antiterminator.