tRNA binding is a method of gene expression regulation used with amino acid biosynthetic pathways. The tRNA molecule binds to stem I of the regulatory region of the mRNA, through the anticodon. If the tRNA is charged, and has an amino acid bound, it is unable to interact with the second loop, leaving the terminator helix in the mRNA and preventing the expression of protein. However, when the tRNA is uncharged, it is able to interact with the second helix, bending the mRNA and allowing an anti-terminator helix to form – and the enzyme coded on the mRNA can be expressed. For example, the t-box riboswitch.
Metabolite binding is another regulatory mechanism found on mRNAs. The metabolite binds to the mRNA, changing the structure of it and allowing successful expression. This is similar to how methionine and cysteine biosynthetic pathways are controlled. The binding of S-adenosyl methionine (SAM) to the aptamer domain upstream of the de novo biosynthetic genes, modifies the position of the expression platform through the switching sequence, terminating protein expression when high levels of SAM are present in the cell. When SAM is not bound to the mRNA, an anti-terminator loop can form and expression is successful. Another example would be the thiamine pyrophosphate (TPP) expression regulation mechanism, which works in much the same way as the SAM riboswitch.
Ribosome stalling is another regulatory mechanism found in the 5’ UTR of mRNA transcripts. The formation of a stem-loop structure can lead to the ribosome detaching from the mRNA, preventing successful protein synthesis. The formation of the loop structure could be temperature dependent, preventing expression below a specific temperature.
The Shine-Dalgarno sequence (ribosome binding site, RBS) may be occluded on the mRNA, by forming a secondary structure preventing binding. This also stalls the ribosome, leading to unsuccessful translation.
Cofactors can be required to regulate the expression of protein from mRNAs, binding to the 5’ UTR of the transcript. These terminator/anti-terminator proteins are able to control expression by feedback inhibition. For example, the ATP synthetic enzyme expression may be regulated by the cellular ADP / ATP ratio. This can help maintain a high concentration ratio while not continuously expressing these enzymes and proteins until there is no ADP left in the cell – these would waste energy and potentially prevent the cell from having metabolic flexibility. These proteins bind to regulatory helix structures in the 5’ UTR, modulating the presence of the terminator/anti-terminator loops in the mRNA.