Certain sequences trigger a bypass event, when a ribosome stops translation, slides along mRNA with peptidyl-tRNA remaining in the P site, and then resumes translation (see Figure 7.30). This is a rather rare phenomenon, with only ~3 authenticated examples (for review see Herr, Atkins, and Gesteland, 2000). The most dramatic example of bypassing is in gene 60 of phage T4, where the ribosome moves 60 nucleotides along the mRNA (Huang et al., 1988).
The key to the bypass system is that there are identical (or synonymous) codons at either end of the sequence that is skipped. They are sometimes referred to as the "take-off" and "landing" sites. Before bypass, the ribosome is positioned with a peptidyl-tRNA paired with the take-off codon in the P site, with an empty A site waiting for an aminoacyl-tRNA to enter. Figure 7.32 shows that the ribosome slides along mRNA in this condition until the peptidyl-tRNA can become paired with the codon in the landing site. A remarkable feature of the system is its high efficiency, ~50%.
The sequence of the mRNA triggers the bypass. The important features are the two GGA codons for take-off and landing, the spacing between them, a stem-loop structure that includes the take-off codon, and the stop codon adjacent to the take-off codon. The protein under synthesis is also involved.
The take-off stage requires the peptidyl-tRNA to unpair from its codon. This is followed by a movement of the mRNA that prevents it from re-pairing. Then the ribosome scans the mRNA until the peptidyl-tRNA can repair with the codon in the landing reaction. This is followed by the resumption of protein synthesis when aminoacyl-tRNA enters the A site in the usual way.
Like frameshifting, the bypass reaction depends on a pause by the ribosome. The probability that peptidyl-tRNA will dissociate from its codon in the P site is increased by delays in the entry of aminoacyl-tRNA into the A site. Starvation for an amino acid can trigger bypassing in bacterial genes because of the delay that occurs when there is no aminoacyl-tRNA available to enter the A site (Gallant and Lindsley, 1998). In phage T4 gene 60, one role of mRNA structure may be to reduce the efficiency of termination, thus creating the delay that is needed for the take-off reaction.