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.