October 16, 2012

Translocation moves the ribosome

  • Translocation is the movement of the ribosome one codon along mRNA after the addition of each amino acid to the polypeptide chain.
  • Ribosomal translocation moves the mRNA through the ribosome by 3 bases.
  • Translocation moves deacylated tRNA into the E site, peptidyl-tRNA into the P site, and empties the A site.
  • The hybrid state model proposes that translocation occurs in two stages, in which the 50S moves relative to the 30S, and then the 30S moves along mRNA to restore the original conformation. 

The cycle of addition of amino acids to the growing polypeptide chain is completed by translocation, when the ribosome advances three nucleotides along the mRNA. Figure 6.28 shows that translocation expels the uncharged tRNA from the P site, so that the new peptidyl-tRNA can enter. The ribosome then has an empty A site ready for entry of the aminoacyl-tRNA corresponding to the next codon. As the figure shows, in bacteria the discharged tRNA is transferred from the P site to the E site (from which it is then expelled into the cytoplasm). In eukaryotes it is expelled directly into the cytosol. The A and P sites straddle both the large and small subunits; the E site (in bacteria) is located largely on the 50S subunit, but has some contacts in the 30S subunit.

Most thinking about translocation follows the hybrid state model, which proposes that translocation occurs in two stages (for review see Ramakrishnan, 2002). Figure 6.29 shows that first there is a shift of the 50S subunit relative to the 30S subunit; then a second shift occurs when the 30S subunit moves along mRNA to restore the original conformation. The basis for this model was the observation that the pattern of contacts that tRNA makes with the ribosome (measured by chemical footprinting) changes in two stages (Moazed and Noller, 1986). When puromycin is added to a ribosome that has an aminoacylated tRNA in the P site, the contacts of tRNA on the 50S subunit change from the P site to the E site, but the contacts on the 30S subunit do not change. This suggests that the 50S subunit has moved to a post-transfer state, but the 30S subunit has not changed.
The interpretation of these results is that first the aminoacyl ends of the tRNAs (located in the 50S subunit) move into the new sites (while the anticodon ends remain bound to their anticodons in the 30S subunit). At this stage, the tRNAs are effectively bound in hybrid sites, consisting of the 50S E/ 30S P and the 50S P/ 30S A sites. Then movement is extended to the 30S subunits, so that the anticodon-codon pairing region finds itself in the right site. The most likely means of creating the hybrid state is by a movement of one ribosomal subunit relative to the other, so that translocation in effect involves two stages, the normal structure of the ribosome being restored by the second stage (Moazed and Noller, 1989).
The ribosome faces an interesting dilemma at translocation. It needs to break many of its contacts with tRNA in order to allow movement. But at the same time it must maintain pairing between tRNA and the anticodon (breaking the pairing of the deacylated tRNA only at the right moment). One possibility is that the ribosome switches between alternative, discrete conformations. The switch could consist of changes in rRNA base pairing. The accuracy of translation is influenced by certain mutations that influence alternative base pairing arrangements. The most likely interpretation is that the effect is mediated by the tightness of binding to tRNA of the alternative conformations (Wilson and Noller, 1998).