Direct recognition of mRNA stop signals by Escherichia coli polypeptide chain release factor two

The interaction between the translational stop signal and the polypeptide chain release factor protein (RF) within complexes of Escherichia coli ribosomes has been investigated by site-directed photochemical cross-linking experiments. Twelve mRNA analogues containing 4-thiouridine residues as part of stop signals were synthesized. Highly efficient cross-linking to RF-2 from 4-thiouridine (sU) residues of sUGAN-containing mRNAs was observed, and cross-linking from those of sUAAN was observed at a lower efficiency. This indicates that RF-2 is in close physical contact with the stop signal on the ribosome. The yield of the RF-2-mRNA cross-link depended on the identity of the fourth base for the sUGAN set of signals, suggesting that the fourth base of the stop signal affects the interaction between RF-2 and the stop codon. A region previously implicated as part of the decoding site of the small ribosomal subunit, 1385-1420 of the 16 S rRNA, was also cross-linked with these mRNAs. No new cross-links were obtained in the presence of the release factor. The data are consistent with models in which the RF has an anticodon-like domain that contacts the stop signal directly at or near the ribosomal site in which sense codons are decoded.