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Nucleic Acids Research, 1990, Vol. 18, No. 22 6537-6544
© 1990

MOLECULAR BIOLOGY

Codon recognition in polypeptide chain termination:site directed crosslinking of termination codon to Escherichia coli release factor 2

Warren Tate*,, Barbara Greuer1 and Richard Brimacombe1

Department of Biochemistry, University of Otago Dunedin, New Zealand 1Max Planck Institute for Molecular Genetics Berlin, FRG

* To whom correspondence should be addressed at Institute of Molecular Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA

Received August 15, 1990. Revised October 19, 1990. Accepted October 19, 1990.

An RNA synthesized in vitro was positioned on the Escherichia coil ribosome at the P site with tRNAala, and with a termination codon, UAA, as the next codon in the A site. Such a complex bound stoichiometric amounts of release factor 2 (RF-2); a corresponding RNA with UAC in place of UAA was not a template for the factor. An RNA containing 4-thio-UAA in place of the UAA supported binding of RF-2, and this has allowed site-directed crosslinking from the first position of the termination codon to answer two long standing questions about the termination of protein biosynthesis, the position of the termination codon and its proximity to the release factor during codon recognition. An RF-2.mRNA crossllnked product was detected, indicating the release factor and the termination codon are in close physical contact during the codon recognition event of termination. The 4-thio-U crosslinked also to the ribosome but only to the 30S subunit, and the proteins and the rRNA site concerned were identified. RF-2 decreased significantly the crosslinking to the ribosomal components, but no new crosslink sites were found. If the stop codon was deliberately displaced from the decoding site by one codon's length then a different pattern of crosslinking in particular to the rRNA resulted. These observations are consistent with a model of codon recognition by RF-2 at the decoding site, without a major shift in position of the codon.

Present address: Institute of Molecular Genetics, Baylor College of Medicine, I Baylor Plaza, Houston, Texas 77030, USA


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