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A tripeptide ‘anticodon’ deciphers stop codons in messenger RNA

Nature volume 403, pages 680–684 (2000)Cite this article

Abstract

The two translational release factors of prokaryotes, RF1 and RF2, catalyse the termination of polypeptide synthesis at UAG/UAA and UGA/UAA stop codons, respectively1,2,3. However, how these polypeptide release factors read both non-identical and identical stop codons is puzzling4. Here we describe the basis of this recognition. Swaps of each of the conserved domains between RF1 and RF2 in an RF1–RF2 hybrid led to the identification of a domain that could switch recognition specificity. A genetic selection among clones encoding random variants of this domain showed that the tripeptides Pro-Ala-Thr and Ser-Pro-Phe determine release-factor specificity in vivo in RF1 and RF2, respectively. An in vitro release study of tripeptide variants indicated that the first and third amino acids independently discriminate the second and third purine bases, respectively. Analysis with stop codons containing base analogues indicated that the C2 amino group of purine may be the primary target of discrimination of G from A. These findings show that the discriminator tripeptide of bacterial release factors is functionally equivalent to that of the anticodon of transfer RNA, irrespective of the difference between protein and RNA.

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Figure 1: A seven-domain model of release factors and release-factor hybrids developed for the pep-anticodon assignment.
Figure 2: The assessment of the discriminator tripeptide within domain D.
Figure 3: Polypeptide release activity of the discriminator variants and inosine variants of stop triplets.
Figure 4: The discriminator amino acids of pep-anticodon tripeptides and their target group of purine bases.

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Acknowledgements

We thank C. Yanofsky and J. Atkins for critical reading of the manuscript and valuable comments. This work was supported in part by grants from The Ministry of Education, Science, Sports and Culture, Japan; the Human Frontier Science Program (awarded in 1993 and 1997); and the Basic Research for Innovation Biosciences Program of Bio-oriented Technology Research Advancement Institution (BRAIN).

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  1. Department of Tumor Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 108-8639, Tokyo, Japan

    Koichi Ito, Makiko Uno & Yoshikazu Nakamura

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  1. Koichi Ito
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Correspondence to Yoshikazu Nakamura.

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Ito, K., Uno, M. & Nakamura, Y. A tripeptide ‘anticodon’ deciphers stop codons in messenger RNA. Nature 403, 680–684 (2000). https://doi.org/10.1038/35001115

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