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Decoding the decoding region: analysis of eukaryotic release factor (eRF1) stop codon-binding residues.

Han Liang·Jonathan Y Wong·Qing Bao·Andre R O Cavalcanti·Laura F Landweber
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Abstract

Peptide synthesis in eukaryotes terminates when eukaryotic release factor 1 (eRF1) binds to an mRNA stop codon and occupies the ribosomal A site. Domain 1 of the eRF1 protein has been implicated in stop codon recognition in a number of experimental studies. In order to further pinpoint the residues of this protein involved in stop codon recognition, we sequenced and compared eRF1 genes from a variety of ciliated protozoan species. We then performed a series of computational analyses to evaluate the conservation, accessibility, and structural environment of each amino acid located in domain 1. With this new dataset and methodology, we were able to identify eight specific amino acid sites important for stop codon recognition and also to propose a set of cooperative paired substitutions that may underlie stop codon reassignment. Our results are more consistent with current experimental data than previously described models.

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Amino Acid SequenceAnimalsBase SequenceCiliophoraCluster AnalysisCodon, TerminatorComputational BiologyConserved SequenceDNA PrimersModels, MolecularMolecular Sequence DataPeptide Termination FactorsProtein Structure, TertiarySequence AlignmentSequence Analysis, DNASpecies SpecificityComparative StudyJournal ArticleResearch Support, N.I.H., ExtramuralResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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Han Liang, Jonathan Y Wong, Qing Bao, Andre R O Cavalcanti, Laura F Landweber. 2005. Decoding the decoding region: analysis of eukaryotic release factor (eRF1) stop codon-binding residues.. https://doi.org/10.1007/s00239-004-0211-8

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