Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity.
Class 1 release factor in eukaryotes (eRF1) recognizes stop codons and promotes peptide release from the ribosome. The 'molecular mimicry' hypothesis suggests that domain 1 of eRF1 is analogous to the tRNA anticodon stem-loop. Recent studies strongly support this hypothesis and several models for specific interactions between stop codons and residues in domain 1 have been proposed. In this study we have sequenced and identified novel eRF1 sequences across a wide diversity of eukaryotes and re-evaluated the codon-binding site by bioinformatic analyses of a large eRF1 dataset. Analyses of the eRF1 structure combined with estimates of evolutionary rates at amino acid sites allow us to define the residues that are under structural (i.e. those involved in intramolecular interactions) versus non-structural selective constraints. Furthermore, we have re-assessed convergent substitutions in the ciliate variant code eRF1s using maximum likelihood-based phylogenetic approaches. Our results favor the model proposed by Bertram et al. that stop codons bind to three 'cavities' on the protein surface, although we suggest that the stop codon may bind in the opposite orientation to the original model. We assess the feasibility of this alternative binding orientation with a triplet stop codon and the eRF1 domain 1 structures using molecular modeling techniques.
Inagaki
Yuji
Y
Program in Evolutionary Biology, Canadian Institute for Advanced Research, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada. yinagai@is.dal.ca
Blouin
Christian
C
Doolittle
W Ford
WF
Roger
Andrew J
AJ
D000595:Amino Acid Sequence; D000818:Animals; D000926:Anticodon / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D018388:Codon, Terminator / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017124:Conserved Sequence / Q000235:genetics; D030541:Databases, Genetic; D005057:Eukaryotic Cells / Q000737:chemistry*; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006801:Humans; D008954:Models, Biological; D008958:Models, Molecular; D018716:Molecular Mimicry; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010454:Peptide Termination Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity
D000926:Anticodon; D018388:Codon, Terminator; C489002:ETF1 protein, human; D005656:Fungal Proteins; D010454:Peptide Termination Factors; D010940:Plant Proteins; D015800:Protozoan Proteins