title: A single amino acid substitution alters omnipotent eRF1 of Dileptus to euplotes-type dualpotent eRF1: standard codon usage may be advantageous in raptorial ciliates.
abstract: Most ciliates use a deviant genetic code. Eukaryotic release factor (eRF1) appears to play an important role in the process of reassignment of stop codons. Although the precise site on eRF1 for recognition of stop codons remains obscure, studies have suggested that the tip region NIKS and its adjacent YxCxxxF motifs in domain 1 are important for stop codon recognition. Litostomatea is a class of ciliate that appears to use the standard genetic code. We used Dileptus (Litostomatea) eRF1 in this study to identify key residues located in or near the YxCxxxF motif. We predicted sites involving stop codon recognition by computational calculation of RNA-protein interaction propensity. We introduced mutations at the predicted sites of Dileptus eRF1 and examined the activity of the mutated Dileptus eRF1 using in vivo assay systems. The results show that the single mutation R128I (Dileptus eRF1 numbering) in the YxCxxxF motif converted the omnipotent recognition of Dileptus eRF1 to Euplotes-type dualpotent eRF1. Our results indicate that R128 is one of the key residues preserving the ability to recognize all three stop codons, especially UGA, in Dileptus. We discuss a possible advantage that ciliates from the Litostomatea class may gain from using the standard genetic code.
authors.affiliation: Graduate School of Natural Science and Ecological Awareness, Nara Women's University, Kitauoyanishi-machi, Nara 630-8506, Japan.
authors.forename: Ying
authors.initials: Y
authors.lastname: Li
authors.forename: Oanh Thi Phuong
authors.initials: OT
authors.lastname: Kim
authors.forename: Koichi
authors.initials: K
authors.lastname: Ito
authors.forename: Kazuki
authors.initials: K
authors.lastname: Saito
authors.forename: Toshinobu
authors.initials: T
authors.lastname: Suzaki
authors.forename: Terue
authors.initials: T
authors.lastname: Harumoto
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D016798:Ciliophora / Q000235:genetics*; D003062:Codon; D018388:Codon, Terminator; D016812:Euplotes / Q000235:genetics*; D005815:Genetic Code; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010454:Peptide Termination Factors / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D003062:Codon; D018388:Codon, Terminator; D010454:Peptide Termination Factors; D015800:Protozoan Proteins