title: Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions.
abstract: The genetic code of nuclear genes in some ciliates was found to differ from that of other organisms in the assignment of UGA, UAG, and UAA codons, which are normally assigned as stop codons. In some ciliate species, the universal stop codons UAA and UAG instead encode glutamine. In some other ciliates, the universal stop codon UGA appears to be translated as cysteine or tryptophan. Eukaryotic release factor 1 (eRF1) is a key protein in stop codon recognition, thus, the protein is believed to play an important role in the stop codon reassignment in ciliates. We have cloned, sequenced, and analyzed the cDNA of eRF1 from four ciliate species of three different classes: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Phylogenetic analysis of these eRF1s supports the hypothesis that the genetic code in ciliates has deviated independently several times from the universal genetic code, and that different ciliate eRF1s may have undergone different processes to change the codon specificity. Using computational methods, we have also suggested areas on the surface of eRF1s that are important for stop codon recognition in ciliate eRF1s.
authors.affiliation: The Division of Human Environmental Sciences, Graduate School of Human Culture, Nara Women's University, Kitauoyanishi-machi, Nara 630-8506, Japan.
authors.forename: Oanh Thi Phuong
authors.initials: OT
authors.lastname: Kim
authors.forename: Kei
authors.initials: K
authors.lastname: Yura
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Go
authors.forename: Terue
authors.initials: T
authors.lastname: Harumoto
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016798:Ciliophora / Q000235:genetics*; D003001:Cloning, Molecular; D018388:Codon, Terminator; D017931:DNA Primers; D018076:DNA, Complementary; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010454:Peptide Termination Factors / Q000737:chemistry / Q000235:genetics*; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid
chemical_list: D018388:Codon, Terminator; D017931:DNA Primers; D018076:DNA, Complementary; D010454:Peptide Termination Factors