Newly sequenced eRF1s from ciliates: The diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions

Oanh Thi Phuong Kim, Kei Yura, Nobuhiro Go, Terue Harumoto

Research output: Contribution to journalArticle

26 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)277-286
Number of pages10
JournalGene
Volume346
DOIs
Publication statusPublished - 2005 Feb 14
Externally publishedYes

Keywords

  • Codon reassignment
  • Computational biology
  • Eukaryotic release factor
  • Phylogenetic tree
  • RNA-binding site
  • Stop codon recognition

ASJC Scopus subject areas

  • Genetics

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