Class I release factors in ciliates with variant genetic codes

In eukaryotes with the universal genetic code a single class I release fact or (eRF1) most probably recognizes all stop codons (UAA, UAG and UGA) and i s essential for termination of nascent peptide synthesis. It is well establ ished that stop codons have been reassigned to amino acid codons at least t hree times among ciliates. The codon specificities of ciliate eRF1s must ha ve been modified to accommodate the variant codes, In this study we have am plified, cloned and sequenced eRF1 genes of two hypo-trichous ciliates, Oxy tricha trifallax (UAA and UAG for Gin) and Euplotes aediculatus (UGA for Cy s), We also sequenced/identified three protist and two archaeal class I RF genes to enlarge the database of eRF1/aRF1s with the universal code, Extens ive comparisons between universal code eRF1s and those of Oxytricha, Euplot es and Tetrahymena, which represent three lineages that acquired variant co des independently, provide important clues to identify stop codon-binding r egions in eRF1, Domain 1 in the five ciliate eRF1s, particulary the TASNIKS heptapeptide and its adjacent region, differs significantly from domain 1 in universal code eRF1s, This observation suggests that domain 1 contains t he codon recognition site, but that the mechanism of eRF1 codon recognition may be more complex than proposed by Nakamura at al. or Knight and Landweb er.