Directionally Evolving Genetic Code: The UGA Codon from Stop to Tryptophan in Mitochondria Yuji Inagaki, 1, * Megumi Ehara, 2 Kazuo I. Watanabe, 2 Yasuko Hayashi-Ishimaru, 1, ** Takeshi Ohama 1 1 JT Biohistory Research Hall, 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan 2 Department of Biology, Faculty of Science, Osaka University, Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan Received: 26 January 1998 / Accepted: 24 April 1998 Abstract. For the comprehensive analyses of deviant codesin protistan mitochondria (mt), we sequenced about a 1.1-kb region of a mitochondrial (mt) gene, the cytochrome c oxidase subunit I (coxI) in two chlorarach- niophytes, the filose amoeba Euglypha rotunda, the cryptomonad Cryptomonas ovata, the prymnesiophyte (haptophyte) Diacronema vlkianum (Pavlovales), and the diatom Melosira ambigua. As a result of this analysis, we noticed that the UGA codon is assigned to tryptophan (Trp) instead of being a signal for translational termina- tion in two chlorarachniophytes and in E. rotunda. The same type of deviantcode was reported previously in animals, fungi, ciliates, kinetoplastids, Chondrus crispus (a red alga), Acanthamoeba castellanii (an amoeboid protozoon), and three of the four prymnesiophyte orders with the exception of the Pavlovales. A phylogenetic analysis based on the COXI sequences of 56 eukaryotes indicated that the organisms bearing the modified code, UGA for Trp, are not monophyletic. Based on these stud- ies,we propose that the ancestral mitochondrion was bearing the universal genetic code and subsequently re- assigned the codon to Trp independently, at least in the lineage of ciliates, kinetoplastids, rhodophytes, prymne- siophytes, and fungi. We also discuss how this codon was directionally captured by Trp tRNA. Key words: COXI phylogenetic tree — UGA codon — Deviant genetic code — Directional codon reassign- ment Introduction A wide variety of metazoan mitochondrial (mt) genomes has been completely sequenced and many types of devi- ant genetic codes have been reported (for a review, see Wolstenholme 1992). Of especial interest is the codon UGA, which usually serves as a translational termination signal(stop),butwhich is used for Trp in the mt ge- nomes of animals, fungi, ciliates, and kinetoplastids (re- viewed by Osawa et al. 1992). Recent studies on protis- tan mitochondria (mt) revealed the same kind of reassignment for the UGA codon in Acanthamoeba (Ac.) castellanii (an amoeboid protozoon) (Burger et al. 1995), Chondrus (Cho.) crispus (Rhodophyta/red alga) (Boyen et al.1994), and prymnesiophytes (haptophytes) (Haya- shi-Ishimaru et al.1997).It has been reported that the codon is utilized as a stop codon in land plants (e.g., Oda et al.1992), a phaeophyte (brown alga) (Fontaine et al. 1995),a rhodophyte (Viehmann et al. 1996),an oomy- cete (see the public database site, http://megasun.bch. umontreal.ca/People/lang/FMGP/), and a freshwater het- erotrophic flagellate, Reclinomonas americana (Lang et al.1997).Curiously, the UGA codon was not detected throughout the mt genomes of apicomplexans (Feagin et al.1992; Kairo et al. 1994),chlorophytes (green algae) (Boer et al. 1985; Feagin et al. 1992; Wolff et al. 1994), * Present address: Department of Biochemistry, Dalhause University, Halifax NS, B3H 4H7, Canada ** Present address: Department of Cell Biology, National Institute for Basic Biology, Okazaki, Aichi 444-0867, Japan Correspondence to: TakeshiOhama; e-mail: Takeshi.Ohama@ims. brh.co.jp J Mol Evol (1998) 47:378–384 © Springer-Verlag New York Inc. 1998