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Nucleic Acids Research, 2000, Vol. 28, No. 21 4105-4112
© 2000 Oxford University Press

A family of developmentally excised DNA elements in Tetrahymena is under selective pressure to maintain an open reading frame encoding an integrase-like protein

Jill A. Gershan and Kathleen M. Karrer*

Department of Biology, Marquette University, Milwaukee, WI 53201-1881, USA

Tlr1 is a member of a family of ~20–30 DNA elements that undergo developmentally regulated excision during formation of the macronucleus in the ciliated protozoan Tetrahymena. Analysis of sequence internal to the right boundary of Tlr1 revealed the presence of a 2 kb open reading frame (ORF) encoding a deduced protein with similarity to retrotransposon integrases. The ORFs of five unique clones were sequenced. The ORFs have 98% sequence conservation and align without frameshifts, although one has an additional trinucleotide at codon 561. Nucleotide changes among the five clones are highly non-random with respect to the position in the codon and 93% of the nucleotide changes among the five clones encode identical or similar amino acids, suggesting that the ORF has evolved under selective pressure to preserve a functional protein. Nineteen T/C transitions in T/CAA and T/CAG codons suggest selection has occurred in the context of the Tetrahymena genome, where TAA and TAG encode Gln. Similarities between the ORF and those encoding retrotransposon integrases suggest that the Tlr family of elements may encode a polynucleotide transferase. Possible roles for the protein in transposition of the elements within the micronuclear genome and/or their developmentally regulated excision from the macronucleus are discussed.

* To whom correspondence should be addressed. Tel: +1 414 288 1474; Fax: +1 414 288 7357; Email: kathleen.karrer@marquette.edu Present address: Jill A. Gershan, Platelet Immunology, Blood Research Institute of Southeastern Wisconsin, 8727 Watertown Plank Road, Wauwatosa, WI 53226, USA


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