title: A family of developmentally excised DNA elements in Tetrahymena is under selective pressure to maintain an open reading frame encoding an integrase-like protein.
abstract: Tlr1 is a member of a family of approximately 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.
authors.affiliation: Department of Biology, Marquette University, Milwaukee, WI 53201-1881, USA.
authors.forename: J A
authors.initials: JA
authors.lastname: Gershan
authors.forename: K M
authors.initials: KM
authors.lastname: Karrer
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D015139:Blotting, Southern; D003001:Cloning, Molecular; D003062:Codon / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics / Q000502:physiology; D016054:DNA, Protozoan / Q000235:genetics* / Q000378:metabolism; D017353:Gene Deletion; D018628:Gene Dosage; D018507:Gene Expression Regulation, Developmental; D005815:Genetic Code / Q000235:genetics; D018503:Genome, Protozoan; D019426:Integrases / Q000235:genetics* / Q000378:metabolism; D048631:Micronucleus, Germline / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics; D015183:Restriction Mapping; D012641:Selection, Genetic; D016415:Sequence Alignment; D013768:Tetrahymena / Q000166:cytology / Q000201:enzymology / Q000235:genetics*; D019895:Transposases / Q000235:genetics / Q000378:metabolism
chemical_list: D003062:Codon; D016054:DNA, Protozoan; D019426:Integrases; D019895:Transposases