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

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.

Tlr1是一类由约20~30个DNA元件组成的家族成员，该家族元件在纤毛原生动物四膜虫（Tetrahymena）的大核（macronucleus）形成过程中，会发生发育调控性切除。对Tlr1右侧边界内侧的序列进行分析后，发现一段2kb的开放阅读框（open reading frame, ORF），其编码的推定蛋白与反转录转座子整合酶（retrotransposon integrase）具有序列相似性。本研究对5个独立克隆的ORF进行了测序，结果显示这些ORF的序列保守性高达98%，且可无移码地进行序列比对，仅其中一个克隆在第561位密码子处额外携带一段三核苷酸序列。五个克隆间的核苷酸变异在密码子中的位置分布呈现高度非随机性，且其中93%的核苷酸变异所编码的氨基酸仍为相同或性质相似的氨基酸，这表明该ORF在进化过程中受到选择压力以维持其编码蛋白的功能。五个克隆中共存在19处T/C转换突变，且均发生于T/CAA和T/CAG密码子位点，这提示选择作用的发生契合四膜虫基因组的密码子使用语境——该基因组中TAA与TAG编码谷氨酰胺。该ORF与编码反转录转座子整合酶的序列具有相似性，这提示Tlr家族元件或许可编码一种多核苷酸转移酶。本文还讨论了该蛋白在微核（micronucleus）基因组内的元件转座过程中，以及从大核中发育调控性切除这些元件的过程中可能发挥的作用。