Identification of an open reading frame with similarity to integrase in a Tetrahymena thermophila micronucleus-limited element

Jill Alane Genshan, Marquette University


Protozoa belonging to the phylum Ciliophora are model systems for the study of DNA rearrangement because large numbers of deletion events result in sequence reorganization during the transition from a germline micronuclear to a somatic macronuclear genome. One element that is excised during development of the macronucleus in Tetrahymena thermophila is T etrahymena HASH(0xc00ee0c)l ong r epeat 1 (Tlr1). This element is greater than 13 kb and structurally resembles class II transposable elements in that there is an 825 bp inverted repeat near the element boundaries. A family of approximately 30 elements contain Tlr1 inverted repeat sequences (Wells et al ., 1994). There is conservation of the innermost 276 bp of this inverted repeat in 2 different clones isolated in this study. Analysis of sequence internal to the right Tlr1 boundary revealed the presence of a 2 kb open reading frame (ORF) that has similarity to polynucleotidyl transferases encoded by retroviruses and retrotransposons (class I elements). Within the Tetrahymena thermophila micronuclear genome, there is a family of 20-25 elements that contain this ORF. The ORF was completely sequenced in 5 unique clones including Tlr1. These ORFs align without frameshifts, have 98% nucleotide conservation, and 92% of the nucleotide changes encode identical or similar amino acids, suggesting that this ORF has evolved under selective pressure to preserve a functional protein. A transcript was not detected by northern analysis. This approach may not be sensitive enough to detect a transcript if it has low abundance or a short half-life. Similarities between retrotransposon integrase and this ORF suggests that Tlr elements may encode a protein that catalyzes their excision.

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Recommended Citation

Genshan, Jill Alane, "Identification of an open reading frame with similarity to integrase in a Tetrahymena thermophila micronucleus-limited element" (2000). Dissertations (1962 - 2010) Access via Proquest Digital Dissertations. AAI9977731.