Internal eliminated sequences interrupting the Oxytricha 81 locus: allelic divergence, conservation, conversions, and possible transposon origins

Internal eliminated sequences (IESs) often interrupt ciliate genes in thesilent germline nucleus but are exactly excised and eliminated from thedeveloping somatic nucleus from which genes are then expressed. Some longIESs are transposons, supporting the hypothesis that short IESs are ancienttransposon relics. In light of that hypothesis and to explore theevolutionary history of a collection of IESs, we have compared variousalleles of a particular locus (the 81 locus) of the ciliated protozoaOxytricha trifallax and O. fallax. Three short IESs that interrupt twogenes of the locus are found in alleles from both species, and thus must berelatively ancient, consistent with the hypothesis that short IESs aretransposon relics. In contrast, TBE1 transposon interruptions of the locusare allele-specific and probably the results of recent transpositions.These IESs (and the TBE1s) are precisely excised from the DNA of thedeveloping somatic macronucleus. Each IES interrupts a highly conservedsequence. A few nucleotides at the ends of each IES are also conserved,suggesting that they interact critically with IES excision machinery.However, most IES nucleotide positions have evolved at high rates, showinglittle or no selective constraint for function. Nonetheless, the length ofeach IES has been maintained (+/- 3 bp). While one IES is approximately 33bp long, three other IESs have very similar sizes, approximately 70 bplong. Two IESs are surrounded by direct repeats of the sequence TTCTT. Noother sequence similarities were found between any of the four IESs.However, the ends of one IES do match the inverted terminal repeatconsensus sequence of the "TA" IESs of Paramecium. Three O. trifallaxalleles appear to have been recipients in recent conversion events thatcould have been provoked by double-strand breaks associated with IES endssubsequent to IES transposition. Our findings support the hypothesis thatshort IESs evolved from ancient transposons that have lost most of theirsequences, except those necessary for precise excision during macronucleardevelopment.