Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O-trifallax

TBEls are ''cut-and-paste'' transposable elements found in high copy number in the germline genomes of the ciliates Oxytricha fallax and O. trifallax. TBEl ''family'' sequence (sequence of mixed polymerase chain reaction products generated using primers that match roughly half the TBEls in host whole-cell DNA) was obtained from both host species. Although family sequence autoradiograms represent thousands of different elements, they are as legible as those representing corresponding sequences of a single TBEl, implying that indel polymorphisms are rare within the genes examined. Nucleotide polymorphisms among TBEls (indicated by ambiguities in family sequence) are far more common at third than at first or second positions of codons of genes, implying that selection has conserved the amino acid sequences of these genes in the majority of TBEls. Portions of the transposase gene and another TBEl gene have been sequenced from 10 individual TBEls. None of these portions is interrupted by stop codons or frameshifts, and, for both genes, pairwise comparisons of these sequences show that nonsynonymous differences are significantly less common than synonymous differences, again implicating conservative selection. Phylogenetic analysis shows that multiple divergent lineages of TBEls have evolved under this selection within O. fallax. All these results are unexpected for cut-and-paste transposons in eukaryotic hosts: since transposase encoded by intact elements presumably acts in trans, it can duplicate mutant copies (those that do not encode functional transposase) found in the same genome, and thus no selection is expected to maintain the transposase gene. The selection demonstrated here could act at transposition (if functional TBEls are preferentially transposed) or at the level of the host (if the host's fitness depends on functional TBEl genes). TBEl-encoded proteins might be responsible for the precise excision of TBEls that occurs during development of the host somatic nucleus; selection on hosts for uninterrupted somatic genes, would then translate into selection for TBEl protein-coding competence. We suggest a method for distinguishing between these two classes of explanations by finding and analyzing divergent alleles of ancestral transposable element insertions.