Domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium

Transposable elements have repeatedly been the source of novel cellular functions during evolution, as illustrated in ciliates, which extensively rearrange their genome following sexual reproduction, during the development of their somatic macronucleus. In Paramecium, rearrangements include the precise excision of ~45,000 Internal Eliminated Sequences (IESs), which starts with programmed DNA double-strand cleavage catalyzed by a domesticated PiggyBac transposase, PiggyMac.We report here the identification of nine distant PiggyMac-like proteins (PgmLs), using a hidden Markov model-based search of the P. tetraurelia protein database. PGML genes form five families (PGML1, PGML2, PGML3a,b&c, PGML4a&b and PGML5a&b), all specifically expressed during macronuclear development. PgmLs lack a canonical DDD catalytic triad, but each family is essential to recover a viable progeny. Each PgmL directly interacts with Pgm in heterologous cell extracts and depletion of each family compromises the correct nuclear localization of Pgm, suggesting that Pgm and PgmLs work as a complex in vivo. Genome-wide analyses revealed that IES excision is severely impaired in all PGML knockdowns. Furthermore, PgmL1- or PgmL3-depleted cells accumulate errors in targeting IES boundaries, suggesting that PgmLs contribute to IES end recognition. DNA rearrangements in Paramecium constitute a rare example of a biological process jointly managed by six distinct domesticated transposases.