A developmental condensin I complex assists the Paramecium PiggyMac domesticated transposase during programmed DNA elimination

Prokaryotes and eukaryotes have evolved various strategies to cope with invading mobile genetic elements, including programmed DNA elimination (PDE) from the genome during differentiation. In the ciliate Paramecium, elimination of transposable elements and their relics requires the PiggyMac (Pgm) endonuclease and its five partners (PgmLs), yet how this machinery is targeted to its cleavage sites remains unclear. Here, we identified condensin I subunits in the proximity proteomes of Pgm and PgmL4. We show that a development-specific condensin I complex localizes to the somatic nuclei during PDE. Depletion of its development-specific subunits inhibits elimination, phenocopying a Pgm depletion. Developmental condensin I is required for the correct nuclear localization of Pgm and some of the PgmLs. Moreover, Pgm and these PgmLs co-immunoprecipitate with condensin I. Our findings reveal both functional and physical interactions between the elimination machinery and a specialized condensin complex, which is critical for PDE in the non-dividing somatic nucleus.