Tim29 is a mitochondrial inner membrane protein that interacts with the protein import complex TIM22. Tim29 was shown to stabilize the TIM22 complex but its biological function remains largely unknown. Until recently it was classified as one of the Domain of Unknown Function (DUF) genes, with a conserved protein domain DUF2366 of unclear function. Since characterizing DUF genes can provide novel biological insight, we used previously established transcriptional profiles of the germline and stem cells of the flatworm Macrostomum lignano to probe conserved DUFs for their potential role in germline biology, stem cell function, and regeneration. Here, we demonstrate that DUF2366/Tim29 is dispensable in normal homeostatic condition in M. lignano but is essential to adapt to a highly proliferative state required for regeneration. Our results show that 'de-DUFing' the function of DUF genes might require special biological conditions, such as regeneration, and establishes M. lignano as an informative platform to study DUF genes.