A ubiquitin network safeguards cell identity by continuously degrading a stem cell-related translational machinery

How cell identity is maintained is a fundamental question, and loss of cell identity is a hallmark of aging associated with multiple age-related diseases. In the adult Drosophila midgut, we identified a posttranscriptional regulatory layer that supervises enterocyte (EC) identity and fails upon aging. Combining single-cell RNA-seq with lineage tracing in aging ECs and classical genetics, we found that aging ECs express genes that unlock the differentiated state. Upon aging, the protein Rogue (CG13928), a translational repressor, along with its partner, Orb2, orchestrates reactivation of a stem cell-related translational repression machinery involving P-body-associated RNA-binding proteins canceling the differentiated state. In young ECs, this machinery is continuously suppressed by the deubiquitinase nonstop (dUSP22) and the ubiquitin E2 dUbcH8/Kdo and E3 CTLH complex, mediating the degradation of the stem cell-related RNA binding proteins safeguarding EC identity. Upon aging, levels of dUSP22 decline and Rogue is ectopically expressed. RNA immunoprecipitation followed by nanopore-based direct RNA sequencing identified that Rogue binds to the RNA transcripts of dUbcH8/Kdo and eEF2, shortening their poly(A) tail and suppressing Kdo protein, resulting in accelerated proteasomal clearance of the CTLH complex. Subsequently, the stem cell-related P-bodies are reactivated, leading to decline in EC gene signatures and unlocking EC identity.