Eukaryotes inherited the core ribosome biogenesis apparatus from archaea. However, nucleocytoplasmic compartmentalisation and expansion to >200 assembly factors created the challenge of integrating this ancestral machinery into a complex maturation programme. One solution is the formation of transient modules in which newly acquired assembly factors support deeply conserved components. Here, we identify such a module, centred on the ancestral isoaspartylase Fap7, which couples the modification of the ribosomal protein uS11 to its incorporation into pre-ribosomes. Fap7 partners with Krr1 to capture uS11, forming an early checkpoint in which uS11 loading licenses Kri1 engagement and assembly progression. Loss of uS11 modification triggers a late checkpoint, preventing aberrant pre-ribosomes from acquiring translational competence. Integrative structure-function studies reveal how the ancestral isoaspartylase is embedded within a conserved eukaryotic assembly-factor network to safeguard the timing, order, and fidelity of ribosome production.
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