Architecture of the intact yeast and human rixosomes
Abstract
The rixosome is an essential, evolutionarily conserved complex that removes internal transcribed spacer 2 (ITS2) during ribosome biogenesis and silences transcription by degrading nascent RNA at heterochromatin. How these two activities are organized within the intact complex is unknown. We report cryo-electron microscopy structures of intact rixosomes purified endogenously from yeast and human cells, and of native rixosome-bound pre-60S intermediates. The yeast holoenzyme comprises a twofold-symmetric Las1₂–Grc3₂ catalytic core flanked by two Rix1₂–Crb3₂–Ipi1₂ scaffold modules; the human complex adopts the same architecture with a single scaffold. In both species, multivalent interfaces join scaffold to core, and disrupting them impairs ITS2 processing and silencing in vivo. Assembly with the scaffold markedly enhances nuclease and kinase activity relative to the isolated core. On the pre-60S particle, the scaffold anchors adjacent to the ITS2 foot while the catalytic core remains flexibly tethered, and the rixosome stays bound after ITS2 removal, defining the order of ITS2 processing and rixosome release. These results identify the scaffold as the organizational and regulatory hub of the rixosome and provide a framework for interpreting disease-associated rixosome variants.
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