A comprehensive landscape of 60S ribosome biogenesis factors

Abstract

Eukaryotic ribosome biogenesis is facilitated and regulated by numerous ribosome biogenesis factors (RBFs). High-resolution cryo-EM maps have defined the molecular interactions of RBFs during maturation, but many transient and dynamic interactions, particularly during early assembly, remain uncharacterized. Using quantitative proteomics and crosslinking coupled to mass spectrometry (XL-MS) data from a extensive set of pre-ribosomal particles, we derived a comprehensive and time-resolved interaction map of RBF engagement during 60S maturation. A novel filter that efficiently eliminates false positive interactions and integration of our MS data with known structural information allowed us to localize 22 unmapped RBFs to specific biogenesis intermediates and to identify 9 proteins that represent potentially new RBFs. Our analysis reveals an extensive interaction network for the casein kinase complex in 60S maturation and elucidates the timing and molecular function of 60S engagement by DEAD-box ATPases. Our data provide a powerful resource for future studies of 60S ribosome biogenesis.