@article{2cd22bb0232f4776b3f46a2ac09fd748,
title = "A comprehensive landscape of 60S ribosome biogenesis factors",
abstract = "Eukaryotic ribosome biogenesis is facilitated and regulated by numerous ribosome biogenesis factors (RBFs). High-resolution cryoelectron microscopy (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 an extensive set of pre-ribosomal particles, we derive a comprehensive and time-resolved interaction map of RBF engagement during 60S maturation. We localize 22 previously unmapped RBFs to specific biogenesis intermediates and validate our results by mapping the catalytic activity of the methyltransferases Bmt2 and Rcm1 to their predicted nucleolar 60S intermediates. Our analysis reveals the interaction sites for the RBFs Noc2 and Ecm1 and elucidates the interaction map and timing of 60S engagement by the DEAD-box ATPases Dbp9 and Dbp10. Our data provide a powerful resource for future studies of 60S ribosome biogenesis.",
keywords = "AFs, DEAD-box ATPase, FDR, RBFs, XL-MS, crosslinking coupled to mass spectrometry, false discovery rate, ribosome assembly factors, ribosome biogenesis, ribosome biogenesis factors",
author = "Carolin Sailer and Jasmin Jansen and Kamil Sekulski and Cruz, {Victor E.} and Erzberger, {Jan P.} and Florian Stengel",
note = "Funding Information: We thank Christoph Hanselka for help with reviewing the crosslink database; Antonia Vogel, Niginia Borlinghaus, and Philipp Schmid for help with the affinity enrichments; Patrick Arner, Cornelia Hauser, Melanie Henkel, and Luisa Huber for help with the primer extension assay; Kai-Michael Kammer and Robin Marzucca for help with python/pandas scripts for FDR calculation and data analysis; and Christine Weirich for help with live imaging and critical reading of the manuscript. We thank the lab of Elke Deuerling for S. cerevisiae strains Arx1-TAP, Lsg1-TAP, and wild-type BY4741. This work was supported by the German Research Foundation Collaborative Research Centre 969 (Project A06). J.P.E. was supported by the Cancer Prevention and Research Institute of Texas ( RR150074 ), the Welch Foundation ( I-1897 ), the UTSW Endowed Scholars Fund , and the National Institutes of Health ( GM135617-01 ). F.S. is grateful for funding from the Emmy Noether Programme of the German Research Foundation ( STE 2517/1-1 ). Funding Information: We thank Christoph Hanselka for help with reviewing the crosslink database; Antonia Vogel, Niginia Borlinghaus, and Philipp Schmid for help with the affinity enrichments; Patrick Arner, Cornelia Hauser, Melanie Henkel, and Luisa Huber for help with the primer extension assay; Kai-Michael Kammer and Robin Marzucca for help with python/pandas scripts for FDR calculation and data analysis; and Christine Weirich for help with live imaging and critical reading of the manuscript. We thank the lab of Elke Deuerling for S. cerevisiae strains Arx1-TAP, Lsg1-TAP, and wild-type BY4741. This work was supported by the German Research Foundation Collaborative Research Centre 969 (Project A06). J.P.E. was supported by the Cancer Prevention and Research Institute of Texas (RR150074), the Welch Foundation (I-1897), the UTSW Endowed Scholars Fund, and the National Institutes of Health (GM135617-01). F.S. is grateful for funding from the Emmy Noether Programme of the German Research Foundation (STE 2517/1-1). C.S. J.J. J.P.E. and F.S. conceived the study and experimental approach. C.S. expressed, purified, and crosslinked pre-ribosomal particles, with help from J.J. C.S. implemented and applied the mi-filter. J.J. K.S. and V.E.C. validated the timeline. C.S. J.J. J.P.E. and F.S. analyzed the data. C.S. J.P.E. and F.S. wrote the paper, with input from all of the authors. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2022 The Author(s)",
year = "2022",
month = feb,
day = "8",
doi = "10.1016/j.celrep.2022.110353",
language = "English (US)",
volume = "38",
journal = "Cell Reports",
issn = "2211-1247",
publisher = "Cell Press",
number = "6",
}