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bioRxiv · 10.1101/2025.09.18.677003

Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1

Favre, S.·Pillet, B.·Burchert, F.·Siva Sankar, D.·Mendez-Godoy, A.·Dengjel, J.·Bange, G.·Kressler, D.
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Abstract

In eukaryotes, most newly synthesized ribosomal proteins (r-proteins) need to rapidly and safely get into the nucleus to reach their assembly site on pre-ribosomal particles. However, only for few r-proteins tailored support mechanisms involving so-called dedicated chaperones could so far be revealed. Here, with the primary aim of identifying novel dedicated chaperones, we performed TurboID-based proximity labelling with all 46 large subunit r-proteins of Saccharomyces cerevisiae, which unveiled the fungi-specific Acl1 and the conserved Bcl1 as candidate dedicated chaperones of Rpl1. We show that the functionally cooperating Acl1 and Bcl1 both directly interact with Rpl1, form a trimeric Acl1-Rpl1-Bcl1 complex, and enable the nuclear import of Rpl1. Moreover, our crystal structure of the minimal Acl1-Rpl1 complex reveals how Acl1s ankyrin repeat domain shields a positively charged rRNA-binding surface of Rpl1. Our proximity labelling approach also permitted to establish novel interactions between four r-proteins and distinct importins and to illuminate r-protein neighbourhoods on successive pre-60S particles. Additionally, reciprocal proximity labelling with the known dedicated chaperones indicates that almost all appear to be transiently associated with pre-ribosomal particles. Our study provides for the first time comprehensive insight into the physical proximities of large subunit r-proteins along their entire life cycle. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/677003v2_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1167c6corg.highwire.dtl.DTLVardef@1429c23org.highwire.dtl.DTLVardef@18f7ecorg.highwire.dtl.DTLVardef@13ccdfb_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT C_FIG

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Favre, S., Pillet, B., Burchert, F., Siva Sankar, D., Mendez-Godoy, A., Dengjel, J., Bange, G., Kressler, D.. 2025-09-18. Exploration of the proxiOME of large subunit ribosomal proteins reveals Acl1 and Bcl1 as cooperating dedicated chaperones of Rpl1. https://doi.org/10.1101/2025.09.18.677003

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