RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages

Teodorus Theo Susanto; Victoria Hung; Andrew G Levine; Craig H Kerr; Yongjin Yoo; Yuxiang Chen; Juan A Oses-Prieto; Lisa Fromm; Kotaro Fujii; Marius Wernig; Alma L Burlingame; Davide Ruggero; Maria Barna

doi:10.1101/2023.12.07.570613

RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages

bioRxiv [Preprint]. 2023 Dec 7:2023.12.07.570613. doi: 10.1101/2023.12.07.570613.

Authors

Teodorus Theo Susanto¹, Victoria Hung¹, Andrew G Levine^{2

3

4}, Craig H Kerr¹, Yongjin Yoo⁵, Yuxiang Chen¹, Juan A Oses-Prieto⁶, Lisa Fromm^{3

4

7}, Kotaro Fujii¹, Marius Wernig^{5

8}, Alma L Burlingame⁶, Davide Ruggero^{3

4

7}, Maria Barna¹

Affiliations

¹ Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
² Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
³ Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
⁴ Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
⁵ Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
⁶ Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA.
⁷ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA.
⁸ Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Abstract

Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translational control. However, a lack of technologies to enrich RAPs across many sample types has prevented systematic analysis of RAP number, dynamics, and functions. Here, we have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development that is linked to the translation of genes with long coding sequences. Finally, we characterized ribosome composition remodeling during immune activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs ranging from those with neuroregulatory functions to those activated by immune stimuli, thereby providing critical insights into how ribosomes are remodeled.

Keywords: embryonic development; macrophages; proteomics; ribosome; ribosome heterogeneity; ribosome-associated proteins; translational control.

Publication types

Preprint

Abstract

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