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The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity
Open accessAbstract
During eukaryotic evolution, ribosomes have considerably increased in size, forming a surface-exposed ribosomal RNA (rRNA) shell of unknown function, which may create an interface for yet uncharacterized interacting proteins. To investigate such protein interactions, we establish a ribosome affinity purification method that unexpectedly identifies hundreds of ribosome-associated proteins (RAPs) from categories including metabolism and cell cycle, as well as RNA- and protein-modifying enzymes that functionally diversify mammalian ribosomes. By further characterizing RAPs, we discover the presence of ufmylation, a metazoan-specific post-translational modification (PTM), on ribosomes and define its direct substrates. Moreover, we show that the metabolic enzyme, pyruvate kinase muscle (PKM), interacts with sub-pools of endoplasmic reticulum (ER)-associated ribosomes, exerting a non-canonical function as an RNA-binding protein in the translation of ER-destined mRNAs. Therefore, RAPs interconnect one of life's most ancient molecular machines with diverse cellular processes, providing an additional layer of regulatory potential to protein expression.
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“This is characterized by the striated muscle-specific paralog RPL3L, which is prevalent in resting tissue. Following hypertrophic overload, RPL3L expression plummets and is replaced by the ubiquitous isoform RPL3.”
From Ribosome Biogenesis as a Putative Bottleneck to Skeletal Muscle Hypertrophy: Mechanisms, Human Evidence, and Practical Modulators (2026) · cites this paper as [189]
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“Rather than altering mRNA selectivity for contractile proteins, this paralog switch enables the RPL3-containing ribosomes to physically anchor to mitochondria, maximizing the local ATP supply required to sustain the massive energetic cost of hypertrophy [187,189].”
From Ribosome Biogenesis as a Putative Bottleneck to Skeletal Muscle Hypertrophy: Mechanisms, Human Evidence, and Practical Modulators (2026) · cites this paper as [189]
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Metadata
- Authors
- Simsek, D., Tiu, G. C., Flynn, R. A., Byeon, G. W., Leppek, K., Xu, A. F., Chang, H. Y., & Barna, M.
- Affiliations
- Stanford University (US)
- Stanford Medicine (US)
- Corresponding author
- Barna, Maria
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2017-06
- Volume
- 169
- Issue
- 6
- Pages
- 1051-1065.e18
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5548193
- OpenAlex
- W2621126205
- Cited by
- 439
- References
- 74
- Citations by year
- 2026: 34 · 2025: 62 · 2024: 44 · 2023: 40 · 2022: 29 · 2021: 53 · 2020: 63 · 2019: 48 · 2018: 47 · 2017: 18
- FWCI
- 19.65
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- New York Stem Cell Foundation (NYSCF-R-I36)
- NIH Director’s New Innovator Award (7DP2OD008509, R21HD086730)
- Alfred P. Sloan Research Fellowship (BR2014)
- Mallinckrodt Foundation Award
- Pew Scholars Award (P50-HG007735, R01-HG004361, R01-ES023168)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- ribosome-associated proteins, ribosome heterogeneity, UFMylation, post-translational modification, RNA-binding proteins
- MeSH terms
- Thyroid Hormone-Binding Proteins, Animals, Carrier Proteins, Endoplasmic Reticulum, Membrane Proteins, Protein Processing, Post-Translational, Ribosomal Proteins, Ribosomes, Mass Spectrometry, Thyroid Hormones, Protein Biosynthesis, Protein Interaction Mapping, Ubiquitin-Protein Ligases, Mice, Embryonic Stem Cells
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