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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RPL3L is prevalent in resting skeletal muscle tissue; following hypertrophic overload, RPL3L expression plummets and is replaced by the ubiquitous isoform RPL3.
“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]
The supplied Results passages discuss PKM isoforms and ribosome interactions, not RPL3L in skeletal muscle. Searches for RPL3L and hypertrophic overload found no passage in our copy addressing resting-muscle prevalence or replacement by RPL3. (LLM, conf=0.75)
Experimental — accuracy not yet measuredThe RPL3L-to-RPL3 paralog switch enables RPL3-containing ribosomes to physically anchor to mitochondria, maximizing local ATP supply required for hypertrophy, rather than altering mRNA selectivity for contractile proteins.
“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]
The Introduction and Results describe ribosome-associated proteins in mouse embryonic stem cells, particularly PKM at ER-associated ribosomes, not an RPL3L-to-RPL3 switch. Searches for RPL3L and mitochondrial anchoring found no passage addressing the proposed switch, local ATP supply during hypertrophy, or contractile-protein mRNA selectivity. The cited paper therefore does not verify this claim in our copy. (LLM, conf=0.76)
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- 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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