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Title:
Proteomics-based characterization of ribosome heterogeneity in adult mouse organs | Cellular and Molecular Life Sciences
Description:
The translation process, leading to protein synthesis from mRNA, has been long thought to be invariable in all cellular organisms. Increasing evidence shows that it is finely regulated by variable features of the translation machinery. Notably, ribosomes, the functional units of protein synthesis, are suggested to display variations in their composition, depending on the developmental stage, cell type or physio-pathological context, thus hinting a new level of actionable regulation of gene expression. Yet, a comprehensive map of the heterogeneity of ribosome composition in ribosomal proteins (RPs) in different organs and tissues is not available. In this work, we explored tissue-specific ribosome heterogeneity using mass spectrometry-based quantitative proteomic characterization of ribosomal fractions purified from 14 adult mouse organs and tissues. We performed crossed clustering and statistical analyses of RP composition to highlight stable, variable and tissue-specific RPs across organs and tissues. Focusing on specific RPs, we validated their varying abundances using a targeted proteomic approach and western blot analyses, providing further insights into the tissue-specific ribosome RP signature. Finally, we investigated the origin of RP variations in ribosome fraction of the different tissues, by comparing RP relative amounts in our ribosomal proteomic dataset with their corresponding transcript abundances in three independent transcriptomic datasets. Interestingly, we found that, in some tissues, the RP abundance in purified ribosomes does not always correlate with the corresponding RP transcript level, arguing for a translational regulation of RP expression, and/or a regulated incorporation of RPs into ribosomes. Altogether, our data support the notion of a tissue-specific RP signature of ribosomes, which opens avenues to study how specific ribosomal composition provides an additional level of regulation to control gene expression in different tissues and organs. Graphical abstract
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Keywords {🔍}
rps, ribosomal, pubmed, tissues, article, ribosome, google, scholar, protein, cas, fig, expression, fractions, rpl, ribosomes, central, proteins, specific, rpll, mouse, organs, analysis, composition, cell, tissue, fraction, peptides, relative, abundance, translation, test, mrna, regulation, detected, level, data, adult, testis, variable, heterogeneity, found, rplp, human, replicates, qvalue, normalized, proteomic, transcript, transcriptomic, analyzed,
Topics {✒️}
/science/article/pii/s1097276520307309 akirtava /profiproteomics/mzdb/tree/mzdb-processing_0 mono-charged y-type ions /trends/biochemical-sciences/abstract/s0968-0004 mass-spectrometry-based draft ms-based quantitative proteomics article download pdf discovery lc–ms/ms data reprosil-pur 120 c18-aq unidirectional flow “dna-mrna-protein” x-linked dyskeratosis congenita higher-energy collisional dissociation targeted proteomics-based quantification central nervous systems multiple unpaired t-tests bis–tris polyacrylamide gel cell type-specific control ms-based proteomic analysis based quantitative proteomics 60 min multi-linear gradient ultrapure ice-cold water tandem mass spectrometry user-friendly software suite nano-lc method consisted log10-transformed protein abundances quantitative discovery proteomics log-transformed protein abundance log-transformed relative abundances stroke-induced peripheral immunosuppression log-transformed relative expression rrna 2′-o-methylation plasticity identifying intra-cellular populations proteomics-based characterization intensity-based absolute quantification high energy-consuming process cell type-specific versus show organ-specific compensations c57bl/6j adult mice specific hox-coding mrnas mix male/female tissues heavy isotope-labeled peptides physio-pathological conditions revealed tissue-specific rp signature heavy isotope-labelled peptides full size image ires-mediated translation run limma t-test organ-specific rp signature malignant human cells home-made mus database
Questions {❓}
- Fortelny N, Overall CM, Pavlidis P, Freue GVC (2017) Can we predict protein from mRNA levels?
- Then the next key question is: what mechanisms are at play to control inter-organ variation in RP ribosomal composition?
- Warner JR, McIntosh KB (2009) How common are extra-ribosomal functions of ribosomal proteins?
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headline:Proteomics-based characterization of ribosome heterogeneity in adult mouse organs
description:The translation process, leading to protein synthesis from mRNA, has been long thought to be invariable in all cellular organisms. Increasing evidence shows that it is finely regulated by variable features of the translation machinery. Notably, ribosomes, the functional units of protein synthesis, are suggested to display variations in their composition, depending on the developmental stage, cell type or physio-pathological context, thus hinting a new level of actionable regulation of gene expression. Yet, a comprehensive map of the heterogeneity of ribosome composition in ribosomal proteins (RPs) in different organs and tissues is not available. In this work, we explored tissue-specific ribosome heterogeneity using mass spectrometry-based quantitative proteomic characterization of ribosomal fractions purified from 14 adult mouse organs and tissues. We performed crossed clustering and statistical analyses of RP composition to highlight stable, variable and tissue-specific RPs across organs and tissues. Focusing on specific RPs, we validated their varying abundances using a targeted proteomic approach and western blot analyses, providing further insights into the tissue-specific ribosome RP signature. Finally, we investigated the origin of RP variations in ribosome fraction of the different tissues, by comparing RP relative amounts in our ribosomal proteomic dataset with their corresponding transcript abundances in three independent transcriptomic datasets. Interestingly, we found that, in some tissues, the RP abundance in purified ribosomes does not always correlate with the corresponding RP transcript level, arguing for a translational regulation of RP expression, and/or a regulated incorporation of RPs into ribosomes. Altogether, our data support the notion of a tissue-specific RP signature of ribosomes, which opens avenues to study how specific ribosomal composition provides an additional level of regulation to control gene expression in different tissues and organs.
datePublished:2025-04-24T00:00:00Z
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keywords:
Ribosome
Ribosome heterogeneity
Mass spectrometry
Quantitative proteomic
Translational control
Transcriptomic analysis
Cell Biology
Biomedicine
general
Life Sciences
Biochemistry
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headline:Proteomics-based characterization of ribosome heterogeneity in adult mouse organs
description:The translation process, leading to protein synthesis from mRNA, has been long thought to be invariable in all cellular organisms. Increasing evidence shows that it is finely regulated by variable features of the translation machinery. Notably, ribosomes, the functional units of protein synthesis, are suggested to display variations in their composition, depending on the developmental stage, cell type or physio-pathological context, thus hinting a new level of actionable regulation of gene expression. Yet, a comprehensive map of the heterogeneity of ribosome composition in ribosomal proteins (RPs) in different organs and tissues is not available. In this work, we explored tissue-specific ribosome heterogeneity using mass spectrometry-based quantitative proteomic characterization of ribosomal fractions purified from 14 adult mouse organs and tissues. We performed crossed clustering and statistical analyses of RP composition to highlight stable, variable and tissue-specific RPs across organs and tissues. Focusing on specific RPs, we validated their varying abundances using a targeted proteomic approach and western blot analyses, providing further insights into the tissue-specific ribosome RP signature. Finally, we investigated the origin of RP variations in ribosome fraction of the different tissues, by comparing RP relative amounts in our ribosomal proteomic dataset with their corresponding transcript abundances in three independent transcriptomic datasets. Interestingly, we found that, in some tissues, the RP abundance in purified ribosomes does not always correlate with the corresponding RP transcript level, arguing for a translational regulation of RP expression, and/or a regulated incorporation of RPs into ribosomes. Altogether, our data support the notion of a tissue-specific RP signature of ribosomes, which opens avenues to study how specific ribosomal composition provides an additional level of regulation to control gene expression in different tissues and organs.
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Ribosome
Ribosome heterogeneity
Mass spectrometry
Quantitative proteomic
Translational control
Transcriptomic analysis
Cell Biology
Biomedicine
general
Life Sciences
Biochemistry
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name:Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, Grenoble, France
name:Univ. Grenoble Alpes, Inserm, U1216, Grenoble Institut Neurosciences, Grenoble, France
name:Univ. Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, Grenoble, France
name:Univ. Grenoble Alpes, Inserm, U1216, Grenoble Institut Neurosciences, Grenoble, France
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