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Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation
Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods relying on pulsed metabolic labeling are popular to quantify turnover rates on a proteome-wide scale. Such data have traditionally been interpreted in the context o...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9718778/ https://www.ncbi.nlm.nih.gov/pubmed/36460637 http://dx.doi.org/10.1038/s41467-022-35054-2 |
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author | Hammarén, Henrik M. Geissen, Eva-Maria Potel, Clement M. Beck, Martin Savitski, Mikhail M. |
author_facet | Hammarén, Henrik M. Geissen, Eva-Maria Potel, Clement M. Beck, Martin Savitski, Mikhail M. |
author_sort | Hammarén, Henrik M. |
collection | PubMed |
description | Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods relying on pulsed metabolic labeling are popular to quantify turnover rates on a proteome-wide scale. Such data have traditionally been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture (pSILAC) for the study of protein phosphorylation. We demonstrate that metabolic labeling combined with PTM-specific enrichment does not measure effects of PTMs on protein stability. Rather, it reveals the relative order of PTM addition and removal along a protein’s lifetime—a fundamentally different metric. This is due to interconversion of the measured proteoform species. Using this framework, we identify temporal phosphorylation sites on cell cycle-specific factors and protein complex assembly intermediates. Our results thus allow tying PTMs to the age of the modified proteins. |
format | Online Article Text |
id | pubmed-9718778 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-97187782022-12-04 Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation Hammarén, Henrik M. Geissen, Eva-Maria Potel, Clement M. Beck, Martin Savitski, Mikhail M. Nat Commun Article Post-translational modifications (PTMs) regulate various aspects of protein function, including degradation. Mass spectrometric methods relying on pulsed metabolic labeling are popular to quantify turnover rates on a proteome-wide scale. Such data have traditionally been interpreted in the context of protein proteolytic stability. Here, we combine theoretical kinetic modeling with experimental pulsed stable isotope labeling of amino acids in cell culture (pSILAC) for the study of protein phosphorylation. We demonstrate that metabolic labeling combined with PTM-specific enrichment does not measure effects of PTMs on protein stability. Rather, it reveals the relative order of PTM addition and removal along a protein’s lifetime—a fundamentally different metric. This is due to interconversion of the measured proteoform species. Using this framework, we identify temporal phosphorylation sites on cell cycle-specific factors and protein complex assembly intermediates. Our results thus allow tying PTMs to the age of the modified proteins. Nature Publishing Group UK 2022-12-02 /pmc/articles/PMC9718778/ /pubmed/36460637 http://dx.doi.org/10.1038/s41467-022-35054-2 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Hammarén, Henrik M. Geissen, Eva-Maria Potel, Clement M. Beck, Martin Savitski, Mikhail M. Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation |
title | Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation |
title_full | Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation |
title_fullStr | Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation |
title_full_unstemmed | Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation |
title_short | Protein-Peptide Turnover Profiling reveals the order of PTM addition and removal during protein maturation |
title_sort | protein-peptide turnover profiling reveals the order of ptm addition and removal during protein maturation |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9718778/ https://www.ncbi.nlm.nih.gov/pubmed/36460637 http://dx.doi.org/10.1038/s41467-022-35054-2 |
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