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Ubiquitin Chain Enrichment Middle-Down Mass Spectrometry (UbiChEM-MS) Reveals Cell-Cycle Dependent Formation of Lys11/Lys48 Branched Ubiquitin Chains

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Department of Chemistry, University of Massachusetts − Amherst, Amherst, Massachusetts 01003, United States
Department of Chemistry, University of Wisconsin − Madison, Madison, Wisconsin 53706, United States
§ Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin − Madison, Madison, Wisconsin 53706, United States
Human Proteomics Program, University of Wisconsin − Madison, Madison, Wisconsin 53706, United States
Department of Biochemistry and Molecular Biology, University of Massachusetts − Amherst, Amherst, Massachusetts 01003, United States
Cite this: J. Proteome Res. 2017, 16, 9, 3363–3369
Publication Date (Web):July 24, 2017
https://doi.org/10.1021/acs.jproteome.7b00381
Copyright © 2017 American Chemical Society
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Abstract

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The dynamics of cellular signaling events are tightly regulated by a diverse set of ubiquitin chains. Recent work has suggested that branched ubiquitin chains composed of Lys11 and Lys48 isopeptide linkages play a critical role in regulating cell cycle progression. Yet, endogenous Lys11/Lys48 branched chains could not be detected. By combining a Lys11 linkage specific antibody with high-resolution middle-down mass spectrometry (an approach termed UbiChEM-MS) we sought to identify endogenous Lys11/Lys48 branched ubiquitin chains in cells. Using asynchronous cells, we find that Lys11-linked branched chains can only be detected upon cotreatment with a proteasome and nonselective deubiquitinase inhibitor. Releasing cells from mitotic arrest results in a marked accumulation of Lys11/Lys48 branched chains in which branch points represent ∼3–4% of the total ubiquitin population. This report highlights the utility of UbiChEM-MS in characterizing the architecture of Lys11 Ub chains under various cellular conditions and corroborates the formation of Lys11/Lys48 branched chains during mitosis.

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This article is cited by 18 publications.

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  2. Kirandeep K. Deol, Stephen J. Eyles, Eric R. Strieter. Quantitative Middle-Down MS Analysis of Parkin-Mediated Ubiquitin Chain Assembly. Journal of the American Society for Mass Spectrometry 2020, 31 (5) , 1132-1139. https://doi.org/10.1021/jasms.0c00058
  3. Nicholas M. Riley and Joshua J. Coon . The Role of Electron Transfer Dissociation in Modern Proteomics. Analytical Chemistry 2018, 90 (1) , 40-64. https://doi.org/10.1021/acs.analchem.7b04810
  4. Anita Waltho, Thomas Sommer. Getting to the Root of Branched Ubiquitin Chains: A Review of Current Methods and Functions. 2023, 19-38. https://doi.org/10.1007/978-1-0716-2859-1_2
  5. Mingwei Sun, Xiaofei Zhang. Current methodologies in protein ubiquitination characterization: from ubiquitinated protein to ubiquitin chain architecture. Cell & Bioscience 2022, 12 (1) https://doi.org/10.1186/s13578-022-00870-y
  6. SriDurgaDevi Kolla, Mengchen Ye, Kevin G. Mark, Michael Rapé. Assembly and function of branched ubiquitin chains. Trends in Biochemical Sciences 2022, 47 (9) , 759-771. https://doi.org/10.1016/j.tibs.2022.04.003
  7. Benjamin Foster, Martin Attwood, Ian Gibbs-Seymour. Tools for Decoding Ubiquitin Signaling in DNA Repair. Frontiers in Cell and Developmental Biology 2021, 9 https://doi.org/10.3389/fcell.2021.760226
  8. Michael E. French, Chad F. Koehler, Tony Hunter. Emerging functions of branched ubiquitin chains. Cell Discovery 2021, 7 (1) https://doi.org/10.1038/s41421-020-00237-y
  9. Kirandeep K. Deol, Eric R. Strieter. The ubiquitin proteoform problem. Current Opinion in Chemical Biology 2021, 63 , 95-104. https://doi.org/10.1016/j.cbpa.2021.02.015
  10. Giovanna Berruti. Destruction or Reconstruction: A Subtle Liaison between the Proteolytic and Signaling Role of Protein Ubiquitination in Spermatogenesis. 2021, 215-240. https://doi.org/10.1007/978-3-030-77779-1_11
  11. Xiao Hua, Guo‐Chao Chu, Yi‐Ming Li. The Ubiquitin Enigma: Progress in the Detection and Chemical Synthesis of Branched Ubiquitin Chains. ChemBioChem 2020, 21 (23) , 3313-3318. https://doi.org/10.1002/cbic.202000295
  12. Yane-Shih Wang, Kuen-Phon Wu, Han-Kai Jiang, Prashant Kurkute, Ruey-Hwa Chen. Branched Ubiquitination: Detection Methods, Biological Functions and Chemical Synthesis. Molecules 2020, 25 (21) , 5200. https://doi.org/10.3390/molecules25215200
  13. Yan-Yan Liang, Jie Zhang, Hui Cui, Zhen-Shu Shao, Chen Cheng, Yue-Bo Wang, Huai-Song Wang. Fluorescence resonance energy transfer (FRET)-based nanoarchitecture for monitoring deubiquitinating enzyme activity. Chemical Communications 2020, 56 (21) , 3183-3186. https://doi.org/10.1039/C9CC09808A
  14. Gunnar Dittmar, Konstanze F. Winklhofer. Linear Ubiquitin Chains: Cellular Functions and Strategies for Detection and Quantification. Frontiers in Chemistry 2020, 7 https://doi.org/10.3389/fchem.2019.00915
  15. Ian G. Cowell, Elise M. Ling, Rebecca L. Swan, Matilda L.W. Brooks, Caroline A. Austin. The Deubiquitinating Enzyme Inhibitor PR-619 is a Potent DNA Topoisomerase II Poison. Molecular Pharmacology 2019, 96 (5) , 562-572. https://doi.org/10.1124/mol.119.117390
  16. Diane L. Haakonsen, Michael Rape. Branching Out: Improved Signaling by Heterotypic Ubiquitin Chains. Trends in Cell Biology 2019, 29 (9) , 704-716. https://doi.org/10.1016/j.tcb.2019.06.003
  17. Hiroyuki Yamano. APC/C: current understanding and future perspectives. F1000Research 2019, 8 , 725. https://doi.org/10.12688/f1000research.18582.1
  18. Jennifer Kernan, Thomas Bonacci, Michael J. Emanuele. Who guards the guardian? Mechanisms that restrain APC/C during the cell cycle. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 2018, 1865 (12) , 1924-1933. https://doi.org/10.1016/j.bbamcr.2018.09.011

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