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Cockman ME, Sugimoto Y, Pegg HB, Masson N, Salah E, Tumber A, Flynn HR, Kirkpatrick JM, Schofield CJ, Ratcliffe PJ. Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6. Proc Natl Acad Sci U S A 2022; 119:e2201483119. [PMID: 35930668 PMCID: PMC9371714 DOI: 10.1073/pnas.2201483119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
The Jumonji domain-containing protein JMJD6 is a 2-oxoglutarate-dependent dioxygenase associated with a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing, and cotranscriptional processing. Although not all studies agree, JMJD6 has been reported to catalyze both hydroxylation of lysine residues and demethylation of arginine residues. However, despite extensive study and indirect evidence for JMJD6 catalysis in many cellular processes, direct assignment of JMJD6 catalytic substrates has been limited. Examination of a reported site of proline hydroxylation within a lysine-rich region of the tandem bromodomain protein BRD4 led us to conclude that hydroxylation was in fact on lysine and catalyzed by JMJD6. This prompted a wider search for JMJD6-catalyzed protein modifications deploying mass spectrometric methods designed to improve the analysis of such lysine-rich regions. Using lysine derivatization with propionic anhydride to improve the analysis of tryptic peptides and nontryptic proteolysis, we report 150 sites of JMJD6-catalyzed lysine hydroxylation on 48 protein substrates, including 19 sites of hydroxylation on BRD4. Most hydroxylations were within lysine-rich regions that are predicted to be unstructured; in some, multiple modifications were observed on adjacent lysine residues. Almost all of the JMJD6 substrates defined in these studies have been associated with membraneless organelle formation. Given the reported roles of lysine-rich regions in subcellular partitioning by liquid-liquid phase separation, our findings raise the possibility that JMJD6 may play a role in regulating such processes in response to stresses, including hypoxia.
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Affiliation(s)
- Matthew E. Cockman
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Yoichiro Sugimoto
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Hamish B. Pegg
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Norma Masson
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Helen R. Flynn
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Joanna M. Kirkpatrick
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Peter J. Ratcliffe
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
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Linthwaite VL, Pawloski W, Pegg HB, Townsend PD, Thomas MJ, So VKH, Brown AP, Hodgson DRW, Lorimer GH, Fushman D, Cann MJ. Ubiquitin is a carbon dioxide-binding protein. Sci Adv 2021; 7:eabi5507. [PMID: 34559559 PMCID: PMC8462908 DOI: 10.1126/sciadv.abi5507] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The identification of CO2-binding proteins is crucial to understanding CO2-regulated molecular processes. CO2 can form a reversible posttranslational modification through carbamylation of neutral N-terminal α-amino or lysine ε-amino groups. We have previously developed triethyloxonium (TEO) ion as a chemical proteomics tool for covalent trapping of carbamates, and here, we deploy TEO to identify ubiquitin as a mammalian CO2-binding protein. We use 13C-NMR spectroscopy to demonstrate that CO2 forms carbamates on the ubiquitin N terminus and ε-amino groups of lysines 6, 33, 48, and 63. We demonstrate that biologically relevant pCO2 levels reduce ubiquitin conjugation at lysine-48 and down-regulate ubiquitin-dependent NF-κB pathway activation. Our results show that ubiquitin is a CO2-binding protein and demonstrates carbamylation as a viable mechanism by which mammalian cells can respond to fluctuating pCO2.
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Affiliation(s)
| | - Wes Pawloski
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Hamish B. Pegg
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | | | | | - Victor K. H. So
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - Adrian P. Brown
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
| | - David R. W. Hodgson
- Department of Chemistry, Durham University, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Durham DH1 3LE, UK
| | - George H. Lorimer
- Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Martin J. Cann
- Department of Biosciences, Durham University, Durham DH1 3LE, UK
- Biophysical Sciences Institute, Durham University, Durham DH1 3LE, UK
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Cockman ME, Lippl K, Tian YM, Pegg HB, Figg WD, Abboud MI, Heilig R, Fischer R, Myllyharju J, Schofield CJ, Ratcliffe PJ. Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates. eLife 2019; 8:e46490. [PMID: 31500697 PMCID: PMC6739866 DOI: 10.7554/elife.46490] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Human and other animal cells deploy three closely related dioxygenases (PHD 1, 2 and 3) to signal oxygen levels by catalysing oxygen regulated prolyl hydroxylation of the transcription factor HIF. The discovery of the HIF prolyl-hydroxylase (PHD) enzymes as oxygen sensors raises a key question as to the existence and nature of non-HIF substrates, potentially transducing other biological responses to hypoxia. Over 20 such substrates are reported. We therefore sought to characterise their reactivity with recombinant PHD enzymes. Unexpectedly, we did not detect prolyl-hydroxylase activity on any reported non-HIF protein or peptide, using conditions supporting robust HIF-α hydroxylation. We cannot exclude PHD-catalysed prolyl hydroxylation occurring under conditions other than those we have examined. However, our findings using recombinant enzymes provide no support for the wide range of non-HIF PHD substrates that have been reported.
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Affiliation(s)
| | - Kerstin Lippl
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Ya-Min Tian
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | | | - William D Figg
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Raphael Heilig
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Peter J Ratcliffe
- The Francis Crick InstituteLondonUnited Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
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