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Article ; Online: Corrigendum: Contrasting effects on HIF-1α regulation by disease-causing pVHL mutations correlate with patterns of tumourigenesis in von Hippel-Lindau disease.

Clifford, Steven C / Cockman, Matthew E / Smallwood, Alan C / Mole, David R / Woodward, Emma R / Maxwell, Patrick H / Ratcliffe, Peter J / Maher, Eamonn R

Human molecular genetics

2021 Volume 30, Issue 9, Page(s) 844–845

Language	English
Publishing date	2021-03-24
Publishing country	England
Document type	Published Erratum
ZDB-ID	1108742-0
ISSN	1460-2083 ; 0964-6906
ISSN (online)	1460-2083
ISSN	0964-6906
DOI	10.1093/hmg/ddab037
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Article ; Online: Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6.

Cockman, Matthew E / Sugimoto, Yoichiro / Pegg, Hamish B / Masson, Norma / Salah, Eidarus / Tumber, Anthony / Flynn, Helen R / Kirkpatrick, Joanna M / Schofield, Christopher J / Ratcliffe, Peter J

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 32, Page(s) e2201483119

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 ... ...

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.
MeSH term(s)	Cell Cycle Proteins/metabolism ; Humans ; Hydroxylation ; Intrinsically Disordered Proteins/metabolism ; Jumonji Domain-Containing Histone Demethylases/chemistry ; Jumonji Domain-Containing Histone Demethylases/metabolism ; Lysine/metabolism ; Protein Domains ; Transcription Factors/metabolism
Chemical Substances	BRD4 protein, human ; Cell Cycle Proteins ; Intrinsically Disordered Proteins ; Transcription Factors ; JMJD6 protein, human (EC 1.14.11.-) ; Jumonji Domain-Containing Histone Demethylases (EC 1.14.11.-) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2022-08-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2201483119
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Article ; Online: Factor inhibiting HIF can catalyze two asparaginyl hydroxylations in VNVN motifs of ankyrin fold proteins.

Leissing, Thomas M / Hardy, Adam P / Chan, Hokfung / Wang, Yihua / Tumber, Anthony / Chowdhury, Rasheduzzaman / Feng, Tianshu / Coleman, Mathew L / Cockman, Matthew E / Kramer, Holger B / Berridge, Georgina / Fischer, Roman / Kessler, Benedikt M / Ratcliffe, Peter J / Lu, Xin / Schofield, Christopher J

The Journal of biological chemistry

2022 Volume 298, Issue 6, Page(s) 102020

Abstract: ... of ankyrin repeat domains in ASPPs (i.e., ASPP1, ASPP2, and iASPP) and the related ASB11 and p18-INK4C proteins ...

Abstract	The aspariginyl hydroxylase human factor inhibiting hypoxia-inducible factor (FIH) is an important regulator of the transcriptional activity of hypoxia-inducible factor. FIH also catalyzes the hydroxylation of asparaginyl and other residues in ankyrin repeat domain-containing proteins, including apoptosis stimulating of p53 protein (ASPP) family members. ASPP2 is reported to undergo a single FIH-catalyzed hydroxylation at Asn-986. We report biochemical and crystallographic evidence showing that FIH catalyzes the unprecedented post-translational hydroxylation of both asparaginyl residues in "VNVN" and related motifs of ankyrin repeat domains in ASPPs (i.e., ASPP1, ASPP2, and iASPP) and the related ASB11 and p18-INK4C proteins. Our biochemical results extend the substrate scope of FIH catalysis and may have implications for its biological roles, including in the hypoxic response and ASPP family function.
MeSH term(s)	Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Ankyrin Repeat ; Apoptosis Regulatory Proteins ; Catalysis ; Humans ; Hydroxylation ; Hypoxia ; Mixed Function Oxygenases/metabolism ; Repressor Proteins/metabolism
Chemical Substances	Adaptor Proteins, Signal Transducing ; Apoptosis Regulatory Proteins ; PPP1R13B protein, human ; Repressor Proteins ; TP53BP2 protein, human ; Mixed Function Oxygenases (EC 1.-) ; HIF1AN protein, human (EC 1.14.11.-)
Language	English
Publishing date	2022-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.102020
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Article ; Online: Ogfod1 deletion increases cardiac beta-alanine levels and protects mice against ischaemia- reperfusion injury.

Harris, Michael / Sun, Junhui / Keeran, Karen / Aponte, Angel / Singh, Komudi / Springer, Danielle / Gucek, Marjan / Pirooznia, Mehdi / Cockman, Matthew E / Murphy, Elizabeth / Kennedy, Leslie M

Cardiovascular research

2021 Volume 118, Issue 13, Page(s) 2847–2858

Abstract: Aims: Prolyl hydroxylation is a post-translational modification that regulates protein stability, turnover, and activity. The proteins that catalyze prolyl hydroxylation belong to the 2-oxoglutarate- and iron-dependent oxygenase family of proteins. 2- ... ...

Abstract	Aims: Prolyl hydroxylation is a post-translational modification that regulates protein stability, turnover, and activity. The proteins that catalyze prolyl hydroxylation belong to the 2-oxoglutarate- and iron-dependent oxygenase family of proteins. 2-oxoglutarate- and iron-dependent oxygenase domain-containing protein 1 (Ogfod1), which hydroxylates a proline in ribosomal protein s23 is a newly described member of this family. The aims of this study were to investigate roles for Ogfod1 in the heart, and in the heart's response to stress. Methods and results: We isolated hearts from wild-type (WT) and Ogfod1 knockout (KO) mice and performed quantitative proteomics using tandem mass Tag labelling coupled to liquid chromatography and tandem mass spectrometry (LC-MS/MS) to identify protein changes. Ingenuity pathway analysis identified 'Urate Biosynthesis/Inosine 5'-phosphate Degradation' and 'Purine Nucleotides Degradation II (Aerobic)' as the most significantly enriched pathways. We performed metabolomics analysis and found that both purine and pyrimidine pathways were altered with the purine nucleotide inosine 5'-monophosphate showing a 3.5-fold enrichment in KO hearts (P = 0.011) and the pyrimidine catabolism product beta-alanine showing a 1.7-fold enrichment in KO hearts (P = 0.014). As changes in these pathways have been shown to contribute to cardioprotection, we subjected isolated perfused hearts to ischaemia and reperfusion (I/R). KO hearts showed a 41.4% decrease in infarct size and a 34% improvement in cardiac function compared to WT hearts. This protection was also evident in an in vivo I/R model. Additionally, our data show that treating isolated perfused WT hearts with carnosine, a metabolite of beta-alanine, improved protection in the context of I/R injury, whereas treating KO hearts with carnosine had no impact on recovery of function or infarct size. Conclusions: Taken together, these data show that Ogfod1 deletion alters the myocardial proteome and metabolome to confer protection against I/R injury.
MeSH term(s)	Animals ; Mice ; beta-Alanine/metabolism ; Carnosine/pharmacology ; Chromatography, Liquid ; Infarction ; Inosine ; Iron ; Ischemia ; Ketoglutaric Acids ; Mice, Knockout ; Myocardial Reperfusion Injury/genetics ; Myocardial Reperfusion Injury/prevention & control ; Myocardial Reperfusion Injury/metabolism ; Nucleotides ; Oxygenases ; Phosphates ; Proline ; Proteome ; Purine Nucleotides ; Pyrimidines ; Ribosomal Proteins ; Tandem Mass Spectrometry ; Uric Acid ; Nuclear Proteins/genetics ; Carrier Proteins/genetics
Chemical Substances	beta-Alanine (11P2JDE17B) ; Carnosine (8HO6PVN24W) ; Inosine (5A614L51CT) ; Iron (E1UOL152H7) ; Ketoglutaric Acids ; Nucleotides ; Oxygenases (EC 1.13.-) ; Phosphates ; Proline (9DLQ4CIU6V) ; Proteome ; Purine Nucleotides ; Pyrimidines ; Ribosomal Proteins ; Uric Acid (268B43MJ25) ; Nuclear Proteins ; Carrier Proteins
Language	English
Publishing date	2021-10-19
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
ZDB-ID	80340-6
ISSN	1755-3245 ; 0008-6363
ISSN (online)	1755-3245
ISSN	0008-6363
DOI	10.1093/cvr/cvab323
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Zs.A 565: Show issues

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Article ; Online: Oxygen sensing.

Cockman, Matthew E / Pugh, Christopher W

Haematologica

2005 Volume 90, Issue 1, Page(s) 8–12

MeSH term(s)	Anaerobiosis/genetics ; Anaerobiosis/physiology ; Dioxygenases/metabolism ; Gene Expression/physiology ; Humans ; Hypoxia/genetics ; Hypoxia/metabolism ; Hypoxia-Inducible Factor-Proline Dioxygenases ; Oxygen Consumption ; Protein Binding
Chemical Substances	Dioxygenases (EC 1.13.11.-) ; EGLN3 protein, human (EC 1.14.11.29) ; Hypoxia-Inducible Factor-Proline Dioxygenases (EC 1.14.11.29)
Language	English
Publishing date	2005-01
Publishing country	Italy
Document type	Editorial
ZDB-ID	2333-4
ISSN	1592-8721 ; 0017-6567 ; 0390-6078
ISSN (online)	1592-8721
ISSN	0017-6567 ; 0390-6078
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Article ; Online: Selective Inhibitors of a Human Prolyl Hydroxylase (OGFOD1) Involved in Ribosomal Decoding.

Thinnes, Cyrille C / Lohans, Christopher T / Abboud, Martine I / Yeh, Tzu-Lan / Tumber, Anthony / Nowak, Radosław P / Attwood, Martin / Cockman, Matthew E / Oppermann, Udo / Loenarz, Christoph / Schofield, Christopher J

Chemistry (Weinheim an der Bergstrasse, Germany)

2019 Volume 25, Issue 8, Page(s) 2019–2024

Abstract: Human prolyl hydroxylases are involved in the modification of transcription factors, procollagen, and ribosomal proteins, and are current medicinal chemistry targets. To date, there are few reports on inhibitors selective for the different types of ... ...

Abstract	Human prolyl hydroxylases are involved in the modification of transcription factors, procollagen, and ribosomal proteins, and are current medicinal chemistry targets. To date, there are few reports on inhibitors selective for the different types of prolyl hydroxylases. We report a structurally informed template-based strategy for the development of inhibitors selective for the human ribosomal prolyl hydroxylase OGFOD1. These inhibitors did not target the other human oxygenases tested, including the structurally similar hypoxia-inducible transcription factor prolyl hydroxylase, PHD2.
MeSH term(s)	Carrier Proteins/antagonists & inhibitors ; Drug Design ; Humans ; Nuclear Proteins/antagonists & inhibitors ; Prolyl Hydroxylases/metabolism ; Prolyl-Hydroxylase Inhibitors/chemistry ; Prolyl-Hydroxylase Inhibitors/metabolism ; Prolyl-Hydroxylase Inhibitors/pharmacology ; Ribosomes/drug effects ; Ribosomes/metabolism ; Structure-Activity Relationship ; Substrate Specificity
Chemical Substances	Carrier Proteins ; Nuclear Proteins ; OGFOD1 protein, human ; Prolyl-Hydroxylase Inhibitors ; Prolyl Hydroxylases (EC 1.14.11.-)
Language	English
Publishing date	2019-01-08
Publishing country	Germany
Document type	Journal Article
ZDB-ID	1478547-X
ISSN	1521-3765 ; 0947-6539
ISSN (online)	1521-3765
ISSN	0947-6539
DOI	10.1002/chem.201804790
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Article ; Online: Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates.

Cockman, Matthew E / Lippl, Kerstin / Tian, Ya-Min / Pegg, Hamish B / Figg, William D / Abboud, Martine I / Heilig, Raphael / Fischer, Roman / Myllyharju, Johanna / Schofield, Christopher J / Ratcliffe, Peter J

eLife

2019 Volume 8

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 ...

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.
MeSH term(s)	Hydroxylation ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Hypoxia-Inducible Factor-Proline Dioxygenases/genetics ; Hypoxia-Inducible Factor-Proline Dioxygenases/metabolism ; Oxygen/metabolism ; Peptides/metabolism ; Protein Processing, Post-Translational ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Substrate Specificity
Chemical Substances	HIF1A protein, human ; Hypoxia-Inducible Factor 1, alpha Subunit ; Peptides ; Recombinant Proteins ; EGLN1 protein, human (EC 1.14.11.2) ; EGLN2 protein, human (EC 1.14.11.29) ; EGLN3 protein, human (EC 1.14.11.29) ; Hypoxia-Inducible Factor-Proline Dioxygenases (EC 1.14.11.29) ; Oxygen (S88TT14065)
Language	English
Publishing date	2019-09-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.46490
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Article ; Online: FIH-dependent asparaginyl hydroxylation of ankyrin repeat domain-containing proteins.

Cockman, Matthew E / Webb, James D / Ratcliffe, Peter J

Annals of the New York Academy of Sciences

2009 Volume 1177, Page(s) 9–18

Abstract: Studies on hypoxia-sensitive pathways have identified a series of Fe(II)-dependent dioxygenases that regulate hypoxia-inducible factor (HIF) by prolyl and asparaginyl hydroxylation. The asparaginyl hydroxylase factor inhibiting HIF (FIH) targets a ... ...

Abstract	Studies on hypoxia-sensitive pathways have identified a series of Fe(II)-dependent dioxygenases that regulate hypoxia-inducible factor (HIF) by prolyl and asparaginyl hydroxylation. The asparaginyl hydroxylase factor inhibiting HIF (FIH) targets a conserved asparaginyl residue in the C-terminal transactivation domain of HIF-alpha. This modification suppresses HIF transcriptional activity by inhibiting co-activator recruitment. Recent work has demonstrated that FIH targets an alternative class of substrate. Proteins containing a common interaction motif known as the ankyrin repeat domain (ARD) have been shown to be efficiently hydroxylated by FIH. This review aims to summarize what is currently known regarding ARD hydroxylation, including the kinetics and determinants of FIH-mediated ARD hydroxylation, the structural and functional consequences of ARD hydroxylation, and the potential for cross-talk between ARD proteins and HIF signaling.
MeSH term(s)	Animals ; Ankyrin Repeat ; Asparagine/metabolism ; Humans ; Hydroxylation ; Mixed Function Oxygenases ; Proteins/chemistry ; Proteins/metabolism ; Repressor Proteins/metabolism
Chemical Substances	Proteins ; Repressor Proteins ; Asparagine (7006-34-0) ; Mixed Function Oxygenases (EC 1.-) ; HIF1AN protein, human (EC 1.14.11.-)
Language	English
Publishing date	2009-10-21
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	211003-9
ISSN	1749-6632 ; 0077-8923
ISSN (online)	1749-6632
ISSN	0077-8923
DOI	10.1111/j.1749-6632.2009.05042.x
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Article ; Online: Inherent DNA-binding specificities of the HIF-1α and HIF-2α transcription factors in chromatin.

Smythies, James A / Sun, Min / Masson, Norma / Salama, Rafik / Simpson, Peter D / Murray, Elizabeth / Neumann, Viviana / Cockman, Matthew E / Choudhry, Hani / Ratcliffe, Peter J / Mole, David R

EMBO reports

2018 Volume 20, Issue 1

Abstract: Hypoxia-inducible factor (HIF) is the major transcriptional regulator of cellular responses to hypoxia. The two principal HIF-α isoforms, HIF-1α and HIF-2α, are progressively stabilized in response to hypoxia and form heterodimers with HIF-1β to activate ...

Abstract	Hypoxia-inducible factor (HIF) is the major transcriptional regulator of cellular responses to hypoxia. The two principal HIF-α isoforms, HIF-1α and HIF-2α, are progressively stabilized in response to hypoxia and form heterodimers with HIF-1β to activate a broad range of transcriptional responses. Here, we report on the pan-genomic distribution of isoform-specific HIF binding in response to hypoxia of varying severity and duration, and in response to genetic ablation of each HIF-α isoform. Our findings reveal that, despite an identical consensus recognition sequence in DNA, each HIF heterodimer loads progressively at a distinct repertoire of cell-type-specific sites across the genome, with little evidence of redistribution under any of the conditions examined. Marked biases towards promoter-proximal binding of HIF-1 and promoter-distant binding of HIF-2 were observed under all conditions and were consistent in multiple cell type. The findings imply that each HIF isoform has an inherent property that determines its binding distribution across the genome, which might be exploited to therapeutically target the specific transcriptional output of each isoform independently.
MeSH term(s)	Basic Helix-Loop-Helix Transcription Factors/genetics ; Cell Hypoxia/genetics ; Cell Line ; Chromatin/genetics ; DNA/genetics ; DNA-Binding Proteins/genetics ; Epigenomics ; Gene Expression Regulation/genetics ; Humans ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics ; Promoter Regions, Genetic ; Protein Isoforms/genetics ; Transcription, Genetic
Chemical Substances	Basic Helix-Loop-Helix Transcription Factors ; Chromatin ; DNA-Binding Proteins ; HIF1A protein, human ; Hypoxia-Inducible Factor 1, alpha Subunit ; Protein Isoforms ; endothelial PAS domain-containing protein 1 (1B37H0967P) ; DNA (9007-49-2)
Language	English
Publishing date	2018-11-14
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.15252/embr.201846401
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Article ; Online: Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates

Matthew E Cockman / Kerstin Lippl / Ya-Min Tian / Hamish B Pegg / William D Figg Jnr / Martine I Abboud / Raphael Heilig / Roman Fischer / Johanna Myllyharju / Christopher J Schofield / Peter J Ratcliffe

eLife, Vol

2019 Volume 8

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.
Keywords	hydroxylation ; prolyl hydroxylase ; oxygenase ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2019-09-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
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