1
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Volkova YL, Jucht AE, Oechsler N, Krishnankutty R, von Kriegsheim A, Wenger RH, Scholz CC. Selective Hypoxia-Sensitive Oxomer Formation by FIH Prevents Binding of the NF-κB Inhibitor IκBβ to NF-κB Subunits. Mol Cell Biol 2024; 44:138-148. [PMID: 38644795 PMCID: PMC11110689 DOI: 10.1080/10985549.2024.2338727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/31/2024] [Indexed: 04/23/2024] Open
Abstract
Pharmacologic inhibitors of cellular hydroxylase oxygen sensors are protective in multiple preclinical in vivo models of inflammation. However, the molecular mechanisms underlying this regulation are only partly understood, preventing clinical translation. We previously proposed a new mechanism for cellular oxygen sensing: oxygen-dependent, (likely) covalent protein oligomer (oxomer) formation. Here, we report that the oxygen sensor factor inhibiting HIF (FIH) forms an oxomer with the NF-κB inhibitor β (IκBβ). The formation of this protein complex required FIH enzymatic activity and was prevented by pharmacologic inhibitors. Oxomer formation was highly hypoxia-sensitive and very stable. No other member of the IκB protein family formed an oxomer with FIH, demonstrating that FIH-IκBβ oxomer formation was highly selective. In contrast to the known FIH-dependent oxomer formation with the deubiquitinase OTUB1, FIH-IκBβ oxomer formation did not occur via an IκBβ asparagine residue, but depended on the amino acid sequence VAERR contained within a loop between IκBβ ankyrin repeat domains 2 and 3. Oxomer formation prevented IκBβ from binding to its primary interaction partners p65 and c-Rel, subunits of NF-κB, the master regulator of the cellular transcriptional response to pro-inflammatory stimuli. We therefore propose that FIH-mediated oxomer formation with IκBβ contributes to the hypoxia-dependent regulation of inflammation.
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Affiliation(s)
- Yulia L. Volkova
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Nina Oechsler
- Institute of Physiology, University Medicine Greifswald, Greifswald, Germany
| | | | | | - Roland H. Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Carsten C. Scholz
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Institute of Physiology, University Medicine Greifswald, Greifswald, Germany
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2
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Corner TP, Teo RZR, Wu Y, Salah E, Nakashima Y, Fiorini G, Tumber A, Brasnett A, Holt-Martyn JP, Figg WD, Zhang X, Brewitz L, Schofield CJ. Structure-guided optimisation of N-hydroxythiazole-derived inhibitors of factor inhibiting hypoxia-inducible factor-α. Chem Sci 2023; 14:12098-12120. [PMID: 37969593 PMCID: PMC10631261 DOI: 10.1039/d3sc04253g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023] Open
Abstract
The human 2-oxoglutarate (2OG)- and Fe(ii)-dependent oxygenases factor inhibiting hypoxia-inducible factor-α (FIH) and HIF-α prolyl residue hydroxylases 1-3 (PHD1-3) regulate the response to hypoxia in humans via catalysing hydroxylation of the α-subunits of the hypoxia-inducible factors (HIFs). Small-molecule PHD inhibitors are used for anaemia treatment; by contrast, few selective inhibitors of FIH have been reported, despite their potential to regulate the hypoxic response, either alone or in combination with PHD inhibition. We report molecular, biophysical, and cellular evidence that the N-hydroxythiazole scaffold, reported to inhibit PHD2, is a useful broad spectrum 2OG oxygenase inhibitor scaffold, the inhibition potential of which can be tuned to achieve selective FIH inhibition. Structure-guided optimisation resulted in the discovery of N-hydroxythiazole derivatives that manifest substantially improved selectivity for FIH inhibition over PHD2 and other 2OG oxygenases, including Jumonji-C domain-containing protein 5 (∼25-fold), aspartate/asparagine-β-hydroxylase (>100-fold) and histone Nε-lysine demethylase 4A (>300-fold). The optimised N-hydroxythiazole-based FIH inhibitors modulate the expression of FIH-dependent HIF target genes and, consistent with reports that FIH regulates cellular metabolism, suppressed lipid accumulation in adipocytes. Crystallographic studies reveal that the N-hydroxythiazole derivatives compete with both 2OG and the substrate for binding to the FIH active site. Derivatisation of the N-hydroxythiazole scaffold has the potential to afford selective inhibitors for 2OG oxygenases other than FIH.
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Affiliation(s)
- Thomas P Corner
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Ryan Z R Teo
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Yue Wu
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization and Department of Chemistry, China Pharmaceutical University Nanjing 211198 China
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Yu Nakashima
- Institute of Natural Medicine, University of Toyama 2630-Sugitani 930-0194 Toyama Japan
| | - Giorgia Fiorini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Amelia Brasnett
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - James P Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - William D Figg
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Xiaojin Zhang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization and Department of Chemistry, China Pharmaceutical University Nanjing 211198 China
| | - Lennart Brewitz
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford 12 Mansfield Road OX1 3TA Oxford United Kingdom
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3
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Bonnici J, Oueini R, Salah E, Johansson C, Schofield CJ, Kawamura A. The catalytic domains of all human KDM5 JmjC demethylases catalyse N-methyl arginine demethylation. FEBS Lett 2023; 597:933-946. [PMID: 36700827 PMCID: PMC10952680 DOI: 10.1002/1873-3468.14586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/13/2022] [Accepted: 12/28/2022] [Indexed: 01/27/2023]
Abstract
The demethylation of Nε -methyllysine residues on histones by Jumonji-C lysine demethylases (JmjC-KDMs) has been established. A subset of JmjC-KDMs has also been reported to have Nω -methylarginine residue demethylase (RDM) activity. Here, we describe biochemical screening studies, showing that the catalytic domains of all human KDM5s (KDM5A-KDM5D), KDM4E and, to a lesser extent, KDM4A/D, have both KDM and RDM activities with histone peptides. Ras GTPase-activating protein-binding protein 1 peptides were shown to be RDM substrates for KDM5C/D. No RDM activity was observed with KDM1A and the other JmjC-KDMs tested. The results highlight the potential of JmjC-KDMs to catalyse reactions other than Nε -methyllysine demethylation. Although our study is limited to peptide fragments, the results should help guide biological studies investigating JmjC functions.
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Affiliation(s)
- Joanna Bonnici
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Chemistry – School of Natural and Environmental SciencesNewcastle UniversityUK
| | - Razanne Oueini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Catrine Johansson
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Botnar Research Centre, NIHR Oxford Biomedical Research UnitUniversity of OxfordUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordUK
- Chemistry – School of Natural and Environmental SciencesNewcastle UniversityUK
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4
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Türkmen VA, Hintzen JCJ, Tumber A, Moesgaard L, Salah E, Kongsted J, Schofield CJ, Mecinović J. Substrate selectivity and inhibition of histidine JmjC hydroxylases MINA53 and NO66. RSC Chem Biol 2023; 4:235-243. [PMID: 36908702 PMCID: PMC9994133 DOI: 10.1039/d2cb00182a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
Non-haem Fe(ii) and 2-oxoglutarate (2OG) dependent oxygenases catalyse oxidation of multiple proteins in organisms ranging from bacteria to humans. We describe studies on the substrate selectivity and inhibition of the human ribosomal oxygenases (ROX) MINA53 and NO66, members of the JmjC 2OG oxygenase subfamily, which catalyse C-3 hydroxylation of histidine residues in Rpl27a and Rpl8, respectively. Assays with natural and unnatural histidine analogues incorporated into Rpl peptides provide evidence that MINA53 and NO66 have narrow substrate selectivities compared to some other human JmjC hydroxylases, including factor inhibiting HIF and JMJD6. Notably, the results of inhibition assays with Rpl peptides containing histidine analogues with acyclic side chains, including Asn, Gln and homoGln, suggest the activities of MINA53/NO66, and by implication related 2OG dependent protein hydroxylases/demethylases, might be regulated in vivo by competition with non-oxidised proteins/peptides. The inhibition results also provide avenues for development of inhibitors selective for MINA53 and NO66.
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Affiliation(s)
- Vildan A Türkmen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Jordi C J Hintzen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Anthony Tumber
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Eidarus Salah
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
| | - Christopher J Schofield
- Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road OX1 3TA Oxford UK
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55 5230 Odense Denmark
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5
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Volkova YL, Pickel C, Jucht AE, Wenger RH, Scholz CC. The Asparagine Hydroxylase FIH: A Unique Oxygen Sensor. Antioxid Redox Signal 2022; 37:913-935. [PMID: 35166119 DOI: 10.1089/ars.2022.0003] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Significance: Limited oxygen availability (hypoxia) commonly occurs in a range of physiological and pathophysiological conditions, including embryonic development, physical exercise, inflammation, and ischemia. It is thus vital for cells and tissues to monitor their local oxygen availability to be able to adjust in case the oxygen supply is decreased. The cellular oxygen sensor factor inhibiting hypoxia-inducible factor (FIH) is the only known asparagine hydroxylase with hypoxia sensitivity. FIH uniquely combines oxygen and peroxide sensitivity, serving as an oxygen and oxidant sensor. Recent Advances: FIH was first discovered in the hypoxia-inducible factor (HIF) pathway as a modulator of HIF transactivation activity. Several other FIH substrates have now been identified outside the HIF pathway. Moreover, FIH enzymatic activity is highly promiscuous and not limited to asparagine hydroxylation. This includes the FIH-mediated catalysis of an oxygen-dependent stable (likely covalent) bond formation between FIH and selected substrate proteins (called oxomers [oxygen-dependent stable protein oligomers]). Critical Issues: The (patho-)physiological function of FIH is only beginning to be understood and appears to be complex. Selective pharmacologic inhibition of FIH over other oxygen sensors is possible, opening new avenues for therapeutic targeting of hypoxia-associated diseases, increasing the interest in its (patho-)physiological relevance. Future Directions: The contribution of FIH enzymatic activity to disease development and progression should be analyzed in more detail, including the assessment of underlying molecular mechanisms and relevant FIH substrate proteins. Also, the molecular mechanism(s) involved in the physiological functions of FIH remain(s) to be determined. Furthermore, the therapeutic potential of recently developed FIH-selective pharmacologic inhibitors will need detailed assessment. Antioxid. Redox Signal. 37, 913-935.
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Affiliation(s)
- Yulia L Volkova
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Christina Pickel
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | | | - Roland H Wenger
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Carsten C Scholz
- Institute of Physiology, University of Zurich, Zurich, Switzerland
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6
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Leissing TM, Hardy AP, Chan H, Wang Y, Tumber A, Chowdhury R, Feng T, Coleman ML, Cockman ME, Kramer HB, Berridge G, Fischer R, Kessler BM, Ratcliffe PJ, Lu X, Schofield CJ. Factor inhibiting HIF can catalyze two asparaginyl hydroxylations in VNVN motifs of ankyrin fold proteins. J Biol Chem 2022; 298:102020. [PMID: 35537551 PMCID: PMC9189129 DOI: 10.1016/j.jbc.2022.102020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/28/2022] [Accepted: 04/15/2022] [Indexed: 10/28/2022] Open
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.
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Affiliation(s)
- Thomas M Leissing
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Adam P Hardy
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Hokfung Chan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Yihua Wang
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Tianshu Feng
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; NDM Research Building, University of Oxford, Oxford, United Kingdom
| | - Mathew L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Matthew E Cockman
- The Francis Crick Institute, Ratcliffe Laboratory, London, United Kingdom
| | - Holger B Kramer
- MRC London Institute of Medical Sciences, London, United Kingdom; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | | | - Roman Fischer
- NDM Research Building, University of Oxford, Oxford, United Kingdom
| | | | - Peter J Ratcliffe
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; The Francis Crick Institute, Ratcliffe Laboratory, London, United Kingdom.
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom.
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7
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Hydroxylation of the Acetyltransferase NAA10 Trp38 Is Not an Enzyme-Switch in Human Cells. Int J Mol Sci 2021; 22:ijms222111805. [PMID: 34769235 PMCID: PMC8583962 DOI: 10.3390/ijms222111805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/27/2021] [Accepted: 10/27/2021] [Indexed: 02/06/2023] Open
Abstract
NAA10 is a major N-terminal acetyltransferase (NAT) that catalyzes the cotranslational N-terminal (Nt-) acetylation of 40% of the human proteome. Several reports of lysine acetyltransferase (KAT) activity by NAA10 exist, but others have not been able to find any NAA10-derived KAT activity, the latter of which is supported by structural studies. The KAT activity of NAA10 towards hypoxia-inducible factor 1α (HIF-1α) was recently found to depend on the hydroxylation at Trp38 of NAA10 by factor inhibiting HIF-1α (FIH). In contrast, we could not detect hydroxylation of Trp38 of NAA10 in several human cell lines and found no evidence that NAA10 interacts with or is regulated by FIH. Our data suggest that NAA10 Trp38 hydroxylation is not a switch in human cells and that it alters its catalytic activity from a NAT to a KAT.
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8
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Wu Y, Li Z, McDonough MA, Schofield CJ, Zhang X. Inhibition of the Oxygen-Sensing Asparaginyl Hydroxylase Factor Inhibiting Hypoxia-Inducible Factor: A Potential Hypoxia Response Modulating Strategy. J Med Chem 2021; 64:7189-7209. [PMID: 34029087 DOI: 10.1021/acs.jmedchem.1c00415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Factor inhibiting hypoxia-inducible factor (FIH) is a JmjC domain 2-oxogluarate and Fe(II)-dependent oxygenase that catalyzes hydroxylation of specific asparagines in the C-terminal transcriptional activation domain of hypoxia-inducible factor alpha (HIF-α) isoforms. This modification suppresses the transcriptional activity of HIF by reducing its interaction with the transcriptional coactivators p300/CBP. By contrast with inhibition of the HIF prolyl hydroxylases (PHDs), inhibitors of FIH, which accepts multiple non-HIF substrates, are less studied; they are of interest due to their potential ability to alter metabolism (either in a HIF-dependent and/or -independent manner) and, provided HIF is upregulated, to modulate the course of the HIF-mediated hypoxic response. Here we review studies on the mechanism and inhibition of FIH. We discuss proposed biological roles of FIH including its regulation of HIF activity and potential roles of FIH-catalyzed oxidation of non-HIF substrates. We highlight potential therapeutic applications of FIH inhibitors.
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Affiliation(s)
- Yue Wu
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Zhihong Li
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Xiaojin Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization, and Department of Chemistry, China Pharmaceutical University, Nanjing 211198, China
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9
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Abstract
Hypoxia can be defined as a relative deficiency in the amount of oxygen reaching the tissues. Hypoxia-inducible factors (HIFs) are critical regulators of the mammalian response to hypoxia. In normal circumstances, HIF-1α protein turnover is rapid, and hyperglycemia further destabilizes the protein. In addition to their role in diabetes pathogenesis, HIFs are implicated in development of the microvascular and macrovascular complications of diabetes. Improving glucose control in people with diabetes increases HIF-1α protein and has wide-ranging benefits, some of which are at least partially mediated by HIF-1α. Nevertheless, most strategies to improve diabetes or its complications via regulation of HIF-1α have not currently proven to be clinically useful. The intersection of HIF biology with diabetes is a complex area in which many further questions remain, especially regarding the well-conducted studies clearly describing discrepant effects of different methods of increasing HIF-1α, even within the same tissues. This Review presents a brief overview of HIFs; discusses the range of evidence implicating HIFs in β cell dysfunction, diabetes pathogenesis, and diabetes complications; and examines the differing outcomes of HIF-targeting approaches in these conditions.
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Affiliation(s)
- Jenny E Gunton
- Centre for Diabetes, Obesity and Endocrinology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Westmead Hospital, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
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10
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Hypoxia and Oxygen-Sensing Signaling in Gene Regulation and Cancer Progression. Int J Mol Sci 2020; 21:ijms21218162. [PMID: 33142830 PMCID: PMC7663541 DOI: 10.3390/ijms21218162] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/19/2022] Open
Abstract
Oxygen homeostasis regulation is the most fundamental cellular process for adjusting physiological oxygen variations, and its irregularity leads to various human diseases, including cancer. Hypoxia is closely associated with cancer development, and hypoxia/oxygen-sensing signaling plays critical roles in the modulation of cancer progression. The key molecules of the hypoxia/oxygen-sensing signaling include the transcriptional regulator hypoxia-inducible factor (HIF) which widely controls oxygen responsive genes, the central members of the 2-oxoglutarate (2-OG)-dependent dioxygenases, such as prolyl hydroxylase (PHD or EglN), and an E3 ubiquitin ligase component for HIF degeneration called von Hippel–Lindau (encoding protein pVHL). In this review, we summarize the current knowledge about the canonical hypoxia signaling, HIF transcription factors, and pVHL. In addition, the role of 2-OG-dependent enzymes, such as DNA/RNA-modifying enzymes, JmjC domain-containing enzymes, and prolyl hydroxylases, in gene regulation of cancer progression, is specifically reviewed. We also discuss the therapeutic advancement of targeting hypoxia and oxygen sensing pathways in cancer.
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11
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Brewitz L, Tumber A, Schofield CJ. Kinetic parameters of human aspartate/asparagine-β-hydroxylase suggest that it has a possible function in oxygen sensing. J Biol Chem 2020; 295:7826-7838. [PMID: 32107312 PMCID: PMC7278358 DOI: 10.1074/jbc.ra119.012202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/24/2020] [Indexed: 12/31/2022] Open
Abstract
Human aspartate/asparagine-β-hydroxylase (AspH) is a 2-oxoglutarate (2OG)-dependent oxygenase that catalyzes the post-translational hydroxylation of Asp and Asn residues in epidermal growth factor-like domains (EGFDs). Despite its biomedical significance, studies on AspH have long been limited by a lack of assays for its isolated form. Recent structural work has revealed that AspH accepts substrates with a noncanonical EGFD disulfide connectivity (i.e. the Cys 1-2, 3-4, 5-6 disulfide pattern). We developed stable cyclic thioether analogues of the noncanonical EGFD AspH substrates to avoid disulfide shuffling. We monitored their hydroxylation by solid-phase extraction coupled to MS. The extent of recombinant AspH-catalyzed cyclic peptide hydroxylation appears to reflect levels of EGFD hydroxylation observed in vivo, which vary considerably. We applied the assay to determine the kinetic parameters of human AspH with respect to 2OG, Fe(II), l-ascorbic acid, and substrate and found that these parameters are in the typical ranges for 2OG oxygenases. Of note, a relatively high Km for O2 suggested that O2 availability may regulate AspH activity in a biologically relevant manner. We anticipate that the assay will enable the development of selective small-molecule inhibitors for AspH and other human 2OG oxygenases.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, OX1 3TA Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, OX1 3TA Oxford, United Kingdom
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12
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Choi H, Hardy AP, Leissing TM, Chowdhury R, Nakashima Y, Ge W, Markoulides M, Scotti JS, Gerken PA, Thorbjornsrud H, Kang D, Hong S, Lee J, McDonough MA, Park H, Schofield CJ. A human protein hydroxylase that accepts D-residues. Commun Chem 2020; 3:52. [PMID: 36703414 PMCID: PMC9814778 DOI: 10.1038/s42004-020-0290-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/12/2020] [Indexed: 01/29/2023] Open
Abstract
Factor inhibiting hypoxia-inducible factor (FIH) is a 2-oxoglutarate-dependent protein hydroxylase that catalyses C3 hydroxylations of protein residues. We report FIH can accept (D)- and (L)-residues for hydroxylation. The substrate selectivity of FIH differs for (D) and (L) epimers, e.g., (D)- but not (L)-allylglycine, and conversely (L)- but not (D)-aspartate, undergo monohydroxylation, in the tested sequence context. The (L)-Leu-containing substrate undergoes FIH-catalysed monohydroxylation, whereas (D)-Leu unexpectedly undergoes dihydroxylation. Crystallographic, mass spectrometric, and DFT studies provide insights into the selectivity of FIH towards (L)- and (D)-residues. The results of this work expand the potential range of known substrates hydroxylated by isolated FIH and imply that it will be possible to generate FIH variants with altered selectivities.
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Affiliation(s)
- Hwanho Choi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK.,Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006, Korea
| | - Adam P Hardy
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Thomas M Leissing
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Yu Nakashima
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Marios Markoulides
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - John S Scotti
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Philip A Gerken
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Helen Thorbjornsrud
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Dahye Kang
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Sungwoo Hong
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon, 34141, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Joongoo Lee
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 05006, Korea.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12, Mansfield Road, Oxford, OX1 3TA, UK.
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13
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Mechanisms of hypoxia signalling: new implications for nephrology. Nat Rev Nephrol 2019; 15:641-659. [PMID: 31488900 DOI: 10.1038/s41581-019-0182-z] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2019] [Indexed: 12/14/2022]
Abstract
Studies of the regulation of erythropoietin (EPO) production by the liver and kidneys, one of the classical physiological responses to hypoxia, led to the discovery of human oxygen-sensing mechanisms, which are now being targeted therapeutically. The oxygen-sensitive signal is generated by 2-oxoglutarate-dependent dioxygenases that deploy molecular oxygen as a co-substrate to catalyse the post-translational hydroxylation of specific prolyl and asparaginyl residues in hypoxia-inducible factor (HIF), a key transcription factor that regulates transcriptional responses to hypoxia. Hydroxylation of HIF at different sites promotes both its degradation and inactivation. Under hypoxic conditions, these processes are suppressed, enabling HIF to escape destruction and form active transcriptional complexes at thousands of loci across the human genome. Accordingly, HIF prolyl hydroxylase inhibitors stabilize HIF and stimulate expression of HIF target genes, including the EPO gene. These molecules activate endogenous EPO gene expression in diseased kidneys and are being developed, or are already in clinical use, for the treatment of renal anaemia. In this Review, we summarize information on the molecular circuitry of hypoxia signalling pathways underlying these new treatments and highlight some of the outstanding questions relevant to their clinical use.
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14
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Von Dwingelo J, Chung IYW, Price CT, Li L, Jones S, Cygler M, Abu Kwaik Y. Interaction of the Ankyrin H Core Effector of Legionella with the Host LARP7 Component of the 7SK snRNP Complex. mBio 2019; 10:e01942-19. [PMID: 31455655 PMCID: PMC6712400 DOI: 10.1128/mbio.01942-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/18/2022] Open
Abstract
Species of the Legionella genus encode at least 18,000 effector proteins that are translocated through the Dot/Icm type IVB translocation system into macrophages and protist hosts to enable intracellular growth. Eight effectors, including ankyrin H (AnkH), are common to all Legionella species. The AnkH effector is also present in Coxiella and Rickettsiella To date, no pathogenic effectors have ever been described that directly interfere with host cell transcription. We determined that the host nuclear protein La-related protein 7 (LARP7), which is a component of the 7SK small nuclear ribonucleoprotein (snRNP) complex, interacts with AnkH in the host cell nucleus. The AnkH-LARP7 interaction partially impedes interactions of the 7SK snRNP components with LARP7, interfering with transcriptional elongation by polymerase (Pol) II. Consistent with that, our data show AnkH-dependent global reprogramming of transcription of macrophages infected by Legionella pneumophila The crystal structure of AnkH shows that it contains four N-terminal ankyrin repeats, followed by a cysteine protease-like domain and an α-helical C-terminal domain. A substitution within the β-hairpin loop of the third ankyrin repeat results in diminishment of LARP7-AnkH interactions and phenocopies the ankH null mutant defect in intracellular growth. LARP7 knockdown partially suppresses intracellular proliferation of wild-type (WT) bacteria and increases the severity of the defect of the ΔankH mutant, indicating a role for LARP7 in permissiveness of host cells to intracellular bacterial infection. We conclude that the AnkH-LARP7 interaction impedes interaction of LARP7 with 7SK snRNP, which would block transcriptional elongation by Pol II, leading to host global transcriptional reprogramming and permissiveness to L. pneumophilaIMPORTANCE For intracellular pathogens to thrive in host cells, an environment that supports survival and replication needs to be established. L. pneumophila accomplishes this through the activity of the ∼330 effector proteins that are injected into host cells during infection. Effector functions range from hijacking host trafficking pathways to altering host cell machinery, resulting in altered cell biology and innate immunity. One such pathway is the host protein synthesis pathway. Five L. pneumophila effectors have been identified that alter host cell translation, and 2 effectors have been identified that indirectly affect host cell transcription. No pathogenic effectors have been described that directly interfere with host cell transcription. Here we show a direct interaction of the AnkH effector with a host cell transcription complex involved in transcriptional elongation. We identify a novel process by which AnkH interferes with host transcriptional elongation through interference with formation of a functional complex and show that this interference is required for pathogen proliferation.
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Affiliation(s)
- Juanita Von Dwingelo
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Ivy Yeuk Wah Chung
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Christopher T Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Lei Li
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Snake Jones
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
| | - Miroslaw Cygler
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, Kentucky, USA
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, Kentucky, USA
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15
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Pickel C, Günter J, Ruiz-Serrano A, Spielmann P, Fabrizio JA, Wolski W, Peet DJ, Wenger RH, Scholz CC. Oxygen-dependent bond formation with FIH regulates the activity of the client protein OTUB1. Redox Biol 2019; 26:101265. [PMID: 31299612 PMCID: PMC6624438 DOI: 10.1016/j.redox.2019.101265] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/28/2019] [Accepted: 06/30/2019] [Indexed: 12/30/2022] Open
Abstract
Protein:protein interactions are the basis of molecular communication and are usually of transient non-covalent nature, while covalent interactions other than ubiquitination are rare. For cellular adaptations, the cellular oxygen and peroxide sensor factor inhibiting HIF (FIH) confers oxygen and oxidant stress sensitivity to the hypoxia inducible factor (HIF) by asparagine hydroxylation. We investigated whether FIH contributes to hypoxia adaptation also through other mechanisms and identified a hypoxia sensitive, likely covalent, bond formation by FIH with several client proteins, including the deubiquitinase ovarian tumor domain containing ubiquitin aldehyde binding protein 1 (OTUB1). Biochemical analyses were consistent with a co-translational amide bond formation between FIH and OTUB1, occurring within mammalian and bacterial cells but not between separately purified proteins. Bond formation is catalysed by FIH and highly dependent on oxygen availability in the cellular microenvironment. Within cells, a heterotrimeric complex is formed, consisting of two FIH and one covalently linked OTUB1. Complexation of OTUB1 by FIH regulates OTUB1 deubiquitinase activity. Our findings reveal an alternative mechanism for hypoxia adaptation with remarkably high oxygen sensitivity, mediated through covalent protein-protein interactions catalysed by an asparagine modifying dioxygenase. FIH forms a (likely amide) bond with client proteins. Bond formation is highly hypoxia sensitive and occurs co-translationally. FIH forms a heterotrimer with the client protein OTUB1 (FIH2OTUB11). Complex formation between OTUB1 and FIH regulates OTUB1 deubiquitinase activity. Bond formation by hydroxylases is an alternative mechanism for hypoxia adaptation.
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Affiliation(s)
- Christina Pickel
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | - Julia Günter
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland
| | | | - Patrick Spielmann
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland
| | | | - Witold Wolski
- Functional Genomics Center Zurich, University of Zurich, 8057, Zurich, Switzerland
| | - Daniel J Peet
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Roland H Wenger
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland.
| | - Carsten C Scholz
- Institute of Physiology, University of Zurich, 8057, Zurich, Switzerland; National Centre of Competence in Research 'Kidney.CH', Switzerland.
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16
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Hampton-Smith RJ, Davenport BA, Nagarajan Y, Peet DJ. The conservation and functionality of the oxygen-sensing enzyme Factor Inhibiting HIF (FIH) in non-vertebrates. PLoS One 2019; 14:e0216134. [PMID: 31034531 PMCID: PMC6488082 DOI: 10.1371/journal.pone.0216134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 04/15/2019] [Indexed: 12/30/2022] Open
Abstract
The asparaginyl hydroxylase, Factor Inhibiting HIF (FIH), is a cellular dioxygenase. Originally identified as oxygen sensor in the cellular response to hypoxia, where FIH acts as a repressor of the hypoxia inducible transcription factor alpha (HIF-α) proteins through asparaginyl hydroxylation, FIH also hydroxylates many proteins that contain ankyrin repeat domains (ARDs). Given FIH's promiscuity and the unclear functional effects of ARD hydroxylation, the biological relevance of HIF-α and ARD hydroxylation remains uncertain. Here, we have employed evolutionary and enzymatic analyses of FIH, and both HIF-α and ARD-containing substrates, in a broad range of metazoa to better understand their conservation and functional importance. Utilising Tribolium castaneum and Acropora millepora, we provide evidence that FIH from both species are able to hydroxylate HIF-α proteins, supporting conservation of this function beyond vertebrates. We further demonstrate that T. castaneum and A. millepora FIH homologs can also hydroxylate specific ARD proteins. Significantly, FIH is also conserved in several species with inefficiently-targeted or absent HIF, supporting the hypothesis of important HIF-independent functions for FIH. Overall, these data show that while oxygen-dependent HIF-α hydroxylation by FIH is highly conserved in many species, HIF-independent roles for FIH have evolved in others.
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Affiliation(s)
| | - Briony A. Davenport
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Yagnesh Nagarajan
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Daniel J. Peet
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- * E-mail:
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17
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Oh S, Shin S, Janknecht R. The small members of the JMJD protein family: Enzymatic jewels or jinxes? Biochim Biophys Acta Rev Cancer 2019; 1871:406-418. [PMID: 31034925 DOI: 10.1016/j.bbcan.2019.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/07/2019] [Accepted: 04/08/2019] [Indexed: 02/07/2023]
Abstract
Jumonji C domain-containing (JMJD) proteins are mostly epigenetic regulators that demethylate histones. However, a hitherto neglected subfamily of JMJD proteins, evolutionarily distant and characterized by their relatively small molecular weight, exerts different functions by hydroxylating proteins and RNA. Recently, unsuspected proteolytic and tyrosine kinase activities were also ascribed to some of these small JMJD proteins, further increasing their enzymatic versatility. Here, we discuss the ten human small JMJD proteins (HIF1AN, HSPBAP1, JMJD4, JMJD5, JMJD6, JMJD7, JMJD8, RIOX1, RIOX2, TYW5) and their diverse physiological functions. In particular, we focus on the roles of these small JMJD proteins in cancer and other maladies and how they are modulated in diseased cells by an altered metabolic milieu, including hypoxia, reactive oxygen species and oncometabolites. Because small JMJD proteins are enzymes, they are amenable to inhibition by small molecules and may represent novel targets in the therapy of cancer and other diseases.
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Affiliation(s)
- Sangphil Oh
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Sook Shin
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Ralf Janknecht
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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18
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Devabhaktuni A, Lin S, Zhang L, Swaminathan K, Gonzalez CG, Olsson N, Pearlman SM, Rawson K, Elias JE. TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. Nat Biotechnol 2019; 37:469-479. [PMID: 30936560 PMCID: PMC6447449 DOI: 10.1038/s41587-019-0067-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
Although mass spectrometry is well suited to identifying thousands of potential protein post-translational modifications (PTMs), it has historically been biased towards just a few. To measure the entire set of PTMs across diverse proteomes, software must overcome the dual challenges of covering enormous search spaces and distinguishing correct from incorrect spectrum interpretations. Here, we describe TagGraph, a computational tool that overcomes both challenges with an unrestricted string-based search method that is as much as 350-fold faster than existing approaches, and a probabilistic validation model that we optimized for PTM assignments. We applied TagGraph to a published human proteomic dataset of 25 million mass spectra and tripled confident spectrum identifications compared to its original analysis. We identified thousands of modification types on almost 1 million sites in the proteome. We show alternative contexts for highly abundant yet understudied PTMs such as proline hydroxylation, and its unexpected association with cancer mutations. By enabling broad characterization of PTMs, TagGraph informs as to how their functions and regulation intersect.
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Affiliation(s)
- Arun Devabhaktuni
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Sarah Lin
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Lichao Zhang
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Kavya Swaminathan
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Carlos G Gonzalez
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Niclas Olsson
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Samuel M Pearlman
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Keith Rawson
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology Stanford School of Medicine, Stanford University, Stanford, CA, USA.
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19
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Abstract
Cells respond to hypoxia by shifting cellular processes from general housekeeping functions to activating specialized hypoxia-response pathways. Oxygen plays an important role in generating ATP to maintain a productive rate of protein synthesis in normoxia. In hypoxia, the rate of the canonical protein synthesis pathway is significantly slowed and impaired due to limited ATP availability, necessitating an alternative mechanism to mediate protein synthesis and facilitate adaptation. Hypoxia adaptation is largely mediated by hypoxia-inducible factors (HIFs). While HIFs are well known for their transcriptional functions, they also play imperative roles in translation to mediate hypoxic protein synthesis. Such adaptations to hypoxia are often hyperactive in solid tumors, contributing to the expression of cancer hallmarks, including treatment resistance. The current literature on protein synthesis in hypoxia is reviewed here, inclusive of hypoxia-specific mRNA selection to translation termination. Current HIF targeting therapies are also discussed as are the opportunities involved with targeting hypoxia specific protein synthesis pathways.
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Affiliation(s)
- Nancy T Chee
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Ines Lohse
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA
| | - Shaun P Brothers
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami, FL, 33136, USA.
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20
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Walport LJ, Schofield CJ. Adventures in Defining Roles of Oxygenases in the Regulation of Protein Biosynthesis. CHEM REC 2018; 18:1760-1781. [PMID: 30151867 DOI: 10.1002/tcr.201800056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The 2-oxoglutarate (2OG) dependent oxygenases were first identified as having roles in the post-translational modification of procollagen in animals. Subsequently in plants and microbes, they were shown to have roles in the biosynthesis of many secondary metabolites, including signalling molecules and the penicillin/cephalosporin antibiotics. Crystallographic studies of microbial 2OG oxygenases and related enzymes, coupled to DNA sequence analyses, led to the prediction that 2OG oxygenases are widely distributed in aerobic biology. This personal account begins with examples of the roles of 2OG oxygenases in antibiotic biosynthesis, and then describes efforts to assign functions to other predicted 2OG oxygenases. In humans, 2OG oxygenases have been found to have roles in small molecule metabolism, as well as in the epigenetic regulation of protein and nucleic acid biosynthesis and function. The roles and functions of human 2OG oxygenases are compared, focussing on discussion of their substrate and product selectivities. The account aims to emphasize how scoping the substrate selectivity of, sometimes promiscuous, enzymes can provide insights into their functions and so enable therapeutic work.
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Affiliation(s)
- Louise J Walport
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK
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21
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Smith AR, Smith RG, Burrage J, Troakes C, Al-Sarraj S, Kalaria RN, Sloan C, Robinson AC, Mill J, Lunnon K. A cross-brain regions study of ANK1 DNA methylation in different neurodegenerative diseases. Neurobiol Aging 2018; 74:70-76. [PMID: 30439595 DOI: 10.1016/j.neurobiolaging.2018.09.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 07/11/2018] [Accepted: 09/18/2018] [Indexed: 10/28/2022]
Abstract
Recent epigenome-wide association studies in Alzheimer's disease have highlighted consistent robust neuropathology-associated DNA hypermethylation of the ankyrin 1 (ANK1) gene in the cortex. The extent to which altered ANK1 DNA methylation is also associated with other neurodegenerative diseases is not currently known. In the present study, we used bisulfite pyrosequencing to quantify DNA methylation across 8 CpG sites within a 118 bp region of the ANK1 gene across multiple brain regions in Alzheimer's disease, Vascular dementia, Dementia with Lewy bodies, Huntington's disease, and Parkinson's disease. We demonstrate disease-associated ANK1 hypermethylation in the entorhinal cortex in Alzheimer's disease, Huntington's disease, and Parkinson's disease, whereas in donors with Vascular dementia and Dementia with Lewy bodies, we observed elevated ANK1 DNA methylation only in individuals with coexisting Alzheimer's disease pathology. We did not observe any disease-associated differential ANK1 DNA methylation in the striatum in Huntington's disease or the substantia nigra in Parkinson's disease. Our data suggest that ANK1 is characterized by region and disease-specific differential DNA methylation in multiple neurodegenerative diseases.
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Affiliation(s)
- Adam R Smith
- University of Exeter Medical School, University of Bristol, Exeter, UK
| | - Rebecca G Smith
- University of Exeter Medical School, University of Bristol, Exeter, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Bristol, Exeter, UK
| | - Claire Troakes
- Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | - Safa Al-Sarraj
- Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King's College London, London, UK
| | | | - Carolyn Sloan
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Andrew C Robinson
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Bristol, Exeter, UK
| | - Katie Lunnon
- University of Exeter Medical School, University of Bristol, Exeter, UK.
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22
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Kang J, Chun YS, Huh J, Park JW. FIH permits NAA10 to catalyze the oxygen-dependent lysyl-acetylation of HIF-1α. Redox Biol 2018; 19:364-374. [PMID: 30237125 PMCID: PMC6142190 DOI: 10.1016/j.redox.2018.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 12/15/2022] Open
Abstract
The N-terminal acetyltransferase A (NatA) complex, which is composed of NAA10 and NAA15, catalyzes N-terminal acetylation of many proteins in a co-translational manner. Structurally, the catalytic subunit NAA10 was believed to have no activity toward an internal lysine residue because the gate of its catalytic pocket is too narrow. However, several studies have demonstrated that the monomeric NAA10 can acetylate the internal lysine residues of several substrates including hypoxia-inducible factor 1α (HIF-1α). How NAA10 acetylates lysine residues has been an unsolved question. We here found that human FIH (factor inhibiting HIF) hydroxylates human NAA10 at W38 oxygen-dependently and this permits NAA10 to express the lysyl-acetyltransferase activity. The hydroxylated W38 forms a new hydrogen-bond with A67 and widens the gate at the catalytic pocket, which allows the entrance of a lysine residue to the site. Since the FIH-dependent hydroxylation of NAA10 occurs oxygen-dependently, NAA10 acetylates HIF-1α under normoxia but does not under hypoxia. Consequently, the acetylation promotes the pVHL binding to HIF-1α, and in turn HIF-1α is destructed via the ubiquitin-proteasome system. This study provides a novel oxygen-sensing process that determines the substrate specificity of NAA10 depending on an ambient oxygen tension.
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Affiliation(s)
- Jengmin Kang
- Department of Biomedical Science, BK21-plus education program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Yang-Sook Chun
- Department of Biomedical Science, BK21-plus education program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - June Huh
- Department of Chemical and Biological Engineering, Korea University, Anam-dong, Seongbuk-gu, Seoul 136-713, Republic of Korea.
| | - Jong-Wan Park
- Department of Biomedical Science, BK21-plus education program, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Pharmacology, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea.
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23
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Hypermethylated gene ANKDD1A is a candidate tumor suppressor that interacts with FIH1 and decreases HIF1α stability to inhibit cell autophagy in the glioblastoma multiforme hypoxia microenvironment. Oncogene 2018; 38:103-119. [PMID: 30082910 PMCID: PMC6318269 DOI: 10.1038/s41388-018-0423-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 06/01/2018] [Accepted: 06/25/2018] [Indexed: 01/28/2023]
Abstract
Ectopic epigenetic mechanisms play important roles in facilitating tumorigenesis. Here, we first demonstrated that ANKDD1A is a functional tumor suppressor gene, especially in the hypoxia microenvironment. ANKDD1A directly interacts with FIH1 and inhibits the transcriptional activity of HIF1α by upregulating FIH1. In addition, ANKDD1A decreases the half-life of HIF1α by upregulating FIH1, decreases glucose uptake and lactate production, inhibits glioblastoma multiforme (GBM) autophagy, and induces apoptosis in GBM cells under hypoxia. Moreover, ANKDD1A is highly frequently methylated in GBM. The tumor-specific methylation of ANKDD1A indicates that it could be used as a potential epigenetic biomarker as well as a possible therapeutic target.
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24
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Genomic comparisons of Rhizobium species using in silico AFLP-PCR, endonuclease restriction, and AMPylating enzymes. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2018.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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25
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Herr CQ, Hausinger RP. Amazing Diversity in Biochemical Roles of Fe(II)/2-Oxoglutarate Oxygenases. Trends Biochem Sci 2018; 43:517-532. [PMID: 29709390 DOI: 10.1016/j.tibs.2018.04.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/21/2018] [Accepted: 04/01/2018] [Indexed: 12/13/2022]
Abstract
Since their discovery in the 1960s, the family of Fe(II)/2-oxoglutarate-dependent oxygenases has undergone a tremendous expansion to include enzymes catalyzing a vast diversity of biologically important reactions. Recent examples highlight roles in controlling chromatin modification, transcription, mRNA demethylation, and mRNA splicing. Others generate modifications in tRNA, translation factors, ribosomes, and other proteins. Thus, oxygenases affect all components of molecular biology's central dogma, in which information flows from DNA to RNA to proteins. These enzymes also function in biosynthesis and catabolism of cellular metabolites, including antibiotics and signaling molecules. Due to their critical importance, ongoing efforts have targeted family members for the development of specific therapeutics. This review provides a general overview of recently characterized oxygenase reactions and their key biological roles.
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Affiliation(s)
- Caitlyn Q Herr
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.
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26
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Abstract
The EGLN (also called PHD) prolyl hydroxylase enzymes and their canonical targets, the HIFα subunits, represent the core of an ancient oxygen-monitoring machinery used by metazoans. In this review, we highlight recent progress in understanding the overlapping versus specific roles of EGLN enzymes and HIF isoforms and discuss how feedback loops based on recently identified noncoding RNAs introduce additional layers of complexity to the hypoxic response. Based on novel interactions identified upstream and downstream of EGLNs, an integrated network connecting oxygen-sensing functions to metabolic and signaling pathways is gradually emerging with broad therapeutic implications.
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Affiliation(s)
- Mircea Ivan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
| | - William G Kaelin
- Howard Hughes Medical Institute, Boston, MA 02215, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
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LC-MS/MS Analysis Unravels Deep Oxidation of Manganese Superoxide Dismutase in Kidney Cancer. Int J Mol Sci 2017; 18:ijms18020319. [PMID: 28165386 PMCID: PMC5343855 DOI: 10.3390/ijms18020319] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/11/2017] [Accepted: 01/25/2017] [Indexed: 01/11/2023] Open
Abstract
Manganese superoxide dismutase (MNSOD) is one of the major scavengers of reactive oxygen species (ROS) in mitochondria with pivotal regulatory role in ischemic disorders, inflammation and cancer. Here we report oxidative modification of MNSOD in human renal cell carcinoma (RCC) by the shotgun method using data-dependent liquid chromatography tandem mass spectrometry (LC-MS/MS). While 5816 and 5571 proteins were identified in cancer and adjacent tissues, respectively, 208 proteins were found to be up- or down-regulated (p < 0.05). Ontological category, interaction network and Western blotting suggested a close correlation between RCC-mediated proteins and oxidoreductases such as MNSOD. Markedly, oxidative modifications of MNSOD were identified at histidine (H54 and H55), tyrosine (Y58), tryptophan (W147, W149, W205 and W210) and asparagine (N206 and N209) residues additional to methionine. These oxidative insults were located at three hotspots near the hydrophobic pocket of the manganese binding site, of which the oxidation of Y58, W147 and W149 was up-regulated around three folds and the oxidation of H54 and H55 was detected in the cancer tissues only (p < 0.05). When normalized to MNSOD expression levels, relative MNSOD enzymatic activity was decreased in cancer tissues, suggesting impairment of MNSOD enzymatic activity in kidney cancer due to modifications. Thus, LC-MS/MS analysis revealed multiple oxidative modifications of MNSOD at different amino acid residues that might mediate the regulation of the superoxide radicals, mitochondrial ROS scavenging and MNSOD activity in kidney cancer.
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29
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Zurlo G, Guo J, Takada M, Wei W, Zhang Q. New Insights into Protein Hydroxylation and Its Important Role in Human Diseases. Biochim Biophys Acta Rev Cancer 2016; 1866:208-220. [PMID: 27663420 DOI: 10.1016/j.bbcan.2016.09.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 09/15/2016] [Accepted: 09/17/2016] [Indexed: 12/26/2022]
Abstract
Protein hydroxylation is a post-translational modification catalyzed by 2-oxoglutarate-dependent dioxygenases. The hydroxylation modification can take place on various amino acids, including but not limited to proline, lysine, asparagine, aspartate and histidine. A classical example of this modification is hypoxia inducible factor alpha (HIF-α) prolyl hydroxylation, which affects HIF-α protein stability via the Von-Hippel Lindau (VHL) tumor suppressor pathway, a Cullin 2-based E3 ligase adaptor protein frequently mutated in kidney cancer. In addition to protein stability regulation, protein hydroxylation may influence other post-translational modifications or the kinase activity of the modified protein (such as Akt and DYRK1A/B). In other cases, protein hydroxylation may alter protein-protein interaction and its downstream signaling events in vivo (such as OTUB1, MAPK6 and eEF2K). In this review, we highlight the recently identified protein hydroxylation targets and their pathophysiological roles, especially in cancer settings. Better understanding of protein hydroxylation will help identify novel therapeutic targets and their regulation mechanisms to foster development of more effective treatment strategies for various human cancers.
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Affiliation(s)
- Giada Zurlo
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jianping Guo
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Mamoru Takada
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA.
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA.
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30
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Walport LJ, Hopkinson RJ, Chowdhury R, Schiller R, Ge W, Kawamura A, Schofield CJ. Arginine demethylation is catalysed by a subset of JmjC histone lysine demethylases. Nat Commun 2016; 7:11974. [PMID: 27337104 PMCID: PMC4931022 DOI: 10.1038/ncomms11974] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 05/17/2016] [Indexed: 12/11/2022] Open
Abstract
While the oxygen-dependent reversal of lysine N(ɛ)-methylation is well established, the existence of bona fide N(ω)-methylarginine demethylases (RDMs) is controversial. Lysine demethylation, as catalysed by two families of lysine demethylases (the flavin-dependent KDM1 enzymes and the 2-oxoglutarate- and oxygen-dependent JmjC KDMs, respectively), proceeds via oxidation of the N-methyl group, resulting in the release of formaldehyde. Here we report detailed biochemical studies clearly demonstrating that, in purified form, a subset of JmjC KDMs can also act as RDMs, both on histone and non-histone fragments, resulting in formaldehyde release. RDM catalysis is studied using peptides of wild-type sequences known to be arginine-methylated and sequences in which the KDM's methylated target lysine is substituted for a methylated arginine. Notably, the preferred sequence requirements for KDM and RDM activity vary even with the same JmjC enzymes. The demonstration of RDM activity by isolated JmjC enzymes will stimulate efforts to detect biologically relevant RDM activity.
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Affiliation(s)
- Louise J. Walport
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Richard J. Hopkinson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Rasheduzzaman Chowdhury
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Rachel Schiller
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Wei Ge
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Akane Kawamura
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher J. Schofield
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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31
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Wilkins SE, Abboud MI, Hancock RL, Schofield CJ. Targeting Protein-Protein Interactions in the HIF System. ChemMedChem 2016; 11:773-86. [PMID: 26997519 PMCID: PMC4848768 DOI: 10.1002/cmdc.201600012] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 02/24/2016] [Indexed: 12/18/2022]
Abstract
Animals respond to chronic hypoxia by increasing the levels of a transcription factor known as the hypoxia-inducible factor (HIF). HIF upregulates multiple genes, the products of which work to ameliorate the effects of limited oxygen at cellular and systemic levels. Hypoxia sensing by the HIF system involves hydroxylase-catalysed post-translational modifications of the HIF α-subunits, which 1) signal for degradation of HIF-α and 2) limit binding of HIF to transcriptional coactivator proteins. Because the hypoxic response is relevant to multiple disease states, therapeutic manipulation of the HIF-mediated response has considerable medicinal potential. In addition to modulation of catalysis by the HIF hydroxylases, the HIF system manifests other possibilities for therapeutic intervention involving protein-protein and protein-nucleic acid interactions. Recent advances in our understanding of the structural biology and biochemistry of the HIF system are facilitating medicinal chemistry efforts. Herein we give an overview of the HIF system, focusing on structural knowledge of protein-protein interactions and how this might be used to modulate the hypoxic response for therapeutic benefit.
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Affiliation(s)
- Sarah E Wilkins
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Rebecca L Hancock
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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32
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Padayatty SJ, Levine M. Vitamin C: the known and the unknown and Goldilocks. Oral Dis 2016; 22:463-93. [PMID: 26808119 DOI: 10.1111/odi.12446] [Citation(s) in RCA: 382] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 12/11/2022]
Abstract
Vitamin C (Ascorbic Acid), the antiscorbutic vitamin, cannot be synthesized by humans and other primates, and has to be obtained from diet. Ascorbic acid is an electron donor and acts as a cofactor for fifteen mammalian enzymes. Two sodium-dependent transporters are specific for ascorbic acid, and its oxidation product dehydroascorbic acid is transported by glucose transporters. Ascorbic acid is differentially accumulated by most tissues and body fluids. Plasma and tissue vitamin C concentrations are dependent on amount consumed, bioavailability, renal excretion, and utilization. To be biologically meaningful or to be clinically relevant, in vitro and in vivo studies of vitamin C actions have to take into account physiologic concentrations of the vitamin. In this paper, we review vitamin C physiology; the many phenomena involving vitamin C where new knowledge has accrued or where understanding remains limited; raise questions about the vitamin that remain to be answered; and explore lines of investigations that are likely to be fruitful.
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Affiliation(s)
- S J Padayatty
- Molecular and Clinical Nutrition Section, Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - M Levine
- Molecular and Clinical Nutrition Section, Digestive Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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33
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Maxwell PH, Eckardt KU. HIF prolyl hydroxylase inhibitors for the treatment of renal anaemia and beyond. Nat Rev Nephrol 2015; 12:157-68. [DOI: 10.1038/nrneph.2015.193] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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34
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Abstract
The post-translational hydroxylation of prolyl and lysyl residues, as catalyzed by 2-oxoglutarate (2OG)-dependent oxygenases, was first identified in collagen biosynthesis. 2OG oxygenases also catalyze prolyl and asparaginyl hydroxylation of the hypoxia-inducible factors that play important roles in the adaptive response to hypoxia. Subsequently, they have been shown to catalyze N-demethylation (via hydroxylation) of N(ϵ)-methylated histone lysyl residues, as well as hydroxylation of multiple other residues. Recent work has identified roles for 2OG oxygenases in the modification of translation-associated proteins, which in some cases appears to be conserved from microorganisms through to humans. Here we give an overview of protein hydroxylation catalyzed by 2OG oxygenases, focusing on recent discoveries.
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Affiliation(s)
- Suzana Markolovic
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Sarah E Wilkins
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom.
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, United Kingdom.
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35
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Chan MC, Atasoylu O, Hodson E, Tumber A, Leung IKH, Chowdhury R, Gómez-Pérez V, Demetriades M, Rydzik AM, Holt-Martyn J, Tian YM, Bishop T, Claridge TDW, Kawamura A, Pugh CW, Ratcliffe PJ, Schofield CJ. Potent and Selective Triazole-Based Inhibitors of the Hypoxia-Inducible Factor Prolyl-Hydroxylases with Activity in the Murine Brain. PLoS One 2015; 10:e0132004. [PMID: 26147748 PMCID: PMC4492579 DOI: 10.1371/journal.pone.0132004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/09/2015] [Indexed: 01/01/2023] Open
Abstract
As part of the cellular adaptation to limiting oxygen availability in animals, the expression of a large set of genes is activated by the upregulation of the hypoxia-inducible transcription factors (HIFs). Therapeutic activation of the natural human hypoxic response can be achieved by the inhibition of the hypoxia sensors for the HIF system, i.e. the HIF prolyl-hydroxylases (PHDs). Here, we report studies on tricyclic triazole-containing compounds as potent and selective PHD inhibitors which compete with the 2-oxoglutarate co-substrate. One compound (IOX4) induces HIFα in cells and in wildtype mice with marked induction in the brain tissue, revealing that it is useful for studies aimed at validating the upregulation of HIF for treatment of cerebral diseases including stroke.
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Affiliation(s)
- Mun Chiang Chan
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Onur Atasoylu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Emma Hodson
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Anthony Tumber
- Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Ivanhoe K. H. Leung
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Verónica Gómez-Pérez
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Marina Demetriades
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Anna M. Rydzik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - James Holt-Martyn
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Ya-Min Tian
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Tammie Bishop
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Timothy D. W. Claridge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Christopher W. Pugh
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Peter J. Ratcliffe
- Centre for Cellular and Molecular Physiology, University of Oxford, Oxford, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, United Kingdom
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36
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Böttger A, Islam MS, Chowdhury R, Schofield CJ, Wolf A. The oxygenase Jmjd6--a case study in conflicting assignments. Biochem J 2015; 468:191-202. [PMID: 25997831 DOI: 10.1042/bj20150278] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Jumonji domain-containing protein 6 (Jmjd6) is a member of the superfamily of non-haem iron(II) and 2-oxoglutarate (2OG)-dependent oxygenases; it plays an important developmental role in higher animals. Jmjd6 was initially assigned a role as the phosphatidylserine receptor responsible for engulfment of apoptotic cells but this now seems unlikely. Jmjd6 has been shown to be a nuclear localized protein with a JmjC domain comprising a distorted double-stranded β-helical structure characteristic of the 2OG-dependent oxygenases. Jmjd6 was subsequently assigned a role in catalysing N-methyl-arginine residue demethylation on the N-terminus of the human histones H3 and H4; however, this function is also subject to conflicting reports. Jmjd6 does catalyse 2OG-dependent C-5 hydroxylation of lysine residues in mRNA splicing-regulatory proteins and histones; there is also accumulating evidence that Jmjd6 plays a role in splicing (potentially in an iron- and oxygen-dependent manner) as well as in other processes regulating gene expression, including transcriptional pause release. Moreover, a link with tumour progression has been suggested. In the present review we look at biochemical, structural and cellular work on Jmjd6, highlighting areas of controversy and consensus.
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Affiliation(s)
- Angelika Böttger
- *Department of Biology II, Ludwig Maximillians University, Munich, Germany
| | - Md Saiful Islam
- †Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
| | - Rasheduzzaman Chowdhury
- †Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
| | - Christopher J Schofield
- †Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, UK
| | - Alexander Wolf
- ‡Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
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37
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Khater S, Mohanty D. novPTMenzy: a database for enzymes involved in novel post-translational modifications. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav039. [PMID: 25931459 PMCID: PMC4414956 DOI: 10.1093/database/bav039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 04/01/2015] [Indexed: 12/03/2022]
Abstract
With the recent discoveries of novel post-translational modifications (PTMs) which play important roles in signaling and biosynthetic pathways, identification of such PTM catalyzing enzymes by genome mining has been an area of major interest. Unlike well-known PTMs like phosphorylation, glycosylation, SUMOylation, no bioinformatics resources are available for enzymes associated with novel and unusual PTMs. Therefore, we have developed the novPTMenzy database which catalogs information on the sequence, structure, active site and genomic neighborhood of experimentally characterized enzymes involved in five novel PTMs, namely AMPylation, Eliminylation, Sulfation, Hydroxylation and Deamidation. Based on a comprehensive analysis of the sequence and structural features of these known PTM catalyzing enzymes, we have created Hidden Markov Model profiles for the identification of similar PTM catalyzing enzymatic domains in genomic sequences. We have also created predictive rules for grouping them into functional subfamilies and deciphering their mechanistic details by structure-based analysis of their active site pockets. These analytical modules have been made available as user friendly search interfaces of novPTMenzy database. It also has a specialized analysis interface for some PTMs like AMPylation and Eliminylation. The novPTMenzy database is a unique resource that can aid in discovery of unusual PTM catalyzing enzymes in newly sequenced genomes. Database URL: http://www.nii.ac.in/novptmenzy.html
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Affiliation(s)
- Shradha Khater
- Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasisa Mohanty
- Bioinformatics Centre, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
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38
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Lv G, Li Y, Wang Z, Lin H. Hypoxia stimulates the proliferation of neonatal rat vascular smooth muscle cells through activation of hypoxia-inducible factor-1α. Int J Clin Exp Med 2015; 8:496-503. [PMID: 25785022 PMCID: PMC4358477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 01/09/2015] [Indexed: 06/04/2023]
Abstract
Exposure to an adverse intrauterine environment increases the risk of cardiovascular disease later in adult life. It has been shown that hypoxia plays a critical role in vascular remodeling and directly affects vascular smooth muscle cells functions. In the present study, we aimed to investigate the effect of hypoxia on neonatal rat aorta smooth muscle cells (NRSMCs). Our study demonstrated that hypoxia stimulation at 2% oxygen could significantly enhance NRSMCs proliferation in a time dependent manner. Moreover, hypoxia treatment resulted in an increased percentage in the S + G2/M phase and decreased apoptosis rate in NRSMCs. On the molecular level, the protein levels of pro-apoptotic proteins BNIP3 and bax were obviously reduced, while the anti-apoptotic factor bcl-2 was enhanced under hypoxia condition. Furthermore, we found that hypoxia activated hypoxia-inducible factor-1α (HIF-1α) expression and subsequently promoted NRSMCs proliferation. Specific down-regulation of HIF-1α partly abolished the proliferative effect of hypoxia on NRSMCs growth. Taken together, the present study demonstrated that hypoxia treatment promoted NRSMCs growth through activation of HIF-1α, which may contribute to the understanding of the pathogenesis of atherosclerosis.
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Affiliation(s)
- Guorong Lv
- Department of Ultrasound, Second Affiliated Hospital of Fujian Medical UniversityQuanzhou 362000, P. R. China
- Department of Clinical Medicine, Quanzhou Medical CollegeQuanzhou 362100, P. R. China
| | - Yanru Li
- Department of Ultrasound, Second Affiliated Hospital of Fujian Medical UniversityQuanzhou 362000, P. R. China
| | - Zhenhua Wang
- Department of Ultrasound, Second Affiliated Hospital of Fujian Medical UniversityQuanzhou 362000, P. R. China
| | - Huitong Lin
- Department of Ultrasound, Second Affiliated Hospital of Fujian Medical UniversityQuanzhou 362000, P. R. China
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39
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Bishop T, Ratcliffe PJ. Signaling hypoxia by hypoxia-inducible factor protein hydroxylases: a historical overview and future perspectives. HYPOXIA 2014; 2:197-213. [PMID: 27774477 PMCID: PMC5045067 DOI: 10.2147/hp.s47598] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
By the early 1900s, the close matching of oxygen supply with demand was recognized to be a fundamental requirement for physiological function, and multiple adaptive responses to environment hypoxia had been described. Nevertheless, the widespread operation of mechanisms that directly sense and respond to levels of oxygen in animal cells was not appreciated for most of the twentieth century with investigators generally stressing the regulatory importance of metabolic products. Work over the last 25 years has overturned that paradigm. It has revealed the existence of a set of “oxygen-sensing” 2-oxoglutarate dependent dioxygenases that catalyze the hydroxylation of specific amino acid residues and thereby control the stability and activity of hypoxia-inducible factor. The hypoxia-inducible factor hydroxylase pathway regulates a massive transcriptional cascade that is operative in essentially all animal cells. It transduces a wide range of responses to hypoxia, extending well beyond the classical boundaries of hypoxia physiology. Here we review the discovery and elucidation of these pathways, and consider the opportunities and challenges that have been brought into focus by the findings, including new implications for the integrated physiology of hypoxia and therapeutic approaches to ischemic/hypoxic disease.
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Affiliation(s)
- Tammie Bishop
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
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40
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Williams ST, Walport LJ, Hopkinson RJ, Madden SK, Chowdhury R, Schofield CJ, Kawamura A. Studies on the catalytic domains of multiple JmjC oxygenases using peptide substrates. Epigenetics 2014; 9:1596-603. [PMID: 25625844 PMCID: PMC4623018 DOI: 10.4161/15592294.2014.983381] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/22/2014] [Accepted: 10/28/2014] [Indexed: 11/28/2022] Open
Abstract
The JmjC-domain-containing 2-oxoglutarate-dependent oxygenases catalyze protein hydroxylation and N(ϵ)-methyllysine demethylation via hydroxylation. A subgroup of this family, the JmjC lysine demethylases (JmjC KDMs) are involved in histone modifications at multiple sites. There are conflicting reports as to the substrate selectivity of some JmjC oxygenases with respect to KDM activities. In this study, a panel of modified histone H3 peptides was tested for demethylation against 15 human JmjC-domain-containing proteins. The results largely confirmed known N(ϵ)-methyllysine substrates. However, the purified KDM4 catalytic domains showed greater substrate promiscuity than previously reported (i.e., KDM4A was observed to catalyze demethylation at H3K27 as well as H3K9/K36). Crystallographic analyses revealed that the N(ϵ)-methyllysine of an H3K27me3 peptide binds similarly to N(ϵ)-methyllysines of H3K9me3/H3K36me3 with KDM4A. A subgroup of JmjC proteins known to catalyze hydroxylation did not display demethylation activity. Overall, the results reveal that the catalytic domains of the KDM4 enzymes may be less selective than previously identified. They also draw a distinction between the N(ϵ)-methyllysine demethylation and hydroxylation activities within the JmjC subfamily. These results will be of use to those working on functional studies of the JmjC enzymes.
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Key Words
- 2OG oxygenases
- 2OG, 2-oxoglutarate
- Epigenetics
- FIH, Factor Inhibiting HIF
- H3, histone 3
- HIF, Hypoxia Inducible Factor
- JmjC histone demethylase
- JmjC, Jumonji C-terminal
- JmjN, Jumonji N-terminal
- KDM, Lysine Demethylase
- LSD, Lysine Specific Demethylase
- MALDI-TOF MS, Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry
- MINA53, Myc-Induced Nuclear Antigen with a molecular mass of 53 kDa
- NO66, Nucleolar protein 66
- PHD, Plant Homeodomain
- Rp, Ribosomal protein
- TPR, Tetratricopeptide repeat
- demethylation
- histone
- methyllysine
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Affiliation(s)
| | | | | | | | | | | | - Akane Kawamura
- Chemistry Research Laboratory; Oxford, UK
- Radcliffe Department of Medicine; Division of Cardiovascular Medicine; Wellcome Trust Center for Human Genetics; Oxford, UK
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41
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Kobayashi K, Katz A, Rajkovic A, Ishii R, Branson OE, Freitas MA, Ishitani R, Ibba M, Nureki O. The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation. Nucleic Acids Res 2014; 42:12295-305. [PMID: 25274739 PMCID: PMC4231759 DOI: 10.1093/nar/gku898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
EF-P is a bacterial tRNA-mimic protein, which accelerates the ribosome-catalyzed polymerization of poly-prolines. In Escherichia coli, EF-P is post-translationally modified on a conserved lysine residue. The post-translational modification is performed in a two-step reaction involving the addition of a β-lysine moiety and the subsequent hydroxylation, catalyzed by PoxA and YfcM, respectively. The β-lysine moiety was previously shown to enhance the rate of poly-proline synthesis, but the role of the hydroxylation is poorly understood. We solved the crystal structure of YfcM and performed functional analyses to determine the hydroxylation mechanism. In addition, YfcM appears to be structurally distinct from any other hydroxylase structures reported so far. The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology. Furthermore, YfcM has a metal ion-coordinating motif, similar to YbeY. The metal ion-coordinating motif of YfcM resembles a 2-His-1-carboxylate motif, which coordinates an Fe(II) ion and forms the catalytic site of non-heme iron enzymes. Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the β-lysylated lysine residue of EF-P. Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM.
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Affiliation(s)
- Kan Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Assaf Katz
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Andrei Rajkovic
- Molecular, Cell, and Developmental Biology Program, Ohio State University, Columbus, OH 43210, USA
| | - Ryohei Ishii
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Owen E Branson
- Department of Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael A Freitas
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
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42
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Yang M, Su H, Soga T, Kranc KR, Pollard PJ. Prolyl hydroxylase domain enzymes: important regulators of cancer metabolism. HYPOXIA 2014; 2:127-142. [PMID: 27774472 PMCID: PMC5045062 DOI: 10.2147/hp.s47968] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The hypoxia-inducible factor (HIF) prolyl hydroxylase domain enzymes (PHDs) regulate the stability of HIF protein by post-translational hydroxylation of two conserved prolyl residues in its α subunit in an oxygen-dependent manner. Trans-4-prolyl hydroxylation of HIFα under normal oxygen (O2) availability enables its association with the von Hippel-Lindau (VHL) tumor suppressor pVHL E3 ligase complex, leading to the degradation of HIFα via the ubiquitin-proteasome pathway. Due to the obligatory requirement of molecular O2 as a co-substrate, the activity of PHDs is inhibited under hypoxic conditions, resulting in stabilized HIFα, which dimerizes with HIFβ and, together with transcriptional co-activators CBP/p300, activates the transcription of its target genes. As a key molecular regulator of adaptive response to hypoxia, HIF plays important roles in multiple cellular processes and its overexpression has been detected in various cancers. The HIF1α isoform in particular has a strong impact on cellular metabolism, most notably by promoting anaerobic, whilst inhibiting O2-dependent, metabolism of glucose. The PHD enzymes also seem to have HIF-independent functions and are subject to regulation by factors other than O2, such as by metabolic status, oxidative stress, and abnormal levels of endogenous metabolites (oncometabolites) that have been observed in some types of cancers. In this review, we aim to summarize current understandings of the function and regulation of PHDs in cancer with an emphasis on their roles in metabolism.
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Affiliation(s)
- Ming Yang
- Cancer Biology and Metabolism Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Huizhong Su
- Cancer Biology and Metabolism Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Mizukami, Tsuruoka, Yamagata, Japan
| | - Kamil R Kranc
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Patrick J Pollard
- Cancer Biology and Metabolism Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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Johansson C, Tumber A, Che K, Cain P, Nowak R, Gileadi C, Oppermann U. The roles of Jumonji-type oxygenases in human disease. Epigenomics 2014; 6:89-120. [PMID: 24579949 PMCID: PMC4233403 DOI: 10.2217/epi.13.79] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The iron- and 2-oxoglutarate-dependent oxygenases constitute a phylogenetically conserved class of enzymes that catalyze hydroxylation reactions in humans by acting on various types of substrates, including metabolic intermediates, amino acid residues in different proteins and various types of nucleic acids. The discovery of jumonji (Jmj), the founding member of a class of Jmj-type chromatin modifying enzymes and transcriptional regulators, has culminated in the discovery of several branches of histone lysine demethylases, with essential functions in regulating the epigenetic landscape of the chromatin environment. This work has now been considerably expanded into other aspects of epigenetic biology and includes the discovery of enzymatic steps required for methyl-cytosine demethylation as well as modification of RNA and ribosomal proteins. This overview aims to summarize the current knowledge on the human Jmj-type enzymes and their involvement in human pathological processes, including development, cancer, inflammation and metabolic diseases.
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Affiliation(s)
- Catrine Johansson
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Anthony Tumber
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - KaHing Che
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
| | - Peter Cain
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
| | - Radoslaw Nowak
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
- Systems Approaches to Biomedical Sciences, Industrial Doctorate Center (SABS IDC) Oxford, UK
| | - Carina Gileadi
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
| | - Udo Oppermann
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington, OX3 7DQ, UK
- Botnar Research Center, NIHR Oxford Biomedical Research Unit, Nuffield Department of Orthopaedics, Rheumatology & Musculoskeletal Sciences, Oxford, OX3 7LD, UK
- Systems Approaches to Biomedical Sciences, Industrial Doctorate Center (SABS IDC) Oxford, UK
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44
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Regulation of IL-1β-induced NF-κB by hydroxylases links key hypoxic and inflammatory signaling pathways. Proc Natl Acad Sci U S A 2013; 110:18490-5. [PMID: 24145445 DOI: 10.1073/pnas.1309718110] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Hypoxia is a prominent feature of chronically inflamed tissues. Oxygen-sensing hydroxylases control transcriptional adaptation to hypoxia through the regulation of hypoxia-inducible factor (HIF) and nuclear factor κB (NF-κB), both of which can regulate the inflammatory response. Furthermore, pharmacologic hydroxylase inhibitors reduce inflammation in multiple animal models. However, the underlying mechanism(s) linking hydroxylase activity to inflammatory signaling remains unclear. IL-1β, a major proinflammatory cytokine that regulates NF-κB, is associated with multiple inflammatory pathologies. We demonstrate that a combination of prolyl hydroxylase 1 and factor inhibiting HIF hydroxylase isoforms regulates IL-1β-induced NF-κB at the level of (or downstream of) the tumor necrosis factor receptor-associated factor 6 complex. Multiple proteins of the distal IL-1β-signaling pathway are subject to hydroxylation and form complexes with either prolyl hydroxylase 1 or factor inhibiting HIF. Thus, we hypothesize that hydroxylases regulate IL-1β signaling and subsequent inflammatory gene expression. Furthermore, hydroxylase inhibition represents a unique approach to the inhibition of IL-1β-dependent inflammatory signaling.
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45
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Hopkinson RJ, Walport LJ, Münzel M, Rose NR, Smart TJ, Kawamura A, Claridge TDW, Schofield CJ. Is JmjC Oxygenase Catalysis Limited to Demethylation? Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303282] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hopkinson RJ, Walport LJ, Münzel M, Rose NR, Smart TJ, Kawamura A, Claridge TDW, Schofield CJ. Is JmjC oxygenase catalysis limited to demethylation? Angew Chem Int Ed Engl 2013; 52:7709-13. [PMID: 23788451 PMCID: PMC3798130 DOI: 10.1002/anie.201303282] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Richard J Hopkinson
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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47
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Janke K, Brockmeier U, Kuhlmann K, Eisenacher M, Nolde J, Meyer HE, Mairbäurl H, Metzen E. Factor inhibiting HIF-1 (FIH-1) modulates protein interactions of apoptosis-stimulating p53 binding protein 2 (ASPP2). J Cell Sci 2013; 126:2629-40. [PMID: 23606740 DOI: 10.1242/jcs.117564] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The asparaginyl hydroxylase factor inhibiting HIF-1 (FIH-1) is an important suppressor of hypoxia-inducible factor (HIF) activity. In addition to HIF-α, FIH-1 was previously shown to hydroxylate other substrates within a highly conserved protein interaction domain, termed the ankyrin repeat domain (ARD). However, to date, the biological role of FIH-1-dependent ARD hydroxylation could not be clarified for any ARD-containing substrate. The apoptosis-stimulating p53-binding protein (ASPP) family members were initially identified as highly conserved regulators of the tumour suppressor p53. In addition, ASPP2 was shown to be important for the regulation of cell polarity through interaction with partitioning defective 3 homolog (Par-3). Using mass spectrometry we identified ASPP2 as a new substrate of FIH-1 but inhibitory ASPP (iASPP) was not hydroxylated. We demonstrated that ASPP2 asparagine 986 (N986) is a single hydroxylation site located within the ARD. ASPP2 protein levels and stability were not affected by depletion or inhibition of FIH-1. However, FIH-1 depletion did lead to impaired binding of Par-3 to ASPP2 while the interaction between ASPP2 and p53, apoptosis and proliferation of the cancer cells were not affected. Depletion of FIH-1 and incubation with the hydroxylase inhibitor dimethyloxalylglycine (DMOG) resulted in relocation of ASPP2 from cell-cell contacts to the cytosol. Our data thus demonstrate that protein interactions of ARD-containing substrates can be modified by FIH-1-dependent hydroxylation. The large cellular pool of ARD-containing proteins suggests that FIH-1 can affect a broad range of cellular functions and signalling pathways under certain conditions, for example, in response to severe hypoxia.
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Affiliation(s)
- Kirsten Janke
- Institute of Physiology, Faculty of Medicine, University Duisburg-Essen, 45147 Essen, Germany
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48
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Yang M, Hardy AP, Chowdhury R, Loik ND, Scotti JS, McCullagh JSO, Claridge TDW, McDonough MA, Ge W, Schofield CJ. Substrate Selectivity Analyses of Factor Inhibiting Hypoxia-Inducible Factor. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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49
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Yang M, Hardy AP, Chowdhury R, Loik ND, Scotti JS, McCullagh JSO, Claridge TDW, McDonough MA, Ge W, Schofield CJ. Substrate selectivity analyses of factor inhibiting hypoxia-inducible factor. Angew Chem Int Ed Engl 2013; 52:1700-4. [PMID: 23296631 DOI: 10.1002/anie.201208046] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Ming Yang
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
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50
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Walport LJ, Hopkinson RJ, Schofield CJ. Mechanisms of human histone and nucleic acid demethylases. Curr Opin Chem Biol 2012; 16:525-34. [PMID: 23063108 DOI: 10.1016/j.cbpa.2012.09.015] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/17/2012] [Accepted: 09/19/2012] [Indexed: 01/31/2023]
Abstract
The discovery that protein and nucleic acid demethylation is common opens up the possibility of 'methylation cycles' of functional importance, including in the regulation of gene expression. The mechanisms of known demethylases can be broadly divided into those involving nucleophilic catalysis and those involving oxidative catalysis. The latter group appear more common; they produce formaldehyde as a co-product. Nucleophilic demethylases include those proceeding via irreversible S-methylation and methyl esterases. In addition to the direct reversal of methylation, demethylation can occur concurrent with loss of other groups, such as in methylarginine hydrolysis, oxidation of N(ɛ)-methyllysine to allysine, and indirectly, for example via base-excision repair. We discuss chemically viable mechanisms for biological demethylation and summarise mechanistic knowledge of the major known families of demethylases.
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Affiliation(s)
- Louise J Walport
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
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