1
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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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2
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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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3
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Ferrante F, Giaimo BD, Friedrich T, Sugino T, Mertens D, Kugler S, Gahr BM, Just S, Pan L, Bartkuhn M, Potente M, Oswald F, Borggrefe T. Hydroxylation of the NOTCH1 intracellular domain regulates Notch signaling dynamics. Cell Death Dis 2022; 13:600. [PMID: 35821235 PMCID: PMC9276811 DOI: 10.1038/s41419-022-05052-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 01/21/2023]
Abstract
Notch signaling plays a pivotal role in the development and, when dysregulated, it contributes to tumorigenesis. The amplitude and duration of the Notch response depend on the posttranslational modifications (PTMs) of the activated NOTCH receptor - the NOTCH intracellular domain (NICD). In normoxic conditions, the hydroxylase FIH (factor inhibiting HIF) catalyzes the hydroxylation of two asparagine residues of the NICD. Here, we investigate how Notch-dependent gene transcription is regulated by hypoxia in progenitor T cells. We show that the majority of Notch target genes are downregulated upon hypoxia. Using a hydroxyl-specific NOTCH1 antibody we demonstrate that FIH-mediated NICD1 hydroxylation is reduced upon hypoxia or treatment with the hydroxylase inhibitor dimethyloxalylglycine (DMOG). We find that a hydroxylation-resistant NICD1 mutant is functionally impaired and more ubiquitinated. Interestingly, we also observe that the NICD1-deubiquitinating enzyme USP10 is downregulated upon hypoxia. Moreover, the interaction between the hydroxylation-defective NICD1 mutant and USP10 is significantly reduced compared to the NICD1 wild-type counterpart. Together, our data suggest that FIH hydroxylates NICD1 in normoxic conditions, leading to the recruitment of USP10 and subsequent NICD1 deubiquitination and stabilization. In hypoxia, this regulatory loop is disrupted, causing a dampened Notch response.
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Affiliation(s)
- Francesca Ferrante
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Benedetto Daniele Giaimo
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Tobias Friedrich
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany ,Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Aulweg 128, 35392 Giessen, Germany
| | - Toshiya Sugino
- grid.418032.c0000 0004 0491 220XMax Planck Institute for Heart and Lung Research, Angiogenesis and Metabolism Laboratory, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Daniel Mertens
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, Albert-Einstein-Allee 23, 89081 Ulm, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Bridging Group Mechanisms of Leukemogenesis, B061, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Sabrina Kugler
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine III, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Bernd Martin Gahr
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Molecular Cardiology, Department of Internal Medicine II, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Steffen Just
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Molecular Cardiology, Department of Internal Medicine II, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Leiling Pan
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Marek Bartkuhn
- Biomedical Informatics and Systems Medicine, Science Unit for Basic and Clinical Medicine, Aulweg 128, 35392 Giessen, Germany ,Institute for Lung Health (ILH), Aulweg 132, 35392 Giessen, Germany
| | - Michael Potente
- grid.418032.c0000 0004 0491 220XMax Planck Institute for Heart and Lung Research, Angiogenesis and Metabolism Laboratory, Ludwigstr. 43, 61231 Bad Nauheim, Germany ,grid.484013.a0000 0004 6879 971XBerlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany ,grid.419491.00000 0001 1014 0849Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Franz Oswald
- grid.410712.10000 0004 0473 882XUniversity Medical Center Ulm, Center for Internal Medicine, Department of Internal Medicine I, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Tilman Borggrefe
- grid.8664.c0000 0001 2165 8627Institute of Biochemistry, University of Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
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4
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Folding and Stability of Ankyrin Repeats Control Biological Protein Function. Biomolecules 2021; 11:biom11060840. [PMID: 34198779 PMCID: PMC8229355 DOI: 10.3390/biom11060840] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
Ankyrin repeat proteins are found in all three kingdoms of life. Fundamentally, these proteins are involved in protein-protein interaction in order to activate or suppress biological processes. The basic architecture of these proteins comprises repeating modules forming elongated structures. Due to the lack of long-range interactions, a graded stability among the repeats is the generic properties of this protein family determining both protein folding and biological function. Protein folding intermediates were frequently found to be key for the biological functions of repeat proteins. In this review, we discuss most recent findings addressing this close relation for ankyrin repeat proteins including DARPins, Notch receptor ankyrin repeat domain, IκBα inhibitor of NFκB, and CDK inhibitor p19INK4d. The role of local folding and unfolding and gradual stability of individual repeats will be discussed during protein folding, protein-protein interactions, and post-translational modifications. The conformational changes of these repeats function as molecular switches for biological regulation, a versatile property for modern drug discovery.
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5
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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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6
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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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7
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Bonnici J, Tumber A, Kawamura A, Schofield CJ. Inhibitors of both the N-methyl lysyl- and arginyl-demethylase activities of the JmjC oxygenases. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170071. [PMID: 29685975 PMCID: PMC5915715 DOI: 10.1098/rstb.2017.0071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2017] [Indexed: 12/22/2022] Open
Abstract
The Jumonji C (JmjC) family of 2-oxoglutarate (2OG)-dependent oxygenases have established roles in the regulation of transcription via the catalysis of demethylation of Nε-methylated lysine residues in histone tails, especially the N-terminal tail of histone H3. Most human JmjC Nɛ -methyl lysine demethylases (KDMs) are complex enzymes, with 'reader domains' in addition to their catalytic domains. Recent biochemical evidence has shown that some, but not all, JmjC KDMs also have Nω-methyl arginyl demethylase (RDM) activity. JmjC KDM activity has been linked to multiple cancers and some JmjC proteins are therapeutic targets. It is, therefore, important to test not only whether compounds in development inhibit the KDM activity of targeted JmjC demethylases, but also whether they inhibit other activities of these proteins. Here we report biochemical studies on the potential dual inhibition of JmjC KDM and RDM activities using a model JmjC demethylase, KDM4E (JMJD2E). The results reveal that all of the tested compounds inhibit both the KDM and RDM activities, raising questions about the in vivo effects of the inhibitors.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'.
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Affiliation(s)
- Joanna Bonnici
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Anthony Tumber
- 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, University of Oxford, 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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8
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Bailey PSJ, Nathan JA. Metabolic Regulation of Hypoxia-Inducible Transcription Factors: The Role of Small Molecule Metabolites and Iron. Biomedicines 2018; 6:biomedicines6020060. [PMID: 29772792 PMCID: PMC6027492 DOI: 10.3390/biomedicines6020060] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 02/02/2023] Open
Abstract
Hypoxia-inducible transcription factors (HIFs) facilitate cellular adaptations to low-oxygen environments. However, it is increasingly recognised that HIFs may be activated in response to metabolic stimuli, even when oxygen is present. Understanding the mechanisms for the crosstalk that exists between HIF signalling and metabolic pathways is therefore important. This review focuses on the metabolic regulation of HIFs by small molecule metabolites and iron, highlighting the latest studies that explore how tricarboxylic acid (TCA) cycle intermediates, 2-hydroxyglutarate (2-HG) and intracellular iron levels influence the HIF response through modulating the activity of prolyl hydroxylases (PHDs). We also discuss the relevance of these metabolic pathways in physiological and disease contexts. Lastly, as PHDs are members of a large family of 2-oxoglutarate (2-OG) dependent dioxygenases that can all respond to metabolic stimuli, we explore the broader role of TCA cycle metabolites and 2-HG in the regulation of 2-OG dependent dioxygenases, focusing on the enzymes involved in chromatin remodelling.
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Affiliation(s)
- Peter S J Bailey
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge CB2 0XY, UK.
| | - James A Nathan
- Cambridge Institute for Medical Research, Department of Medicine, University of Cambridge, Cambridge CB2 0XY, UK.
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9
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The Factor Inhibiting HIF Asparaginyl Hydroxylase Regulates Oxidative Metabolism and Accelerates Metabolic Adaptation to Hypoxia. Cell Metab 2018; 27:898-913.e7. [PMID: 29617647 PMCID: PMC5887987 DOI: 10.1016/j.cmet.2018.02.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/29/2017] [Accepted: 02/20/2018] [Indexed: 01/16/2023]
Abstract
Animals require an immediate response to oxygen availability to allow rapid shifts between oxidative and glycolytic metabolism. These metabolic shifts are highly regulated by the HIF transcription factor. The factor inhibiting HIF (FIH) is an asparaginyl hydroxylase that controls HIF transcriptional activity in an oxygen-dependent manner. We show here that FIH loss increases oxidative metabolism, while also increasing glycolytic capacity, and that this gives rise to an increase in oxygen consumption. We further show that the loss of FIH acts to accelerate the cellular metabolic response to hypoxia. Skeletal muscle expresses 50-fold higher levels of FIH than other tissues: we analyzed skeletal muscle FIH mutants and found a decreased metabolic efficiency, correlated with an increased oxidative rate and an increased rate of hypoxic response. We find that FIH, through its regulation of oxidation, acts in concert with the PHD/vHL pathway to accelerate HIF-mediated metabolic responses to hypoxia.
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10
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Mills DB, Francis WR, Vargas S, Larsen M, Elemans CP, Canfield DE, Wörheide G. The last common ancestor of animals lacked the HIF pathway and respired in low-oxygen environments. eLife 2018; 7:31176. [PMID: 29402379 PMCID: PMC5800844 DOI: 10.7554/elife.31176] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 12/21/2017] [Indexed: 12/30/2022] Open
Abstract
Animals have a carefully orchestrated relationship with oxygen. When exposed to low environmental oxygen concentrations, and during periods of increased energy expenditure, animals maintain cellular oxygen homeostasis by enhancing internal oxygen delivery, and by enabling the anaerobic production of ATP. These low-oxygen responses are thought to be controlled universally across animals by the hypoxia-inducible factor (HIF). We find, however, that sponge and ctenophore genomes lack key components of the HIF pathway. Since sponges and ctenophores are likely sister to all remaining animal phyla, the last common ancestor of extant animals likely lacked the HIF pathway as well. Laboratory experiments show that the marine sponge Tethya wilhelma maintains normal transcription under oxygen levels down to 0.25% of modern atmospheric saturation, the lowest levels we investigated, consistent with the predicted absence of HIF or any other HIF-like pathway. Thus, the last common ancestor of all living animals could have metabolized aerobically under very low environmental oxygen concentrations. Almost all animals need oxygen to live. This is because they use oxygen to release much of the energy locked up in their diets. Oxygen may have also played a crucial role in the early evolution of animal life. Animals evolved from single-celled ancestors in the ocean over 800 million years ago. Before then, it is debated whether the atmosphere and ocean had enough oxygen to permit animals to evolve. Oxygen levels are much higher now, but oxygen availability still varies in some environments. If oxygen becomes limited (a condition known as hypoxia), almost all animals react using a specific set of molecules known as the HIF pathway. This pathway – which is named after proteins called “hypoxia-inducible factors” – triggers changes that help the animal to maintain a stable level of oxygen in its cells. Yet it was not clear if the capacity to sense hypoxia and regulate oxygen demands within the body evolved in the ancestor of all animals, or if it evolved more recently. When trying to understand early evolution, scientists often turn to some living species that sit on the oldest branches of a group’s family tree. In the animal kingdom, sponges and comb jellies occupy those branches. Mills, Francis et al. have now searched the genomes of several of these animals to ask how oxygen sensing evolved. The genomes of the sponges and comb jellies surveyed lack key components of the HIF pathway, suggesting that the last common ancestor of living animals lacked the HIF pathway as well. This also implies that the ancestor of all animals probably did not respond to oxygen stress or used unknown mechanisms to deal with it instead. In laboratory experiments, Mills, Francis et al. saw that a marine sponge named Tethya wilhelma does not alter its gene activity even when the oxygen levels are reduced to 0.25% of modern levels. This is consistent with the predicted absence of a HIF pathway or anything similar. Together these finding may indicate that the last common ancestor of all living animals maintained normal gene activity even at very low concentrations of oxygen. These findings help scientists understand how life and the global environment have shaped each other since the origin of life over 3.5 billion years ago. This fundamental knowledge may provide the context needed to help society navigate through current and on-going environmental changes, including the dropping oxygen levels in the world’s oceans.
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Affiliation(s)
- Daniel B Mills
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Warren R Francis
- Paleontology & Geobiology, Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sergio Vargas
- Paleontology & Geobiology, Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Morten Larsen
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Coen Ph Elemans
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Donald E Canfield
- Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Gert Wörheide
- Paleontology & Geobiology, Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany.,GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany.,SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany
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11
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Price C, Merchant M, Jones S, Best A, Von Dwingelo J, Lawrenz MB, Alam N, Schueler-Furman O, Kwaik YA. Host FIH-Mediated Asparaginyl Hydroxylation of Translocated Legionella pneumophila Effectors. Front Cell Infect Microbiol 2017; 7:54. [PMID: 28321389 PMCID: PMC5337513 DOI: 10.3389/fcimb.2017.00054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/13/2017] [Indexed: 01/15/2023] Open
Abstract
FIH-mediated post-translational modification through asparaginyl hydroxylation of eukaryotic proteins impacts regulation of protein-protein interaction. We have identified the FIH recognition motif in 11 Legionella pneumophila translocated effectors, YopM of Yersinia, IpaH4.5 of Shigella and an ankyrin protein of Rickettsia. Mass spectrometry analyses of the AnkB and AnkH effectors of L. pneumophila confirm their asparaginyl hydroxylation. Consistent with localization of the AnkB effector to the Legionella-containing vacuole (LCV) membrane and its modification by FIH, our data show that FIH and its two interacting proteins, Mint3 and MT1-MMP are acquired by the LCV in a Dot/Icm type IV secretion-dependent manner. Chemical inhibition or RNAi-mediated knockdown of FIH promotes LCV-lysosomes fusion, diminishes decoration of the LCV with polyubiquitinated proteins, and abolishes intra-vacuolar replication of L. pneumophila. These data show acquisition of the host FIH by a pathogen-containing vacuole and that asparaginyl-hydroxylation of translocated effectors is indispensable for their function.
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Affiliation(s)
- Christopher Price
- Department of Microbiology and Immunology, College of Medicine, University of Louisville Louisville, KY, USA
| | - Michael Merchant
- Department of Medicine-Renal, College of Medicine, University of Louisville Louisville, KY, USA
| | - Snake Jones
- Department of Microbiology and Immunology, College of Medicine, University of Louisville Louisville, KY, USA
| | - Ashley Best
- Department of Microbiology and Immunology, College of Medicine, University of Louisville Louisville, KY, USA
| | - Juanita Von Dwingelo
- Department of Microbiology and Immunology, College of Medicine, University of Louisville Louisville, KY, USA
| | - Matthew B Lawrenz
- Department of Microbiology and Immunology, College of Medicine, University of LouisvilleLouisville, KY, USA; Center for Predictive Medicine, College of Medicine, University of LouisvilleLouisville, KY, USA
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), Faculty of Medicine, Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), Faculty of Medicine, Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Yousef A Kwaik
- Department of Microbiology and Immunology, College of Medicine, University of LouisvilleLouisville, KY, USA; Center for Predictive Medicine, College of Medicine, University of LouisvilleLouisville, KY, USA
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12
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Ankyrin Repeat Proteins of Orf Virus Influence the Cellular Hypoxia Response Pathway. J Virol 2016; 91:JVI.01430-16. [PMID: 27795413 DOI: 10.1128/jvi.01430-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/18/2016] [Indexed: 11/20/2022] Open
Abstract
Hypoxia-inducible factor (HIF) is a transcriptional activator with a central role in regulating cellular responses to hypoxia. It is also emerging as a major target for viral manipulation of the cellular environment. Under normoxic conditions, HIF is tightly suppressed by the activity of oxygen-dependent prolyl and asparaginyl hydroxylases. The asparaginyl hydroxylase active against HIF, factor inhibiting HIF (FIH), has also been shown to hydroxylate some ankyrin repeat (ANK) proteins. Using bioinformatic analysis, we identified the five ANK proteins of the parapoxvirus orf virus (ORFV) as potential substrates of FIH. Consistent with this prediction, coimmunoprecipitation of FIH was detected with each of the ORFV ANK proteins, and for one representative ORFV ANK protein, the interaction was shown to be dependent on the ANK domain. Immunofluorescence studies revealed colocalization of FIH and the viral ANK proteins. In addition, mass spectrometry confirmed that three of the five ORFV ANK proteins are efficiently hydroxylated by FIH in vitro While FIH levels were unaffected by ORFV infection, transient expression of each of the ORFV ANK proteins resulted in derepression of HIF-1α activity in reporter gene assays. Furthermore, ORFV-infected cells showed upregulated HIF target gene expression. Our data suggest that sequestration of FIH by ORFV ANK proteins leads to derepression of HIF activity. These findings reveal a previously unknown mechanism of viral activation of HIF that may extend to other members of the poxvirus family. IMPORTANCE The protein-protein binding motif formed from multiple repeats of the ankyrin motif is common among chordopoxviruses. However, information on the roles of these poxviral ankyrin repeat (ANK) proteins remains limited. Our data indicate that the parapoxvirus orf virus (ORFV) is able to upregulate hypoxia-inducible factor (HIF) target gene expression. This response is mediated by the viral ANK proteins, which sequester the HIF regulator FIH (factor inhibiting HIF). This is the first demonstration of any viral protein interacting directly with FIH. Our data reveal a new mechanism by which viruses reprogram HIF, a master regulator of cellular metabolism, and also show a new role for the ANK family of poxvirus proteins.
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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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FIH Regulates Cellular Metabolism through Hydroxylation of the Deubiquitinase OTUB1. PLoS Biol 2016; 14:e1002347. [PMID: 26752685 PMCID: PMC4709136 DOI: 10.1371/journal.pbio.1002347] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 12/07/2015] [Indexed: 12/30/2022] Open
Abstract
The asparagine hydroxylase, factor inhibiting HIF (FIH), confers oxygen-dependence upon the hypoxia-inducible factor (HIF), a master regulator of the cellular adaptive response to hypoxia. Studies investigating whether asparagine hydroxylation is a general regulatory oxygen-dependent modification have identified multiple non-HIF targets for FIH. However, the functional consequences of this outside of the HIF pathway remain unclear. Here, we demonstrate that the deubiquitinase ovarian tumor domain containing ubiquitin aldehyde binding protein 1 (OTUB1) is a substrate for hydroxylation by FIH on N22. Mutation of N22 leads to a profound change in the interaction of OTUB1 with proteins important in cellular metabolism. Furthermore, in cultured cells, overexpression of N22A mutant OTUB1 impairs cellular metabolic processes when compared to wild type. Based on these data, we hypothesize that OTUB1 is a target for functional hydroxylation by FIH. Additionally, we propose that our results provide new insight into the regulation of cellular energy metabolism during hypoxic stress and the potential for targeting hydroxylases for therapeutic benefit. The oxygen-dependent asparagine hydroxylase FIH regulates the transcription factor HIF during the cellular response to hypoxia. This study suggests that FIH may also contribute to the hypoxia response by affecting cellular metabolism via altered deubiquitinase targeting. Hypoxia is a commonly encountered physiologic and pathophysiologic stress to which mammalian cells have evolved an effective adaptive response. This response is governed by a transcription factor termed the hypoxia-inducible factor (HIF). The mechanisms linking the cellular sensing of oxygen levels to HIF activation have been elucidated and involve oxygen-dependent hydroxylation of HIF on proline and asparagine residues by a family of hydroxylases. A key question that remains unclear is the extent to which oxygen-dependent hydroxylation occurs as a functional post-translational modification outside of the HIF pathway. This is key to developing our understanding of whether hydroxylation is a general regulatory modification or one which has specifically evolved for the regulation of HIF. Here, we demonstrate that the deubiquitinase ovarian tumor domain containing ubiquitin aldehyde binding protein 1 (OTUB1) is a target for functional hydroxylation by the FIH hydroxylase. Hydroxylation of OTUB1 by FIH on asparagine residue N22 results in a restriction in its interactome, leading us to hypothesize a possible role for hydroxylation in substrate targeting. Of interest, interactions of OTUB1 with a number of proteins involved in metabolism are altered upon removal of the hydroxylation site—implicating OTUB1 as a possible link between oxygen sensing and the regulation of metabolism.
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Pharmacological targeting of the HIF hydroxylases--A new field in medicine development. Mol Aspects Med 2016; 47-48:54-75. [PMID: 26791432 DOI: 10.1016/j.mam.2016.01.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/11/2015] [Accepted: 01/04/2016] [Indexed: 12/13/2022]
Abstract
In human cells oxygen levels are 'sensed' by a set of ferrous iron and 2-oxoglutarate dependent dioxygenases. These enzymes regulate a broad range of cellular and systemic responses to hypoxia by catalysing the post-translational hydroxylation of specific residues in the alpha subunits of hypoxia inducible factor (HIF) transcriptional complexes. The HIF hydroxylases are now the subject of pharmaceutical targeting by small molecule inhibitors that aim to activate or augment the endogenous HIF transcriptional response for the treatment of anaemia and other hypoxic human diseases. Here we consider the rationale for this therapeutic strategy from the biochemical, biological and medical perspectives. We outline structural and mechanistic considerations that are relevant to the design of HIF hydroxylase inhibitors, including likely determinants of specificity, and review published reports on their activity in pre-clinical models and clinical trials.
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16
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Tarhonskaya H, Hardy AP, Howe EA, Loik ND, Kramer HB, McCullagh JSO, Schofield CJ, Flashman E. Kinetic Investigations of the Role of Factor Inhibiting Hypoxia-inducible Factor (FIH) as an Oxygen Sensor. J Biol Chem 2015; 290:19726-42. [PMID: 26112411 PMCID: PMC4528135 DOI: 10.1074/jbc.m115.653014] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 06/24/2015] [Indexed: 01/23/2023] Open
Abstract
The hypoxia-inducible factor (HIF) hydroxylases regulate hypoxia sensing in animals. In humans, they comprise three prolyl hydroxylases (PHD1-3 or EGLN1-3) and factor inhibiting HIF (FIH). FIH is an asparaginyl hydroxylase catalyzing post-translational modification of HIF-α, resulting in reduction of HIF-mediated transcription. Like the PHDs, FIH is proposed to have a hypoxia-sensing role in cells, enabling responses to changes in cellular O2 availability. PHD2, the most important human PHD isoform, is proposed to be biochemically/kinetically suited as a hypoxia sensor due to its relatively high sensitivity to changes in O2 concentration and slow reaction with O2. To ascertain whether these parameters are conserved among the HIF hydroxylases, we compared the reactions of FIH and PHD2 with O2. Consistent with previous reports, we found lower Km(app)(O2) values for FIH than for PHD2 with all HIF-derived substrates. Under pre-steady-state conditions, the O2-initiated FIH reaction is significantly faster than that of PHD2. We then investigated the kinetics with respect to O2 of the FIH reaction with ankyrin repeat domain (ARD) substrates. FIH has lower Km(app)(O2) values for the tested ARDs than HIF-α substrates, and pre-steady-state O2-initiated reactions were faster with ARDs than with HIF-α substrates. The results correlate with cellular studies showing that FIH is active at lower O2 concentrations than the PHDs and suggest that competition between HIF-α and ARDs for FIH is likely to be biologically relevant, particularly in hypoxic conditions. The overall results are consistent with the proposal that the kinetic properties of individual oxygenases reflect their biological capacity to act as hypoxia sensors.
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Affiliation(s)
- Hanna Tarhonskaya
- From the Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom and
| | - Adam P Hardy
- From the Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom and
| | - Emily A Howe
- From the Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom and
| | - Nikita D Loik
- From the Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom and
| | - Holger B Kramer
- the OXION Proteomics Facility, Department of Physiology, Anatomy, and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, United Kingdom
| | - James S O McCullagh
- From the Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom and
| | - Christopher J Schofield
- From the Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom and
| | - Emily Flashman
- From the Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom and
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Kiriakidis S, Henze A, Kruszynska‐Ziaja I, Skobridis K, Theodorou V, Paleolog EM, Mazzone M. Factor‐inhibiting HIF‐1 (FIH‐1) is required for human vascular endothelial cell survival. FASEB J 2015; 29:2814-27. [DOI: 10.1096/fj.14-252379] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 03/06/2015] [Indexed: 01/22/2023]
Affiliation(s)
- Serafim Kiriakidis
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesKennedy Institute of Rheumatology, University of OxfordUnited Kingdom
| | - Anne‐Theres Henze
- Laboratory of Molecular Oncology and Angiogenesis, Vesalius Research Center, Vlaams Instituut voor Biotechnologie (VIB)LeuvenBelgium
- Laboratory of Molecular Oncology and Angiogenesis, Vesalius Research CenterDepartment of OncologyKatholieke Universiteit (KU)LeuvenBelgium
| | - Ilona Kruszynska‐Ziaja
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesKennedy Institute of Rheumatology, University of OxfordUnited Kingdom
| | - Konstantinos Skobridis
- Department of ChemistrySection of Organic Chemistry and BiochemistryUniversity of IoanninaGreece
| | - Vassiliki Theodorou
- Department of ChemistrySection of Organic Chemistry and BiochemistryUniversity of IoanninaGreece
| | - Ewa M. Paleolog
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal SciencesKennedy Institute of Rheumatology, University of OxfordUnited Kingdom
| | - Massimiliano Mazzone
- Laboratory of Molecular Oncology and Angiogenesis, Vesalius Research Center, Vlaams Instituut voor Biotechnologie (VIB)LeuvenBelgium
- Laboratory of Molecular Oncology and Angiogenesis, Vesalius Research CenterDepartment of OncologyKatholieke Universiteit (KU)LeuvenBelgium
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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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19
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Hangasky JA, Ivison GT, Knapp MJ. Substrate positioning by Gln(239) stimulates turnover in factor inhibiting HIF, an αKG-dependent hydroxylase. Biochemistry 2014; 53:5750-8. [PMID: 25119663 PMCID: PMC4165446 DOI: 10.1021/bi500703s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Nonheme Fe(II)/αKG-dependent
oxygenases catalyze diverse
reactions, typically inserting an O atom from O2 into a
C–H bond. Although the key to their catalytic cycle is the
fact that binding and positioning of primary substrate precede O2 activation, the means by which substrate binding stimulates
turnover is not well understood. Factor Inhibiting HIF (FIH) is a
Fe(II)/αKG-dependent oxygenase that acts as a cellular oxygen
sensor in humans by hydroxylating the target residue Asn803, found in the C-terminal transactivation domain (CTAD) of hypoxia
inducible factor-1. FIH-Gln239 makes two hydrogen bonds
with CTAD-Asn803, positioning this target residue over
the Fe(II). We hypothesized the positioning of the side chain of CTAD-Asn803 by FIH-Gln239 was critical for stimulating O2 activation and subsequent substrate hydroxylation. The steady-state
characterization of five FIH-Gln239 variants (Ala, Asn,
Glu, His, and Leu) tested the role of hydrogen bonding potential and
sterics near the target residue. Each variant exhibited a 20–1200-fold
decrease in kcat and kcat/KM(CTAD), but no change
in KM(CTAD), indicating that the step
after CTAD binding was affected by point mutation. Uncoupled O2 activation was prominent in these variants, as shown by large
coupling ratios (C = [succinate]/[CTAD-OH] = 3–5)
for each of the FIH-Gln239 → X variants. The coupling
ratios decreased in D2O, indicating an isotope-sensitive
inactivation for variants, not observed in the wild type. The data
presented indicate that the proper positioning of CTAD-Asn803 by FIH-Gln239 is necessary to suppress uncoupled turnover
and to support substrate hydroxylation, suggesting substrate positioning
may be crucial for directing O2 reactivity within the broader
class of αKG hydroxylases.
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Affiliation(s)
- John A Hangasky
- Department of Chemistry, University of Massachusetts at Amherst , Amherst, Massachusetts 01003, United States
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20
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Karttunen S, Duffield M, Scrimgeour NR, Squires L, Lim WL, Dallas ML, Scragg JL, Chicher J, Dave KA, Whitelaw ML, Peers C, Gorman JJ, Gleadle JM, Rychkov GY, Peet DJ. Oxygen-dependent hydroxylation by Factor Inhibiting HIF (FIH) regulates the TRPV3 ion channel. J Cell Sci 2014; 128:225-31. [DOI: 10.1242/jcs.158451] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Factor Inhibiting HIF (FIH) is an oxygen-dependent asparaginyl hydroxylase that regulates the hypoxia-inducible factors (HIFs). Several proteins containing ankyrin repeat domains have been characterised as substrates of FIH, although there is little evidence for a functional consequence of hydroxylation on these substrates. This study demonstrates that the transient receptor potential vanilloid 3 (TRPV3) channel is hydroxylated by FIH on asparagine 242 within the cytoplasmic ankyrin repeat domain. Hypoxia, FIH inhibitors and mutation of asparagine 242 all potentiated TRPV3-mediated current, without altering TRPV3 protein levels, indicating that oxygen-dependent hydroxylation inhibits TRPV3 activity. This novel mechanism of channel regulation by oxygen-dependent asparaginyl hydroxylation is likely to extend to other ion channels.
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Hoff S, Halbritter J, Epting D, Frank V, Nguyen TMT, van Reeuwijk J, Boehlke C, Schell C, Yasunaga T, Helmstädter M, Mergen M, Filhol E, Boldt K, Horn N, Ueffing M, Otto EA, Eisenberger T, Elting MW, van Wijk JAE, Bockenhauer D, Sebire NJ, Rittig S, Vyberg M, Ring T, Pohl M, Pape L, Neuhaus TJ, Elshakhs NAS, Koon SJ, Harris PC, Grahammer F, Huber TB, Kuehn EW, Kramer-Zucker A, Bolz HJ, Roepman R, Saunier S, Walz G, Hildebrandt F, Bergmann C, Lienkamp SS. ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3. Nat Genet 2013; 45:951-6. [PMID: 23793029 PMCID: PMC3786259 DOI: 10.1038/ng.2681] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 06/03/2013] [Indexed: 11/09/2022]
Abstract
Nephronophthisis (NPH) is an autosomal recessive cystic kidney disease that leads to renal failure in childhood or adolescence. Most NPHP gene products form molecular networks. We have identified ANKS6 as a new NPHP family member that connects NEK8 (NPHP9) to INVERSIN (INVS, NPHP2) and NPHP3 to form a distinct NPHP module. ANKS6 localizes to the proximal cilium and knockdown experiments in zebrafish and Xenopus confirmed a role in renal development. Genetic screening identified six families with ANKS6 mutations and NPH, including severe cardiovascular abnormalities, liver fibrosis and situs inversus. The oxygen sensor HIF1AN (FIH) hydroxylates ANKS6 and INVS, while knockdown of Hif1an in Xenopus resembled the loss of other NPHP proteins. HIF1AN altered the composition of the ANKS6/INVS/NPHP3 module. Network analyses, uncovering additional putative NPHP-associated genes, placed ANKS6 at the center of the NPHP module, explaining the overlapping disease manifestation caused by mutations of either ANKS6, NEK8, INVS or NPHP3.
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Affiliation(s)
- Sylvia Hoff
- Department of Medicine, Renal Division, University of Freiburg Medical Center, Freiburg, Germany
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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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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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Liu Y, Higashitsuji H, Higashitsuji H, Itoh K, Sakurai T, Koike K, Hirota K, Fukumoto M, Fujita J. Overexpression of gankyrin in mouse hepatocytes induces hemangioma by suppressing factor inhibiting hypoxia-inducible factor-1 (FIH-1) and activating hypoxia-inducible factor-1. Biochem Biophys Res Commun 2013; 432:22-7. [PMID: 23376718 DOI: 10.1016/j.bbrc.2013.01.093] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/25/2013] [Indexed: 11/19/2022]
Abstract
Gankyrin (also called p28 or PSMD10) is an oncoprotein commonly overexpressed in hepatocellular carcinomas. It consists of 7 ankyrin repeats and interacts with multiple proteins including Rb, Cdk4, MDM2 and NF-κB. To assess the oncogenic activity in vivo, we produced transgenic mice that overexpress gankyrin specifically in the hepatocytes. Unexpectedly, 5 of 7 F2 transgenic mice overexpressing hepatitis B virus X protein (HBX) promoter-driven gankyrin, and one of 3 founder mice overexpressing serum amyloid P component (SAP) promoter-driven gankyrin developed hepatic vascular neoplasms (hemangioma/hemangiosarcomas) whereas none of the wild-type mice did. Endothelial overgrowth was more frequent in the livers of diethylnitrosamine-treated transgenic mice than wild-type mice. Mouse hepatoma Hepa1-6 cells overexpressing gankyrin formed tumors with more vascularity than parental Hepa1-6 cells in the transplanted mouse skin. We found that gankyrin binds to and sequester factor inhibiting hypoxia-inducible factor-1 (FIH-1), which results in decreased interaction between FIH-1 and hypoxia-inducible factor-1α (HIF-1α) and increased activity of HIF-1 to promote VEGF production. The effects of gankyrin were more prominent under 3% O2 than 1% or 20% O2 conditions. Thus, the present study clarified, at least partly, mechanisms of vascular tumorigenesis, and suggests that gankyrin might play a physiological role in hypoxic responses besides its roles as an oncoprotein.
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Affiliation(s)
- Yu Liu
- Department of Clinical Molecular Biology, Graduate School of Medicine, Kyoto University, 54 Shogoin Kawaharacho, Sakyo-ku, Kyoto 606-8507, Japan
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25
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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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