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Figg WD, Fiorini G, Chowdhury R, Nakashima Y, Tumber A, McDonough MA, Schofield CJ. Structural basis for binding of the renal carcinoma target hypoxia-inducible factor 2α to prolyl hydroxylase domain 2. Proteins 2023; 91:1510-1524. [PMID: 37449559 PMCID: PMC10952196 DOI: 10.1002/prot.26541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023]
Abstract
The hypoxia-inducible factor (HIF) prolyl-hydroxylases (human PHD1-3) catalyze prolyl hydroxylation in oxygen-dependent degradation (ODD) domains of HIFα isoforms, modifications that signal for HIFα proteasomal degradation in an oxygen-dependent manner. PHD inhibitors are used for treatment of anemia in kidney disease. Increased erythropoietin (EPO) in patients with familial/idiopathic erythrocytosis and pulmonary hypertension is associated with mutations in EGLN1 (PHD2) and EPAS1 (HIF2α); a drug inhibiting HIF2α activity is used for clear cell renal cell carcinoma (ccRCC) treatment. We report crystal structures of PHD2 complexed with the C-terminal HIF2α-ODD in the presence of its 2-oxoglutarate cosubstrate or N-oxalylglycine inhibitor. Combined with the reported PHD2.HIFα-ODD structures and biochemical studies, the results inform on the different PHD.HIFα-ODD binding modes and the potential effects of clinically observed mutations in HIFα and PHD2 genes. They may help enable new therapeutic avenues, including PHD isoform-selective inhibitors and sequestration of HIF2α by the PHDs for ccRCC treatment.
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Affiliation(s)
- William D. Figg
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Giorgia Fiorini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Yu Nakashima
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
- Institute of Natural Medicine, University of ToyamaToyamaJapan
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Michael A. McDonough
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
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2
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Windsor P, Ouyang H, da Costa JAG, Damodaran AR, Chen Y, Bhagi-Damodaran A. Gas tunnel engineering of prolyl hydroxylase reprograms hypoxia signaling in cells. bioRxiv 2023:2023.08.07.552357. [PMID: 37609209 PMCID: PMC10441328 DOI: 10.1101/2023.08.07.552357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Molecular engineering of biocatalysts has revolutionized complex synthetic chemistry and sustainable catalysis. Here, we show that it is also possible to use engineered biocatalysts to reprogram signal transduction in human cells. More specifically, we manipulate cellular hypoxia (low O2) signaling by engineering the gas-delivery tunnel of prolyl hydroxylase 2 (PHD2), an iron-dependent enzymatic O2 sensor. Using computational modeling and rational protein design techniques, we resolve PHD2's gas tunnel and critical residues therein that limit the flow of O2 to PHD2's catalytic core. Systematic modification of these residues open the constriction topology of PHD2's gas tunnel with the most effectively designed mutant displaying 11-fold enhanced hydroxylation efficiency. Furthermore, transfection of plasmids that express these engineered PHD2 mutants in HEK-293T cells reveal significant reduction in the levels of hypoxia inducible factor (HIF-1α) even under hypoxic conditions. Our studies reveal that activated PHD2 mutants can reprogram downstream HIF pathways in cells to simulate physiological O2-like conditions despite extreme hypoxia and underscores the potential of engineered biocatalysts in controlling cellular function.
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Affiliation(s)
- Peter Windsor
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN-55455, USA
| | - Haiping Ouyang
- Department of Biochemistry and Molecular Biology, University of Minnesota, Twin Cities, Minneapolis, MN-55455, USA
| | - Joseph A. G. da Costa
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN-55455, USA
| | - Anoop Rama Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN-55455, USA
| | - Yue Chen
- Department of Biochemistry and Molecular Biology, University of Minnesota, Twin Cities, Minneapolis, MN-55455, USA
| | - Ambika Bhagi-Damodaran
- Department of Chemistry, University of Minnesota, Twin Cities, Minneapolis, MN-55455, USA
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Meng J, Wang T, Li B, Li L, Zhang G. Oxygen sensing and transcriptional regulation under hypoxia exposure in the mollusk Crassostrea gigas. Sci Total Environ 2022; 853:158557. [PMID: 36084780 DOI: 10.1016/j.scitotenv.2022.158557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/23/2022] [Accepted: 09/01/2022] [Indexed: 06/15/2023]
Abstract
Hypoxia caused by global climate change and anthropogenic pollution has exposed marine species to increasing stress. Oxygen sensing mediated by prolyl hydroxylase (PHD) is regarded as the first line of defense under hypoxia exposure; however, the function of PHD in marine molluscan species remains unclear. In this study, we identified two PHD2 gene in the oyster Crassostrea gigas using phylogenetic tree analysis with 36 species, namely, CgPHD2A/B. Under hypoxia, the mRNA and protein expression of CgPHD2A displayed a time-dependent pattern, revealing a critical role in the response to hypoxia-induced stress. Observation of interactions between CgPHD2 and CgHIF-1α proteins under normoxia using co-immunoprecipitation and GST-pull down experiments showed that the β2β3 loop in CgPHD2A hydroxylates CgHIF-1α to promote its ubiquitination with CgVHL. With the protein recombination and site-directed mutagenesis, the hydroxylation domain and two target proline loci (P404A and 504A) in CgPHDs and CgHIF-1α were identified respectively. Moreover, the electrophoretic mobility-shift assay (EMSA) and luciferase double reporter gene assay revelaed that CgHIF-1α could regulate CgPHD2A expression through binding with the hypoxia-responsive element in the promoter region (320 bp upstream), forming a feedback loop. However, protein structure analysis indicated that six extra amino acids formed an α-helix in the β2β3 loop of CgPHD2B, inhibiting its activity. Overall, this study revealed that two CgPHD2 proteins have evolved, which encode enzymes with different activities in oyster, potentially representing a specific hypoxia-sensing mechanism in mollusks. Illustrating the functional diversity of CgPHDs could help to assess the physiological status of oyster and guide their aquaculture.
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Affiliation(s)
- Jie Meng
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China
| | - Ting Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China
| | - Busu Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, Shandong, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China; National and Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, 266071, Shandong, China.
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4
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Tao H, Ushimaru R, Awakawa T, Mori T, Uchiyama M, Abe I. Stereoselectivity and Substrate Specificity of the Fe(II)/α-Ketoglutarate-Dependent Oxygenase TqaL. J Am Chem Soc 2022; 144:21512-21520. [DOI: 10.1021/jacs.2c08116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Hui Tao
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-0033, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-0033, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Research Initiative for Supra-Materials (RISM), Shinshu University, Ueda 386-8567, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-0033, Japan
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5
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Bunno R, Awakawa T, Mori T, Abe I. Aziridine Formation by a Fe II /α-Ketoglutarate Dependent Oxygenase and 2-Aminoisobutyrate Biosynthesis in Fungi. Angew Chem Int Ed Engl 2021; 60:15827-15831. [PMID: 33973699 DOI: 10.1002/anie.202104644] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/03/2021] [Indexed: 11/08/2022]
Abstract
Aziridine is a characteristically reactive molecule with increased bioactivity due to its strained ring structure. Here, we investigated the biosynthesis of 2-aminoisobutyric acid (AIB) in Penicillium, and successfully reconstituted the three-step biosynthesis from L-Val to AIB in vitro. This previously unknown aziridine formation pathway proceeded with the non-heme iron and α-ketoglutarate-dependent (FeII /αKG) oxygenase TqaL, followed by aziridine ring opening by the haloalkanoic acid dehalogenase (HAD)-type hydrolase TqaF, and subsequent oxidative decarboxylation by the NovR/CloR-like non-heme iron oxygenase TqaM. Furthermore, the X-ray crystal structure of the C-N bond forming FeII /αKG oxygenase TqaL was solved at 2.0 Å resolution. This work presents the first molecular basis for aziridine biogenesis, thereby expanding the catalytic repertoire of the FeII /αKG oxygenases. We also report the unique aziridine ring opening by a HAD-type hydrolase and the remarkable oxidative decarboxylation by a non-heme iron oxygenase to produce AIB.
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Affiliation(s)
- Reito Bunno
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan.,PRESTO (Japan) Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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6
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Bunno R, Awakawa T, Mori T, Abe I. Aziridine Formation by a Fe
II
/α‐Ketoglutarate Dependent Oxygenase and 2‐Aminoisobutyrate Biosynthesis in Fungi. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Reito Bunno
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
| | - Takahiro Mori
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
- PRESTO (Japan) Science and Technology Agency Kawaguchi Saitama 332-0012 Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Collaborative Research Institute for Innovative Microbiology The University of Tokyo Yayoi 1-1-1, Bunkyo-ku Tokyo 113-8657 Japan
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Liu T, Abboud MI, Chowdhury R, Tumber A, Hardy AP, Lippl K, Lohans CT, Pires E, Wickens J, McDonough MA, West CM, Schofield CJ. Biochemical and biophysical analyses of hypoxia sensing prolyl hydroxylases from Dictyostelium discoideum and Toxoplasma gondii. J Biol Chem 2020; 295:16545-16561. [PMID: 32934009 PMCID: PMC7864055 DOI: 10.1074/jbc.ra120.013998] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 08/14/2020] [Indexed: 12/30/2022] Open
Abstract
In animals, the response to chronic hypoxia is mediated by prolyl hydroxylases (PHDs) that regulate the levels of hypoxia-inducible transcription factor α (HIFα). PHD homologues exist in other types of eukaryotes and prokaryotes where they act on non HIF substrates. To gain insight into the factors underlying different PHD substrates and properties, we carried out biochemical and biophysical studies on PHD homologues from the cellular slime mold, Dictyostelium discoideum, and the protozoan parasite, Toxoplasma gondii, both lacking HIF. The respective prolyl-hydroxylases (DdPhyA and TgPhyA) catalyze prolyl-hydroxylation of S-phase kinase-associated protein 1 (Skp1), a reaction enabling adaptation to different dioxygen availability. Assays with full-length Skp1 substrates reveal substantial differences in the kinetic properties of DdPhyA and TgPhyA, both with respect to each other and compared with human PHD2; consistent with cellular studies, TgPhyA is more active at low dioxygen concentrations than DdPhyA. TgSkp1 is a DdPhyA substrate and DdSkp1 is a TgPhyA substrate. No cross-reactivity was detected between DdPhyA/TgPhyA substrates and human PHD2. The human Skp1 E147P variant is a DdPhyA and TgPhyA substrate, suggesting some retention of ancestral interactions. Crystallographic analysis of DdPhyA enables comparisons with homologues from humans, Trichoplax adhaerens, and prokaryotes, informing on differences in mobile elements involved in substrate binding and catalysis. In DdPhyA, two mobile loops that enclose substrates in the PHDs are conserved, but the C-terminal helix of the PHDs is strikingly absent. The combined results support the proposal that PHD homologues have evolved kinetic and structural features suited to their specific sensing roles.
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Affiliation(s)
- Tongri Liu
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Adam P Hardy
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Kerstin Lippl
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Elisabete Pires
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - James Wickens
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | | | - Christopher M West
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia, USA
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9
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Domene C, Jorgensen C, Schofield CJ. Mechanism of Molecular Oxygen Diffusion in a Hypoxia-Sensing Prolyl Hydroxylase Using Multiscale Simulation. J Am Chem Soc 2020; 142:2253-2263. [DOI: 10.1021/jacs.9b09236] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Carmen Domene
- Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, United Kingdom
- Department of Chemistry, Britannia House, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
- Department of Chemistry, University of Bath, Claverton Down Bath BA2 7AY, United Kingdom
| | - Christian Jorgensen
- Department of Chemistry, Britannia House, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, United Kingdom
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10
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Tarade D, Lee JE, Ohh M. Evolution of metazoan oxygen-sensing involved a conserved divergence of VHL affinity for HIF1α and HIF2α. Nat Commun 2019; 10:3293. [PMID: 31337753 PMCID: PMC6650433 DOI: 10.1038/s41467-019-11149-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/26/2019] [Indexed: 12/18/2022] Open
Abstract
Duplication of ancestral hypoxia-inducible factor (HIF)α coincided with the evolution of vertebrate species. Paralogs HIF1α and HIF2α are the most well-known factors for modulating the cellular transcriptional profile following hypoxia. However, how the processes of natural selection acted upon the coding region of these two genes to optimize the cellular response to hypoxia during evolution remains unclear. A key negative regulator of HIFα is von Hippel-Lindau (VHL) tumour suppressor protein. Here we show that evolutionarily-relevant substitutions can modulate a secondary contact between HIF1α Met561 and VHL Phe91. Notably, HIF1α binds more tightly than HIF2α to VHL due to a conserved Met to Thr substitution observed in the vertebrate lineage. Similarly, substitution of VHL Phe91 with Tyr, as seen in invertebrate species, decreases VHL affinity for both HIF1α and HIF2α. We propose that vertebrate evolution involved a more complex hypoxia response with fine-tuned divergence of VHL affinity for HIF1α and HIF2α. Paralogs HIF1α and HIF2α are important modulators regulating cellular transcriptional profile following hypoxia. Here, the authors investigate evolutionary substitutions that fine tune the interaction between HIFα and their regulator VHL in the vertebrate and invertebrate lineages.
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Affiliation(s)
- Daniel Tarade
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Jeffrey E Lee
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Michael Ohh
- Department of Laboratory Medicine & Pathobiology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada. .,Department of Biochemistry, University of Toronto, 661 University Avenue, Toronto, ON, M5G 1M1, Canada.
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