EGLN1 prolyl hydroxylation of hypoxia-induced transcription factor HIF1α is repressed by SET7-catalyzed lysine methylation
Jinhua Tang, Hongyan Deng, Zixuan Wang, Huangyuan Zha, Qian Liao, Chunchun Zhu, Xiaoyun Chen, Xueyi Sun, Shuke Jia, Gang Ouyang, Xing Liu, Wuhan Xiao
Abstract
Egg-laying defective nine 1 (EGLN1) functions as an oxygen sensor to catalyze prolyl hydroxylation of the transcription factor hypoxia-inducible factor-1 α under normoxia conditions, leading to its proteasomal degradation. Thus, EGLN1 plays a central role in the hypoxia-inducible factor–mediated hypoxia signaling pathway; however, the posttranslational modifications that control EGLN1 function remain largely unknown. Here, we identified that a lysine monomethylase, SET7, catalyzes EGLN1 methylation on lysine 297, resulting in the repression of EGLN1 activity in catalyzing prolyl hydroxylation of hypoxia-inducible factor-1 α. Notably, we demonstrate that the methylation mimic mutant of EGLN1 loses the capability to suppress the hypoxia signaling pathway, leading to the enhancement of cell proliferation and the oxygen consumption rate. Collectively, our data identify a novel modification of EGLN1 that is critical for inhibiting its enzymatic activity and which may benefit cellular adaptation to conditions of hypoxia. Egg-laying defective nine 1 (EGLN1) functions as an oxygen sensor to catalyze prolyl hydroxylation of the transcription factor hypoxia-inducible factor-1 α under normoxia conditions, leading to its proteasomal degradation. Thus, EGLN1 plays a central role in the hypoxia-inducible factor–mediated hypoxia signaling pathway; however, the posttranslational modifications that control EGLN1 function remain largely unknown. Here, we identified that a lysine monomethylase, SET7, catalyzes EGLN1 methylation on lysine 297, resulting in the repression of EGLN1 activity in catalyzing prolyl hydroxylation of hypoxia-inducible factor-1 α. Notably, we demonstrate that the methylation mimic mutant of EGLN1 loses the capability to suppress the hypoxia signaling pathway, leading to the enhancement of cell proliferation and the oxygen consumption rate. Collectively, our data identify a novel modification of EGLN1 that is critical for inhibiting its enzymatic activity and which may benefit cellular adaptation to conditions of hypoxia. Egg-laying defective nine (EGLN) 1, EGLN2, and EGLN3 (also known as prolyl hydroxylase domain [PHD] enzyme, PHD2, PHD1, and PHD3) are evolutionarily conserved oxygen sensors, which target hypoxia-inducible factor (HIF)-α subunits for hydroxylation and subsequent proteasomal degradation under normoxia, thus playing a central role in hypoxia signaling pathway (1Fong G.H. Takeda K. Role and regulation of prolyl hydroxylase domain proteins.Cell Death Differ. 2008; 15: 635-641Crossref PubMed Scopus (225) Google Scholar, 2Wong B.W. Kuchnio A. Bruning U. Carmeliet P. 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Takeda K. Role and regulation of prolyl hydroxylase domain proteins.Cell Death Differ. 2008; 15: 635-641Crossref PubMed Scopus (225) Google Scholar). FK506-binding protein (FKBP) 38 has been shown to negatively regulate PHD2 (EGLN1) activity (13Barth S. Edlich F. Berchner-Pfannschmidt U. Gneuss S. Jahreis G. Hasgall P.A. Fandrey J. Wenger R.H. Camenisch G. Hypoxia-inducible factor prolyl-4-hydroxylase PHD2 protein abundance depends on integral membrane anchoring of FKBP38.J. Biol. Chem. 2009; 284: 23046-23058Abstract Full Text Full Text PDF PubMed Scopus (57) Google Scholar), whereas seven in absentia homolog 2 (SIAH2) has been identified to degrade PHD3 (EGLN3) (14Nakayama K. Gazdoiu S. Abraham R. Pan Z.Q. Ronai Z. Hypoxia-induced assembly of prolyl hydroxylase PHD3 into complexes: Implications for its activity and susceptibility for degradation by the E3 ligase Siah2.Biochem. J. 2007; 401: 217-226Crossref PubMed Scopus (49) Google Scholar). 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Cystathione beta-synthase regulates HIF-1alpha stability through persulfidation of PHD2.Sci. Adv. 2020; 6eaaz8534Crossref Scopus (10) Google Scholar). In response to oxidative stress, PHD2 is dimerized and its activity is inhibited, resulting in the stabilization of HIF1α (17Lee G. Won H.S. Lee Y.M. Choi J.W. Oh T.I. Jang J.H. Choi D.K. Lim B.O. Kim Y.J. Park J.W. Puigserver P. Lim J.H. Oxidative dimerization of PHD2 is responsible for its inactivation and contributes to metabolic reprogramming via HIF-1alpha activation.Sci. Rep. 2016; 6: 18928Crossref PubMed Scopus (87) Google Scholar). Given the importance of posttranslational modifications (PTMs) in the regulation of protein functions, other unidentified PTMs of PHDs should affect PHD activity and subsequent hypoxia signaling pathway. SET7 (also known as SETD7, SET9, and SET7/9) was originally identified as a monomethylase of histone H3 lysine 4, involved in gene activation (18Nishioka K. Chuikov S. Sarma K. Erdjument-Bromage H. 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Commun. 2016; 7: 10347Crossref PubMed Scopus (113) Google Scholar) In this study, we found that that EGLN1 contains a SET7 targeting motif (RS/TK). Further assays show that SET7 mediated monomethylation of EGLN1 on lysine 297, leading to the relief of its suppressive role on HIF1α activity and promoting cellular hypoxia adaptation. In addition to histone H3, SET7 was also found to monomethylate nonhistone proteins by recognizing a conserved core domain ([K/R] [S/T] K) (24Subramanian K. Jia D. Kapoor-Vazirani P. Powell D.R. Collins R.E. Sharma D. Peng J. Cheng X. Vertino P.M. Regulation of estrogen receptor alpha by the SET7 lysine methyltransferase.Mol. Cell. 2008; 30: 336-347Abstract Full Text Full Text PDF PubMed Scopus (217) Google Scholar, 27Liu X. Chen Z. Xu C. Leng X. Cao H. Ouyang G. Xiao W. Repression of hypoxia-inducible factor alpha signaling by Set7-mediated methylation.Nucleic Acids Res. 2015; 43: 5081-5098Crossref PubMed Scopus (62) Google Scholar, 29Couture J.F. Collazo E. Hauk G. Trievel R.C. Structural basis for the methylation site specificity of SET7/9.Nat. Struct. Mol. Biol. 2006; 13: 140-146Crossref PubMed Scopus (136) Google Scholar, 30Pradhan S. Chin H.G. Esteve P.O. Jacobsen S.E. SET7/9 mediated methylation of non-histone proteins in mammalian cells.Epigenetics. 2009; 4: 383-387Crossref PubMed Scopus (101) Google Scholar, 31Esteve P.O. Chin H.G. Benner J. Feehery G.R. Samaranayake M. Horwitz G.A. Jacobsen S.E. Pradhan S. Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells.Proc. Natl. Acad. Sci. U. S. A. 2009; 106: 5076-5081Crossref PubMed Scopus (225) Google Scholar) in these proteins. After searching the amino acid sequences of EGLN1 from different organisms, the three “RTK (Argnine-Threonine-Lysine)” residues were identified in the catalytic domain (PH domain) of EGLN1 (Fig. 1A), in which lysine 297 might be methylated by SET7. To confirm this hypothesis, we developed an antibody (anti-EGLN1-K297me1) to specifically recognize lysine 297 of human EGLN1. When WT hemagglutinin (HA)-tagged EGLN1 (HA-EGLN1) was cotransfected with SET7, the methylated EGLN1 was readily detected by anti-EGLN1-K297me1 antibody after the coimmunoprecipitation with anti-HA–conjugated agarose beads (Fig. 1B). However, the methylated EGLN1 was not shown up when the mutant (H297A) was cotransfected (Fig. 1B). To further validate this result, we performed mass spectrometry assay. As shown in Figure 1C, the monomethylated K297 was identified in EGLN1 when SET7 was coexpressed (Fig. 1C). To determine whether endogenous EGLN1 was methylated by SET7, we examined methylation of EGLN1 in SET7+/+ and SET7−/− HEK293T cells after coimmunoprecipitation with anti-EGLN1 antibody. of EGLN1 in SET7+/+ HEK293T cells was that in SET7−/− HEK293T cells (Fig. we WT SET7 and its mutant (H297A) into SET7−/− HEK293T cells and examined methylation of endogenous EGLN1 after coimmunoprecipitation with anti-EGLN1 antibody. of EGLN1 in the cells with WT SET7 was in the cells with (Fig. we examined whether EGLN1 with SET7 by coimmunoprecipitation assay. EGLN1 with SET7 (Fig. and Moreover, endogenous SET7 with endogenous EGLN1 in HEK293T cells (Fig. and SET7 also with endogenous EGLN1 (Fig. that SET7 with the of EGLN1 (Fig. and To determine whether SET7 has on EGLN1 protein we into HEK293T cells with an and found that endogenous EGLN1 protein was not at (Fig. EGLN1 was the SET7+/+ and SET7−/− HEK293T cells (Fig. EGLN1 protein was also detected in SET7−/− HEK293T cells with WT SET7, and the SET7 (H297A) (Fig. In of SET7 also on EGLN1 protein (Fig. EGLN1 on SET7 protein (Fig. and The data that EGLN1 and SET7 not affect other at protein are in these that SET7 with EGLN1 to catalyze monomethylation of EGLN1 on Given the function of EGLN1 in catalyzing prolyl hydroxylation of we to determine whether methylation of EGLN1 by SET7 affect the prolyl hydroxylase activity of EGLN1 on In as of WT EGLN1 a of cotransfected However, of the mutant of EGLN1 the protein of cotransfected was not as as of the mutant of EGLN1 suggesting that methylation of EGLN1 on K297 a of enzymatic activity of EGLN1 (Fig. 4, and we that to cells with of WT HIF1α hydroxylation was in cells with of the mutant of EGLN1 (Fig. we that of SET7 HIF1α hydroxylation when EGLN1 was coexpressed (Fig. Notably, in of WT EGLN1 a more of endogenous HIF1α of the mutant of EGLN1 (Fig. In of WT EGLN1 a more enhancement of HIF1α hydroxylation of the mutant (Fig. In the of HIF1α hydroxylation was in cells that in cells (Fig. in of SET7 degradation of HIF1α when EGLN1 was coexpressed (Fig. data that the prolyl hydroxylase activity of EGLN1 is by SET7-mediated To determine whether methylation of EGLN1 on K297 by SET7 has impacts on hypoxia we examined the of mutant of EGLN1 on activity of for hypoxia response (27Liu X. Chen Z. Xu C. Leng X. Cao H. Ouyang G. Xiao W. Repression of hypoxia-inducible factor alpha signaling by Set7-mediated methylation.Nucleic Acids Res. 2015; 43: 5081-5098Crossref PubMed Scopus (62) Google Scholar). of WT EGLN1 a of activity, including hypoxia response and but of the suppressive of WT EGLN1 on HIF1α (Fig. HIF1α is a for metabolic adaptation under hypoxia and in the Rev. Cancer. 2008; 8: PubMed Scopus Google Scholar, G.L. Regulation of by hypoxia-inducible factor Biol. 2011; 76: PubMed Scopus Google Scholar, M. suppressor regulates via alpha Death Differ. 2014; 21: PubMed Scopus Google Scholar). we the of mutant of EGLN1 on cellular hypoxia adaptation. As shown in Figure of WT EGLN1 in an of a of G.L. regulation of by hypoxia-inducible factor J. 2007; PubMed Scopus Google Scholar) (Fig. However, of this (Fig. In the proliferation of cells with was cells with WT EGLN1 as revealed by (Fig. and the and of cells with was cells with WT EGLN1 (Fig. and Collectively, these data that methylation of EGLN1 facilitates hypoxia which might benefit cell EGLN1 was identified as a prolyl hydroxylase of its function and molecular on hypoxia signaling has been Jr., W.G. Ratcliffe P.J. Oxygen sensing by metazoans: The central role of the HIF hydroxylase pathway.Mol. Cell. 2008; 30: 393-402Abstract Full Text Full Text PDF PubMed Scopus (2105) Google Scholar, P. D.R. Y.M. Wilson J. S.J. A. M. Ratcliffe P.J. of to the by prolyl 2001; PubMed Scopus Google Scholar, M. K. Kim W. J. M. A. W.G. HIF alpha for by Implications for 2001; PubMed Scopus Google Scholar). of its activity on oxygen, is as an oxygen sensor involved in multiple biological by targeting different J. T. J. M. R. Fan C. X.D. E. L. Chen X. P. Li substrate transcription factor as an in cell cell PubMed Scopus Google Scholar, H. B. Zhang J.F. Zhang M. J. Cheng A. S. Zhang Q. kinase activity of in a 2016; PubMed Scopus (113) Google Scholar, B. P. S.J. G. C. X. Chen X. Chen Zhang J. hydroxylation by by its with the Dev. 2014; 28: PubMed Scopus Google Scholar). However, whether the activity of EGLN1 is regulated by other factors, by is not (15Di Conza G. Trusso Cafarello S. Loroch S. Mennerich D. Deschoemaeker S. Di Matteo M. Ehling M. Gevaert K. Prenen H. Zahedi R.P. Sickmann A. Kietzmann T. Moretti F. Mazzone M. The mTOR and PP2A pathways regulate PHD2 phosphorylation to fine-tune HIF1alpha levels and colorectal cancer cell survival under hypoxia.Cell Rep. 2017; 18: 1699-1712Abstract Full Text Full Text PDF PubMed Scopus (67) Google Scholar, A. Prabhudesai S. Zhang Y. Rao G. Thirugnanam K. Hossen M.N. Dwivedi S.K.D. Ramchandran R. Mukherjee P. Bhattacharya R. Cystathione beta-synthase regulates HIF-1alpha stability through persulfidation of PHD2.Sci. Adv. 2020; 6eaaz8534Crossref Scopus (10) Google Scholar). In this study, we identified that SET7 EGLN1 on K297 to its enzymatic activity on that PTMs also affect To further the of PTMs or factors of EGLNs on their activity for HIFα may not our the modulation of hypoxia signaling but also to the fine-tuning of cellular hypoxia adaptation. Notably, we to show that the methylation of EGLN1 by SET7 the activity of EGLN1 on the mutant of EGLN1 which lysine 297 is into not its enzymatic activity on different from the mutant of EGLN1 the of lysine to on K297 of EGLN1 might not mimic methylation of EGLN1 by SET7 in other lysine residues might be also methylated by SET7, which are not identified in this the regulation of hypoxia in addition to EGLN1 identified SET7 is also found to directly HIFα (27Liu X. Chen Z. Xu C. Leng X. Cao H. Ouyang G. Xiao W. Repression of hypoxia-inducible factor alpha signaling by Set7-mediated methylation.Nucleic Acids Res. 2015; 43: 5081-5098Crossref PubMed Scopus (62) Google Scholar, 28Kim Y. Nam H.J. Lee J. Park D.Y. Kim C. Yu Y.S. Kim D. Park S.W. Bhin J. Hwang D. Lee H. Koh G.Y. Baek S.H. Methylation-dependent regulation of HIF-1alpha stability restricts retinal and tumour angiogenesis.Nat. Commun. 2016; 7: 10347Crossref PubMed Scopus (113) Google Scholar). SET7 to affect hypoxia signaling through multiple Given that the importance of hypoxia signaling in cellular B.W. Kuchnio A. Bruning U. Carmeliet P. Emerging novel functions of the oxygen-sensing prolyl hydroxylase domain enzymes.Trends Biochem. Sci. 2013; 38: 3-11Abstract Full Text Full Text PDF PubMed Scopus (102) Google Scholar, 3Aragones J. Fraisl P. Baes M. Carmeliet P. Oxygen sensors at the crossroad of metabolism.Cell Metab. 2009; 9: 11-22Abstract Full Text Full Text PDF PubMed Scopus (215) Google Scholar), SET7 to an role in cellular hypoxia adaptation through the key factors of hypoxia To further the of SET7 in may benefit for the of metabolic HEK293T and cells originally from were in with The cells were at in a including anti-EGLN1 and were from Cell was from was from was from and antibody was from was from was from was from methylation antibody was by a human as an After the with the specificity of antibody was by and were performed as (27Liu X. Chen Z. Xu C. Leng X. Cao H. 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