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Hsieh JY, Chen KC, Wang CH, Liu GY, Ye JA, Chou YT, Lin YC, Lyu CJ, Chang RY, Liu YL, Li YH, Lee MR, Ho MC, Hung HC. Suppression of the human malic enzyme 2 modifies energy metabolism and inhibits cellular respiration. Commun Biol 2023; 6:548. [PMID: 37217557 DOI: 10.1038/s42003-023-04930-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 05/12/2023] [Indexed: 05/24/2023] Open
Abstract
Human mitochondrial NAD(P)+-dependent malic enzyme (ME2) is well-known for its role in cell metabolism, which may be involved in cancer or epilepsy. We present potent ME2 inhibitors based on cyro-EM structures that target ME2 enzyme activity. Two structures of ME2-inhibitor complexes demonstrate that 5,5'-Methylenedisalicylic acid (MDSA) and embonic acid (EA) bind allosterically to ME2's fumarate-binding site. Mutagenesis studies demonstrate that Asn35 and the Gln64-Tyr562 network are required for both inhibitors' binding. ME2 overexpression increases pyruvate and NADH production while decreasing the cell's NAD+/NADH ratio; however, ME2 knockdown has the opposite effect. MDSA and EA inhibit pyruvate synthesis and thus increase the NAD+/NADH ratio, implying that these two inhibitors interfere with metabolic changes by inhibiting cellular ME2 activity. ME2 silence or inhibiting ME2 activity with MDSA or EA decreases cellular respiration and ATP synthesis. Our findings suggest that ME2 is crucial for mitochondrial pyruvate and energy metabolism, as well as cellular respiration, and that ME2 inhibitors could be useful in the treatment of cancer or other diseases that involve these processes.
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Affiliation(s)
- Ju-Yi Hsieh
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Kun-Chi Chen
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan ROC
| | - Guang-Yaw Liu
- Institute of Medicine, College of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan ROC
| | - Jie-An Ye
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
- Institute of Medicine, College of Medicine, Chung Shan Medical University, Taichung, 402, Taiwan ROC
| | - Yu-Tung Chou
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Yi-Chun Lin
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Cheng-Jhe Lyu
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Rui-Ying Chang
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Yi-Liang Liu
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Yen-Hsien Li
- Instrument Center, Office of Research and Development, National Chung Hsing University, Taichung, 40227, Taiwan ROC
- Department of Chemistry, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Mau-Rong Lee
- Department of Chemistry, National Chung Hsing University, Taichung, 402, Taiwan ROC
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan ROC.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan ROC.
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan ROC.
- Ph.D. Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung, 402, Taiwan ROC.
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan ROC.
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan ROC.
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Single nucleotide variants lead to dysregulation of the human mitochondrial NAD(P) +-dependent malic enzyme. iScience 2021; 24:102034. [PMID: 33554057 PMCID: PMC7847962 DOI: 10.1016/j.isci.2021.102034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/16/2020] [Accepted: 12/31/2020] [Indexed: 11/23/2022] Open
Abstract
Human mitochondrial NAD(P)+-dependent malic enzyme (ME2) is well recognized to associate with cancer cell metabolism, and the single nucleotide variants (SNVs) of ME2 may play a role in enzyme regulation. Here we reported that the SNVs of ME2 occurring in the allosteric sites lead to inactivation or overactivation of ME2. Two ME2-SNVs, ME2_R67Q and ME2-R484W, that demonstrated inactivating or overactivating enzyme activities of ME2, respectively, have different impact toward the cells. The cells with overactivating SNV enzyme, ME2_R484W, grow more rapidly and are more resistant to cellular senescence than the cells with wild-type or inactivating SNV enzyme, ME2_R67Q. Crystal structures of these two ME2-SNVs reveal that ME2_R67Q was an inactivating "dead form," and ME2_R484W was an overactivating "closed form" of the enzyme. The resolved ME2-SNV structures provide a molecular basis to explain the abnormal kinetic properties of these SNV enzymes.
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Lobos M, Figueroa M, Martínez-Oyanedel J, López V, García-Robles MDLÁ, Tarifeño-Saldivia E, Carvajal N, Uribe E. Insights on the participation of Glu256 and Asp204 in the oligomeric structure and cooperative effects of human arginase type I. J Struct Biol 2020; 211:107533. [PMID: 32450233 DOI: 10.1016/j.jsb.2020.107533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 11/20/2022]
Abstract
Arginase (EC 3.5.3.1) catalyzes the hydrolysis of L-arginine to L-ornithine and urea, and requires a bivalent cation, especially Mn2+ for its catalytic activity. It is a component of the urea cycle and regulates the intracellular levels of l-arginine, which makes the arginase a target for treatment of vascular diseases and asthma. Mammalian arginases contain an unusual S-shaped motif located at the intermonomeric interface. Until now, the studies were limited to structural role of the motif. Then, our interest was focused on functional aspects and our hypothesis has been that the motif is essential for maintain the oligomeric state, having Arg308 as a central axis. Previously, we have shown that the R308A mutant is monomeric and re-associates to the trimeric-cooperative state in the presence of low concentrations of guanidine chloride. We have now mutated Asp204 that interacts with Arg308 in the neighbor subunit, and also we mutated Glu256, proposed as important for oligomerization. Concretely, the human arginase I mutants D204A, D204E, E256A, E256Q and E256D were generated and examined. No differences were observed in the kinetic parameters at pH 9.5 or in tryptophan fluorescence. However, the D204A and E256Q variants were monomeric. On the other hand, D204E and E256D proved to be trimeric and kinetically cooperative at pH 7.5, whereas hyperbolic kinetics was exhibited by E256A, also trimeric. The results obtained strongly support the importance of the interaction between Arg255 and Glu256 in the cooperative properties of arginase, and Asp204 would be relevant to maintain the oligomeric state through salt bridges with Arg255 and Arg308.
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Affiliation(s)
- Marcela Lobos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Maximiliano Figueroa
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción, Chile.
| | - José Martínez-Oyanedel
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Vasthi López
- Departamento de Ciencias Biomédicas. Universidad Católica del Norte, Coquimbo, Chile
| | | | - Estefanía Tarifeño-Saldivia
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Nelson Carvajal
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción, Chile
| | - Elena Uribe
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Casilla 160-C, Concepción, Chile.
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Hsieh JY, Li SY, Tsai WC, Liu JH, Lin CL, Liu GY, Hung HC. A small-molecule inhibitor suppresses the tumor-associated mitochondrial NAD(P)+-dependent malic enzyme (ME2) and induces cellular senescence. Oncotarget 2016; 6:20084-98. [PMID: 26008970 PMCID: PMC4652989 DOI: 10.18632/oncotarget.3907] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/06/2015] [Indexed: 11/25/2022] Open
Abstract
Here, we found a natural compound, embonic acid (EA), that can specifically inhibit the enzymatic activity of mitochondrial NAD(P)+-dependent malic enzyme (m-NAD(P)-ME, ME2) either in vitro or in vivo. The in vitro IC50 value of EA for m-NAD(P)-ME was 1.4 ± 0.4 μM. Mutagenesis and binding studies revealed that the putative binding site of EA on m-NAD(P)-ME is located at the fumarate binding site or at the dimer interface near the site. Inhibition studies reveal that EA displayed a non-competitive inhibition pattern, which demonstrated that the binding site of EA was distinct from the active site of the enzyme. Therefore, EA is thought to be an allosteric inhibitor of m-NAD(P)-ME. Both EA treatment and knockdown of m-NAD(P)-ME by shRNA inhibited the growth of H1299 cancer cells. The protein expression and mRNA synthesis of m-NAD(P)-ME in H1299 cells were not influenced by EA, suggesting that the EA-inhibited H1299 cell growth occurs through the suppression of in vivo m-NAD(P)-ME activity EA treatment further induced the cellular senescence of H1299 cells. However, down-regulation of the enzyme-induced cellular senescence was not through p53. Therefore, the EA-evoked senescence of H1299 cells may occur directly through the inhibition of ME2 or a p53-independent pathway.
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Affiliation(s)
- Ju-Yi Hsieh
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Institute of Microbiology & Immunology, Chung Shan Medical University, and Division of Allergy, Immunology, and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shao-Yu Li
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Wen-Chen Tsai
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Institute of Microbiology & Immunology, Chung Shan Medical University, and Division of Allergy, Immunology, and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Jyung-Hurng Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Agricultural Biotechnology Center (ABC), National Chung Hsing University, Taichung, Taiwan
| | - Chih-Li Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Guang-Yaw Liu
- Institute of Microbiology & Immunology, Chung Shan Medical University, and Division of Allergy, Immunology, and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.,Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.,Agricultural Biotechnology Center (ABC), National Chung Hsing University, Taichung, Taiwan
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Chang YL, Gao HW, Chiang CP, Wang WM, Huang SM, Ku CF, Liu GY, Hung HC. Human mitochondrial NAD(P)(+)-dependent malic enzyme participates in cutaneous melanoma progression and invasion. J Invest Dermatol 2014; 135:807-815. [PMID: 25202825 DOI: 10.1038/jid.2014.385] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 08/06/2014] [Accepted: 08/07/2014] [Indexed: 12/25/2022]
Abstract
Cutaneous melanoma is the most life-threatening neoplasm of the skin, accounting for most of the skin cancer deaths. Accumulating evidence suggests that targeting metabolism is an appealing strategy for melanoma therapy. Mitochondrial NAD(P)(+)-dependent malic enzyme (ME2), an oxidative decarboxylase, was evaluated for its biological significance in cutaneous melanoma progression. ME2 mRNA and protein expression significantly increased during melanoma progression, as evidenced by Gene Expression Omnibus analysis and immunohistochemistry on clinically annotated tissue microarrays, respectively. In addition, ME2 knockdown attenuated melanoma cell proliferation in vitro. ME2 ablation resulted in reduced cellular ATP levels and elevated cellular reactive oxygen species production, which activated the AMP-activated protein kinase pathway and inhibited acetyl-CoA carboxylase. Furthermore, ME2 expression was associated with cell migration and invasion. ME2 knockdown decreased anchorage-independent growth in vitro and tumor cell growth in vivo. These results suggested that ME2 might be an important factor in melanoma progression and a novel biomarker of invasion.
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Affiliation(s)
- Yung-Lung Chang
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan; Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Hong-Wei Gao
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chien-Ping Chiang
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan; Department of Dermatology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wei-Ming Wang
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan; Department of Dermatology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Shih-Ming Huang
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Chien-Fen Ku
- Department of Biochemistry, National Defense Medical Center, Taipei, Taiwan
| | - Guang-Yaw Liu
- Institute of Microbiology and Immunology and Division of Allergy, Immunology and Rheumatology, Chung Shan Medical University and Hospital, Taichung, Taiwan.
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung-Hsing University, Taichung, Taiwan; Institute of Genomics and Bioinformatics, National Chung-Hsing University, Taichung, Taiwan.
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Structural characteristics of the nonallosteric human cytosolic malic enzyme. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1773-83. [PMID: 24998673 DOI: 10.1016/j.bbapap.2014.06.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 06/24/2014] [Accepted: 06/26/2014] [Indexed: 11/22/2022]
Abstract
Human cytosolic NADP(+)-dependent malic enzyme (c-NADP-ME) is neither a cooperative nor an allosteric enzyme, whereas mitochondrial NAD(P)(+)-dependent malic enzyme (m-NAD(P)-ME) is allosterically activated by fumarate. This study examines the molecular basis for the different allosteric properties and quaternary structural stability of m-NAD(P)-ME and c-NADP-ME. Multiple residues corresponding to the fumarate-binding site were mutated in human c-NADP-ME to correspond to those found in human m-NAD(P)-ME. Additionally, the crystal structure of the apo (ligand-free) human c-NADP-ME conformation was determined. Kinetic studies indicated no significant difference between the wild-type and mutant enzymes in Km,NADP, Km,malate, and kcat. A chimeric enzyme, [51-105]_c-NADP-ME, was designed to include the putative fumarate-binding site of m-NAD(P)-ME at the dimer interface of c-NADP-ME; however, this chimera remained nonallosteric. In addition to fumarate activation, the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME is quite different; c-NADP-ME is a stable tetramer, whereas m-NAD(P)-ME exists in equilibrium between a dimer and a tetramer. The quaternary structures for the S57K/N59E/E73K/S102D and S57K/N59E/E73K/S102D/H74K/D78P/D80E/D87G mutants of c-NADP-ME are tetrameric, whereas the K57S/E59N/K73E/D102S m-NAD(P)-ME quadruple mutant is primarily monomeric with some dimer formation. These results strongly suggest that the structural features near the fumarate-binding site and the dimer interface are highly related to the quaternary structural stability of c-NADP-ME and m-NAD(P)-ME. In this study, we attempt to delineate the structural features governing the fumarate-induced allosteric activation of malic enzyme.
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Hsieh JY, Liu JH, Yang PC, Lin CL, Liu GY, Hung HC. Fumarate analogs act as allosteric inhibitors of the human mitochondrial NAD(P)+-dependent malic enzyme. PLoS One 2014; 9:e98385. [PMID: 24911153 PMCID: PMC4049574 DOI: 10.1371/journal.pone.0098385] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/02/2014] [Indexed: 11/20/2022] Open
Abstract
Human mitochondrial NAD(P)+-dependent malic enzyme (m-NAD(P)-ME) is allosterically activated by the four-carbon trans dicarboxylic acid, fumarate. Previous studies have suggested that the dicarboxylic acid in a trans conformation around the carbon-carbon double bond is required for the allosteric activation of the enzyme. In this paper, the allosteric effects of fumarate analogs on m-NAD(P)-ME are investigated. Two fumarate-insensitive mutants, m-NAD(P)-ME_R67A/R91A and m-NAD(P)-ME_K57S/E59N/K73E/D102S, as well as c-NADP-ME, were used as the negative controls. Among these analogs, mesaconate, trans-aconitate, monomethyl fumarate and monoethyl fumarate were allosteric activators of the enzyme, while oxaloacetate, diethyl oxalacetate, and dimethyl fumarate were found to be allosteric inhibitors of human m-NAD(P)-ME. The IC50 value for diethyl oxalacetate was approximately 2.5 mM. This paper suggests that the allosteric inhibitors may impede the conformational change from open form to closed form and therefore inhibit m-NAD(P)-ME enzyme activity.
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Affiliation(s)
- Ju-Yi Hsieh
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Jyung-Hurng Liu
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
| | - Pai-Chun Yang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Chi-Li Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Guang-Yaw Liu
- Institute of Microbiology & Immunology, Chung Shan Medical University, and Division of Allergy, Immunology, and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
- * E-mail: (HCH); (GYL)
| | - Hui-Chih Hung
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center (ABC), National Chung Hsing University, Taichung, Taiwan
- * E-mail: (HCH); (GYL)
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