1
|
Wang H, Cui W, Yue S, Zhu X, Li X, He L, Zhang M, Yang Y, Wei M, Wu H, Wang S. Malic enzymes in cancer: Regulatory mechanisms, functions, and therapeutic implications. Redox Biol 2024; 75:103273. [PMID: 39142180 DOI: 10.1016/j.redox.2024.103273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/21/2024] [Accepted: 07/17/2024] [Indexed: 08/16/2024] Open
Abstract
Malic enzymes (MEs) are metabolic enzymes that catalyze the oxidation of malate to pyruvate and NAD(P)H. While researchers have well established the physiological metabolic roles of MEs in organisms, recent research has revealed a link between MEs and carcinogenesis. This review collates evidence of the molecular mechanisms by which MEs promote cancer occurrence, including transcriptional regulation, post-transcriptional regulation, post-translational protein modifications, and protein-protein interactions. Additionally, we highlight the roles of MEs in reprogramming energy metabolism, suppressing senescence, and modulating the tumor immune microenvironment. We also discuss the involvement of these enzymes in mediating tumor resistance and how the development of novel small-molecule inhibitors targeting MEs might be a good therapeutic approach. Insights through this review are expected to provide a comprehensive understanding of the intricate relationship between MEs and cancer, while facilitating future research on the potential therapeutic applications of targeting MEs in cancer management.
Collapse
Affiliation(s)
- Huan Wang
- Department of Radiotherapy, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning Province, PR China.
| | - Wanlin Cui
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, Liaoning Province, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, PR China.
| | - Song Yue
- Department of Ophthalmology, The First Hospital of China Medical University, Shenyang, Liaoning Province, PR China.
| | - Xianglong Zhu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, Liaoning Province, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, PR China
| | - Xiaoyan Li
- Department of Pathology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning Province, PR China
| | - Lian He
- Department of Pathology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning Province, PR China
| | - Mingrong Zhang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, Liaoning Province, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, PR China
| | - Yan Yang
- Department of Gastroenterology, The Fourth Affiliated Hospital of China Medical University, No.4, Chongshan Road, Huanggu District, Shenyang, Liaoning Province, PR China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, Liaoning Province, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, PR China; Shenyang Kangwei Medical Laboratory Analysis Co. LTD, Shenyang City, Liaoning Province, PR China.
| | - Huizhe Wu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, Liaoning Province, PR China; Liaoning Key Laboratory of Molecular Targeted Anti-tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, PR China.
| | - Shuo Wang
- Department of Gynecology Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, No.44 Xiaoheyan Road, Dadong District, Shenyang, 110042, Liaoning Province, PR China.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
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.
Collapse
|
4
|
Liu Y, Feng Y, Wang L, Guo X, Liu W, Li Q, Wang X, Xue S, Zhao ZK. Structural Insights into Phosphite Dehydrogenase Variants Favoring a Non-natural Redox Cofactor. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04822] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yuxue Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanbin Feng
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lei Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaojia Guo
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wujun Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qing Li
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueying Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Song Xue
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zongbao Kent Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Nargund S, Qiu J, Goudar CT. Elucidating the role of copper in CHO cell energy metabolism using13C metabolic flux analysis. Biotechnol Prog 2015; 31:1179-86. [DOI: 10.1002/btpr.2131] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 06/09/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Shilpa Nargund
- Drug Substance Technologies, Process Development; Amgen Inc., One Amgen Center Drive; Thousand Oaks CA 91320
| | - Jinshu Qiu
- Attribute Sciences, Process Development, Amgen Inc., One Amgen Center Drive; Thousand Oaks CA 91320
| | - Chetan T. Goudar
- Drug Substance Technologies, Process Development; Amgen Inc., One Amgen Center Drive; Thousand Oaks CA 91320
| |
Collapse
|
7
|
Spaans SK, Weusthuis RA, van der Oost J, Kengen SWM. NADPH-generating systems in bacteria and archaea. Front Microbiol 2015; 6:742. [PMID: 26284036 PMCID: PMC4518329 DOI: 10.3389/fmicb.2015.00742] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/06/2015] [Indexed: 12/22/2022] Open
Abstract
Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is an essential electron donor in all organisms. It provides the reducing power that drives numerous anabolic reactions, including those responsible for the biosynthesis of all major cell components and many products in biotechnology. The efficient synthesis of many of these products, however, is limited by the rate of NADPH regeneration. Hence, a thorough understanding of the reactions involved in the generation of NADPH is required to increase its turnover through rational strain improvement. Traditionally, the main engineering targets for increasing NADPH availability have included the dehydrogenase reactions of the oxidative pentose phosphate pathway and the isocitrate dehydrogenase step of the tricarboxylic acid (TCA) cycle. However, the importance of alternative NADPH-generating reactions has recently become evident. In the current review, the major canonical and non-canonical reactions involved in the production and regeneration of NADPH in prokaryotes are described, and their key enzymes are discussed. In addition, an overview of how different enzymes have been applied to increase NADPH availability and thereby enhance productivity is provided.
Collapse
Affiliation(s)
| | - Ruud A. Weusthuis
- Bioprocess Engineering, Wageningen UniversityWageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Servé W. M. Kengen
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| |
Collapse
|
8
|
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.
Collapse
|
9
|
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.
Collapse
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)
| |
Collapse
|
10
|
Identification of malic enzyme mutants depending on 1,2,3-triazole moiety-containing nicotinamide adenine dinucleotide analogs. Bioorg Med Chem Lett 2014; 24:1307-9. [PMID: 24513047 DOI: 10.1016/j.bmcl.2014.01.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/15/2014] [Accepted: 01/20/2014] [Indexed: 11/22/2022]
Abstract
An activity screening between 1,2,3-triazole moiety-containing nicotinamide adenine dinucleotide (NAD) analogs and malic enzyme (ME) mutants identified some mutants capable of taking NAD analogs as the cofactor. One particular pair, ME-L310K/L404S and the analog B-8 had good catalytic efficiency and cofactor specificity. The new system gained about 1200-fold cofactor specificity shift from NAD toward B-8 in terms of oxidative decarboxylation of l-malate. Our results provided insightful information for the development of orthogonal redox system that is of particular important to precisely control engineered metabolic pathways.
Collapse
|
11
|
Li Y, Tschaplinski TJ, Engle NL, Hamilton CY, Rodriguez M, Liao JC, Schadt CW, Guss AM, Yang Y, Graham DE. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:2. [PMID: 22214220 PMCID: PMC3268733 DOI: 10.1186/1754-6834-5-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/04/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND The model bacterium Clostridium cellulolyticum efficiently degrades crystalline cellulose and hemicellulose, using cellulosomes to degrade lignocellulosic biomass. Although it imports and ferments both pentose and hexose sugars to produce a mixture of ethanol, acetate, lactate, H2 and CO2, the proportion of ethanol is low, which impedes its use in consolidated bioprocessing for biofuels production. Therefore genetic engineering will likely be required to improve the ethanol yield. Plasmid transformation, random mutagenesis and heterologous expression systems have previously been developed for C. cellulolyticum, but targeted mutagenesis has not been reported for this organism, hindering genetic engineering. RESULTS The first targeted gene inactivation system was developed for C. cellulolyticum, based on a mobile group II intron originating from the Lactococcus lactis L1.LtrB intron. This markerless mutagenesis system was used to disrupt both the paralogous L-lactate dehydrogenase (Ccel_2485; ldh) and L-malate dehydrogenase (Ccel_0137; mdh) genes, distinguishing the overlapping substrate specificities of these enzymes. Both mutations were then combined in a single strain, resulting in a substantial shift in fermentation toward ethanol production. This double mutant produced 8.5-times more ethanol than wild-type cells growing on crystalline cellulose. Ethanol constituted 93% of the major fermentation products, corresponding to a molar ratio of ethanol to organic acids of 15, versus 0.18 in wild-type cells. During growth on acid-pretreated switchgrass, the double mutant also produced four times as much ethanol as wild-type cells. Detailed metabolomic analyses identified increased flux through the oxidative branch of the mutant's tricarboxylic acid pathway. CONCLUSIONS The efficient intron-based gene inactivation system produced the first non-random, targeted mutations in C. cellulolyticum. As a key component of the genetic toolbox for this bacterium, markerless targeted mutagenesis enables functional genomic research in C. cellulolyticum and rapid genetic engineering to significantly alter the mixture of fermentation products. The initial application of this system successfully engineered a strain with high ethanol productivity from cellobiose, cellulose and switchgrass.
Collapse
Affiliation(s)
- Yongchao Li
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Choo Y Hamilton
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James C Liao
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yunfeng Yang
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David E Graham
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
| |
Collapse
|
12
|
Determinants of nucleotide-binding selectivity of malic enzyme. PLoS One 2011; 6:e25312. [PMID: 21980421 PMCID: PMC3183043 DOI: 10.1371/journal.pone.0025312] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/31/2011] [Indexed: 11/19/2022] Open
Abstract
Malic enzymes have high cofactor selectivity. An isoform-specific distribution of residues 314, 346, 347 and 362 implies that they may play key roles in determining the cofactor specificity. Currently, Glu314, Ser346, Lys347 and Lys362 in human c-NADP-ME were changed to the corresponding residues of human m-NAD(P)-ME (Glu, Lys, Tyr and Gln, respectively) or Ascaris suum m-NAD-ME (Ala, Ile, Asp and His, respectively). Kinetic data demonstrated that the S346K/K347Y/K362Q c-NADP-ME was transformed into a debilitated NAD⁺-utilizing enzyme, as shown by a severe decrease in catalytic efficiency using NADP⁺ as the cofactor without a significant increase in catalysis using NAD⁺ as the cofactor. However, the S346K/K347Y/K362H enzyme displayed an enhanced value for k(cat,NAD), suggesting that His at residue 362 may be more beneficial than Gln for NAD⁺ binding. Furthermore, the S346I/K347D/K362H mutant had a very large K(m,NADP) value compared to other mutants, suggesting that this mutant exclusively utilizes NAD⁺ as its cofactor. Since the S346K/K347Y/K362Q, S346K/K347Y/K362H and S346I/K347D/K362H c-NADP-ME mutants did not show significant reductions in their K(m,NAD) values, the E314A mutation was then introduced into these triple mutants. Comparison of the kinetic parameters of each triple-quadruple mutant pair (for example, S346K/K347Y/K362Q versus E314A/S346K/K347Y/K362Q) revealed that all of the K(m) values for NAD⁺ and NADP(+) of the quadruple mutants were significantly decreased, while either k(cat,NAD) or k(cat,NADP) was substantially increased. By adding the E314A mutation to these triple mutant enzymes, the E314A/S346K/K347Y/K362Q, E314A/S346K/K347Y/K362H and E314A/S346I/K347D/K362H c-NADP-ME variants are no longer debilitated but become mainly NAD⁺-utilizing enzymes by a considerable increase in catalysis using NAD⁺ as the cofactor. These results suggest that abolishing the repulsive effect of Glu314 in these quadruple mutants increases the binding affinity of NAD⁺. Here, we demonstrate that a series of E314A-containing c-NADP-ME quadruple mutants have been changed to NAD⁺-utilizing enzymes by abrogating NADP⁺ binding and increasing NAD⁺ binding.
Collapse
|