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Grzechowiak M, Sliwiak J, Link A, Ruszkowski M. Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies. Int J Biol Macromol 2024; 278:134648. [PMID: 39142482 DOI: 10.1016/j.ijbiomac.2024.134648] [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: 02/28/2024] [Revised: 06/28/2024] [Accepted: 08/08/2024] [Indexed: 08/16/2024]
Abstract
Glutamate dehydrogenases (GDHs) are key enzymes at the crossroads of N and C metabolism in plants. Legumes, whose N metabolism is particularly intricate, possess a unique type of GDH. This study presents an analysis of a legume-type GDH (isoform 2) from Medicago truncatula (MtGDH2). We measured MtGDH2 activity in both the Glu → 2-oxoglutarate (2OG) and 2OG → Glu reaction directions and obtained kinetic parameters for Glu, 2OG, NAD+, and NADH. Inhibition assays revealed that compounds possessing di- or tricarboxylates act as inhibitors of plant GDHs. Interestingly, 2,6-pyridinedicarboxylate (PYR) weakly inhibits MtGDH2 compared to Arabidopsis thaliana homologs. Furthermore, we explored tetrazole derivatives to discover 3-(1H-tetrazol-5-yl)benzoic acid (TBA) as an MtGDH2 inhibitor. The kinetic experiments are supported by six crystal structures, solved as: (i) unliganded enzyme, (ii) trapping the reaction intermediate 2-amino-2-hydroxyglutarate and NAD+, and also complexed with NAD+ and inhibitors such as (iii) citrate, (iv) PYR, (v) isophthalate, and (vi) TBA. The complex with TBA revealed a new mode of action that, in contrast to other inhibitors, prevents domain closure. This discovery points to TBA as a starting point for the development of novel GDH inhibitors to study the functions of GDH in plants and potentially boost biomass production.
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Affiliation(s)
- Marta Grzechowiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Joanna Sliwiak
- Laboratory of Protein Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland
| | - Andreas Link
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.
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2
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Zhang Q, Chen Y, Duan L, Dong L, Wang S. Design Glutamate Dehydrogenase for Nonaqueous System by Motifs Reassembly and Interaction Network Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:19931-19939. [PMID: 39222309 DOI: 10.1021/acs.jafc.4c02995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Glutamate dehydrogenases (GDH) serve as the key regulated enzyme that links protein and carbohydrate metabolism. Combined with motif reassembly and mutation, novel GDHs were designed. Motif reassembly of thermophilic GDH and malate dehydrogenase aims to overcome stability and activity tradeoff in nonaqueous systems. Structural compatibility and dynamic cooperation of the designed AaDHs were studied by molecular dynamics simulation. Furthermore, multipoint mutations improved its catalytic activity for unnatural substrates. Amino acid interaction network analysis indicated that the high density of hydrogen-bonded salt bridges is beneficial to the stability. Finally, the experimental verification determines the kinetics of AaDHs in a nonaqueous system. The activity of Aa05 was increased by 1.78-fold with ionic liquid [EMIM]BF4. This study presents the strategy of a combination of rigid motif assembly and mutations of active sites for robust dehydrogenases with high activity in the nonaqueous system, which overcomes the activity-stability tradeoff effect.
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Affiliation(s)
- Qian Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuxin Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Lingxuan Duan
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Lingling Dong
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen, Fujian 361005, P. R. China
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Grzechowiak M, Sliwiak J, Jaskolski M, Ruszkowski M. Structural and functional studies of Arabidopsis thaliana glutamate dehydrogenase isoform 2 demonstrate enzyme dynamics and identify its calcium binding site. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107895. [PMID: 37478728 DOI: 10.1016/j.plaphy.2023.107895] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 06/26/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Glutamate dehydrogenase (GDH) is an enzyme at the crossroad of plant nitrogen and carbon metabolism. GDH catalyzes the conversion of 2-oxoglutarate into glutamate (2OG → Glu), utilizing ammonia as cosubstrate and NADH as coenzyme. The GDH reaction is reversible, meaning that the NAD+-dependent reaction (Glu → 2OG) releases ammonia. In Arabidopsis thaliana, three GDH isoforms exist, AtGDH1, AtGDH2, and AtGDH3. The subject of this work is AtGDH2. Previous reports have suggested that enzymes homologous to AtGDH2 contain a calcium-binding EF-hand motif located in the coenzyme binding domain. Here, we show that while AtGDH2 indeed does bind calcium, the binding occurs elsewhere and the region predicted to be the EF-hand motif has a completely different structure. As the true calcium binding site is > 20 Å away from the active site, it seems to play a structural, rather than catalytic role. We also performed comparative kinetic characterization of AtGDH1 and AtGDH2 using spectroscopic methods and isothermal titration calorimetry, to note that the isoenzymes generally exhibit similar behavior, with calcium having only a minor effect. However, the spatial and temporal changes in the gene expression profiles of the three AtGDH genes point to AtGDH2 as the most prevalent isoform.
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Affiliation(s)
- Marta Grzechowiak
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Joanna Sliwiak
- Laboratory of Protein Engineering, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland
| | - Mariusz Jaskolski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland; Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznan, 61-614, Poland
| | - Milosz Ruszkowski
- Department of Structural Biology of Eukaryotes, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, 61-704, Poland.
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Transcriptome and Metabolome Reveal the Molecular Mechanism of Barley Genotypes Underlying the Response to Low Nitrogen and Resupply. Int J Mol Sci 2023; 24:ijms24054706. [PMID: 36902137 PMCID: PMC10003240 DOI: 10.3390/ijms24054706] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Nitrogen is one of the most important mineral elements for plant growth and development. Excessive nitrogen application not only pollutes the environment, but also reduces the quality of crops. However, are few studies on the mechanism of barley tolerance to low nitrogen at both the transcriptome and metabolomics levels. In this study, the nitrogen-efficient genotype (W26) and the nitrogen-sensitive genotype (W20) of barley were treated with low nitrogen (LN) for 3 days and 18 days, then treated with resupplied nitrogen (RN) from 18 to 21 days. Later, the biomass and the nitrogen content were measured, and RNA-seq and metabolites were analyzed. The nitrogen use efficiency (NUE) of W26 and W20 treated with LN for 21 days was estimated by nitrogen content and dry weight, and the values were 87.54% and 61.74%, respectively. It turned out to have a significant difference in the two genotypes under the LN condition. According to the transcriptome analysis, 7926 differentially expressed genes (DEGs) and 7537 DEGs were identified in the leaves of W26 and W20, respectively, and 6579 DEGs and 7128 DEGs were found in the roots of W26 and W20, respectively. After analysis of the metabolites, 458 differentially expressed metabolites (DAMs) and 425 DAMs were found in the leaves of W26 and W20, respectively, and 486 DAMs and 368 DAMs were found in the roots of W26 and W20, respectively. According to the KEGG joint analysis of DEGs and DAMs, it was discovered that glutathione (GSH) metabolism was the pathway of significant enrichment in the leaves of both W26 and W20. In this study, the metabolic pathways of nitrogen metabolism and GSH metabolism of barley under nitrogen were constructed based on the related DAMs and DEGs. In leaves, GSH, amino acids, and amides were the main identified DAMs, while in roots, GSH, amino acids, and phenylpropanes were mainly found DAMs. Finally, some nitrogen-efficient candidate genes and metabolites were selected based on the results of this study. The responses of W26 and W20 to low nitrogen stress were significantly different at the transcriptional and metabolic levels. The candidate genes that have been screened will be verified in future. These data not only provide new insights into how barley responds to LN, but also provide new directions for studying the molecular mechanisms of barley under abiotic stress.
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Sun L, Cheng L, Fu H, Wang R, Gu Y, Qiu Y, Sun K, Xu H, Lei P. A strategy for nitrogen conversion in aquaculture water based on poly-γ-glutamic acid synthesis. Int J Biol Macromol 2023; 229:1036-1043. [PMID: 36603727 DOI: 10.1016/j.ijbiomac.2022.12.314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Ammonia and nitrite are nitrogenous pollutants in aquaculture effluents, which pose a major threat to the health of aquatic animals. In this study, we developed a nitrogen conversion strategy based on synthesis of poly-γ-glutamic acid (γ-PGA) by Bacillus subtilis NX-2. The nitrogen removal efficiency of NX-2 was closely related to synthesizing γ-PGA, and was positively correlated with the inoculum level. The degradation rates of ammonia nitrogen and nitrite at 104 CFU/mL were 84.42 % and 62.56 %, respectively. Through adaptive laboratory evolution (ALE) experiment, we obtained a strain named ALE 5 M with ammonia degradation rate of 98.03 % and nitrite of 93.62 % at the inoculum level of 104 CFU/mL. Transcriptome analysis showed that the strain was more likely to produce γ-PGA after ALE. By enzyme activity and qPCR analysis, we confirmed that ALE 5 M degraded ammonia nitrogen through γ-PGA synthesis, which provided a new way for nitrogen removal in aquaculture water.
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Affiliation(s)
- Liang Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Lifangyu Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Heng Fu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Rui Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yian Gu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Yibin Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Ke Sun
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Hong Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China
| | - Peng Lei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China.
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Ying M, Hu X. Tracing the electron flow in redox metabolism: The appropriate distribution of electrons is essential to maintain redox balance in cancer cells. Semin Cancer Biol 2022; 87:32-47. [PMID: 36374644 DOI: 10.1016/j.semcancer.2022.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
Cancer cells are characterized by sustained proliferation, which requires a huge demand of fuels to support energy production and biosynthesis. Energy is produced by the oxidation of the fuels during catabolism, and biosynthesis is achieved by the reduction of smaller units or precursors. Therefore, the oxidation-reduction (redox) reactions in cancer cells are more active compared to those in the normal counterparts. The higher activity of redox metabolism also induces a more severe oxidative stress, raising the question of how cancer cells maintain the redox balance. In this review, we overview the redox metabolism of cancer cells in an electron-tracing view. The electrons are derived from the nutrients in the tumor microenvironment and released during catabolism. Most of the electrons are transferred to NAD(P) system and then directed to four destinations: energy production, ROS generation, reductive biosynthesis and antioxidant system. The appropriate distribution of these electrons achieved by the function of redox regulation network is essential to maintain redox homeostasis in cancer cells. Interfering with the electron distribution and disrupting redox balance by targeting the redox regulation network may provide therapeutic implications for cancer treatment.
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Affiliation(s)
- Minfeng Ying
- Cancer Institute (Key Laboratory for Cancer Intervention and Prevention, China National Ministry of Education, Zhejiang Provincial Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009 Hangzhou, Zhejiang, China.
| | - Xun Hu
- Cancer Institute (Key Laboratory for Cancer Intervention and Prevention, China National Ministry of Education, Zhejiang Provincial Key Laboratory of Molecular Biology in Medical Sciences), The Second Affiliated Hospital, Zhejiang University School of Medicine, 310009 Hangzhou, Zhejiang, China.
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Mayer RJ, Moran J. Quantifying Reductive Amination in Nonenzymatic Amino Acid Synthesis. Angew Chem Int Ed Engl 2022; 61:e202212237. [PMID: 36121198 PMCID: PMC9828492 DOI: 10.1002/anie.202212237] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Indexed: 01/12/2023]
Abstract
Amino acid biosynthesis initiates with the reductive amination of α-ketoglutarate with ammonia to produce glutamate. However, the other α-keto acids derived from the glyoxylate and Krebs cycles are converted into amino acids by transamination, rather than by reductive amination. Why is only one amino acid synthesized by reductive amination and not the others? To explore this question, we quantified the inherent reactivities of keto acids in nonenzymatic reduction and reductive amination by using BH3 CN- as a model nucleophile. Biological α-keto acids were found to show pronounced nonenzymatic reactivity differences for the formation of amino acids (α-ketoglutarate
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Affiliation(s)
- Robert J. Mayer
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS)CNRS UMR 7006Université de Strasbourg8 Allée Gaspard Monge67000StrasbourgFrance
| | - Joseph Moran
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS)CNRS UMR 7006Université de Strasbourg8 Allée Gaspard Monge67000StrasbourgFrance
- Institut Universitaire de France (IUF)75005ParisFrance
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Substrate-Specific Engineering of Amino Acid Dehydrogenase Superfamily for Synthesis of a Variety of Chiral Amines and Amino Acids. Catalysts 2022. [DOI: 10.3390/catal12040380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Amino acid dehydrogenases (AADHs) are a group of enzymes that catalyze the reversible reductive amination of keto acids with ammonia to produce chiral amino acids using either nicotinamide adenine dinucleotide (NAD+) or nicotinamide adenine dinucleotide phosphate (NADP+) as cofactors. Among them, glutamate dehydrogenase, valine dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and tryptophan dehydrogenase have been classified as a superfamily of amino acid dehydrogenases (s-AADHs) by previous researchers because of their conserved structures and catalytic mechanisms. Owing to their excellent stereoselectivity, high atom economy, and low environmental impact of the reaction pathway, these enzymes have been extensively engineered to break strict substrate specificities for the synthesis of high value-added chiral compounds (chiral amino acids, chiral amines, and chiral amino alcohols). Substrate specificity engineering of s-AADHs mainly focuses on recognition engineering of the substrate side chain R group and substrate backbone carboxyl group. This review summarizes the reported studies on substrate specificity engineering of s-AADHs and reports that this superfamily of enzymes shares substrate specificity engineering hotspots (the inside of the pocket, substrate backbone carboxyl anchor sites, substrate entrance tunnel, and hinge region), which sheds light on the substrate-specific tailoring of these enzymes.
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A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nat Chem Biol 2022; 18:161-170. [PMID: 34931064 PMCID: PMC8810680 DOI: 10.1038/s41589-021-00919-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/12/2021] [Indexed: 12/18/2022]
Abstract
Multi-enzyme assemblies composed of metabolic enzymes catalyzing sequential reactions are being increasingly studied. Here, we report the discovery of a 1.6 megadalton multi-enzyme complex from Bacillus subtilis composed of two enzymes catalyzing opposite ('counter-enzymes') rather than sequential reactions: glutamate synthase (GltAB) and glutamate dehydrogenase (GudB), which make and break glutamate, respectively. In vivo and in vitro studies show that the primary role of complex formation is to inhibit the activity of GudB. Using cryo-electron microscopy, we elucidated the structure of the complex and the molecular basis of inhibition of GudB by GltAB. The complex exhibits unusual oscillatory progress curves and is necessary for both planktonic growth, in glutamate-limiting conditions, and for biofilm growth, in glutamate-rich media. The regulation of a key metabolic enzyme by complexing with its counter enzyme may thus enable cell growth under fluctuating glutamate concentrations.
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Song C, Wu M, Zhang Y, Li J, Yang J, Wei D, Li H, Guo L, Qin J. Bioactive Monomer and Polymer Polyketides from Edible Mushroom Cortinarius caerulescens as Glutamate Dehydrogenase Inhibitors and Antioxidants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:804-814. [PMID: 35029386 DOI: 10.1021/acs.jafc.1c07119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Two new polyketides named rufoolivacin E and viocristin B, a new natural product named 1-hydroxy-3,6,8-trimethoxyanthraquinone, and 13 known compounds were isolated from edible mushroom Cortinarius purpurascens in this work. Their structures were assigned on the basis of high-resolution electrospray ionization mass spectrometry, 1D and 2D nuclear magnetic resonance, and electronic circular dichroism data. Notably, the enzyme activity test on glutamate dehydrogenase indicated that 1, 3, 4, 5, 6, 10, 11, and 15 displayed an excellent inhibition effect. Further kinetic studies showed that the most potent compounds, 4 and 10, possess great potential as competitive inhibitors of glutamate dehydrogenase. Molecular docking and computational chemistry were applied to illustrate the binding mechanism in detail. 2,2-Diphenyl-1-picrylhydrazyl and reactive oxygen species assay results showed that compounds 1, 2, 3, and 8 exhibited significant antioxidant activities with IC50 values of 7.0 ± 0.3, 8.6 ± 0.1, 7.5 ± 0.1, and 2.8 ± 0.2 μg mL-1, respectively. Thus, Cortinarius caerulescens represents a novel resource of these polyketides to be utilized in food selection and drug discovery.
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Affiliation(s)
- Chenggang Song
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Mingyue Wu
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Yanxin Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Jie Li
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Jian Yang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100193, P. R. China
| | - Dongsheng Wei
- Institute of Wood Science, Department of Biology, University of Hamburg, Leuschnerstrasse 91, Hamburg 21031, Germany
| | - He Li
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100193, P. R. China
| | - Jianchun Qin
- College of Plant Sciences, Jilin University, Changchun 130062, China
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Yin X, Zeng Y, Chen J, Liu L, Gao Z. Combined active pocket and hinge region engineering to develop an NADPH-dependent phenylglycine dehydrogenase. Bioorg Chem 2022; 120:105601. [PMID: 35033816 DOI: 10.1016/j.bioorg.2022.105601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/20/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022]
Abstract
NADPH-dependent amino acid dehydrogenases (AADHs) are favorable enzymes to construct artificial biosynthetic pathways in whole-cell for high-value noncanonical amino acids (NcAAs) production. Glutamate dehydrogenases (GluDHs) represent attractive candidates for the development of novel NADPH-dependent AADHs. Here, we report the development of a novel NADPH-dependent phenylglycine dehydrogenase by combining active pocket engineering and hinge region engineering of a GluDH from Pseudomonas putida (PpGluDH). The active pocket of PpGluDH was firstly tailored to optimize its binding mode with bulky substrate α-oxobenzeneacetic acid (α-OA), and then, the hinge region was further engineered to tune the protein conformational dynamics, which finally resulted in a mutant M3 (T196A/T121I/L123D) with a 103-fold increase of catalytic efficiency (kcat/Km) toward α-OA. The M3 mutant exhibited high catalytic performance in both in vitro biocatalysis preparation and in vivo biosynthesis of l-phenylglycine, indicating its promising practical applications. Our results demonstrated that co-engineering of the active pocket and hinge region is an effective strategy for developing novel NADPH-dependent AADHs from GluDHs for NcAAs production.
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Affiliation(s)
- Xinjian Yin
- School of Marine Science, Sun Yat-sen University, Zhuhai 519080, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Yujing Zeng
- School of Marine Science, Sun Yat-sen University, Zhuhai 519080, China
| | - Jun Chen
- School of Marine Science, Sun Yat-sen University, Zhuhai 519080, China
| | - Lan Liu
- School of Marine Science, Sun Yat-sen University, Zhuhai 519080, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China
| | - Zhizeng Gao
- School of Marine Science, Sun Yat-sen University, Zhuhai 519080, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519080, China.
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12
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Nitrogen Availability Affects the Metabolic Profile in Cyanobacteria. Metabolites 2021; 11:metabo11120867. [PMID: 34940625 PMCID: PMC8707274 DOI: 10.3390/metabo11120867] [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: 12/02/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Nitrogen is essential for the biosynthesis of various molecules in cells, such as amino acids and nucleotides, as well as several types of lipids and sugars. Cyanobacteria can assimilate several forms of nitrogen, including nitrate, ammonium, and urea, and the physiological and genetic responses to these nitrogen sources have been studied previously. However, the metabolic changes in cyanobacteria caused by different nitrogen sources have not yet been characterized. This study aimed to elucidate the influence of nitrate and ammonium on the metabolic profiles of the cyanobacterium Synechocystis sp. strain PCC 6803. When supplemented with NaNO3 or NH4Cl as the nitrogen source, Synechocystis sp. PCC 6803 grew faster in NH4Cl medium than in NaNO3 medium. Metabolome analysis indicated that some metabolites in the CBB cycle, glycolysis, and TCA cycle, and amino acids were more abundant when grown in NH4Cl medium than NaNO3 medium. 15N turnover rate analysis revealed that the nitrogen assimilation rate in NH4Cl medium was higher than in NaNO3 medium. These results indicate that the mechanism of nitrogen assimilation in the GS-GOGAT cycle differs between NaNO3 and NH4Cl. We conclude that the amounts and biosynthetic rate of cyanobacterial metabolites varies depending on the type of nitrogen.
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Borvinskaya E, Kochneva A, Bedulina D, Sukhovskaya I, Smirnov L, Babkina I. Comparative Analysis of Proteins of Functionally Different Body Parts of the Fish Parasites Triaenophorus nodulosus and Triaenophorus crassus. Acta Parasitol 2021; 66:1137-1150. [PMID: 33818717 DOI: 10.1007/s11686-021-00384-6] [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: 11/16/2020] [Accepted: 03/23/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE Studies of proteins expressed in the morphological structures of the parasite are necessary for elucidating the biological functions of unknown proteins and understanding the molecular basis of parasitism. The research aim was to investigate the spatial distribution of major proteins in scolex, immature and gravid proglottids of Triaenophorus nodulosus and Triaenophorus crassus. METHODS Protein extracts of worm body parts were analyzed using two-dimensional difference gel electrophoresis (DIGE) and mass spectrometry. RESULTS Comparison of the protein repertoire of the adult worm and the encysted plerocercoid revealed differences between the worm body parts, life stages and parasite species. The content of proteins associated with the cytoskeleton and musculature (actin, myosin regulatory light chain, and tropomyosin 2) decreased with distance from the scolex. Mature proglottids were rich in transforming growth factor-beta-induced protein, propionyl-CoA carboxylase, glutamate dehydrogenase and beta-tubulin. Interspecific variation in T. nodulosus and T. crassus was found in the content of the myosin, paramyosin, the major vault protein and an uncharacterized secreted protein TRINITY_DN24645. Differential expression of TRINITY_DN24645, paramyosin and tropomyosin 2 was found between plerocercoids and adult worms. CONCLUSION The present study provides the first characteristics of the spatial distribution of the major proteins of T. crassus and T. nodulosus. Comparison of the protein composition of plerocercoids and adult parasites indicates a significant similarity in the proteomic organization of Triaenophorus sp. in the second intermediate and final hosts. The gradual change in the morphological organization of tapeworms in the longitudinal direction coincided with the expression of some structural and metabolic proteins.
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Affiliation(s)
- Ekaterina Borvinskaya
- Institute of Biology At Irkutsk State University, 3 Lenin St, 664025, Irkutsk, Russia.
| | - Albina Kochneva
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, 11 Pushkinskaya St, 185910, Petrozavodsk, Russia
| | - Daria Bedulina
- Institute of Biology At Irkutsk State University, 3 Lenin St, 664025, Irkutsk, Russia
| | - Irina Sukhovskaya
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, 11 Pushkinskaya St, 185910, Petrozavodsk, Russia
| | - Lev Smirnov
- Institute of Biology of the Karelian Research Centre of the Russian Academy of Sciences, 11 Pushkinskaya St, 185910, Petrozavodsk, Russia
| | - Irina Babkina
- Department of Invertebrate Zoology, St Petersburg State University, 7/9A Universitetskaya St, 199034, St Petersburg, Russia
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14
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Borvinskaya EV, Kochneva AA, Drozdova PB, Balan OV, Zgoda VG. Temperature-induced reorganisation of Schistocephalus solidus (Cestoda) proteome during the transition to the warm-blooded host. Biol Open 2021; 10:bio058719. [PMID: 34787304 PMCID: PMC8609239 DOI: 10.1242/bio.058719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/10/2021] [Indexed: 11/30/2022] Open
Abstract
The protein composition of the cestode Schistocephalus solidus was measured in an experiment simulating the trophic transmission of the parasite from a cold-blooded to a warm-blooded host. The first hour of host colonisation was studied in a model experiment, in which sticklebacks Gasterosteus aculeatus infected with S. solidus were heated at 40°C for 1 h. As a result, a decrease in the content of one tegument protein was detected in the plerocercoids of S. solidus. Sexual maturation of the parasites was initiated in an experiment where S. solidus larvae were taken from fish and cultured in vitro at 40°C for 48 h. Temperature-independent changes in the parasite proteome were investigated by incubating plerocercoids at 22°C for 48 h in culture medium. Analysis of the proteome allowed us to distinguish the temperature-induced genes of S. solidus, as well as to specify the molecular markers of the plerocercoid and adult worms. The main conclusion of the study is that the key enzymes of long-term metabolic changes (glycogen consumption, protein production, etc.) in parasites during colonisation of a warm-blooded host are induced by temperature.
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Affiliation(s)
| | - Albina A. Kochneva
- Institute of Biology, Karelian Research Centre of the Russian Academy of Sciences, 11 Pushkinskaya Street, 185910 Petrozavodsk, Karelia, Russia
| | - Polina B. Drozdova
- Institute of Biology, Irkutsk State University, 3 Lenin St, 664025 Irkutsk, Russia
| | - Olga V. Balan
- Institute of Biology, Karelian Research Centre of the Russian Academy of Sciences, 11 Pushkinskaya Street, 185910 Petrozavodsk, Karelia, Russia
| | - Victor G. Zgoda
- Department of Proteomic Research and Mass Spectrometry, Institute of Biomedical Chemistry (IBMC), 10 Pogodinskaya street, 119121 Moscow, Russia
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15
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Godsora BKJ, Prakash P, Punekar NS, Bhaumik P. Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites. Proteins 2021; 90:810-823. [PMID: 34748226 DOI: 10.1002/prot.26276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022]
Abstract
Glutamate dehydrogenase (GDH) is a salient metabolic enzyme which catalyzes the NAD+ - or NADP+ -dependent reversible conversion of α-ketoglutarate (AKG) to l-glutamate; and thereby connects the carbon and nitrogen metabolism cycles in all living organisms. The function of GDH is extensively regulated by both metabolites (citrate, succinate, etc.) and non-metabolites (ATP, NADH, etc.) but sufficient molecular evidences are lacking to rationalize the inhibitory effects by the metabolites. We have expressed and purified NADP+ -dependent Aspergillus terreus GDH (AtGDH) in recombinant form. Succinate, malonate, maleate, fumarate, and tartrate independently inhibit the activity of AtGDH to different extents. The crystal structures of AtGDH complexed with the dicarboxylic acid metabolites and the coenzyme NADPH have been determined. Although AtGDH structures are not complexed with substrate; surprisingly, they acquire super closed conformation like previously reported for substrate and coenzyme bound catalytically competent Aspergillus niger GDH (AnGDH). These dicarboxylic acid metabolites partially occupy the same binding pocket as substrate; but interact with varying polar interactions and the coenzyme NADPH binds to the Domain-II of AtGDH. The low inhibition potential of tartrate as compared to other dicarboxylic acid metabolites is due to its weaker interactions of carboxylate groups with AtGDH. Our results suggest that the length of carbon skeleton and positioning of the carboxylate groups of inhibitors between two conserved lysine residues at the GDH active site might be the determinants of their inhibitory potency. Molecular details on the dicarboxylic acid metabolites bound AtGDH active site architecture presented here would be applicable to GDHs in general.
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Affiliation(s)
| | - Prem Prakash
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Narayan S Punekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Prasenjit Bhaumik
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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16
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Singh P, Srivastava R. Utilization of bio-inspired catalyst for CO2 reduction into green fuels: Recent advancement and future perspectives. J CO2 UTIL 2021. [DOI: 10.1016/j.jcou.2021.101748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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17
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Li N, Wang W, Zeng X, Liu M, Li M, Li C, Wang M. Crystal structure of glutamate dehydrogenase 3 from Candida albicans. Biochem Biophys Res Commun 2021; 570:15-20. [PMID: 34271431 DOI: 10.1016/j.bbrc.2021.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/06/2021] [Indexed: 10/20/2022]
Abstract
Glutamate dehydrogenase 3 from Candida albicans (CaGdh3) catalyzes the reversible oxidative deamination of l-glutamate, playing an important role in the yeast-to-hyphal transition of C. albicans. Here we report the crystal structures of CaGdh3 and its complex with α-ketoglutarate and NADPH. CaGdh3 exists as a hexamer, with each subunit containing two domains. The substrate and coenzyme bind in the cleft between the two domains and their binding induces a conformational change in CaGdh3. Our results will help to understand the catalytic mechanism of CaGdh3 and will provide a structural basis for the design of antifungal drugs targeting the CaGdh3 pathway.
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Affiliation(s)
- Na Li
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Wenfeng Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China; School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China
| | - Xue Zeng
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China
| | - Mingjie Liu
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China; School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China
| | - Mengyu Li
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China; School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China
| | - Changrun Li
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China.
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, Anhui, China; School of Life Sciences, Anhui University, Hefei, 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, 230601, Anhui, China.
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18
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Zhao Y, Gao J, Su S, Shan X, Li S, Liu H, Yuan Y, Li H. Regulation of the activity of maize glutamate dehydrogenase by ammonium and potassium. Biosci Biotechnol Biochem 2021; 85:262-271. [PMID: 33604622 DOI: 10.1093/bbb/zbaa020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/18/2020] [Indexed: 11/14/2022]
Abstract
Glutamate dehydrogenase (GDH) is an important enzyme in ammonium metabolism, the activity of which is regulated by multiple factors. In this study, we investigate the effects of ammonium and potassium on the activity of maize GDH. Our results show that both ammonium and potassium play multiple roles in regulating the activity of maize GDH, with the specific roles depending on the concentration of potassium. Together with the structural information of GDH, we propose models for the substrate inhibition of ammonium, and the elimination of substrate inhibition by potassium. These models are supported by the analysis of statistic thermodynamics. We also analyze the binding sites of ammonium and potassium on maize GDH, and the conformational changes of maize GDH. The findings provide insight into the regulation of maize GDH activity by ammonium and potassium and reveal the importance of the dose and ratio of nitrogen and potassium in crop cultivation.
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Affiliation(s)
- Yanjie Zhao
- College of Plant Science, Jilin University, Changchun, China
| | - Jie Gao
- College of Plant Science, Jilin University, Changchun, China
| | - Shengzhong Su
- College of Plant Science, Jilin University, Changchun, China
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun, China
| | - Shipeng Li
- College of Plant Science, Jilin University, Changchun, China
| | - Hongkui Liu
- College of Plant Science, Jilin University, Changchun, China
| | - Yaping Yuan
- College of Plant Science, Jilin University, Changchun, China
| | - He Li
- College of Plant Science, Jilin University, Changchun, China
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19
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Simultaneous directed evolution of coupled enzymes for efficient asymmetric synthesis of l-phosphinothricin. Appl Environ Microbiol 2021; 87:AEM.02563-20. [PMID: 33310717 PMCID: PMC8090864 DOI: 10.1128/aem.02563-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The traditional strategy to improve the efficiency of an entire coupled enzyme system relies on separate direction of the evolution of enzymes involved in their respective enzymatic reactions. This strategy can lead to enhanced single-enzyme catalytic efficiency but may also lead to loss of coordination among enzymes. This study aimed to overcome such shortcomings by executing a directed evolution strategy on multiple enzymes in one combined group that catalyzes the asymmetric biosynthesis of l-phosphinothricin. The genes of a glutamate dehydrogenase from Pseudomonas moorei (PmGluDH) and a glucose dehydrogenase from Exiguobacterium sibiricum (EsGDH), along with other gene parts (promoters, ribosomal binding sites (RBSs), and terminators) were simultaneously evolved. The catalytic efficiency of PmGluDH was boosted by introducing the beneficial mutation A164G (from 1.29 s-1mM-1 to 183.52 s-1mM-1), and the EsGDH expression level was improved by optimizing the linker length between the RBS and the start codon of gdh. The total turnover numbers of the bioreaction increased from 115 (GluDH WTNADPH) to 5846 (A164GNADPH coupled with low expression of EsGDH), and to 33950 (A164GNADPH coupled with high expression of EsGDH). The coupling efficiency was increased from ∼30% (GluDH_WT with low expression of GDH) to 83.3% (GluDH_A164G with high expression of GDH). In the batch production of l-phosphinothricin utilizing whole-cell catalysis, the strongest biocatalytic reaction exhibited a high space-time yield (6410 g·L-1·d-1) with strict stereoselectivity (>99% enantiomeric excess).Importance: The traditional strategy to improve multienzyme-catalyzed reaction efficiency may lead to enhanced single-enzyme catalytic efficiency but may also result in loss of coordination among enzymes. We describe a directed evolution strategy of an entire coupled enzyme system to simultaneously enhance enzyme coordination and catalytic efficiency. The simultaneous evolution strategy was applied to a multienzyme-catalyzed reaction for the asymmetric synthesis of l-phosphinothricin, which not only enhanced the catalytic efficiency of GluDH but also improved the coordination between GluDH and GDH. Since this strategy is enzyme-independent, it may be applicable to other coupled enzyme systems for chiral chemical synthesis.
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20
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Wang L, Diao S, Sun Y, Jiang S, Liu Y, Wang H, Wei D. Rational engineering of Acinetobacter tandoii glutamate dehydrogenase for asymmetric synthesis of l-homoalanine through biocatalytic cascades. Catal Sci Technol 2021. [DOI: 10.1039/d1cy00376c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A high yield of l-homoalanine can be obtained by an engineered dual cofactor-dependent GluDH in a cascade without the addition of NAD(P)H.
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Affiliation(s)
- Liuzhu Wang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai
- China
| | - Shiqing Diao
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai
- China
| | - Yangyang Sun
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai
- China
| | - Shuiqin Jiang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai
- China
| | - Yan Liu
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai
- China
| | - Hualei Wang
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai
- China
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering
- New World Institute of Biotechnology
- East China University of Science and Technology
- Shanghai
- China
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21
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Vadlakonda L, Indracanti M, Kalangi SK, Gayatri BM, Naidu NG, Reddy ABM. The Role of Pi, Glutamine and the Essential Amino Acids in Modulating the Metabolism in Diabetes and Cancer. J Diabetes Metab Disord 2020; 19:1731-1775. [PMID: 33520860 DOI: 10.1007/s40200-020-00566-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
Abstract
Purpose Re-examine the current metabolic models. Methods Review of literature and gene networks. Results Insulin activates Pi uptake, glutamine metabolism to stabilise lipid membranes. Tissue turnover maintains the metabolic health. Current model of intermediary metabolism (IM) suggests glucose is the source of energy, and anaplerotic entry of fatty acids and amino acids into mitochondria increases the oxidative capacity of the TCA cycle to produce the energy (ATP). The reduced cofactors, NADH and FADH2, have different roles in regulating the oxidation of nutrients, membrane potentials and biosynthesis. Trans-hydrogenation of NADH to NADPH activates the biosynthesis. FADH2 sustains the membrane potential during the cell transformations. Glycolytic enzymes assume the non-canonical moonlighting functions, enter the nucleus to remodel the genetic programmes to affect the tissue turnover for efficient use of nutrients. Glycosylation of the CD98 (4F2HC) stabilises the nutrient transporters and regulates the entry of cysteine, glutamine and BCAA into the cells. A reciprocal relationship between the leucine and glutamine entry into cells regulates the cholesterol and fatty acid synthesis and homeostasis in cells. Insulin promotes the Pi transport from the blood to tissues, activates the mitochondrial respiratory activity, and glutamine metabolism, which activates the synthesis of cholesterol and the de novo fatty acids for reorganising and stabilising the lipid membranes for nutrient transport and signal transduction in response to fluctuations in the microenvironmental cues. Fatty acids provide the lipid metabolites, activate the second messengers and protein kinases. Insulin resistance suppresses the lipid raft formation and the mitotic slippage activates the fibrosis and slow death pathways.
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Affiliation(s)
| | - Meera Indracanti
- Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Suresh K Kalangi
- Amity Stem Cell Institute, Amity University Haryana, Amity Education Valley Pachgaon, Manesar, Gurugram, HR 122413 India
| | - B Meher Gayatri
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046 India
| | - Navya G Naidu
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046 India
| | - Aramati B M Reddy
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046 India
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22
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Cheng F, Li H, Zhang K, Li QH, Xie D, Xue YP, Zheng YG. Tuning amino acid dehydrogenases with featured sequences for L-phosphinothricin synthesis by reductive amination. J Biotechnol 2020; 312:35-43. [PMID: 32135177 DOI: 10.1016/j.jbiotec.2020.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/16/2020] [Accepted: 03/01/2020] [Indexed: 01/23/2023]
Abstract
Biosynthesizing unnatural chiral amino acids is challenging due to the limited reductive amination activity of amino acid dehydrogenase (AADH). Here, for the asymmetric synthesis of l-phosphinothricin from 2-oxo-4-[(hydroxy)(methyl)phosphinoyl]butyric acid (PPO), a glutamate dehydrogenase gene (named GluDH3) from Pseudomonas monteilii was selected, cloned and expressed in Escherichia coli (E. coli). To boost its activity, a "two-step"-based computational approach was developed and applied to select the potential beneficial amino acid positions on GluDH3. l-phosphinothricin was synthesized by GluDH-catalyzed asymmetric amination using the d-glucose dehydrogenase from Exiguobacterium sibiricum (EsGDH) for NADPH regeneration. Using lyophilized E. coli cells that co-expressed GluDH3_V375S and EsGDH, up to 89.04 g L-1 PPO loading was completely converted to l-phosphinothricin within 30 min at 35 °C with a space-time yield of up to 4.752 kg·L-1·d-1. The beneficial substitution V375S with increased polar interactions between K90, T193, and substrate PPO exhibited 168.2-fold improved catalytic efficiency (kcat/KM) and 344.8-fold enhanced specific activity. After the introduction of serine residues into other GluDHs at specific positions, forty engineered GluDHs exhibited the catalytic functions of "glufosinate dehydrogenase" towards PPO.
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Affiliation(s)
- Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Heng Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Kai Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Qing-Hua Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Dong Xie
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
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23
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The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase. J Mol Biol 2020; 432:2042-2054. [PMID: 32061937 DOI: 10.1016/j.jmb.2020.01.042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/24/2020] [Accepted: 01/28/2020] [Indexed: 11/22/2022]
Abstract
NADP-dependent methylene-tetrahydromethanopterin (methylene-H4MPT) dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of methylene-H4MPT to form methenyl-H4MPT+ by using NADP+ as a hydride acceptor. This hydride transfer reaction is involved in the oxidative metabolism from formaldehyde to CO2 in methylotrophic and methanotrophic bacteria. Here, we report on the crystal structures of the ternary MtdA-substrate complexes from Methylorubrum extorquens AM1 obtained in open and closed forms. Their conversion is accomplished by opening/closing the active site cleft via a 15° rotation of the NADP, relative to the pterin domain. The 1.08 Å structure of the closed and active enzyme-NADP-methylene-H4MPT complex allows a detailed geometric analysis of the bulky substrates and a precise prediction of the hydride trajectory. Upon domain closure, the bulky substrate rings become compressed resulting in a tilt of the imidazolidine group of methylene-H4MPT that optimizes the geometry for hydride transfer. An additional 1.5 Å structure of MtdA in complex with the nonreactive NADP+ and methenyl-H4MPT+ revealed an extremely short distance between nicotinamide-C4 and imidazoline-C14a of 2.5 Å, which demonstrates the strong pressure imposed. The pterin-imidazolidine-phenyl butterfly angle of methylene-H4MPT bound to MtdA is smaller than that in the enzyme-free state but is similar to that in H2- and F420-dependent methylene-H4MPT dehydrogenases. The concept of compression-driven hydride transfer including quantum mechanical hydrogen tunneling effects, which are established for flavin- and NADP-dependent enzymes, can be expanded to hydride-transferring H4MPT-dependent enzymes.
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24
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Yin X, Liu Y, Meng L, Zhou H, Wu J, Yang L. Semi-rational hinge engineering: modulating the conformational transformation of glutamate dehydrogenase for enhanced reductive amination activity towards non-natural substrates. Catal Sci Technol 2020. [DOI: 10.1039/c9cy02576f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The hinge region was identified to be a promising hotspot for activity engineering of GluDHs, providing a potent alternative for developing high-performance biocatalysts toward valuable optically pure l-amino acid production.
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Affiliation(s)
- Xinjian Yin
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Yayun Liu
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Lijun Meng
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Haisheng Zhou
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Jianping Wu
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Lirong Yang
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
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25
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Trotter PJ, Juco K, Le HT, Nelson K, Tamayo LI, Nicaud JM, Park YK. Glutamate dehydrogenases in the oleaginous yeast Yarrowia lipolytica. Yeast 2019; 37:103-115. [PMID: 31119792 DOI: 10.1002/yea.3425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/25/2019] [Accepted: 05/17/2019] [Indexed: 11/12/2022] Open
Abstract
Glutamate dehydrogenases (GDHs) are fundamental to cellular nitrogen and energy balance. Yet little is known about these enzymes in the oleaginous yeast Yarrowia lipolytica. The YALI0F17820g and YALI0E09603g genes, encoding potential GDH enzymes in this organism, were examined. Heterologous expression in gdh-null Saccharomyces cerevisiae and examination of Y. lipolytica strains carrying gene deletions demonstrate that YALI0F17820g (ylGDH1) encodes a NADP-dependent GDH whereas YALI0E09603g (ylGDH2) encodes a NAD-dependent GDH enzyme. The activity encoded by these two genes accounts for all measurable GDH activity in Y. lipolytica. Levels of the two enzyme activities are comparable during logarithmic growth on rich medium, but the NADP-ylGDH1p enzyme activity is most highly expressed in stationary and nitrogen starved cells by threefold to 12-fold. Replacement of ammonia with glutamate causes a decrease in NADP-ylGdh1p activity, whereas NAD-ylGdh2p activity is increased. When glutamate is both carbon and nitrogen sources, the activity of NAD-ylGDH2p becomes dominant up to 18-fold compared with that of NADP-ylGDH1p. Gene deletion followed by growth on different carbon and nitrogen sources shows that NADP-ylGdh1p is required for efficient nitrogen assimilation whereas NAD-ylGdh2p plays a role in nitrogen and carbon utilization from glutamate. Overexpression experiments demonstrate that ylGDH1 and ylGDH2 are not interchangeable. These studies provide a vital basis for future consideration of how these enzymes function to facilitate energy and nitrogen homeostasis in Y. lipolytica.
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Affiliation(s)
- Pamela J Trotter
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Karen Juco
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Ha T Le
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Kjersten Nelson
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Lizeth I Tamayo
- Guehler Biochemistry Research Laboratory, Department of Chemistry, Augustana College, Rock Island, Illinois
| | - Jean-Marc Nicaud
- Biologie intégrative du Métabolisme Lipidique, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Young-Kyoung Park
- Biologie intégrative du Métabolisme Lipidique, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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26
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Agarwal N, Walvekar AS, Punekar NS. 2-Oxoglutarate cooperativity and biphasic ammonium saturation of Aspergillus niger NADP-glutamate dehydrogenase are structurally coupled. Arch Biochem Biophys 2019; 669:50-60. [PMID: 31136734 DOI: 10.1016/j.abb.2019.05.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/18/2022]
Abstract
NADP-glutamate dehydrogenase from Aspergillus niger (AnGDH) exhibits sigmoidal 2-oxoglutarate saturation. Despite sharing 88% amino acid identity, the homologous enzyme from Aspergillus terreus (AtGDH) shows hyperbolic 2-oxoglutarate saturation. In order to address the structural origins of this phenomenon, six AnGDH-AtGDH chimeras were constructed and characterized. The C-terminal sequence (residues 315-460, named the D-segment) was implicated in the AnGDH cooperativity. The D-segment residues largely contribute to the monomer-monomer interface of each trimer in the native hexamer and are far removed from the enzyme active site. The D-segment appears to be a part of the allosteric network responsible for 2-oxoglutarate homotropic interactions in AnGDH. AnGDH and its C415S mutant, but not AtGDH, also showed atypical, biphasic ammonium saturation, particularly at sub-saturating 2-oxoglutarate concentrations. We found that the sigmoidal 2-oxoglutarate saturation and the biphasic ammonium response are tightly coupled; the analysis of AnGDH-AtGDH chimeras ascribes the two features to the AnGDH D-segment. The two non-Michaelis-Menten substrate saturations of AnGDH were influenced by ionic strength. Increase in ionic strength reduced the nH of 2-oxoglutarate saturation as well as abolished the biphasic response, suggesting that polar/ionic interactions determine the allosteric, inter-subunit communications. The biochemical analysis in the context of available structural data implicates the D-segment of AnGDH in the allosteric feature of this enzyme. The coupling of sigmoidal 2-oxoglutarate saturation and the biphasic ammonium response could possibly confer growth advantage to A. niger experiencing carbon and/or nitrogen limitation.
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Affiliation(s)
- Nupur Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, Maharashtra, India
| | - Adhish S Walvekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, Maharashtra, India
| | - Narayan S Punekar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, Maharashtra, India.
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Chen Z, Yin H, Peng H, Lu G, Liu Z, Dang Z. Identification of novel pathways for biotransformation of tetrabromobisphenol A by Phanerochaete chrysosporium, combined with mechanism analysis at proteome level. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 659:1352-1361. [PMID: 31096345 DOI: 10.1016/j.scitotenv.2018.12.446] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/28/2018] [Accepted: 12/29/2018] [Indexed: 06/09/2023]
Abstract
The investigation of tetrabromobisphenol A (TBBPA) removal by Phanerochaete chrysosporium (P. chrysosporium) was conducted. Under optimal conditions (pH 5, inoculum size of 5% (v/v), initial glucose concentration of 5 g/L, TBBPA concentration of 5 mg/L), >97% of initial TBBPA was removed after 3 days. The TBBPA metabolites, tetrabromobisphenol A glycoside, tribromobisphenol A glycoside and monohydroxylated tetrabromobisphenol A, were identified for the first time by fungi transformation as being produced by glycosylation and oxidative hydroxylation, respectively. Proteome analysis showed that P. chrysosporium significantly upregulated cytochrome P450 monooxygenase, glutathione S-transferases, UDP-glucosyltransferase, O‑methyltransferase and other oxidoreductases for TBBPA oxidative hydroxylation, reductive debromination, glycosylation, O‑methylation and oxidative cleavage for detoxification. Data from cytotoxicity tests with human hepatocellular liver carcinoma (HepG2) confirmed that TBBPA toxicity was effectively decreased by P. chrysosporium treatment. Bioaugmentation with P. chrysosporium significantly improved the removal efficiency of TBBPA in water microcosms to 63.1% within 12 h. This study suggests that P. chrysosporium might be suitable for the removal of TBBPA from contaminated water.
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Affiliation(s)
- Zhanghong Chen
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, PR China
| | - Hua Yin
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, PR China.
| | - Hui Peng
- Department of Chemistry, Jinan University, Guangzhou 510632, Guangdong, PR China
| | - Guining Lu
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, PR China
| | - Zehua Liu
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, PR China
| | - Zhi Dang
- Key Laboratory of Ministry of Education on Pollution Control and Ecosystem Restoration in Industry Clusters, Guangdong Provincial Engineering and Technology Research Center for Environmental Risk Prevention and Emergency Disposal, School of Environment and Energy, South China University of Technology, Guangzhou 510006, Guangdong, PR China
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Shah L, Nadeem MS, Khan JA, Zeyadi MA, Zamzami MA, Mohammed K. Recombinant l-glutaminase obtained from Geobacillus thermodenitrificans DSM-465: characterization and in silico elucidation of conserved structural domains. RSC Adv 2019; 9:4258-4267. [PMID: 35520186 PMCID: PMC9060542 DOI: 10.1039/c8ra04740e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 01/09/2019] [Indexed: 11/21/2022] Open
Abstract
Glutaminase (GLS) is an enzyme essential for amino acid metabolism; in particular, it acts as a catalyst in glutaminolysis, a reaction exploited by the malignant cells to meet the nutrient requirements for their accelerated growth and proliferation. Via regulating the initial reaction of the glutaminolysis pathway, glutaminase offers an intriguing target for the development of anticancer drugs. In the present study, we produced a recombinant glutaminase from Geobacillus thermodenitrificans DSM-465 in E. coli. The enzyme was purified to electrophoretic homogeneity, with 40% recovery and 22.36 fold purity. It exhibited a molecular weight of 33 kDa, with an optimum pH and temperature of 9 and 70 °C, respectively. The K M value of the purified enzyme was 104 μM for l-glutamine. A 3D model was built for the enzyme using Swiss-Model and subjected to molecular docking with the substrate and potential inhibitors. Moreover, the subject enzyme was compared with the human kidney type GLS-K by ConSurf and TM-align servers for evolutionary conserved residues and structural domains. Despite having less than 40% amino acid identity, the superimposed monomers of both enzymes exhibited ∼94% structural identity. With a positional difference, the active site residues Ser65, Asn117, Glu162, Asn169, Tyr193, Tyr245, and Val263 found in the bacterial enzyme were also conserved in the human GLS-K. Molecular docking results have shown that CB-839 is the best inhibitor for GLS-GT and UPGL00004 is the best inhibitor for GLS-K, as designated by the binding free energy changes, i.e. ΔG -388.7 kJ mol-1 and ΔG -375 kJ mol-1, respectively. Moreover, six potential inhibitory molecules were ranked according to their binding free energy change values for both enzymes. The information can be used for the in vivo anticancer studies.
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Affiliation(s)
- Luqman Shah
- Department of Biochemistry, Faculty of Science, King Abdulaziz University Building A 90 Jeddah 21589 Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University Building A 90 Jeddah 21589 Saudi Arabia
| | - Jalaluddin Azam Khan
- Department of Biochemistry, Faculty of Science, King Abdulaziz University Building A 90 Jeddah 21589 Saudi Arabia
| | - Mustafa A Zeyadi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University Building A 90 Jeddah 21589 Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University Building A 90 Jeddah 21589 Saudi Arabia
| | - Kaleemuddin Mohammed
- Department of Biochemistry, Faculty of Science, King Abdulaziz University Building A 90 Jeddah 21589 Saudi Arabia
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Yin X, Liu Y, Meng L, Zhou H, Wu J, Yang L. Rational Molecular Engineering of Glutamate Dehydrogenases for Enhancing Asymmetric Reductive Amination of Bulky α-Keto Acids. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801251] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xinjian Yin
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Yayun Liu
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Lijun Meng
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Haisheng Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
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