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Al-Shameri A, Siebert DL, Sutiono S, Lauterbach L, Sieber V. Hydrogenase-based oxidative biocatalysis without oxygen. Nat Commun 2023; 14:2693. [PMID: 37258512 DOI: 10.1038/s41467-023-38227-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 04/21/2023] [Indexed: 06/02/2023] Open
Abstract
Biocatalysis-based synthesis can provide a sustainable and clean platform for producing chemicals. Many oxidative biocatalytic routes require the cofactor NAD+ as an electron acceptor. To date, NADH oxidase (NOX) remains the most widely applied system for NAD+ regeneration. However, its dependence on O2 implies various technical challenges in terms of O2 supply, solubility, and mass transfer. Here, we present the suitability of a NAD+ regeneration system in vitro based on H2 evolution. The efficiency of the hydrogenase-based system is demonstrated by integrating it into a multi-enzymatic cascade to produce ketoacids from sugars. The total NAD+ recycled using the hydrogenase system outperforms NOX in all different setups reaching up to 44,000 mol per mol enzyme. This system proves to be scalable and superior to NOX in terms of technical simplicity, flexibility, and total output. Furthermore, the system produces only green H2 as a by-product even in the presence of O2.
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Affiliation(s)
- Ammar Al-Shameri
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Dominik L Siebert
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Samuel Sutiono
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany
| | - Lars Lauterbach
- RWTH Universität Aachen, Institute of Applied Microbiology, Worringerweg 1, 52074, Aachen, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, TUM Campus Straubing for Biotechnology and Sustainability, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany.
- Catalytic Research Center, Technical University of Munich, Ernst-Otto-Fischer-Straße 1, 85748, Garching, Germany.
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 16, 94315, Straubing, Germany.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Zhang Y, Cai Y, Wang J, Niu L, Yang S, Liu X, Zheng Z, Zeng L, Liu A. Cobalt-doped MoS2 nanocomposite with NADH oxidase mimetic activity and its application in colorimetric biosensing of NADH. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Zhou Q, Gao J, Zhang YW. Optimal pH shift of the NADH oxidase from Lactobacillus rhamnosus with a single mutation. Biotechnol Lett 2021; 43:1413-1420. [PMID: 33844097 DOI: 10.1007/s10529-021-03129-7] [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: 01/15/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE To improve the activity of a water-forming NADH oxidase from Lactobacillus rhamnosus under neutral or alkaline pH for coupling NAD+-dependent dehydrogenases with an alkaline optimal pH. RESULTS The water-forming NADH oxidase from Lactobacillus rhamnosus was engineered by replacing the aspartic acid or glutamic acid with arginine on the surface. The mutant D251R improved the activity with a 112%, 111%, and 244% relative activity to the wild-type at pH 6.5, pH 7.0, and pH 7.5, respectively. Docking substrate into the D251R mutant reveals that the NADH is access to the substrate-binding site with a larger substrate loop due to the enhanced electrostatic repulsion between ARG-251 and ARG-243. In the D251R-NADH complex, the carboxyl of NADH additionally forms two hydrogen bonds (2.6 and 2.9 Å) with G154 due to the changed interaction of substrate and the residues in the catalytic sites, and the hydrogen bond with the oxygen of carbonyl in P295 is shortened from 2.9 to 2.0 Å, which could account for the enhanced specific activity. CONCLUSIONS The D251R mutant displayed higher catalytic activity than the wild-type in the pH range 6.5-7.5, and further insight into those shorter and newly formed hydrogen bonds in substrate docking analysis could account for the higher bind affinity and catalytic efficiency of D251R mutant.
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Affiliation(s)
- Qiang Zhou
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Jian Gao
- College of Petroleum and Chemical Engineering, Qinzhou, 535100, People's Republic of China
| | - Ye-Wang Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, People's Republic of China.
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Expression, biochemical characterization, and mutation of a water forming NADH: FMN oxidoreductase from Lactobacillus rhamnosus. Enzyme Microb Technol 2019; 134:109464. [PMID: 32044036 DOI: 10.1016/j.enzmictec.2019.109464] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 10/29/2019] [Accepted: 11/02/2019] [Indexed: 01/03/2023]
Abstract
Enzyme-catalyzed cofactor regeneration is a significant approach to avoid large quantities consumption of oxidized cofactor, which is vital in a variety of bioconversion reactions. NADH: FMN oxidoreductase is an ideal regenerating enzyme because innocuous molecular oxygen is required as an oxidant. But the by-product H2O2 limits its further applications at the industrial scale. Here, novel NADH: FMN oxidoreductase (LrFOR) from Lactobacillus rhamnosus comprised of 1146 bp with a predicted molecular weight of 42 kDa was cloned and overexpressed in Escherichia coli BL21 (DE3). Enzyme assay shows that the purified recombinant LrFOR has both the NADPH and NADH oxidation activity. Biochemical characterizations suggested that LrFOR exhibits the specific activity of 39.8 U·mg-1 with the optimal pH and temperature of 5.6 and 35 °C and produces H2O instead of potentially harmful peroxide. To further study its catalytic function, a critical Thr29 residue and its six mutants were investigated. Mutants T29G, T29A, and T29D show notable enhancement in activities compared with the wild type. Molecular docking of NADH into wild type and its mutants reveal that a small size or electronegative of residue in position29 could shorten the distance of NADH and FMN, promoting the electrons transfer and resulting in the increased activity. This work reveals the pivotal role of position 29 in the catalytic function of LrFOR and provides effective catalysts in NAD+ regeneration.
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Varghese F, Kabasakal BV, Cotton CAR, Schumacher J, Rutherford AW, Fantuzzi A, Murray JW. A low-potential terminal oxidase associated with the iron-only nitrogenase from the nitrogen-fixing bacterium Azotobacter vinelandii. J Biol Chem 2019; 294:9367-9376. [PMID: 31043481 PMCID: PMC6579470 DOI: 10.1074/jbc.ra118.007285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 04/26/2019] [Indexed: 11/06/2022] Open
Abstract
The biological route for nitrogen gas entering the biosphere is reduction to ammonia by the nitrogenase enzyme, which is inactivated by oxygen. Three types of nitrogenase exist, the least-studied of which is the iron-only nitrogenase. The Anf3 protein in the bacterium Rhodobacter capsulatus is essential for diazotrophic (i.e. nitrogen-fixing) growth with the iron-only nitrogenase, but its enzymatic activity and function are unknown. Here, we biochemically and structurally characterize Anf3 from the model diazotrophic bacterium Azotobacter vinelandii Determining the Anf3 crystal structure to atomic resolution, we observed that it is a dimeric flavocytochrome with an unusually close interaction between the heme and the FAD cofactors. Measuring the reduction potentials by spectroelectrochemical redox titration, we observed values of -420 ± 10 and -330 ± 10 mV for the two FAD potentials and -340 ± 1 mV for the heme. We further show that Anf3 accepts electrons from spinach ferredoxin and that Anf3 consumes oxygen without generating superoxide or hydrogen peroxide. We predict that Anf3 protects the iron-only nitrogenase from oxygen inactivation by functioning as an oxidase in respiratory protection, with flavodoxin or ferredoxin as the physiological electron donors.
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Affiliation(s)
- Febin Varghese
- From the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Burak Veli Kabasakal
- From the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Charles A R Cotton
- From the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jörg Schumacher
- From the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - A William Rutherford
- From the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrea Fantuzzi
- From the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - James W Murray
- From the Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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Lee SH, Youn H, Kang SG, Lee HS. Oxygen-mediated growth enhancement of an obligate anaerobic archaeon Thermococcus onnurineus NA1. J Microbiol 2019; 57:138-142. [PMID: 30706342 DOI: 10.1007/s12275-019-8592-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/21/2018] [Indexed: 11/27/2022]
Abstract
Thermococcus onnurineus NA1, an obligate anaerobic hyperthermophilic archaeon, showed variable oxygen (O2) sensitivity depending on the types of substrate employed as an energy source. Unexpectedly, the culture with yeast extract as a sole energy source showed enhanced growth by 2-fold in the presence of O2. Genome-wide transcriptome analysis revealed the upregulation of several antioxidant-related genes encoding thioredoxin peroxidase (TON_0862), rubrerythrin (TON_0864), rubrerythrin-related protein (TON_0873), NAD(P)H rubredoxin oxidoreductase (TON_0865), or thioredoxin reductase (TON_1603), which can couple the detoxification of reactive oxygen species with the regeneration of NAD(P)+ from NAD(P)H. We present a plausible mechanism by which O2 serves to maintain the intracellular redox balance. This study demonstrates an unusual strategy of an obligate anaerobe underlying O2-mediated growth enhancement despite not having heme-based or cytochrome-type proteins.
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Affiliation(s)
- Seong Hyuk Lee
- Korea Institute of Ocean Science and Technology, Busan, 49111, Republic of Korea
| | - Hwan Youn
- Department of Biology, California State University, Fresno, CA, 93740-8034, USA
| | - Sung Gyun Kang
- Korea Institute of Ocean Science and Technology, Busan, 49111, Republic of Korea.
- Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Hyun Sook Lee
- Korea Institute of Ocean Science and Technology, Busan, 49111, Republic of Korea.
- Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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Li FL, Shi Y, Zhang JX, Gao J, Zhang YW. Cloning, expression, characterization and homology modeling of a novel water-forming NADH oxidase from Streptococcus mutans ATCC 25175. Int J Biol Macromol 2018. [PMID: 29514042 DOI: 10.1016/j.ijbiomac.2018.03.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A novel nicotinamide adenine dinucleotide (NADH) oxidase from Streptococcus mutans ATCC 25175 (SmNox) was cloned and overexpressed in Escherichia coli BL21 (DE3). Sequence analysis revealed an open reading frame of 1374bp, capable of encoding a polypeptide of 457 amino acid residues. The molecular mass of the purified SmNox was estimated to be ∼49.9kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The purified SmNox had the highest specific activity of 281.2U·mg-1 at optimal pH and temperature of 7.0 and 35°C, with a Km of 57.7μM and a Vmax of 154.3U·mg-1. The good stability at room temperature was observed. Homology modeling and substrate docking were performed to evaluate the catalytic characteristics. The results indicated that Nicotinamide ring of NADH extends vertically toward to re-face of coenzyme (FAD), and the specific conformation of NADH suggested that the charges transfer in SmNox complex could be easier than in its homologous enzyme (LbNox) under alkaline environment. The characterization of the SmNox indicated it has potential in industrial regeneration of coenzyme NAD+ for coupling with dehydrogenases.
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Affiliation(s)
- Fei-Long Li
- School of Pharmacy, United Pharmaceutical Institute of Jiangsu University and Shandong Tianzhilvye Biotechnology Co. Ltd., Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Ying Shi
- School of Pharmacy, United Pharmaceutical Institute of Jiangsu University and Shandong Tianzhilvye Biotechnology Co. Ltd., Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Jiu-Xun Zhang
- School of Pharmacy, United Pharmaceutical Institute of Jiangsu University and Shandong Tianzhilvye Biotechnology Co. Ltd., Jiangsu University, Zhenjiang 212013, People's Republic of China
| | - Jian Gao
- College of Petroleum and Chemical Engineering, Qinzhou University, Qinzhou 535011, People's Republic of China
| | - Ye-Wang Zhang
- School of Pharmacy, United Pharmaceutical Institute of Jiangsu University and Shandong Tianzhilvye Biotechnology Co. Ltd., Jiangsu University, Zhenjiang 212013, People's Republic of China; College of Petroleum and Chemical Engineering, Qinzhou University, Qinzhou 535011, People's Republic of China.
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Chavushyan VA, Simonyan KV, Simonyan RM, Isoyan AS, Simonyan GM, Babakhanyan MA, Hovhannisyian LE, Nahapetyan KH, Avetisyan LG, Simonyan MA. Effects of stevia on synaptic plasticity and NADPH oxidase level of CNS in conditions of metabolic disorders caused by fructose. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 17:540. [PMID: 29258552 PMCID: PMC5735878 DOI: 10.1186/s12906-017-2049-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/06/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Excess dietary fructose intake associated with metabolic syndrome and insulin resistance and increased risk of developing type 2 diabetes. Previous animal studies have reported that diabetic animals have significantly impaired behavioural and cognitive functions, pathological synaptic function and impaired expression of glutamate receptors. Correction of the antioxidant status of laboratory rodents largely prevents the development of fructose-induced plurimetabolic changes in the nervous system. We suggest a novel concept of efficiency of Stevia leaves for treatment of central diabetic neuropathy. METHODS By in vivo extracellular studies induced spike activity of hippocampal neurons during high frequency stimulation of entorhinal cortex, as well as neurons of basolateral amygdala to high-frequency stimulation of the hippocampus effects of Stevia rebaudiana Bertoni plant evaluated in synaptic activity in the brain of fructose-enriched diet rats. In the conditions of metabolic disorders caused by fructose, antioxidant activity of Stevia rebaudiana was assessed by measuring the NOX activity of the hippocampus, amygdala and spinal cord. RESULTS In this study, the characteristic features of the metabolic effects of dietary fructose on synaptic plasticity in hippocampal neurons and basolateral amygdala and the state of the NADPH oxidase (NOX) oxidative system of these brain formations are revealed, as well as the prospects for development of multitarget and polyfunctional phytopreparations (with adaptogenic, antioxidant, antidiabetic, nootropic activity) from native raw material of Stevia rebaudiana. Stevia modulates degree of expressiveness of potentiation/depression (approaches but fails to achieve the norm) by shifting the percentage balance in favor of depressor type of responses during high-frequency stimulation, indicating its adaptogenic role in plasticity of neural networks. Under the action of fructose an increase (3-5 times) in specific quantity of total fraction of NOX isoforms isolated from the central nervous system tissue (amygdala, hippocampus, spinal cord) was revealed. Stevia exhibits an antistress, membrane-stabilizing role reducing the level of total fractions of NOX isoforms from central nervous system tissues and regulates NADPH-dependent O2- -producing activity. CONCLUSION Generally, in condition of metabolic disorders caused by intensive consumption of dietary fructose Stevia leaves contributes to the control of neuronal synaptic plasticity possibly influencing the conjugated NOX-specific targets.
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Affiliation(s)
- V A Chavushyan
- Orbeli Institute of Physiology NAS RA, 22 Orbeli Bros Street, 0028, Yerevan, Armenia
| | - K V Simonyan
- Orbeli Institute of Physiology NAS RA, 22 Orbeli Bros Street, 0028, Yerevan, Armenia.
| | - R M Simonyan
- H. Buniatian Institute of Biochemistry NAS RA, 5/1 P.Sevag str, 0014, Yerevan, Armenia
| | - A S Isoyan
- Orbeli Institute of Physiology NAS RA, 22 Orbeli Bros Street, 0028, Yerevan, Armenia
| | - G M Simonyan
- H. Buniatian Institute of Biochemistry NAS RA, 5/1 P.Sevag str, 0014, Yerevan, Armenia
| | - M A Babakhanyan
- Scientific Centre of Artsakh, 8 Tigran Mets str, Stepanakert, Nagorno Karabakh, Armenia
| | - L E Hovhannisyian
- Scientific Centre of Artsakh, 8 Tigran Mets str, Stepanakert, Nagorno Karabakh, Armenia
| | - Kh H Nahapetyan
- Orbeli Institute of Physiology NAS RA, 22 Orbeli Bros Street, 0028, Yerevan, Armenia
| | - L G Avetisyan
- Orbeli Institute of Physiology NAS RA, 22 Orbeli Bros Street, 0028, Yerevan, Armenia
| | - M A Simonyan
- H. Buniatian Institute of Biochemistry NAS RA, 5/1 P.Sevag str, 0014, Yerevan, Armenia
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Abstract
The NADH oxidase family of enzymes catalyzes the oxidation of NADH by reducing molecular O2 to H2O2, H2O or both. In the protozoan parasite Giardia lamblia, the NADH oxidase enzyme (GlNOX) produces H2O as end product without production of H2O2. GlNOX has been implicated in the parasite metabolism, the intracellular redox regulation and the resistance to drugs currently used against giardiasis; therefore, it is an interesting protein from diverse perspectives. In this work, the GlNOX gene was amplified from genomic G. lamblia DNA and expressed in Escherichia coli as a His-Tagged protein; then, the enzyme was purified by immobilized metal affinity chromatography, characterized, and its properties compared with those of the endogenous enzyme previously isolated from trophozoites (Brown et al. in Eur J Biochem 241(1):155-161, 1996). In comparison with the trophozoite-extracted enzyme, which was scarce and unstable, the recombinant heterologous expression system and one-step purification method produce a stable protein preparation with high yield and purity. The recombinant enzyme mostly resembles the endogenous protein; where differences were found, these were attributable to methodological discrepancies or artifacts. This homogenous, pure and functional protein preparation can be used for detailed structural or functional studies of GlNOX, which will provide a deeper understanding of the biology and pathogeny of G. lamblia.
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Zhang JD, Cui ZM, Fan XJ, Wu HL, Chang HH. Cloning and characterization of two distinct water-forming NADH oxidases from Lactobacillus pentosus for the regeneration of NAD. Bioprocess Biosyst Eng 2016; 39:603-11. [PMID: 26801669 DOI: 10.1007/s00449-016-1542-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 01/08/2016] [Indexed: 11/24/2022]
Abstract
Two uncharacterized nicotinamide adenine dinucleotide (NADH) oxidases (named as LpNox1, LpNox2) from Lactobacillus pentosus ATCC 8041 were cloned and overexpressed in Escherichia coli BL21 (DE3). The sequence analysis revealed that the two enzymes are water-forming Noxs with 64 % and 52 % identity to LbNox from Lactobacillus brevis DSM 20054. The optimal pH and temperature of the purified LpNox1 and LpNox2 were 7.0 and 8.0 and 35 and 40 °C, respectively, with K M of 99.0 μM (LpNox1) and 27.6 μM (LpNox2), and yielding catalytic efficiency k cat/K M of 1.0 and 0.2 μM(-1) s(-1), respectively. Heat inactivation studies revealed that the two enzymes are relatively instable. The application of LpNox1 for the regeneration of NAD(+) was demonstrated by coupling with a glycerol dehydrogenase-catalyzed oxidation of glycerol to 1,3-dihydroxyacetone. The characteristics of the LpNox1 could prove to be of interest in industrial application such as NAD(+) regeneration in dehydrogenase-catalyzed oxidations.
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Affiliation(s)
- Jian-Dong Zhang
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No.79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China.
| | - Zhi-Mei Cui
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No.79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China
| | - Xiao-Jun Fan
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No.79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China.
| | - Hua-Lei Wu
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No.79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China
| | - Hong-Hong Chang
- Department of Biological and Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, No.79 West Yingze Street, Taiyuan, Shanxi, 030024, People's Republic of China
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Tetianec L, Chaleckaja A, Vidziunaite R, Kulys J, Bachmatova I, Marcinkeviciene L, Meskys R. Development of a laccase/syringaldazine system for NAD(P)H oxidation. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.12.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Thioredoxin targets fundamental processes in a methane-producing archaeon, Methanocaldococcus jannaschii. Proc Natl Acad Sci U S A 2014; 111:2608-13. [PMID: 24505058 DOI: 10.1073/pnas.1324240111] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Thioredoxin (Trx), a small redox protein, controls multiple processes in eukaryotes and bacteria by changing the thiol redox status of selected proteins. The function of Trx in archaea is, however, unexplored. To help fill this gap, we have investigated this aspect in methanarchaea--strict anaerobes that produce methane, a fuel and greenhouse gas. Bioinformatic analyses suggested that Trx is nearly universal in methanogens. Ancient methanogens that produce methane almost exclusively from H2 plus CO2 carried approximately two Trx homologs, whereas nutritionally versatile members possessed four to eight. Due to its simplicity, we studied the Trx system of Methanocaldococcus jannaschii--a deeply rooted hyperthermophilic methanogen growing only on H2 plus CO2. The organism carried two Trx homologs, canonical Trx1 that reduced insulin and accepted electrons from Escherichia coli thioredoxin reductase and atypical Trx2. Proteomic analyses with air-oxidized extracts treated with reduced Trx1 revealed 152 potential targets representing a range of processes--including methanogenesis, biosynthesis, transcription, translation, and oxidative response. In enzyme assays, Trx1 activated two selected targets following partial deactivation by O2, validating proteomics observations: methylenetetrahydromethanopterin dehydrogenase, a methanogenesis enzyme, and sulfite reductase, a detoxification enzyme. The results suggest that Trx assists methanogens in combating oxidative stress and synchronizing metabolic activities with availability of reductant, making it a critical factor in the global carbon cycle and methane emission. Because methanogenesis developed before the oxygenation of Earth, it seems possible that Trx functioned originally in metabolic regulation independently of O2, thus raising the question whether a complex biological system of this type evolved at least 2.5 billion years ago.
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Yan Z, Fushinobu S, Wakagi T. Four Cys residues in heterodimeric 2-oxoacid:ferredoxin oxidoreductase are required for CoA-dependent oxidative decarboxylation but not for a non-oxidative decarboxylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:736-43. [PMID: 24491525 DOI: 10.1016/j.bbapap.2014.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/22/2014] [Accepted: 01/24/2014] [Indexed: 11/26/2022]
Abstract
Heterodimeric 2-oxoacid:ferredoxin oxidoreductase (OFOR) from Sulfolobus tokodaii (StOFOR) has only one [4Fe-4S]²⁺ cluster, ligated by 4 Cys residues, C12, C15, C46, and C197. The enzyme has no other Cys. To elucidate the role of these Cys residues in holding of the iron-sulfur cluster in the course of oxidative decarboxylation of a 2-oxoacid, one or two of these Cys residues was/were substituted with Ala to yield C12A, C15A, C46A, C197A and C12/15A mutants. All the mutants showed the loss of iron-sulfur cluster, except the C197A one which retained some unidentified type of iron-sulfur cluster. On addition of pyruvate to OFOR, the wild type enzyme exhibited a chromophore at 320nm and a stable large EPR signal corresponding to a hydroxyethyl-ThDP radical, while the mutant enzymes did not show formation of any radical intermediate or production of acetyl-CoA, suggesting that the intact [4Fe-4S] cluster is necessary for these processes. The stable radical intermediate in wild type OFOR was rapidly decomposed upon addition of CoA in the absence of an electron acceptor. Non-oxidative decarboxylation of pyruvate, yielding acetaldehyde, has been reported to require CoA for other OFORs, but StOFOR catalyzed acetaldehyde production from pyruvate independent of CoA, regardless of whether the iron-sulfur cluster is intact [4Fe-4S] type or not. A comprehensive reaction scheme for StOFOR with a single cluster was proposed.
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Affiliation(s)
- Zhen Yan
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Takayoshi Wakagi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan.
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Yan Z, Nam YW, Fushinobu S, Wakagi T. Sulfolobus tokodaii ST2133 is characterized as a thioredoxin reductase-like ferredoxin:NADP+ oxidoreductase. Extremophiles 2013; 18:99-110. [DOI: 10.1007/s00792-013-0601-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
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Knuuti J, Belevich G, Sharma V, Bloch DA, Verkhovskaya M. A single amino acid residue controls ROS production in the respiratory Complex I from Escherichia coli. Mol Microbiol 2013; 90:1190-200. [PMID: 24325249 DOI: 10.1111/mmi.12424] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2013] [Indexed: 01/08/2023]
Abstract
Reactive oxygen species (ROS) production by respiratory Complex I from Escherichia coli was studied in bacterial membrane fragments and in the isolated and purified enzyme, either solubilized or incorporated in proteoliposomes. We found that the replacement of a single amino acid residue in close proximity to the nicotinamide adenine dinucleotide (NADH)-binding catalytic site (E95 in the NuoF subunit) dramatically increases the reactivity of Complex I towards dioxygen (O2 ). In the E95Q variant short-chain ubiquinones exhibit strong artificial one-electron reduction at the catalytic site, also leading to a stronger increase in ROS production. Two mechanisms can contribute to the observed kinetic effects: (a) a change in the reactivity of flavin mononucleotide (FMN) towards dioxygen at the catalytic site, and (b) a change in the population of the ROS-generating state. We propose the existence of two (closed and open) states of the NAD(+) -bound enzyme as one feature of the substrate-binding site of Complex I. The analysis of the kinetic model of ROS production allowed us to propose that the population of Complex I with reduced FMN is always low in the wild-type enzyme even at low ambient redox potentials, minimizing the rate of reaction with O2 in contrast to E95Q variant.
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Affiliation(s)
- Juho Knuuti
- Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, PO Box 65 (Viikinkaari 1), FIN-00014, Helsinki, Finland
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Identification and expression of genes involved in the conversion of daidzein and genistein by the equol-forming bacterium Slackia isoflavoniconvertens. Appl Environ Microbiol 2013; 79:3494-502. [PMID: 23542626 DOI: 10.1128/aem.03693-12] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gut bacteria play a key role in the metabolism of dietary isoflavones, thereby influencing the availability and bioactivation of these polyphenols in the intestine. The human intestinal bacterium Slackia isoflavoniconvertens converts the main soybean isoflavones daidzein and genistein to equol and 5-hydroxy-equol, respectively. Cell extracts of S. isoflavoniconvertens catalyzed the conversion of daidzein via dihydrodaidzein to equol and that of genistein to dihydrogenistein. Growth of S. isoflavoniconvertens in the presence of daidzein led to the induction of several proteins as observed by two-dimensional difference gel electrophoresis. Based on determined peptide sequences, we identified a cluster of eight genes encoding the daidzein-induced proteins. Heterologous expression of three of these genes in Escherichia coli and enzyme activity tests with the resulting cell extracts identified the corresponding gene products as a daidzein reductase (DZNR), a dihydrodaidzein reductase (DHDR), and a tetrahydrodaidzein reductase (THDR). The recombinant DZNR also converted genistein to dihydrogenistein at higher rates than were observed for the conversion of daidzein to dihydrodaidzein. Higher rates were also observed with cell extracts of S. isoflavoniconvertens. The recombinant DHDR and THDR catalyzed the reduction of dihydrodaidzein to equol, while the corresponding conversion of dihydrogenistein to 5-hydroxy-equol was not observed. The DZNR, DHDR, and THDR were expressed as Strep-tag fusion proteins and subsequently purified by affinity chromatography. The purified enzymes were further characterized with regard to their activity, stereochemistry, quaternary structure, and content of flavin cofactors.
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Nisar MA, Rashid N, Bashir Q, Gardner QTAA, Shafiq MH, Akhtar M. TK1299, a highly thermostable NAD(P)H oxidase from Thermococcus kodakaraensis exhibiting higher enzymatic activity with NADPH. J Biosci Bioeng 2013; 116:39-44. [PMID: 23453203 DOI: 10.1016/j.jbiosc.2013.01.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 01/24/2013] [Accepted: 01/28/2013] [Indexed: 10/27/2022]
Abstract
Seven nicotinamide adenine dinucleotide oxidase homologs have been found in the genome of Thermococcus kodakaraensis. The gene encoding one of them, TK1299, consisted of 1326 nucleotides, corresponding to a polypeptide of 442 amino acids. To examine the molecular properties of TK1299, the structural gene was cloned, expressed in Escherichia coli and the gene product was characterized. Molecular weight of the recombinant protein was 49,375 Da when determined by matrix-assisted laser desorption/ionization time-of-flight and 300 kDa when analyzed by gel filtration chromatography indicating that it existed in a hexameric form. The enzyme was highly thermostable even in boiling water where it exhibited more than 95% of the enzyme activity after incubation of 150 min. TK1299 catalyzed the oxidation of NADH as well as NADPH and predominantly converted O₂ to H₂O (more than 75%). K(m) value of the enzyme towards NADH and NADPH was almost same (24 ± 2 μM) where as specific activity was higher with NADPH compared to NADH. To our knowledge this is the most thermostable and unique NAD(P)H oxidase displaying higher enzyme activity with NADPH.
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Affiliation(s)
- Muhammad Atif Nisar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Punjab, Pakistan
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Zhang YW, Tiwari MK, Gao H, Dhiman SS, Jeya M, Lee JK. Cloning and characterization of a thermostable H2O-forming NADH oxidase from Lactobacillus rhamnosus. Enzyme Microb Technol 2012; 50:255-62. [PMID: 22418266 DOI: 10.1016/j.enzmictec.2012.01.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 01/13/2012] [Accepted: 01/28/2012] [Indexed: 11/30/2022]
Abstract
NADH oxidase (Nox) catalyzes the conversion of NADH to NAD(+). A previously uncharacterized Nox gene (LrNox) was cloned from Lactobacillus rhamnosus and overexpressed in Escherichia coli BL21(DE3). Sequence analysis revealed an open reading frame of 1359 bp, capable of encoding a polypeptide of 453 amino acid residues. The molecular mass of the purified LrNox enzyme was estimated to be ~50 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and 100 kDa by gel filtration chromatography, suggesting that the enzyme is a homodimer. The enzyme had optimal activity at pH 5.6 and temperature 65 °C, and k(cat)/K(m) of 3.77×10(7) s(-1) M(-1), the highest ever reported. Heat inactivation studies revealed that LrNox had high thermostability, with a half-life of 120 min at 80 °C. Molecular dynamics simulation studies shed light on the factors contributing to the high activity of LrNox. Although the properties of Nox from several microorganisms have been reported, this is the first report on the characterization of a recombinant H(2)O-forming Nox with high activity and thermostability. The characteristics of the LrNox enzyme could prove to be of interest in industrial applications such as NAD(+) regeneration.
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Affiliation(s)
- Ye-Wang Zhang
- Department of Chemical Engineering, Konkuk University, Seoul 143-701, Republic of Korea
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Wu X, Kobori H, Orita I, Zhang C, Imanaka T, Xing XH, Fukui T. Application of a novel thermostable NAD(P)H oxidase from hyperthermophilic archaeon for the regeneration of both NAD⁺ and NADP⁺. Biotechnol Bioeng 2011; 109:53-62. [PMID: 21830202 DOI: 10.1002/bit.23294] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 07/25/2011] [Accepted: 08/03/2011] [Indexed: 11/07/2022]
Abstract
A novel thermostable NAD(P)H oxidase from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1 (TkNOX) catalyzes oxidation of NADH and NADPH with oxygen from atmospheric air as an electron acceptor. Although the optimal temperature of TkNOX is >90°C, it also shows activity at 30°C. This enzyme was used for the regeneration of both NADP(+) and NAD(+) in alcohol dehydrogenase (ADH)-catalyzed enantioselective oxidation of racemic 1-phenylethanol. NADP(+) regeneration at 30°C was performed by TkNOX coupled with (R)-specific ADH from Lactobacillus kefir, resulting in successful acquisition of optically pure (S)-1-phenylethanol. The use of TkNOX with moderately thermostable (S)-specific ADH from Rhodococcus erythropolis enabled us to operate the enantioselective bioconversion accompanying NAD(+) regeneration at high temperatures. Optically pure (R)-1-phenylethanol was successfully obtained by this system after a shorter reaction time at 45-60°C than that at 30°C, demonstrating an advantage of the combination of thermostable enzymes. The ability of TkNOX to oxidize both NADH and NADPH with remarkable thermostability renders this enzyme a versatile tool for regeneration of the oxidized nicotinamide cofactors without the need for extra substrates other than dissolved oxygen from air.
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Affiliation(s)
- Xi Wu
- Department of Bioengineering, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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Characterization of NADH oxidase/NADPH polysulfide oxidoreductase and its unexpected participation in oxygen sensitivity in an anaerobic hyperthermophilic archaeon. J Bacteriol 2010; 192:5192-202. [PMID: 20675490 DOI: 10.1128/jb.00235-10] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many genomes of anaerobic hyperthermophiles encode multiple homologs of NAD(P)H oxidase that are thought to function in response to oxidative stress. We investigated one of the seven NAD(P)H oxidase homologs (TK1481) in the sulfur-reducing hyperthermophilic archaeon Thermococcus kodakarensis, focusing on the catalytic properties and roles in oxidative-stress defense and sulfur-dependent energy conservation. The recombinant form of TK1481 exhibited both NAD(P)H oxidase and NAD(P)H:polysulfide oxidoreductase activities. The enzyme also possessed low NAD(P)H peroxidase and NAD(P)H:elemental sulfur oxidoreductase activities under anaerobic conditions. A mutant form of the enzyme, in which the putative redox-active residue Cys43 was replaced by Ala, still showed NADH-dependent flavin adenine dinucleotide (FAD) reduction activity. Although it also retained successive oxidase and anaerobic peroxidase activities, the ability to reduce polysulfide and sulfur was completely lost, suggesting the specific reactivity of the Cys43 residue for sulfur. To evaluate the physiological function of TK1481, we constructed a gene deletant, ΔTK1481, and mutant KUTK1481C43A, into which two base mutations altering Cys43 of TK1481 to Ala were introduced. ΔTK1481 exhibited growth properties nearly identical to those of the parent strain, KU216, in sulfur-containing media. Interestingly, in the absence of elemental sulfur, the growth of ΔTK1481 was not affected by dissolved oxygen, whereas the growth of KU216 and KUTK1481C43A was significantly impaired. These results indicate that although TK1481 does not play a critical role in either sulfur reduction or the response to oxidative stress, the NAD(P)H oxidase activity of TK1481 unexpectedly participates in the oxygen sensitivity of the hyperthermophilic archaeon T. kodakarensis in the absence of sulfur.
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