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Saiapina OY, Berketa K, Sverstiuk AS, Fayura L, Sibirny AA, Dzyadevych S, Soldatkin OO. Adaptation of Conductometric Monoenzyme Biosensor for Rapid Quantitative Analysis of L-arginine in Dietary Supplements. SENSORS (BASEL, SWITZERLAND) 2024; 24:4672. [PMID: 39066069 PMCID: PMC11281210 DOI: 10.3390/s24144672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/05/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
Abstract
The present study reports on the development, adaptation, and optimization of a novel monoenzyme conductometric biosensor based on a recombinant arginine deiminase (ADI) for the determination of arginine in dietary supplements with a high accuracy of results. Aiming for the highly sensitive determination of arginine in real samples, we studied the effect of parameters of the working buffer solution (its pH, buffer capacity, ionic strength, temperature, and protein concentration) on the sensitivity of the biosensor to arginine. Thus, it was determined that the optimal buffer is a 5 mM phosphate buffer solution with pH 6.2, and the optimal temperature is 39.5 °C. The linear functioning range is 2.5-750 µM of L-arginine with a minimal limit of detection of 2 µM. The concentration of arginine in food additive samples was determined using the developed ADI-based biosensor. Based on the obtained results, the most effective method of biosensor analysis using the method of standard additions was chosen. It was also checked how the reproducibility of the biosensor changes during the analysis of pharmaceutical samples. The results of the determination of arginine in real samples using a conductometric biosensor based on ADI clearly correlated with the data obtained using the method of ion-exchange chromatography and enzymatic spectrophotometric analysis. We concluded that the developed biosensor would be effective for the accurate and selective determination of arginine in dietary supplements intended for the prevention and/or elimination of arginine deficiency.
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Affiliation(s)
- Olga Y. Saiapina
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnyi Str., 03680 Kyiv, Ukraine; (O.Y.S.); (S.D.); (O.O.S.)
| | - Kseniia Berketa
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnyi Str., 03680 Kyiv, Ukraine; (O.Y.S.); (S.D.); (O.O.S.)
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Volodymyrska Street 64, 01003 Kyiv, Ukraine
| | - Andrii S. Sverstiuk
- Department of Medical Informatics, I. Horbachevsky Ternopil National Medical University, Maidan Voli Str., 1, 46002 Ternopil, Ukraine
- Department of Computer Sciences, Ternopil National Ivan Puluj Technical University, Rus’ka Str., 56, 46001 Ternopil, Ukraine
| | - Lyubov Fayura
- Institute of Cell Biology, National Academy of Science of Ukraine, 14/16 Drahomanov Str., 79005 Lviv, Ukraine; (L.F.); (A.A.S.)
| | - Andriy A. Sibirny
- Institute of Cell Biology, National Academy of Science of Ukraine, 14/16 Drahomanov Str., 79005 Lviv, Ukraine; (L.F.); (A.A.S.)
- Department of Biotechnology and Microbiology, Rzeszow University, Zelwerowicza 4, 35-601 Rzeszow, Poland
| | - Sergei Dzyadevych
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnyi Str., 03680 Kyiv, Ukraine; (O.Y.S.); (S.D.); (O.O.S.)
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Volodymyrska Street 64, 01003 Kyiv, Ukraine
| | - Oleksandr O. Soldatkin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnyi Str., 03680 Kyiv, Ukraine; (O.Y.S.); (S.D.); (O.O.S.)
- Igor Sikorsky Kyiv Polytechnic Institute, Beresteyskyi ave. 37, 03056 Kyiv, Ukraine
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2
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Stasyuk N, Gayda G, Nogala W, Holdynski M, Demkiv O, Fayura L, Sibirny A, Gonchar M. Ammonium nanochelators in conjunction with arginine-specific enzymes in amperometric biosensors for arginine assay. Mikrochim Acta 2023; 191:47. [PMID: 38133683 PMCID: PMC10987348 DOI: 10.1007/s00604-023-06114-1] [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: 07/20/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Amino acid L-arginine (Arg), usually presented in food products and biological liquids, can serve both as a useful indicator of food quality and an important biomarker in medicine. The biosensors based on Arg-selective enzymes are the most promising devices for Arg assay. In this research, three types of amperometric biosensors have been fabricated. They exploit arginine oxidase (ArgO), recombinant arginase I (ARG)/urease, and arginine deiminase (ADI) coupled with the ammonium-chelating redox-active nanoparticles. Cadmium-copper nanoparticles (nCdCu) as the most effective nanochelators were used for the development of ammonium chemosensors and enzyme-coupled Arg biosensors. The fabricated enzyme/nCdCu-containing bioelectrodes show wide linear ranges (up to 200 µM), satisfactory storage stabilities (14 days), and high sensitivities (A⋅M-1⋅m-2) to Arg: 1650, 1700, and 4500 for ADI-, ArgO- and ARG/urease-based sensors, respectively. All biosensors have been exploited to estimate Arg content in commercial juices. The obtained data correlate well with the values obtained by the reference method. A hypothetic scheme for mechanism of action of ammonium nanochelators in electron transfer reaction on the arginine-sensing electrodes has been proposed.
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Affiliation(s)
- Nataliya Stasyuk
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine.
| | - Galina Gayda
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine
| | - Wojciech Nogala
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland.
| | - Marcin Holdynski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224, Warsaw, Poland
| | - Olha Demkiv
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine
| | - Lyubov Fayura
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine
| | - Andriy Sibirny
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine
- Department of Biotechnology and Microbiology, Rzeszow University, 35-601, Rzeszow, Poland
| | - Mykhailo Gonchar
- Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, 79005, Ukraine.
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3
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Yamamoto K, Masakari Y, Araki Y, Ichiyanagi A, Ito K. Modification of substrate specificity of L-arginine oxidase for detection of L-citrulline. AMB Express 2023; 13:137. [PMID: 38044351 PMCID: PMC10694123 DOI: 10.1186/s13568-023-01636-6] [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: 07/11/2023] [Accepted: 10/30/2023] [Indexed: 12/05/2023] Open
Abstract
Enzymatic detection of citrulline, a potential biomarker for various diseases, is beneficial. However, determining citrulline levels requires expensive instrumental analyses and complicated colorimetric assays. Although L-amino acid oxidase/dehydrogenase is widely used to detect L-amino acids, an L-citrulline-specific oxidase/dehydrogenase has not been reported. Therefore, in this study, we aimed to develop an L-citrulline-specific enzyme by introducing a mutation into L-arginine oxidase (ArgOX) derived from Pseudomonas sp. TPU 7192 to provide a simple enzymatic L-citrulline detection system. The ratio of the oxidase activity against L-arginine to that against L-citrulline (Cit/Arg) was 1.2%, indicating that ArgOX could recognize L-citrulline as a substrate. In the dehydrogenase assay, the specific dehydrogenase activity towards L-arginine was considerably lower than the specific oxidase activity. However, the specific dehydrogenase activity towards L-citrulline was only slightly lower than the oxidase activity, resulting in improved substrate specificity with a Cit/Arg ratio of 49.5%. To enhance the substrate specificity of ArgOX, we performed site-directed mutagenesis using structure-based engineering. The 3D model structure indicated that E486 interacted with the L-arginine side chain. By introducing the E486 mutation, the specific dehydrogenase activity of ArgOX/E486Q for L-citrulline was 3.25 ± 0.50 U/mg, which was 3.8-fold higher than that of ArgOX. The Cit/Arg ratio of ArgOX/E486Q was 150%, which was higher than that of ArgOX. Using ArgOX/E486Q, linear relationships were observed within the range of 10-500 μM L-citrulline, demonstrating its suitability for detecting citrulline in human blood. Consequently, ArgOX/E486Q can be adapted as an enzymatic sensor in the dehydrogenase system.
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Affiliation(s)
- Kei Yamamoto
- Marketing and Planning Division, Kikkoman Biochemifa Company, 1600, Kaisuka, Kamogawa, Chiba, 296-0004, Japan.
| | - Yosuke Masakari
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Yasuko Araki
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Atsushi Ichiyanagi
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
| | - Kotaro Ito
- Research and Development Division, Kikkoman Corporation, 338 Noda, Noda, Chiba, 278-0037, Japan
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4
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Ohshima T, Tanaka M, Ohmori T. NADP +-dependent l-arginine dehydrogenase from Pseudomonas velonii: Purification, characterization and application to an l-arginine assay. Protein Expr Purif 2022; 199:106135. [PMID: 35760253 DOI: 10.1016/j.pep.2022.106135] [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: 03/22/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 10/31/2022]
Abstract
l-Arginine dehydrogenase (L-ArgDH) is an amino acid dehydrogenase which catalyzes the reversible oxidative deamination of l-arginine to the oxo analog in the presence of NAD(P)+. We here found the gene homolog of L-ArgDH in genome data of Pseudomonas veronii and succeeded in expression of P. veronii JCM11942 gene in E. coli. The gene product exhibited strong NADP + -dependent L-ArgDH activity. The enzyme was unstable, but markedly stabilized by the addition of 10% glycerol. The enzyme first purified to homogeneity consisted of a homodimeric protein with a molecular mass of about 65 kDa. The enzyme selectively catalyzed NADP+-dependent l-arginine oxidation with maximal activity at pH 9.5. The apparent Km values for l-arginine and NADP+ were 2.5 and 0.21 mM, respectively. The nucleotide sequence coding the enzyme gene was determined and the amino acid sequence was deduced from the nucleotide sequence. The simple colorimetric microassay for l-arginine using the enzyme was achieved.
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Affiliation(s)
- Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka, 535-8585, Japan.
| | - Masaki Tanaka
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka, 535-8585, Japan.
| | - Taketo Ohmori
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka, 535-8585, Japan.
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5
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Tinikul R, Trisrivirat D, Chinantuya W, Wongnate T, Watthaisong P, Phonbuppha J, Chaiyen P. Detection of cellular metabolites by redox enzymatic cascades. Biotechnol J 2022; 17:e2100466. [PMID: 35192744 DOI: 10.1002/biot.202100466] [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: 08/26/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 11/11/2022]
Abstract
Detection of cellular metabolites that are disease biomarkers is important for human healthcare monitoring and assessing prognosis and therapeutic response. Accurate and rapid detection of microbial metabolites and pathway intermediates is also crucial for the process optimization required for development of bioconversion methods using metabolically engineered cells. Various redox enzymes can generate electrons that can be employed in enzyme-based biosensors and in the detection of cellular metabolites. These reactions can directly transform target compounds into various readout signals. By incorporating engineered enzymes into enzymatic cascades, the readout signals can be improved in terms of accuracy and sensitivity. This review critically discusses selected redox enzymatic and chemoenzymatic cascades currently employed for detection of human- and microbe-related cellular metabolites including, amino acids, d-glucose, inorganic ions (pyrophosphate, phosphate, and sulfate), nitro- and halogenated phenols, NAD(P)H, fatty acids, fatty aldehyde, alkane, short chain acids, and cellular metabolites.
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Affiliation(s)
- Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Duangthip Trisrivirat
- Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
| | - Wachirawit Chinantuya
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Thanyaporn Wongnate
- Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
| | - Pratchaya Watthaisong
- Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
| | - Jittima Phonbuppha
- Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, School of Biomolecular Science and Engineering, Rayong, Thailand
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6
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Trisrivirat D, Sutthaphirom C, Pimviriyakul P, Chaiyen P. Dual activities of oxidation and oxidative decarboxylation by flavoenzymes. Chembiochem 2022; 23:e202100666. [PMID: 35040514 DOI: 10.1002/cbic.202100666] [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: 12/06/2021] [Revised: 01/17/2022] [Indexed: 11/07/2022]
Abstract
Specific flavoenzyme oxidases catalyze oxidative decarboxylation in addition to their classical oxidation reactions in the same active sites. The mechanisms underlying oxidative decarboxylation by these enzymes and how they control their two activities are not clearly known. This article reviews the current state of knowledge of four enzymes from the l-amino acid oxidase and l-hydroxy acid oxidase families, including l-tryptophan 2-monooxygenase, l-phenylalanine 2-oxidase and l-lysine oxidase/monooxygenase and lactate monooxygenase which catalyze substrate oxidation and oxidative decarboxylation. Apart from specific interactions to allow substrate oxidation by the flavin cofactor, specific binding of oxidized product in the active sites appears to be important for enabling subsequent decarboxylation by these enzymes. Based on recent findings of l-lysine oxidase/monooxygenase, we propose that nucleophilic attack of H2O2 on the imino acid product is the mechanism enabling oxidative decarboxylation.
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Affiliation(s)
- Duangthip Trisrivirat
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | - Chalermroj Sutthaphirom
- VISTEC: Vidyasirimedhi Institute of Science and Technology, Biomolecular Science and Engineering, THAILAND
| | | | - Pimchai Chaiyen
- Vidyasirimedhi Institute of Science and Technology (VISTEC), School of Biomolecular Science and Engineering, 555 Moo 1 Payupnai, 21210, Wangchan District, THAILAND
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7
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Yano Y, Matsuo S, Ito N, Tamura T, Kusakabe H, Inagaki K, Imada K. A new l-arginine oxidase engineered from l-glutamate oxidase. Protein Sci 2021; 30:1044-1055. [PMID: 33764624 DOI: 10.1002/pro.4070] [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: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/21/2021] [Indexed: 11/08/2022]
Abstract
The alternation of substrate specificity expands the application range of enzymes in industrial, medical, and pharmaceutical fields. l-Glutamate oxidase (LGOX) from Streptomyces sp. X-119-6 catalyzes the oxidative deamination of l-glutamate to produce 2-ketoglutarate with ammonia and hydrogen peroxide. LGOX shows strict substrate specificity for l-glutamate. Previous studies on LGOX revealed that Arg305 in its active site recognizes the side chain of l-glutamate, and replacement of Arg305 by other amino acids drastically changes the substrate specificity of LGOX. Here we demonstrate that the R305E mutant variant of LGOX exhibits strict specificity for l-arginine. The oxidative deamination activity of LGOX to l-arginine is higher than that of l-arginine oxidase form from Pseudomonas sp. TPU 7192. X-ray crystal structure analysis revealed that the guanidino group of l-arginine is recognized not only by Glu305 but also Asp433, Trp564, and Glu617, which interact with Arg305 in wild-type LGOX. Multiple interactions by these residues provide strict specificity and high activity of LGOX R305E toward l-arginine. LGOX R305E is a thermostable and pH stable enzyme. The amount of hydrogen peroxide, which is a byproduct of oxidative deamination of l-arginine by LGOX R305E, is proportional to the concentration of l-arginine in a range from 0 to 100 μM. The linear relationship is maintained around 1 μM of l-arginine. Thus, LGOX R305E is suitable for the determination of l-arginine.
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Affiliation(s)
- Yoshika Yano
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Shinsaku Matsuo
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Nanako Ito
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | | | - Kenji Inagaki
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
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8
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Assefa AD, Hur OS, Ro NY, Lee JE, Hwang AJ, Kim BS, Rhee JH, Yi JY, Kim JH, Lee HS, Sung JS, Kim MK, Noh JJ. Fruit Morphology, Citrulline, and Arginine Levels in Diverse Watermelon ( Citrullus lanatus) Germplasm Collections. PLANTS 2020; 9:plants9091054. [PMID: 32824928 PMCID: PMC7569901 DOI: 10.3390/plants9091054] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/14/2020] [Accepted: 08/16/2020] [Indexed: 12/13/2022]
Abstract
Watermelon (Citrullus lanatus) is a non-seasonal, economically important, cucurbit cultivated throughout the world, with Asia as a continent contributing the most. As part of the effort to diversify watermelon genetic resources in the already cultivated group, this study was devoted to providing baseline data on morphological quality traits and health-beneficial phytonutrients of watermelon germplasm collections, thereby promoting watermelon research and cultivation programs. To this end, we reported morphological traits, citrulline, and arginine levels of watermelon genetic resources obtained from the gene bank of Agrobiodiversity Center, Republic of Korea, and discussed the relationships between each. Diverse characteristics were observed among many of the traits, but most of the genetic resources (>90%) were either red or pink-fleshed. Korean originated fruits contained intermediate levels of soluble solid content (SSC) while the USA, Russian, Tajikistan, Turkmenistan, Taiwan, and Uruguay originated fruits had generally the highest levels of soluble solids. The citrulline and arginine contents determined using the High Performance Liquid Chromatography (HPLC) method ranged from 6.9 to 52.1 mg/g (average, 27.3 mg/g) and 1.8 to 21.3 mg/g (average, 9.8 mg/g), respectively. The citrulline content determined using the Citrulline Assay Kit ranged from 6.5 to 42.8 mg/g (average, 27.0 mg/g). Resources with high citrulline and arginine levels contained low SSC, whereas red- and pink-colored flesh samples had less citrulline compared to yellow and orange.
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Affiliation(s)
- Awraris Derbie Assefa
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - On-Sook Hur
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - Na-Young Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - Jae-Eun Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - Ae-Jin Hwang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - Bich-Saem Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - Ju-Hee Rhee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - Jung-Yoon Yi
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - Ji-Hyun Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea; (A.D.A.); (O.-S.H.); (N.-Y.R.); (J.-E.L.); (A.-J.H.); (B.-S.K.); (J.-H.R.); (J.-Y.Y.); (J.-H.K.)
| | - Ho-Sun Lee
- International Technology Cooperation Center, RDA, Jeonju 54875, Korea;
| | - Jung-Sook Sung
- Upland Crop Breeding Division, Department of Southern Area Crop Science, National Institute of Crop Science, RDA, Miryang 50424, Korea;
| | - Myung-Kon Kim
- Department of Food Science and Technology, Jeonbuk National University, Jeonju 54896, Korea;
| | - Jae-Jong Noh
- Jeonbuk Agricultural Research and Extension Services, Iksan 54591, Korea
- Correspondence: ; Tel.: +82-63-290-6121
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9
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A novel arginine bioprobe based on up-conversion fluorescence resonance energy transfer. Anal Chim Acta 2019; 1079:200-206. [DOI: 10.1016/j.aca.2019.06.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/16/2019] [Accepted: 06/27/2019] [Indexed: 12/14/2022]
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10
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Asano Y. Screening and development of enzymes for determination and transformation of amino acids. Biosci Biotechnol Biochem 2019; 83:1402-1416. [PMID: 30621552 DOI: 10.1080/09168451.2018.1559027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The high stereo- and substrate specificities of enzymes have been utilized for micro-determination of amino acids. Here, I review the discovery of l-Phe dehydrogenase and its practical use in the diagnosis of phenylketonuria in more than 5,400,000 neonates over two decades in Japan. Screening and uses of other selective enzymes for micro-determination of amino acids have also been discussed. In addition, novel enzymatic assays with the systematic use of known enzymes, including assays based on a pyrophosphate detection system using pyrophosphate dikinase for a variety of l-amino acids with amino-acyl-tRNA synthetase have been reviewed. Finally, I review the substrate specificities of a few amino acid-metabolizing enzymes that have been altered, using protein engineering techniques, mainly for production of useful chemicals, thus enabling the wider use of natural enzymes.
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Affiliation(s)
- Yasuhisa Asano
- a Biotechnology Research Center and Department of Biotechnology , Toyama Prefectural University , Imizu , Toyama , Japan
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11
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Ortiz-Tena JG, Rühmann B, Sieber V. Colorimetric Determination of Sulfate via an Enzyme Cascade for High-Throughput Detection of Sulfatase Activity. Anal Chem 2018; 90:2526-2533. [PMID: 29307190 DOI: 10.1021/acs.analchem.7b03719] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-throughput screening (HTS) methods have become decisive for the discovery and development of new biocatalysts and their application in numerous fields. Sulfatases, a broad class of biocatalysts that hydrolyze sulfate esters, are involved in diverse relevant cellular functions (e.g., signaling and hormonal regulation) and are therefore gaining importance, particularly in the medical field. Additionally, various technical applications have been recently devised. One of the major challenges in the field of enzyme development is the sensitive and high-throughput detection of the actual product of the biocatalyst of interest without the need for chromophore analogues. Addressing this issue, a colorimetric assay for sulfatases was developed and validated for detecting sulfate through a two-step enzymatic cascade, with a linear detection range of 3.3 (limit of detection) up to 250 μM. The procedure is compatible with relevant compounds employed in sulfatase reactions, including cosolvents, cations, and buffers. The assay was optimized and performed as part of a 96-well screening workflow that included bacterial growth, heterologous sulfatase expression, cell lysis, sulfate ester hydrolysis, inactivation of cell lysate, and colorimetric sulfate determination. With this procedure, the activity of an aryl and an alkyl sulfatase could be confirmed and validated. Overall, this assay provides a simple and fast alternative for screening and engineering sulfatases from DNA libraries (e.g., using metagenomics) with medical or synthetic relevance.
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Affiliation(s)
- Jose G Ortiz-Tena
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany
| | - Broder Rühmann
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technische Universität München , 94315 Straubing, Germany.,Fraunhofer IGB , Straubing Branch BioCat, 94315 Straubing, Germany.,TUM Catalysis Research Center , Ernst-Otto-Fischer-Straße 1, 85748 Garching, Germany.,The University of Queensland , School of Chemistry and Molecular Biosciences, 68 Copper Road, St. Lucia 4072, Australia
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12
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Recombinant Forms of Arginase and Arginine Deiminase as Catalytic Components of «Argitest» Enzymatic Kit for L-arginine Analysis. SCIENCE AND INNOVATION 2017. [DOI: 10.15407/scine13.04.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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13
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Shen Q, Tan H, Xing GW, Zheng J, Jia Z. A new method to investigate the catalytic mechanism of YhdE pyrophosphatase by using a pyrophosphate fluorescence probe. Sci Rep 2017; 7:8169. [PMID: 28811554 PMCID: PMC5557916 DOI: 10.1038/s41598-017-08368-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/11/2017] [Indexed: 01/27/2023] Open
Abstract
YhdE is a Maf (multicopy associated filamentation) proteins from Escherichia coli which exhibits pyrophosphatase activity towards selected nucleotides, although its catalytic mechanism remains unclear. Herein we used a novel fluorescence probe (4-isoACBA–Zn(II) complex) to characterize the enzymatic properties of YhdE and its mutant, establishing a new method for assaying pyrophosphatase catalytic function. Our results reveal for the first time that the new fluorescence sensor confers high sensitivity and specificity and pyrophosphate (PPi) is the direct catalytic product of YhdE. Crystal structures of a mutant in the active-site loop (YhdE_E33A) show conformational flexibility implicated in the catalytic mechanism of YhdE. ITC experiments and computational docking further reveal that Asp70 and substrate dTTP coordinate Mn2+. Quantum mechanics calculations indicate that YhdE hydrolysis appears to follow a stepwise pathway in which a water molecule first attacks the α-phosphorus atom in the substrate, followed by the release of PPi from the pentavalent intermediate.
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Affiliation(s)
- Qingya Shen
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Guo-Wen Xing
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing, 100875, China.
| | - Zongchao Jia
- Department of Biochemical and Molecular Science, Queen's University, Kingston, Ontario, K7L 3N6, Canada.
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14
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Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. Biotechnol Adv 2017; 35:950-970. [PMID: 28723577 DOI: 10.1016/j.biotechadv.2017.07.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/07/2017] [Accepted: 07/11/2017] [Indexed: 12/21/2022]
Abstract
Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.
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15
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Translation-dependent bioassay for amino acid quantification using auxotrophic microbes as biocatalysts of protein synthesis. Appl Microbiol Biotechnol 2016; 101:2523-2531. [DOI: 10.1007/s00253-016-8027-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/20/2016] [Accepted: 11/23/2016] [Indexed: 10/20/2022]
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16
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Stasyuk NY, Gayda GZ, Fayura LR, Boretskyy YR, Gonchar MV, Sibirny AA. Novel arginine deiminase-based method to assay L-arginine in beverages. Food Chem 2016; 201:320-6. [PMID: 26868583 DOI: 10.1016/j.foodchem.2016.01.093] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/18/2016] [Accepted: 01/20/2016] [Indexed: 12/01/2022]
Abstract
A highly selective and sensitive enzymatic method for the quantitative determination of L-arginine (Arg) has been developed. The method is based on the use of recombinant bacterial arginine deiminase (ADI) isolated from the cells of a recombinant strain Escherichia coli and o-phthalaldehyde (OPA) as a chemical reagent. Ammonia, the product of the enzymatic digestion of Arg by ADI, reacts with OPA and forms in the presence of sulfite a product, which can be detected by spectrophotometry (S) and fluorometry (F). The linear concentration range for Arg assay in the final reaction mixture varies for ADI-OPA-F variant of the method from 0.35 μM to 24 μM with the detection limit of 0.25 μM. For ADI-OPA-S variant of the assay, the linearity varies from 0.7 μM to 50 μM with the detection limit of 0.55 μM. The new method was tested on real samples of wines and juices. A high correlation (R=0.978) was shown for the results obtained with the proposed and the reference enzymatic method.
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Affiliation(s)
- N Ye Stasyuk
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Str. 14/16, 79005 Lviv, Ukraine
| | - G Z Gayda
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Str. 14/16, 79005 Lviv, Ukraine.
| | - L R Fayura
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Str. 14/16, 79005 Lviv, Ukraine
| | - Y R Boretskyy
- Department of Biochemistry and Hygiene, Lviv State University of Physical Culture, Kosciuszko Street 11, 79000 Lviv, Ukraine; Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Str. 14/16, 79005 Lviv, Ukraine
| | - M V Gonchar
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Str. 14/16, 79005 Lviv, Ukraine; Institute of Applied Biotechnology and Basic Sciences, Rzeszow University, Sokolowska Str. 26, 36-100 Kolbuszowa, Poland
| | - A A Sibirny
- Institute of Cell Biology, National Academy of Science of Ukraine, Drahomanov Str. 14/16, 79005 Lviv, Ukraine; Department of Biotechnology and Microbiology, Rzeszow University, Cwiklinskiej 2, 35-601 Rzeszow, Poland
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17
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Matsui D, Terai A, Asano Y. L-Arginine oxidase from Pseudomonas sp. TPU 7192: Characterization, gene cloning, heterologous expression, and application to L-arginine determination. Enzyme Microb Technol 2015; 82:151-157. [PMID: 26672462 DOI: 10.1016/j.enzmictec.2015.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/01/2015] [Accepted: 10/03/2015] [Indexed: 10/22/2022]
Abstract
L-Arginine oxidase (AROD, EC 1.4.3.-) was discovered in newly discovered Pseudomonas sp. TPU 7192 and its characteristics were described. The molecular mass (MS) of the enzyme was estimated to be 528 kDa, which was accounted for by eight identical subunits with MS of 66 kDa each. AROD was identified as a flavin adenine dinucleotide (FAD)-dependent enzyme with 1 mol of FAD being contained in each subunit. It catalyzed the oxidative deamination of L-arginine and converted L-arginine to 2-ketoarginine, which was non-enzymatically converted into 4-guanidinobutyric acid when the hydrogen peroxide (H2O2) formed by L-arginine oxidation was not removed. In contrast, 2-ketoarginine was present when H2O2was decomposed. AROD was specific to L-arginine with a Km value of 149 μM. It exhibited maximal activity at 55 °C and pH 5.5. AROD was stable in the pH range 5.5-7.5 and >95% of its original activity was below 60 °C at pH 7.0. Since these enzymatic properties are considered suitable for the determination of L-arginine, the gene was cloned and expressed in a heterologous expression system. We herein successfully developed a new simple enzymatic method for the determination of L-arginine using Pseudomonas AROD.
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Affiliation(s)
- Daisuke Matsui
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Anna Terai
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan; Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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18
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Attri P, Park JH, Gaur J, Kumar N, Park DH, Jeon SN, Park BS, Chand S, Uhm HS, Choi EH. Influence of nanosecond pulsed plasma on the non-enzymatic pathway for the generation of nitric oxide from L-arginine and the modification of graphite oxide to increase the solar cell efficiency. Phys Chem Chem Phys 2015; 16:18375-82. [PMID: 25070082 DOI: 10.1039/c4cp02514h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we demonstrated the action of nanosecond pulsed plasma (NPP) on the generation of nitric oxide (NO) from the non-enzymatic pathway and on the modification of graphite oxide (GO) sheets to increase polymer solar cells (PSCs) efficiency. NO is an important signal and an effector molecule in animals, which is generated from the enzyme-catalyzed oxidation of L-arginine to NO and L-citrulline. Hence, L-arginine is an important biological precursor for NO formation. Therefore, we developed a new non-enzymatic pathway for the formation of NO and L-citrulline using NPP and characterized the pathway using NO detection kit, NMR, liquid chromatography/capillary electrophoresis-mass spectrometry (LC/CE-MS) for both quantitative and qualitative bioanalysis. We then synthesized and modified the functional groups of GO using NPP, and it was characterised by X-ray photoelectron spectroscopy (XPS), confocal Raman spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM) imaging, cathodoluminescence (CL) and work function using γ-FIB. Further, we also tested the power conversion efficiency of the PSCs devices with modified GO that is similar to the one obtained with poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) as HTL. This work is perceived to have great implications for inexpensive and efficient methodology for NO generation and modification of GO, which are applicable in materials from nanomaterials to biomolecules.
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Affiliation(s)
- Pankaj Attri
- Plasma BioScience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Korea.
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