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Toyama F, Kimura H, Zhang Y, Nishiya Y. Chemical modification of Arthrobacter sarcosine oxidase by N-methylisothiazolinone reduces reactivity toward oxygen. Biosci Biotechnol Biochem 2024; 88:630-636. [PMID: 38553959 DOI: 10.1093/bbb/zbae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/25/2024] [Indexed: 05/23/2024]
Abstract
N-Methylisothiazolinone (MIT) is a thiol group modifier and antimicrobial agent. Arthrobacter sarcosine oxidase (SoxA), a diagnostic enzyme for assaying creatinine, loses its activity upon the addition of MIT, and its inactivation mechanism remains unclear. In this study, SoxA was chemically modified using MIT (mo-SoxA), and its structural and chemical properties were characterized. Spectral analysis data, oxygen consumption rates, and reactions were compared between intact SoxA and mo-SoxA. These demonstrate that the oxidative half-reaction toward oxygen is inhibited by MIT modification. The oxidase activity of mo-SoxA was approximately 2.1% of that of intact SoxA, and its dehydrogenase activity was approximately 4.2 times higher. The C-to-S mutants revealed that cooperative modification of 2 specific cysteine residues caused a drastic change in the enzyme reaction mode. Based on the modeled tertiary structures, the putative entrance for oxygen uptake is predicted to be blocked by the chemical modification of the 2 cysteine residues.
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Affiliation(s)
- Fuka Toyama
- Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
| | - Hironori Kimura
- Department of Life Science, Faculty of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
| | - Yuqi Zhang
- Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
| | - Yoshiaki Nishiya
- Division of Life Science, Graduate School of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
- Department of Life Science, Faculty of Science and Engineering, Setsunan University, 17-8 Ikeda-Nakamachi, Neyagawa, Osaka, Japan
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2
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Tomari N, Sasamoto K, Sakai H, Tani T, Yamamoto Y, Nishiya Y. New enzymatic assays based on the combination of signal accumulation type of ion sensitive field effect transistor (SA-ISFET) with horseradish peroxidase. Anal Biochem 2019; 584:113353. [PMID: 31271734 DOI: 10.1016/j.ab.2019.113353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 11/18/2022]
Abstract
Peroxidase is widely used for the detection of secondary reactions during measurements of various enzymatic reactions, such as that of oxidase activity, or as an enzyme for immunoassay. Conventional methods utilizing the enzyme require expensive equipment such as a spectrophotometer to measure the absorption of light by the reaction product. Here, we describe a simple and cost-effective method for measuring enzymatic reactions using a signal accumulation type of ion sensitive field effect transistor (SA-ISFET) sensor capable of detecting the proton changes due to the enzymatic reaction. Using this detection principle, we constructed a detection system combining ABTS, an electron mediator, and a horseradish peroxidase activity detection system. As a result, we could quantitatively measure hydrogen peroxide with excellent reproducibility and linearity. As an application of this tool, we describe an oxidase-peroxidase reaction system for the measurement of glucose, sarcosine, uric acid and lactic acid. In addition, we describe an immunoassay system using a peroxidase-labeled antibody for detection of Escherichia coli. We also describe a prototype for a flow-type ISFET device for continuous and routine measurements.
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Affiliation(s)
- Naohiro Tomari
- Kyoto Municipal Institute of Industrial Technology and Culture, 91 Chudouji Awata-cho, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Kohei Sasamoto
- Department of Life Science, Faculty of Science and Engineering, Setsunan University, 17-8 Ikedanaka-machi, Neyagawa, Osaka, 572-8508, Japan
| | - Hanami Sakai
- Department of Life Science, Faculty of Science and Engineering, Setsunan University, 17-8 Ikedanaka-machi, Neyagawa, Osaka, 572-8508, Japan
| | - Toshio Tani
- Bio-X Inc., 121-17 Terada-Imahori, Joyo, Kyoto, 610-0121, Japan
| | - Yoshihiro Yamamoto
- Kyoto Municipal Institute of Industrial Technology and Culture, 91 Chudouji Awata-cho, Shimogyo-ku, Kyoto, 600-8813, Japan
| | - Yoshiaki Nishiya
- Department of Life Science, Faculty of Science and Engineering, Setsunan University, 17-8 Ikedanaka-machi, Neyagawa, Osaka, 572-8508, Japan.
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3
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Kubacka A, Diez MS, Rojo D, Bargiela R, Ciordia S, Zapico I, Albar JP, Barbas C, Martins dos Santos VAP, Fernández-García M, Ferrer M. Understanding the antimicrobial mechanism of TiO₂-based nanocomposite films in a pathogenic bacterium. Sci Rep 2014; 4:4134. [PMID: 24549289 PMCID: PMC3928576 DOI: 10.1038/srep04134] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/05/2014] [Indexed: 02/07/2023] Open
Abstract
Titania (TiO2)-based nanocomposites subjected to light excitation are remarkably effective in eliciting microbial death. However, the mechanism by which these materials induce microbial death and the effects that they have on microbes are poorly understood. Here, we assess the low dose radical-mediated TiO2 photocatalytic action of such nanocomposites and evaluate the genome/proteome-wide expression profiles of Pseudomonas aeruginosa PAO1 cells after two minutes of intervention. The results indicate that the impact on the gene-wide flux distribution and metabolism is moderate in the analysed time span. Rather, the photocatalytic action triggers the decreased expression of a large array of genes/proteins specific for regulatory, signalling and growth functions in parallel with subsequent selective effects on ion homeostasis, coenzyme-independent respiration and cell wall structure. The present work provides the first solid foundation for the biocidal action of titania and may have an impact on the design of highly active photobiocidal nanomaterials.
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Affiliation(s)
- Anna Kubacka
- Institute of Catalysis, CSIC, 28049 Madrid, Spain
| | - María Suárez Diez
- Chair of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, The Netherlands
| | - David Rojo
- Center for Metabolomics and Bioanalysis, University CEU San Pablo, Boadilla del Monte, 28668 Madrid, Spain
| | | | - Sergio Ciordia
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, 28049 Madrid, Spain
| | - Inés Zapico
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, 28049 Madrid, Spain
| | - Juan P Albar
- Proteomic Facility, CNB-National Centre for Biotechnology, CSIC, 28049 Madrid, Spain
| | - Coral Barbas
- Center for Metabolomics and Bioanalysis, University CEU San Pablo, Boadilla del Monte, 28668 Madrid, Spain
| | - Vitor A P Martins dos Santos
- 1] Chair of Systems and Synthetic Biology, Wageningen University, 6703 HB Wageningen, The Netherlands [2] LifeGlimmer GmbH, 12163 Berlin, Germany
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Elucidating the Biosynthetic Pathway for the Polyketide-Nonribosomal Peptide Collismycin A: Mechanism for Formation of the 2,2′-bipyridyl Ring. ACTA ACUST UNITED AC 2012; 19:399-413. [DOI: 10.1016/j.chembiol.2012.01.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Revised: 01/13/2012] [Accepted: 01/17/2012] [Indexed: 11/22/2022]
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5
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Nishiya Y. A mutant sarcosine oxidase in which activity depends on flavin adenine dinucleotide. Protein Expr Purif 2000; 20:95-7. [PMID: 11035956 DOI: 10.1006/prep.2000.1299] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The covalent flavin attachment site in the Arthrobacter sarcosine oxidase (cysteine at position 318) was replaced with serine, and the mutational effect of C318S was analyzed. Wild type and C318S with a C-terminal 6-histidine tag were constructed and homogeneously purified by the single step. The covalently binding to flavin was not essential to the enzyme activity because the C318S mutant exhibited extremely weak activity. Moreover, the activity of the mutant was recovered in the presence of flavin adenine dinucleotide (FAD), and significantly increased as the concentration of FAD increased. This dependence of the mutant on FAD indicates that the noncovalent binding of free FAD to the mutant enzyme is reversible.
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Affiliation(s)
- Y Nishiya
- Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24 Toyo-cho, Tsuruga, Fukui, 914-0047, Japan.
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6
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Abstract
The goal of this review is to present a comprehensive survey of the many intriguing facets of creatine (Cr) and creatinine metabolism, encompassing the pathways and regulation of Cr biosynthesis and degradation, species and tissue distribution of the enzymes and metabolites involved, and of the inherent implications for physiology and human pathology. Very recently, a series of new discoveries have been made that are bound to have distinguished implications for bioenergetics, physiology, human pathology, and clinical diagnosis and that suggest that deregulation of the creatine kinase (CK) system is associated with a variety of diseases. Disturbances of the CK system have been observed in muscle, brain, cardiac, and renal diseases as well as in cancer. On the other hand, Cr and Cr analogs such as cyclocreatine were found to have antitumor, antiviral, and antidiabetic effects and to protect tissues from hypoxic, ischemic, neurodegenerative, or muscle damage. Oral Cr ingestion is used in sports as an ergogenic aid, and some data suggest that Cr and creatinine may be precursors of food mutagens and uremic toxins. These findings are discussed in depth, the interrelationships are outlined, and all is put into a broader context to provide a more detailed understanding of the biological functions of Cr and of the CK system.
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Affiliation(s)
- M Wyss
- F. Hoffmann-La Roche, Vitamins and Fine Chemicals Division, Basel, Switzerland.
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Dodt G, Kim DG, Reimann SA, Reuber BE, McCabe K, Gould SJ, Mihalik SJ. L-Pipecolic acid oxidase, a human enzyme essential for the degradation of L-pipecolic acid, is most similar to the monomeric sarcosine oxidases. Biochem J 2000; 345 Pt 3:487-94. [PMID: 10642506 PMCID: PMC1220782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
L-Pipecolic acid oxidase activity is deficient in patients with peroxisome biogenesis disorders (PBDs). Because its role, if any, in these disorders is unknown, we cloned the associated human gene and expressed its protein product. The cDNA was cloned with the use of a reverse genetics approach based on the amino acid sequence obtained from purified L-pipecolic acid oxidase from monkey. The complete cDNA, obtained by conventional library screening and 5' rapid amplification of cDNA ends, encompassed an open reading frame of 1170 bases, translating to a 390-residue protein. The translated protein terminated with the sequence AHL, a peroxisomal targeting signal 1. Indirect immunofluorescence studies showed that the protein product was expressed in human fibroblasts in a punctate pattern that co-localized with the peroxisomal enzyme catalase. A BLAST search with the amino acid sequence showed 31% identity and 53% similarity with Bacillus sp. NS-129 monomeric sarcosine oxidase, as well as similarity to all sarcosine oxidases and dehydrogenases. No similarity was found to the peroxisomal D-amino acid oxidases. The recombinant enzyme oxidized both L-pipecolic acid and sarcosine. However, PBD patients who lack the enzyme activity accumulate only L-pipecolic acid, suggesting that in humans in vivo, this enzyme is involved mainly in the degradation of L-pipecolic acid.
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Affiliation(s)
- G Dodt
- Institut für Physiologische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Federal Republic of Germany
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Nishiya Y, Imanaka T. Purification and characterization of a novel glycine oxidase from Bacillus subtilis. FEBS Lett 1998; 438:263-6. [PMID: 9827558 DOI: 10.1016/s0014-5793(98)01313-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The open reading frame yjbR which had been sequenced as a part of the Bacillus subtilis genome project encodes a putative 40.9-kDa protein. The yjbR-coding sequence was slightly similar to those of bacterial sarcosine oxidases and possibly compatible with the tertiary structure of the porcine kidney D-amino acid oxidase. The yjbR gene product was overproduced in Escherichia coli, purified to homogeneity from the recombinant strain, and characterized. This protein effectively catalyzed the oxidation of sarcosine (N-methylglycine), N-ethylglycine and glycine. Lower activities on D-alanine, D-valine, and D-proline were detected although no activities were shown on L-amino acids and other D-amino acids. Since glycine is a product and not a substrate for sarcosine oxidase, this protein is not a type of demethylating enzymes but a novel deaminating oxidase, named glycine oxidase as a common name. Several enzymatic properties of the B. subtilis glycine oxidase were also investigated.
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Affiliation(s)
- Y Nishiya
- Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., Fukui, Japan.
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Nishiya Y, Kawamura Y, Imanaka T. Enzymatic assay for chloride ion with chloride-dependent sarcosine oxidase created by site-directed mutagenesis. Anal Biochem 1997; 245:127-32. [PMID: 9056195 DOI: 10.1006/abio.1996.9935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Serum chloride ion is routinely assayed in clinical laboratories. We have developed a new enzymatic assay for determining the chloride ion concentration. The method involves the use of a mutant sarcosine oxidase, which was created as desired by site-directed mutagenesis and showed chloride-dependent activity. The enzyme which is reactivated by the chloride ion forms hydrogen peroxide from sarcosine. The production of hydrogen peroxide is measured by the 4-amino-antipyrine peroxidase system. The increase of the reaction rate was proportional to the chloride ion concentration. A lag time of the time course was not observed, and the reaction rate for a blank was not detected. Therefore, a rate assay could be adopted. A standard curve of the assay reagent was linear up to 180 mM chloride ion of the sample. The specificity for the bromide ion was 43% of that of the chloride ion, although it was 0% for other ion species. When serum samples were used, within-day coefficient variations (CVs) and day-to-day CVs were below 1.5%. A good correlation with the comparison assay was observed by using 160 samples of normal and abnormal patient sera. This method can easily and reliably be used for the accurate determination of chloride ion concentration in serum or other samples.
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Affiliation(s)
- Y Nishiya
- Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., Fukui, Japan
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Nishiya Y, Imanaka T. Highly conservative sequence in the carboxyl terminus of sarcosine oxidase is important for substrate binding. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0922-338x(97)81917-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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11
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Yoshida N, Sakai Y, Isogai A, Fukuya H, Yagi M, Tani Y, Kato N. Primary structures of fungal fructosyl amino acid oxidases and their application to the measurement of glycated proteins. EUROPEAN JOURNAL OF BIOCHEMISTRY 1996; 242:499-505. [PMID: 9022674 DOI: 10.1111/j.1432-1033.1996.0499r.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Fructosyl amino acid oxidase (FAOD), which is active toward model compounds of the glycated proteins in blood, N epsilon-fructosyl N sigma-Z-lysine and N-fructosyl valine, was purified to homogeneity from Aspergillus terreus GP1. Though the enzyme did not use glycated proteins directly as its substrate, it used glycated human serum albumin (HSA) when HSA was treated with a protease. Linear relationships between both the concentration and the increase in absorbance and the glycation rate of glycated HSA and the increase in absorbance were observed. cDNAs coding for FAODs were cloned from cDNA libraries of A. terreus GP1 and Penicillium janthinellum AKU 3413. The coding region for both fungal FAODs consisted of 1314 bp encoding 437 amino acids. The sequence of a dinucleotide-binding motif, GXGXXG, was in the deduced N-terminal region and a similar sequence to that the active site of bacterial sarcosine oxidases was found near the C-terminal region of FAOD. The of C-terminal tripeptides SKL and AKL of FAODs from A. terreus and P. janthinellum, respectively, represent typical peroxisomal-targeting signals. Finally, FAOD protein was produced in Escherichia coli transformants in an active form, and at the same level as in the original fungi.
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Affiliation(s)
- N Yoshida
- Department of Agricultural Chemistry, Faculty of Agriculture, Kyoto University, Japan
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Nishiya Y, Imanaka T. Analysis of interaction between the Arthrobacter sarcosine oxidase and the coenzyme flavin adenine dinucleotide by site-directed mutagenesis. Appl Environ Microbiol 1996; 62:2405-10. [PMID: 8779579 PMCID: PMC168022 DOI: 10.1128/aem.62.7.2405-2410.1996] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Sarcosine oxidase from Arthrobacter sp. TE1826 (SoxA) tightly binds with the coenzyme flavin adenine dinucleotide (FAD). The amino-terminal region of this enzyme was recognized as a part of the FAD-binding domain by homology search analysis. Comparison with other structurally well-known flavoproteins suggested that the aspartate residue at position 35 (D-35) and the motif sequence (six residues at positions 12 to 17) were important for the interaction with FAD. Site-directed mutagenesis of each position was performed, and mutant SoxAs were purified and characterized. When D-35 was substituted with glutamate, asparagine, and alanine, it was indicated that the carboxyl group of the side chain interacted with FAD. Changes in the enzyme-bound FAD were also observed from the altered spectral profiles. Thirteen mutant SoxAs were obtained by replacing amino acids in the motif sequence. Most of them showed inhibited or remarkably decreased sarcosine oxidase activity, and their spectral profiles were altered. However, some of them were reactivated by chloride ion. Their spectral profiles also became close to that of wild type in the presence of chloride ion. These results strongly suggest that the inhibition of interaction of enzyme with FAD was caused by the substitution in the motif and that it could be recovered under different conditions.
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Affiliation(s)
- Y Nishiya
- Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., Fukui Prefecture, Japan
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