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Yu Y, Liu NH, Teng ZJ, Chen Y, Wang P, Zhang YZ, Fu HH, Chen XL, Zhang YQ. Evidence for archaeal metabolism of D-amino acids in the deep marine sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174723. [PMID: 39002603 DOI: 10.1016/j.scitotenv.2024.174723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
The deep marine sediments represent a major repository of organic matter whilst hosting a great number of uncultivated microbes. Microbial metabolism plays a key role in the recycling of organic matter in the deep marine sediments. D-amino acids (DAAs) and DAA-containing muropeptides, an important group of organic matter in the deep marine sediments, are primarily derived from bacterial peptidoglycan decomposition. Archaea are abundant in the deep ocean microbiome, yet their role in DAA metabolism remains poorly studied. Here, we report bioinformatic investigation and enzymatic characterization of deep marine sedimentary archaea involved in DAA metabolism. Our analyses suggest that a variety of archaea, particularly the Candidatus Bathyarchaeota and the Candidatus Lokiarchaeaota, can metabolize DAAs. DAAs are converted into L-amino acids via amino acid racemases (Ala racemase, Asp racemase and broad substrate specificity amino acid racemase), and converted into α-keto acid via d-serine ammonia-lyase, whereas DAA-containing di-/tri-muropeptides can be hydrolyzed by peptidases (dipeptidase and D-aminopeptidase). Overall, this study reveals the identity and activity of deep marine sedimentary archaea involved in DAA metabolism, shedding light on the mineralization and biogeochemical cycling of DAAs in the deep marine sediments.
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Affiliation(s)
- Yang Yu
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Ning-Hua Liu
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Zhao-Jie Teng
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Yin Chen
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; School of Life Sciences, University of Warwick, Coventry, UK; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Hui-Hui Fu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China
| | - Yu-Qiang Zhang
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Joint Research Center for Marine Microbial Science and Technology, Shandong University and Ocean University of China, China.
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Characterization of a Novel Thermostable Dye-Linked l-Lactate Dehydrogenase Complex and Its Application in Electrochemical Detection. Int J Mol Sci 2021; 22:ijms222413570. [PMID: 34948373 PMCID: PMC8704557 DOI: 10.3390/ijms222413570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
Flavoenzyme dye-linked l-lactate dehydrogenase (Dye-LDH) is primarily involved in energy generation through electron transfer and exhibits potential utility in electrochemical devices. In this study, a gene encoding a Dye-LDH homolog was identified in a hyperthermophilic archaeon, Sulfurisphaera tokodaii. This gene was part of an operon that consisted of four genes that were tandemly arranged in the Sf. tokodaii genome in the following order: stk_16540, stk_16550 (dye-ldh homolog), stk_16560, and stk_16570. This gene cluster was expressed in an archaeal host, Sulfolobus acidocaldarius, and the produced enzyme was purified to homogeneity and characterized. The purified recombinant enzyme exhibited Dye-LDH activity and consisted of two different subunits (products of stk_16540 (α) and stk_16550 (β)), forming a heterohexameric structure (α3β3) with a molecular mass of approximately 253 kDa. Dye-LDH also exhibited excellent stability, retaining full activity upon incubation at 70 °C for 10 min and up to 80% activity after 30 min at 50 °C and pH 6.5–8.0. A quasi-direct electron transfer (DET)-type Dye-LDH was successfully developed by modification of the recombinant enzyme with an artificial redox mediator, phenazine ethosulfate, through amine groups on the enzyme’s surface. This study is the first report describing the development of a quasi-DET-type enzyme by using thermostable Dye-LDH.
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Satomura T, Emoto S, Kurosawa N, Ohshima T, Sakuraba H, Suye SI. Characterization of dye-linked d-amino acid dehydrogenase from Sulfurisphaera tokodaii expressed using an archaeal recombinant protein expression system. J Biosci Bioeng 2020; 130:247-252. [PMID: 32451245 DOI: 10.1016/j.jbiosc.2020.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 11/16/2022]
Abstract
A gene encoding a dye-linked d-amino acid dehydrogenase (Dye-DADH) homologue was found in a hyperthermophilic archaeon, Sulfurisphaera tokodaii. The predicted amino acid sequence suggested that the gene product is a membrane-bound type enzyme. The gene was overexpressed in Escherichia coli, but the recombinant protein was exclusively produced as an inclusion body. In order to avoid production of the inclusion body, an expression system using the thermoacidophilic archaeon Sulfolobus acidocaldarius instead of E. coli as the host cell was constructed. The gene was successfully expressed in Sulfolobus acidocaldarius, and its product was purified to homogeneity and characterized. The purified enzyme catalyzed the dehydrogenation of various d-amino acids, with d-phenylalanine being the most preferred substrate. The enzyme retained its full activity after incubation at 90 °C for 30 min and after incubation at pH 4.0-11.0 for 30 min at 50 °C. This is the first report on membrane-bound Dye-DADH from thermophilic archaea that was successfully expressed in an archaeal host.
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Affiliation(s)
- Takenori Satomura
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Life Science Innovation Center, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan.
| | - Shin Emoto
- Department of Applied Chemistry Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Innovation, Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, Ohmiya, 5-16-1 Asahi-ku, Osaka 535-8585, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Shin-Ichiro Suye
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan; Life Science Innovation Center, University of Fukui, 3-9-1 Bunkyo, Fukui 910-8507, Japan
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Watanabe Y, Watanabe S, Itoh Y, Watanabe Y. Crystal structure of substrate-bound bifunctional proline racemase/hydroxyproline epimerase from a hyperthermophilic archaeon. Biochem Biophys Res Commun 2019; 511:135-140. [PMID: 30773259 DOI: 10.1016/j.bbrc.2019.01.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/31/2019] [Indexed: 11/30/2022]
Abstract
The hypothetical OCC_00372 protein from Thermococcus litoralis is a member of the ProR superfamily from hyperthermophilic archaea and exhibits unique bifunctional proline racemase/hydroxyproline 2-epimerase activity. However, the molecular mechanism of the broad substrate specificity and extreme thermostability of this enzyme (TlProR) remains unclear. Here we determined the crystal structure of TlProR at 2.7 Å resolution. Of note, a substrate proline molecule, derived from expression host Escherichia coli cells, was tightly bound in the active site of TlProR. The substrate bound structure and mutational analyses suggested that Trp241 is involved in hydroxyproline recognition by making a hydrogen bond between the indole group of Trp241 and the hydroxyl group of hydroxyproline. Additionally, Tyr171 may contribute to the thermostability by making hydrogen bonds between the hydroxyl group of Tyr171 and catalytic residues. Our structural and functional analyses provide a structural basis for understanding the molecular mechanism of substrate specificity and thermostability of ProR superfamily proteins.
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Affiliation(s)
- Yasunori Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Seiya Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Center for Marine Environmental Studies (CMES), Ehime University, 2-5 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
| | - Yoshika Itoh
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
| | - Yasuo Watanabe
- Department of Bioscience, Graduate School of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan; Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime, 790-8566, Japan
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Satomura T, Hayashi J, Ohshida T, Sakuraba H, Ohshima T, Suye SI. Enzymological characteristics of a novel archaeal dye-linked D-lactate dehydrogenase showing loose binding of FAD. Extremophiles 2018; 22:975-981. [PMID: 30206766 DOI: 10.1007/s00792-018-1054-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 09/06/2018] [Indexed: 11/26/2022]
Abstract
A gene-encoding a dye-linked D-lactate dehydrogenase (Dye-DLDH) homolog was identified in the genome of the hyperthermophilic archaeon Thermoproteus tenax. The gene was expressed in Escherichia coli and the product was purified to homogeneity. The recombinant protein exhibited highly thermostable Dye-DLDH activity. To date, four types of Dye-DLDH have been identified in hyperthermophilic archaea (in Aeropyrum pernix, Sulfolobus tokodaii, Archaeoglobus fulgidus, and Candidatus Caldiarchaeum subterraneum). The amino acid sequence of T. tenax Dye-DLDH showed the highest similarity (45%) to A. pernix Dye-DLDH, but neither contained a known FAD-binding motif. Nonetheless, both homologs required FAD for enzymatic activity, suggesting that FAD binds loosely to the enzyme and is easily released unlike in other Dye-DLDHs. Our findings indicate that Dye-DLDHs from T. tenax and A. pernix are a novel type of Dye-DLDH characterized by loose binding of FAD.
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Affiliation(s)
- Takenori Satomura
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan.
- Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan.
| | - Junji Hayashi
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Biwako-Kusatsu Campus, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan
| | - Tatsuya Ohshida
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan
| | - Toshihisa Ohshima
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, Ohmiya, 5-16-1 Asahi-ku, Osaka, 535-8585, Japan
| | - Shin-Ichiro Suye
- Division of Engineering, Faculty of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
- Organization for Life Science Advancement Programs, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
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Wolff H, Bode HB. The benzodiazepine-like natural product tilivalline is produced by the entomopathogenic bacterium Xenorhabdus eapokensis. PLoS One 2018; 13:e0194297. [PMID: 29596433 PMCID: PMC5875774 DOI: 10.1371/journal.pone.0194297] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/28/2018] [Indexed: 01/05/2023] Open
Abstract
The pyrrolobenzodiazepine tilivalline (1) was originally identified in the human gut pathobiont Klebsiella oxytoca, the causative agent of antibiotic-associated hemorrhagic colitis. Here we show the identification of tilivalline and analogs thereof in the entomopathogenic bacterium Xenorhabdus eapokensis as well as the identification of its biosynthesis gene cluster encoding a bimodular non-ribosomal peptide synthetase. Heterologous expression of both genes in E. coli resulted in the production of 1 and from mutasynthesis and precursor directed biosynthesis 11 new tilivalline analogs were identified in X. eapokensis. These results allowed the prediction of the tilivalline biosynthesis being similar to that in K. oxytoca.
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Affiliation(s)
- Hendrik Wolff
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Fachbereich Biowissenschaften, Merck Stiftungsprofessur für Molekulare Biotechnologie, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe-Universität Frankfurt, Frankfurt am Main, Germany
- * E-mail:
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Xu J, Bai Y, Fan T, Zheng X, Cai Y. Expression, purification, and characterization of a membrane-bound D-amino acid dehydrogenase from Proteus mirabilis JN458. Biotechnol Lett 2017; 39:1559-1566. [PMID: 28676939 DOI: 10.1007/s10529-017-2388-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 06/19/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To characterize a novel membrane-bound D -amino acid dehydrogenase from Proteus mirabilis JN458 (PmDAD). RESULTS The recombinant PmDAD protein, encoding a peptide of 434 amino acids with a MW of 47.7 kDa, exhibited broad substrate specificity with D -alanine the most preferred substrate. The K m and V max values for D -alanine were 9 mM and 20 μmol min-1 mg-1, respectively. Optimal activity was at pH 8 and 45 °C. Additionally, this PmDAD generated H2O2 and exhibited 68 and 60% similarity with E. coli K12 DAD and Pseudomonas aeruginosa DAD, respectively, with low degrees of sequence similarity with other bacterial DADs. CONCLUSIONS D-Amino acid dehydrogenase from Proteus mirabilis JN458 was expressed and characterized for the first time, DAD was confirmed to be an alanine dehydrogenase.
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Affiliation(s)
- Jinjin Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Taiping Fan
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China.,Department of Pharmacology, University of Cambridge, Cambridge, CB2 1T, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, 710069, Shanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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Kubota T, Kobayashi T, Nunoura T, Maruyama F, Deguchi S. Enantioselective Utilization of D-Amino Acids by Deep-Sea Microorganisms. Front Microbiol 2016; 7:511. [PMID: 27148200 PMCID: PMC4836201 DOI: 10.3389/fmicb.2016.00511] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/29/2016] [Indexed: 12/27/2022] Open
Abstract
Microorganisms that utilize various D-amino acids (DAAs) were successfully isolated from deep-sea sediments. The isolates were phylogenetically assigned to Alphaproteobacteria, Gammmaproteobacteria, and Bacilli. Some of the isolates exhibited high enantioselective degradation activities to various DAAs. In particular, the Alphaproteobacteria Nautella sp. strain A04V exhibited robust growth in minimal medium supplemented with D-Val as a sole carbon and nitrogen source, whereas its growth was poor on minimal medium supplemented with L-Val instead of D-Val. Its growth was facilitated most when racemic mixtures of valine were used. In contrast, the Nautella strains isolated from shallow-sea grew only with L-Val. No significant differences were found among the strains in the genome sequences including genes possibly related to DAA metabolisms.
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Affiliation(s)
- Takaaki Kubota
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Tohru Kobayashi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Shigeru Deguchi
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology Yokosuka, Japan
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Satomura T, Sakuraba H, Suye SI, Ohshima T. Dye-linked D-amino acid dehydrogenases: biochemical characteristics and applications in biotechnology. Appl Microbiol Biotechnol 2015; 99:9337-47. [PMID: 26362681 DOI: 10.1007/s00253-015-6944-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/12/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
Abstract
Dye-linked D-amino acid dehydrogenases (Dye-DADHs) catalyze the dehydrogenation of free D-amino acids in the presence of an artificial electron acceptor. Although Dye-DADHs functioning in catabolism of L-alanine and as primary enzymes in electron transport chains are widely distributed in mesophilic Gram-negative bacteria, biochemical and biotechnological information on these enzymes remains scanty. This is in large part due to their instability after isolation. On the other hand, in the last decade, several novel types of Dye-DADH have been found in thermophilic bacteria and hyperthermophilic archaea, where they contribute not only to L-alanine catabolism but also to the catabolism of other amino acids, including D-arginine and L-hydroxyproline. In this minireview, we summarize recent developments in our understanding of the biochemical characteristics of Dye-DADHs and their specific application to electrochemical biosensors.
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Affiliation(s)
- Takenori Satomura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan.
| | - Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan
| | - Shin-Ichiro Suye
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan.,Department of Frontier Fiber Technology and Sciences, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui, 910-8507, Japan
| | - Toshihisa Ohshima
- Department of Biomedical engineering, Faculty of Engineering, Osaka Institute of Technology, Ohmiya, 5-16-1 Asahi-ku, Ohsaka, 535-8585, Japan
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Identification and characterization of bifunctional proline racemase/hydroxyproline epimerase from archaea: discrimination of substrates and molecular evolution. PLoS One 2015; 10:e0120349. [PMID: 25786142 PMCID: PMC4364671 DOI: 10.1371/journal.pone.0120349] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/21/2015] [Indexed: 12/14/2022] Open
Abstract
Proline racemase (ProR) is a member of the pyridoxal 5’-phosphate-independent racemase family, and is involved in the Stickland reaction (fermentation) in certain clostridia as well as the mechanisms underlying the escape of parasites from host immunity in eukaryotic Trypanosoma. Hydroxyproline epimerase (HypE), which is in the same protein family as ProR, catalyzes the first step of the trans-4-hydroxy-L-proline metabolism of bacteria. Their substrate specificities were previously considered to be very strict, in spite of similarities in their structures and catalytic mechanisms, and no racemase/epimerase from the ProR superfamily has been found in archaea. We here characterized the ProR-like protein (OCC_00372) from the hyperthermophilic archaeon, Thermococcus litoralis (TlProR). This protein could reversibly catalyze not only the racemization of proline, but also the epimerization of 4-hydroxyproline and 3-hydroxyproline with similar kinetic constants. Among the four (putative) ligand binding sites, one amino acid substitution was detected between TlProR (tryptophan at the position of 241) and natural ProR (phenylalanine). The W241F mutant showed a significant preference for proline over hydroxyproline, suggesting that this (hydrophobic and bulky) tryptophan residue played an importance role in the recognition of hydroxyproline (more hydrophilic and bulky than proline), and substrate specificity for hydroxyproline was evolutionarily acquired separately between natural HypE and ProR. A phylogenetic analysis indicated that such unique broad substrate specificity was derived from an ancestral enzyme of this superfamily.
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EQUAR MY, TANI Y, MIHARA H. Purification and Properties of Glycine Oxidase from Pseudomonas putida KT2440. J Nutr Sci Vitaminol (Tokyo) 2015; 61:506-10. [DOI: 10.3177/jnsv.61.506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Yasushi TANI
- College of Life Sciences, Ritsumeikan University
- R-GIRO, Ritsumeikan University
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12
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Dye-linked d-amino acid dehydrogenase from the thermophilic bacterium Rhodothermus marinus JCM9785: characteristics and role in trans-4-hydroxy-l-proline catabolism. Appl Microbiol Biotechnol 2014; 99:4265-75. [DOI: 10.1007/s00253-014-6263-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/20/2014] [Accepted: 11/22/2014] [Indexed: 10/24/2022]
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13
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Watanabe S, Tozawa Y, Watanabe Y. Ornithine cyclodeaminase/μ-crystallin homolog from the hyperthermophilic archaeon Thermococcus litoralis functions as a novel Δ(1)-pyrroline-2-carboxylate reductase involved in putative trans-3-hydroxy-l-proline metabolism. FEBS Open Bio 2014; 4:617-26. [PMID: 25161870 PMCID: PMC4141209 DOI: 10.1016/j.fob.2014.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 06/25/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022] Open
Abstract
Ornithine cyclodeaminase homolog from an archeon was characterized biochemically. This protein functions as a novel Δ1-pyrroline-2-carboxylate reductase. This enzyme is probably involved in trans-3-hydroxy-l-proline metabolism as in bacteria and mammals.
l-Ornithine cyclodeaminase (OCD) is involved in l-proline biosynthesis and catalyzes the unique deaminating cyclization of l-ornithine to l-proline via a Δ1-pyrroline-2-carboxyrate (Pyr2C) intermediate. Although this pathway functions in only a few bacteria, many archaea possess OCD-like genes (proteins), among which only AF1665 protein (gene) from Archaeoglobus fulgidus has been characterized as an NAD+-dependent l-alanine dehydrogenase (AfAlaDH). However, the physiological role of OCD-like proteins from archaea has been unclear. Recently, we revealed that Pyr2C reductase, involved in trans-3-hydroxy-l-proline (T3LHyp) metabolism of bacteria, belongs to the OCD protein superfamily and catalyzes only the reduction of Pyr2C to l-proline (no OCD activity) [FEBS Open Bio (2014) 4, 240–250]. In this study, based on bioinformatics analysis, we assumed that the OCD-like gene from Thermococcus litoralis DSM 5473 is related to T3LHyp and/or proline metabolism (TlLhpI). Interestingly, TlLhpI showed three different enzymatic activities: AlaDH; N-methyl-l-alanine dehydrogenase; Pyr2C reductase. Kinetic analysis suggested strongly that Pyr2C is the preferred substrate. In spite of their similar activity, TlLhpI had a poor phylogenetic relationship to the bacterial and mammalian reductases for Pyr2C and formed a close but distinct subfamily to AfAlaDH, indicating convergent evolution. Introduction of several specific amino acid residues for OCD and/or AfAlaDH by site-directed mutagenesis had marked effects on both AlaDH and Pyr2C reductase activities. The OCC_00387 gene, clustered with the TlLhpI gene on the genome, encoded T3LHyp dehydratase, homologous to the bacterial and mammalian enzymes. To our knowledge, this is the first report of T3LHyp metabolism from archaea.
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Affiliation(s)
- Seiya Watanabe
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
- Corresponding author. Tel./fax: +81 89 946 9848.
| | - Yuzuru Tozawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yasuo Watanabe
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
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Gene Expression and Characterization of a Third Type of Dye-LinkedL-Proline Dehydrogenase from the Aerobic Hyperthermophilic Archaeon,Aeropyrum pernix. Biosci Biotechnol Biochem 2014; 76:589-93. [DOI: 10.1271/bbb.110775] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Watanabe S, Morimoto D, Fukumori F, Shinomiya H, Nishiwaki H, Kawano-Kawada M, Sasai Y, Tozawa Y, Watanabe Y. Identification and characterization of D-hydroxyproline dehydrogenase and Delta1-pyrroline-4-hydroxy-2-carboxylate deaminase involved in novel L-hydroxyproline metabolism of bacteria: metabolic convergent evolution. J Biol Chem 2012; 287:32674-88. [PMID: 22833679 DOI: 10.1074/jbc.m112.374272] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
L-hydroxyproline (4-hydroxyproline) mainly exists in collagen, and most bacteria cannot metabolize this hydroxyamino acid. Pseudomonas putida and Pseudomonas aeruginosa convert L-hydroxyproline to α-ketoglutarate via four hypothetical enzymatic steps different from known mammalian pathways, but the molecular background is rather unclear. Here, we identified and characterized for the first time two novel enzymes, D-hydroxyproline dehydrogenase and Δ(1)-pyrroline-4-hydroxy-2-carboxylate (Pyr4H2C) deaminase, involved in this hypothetical pathway. These genes were clustered together with genes encoding other catalytic enzymes on the bacterial genomes. D-hydroxyproline dehydrogenases from P. putida and P. aeruginosa were completely different from known bacterial proline dehydrogenases and showed similar high specificity for substrate (D-hydroxyproline) and some artificial electron acceptor(s). On the other hand, the former is a homomeric enzyme only containing FAD as a prosthetic group, whereas the latter is a novel heterododecameric structure consisting of three different subunits (α(4)β(4)γ(4)), and two FADs, FMN, and [2Fe-2S] iron-sulfur cluster were contained in αβγ of the heterotrimeric unit. These results suggested that the L-hydroxyproline pathway clearly evolved convergently in P. putida and P. aeruginosa. Pyr4H2C deaminase is a unique member of the dihydrodipicolinate synthase/N-acetylneuraminate lyase protein family, and its activity was competitively inhibited by pyruvate, a common substrate for other dihydrodipicolinate synthase/N-acetylneuraminate lyase proteins. Furthermore, disruption of Pyr4H2C deaminase genes led to loss of growth on L-hydroxyproline (as well as D-hydroxyproline) but not L- and D-proline, indicating that this pathway is related only to L-hydroxyproline degradation, which is not linked to proline metabolism.
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Affiliation(s)
- Seiya Watanabe
- Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan.
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Sakuraba H, Satomura T, Kawakami R, Kim K, Hara Y, Yoneda K, Ohshima T. Crystal structure of novel dye-linked L-proline dehydrogenase from hyperthermophilic archaeon Aeropyrum pernix. J Biol Chem 2012; 287:20070-80. [PMID: 22511758 DOI: 10.1074/jbc.m111.319038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two types of dye-linked L-proline dehydrogenase (PDH1, α4β4-type hetero-octamer, and PDH2, αβγδ-type heterotetramer) have been identified so far in hyperthermophilic archaea. Here, we report the crystal structure of a third type of L-proline dehydrogenase, found in the aerobic hyperthermophilic archaeon Aeropyrum pernix, whose structure (homodimer) is much simpler than those of previously studied L-proline dehydrogenases. The structure was determined at a resolution of 1.92 Å. The asymmetric unit contained one subunit, and a crystallographic 2-fold axis generated the functional dimer. The overall fold of the subunit showed similarity to that of the PDH1 β-subunit, which is responsible for catalyzing L-proline dehydrogenation. However, the situation at the subunit-subunit interface of the A. pernix enzyme was totally different from that in PDH1. The presence of additional surface elements in the A. pernix enzyme contributes to a unique dimer association. Moreover, the C-terminal Leu(428), which is provided by a tail extending from the FAD-binding domain, shielded the active site, and an L-proline molecule was entrapped within the active site cavity. The K(m) value of a Leu(428) deletion mutant for L-proline was about 800 times larger than the K(m) value of the wild-type enzyme, although the k(cat) values did not differ much between the two enzymes. This suggests the C-terminal Leu(428) is not directly involved in catalysis, but it is essential for maintaining a high affinity for the substrate. This is the first description of an LPDH structure with L-proline bound, and it provides new insight into the substrate binding of LPDH.
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Affiliation(s)
- Haruhiko Sakuraba
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
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Shahbaz Mohammadi H, Omidinia E. Proline dehydrogenase from Pseudomonas fluorescens: Gene cloning, purification, characterization and homology modeling. APPL BIOCHEM MICRO+ 2012. [DOI: 10.1134/s0003683812020081] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Kawakami R, Satomura T, Sakuraba H, Ohshima T. l-Proline dehydrogenases in hyperthermophilic archaea: distribution, function, structure, and application. Appl Microbiol Biotechnol 2011; 93:83-93. [DOI: 10.1007/s00253-011-3682-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/11/2011] [Accepted: 10/27/2011] [Indexed: 10/15/2022]
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Shibahara T, Satomura T, Kawakami R, Ohshima T, Sakuraba H. Crystallization and preliminary X-ray analysis of a dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1425-7. [PMID: 22102248 DOI: 10.1107/s1744309111036098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 09/05/2011] [Indexed: 11/11/2022]
Abstract
A dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the hanging-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 63.4, b = 119.4, c = 70.2 Å, β = 112.0°, and diffracted to 2.0 Å resolution on the BL26B1 beamline at SPring-8. The overall R(merge) was 4.5% and the completeness was 99.8%.
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Affiliation(s)
- Takenori Shibahara
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Kita-gun, Kagawa 761-0795, Japan
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Satomura T, Sakuraba H, Hara Y, Ohshima T. Crystallization and preliminary X-ray analysis of a novel dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1508-10. [PMID: 21045308 DOI: 10.1107/s1744309110036808] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 09/14/2010] [Indexed: 11/10/2022]
Abstract
A novel dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the sitting-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the tetragonal space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2, with unit-cell parameters a = b = 61.1, c = 276.3 Å, and diffracted to 2.87 Å resolution using a Cu Kα rotating-anode generator with an R-AXIS VII detector. The asymmetric unit contained one protein molecule, giving a crystal volume per enzyme mass (V(M)) of 2.75 Å(3) Da(-1) and a solvent content of 55.3%.
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Affiliation(s)
- Takenori Satomura
- Department of Materials Science, Yonago National College of Technology, 4448 Hikona-cho, Yonago, Tottori 683-8506, Japan
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Satomura T, Zhang XD, Hara Y, Doi K, Sakuraba H, Ohshima T. Characterization of a novel dye-linked L-proline dehydrogenase from an aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis. Appl Microbiol Biotechnol 2010; 89:1075-82. [PMID: 20936278 DOI: 10.1007/s00253-010-2914-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 09/07/2010] [Accepted: 09/09/2010] [Indexed: 11/28/2022]
Abstract
The activity of a dye-linked L-proline dehydrogenase (dye-L: -proDH) was found in the crude extract of an aerobic hyperthermophilic archaeon, Pyrobaculum calidifontis JCM 11548, and was purified 163-fold through four sequential chromatography steps. The enzyme has a molecular mass of about 108 kDa and is a homodimer with a subunit molecular mass of about 46 kDa. The enzyme retained more than 90% of its activity after incubation at 100 °C for 120 min (pH 7.5) or after incubation at pHs 4.5-9.0 for 30 min at 50 °C. The enzyme catalyzed L-proline dehydrogenation to Δ(1)-pyroline-5-carboxylate using 2,6-dichloroindophenol (DCIP) as the electron acceptor and the Michaelis constants for L-proline and DCIP were 1.67 and 0.026 mM, respectively. The prosthetic group on the enzyme was identified as flavin adenine dinucleotide by high-performance liquid chromatography. The subunit N-terminal amino acid sequence was MYDYVVVGAG. Using that sequence and previously reported genome information, the gene encoding the enzyme (Pcal_1655) was identified. The gene was then cloned and expressed in Escherichia coli and found to encode a polypeptide of 415 amino acids with a calculated molecular weight of 46,259. The dye-L-proDH gene cluster in P. calidifontis inherently differs from those in the other hyperthermophiles reported so far.
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Affiliation(s)
- Takenori Satomura
- Department of Materials Science, Yonago National College of Technology, 4448 Hikona-cho, Yonago, Tottori 683-8506, Japan
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D-Amino acid dehydrogenase from Helicobacter pylori NCTC 11637. Amino Acids 2009; 38:247-55. [PMID: 19212808 DOI: 10.1007/s00726-009-0240-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 01/13/2009] [Indexed: 10/21/2022]
Abstract
Helicobacter pylori is a microaerophilic bacterium, associated with gastric inflammation and peptic ulcers. D-Amino acid dehydrogenase is a flavoenzyme that digests free neutral D-amino acids yielding corresponding 2-oxo acids and hydrogen. We sequenced the H. pylori NCTC 11637 D-amino acid dehydrogenase gene, dadA. The primary structure deduced from the gene showed low similarity with other bacterial D-amino acid dehydrogenases. We purified the enzyme to homogeneity from recombinant Escherichia coli cells by cloning dadA. The recombinant protein, DadA, with 44 kDa molecular mass, possessed FAD as cofactor, and showed the highest activity to D-proline. The enzyme mediated electron transport from D-proline to coenzyme Q(1), thus distinguishing it from D-amino acid oxidase. The apparent K(m) and V(max) values were 40.2 mM and 25.0 micromol min(-1) mg(-1), respectively, for dehydrogenation of D-proline, and were 8.2 microM and 12.3 micromol min(-1) mg(-1), respectively, for reduction of Q(1). The respective pH and temperature optima were 8.0 and 37 degrees C. Enzyme activity was inhibited markedly by benzoate, and moderately by SH reagents. DadA showed more similarity with mammalian D-amino acid oxidase than other bacterial D-amino acid dehydrogenases in some enzymatic characteristics. Electron transport from D-proline to a c-type cytochrome was suggested spectrophotometrically.
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TANI Y, ITOYAMA Y, NISHI K, WADA C, SHODA Y, SATOMURA T, SAKURABA H, OHSHIMA T, HAYASHI Y, YABUTANI T, MOTONAKA J. An Amperometric D-Amino Acid Biosensor Prepared with a Thermostable D-Proline Dehydrogenase and a Carbon Nanotube-Ionic Liquid Gel. ANAL SCI 2009; 25:919-23. [DOI: 10.2116/analsci.25.919] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yuji TANI
- Department of Chemical Science and Technology, Institute of Science and Tecnhology, The University of Tokushima
| | - Yukiko ITOYAMA
- Department of Chemical Science and Technology, Institute of Science and Tecnhology, The University of Tokushima
| | - Kenichi NISHI
- Department of Chemical Science and Technology, Institute of Science and Tecnhology, The University of Tokushima
| | - Chikahiro WADA
- Department of Chemical Science and Technology, Institute of Science and Tecnhology, The University of Tokushima
| | - Yoshio SHODA
- Department of Chemical Science and Technology, Institute of Science and Tecnhology, The University of Tokushima
| | - Takenori SATOMURA
- Department of Materials Science, Yonago National College of Technology
| | - Haruhiko SAKURABA
- Department of Applied Biological Science, Faculty of Agriculture & Graduate School of Agriculture, Kagawa University
| | - Toshihisa OHSHIMA
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University
| | - Yukako HAYASHI
- Department of Chemical Science and Technology, Institute of Science and Tecnhology, The University of Tokushima
| | - Tomoki YABUTANI
- Department of Chemical Science and Technology, Institute of Science and Tecnhology, The University of Tokushima
| | - Junko MOTONAKA
- Department of Chemical Science and Technology, Institute of Science and Tecnhology, The University of Tokushima
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Satomura T, Kawakami R, Sakuraba H, Ohshima T. A novel flavin adenine dinucleotide (FAD) containing d-lactate dehydrogenase from the thermoacidophilic crenarchaeota Sulfolobus tokodaii strain 7: purification, characterization and expression in Escherichia coli. J Biosci Bioeng 2008; 106:16-21. [PMID: 18691525 DOI: 10.1263/jbb.106.16] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Accepted: 03/27/2008] [Indexed: 11/17/2022]
Abstract
Dye-linked D-lactate dehydrogenase activity was found in the crude extract of a continental thermoacidophilic crenarchaeota, Sulfolobus tokodaii strain 7, and was purified 375-fold through four sequential chromatography steps. With a molecular mass of about 93 kDa, this enzyme was a homodimer comprised of identical subunits with molecular masses of about 48 kDa. The enzyme retained its full activity after incubation at 80 degrees C for 10 min and after incubation at pHs ranging from 6.5 to 10.0 for 30 min at 50 degrees C. The preferred substrate for this enzyme was D-lactate, with 2,6-dichloroindophenol serving as the electron acceptor. Using high-performance liquid chromatography (HPLC), the enzyme's prosthetic group was determined to be flavin adenine dinucleotide (FAD). Its N-terminal amino acid sequence was MLEGIEYSQGEEREDFVGFKIKPKI. Using that sequence and previously reported genome information, the gene encoding the enzyme (ST0649) was identified. It was subsequently cloned and expressed in Escherichia coli and found to encode a polypeptide of 440 amino acids with a calculated molecular weight of 49,715. The amino acid sequence of this dye-linked D-lactate dehydrogenase showed higher homology (39% identity) with that of a glycolate oxidase subunit homologue from Archaeoglobus fulgidus, but less similarity (32% identity) to D-lactate dehydrogenase from A. fulgidus. Taken together, our findings indicate that the dye-linked D-lactate dehydrogenase from S. tokodaii is a novel type of FAD containing D-lactate dehydrogenase.
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Affiliation(s)
- Takenori Satomura
- Department of Materials Science, Yonago National College of Technology, 4448 Hikona-cho, Yonago, Tottori 683-8506, Japan
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Development of a d-amino acids electrochemical sensor based on immobilization of thermostable d-Proline dehydrogenase within agar gel membrane. Anal Chim Acta 2008; 619:215-20. [DOI: 10.1016/j.aca.2008.04.063] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 04/26/2008] [Accepted: 04/29/2008] [Indexed: 11/19/2022]
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Vedha-Peters K, Gunawardana M, Rozzell JD, Novick SJ. Creation of a broad-range and highly stereoselective D-amino acid dehydrogenase for the one-step synthesis of D-amino acids. J Am Chem Soc 2007; 128:10923-9. [PMID: 16910688 PMCID: PMC2533268 DOI: 10.1021/ja0603960] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using both rational and random mutagenesis, we have created the first known broad substrate range, nicotinamide cofactor dependent, and highly stereoselective d-amino acid dehydrogenase. This new enzyme is capable of producing d-amino acids via the reductive amination of the corresponding 2-keto acid with ammonia. This biocatalyst was the result of three rounds of mutagenesis and screening performed on the enzyme meso-diaminopimelate d-dehydrogenase. The first round targeted the active site of the wild-type enzyme and produced mutants that were no longer strictly dependent on the native substrate. The second and third rounds produced mutants that had an increased substrate range including straight- and branched-aliphatic amino acids and aromatic amino acids. The very high selectivity toward the d-enantiomer (95 to >99% ee) was shown to be preserved even after the addition of the five mutations found in the three rounds of mutagenesis and screening. This new enzyme could complement and improve upon current methods for d-amino acid synthesis.
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Affiliation(s)
- Kavitha Vedha-Peters
- BioCatalytics, Inc., 129 North Hill Avenue, Suite 103, Pasadena, California 91106, USA
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27
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Monaghan PJ, Leys D, Scrutton NS. Mechanistic aspects and redox properties of hyperthermophilic L-proline dehydrogenase from Pyrococcus furiosus related to dimethylglycine dehydrogenase/oxidase. FEBS J 2007; 274:2070-87. [PMID: 17371548 DOI: 10.1111/j.1742-4658.2007.05750.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Two ORFs encoding a protein related to bacterial dimethylglycine oxidase were cloned from Pyrococcus furiosus DSM 3638. The protein was expressed in Escherichia coli, purified, and shown to be a flavoprotein amine dehydrogenase. The enzyme oxidizes the secondary amines L-proline, L-pipecolic acid and sarcosine, with optimal catalytic activity towards L-proline. The holoenzyme contains one FAD, FMN and ATP per alphabeta complex, is not reduced by sulfite, and reoxidizes slowly following reduction, which is typical of flavoprotein dehydrogenases. Isolation of the enzyme in a form containing only FAD cofactor allowed detailed pH dependence studies of the reaction with L-proline, for which a bell-shaped dependence (pK(a) values 7.0 +/- 0.2 and 7.6 +/- 0.2) for k(cat)/K(m) as a function of pH was observed. The pH dependence of k(cat) is sigmoidal, described by a single macroscopic pK(a) of 7.7 +/- 0.1, tentatively attributed to ionization of L-proline in the Michaelis complex. The preliminary crystal structure of the enzyme revealed active site residues conserved in related amine dehydrogenases and potentially implicated in catalysis. Studies with H225A, H225Q and Y251F mutants ruled out participation of these residues in a carbanion-type mechanism. The midpoint potential of enzyme-bound FAD has a linear temperature dependence (- 3.1 +/- 0.05 mV x C degrees (-1)), and extrapolation to physiologic growth temperature for P. furiosus (100 degrees C) yields a value of - 407 +/- 5 mV for the two-electron reduction of enzyme-bound FAD. These studies provide the first detailed account of the kinetic/redox properties of this hyperthermophilic L-proline dehydrogenase. Implications for its mechanism of action are discussed.
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Affiliation(s)
- Phillip J Monaghan
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, UK
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Kawakami R, Sakuraba H, Tsuge H, Goda S, Katunuma N, Ohshima T. A second novel dye-linked L-proline dehydrogenase complex is present in the hyperthermophilic archaeon Pyrococcus horikoshii OT-3. FEBS J 2005; 272:4044-54. [PMID: 16098188 DOI: 10.1111/j.1742-4658.2005.04810.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two distinguishable activity bands for dye-linked l-proline dehydrogenase (PDH1 and PDH2) were detected when crude extract of the hyperthermophilic archaeon Pyrococcus horikoshii OT-3 was run on a polyacrylamide gel. After purification, PDH1 was found to be composed of two different subunits with molecular masses of 56 and 43 kDa, whereas PDH2 was composed of four different subunits with molecular masses of 52, 46, 20 and 8 kDa. The native molecular masses of PDH1 and PDH2 were 440 and 101 kDa, respectively, indicating that PDH1 has an alpha4beta4 structure, while PDH2 has an alphabetagammadelta structure. PDH2 was found to be similar to the dye-linked l-proline dehydrogenase complex from Thermococcus profundus, but PDH1 is a different type of enzyme. After production of the enzyme in Escherichia coli, high-performance liquid chromatography showed the PDH1 complex to contain the flavins FMN and FAD as well as ATP. Gene expression and biochemical analyses of each subunit revealed that the beta subunit bound FAD and exhibited proline dehydrogenase activity, while the alpha subunit bound ATP, but unlike the corresponding subunit in the T. profundus enzyme, it exhibited neither proline dehydrogenase nor NADH dehydrogenase activity. FMN was not bound to either subunit, suggesting it is situated at the interface between the alpha and beta subunits. A comparison of the amino-acid sequences showed that the ADP-binding motif in the alpha subunit of PDH1 clearly differs from that in the alpha subunit of PDH2. It thus appears that a second novel dye-linked l-proline dehydrogenase complex is produced in P. horikoshii.
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Affiliation(s)
- Ryushi Kawakami
- Department of Biological Science and Technology, Faculty of Engineering, The University of Tokushima, Japan
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Tsuge H, Kawakami R, Sakuraba H, Ago H, Miyano M, Aki K, Katunuma N, Ohshima T. Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii. J Biol Chem 2005; 280:31045-9. [PMID: 16027125 DOI: 10.1074/jbc.c500234200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Two novel types of dye-linked L-proline dehydrogenase complex (PDH1 and PDH2) were found in a hyperthermophilic archaeon, Pyrococcus horikoshii OT3. Here we report the first crystal structure of PDH1, which is a heterooctameric complex (alphabeta)4 containing three different cofactors: FAD, FMN, and ATP. The structure was determined by x-ray crystallography to a resolution of 2.86 angstroms. The structure of the beta subunit, which is an L-proline dehydrogenase catalytic component containing FAD as a cofactor, was similar to that of monomeric sarcosine oxidase. On the other hand, the alpha subunit possessed a unique structure composed of a classical dinucleotide fold domain with ATP, a central domain, an N-terminal domain, and a Cys-clustered domain. Serving as a third cofactor, FMN was located at the interface between the alpha and beta subunits in a novel configuration. The observed structure suggests that FAD and FMN are incorporated into an electron transfer system, with electrons passing from the former to the latter. The function of ATP is unknown, but it may play a regulatory role. Although the structure of the alpha subunit differs from that of the beta subunit, except for the presence of an analogous dinucleotide domain with a different cofactor, the structural characteristics of PDH1 suggest that each represents a divergent enzyme that arose from a common ancestral flavoenzyme and that they eventually formed a complex to gain a new function. The structural characteristics described here reveal the PDH1 complex to be a unique diflavin dehydrogenase containing a novel electron transfer system.
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Affiliation(s)
- Hideaki Tsuge
- Institute for Health Sciences, Tokushima Bunri University, 180 Nishihama-bouji, Yamashiro-cho, Tokushima 770-8514, Japan.
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Yoneda K, Sakuraba H, Tsuge H, Katunuma N, Kuramitsu S, Kawabata T, Ohshima T. The first crystal structure of an archaeal helical repeat protein. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:636-9. [PMID: 16511116 PMCID: PMC1952456 DOI: 10.1107/s1744309105019263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2005] [Accepted: 06/17/2005] [Indexed: 11/10/2022]
Abstract
The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 A resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten alpha-helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein.
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Affiliation(s)
- Kazunari Yoneda
- Department of Biological Science and Technology, Faculty of Engineering, University of Tokushima, Tokushima 770-8506, Japan
| | - Haruhiko Sakuraba
- Department of Biological Science and Technology, Faculty of Engineering, University of Tokushima, Tokushima 770-8506, Japan
| | - Hideaki Tsuge
- Institute for Health Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Nobuhiko Katunuma
- Institute for Health Sciences, Tokushima Bunri University, Tokushima 770-8514, Japan
| | - Seiki Kuramitsu
- Department of Biology, Graduate School of Science, Osaka University, Japan
| | - Takeshi Kawabata
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
| | - Toshihisa Ohshima
- Department of Biological Science and Technology, Faculty of Engineering, University of Tokushima, Tokushima 770-8506, Japan
- Correspondence e-mail:
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Nagata K, Nagata Y, Sato T, Fujino MA, Nakajima K, Tamura T. L-Serine, D- and L-proline and alanine as respiratory substrates of Helicobacter pylori: correlation between in vitro and in vivo amino acid levels. MICROBIOLOGY (READING, ENGLAND) 2003; 149:2023-2030. [PMID: 12904542 DOI: 10.1099/mic.0.26203-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Helicobacter pylori whole cells showed high rates of oxygen uptake with L-serine and L-proline as respiratory substrates, and somewhat lower rates with D-alanine and D-proline. These respiratory activities were inhibited by rotenone and antimycin A at low concentrations. Since pyruvate was produced from L-serine and D- and L-alanine in whole cells, the respiratory activities with these amino acids as substrates occurred via pyruvate. Whole cells showed 2,6-dichlorophenolindophenol (DCIP)-reducing activities with D- and L-proline and D-alanine as substrates, suggesting that hydrogen removed from these amino acids also participated in oxygen uptake by the whole cells. High amounts of L-proline, D- and L-alanine, and L-serine were present in H. pylori cells, and these amino acids also predominated in samples of human gastric juice. H. pylori seems to utilize D- and L-proline, D-alanine and L-serine as important energy sources in its habitat of the mucous layer of the stomach.
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Affiliation(s)
- Kumiko Nagata
- Department of Bacteriology, Hyogo College of Medicine, 1-1 Mukogawa, Nishinomiya, Hyogo 663-8501, Japan
| | - Yoko Nagata
- Department of Materials and Applied Chemistry, College of Science and Technology, Nihon University, 1-8-14 Kanda, Surugadai, Chiyoda-ku, Tokyo 101-8308, Japan
| | - Tadashi Sato
- First Department of Medicine, Yamanashi Medical University, Kofu, Yamanashi, 409-3898, Japan
| | - Masayuki A Fujino
- First Department of Medicine, Yamanashi Medical University, Kofu, Yamanashi, 409-3898, Japan
| | - Kazuhiko Nakajima
- Department of Bacteriology, Hyogo College of Medicine, 1-1 Mukogawa, Nishinomiya, Hyogo 663-8501, Japan
| | - Toshihide Tamura
- Department of Bacteriology, Hyogo College of Medicine, 1-1 Mukogawa, Nishinomiya, Hyogo 663-8501, Japan
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