1
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Bi Y, Song A, Pan L, Miao J, Zhou Y, Li Z. Interference mechanism of benzo[a]pyrene exposure on the taste substance metabolisms in Ruditapes philippinarum. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:12019-12035. [PMID: 38228951 DOI: 10.1007/s11356-024-31906-0] [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: 03/05/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024]
Abstract
Aquatic animals are popular for their unique umami and high-quality protein. However, under the realistic background of increasing marine pollution, whether it affects the aquatic animal tastes, and what the interference mechanism is still remains unknown. Benzo[a]pyrene (B[a]P) is a typical Polycyclic aromatic hydrocarbons (PAHs) with high toxicity. In this study, we investigated the effects of B[a]P (0, 0.8, 4 and 20 μg/L) on the content and taste evaluation of Ruditapes philippinarum taste substances, and clarified the interference mechanism of B[a]P on taste substance metabolisms with transcriptome analysis. The results demonstrated that B[a]P significantly altered the contents and taste activity values (TAVs) of free amino acids (FAAs), 5'-nucleotides, organic acids, flavor peptides, organic bases, sugars and inorganic ions, as well as the gene expressions within their synthesis and decomposition, indicating that B[a]P affected these taste substance contents by interfering with their metabolisms, thereby changing the clam tastes (decreases of umami and sweetness, and increase of bitter taste). This study provided scientific basis for quality assurance of bivalve cultivation and control of marine pollution.
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Affiliation(s)
- Yaqi Bi
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Aimin Song
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China.
| | - Jingjing Miao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Yueyao Zhou
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Zeyuan Li
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
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2
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Li C, Wu G, Fan X, Guo S, Qin Y, Hu Y, Ruan L. Directed evolution of glyphosate oxidase and a chemiluminescence system for glyphosate detection: A comprehensive practical laboratory experiment on biotechnology. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:302-311. [PMID: 36971149 DOI: 10.1002/bmb.21721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 01/03/2023] [Accepted: 02/23/2023] [Indexed: 05/15/2023]
Abstract
This article describes a comprehensive practical laboratory method for developing an enzyme to more easily measure glyphosate levels in solution. Through this article, undergraduate students of biology majors can conduct research experiments in critical fields by utilizing various techniques, such as chemiluminescence (CL) biosensors with engineered enzymes and are guided in molecular biology laboratories. A glyphosate oxidase mutant library was constructed by DNA shuffling, and a glyphosate oxidase variant with increased glyphosate degradation activity was selected by using a high-throughput screening assay. Following protein overexpression in Escherichia coli (DE3) and purification by affinity chromatography, the glyphosate oxidase variant protein combined with luminol-H2 O2 reaction was constructed as a new CL biosensor for detecting glyphosate in soils.
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Affiliation(s)
- Chanjuan Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Wuhan Institute of Design and Sciences, Wuhan, China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xuezhu Fan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Siqi Guo
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Qin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yonggang Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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Functional Characterization and Structural Modeling of a Novel Glycine Oxidase from Variovorax paradoxus Iso1. Appl Environ Microbiol 2022; 88:e0107722. [PMID: 36377957 PMCID: PMC9746326 DOI: 10.1128/aem.01077-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The N-acyl-d-amino acid amidohydrolase (N-d-AAase) of Variovorax paradoxus Iso1 can enantioselectively catalyze the zinc-assisted deacetylation of N-acyl-d-amino acids to yield consistent d-amino acids. A putative FAD-binding glycine/d-amino acid oxidase was located immediately upstream of the N-d-AAase gene. The gene encoding this protein was cloned into Escherichia coli BL21 (DE3)pLysS and overexpressed at 25°C for 6 h with 0.5 mM isopropyl β-d-1-thiogalactopyranoside induction. After purification, the tag-free recombinant protein was obtained. The enzyme could metabolize glycine, sarcosine, and d-alanine, but not l-amino acids or bulky d-amino acids. Protein modeling further supported these results, demonstrating that glycine, sarcosine, and d-alanine could fit into the pocket of the enzyme's activation site, while l-alanine and d-threonine were out of position. Therefore, this protein was proposed as a glycine oxidase, and we designated it VpGO. Interestingly, VpGO showed low sequence similarity to other well-characterized glycine oxidases. We found that VpGO and N-d-AAase were expressed on the same mRNA and could be transcriptionally induced by various N-acetyl-d-amino acids. Western blotting and zymography showed that both proteins had similar expression patterns in response to different types of inducers. Thus, we have identified a novel glycine oxidase that is co-regulated with N-d-AAase in an operon, and metabolizes N-acyl-d-amino acids in the metabolically versatile V. paradoxus Iso1. IMPORTANCE The Gram-negative bacterium Variovorax paradoxus has numerous metabolic capabilities, including the association with important catabolic processes and the promotion of plant growth. We had previously identified and characterized an N-acyl-d-amino-acid amidohydrolase (N-d-AAase) gene from the strain of V. paradoxus Iso1. The aim of this study was to isolate and characterize (both in vitro and in vivo) another potential gene found in the promoter region of this N-d-AAase gene. The protein was identified as a glycine oxidase, and the gene existed in an operon with N-d-AAase. The structural basis for its FAD-binding potential and substrate stereo-specificity were also elucidated. This study first reported a novel glycine oxidase from V. paradoxus. We believe that our study makes a significant contribution to the literature, because this enzyme has great potential for use as an industrial catalysis, as a biosensor, and in agricultural biotechnology.
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Robertson CF, Meyers PR. Oxalate utilisation is widespread in the actinobacterial genus Kribbella. Syst Appl Microbiol 2022; 45:126373. [DOI: 10.1016/j.syapm.2022.126373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 10/31/2022]
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5
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Iraninasab S, Sharifian S, Homaei A, Homaee MB, Sharma T, Nadda AK, Kennedy JF, Bilal M, Iqbal HMN. Emerging trends in environmental and industrial applications of marine carbonic anhydrase: a review. Bioprocess Biosyst Eng 2022; 45:431-451. [PMID: 34821989 DOI: 10.1007/s00449-021-02667-8] [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: 09/27/2021] [Accepted: 11/10/2021] [Indexed: 02/08/2023]
Abstract
Biocatalytic conversion of greenhouse gases such as carbon dioxide into commercial products is one of the promising key approaches to solve the problem of climate change. Microbial enzymes, including carbonic anhydrase, NAD-dependent formate dehydrogenase, ribulose bisphosphate carboxylase, and methane monooxygenase, have been exploited to convert atmospheric gases into industrial products. Carbonic anhydrases are Zn2+-dependent metalloenzymes that catalyze the reversible conversion of CO2 into bicarbonate. They are widespread in bacteria, algae, plants, and higher organisms. In higher organisms, they regulate the physiological pH and contribute to CO2 transport in the blood. In plants, algae, and photosynthetic bacteria carbonic anhydrases are involved in photosynthesis. Converting CO2 into bicarbonate by carbonic anhydrases can solidify gaseous CO2, thereby reducing global warming due to the burning of fossil fuels. This review discusses the three-dimensional structures of carbonic anhydrases, their physiological role in marine life, their catalytic mechanism, the types of inhibitors, and their medicine and industry applications.
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Affiliation(s)
- Sudabeh Iraninasab
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, P.O. Box 3995, Bandar Abbas, Iran
| | - Sana Sharifian
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, P.O. Box 3995, Bandar Abbas, Iran
| | - Ahmad Homaei
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, P.O. Box 3995, Bandar Abbas, Iran.
| | | | - Tanvi Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173 234, India
| | - Ashok Kumar Nadda
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, 173 234, India
| | - John F Kennedy
- Chembiotech Laboratories, Advanced Science and Technology Institute, The Kyrewood Centre, Tenbury Wells, Worcs, WR15 8FF, UK
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, 64849, Monterrey, Mexico
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Cappelli J, Khacho P, Wang B, Sokolovski A, Bakkar W, Raymond S, Ahlskog N, Pitney J, Wu J, Chudalayandi P, Wong AYC, Bergeron R. Glycine-induced NMDA receptor internalization provides neuroprotection and preserves vasculature following ischemic stroke. iScience 2022; 25:103539. [PMID: 34977503 PMCID: PMC8689229 DOI: 10.1016/j.isci.2021.103539] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 11/26/2022] Open
Abstract
Ischemic stroke is the second leading cause of death worldwide. Following an ischemic event, neuronal death is triggered by uncontrolled glutamate release leading to overactivation of glutamate sensitive N-methyl-d-aspartate receptor (NMDAR). For gating, NMDARs require not only the binding of glutamate, but also of glycine or a glycine-like compound as a co-agonist. Low glycine doses enhance NMDAR function, whereas high doses trigger glycine-induced NMDAR internalization (GINI) in vitro. Here, we report that following an ischemic event, in vivo, GINI also occurs and provides neuroprotection in the presence of a GlyT1 antagonist (GlyT1-A). Mice pretreated with a GlyT1-A, which increases synaptic glycine levels, exhibited smaller stroke volume, reduced cell death, and minimized behavioral deficits following stroke induction by either photothrombosis or endothelin-1. Moreover, we show evidence that in ischemic conditions, GlyT1-As preserve the vasculature in the peri-infarct area. Therefore, GlyT1 could be a new target for the treatment of ischemic stroke. GINI is a dynamic phenomenon which dampens NMDAR-mediated excitotoxicity during stroke GlyT1-antagonists (GlyT1-As) trigger GINI during stroke in vivo GlyT1-As mitigate post-stroke behavioral deficits and preserve peri-infarct vasculature GlyT1 could be a novel and viable therapeutic target for ischemic stroke
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Affiliation(s)
- Julia Cappelli
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Pamela Khacho
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Boyang Wang
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Alexandra Sokolovski
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Wafae Bakkar
- Ottawa Hospital Research Institute, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Sophie Raymond
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Nina Ahlskog
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Julian Pitney
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Junzheng Wu
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Prakash Chudalayandi
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Adrian Y C Wong
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
| | - Richard Bergeron
- Cellular and Molecular Medicine Department, University of Ottawa, 451 Smyth Road, Roger Guindon Building, Room 3501N, Ottawa, ON K1H 8M5, Canada
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7
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Engineering the Reductive Glycine Pathway: A Promising Synthetic Metabolism Approach for C1-Assimilation. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022; 180:299-350. [DOI: 10.1007/10_2021_181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Moussa S, Rosini E, Chitsaz D, Pollegioni L, Kennedy TE, Mauzeroll J. High-Throughput Strategy for Glycine Oxidase Biosensor Development Reveals Glycine Release from Cultured Cells. Anal Chem 2021; 93:16504-16511. [PMID: 34843206 DOI: 10.1021/acs.analchem.1c03620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycine is an important biomarker in clinical analysis due to its involvement in multiple physiological processes. As such, the need for low-cost analytical tools for glycine detection is growing. As a neurotransmitter, glycine is involved in inhibitory and excitatory neurochemical transmission in the central nervous system. In this work, we present a 10 μM Pt-based electrochemical enzymatic biosensor based on the flavoenzyme glycine oxidase (GO) for localized real-time measurements of glycine. Among GO variants at position 244, the H244K variant with increased glycine turnover was selected to develop a functional biosensor. This biosensor relies on amperometric readouts and does not require additional redox mediators. The biosensor was characterized and applied for glycine detection from cells, mainly HEK 293 cells and primary rat astrocytes. We have identified an enzyme, GO H244K, with increased glycine turnover using mutagenesis but which can be developed into a functional biosensor. Noteworthy, a glycine release of 395.7 ± 123 μM from primary astrocytes was measured, which is ∼fivefold higher than glycine release from HEK 293 cells (75.4 ± 3.91 μM) using the GO H244K biosensor.
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Affiliation(s)
- Siba Moussa
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi deII'Insubria, via J. H. Dunant 3, Varese 21100, Italy
| | - Daryan Chitsaz
- Integrated Program in Neuroscience, McGill University, 1033 Pine Ave. W., Montreal, Quebec H3A 1A1, Canada
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi deII'Insubria, via J. H. Dunant 3, Varese 21100, Italy
| | - Timothy E Kennedy
- McGill Program in Neuroengineering, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec H3A 2B4, Canada
| | - Janine Mauzeroll
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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Rossi F, Carles L, Donnadieu F, Batisson I, Artigas J. Glyphosate-degrading behavior of five bacterial strains isolated from stream biofilms. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126651. [PMID: 34329075 DOI: 10.1016/j.jhazmat.2021.126651] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 07/02/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
The present study investigates the individual degrading behavior of bacterial strains isolated from glyphosate-degrading stream biofilms. In this aim, biofilms were subjected to enrichment experiments using glyphosate or its metabolite AMPA (aminomethyl phosphonic acid) as the sole phosphorus source. Five bacterial strains were isolated and taxonomically affiliated to Ensifer sp. CNII15, Acidovorax sp. CNI26, Agrobacterium tumefaciens CNI28, Novosphingobium sp. CNI35 and Ochrobactrum pituitosum CNI52. All strains were capable of completely dissipating glyphosate after 125-400 h and AMPA after 30-120 h, except for Ensifer sp. CNII15 that was not able to dissipate glyphosate but entirely dissipated AMPA after 200 h. AMPA dissipation was overall faster than glyphosate dissipation. The five strains degraded AMPA completely since formaldehyde and/or glycine accumulation was observed. During glyphosate degradation, the strain CNI26 used the C-P lyase degradation pathway since sarcosine was quantitatively produced, and C-P lyase gene expression was enhanced 30× compared to the control treatment. However, strains CNI28, CNI35 and CNI52 accumulated both formaldehyde and glycine after glyphosate transformation suggesting that both C-P lyase and/or glyphosate oxidase degradation pathways took place. Our study shows different and complementary glyphosate degradation pathways for bacteria co-existing in stream biofilms.
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Affiliation(s)
- Florent Rossi
- Université Clermont-Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Louis Carles
- Department of Environmental Toxicology (Utox), Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Florence Donnadieu
- Université Clermont-Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Isabelle Batisson
- Université Clermont-Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Joan Artigas
- Université Clermont-Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France.
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Brito LF, Irla M, Nærdal I, Le SB, Delépine B, Heux S, Brautaset T. Evaluation of Heterologous Biosynthetic Pathways for Methanol-Based 5-Aminovalerate Production by Thermophilic Bacillus methanolicus. Front Bioeng Biotechnol 2021; 9:686319. [PMID: 34262896 PMCID: PMC8274714 DOI: 10.3389/fbioe.2021.686319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
The use of methanol as carbon source for biotechnological processes has recently attracted great interest due to its relatively low price, high abundance, high purity, and the fact that it is a non-food raw material. In this study, methanol-based production of 5-aminovalerate (5AVA) was established using recombinant Bacillus methanolicus strains. 5AVA is a building block of polyamides and a candidate to become the C5 platform chemical for the production of, among others, δ-valerolactam, 5-hydroxy-valerate, glutarate, and 1,5-pentanediol. In this study, we test five different 5AVA biosynthesis pathways, whereof two directly convert L-lysine to 5AVA and three use cadaverine as an intermediate. The conversion of L-lysine to 5AVA employs lysine 2-monooxygenase (DavB) and 5-aminovaleramidase (DavA), encoded by the well-known Pseudomonas putida cluster davBA, among others, or lysine α-oxidase (RaiP) in the presence of hydrogen peroxide. Cadaverine is converted either to γ-glutamine-cadaverine by glutamine synthetase (SpuI) or to 5-aminopentanal through activity of putrescine oxidase (Puo) or putrescine transaminase (PatA). Our efforts resulted in proof-of-concept 5AVA production from methanol at 50°C, enabled by two pathways out of the five tested with the highest titer of 0.02 g l-1. To our knowledge, this is the first report of 5AVA production from methanol in methylotrophic bacteria, and the recombinant strains and knowledge generated should represent a valuable basis for further improved 5AVA production from methanol.
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Affiliation(s)
- Luciana Fernandes Brito
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marta Irla
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ingemar Nærdal
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Simone Balzer Le
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Baudoin Delépine
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Stéphanie Heux
- Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology, Trondheim, Norway
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11
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Pollegioni L, Molla G, Sacchi S, Murtas G. Human D-aspartate Oxidase: A Key Player in D-aspartate Metabolism. Front Mol Biosci 2021; 8:689719. [PMID: 34250021 PMCID: PMC8260693 DOI: 10.3389/fmolb.2021.689719] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/09/2021] [Indexed: 11/15/2022] Open
Abstract
In recent years, the D-enantiomers of amino acids have been recognized as natural molecules present in all kingdoms, playing a variety of biological roles. In humans, d-serine and d-aspartate attracted attention for their presence in the central nervous system. Here, we focus on d-aspartate, which is involved in glutamatergic neurotransmission and the synthesis of various hormones. The biosynthesis of d-aspartate is still obscure, while its degradation is due to the peroxisomal flavin adenine dinucleotide (FAD)-containing enzyme d-aspartate oxidase. d-Aspartate emergence is strictly controlled: levels decrease in brain within the first days of life while increasing in endocrine glands postnatally and through adulthood. The human d-aspartate oxidase (hDASPO) belongs to the d-amino acid oxidase-like family: its tertiary structure closely resembles that of human d-amino acid oxidase (hDAAO), the enzyme that degrades neutral and basic d-amino acids. The structure-function relationships of the physiological isoform of hDASPO (named hDASPO_341) and the regulation of gene expression and distribution and properties of the longer isoform hDASPO_369 have all been recently elucidated. Beyond the substrate preference, hDASPO and hDAAO also differ in kinetic efficiency, FAD-binding affinity, pH profile, and oligomeric state. Such differences suggest that evolution diverged to create two different ways to modulate d-aspartate and d-serine levels in the human brain. Current knowledge about hDASPO is shedding light on the molecular mechanisms underlying the modulation of d-aspartate levels in human tissues and is pushing novel, targeted therapeutic strategies. Now, it has been proposed that dysfunction in NMDA receptor-mediated neurotransmission is caused by disrupted d-aspartate metabolism in the nervous system during the onset of various disorders (such as schizophrenia): the design of suitable hDASPO inhibitors aimed at increasing d-aspartate levels thus represents a novel and useful form of therapy.
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Affiliation(s)
- Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Gianluca Molla
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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12
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He HY, Ryan KS. Glycine-derived nitronates bifurcate to O-methylation or denitrification in bacteria. Nat Chem 2021; 13:599-606. [PMID: 33782561 DOI: 10.1038/s41557-021-00656-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 02/08/2021] [Indexed: 02/01/2023]
Abstract
Natural products with rare functional groups are likely to be constructed by unique biosynthetic enzymes. One such rare functional group is the O-methyl nitronate, which can undergo [3 + 2] cycloaddition reactions with olefins in mild conditions. O-methyl nitronates are found in some natural products; however, how such O-methyl nitronates are assembled biosynthetically is unknown. Here we show that the assembly of the O-methyl nitronate in the natural product enteromycin carboxamide occurs via activation of glycine on a peptidyl carrier protein, followed by reaction with a diiron oxygenase to give a nitronate intermediate and then with a methyltransferase to give an O-methyl nitronate. Guided by the discovery of this pathway, we then identify related cryptic biosynthetic gene cassettes in other bacteria and show that these alternative gene cassettes can, instead, facilitate oxidative denitrification of glycine-derived nitronates. Altogether, our work reveals bifurcating pathways from a central glycine-derived nitronate intermediate in bacteria.
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Affiliation(s)
- Hai-Yan He
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Katherine S Ryan
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia, Canada.
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13
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Hertel R, Gibhardt J, Martienssen M, Kuhn R, Commichau FM. Molecular mechanisms underlying glyphosate resistance in bacteria. Environ Microbiol 2021; 23:2891-2905. [PMID: 33876549 DOI: 10.1111/1462-2920.15534] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 04/10/2021] [Accepted: 04/14/2021] [Indexed: 11/29/2022]
Abstract
Glyphosate is a nonselective herbicide that kills weeds and other plants competing with crops. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, thereby depleting the cell of EPSP serving as a precursor for biosynthesis of aromatic amino acids. Glyphosate is considered to be toxicologically safe for animals and humans. Therefore, it became the most-important herbicide in agriculture. However, its intensive application in agriculture is a serious environmental issue because it may negatively affect the biodiversity. A few years after the discovery of the mode of action of glyphosate, it has been observed that bacteria evolve glyphosate resistance by acquiring mutations in the EPSP synthase gene, rendering the encoded enzyme less sensitive to the herbicide. The identification of glyphosate-resistant EPSP synthase variants paved the way for engineering crops tolerating increased amounts of the herbicide. This review intends to summarize the molecular mechanisms underlying glyphosate resistance in bacteria. Bacteria can evolve glyphosate resistance by (i) reducing glyphosate sensitivity or elevating production of the EPSP synthase, by (ii) degrading or (iii) detoxifying glyphosate and by (iv) decreasing the uptake or increasing the export of the herbicide. The variety of glyphosate resistance mechanisms illustrates the adaptability of bacteria to anthropogenic substances due to genomic alterations.
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Affiliation(s)
- Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Johannes Gibhardt
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
| | - Marion Martienssen
- Institute of Environmental Technology, Chair of Biotechnology of Water Treatment, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Ramona Kuhn
- Institute of Environmental Technology, Chair of Biotechnology of Water Treatment, BTU Cottbus-Senftenberg, Cottbus, 03046, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
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14
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Watanabe Y, Aoki W, Ueda M. Improved ammonia production from soybean residues by cell surface-displayed l-amino acid oxidase on yeast. Biosci Biotechnol Biochem 2021; 85:972-980. [PMID: 33580695 DOI: 10.1093/bbb/zbaa112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022]
Abstract
Ammonia is critical for agricultural and chemical industries. The extracellular production of ammonia by yeast (Saccharomyces cerevisiae) using cell surface engineering can be efficient approach because yeast can avoid growth deficiencies caused by knockout of genes for ammonia assimilation. In this study, we produced ammonia outside the yeast cells by displaying an l-amino acid oxidase with a wide substrate specificity derived from Hebeloma cylindrosporum (HcLAAO) on yeast cell surfaces. The HcLAAO-displaying yeast successfully produced 12.6 m m ammonia from a mixture of 20 proteinogenic amino acids (the theoretical conversion efficiency was 63%). We also succeeded in producing ammonia from a food processing waste, soybean residues (okara) derived from tofu production. The conversion efficiency was 88.1%, a higher yield than reported in previous studies. Our study demonstrates that ammonia production outside of yeast cells is a promising strategy to utilize food processing wastes.
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Affiliation(s)
- Yukio Watanabe
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Japan Science and Technology Agency (JST), Tokyo, Japan
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15
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Kitagawa M, Ito N, Matsumoto Y, Saito M, Tamura T, Kusakabe H, Inagaki K, Imada K. Structural basis of enzyme activity regulation by the propeptide of l-lysine α-oxidase precursor from Trichoderma viride. JOURNAL OF STRUCTURAL BIOLOGY-X 2021; 5:100044. [PMID: 33554108 PMCID: PMC7844570 DOI: 10.1016/j.yjsbx.2021.100044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/17/2020] [Accepted: 01/07/2021] [Indexed: 11/04/2022]
Abstract
The suppression mechanism of activity by propeptide remains unclear for most LAAOs. The crystal structures of the LysOX precursor (prLysOX) have been determined. The propeptide indirectly changes the active site structure to suppress the activity. prLysOX can adopt another conformation similar to mature LysOX. prLysOX is able to be activated without proteolytic processing.
Harmuful proteins are usually synthesized as inactive precursors and are activated by proteolytic processing. l-Amino acid oxidase (LAAO) is a flavoenzyme that catalyzes the oxidative deamination of l-amino acid to produce a 2-oxo acid with ammonia and highly toxic hydrogen peroxide and, therefore, is expressed as a precursor. The LAAO precursor shows significant variation in size and the cleavage pattern for activation. However, the molecular mechanism of how the propeptide suppresses the enzyme activity remains unclear except for deaminating/decarboxylating Pseudomonasl-phenylalanine oxidase (PAO), which has a short N-terminal propeptide composed of 14 residues. Here we show the inactivation mechanism of the l-lysine oxidase (LysOX) precursor (prLysOX), which has a long N-terminal propeptide composed of 77 residues, based on the crystal structure at 1.97 Å resolution. The propeptide of prLysOX indirectly changes the active site structure to inhibit the enzyme activity. prLysOX retains weak enzymatic activity with strict specificity for l-lysine and shows raised activity in acidic conditions. The structures of prLysOX crystals that soaked in a solution with various concentrations of l-lysine have revealed that prLysOX can adopt two conformations; one is the inhibitory form, and the other is very similar to mature LysOX. The propeptide region of the latter form is disordered, and l-lysine is bound to the latter form. These results indicate that prLysOX uses a different strategy from PAO to suppress the enzyme activity and suggest that prLysOX can be activated quickly in response to the environmental change without proteolytic processing.
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Affiliation(s)
- Masaki Kitagawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Nanako Ito
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Yuya Matsumoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Masaya Saito
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Tamura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | | | - Kenji Inagaki
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Katsumi Imada
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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16
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Seok J, Kim YJ, Kim IK, Kim KJ. Structural basis for stereospecificity to d-amino acid of glycine oxidase from Bacillus cereus ATCC 14579. Biochem Biophys Res Commun 2020; 533:824-830. [PMID: 32993959 DOI: 10.1016/j.bbrc.2020.09.093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 09/22/2020] [Indexed: 11/20/2022]
Abstract
Glycine oxidase (GO) is an enzyme that catalyzes the oxidation of the primary and secondary amines of various chemicals, including glycine, and the enzyme has been applied in a variety of fields, such as biosensor and genetically modified glyphosate resistance plants. Here, we report that the gene product of BC0747 from Bacillus cereus (BcGO) shows oxidase activity for glycine and small d-amino acids, such as d-proline and d-alanine. We also determined the crystal structure of BcGO complexed with the FAD cofactor at a 2.36 Å resolution and revealed how the cofactor binds to the deep pocket of the enzyme. We performed the molecular docking calculation of the glycine substrate to the BcGO structure and identified how the carboxyl- and amine-groups of the d-amino acid are stabilized at the substrate binding site. Structural analysis of BcGO also provided information on the structural basis for the stereospecificity of the enzyme to d-amino acids. In addition, we placed the glyphosate molecule, a plant herbicide, at the substrate binding site, and explained how the mutation of Gly51 to arginine enhances enzyme activity.
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Affiliation(s)
- Jihye Seok
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea
| | - Yeo-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea
| | - Il-Kwon Kim
- KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daehak-ro 80, Buk-ku, Daegu, 41566, Republic of Korea.
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17
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Claassens NJ, Bordanaba-Florit G, Cotton CA, De Maria A, Finger-Bou M, Friedeheim L, Giner-Laguarda N, Munar-Palmer M, Newell W, Scarinci G, Verbunt J, de Vries ST, Yilmaz S, Bar-Even A. Replacing the Calvin cycle with the reductive glycine pathway in Cupriavidus necator. Metab Eng 2020; 62:30-41. [DOI: 10.1016/j.ymben.2020.08.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/07/2020] [Accepted: 08/06/2020] [Indexed: 11/27/2022]
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18
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Qin Y, Wu G, Guo Y, Ke D, Yin J, Wang D, Fan X, Liu Z, Ruan L, Hu Y. Engineered glyphosate oxidase coupled to spore-based chemiluminescence system for glyphosate detection. Anal Chim Acta 2020; 1133:39-47. [PMID: 32993872 DOI: 10.1016/j.aca.2020.07.077] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
The extensive and intensive utilization of glyphosate (Glyp) caused public concerns on the potential risk of environment and health resulted from the chemical residues. Therefore, the development of a high-selective, low-cost and easy-operation Glyp detection methods is highly desired. Screening highly selective enzymes by directed evolution is important in practical applications. Herein, a glyphosate oxidase (GlypO) preferring substrate Glyp to produce H2O2 was obtained via directed evolution from glycine oxidase obtained from Bacillus cereus (BceGO). The catalytic efficiency, specificity constant, and affinity enhancement factor of GlypO toward Glyp were increased by 2.85 × 103-fold; 2.25 × 105-fold; and 9.64 × 104-fold, respectively, compared with those of BceGO. The catalytic efficiency toward glycine decreased by 78.60-fold. The spores of Bacillus subtilis (B. subtilis) effectively catalyzed luminol-H2O2 reaction to create excellent chemiluminescence (CL) signal because CotA-laccase exists on their surface. Based on these findings, a new CL biosensor via coupling to biological reaction system was presented for Glyp detection. The CL biosensor exhibited several advantages, such as eco-friendliness, low cost, high selectivity and sensitivity, and good practical application prospects for environmental pollution control.
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Affiliation(s)
- Yuqing Qin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yiming Guo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Da Ke
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jiakang Yin
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Donglin Wang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuezhu Fan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziduo Liu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yonggang Hu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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19
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Kondo H, Kitagawa M, Matsumoto Y, Saito M, Amano M, Sugiyama S, Tamura T, Kusakabe H, Inagaki K, Imada K. Structural basis of strict substrate recognition of l-lysine α-oxidase from Trichoderma viride. Protein Sci 2020; 29:2213-2225. [PMID: 32894626 DOI: 10.1002/pro.3946] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 11/07/2022]
Abstract
l-Lysine oxidase (LysOX) is a FAD-dependent homodimeric enzyme that catalyzes the oxidative deamination of l-lysine to produce α-keto-ε-aminocaproate with ammonia and hydrogen peroxide. LysOX shows strict substrate specificity for l-lysine, whereas most l-amino acid oxidases (LAAOs) exhibit broad substrate specificity for l-amino acids. Previous studies of LysOX showed that overall structural similarity to the well-studied snake venom LAAOs. However, the molecular mechanism of strict specificity for l-lysine was still unclear. We here determined the structure of LysOX in complex with l-lysine at 1.7 Å resolution. The structure revealed that the hydrogen bonding network formed by D212, D315, and A440 with two water molecules is responsible for the recognition of the side chain amino group. In addition, a narrow hole formed by five hydrophobic residues in the active site contributes to strict substrate specificity. Mutation studies demonstrated that D212 and D315 are essential for l-lysine recognition, and the D212A/D315A double mutant LysOX showed different substrate specificity from LysOX. Moreover, the structural basis of the substrate specificity change has also been revealed by the structural analysis of the mutant variant and its substrate complexes. These results clearly explain the molecular mechanism of the strict specificity of LysOX and suggest that LysOX is a potential candidate for a template to design LAAOs specific to other l-amino acids.
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Affiliation(s)
- Hiroki Kondo
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Osaka, Japan
| | - Masaki Kitagawa
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Osaka, Japan
| | - Yuya Matsumoto
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Masaya Saito
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Marie Amano
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Shigeru Sugiyama
- Faculty of Science and Technology, Kochi University, Kochi, 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, Osaka, Japan
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20
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Pérez-Ràfols C, Liu Y, Wang Q, Cuartero M, Crespo GA. Why Not Glycine Electrochemical Biosensors? SENSORS (BASEL, SWITZERLAND) 2020; 20:E4049. [PMID: 32708149 PMCID: PMC7411573 DOI: 10.3390/s20144049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/14/2020] [Accepted: 07/16/2020] [Indexed: 01/26/2023]
Abstract
Glycine monitoring is gaining importance as a biomarker in clinical analysis due to its involvement in multiple physiological functions, which results in glycine being one of the most analyzed biomolecules for diagnostics. This growing demand requires faster and more reliable, while affordable, analytical methods that can replace the current gold standard for glycine detection, which is based on sample extraction with subsequent use of liquid chromatography or fluorometric kits for its quantification in centralized laboratories. This work discusses electrochemical sensors and biosensors as an alternative option, focusing on their potential application for glycine determination in blood, urine, and cerebrospinal fluid, the three most widely used matrices for glycine analysis with clinical meaning. For electrochemical sensors, voltammetry/amperometry is the preferred readout (10 of the 13 papers collected in this review) and metal-based redox mediator modification is the predominant approach for electrode fabrication (11 of the 13 papers). However, none of the reported electrochemical sensors fulfill the requirements for direct analysis of biological fluids, most of them lacking appropriate selectivity, linear range of response, and/or capability of measuring at physiological conditions. Enhanced selectivity has been recently reported using biosensors (with an enzyme element in the electrode design), although this is still a very incipient approach. Currently, despite the benefits of electrochemistry, only optical biosensors have been successfully reported for glycine detection and, from all the inspected works, it is clear that bioengineering efforts will play a key role in the embellishment of selectivity and storage stability of the sensing element in the sensor.
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Affiliation(s)
| | | | | | | | - Gastón A. Crespo
- Department of Chemistry, School of Engineering Science in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Teknikringen 30, SE-100 44 Stockholm, Sweden; (C.P.-R.); (Y.L.); (Q.W.); (M.C.)
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21
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Tatsumi M, Hoshino W, Kodama Y, Ueatrongchit T, Takahashi K, Yamaguchi H, Tagami U, Miyano H, Asano Y, Mizukoshi T. Development of a rapid and simple glycine analysis method using a stable glycine oxidase mutant. Anal Biochem 2019; 587:113447. [PMID: 31562850 DOI: 10.1016/j.ab.2019.113447] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 09/06/2019] [Accepted: 09/19/2019] [Indexed: 11/27/2022]
Abstract
Glycine analysis is important in research fields such as physiology and healthcare because the concentration of glycine in human plasma has been reported to change with various disorders. Glycine oxidase from Bacillus subtilis (GlyOX) is useful for quantitative analysis of glycine. However, GlyOX is not sufficiently stable for use in physiology-based research or clinical settings. In this report, site-directed mutagenesis was used to engineer a GlyOX mutant suitable for glycine analysis. The GlyOX triple-mutant (T42 A/C245 S/L301V) retained most of its enzymatic activity during storage for over a year at 4 °C. A colorimetric enzyme analysis protocol was established using the GlyOX triple-mutant to determine glycine concentrations in human plasma. The analysis showed high accuracy (-5.4 to 3.5% relative errors when compared with the results from an amino acid analyzer, and 96.0-98.7% recoveries) and high precision (<4% between-run variation). Sample pretreatments of deproteinization and derivatization were not required. Therefore, this novel enzymatic analysis offers an effective and useful method for determining glycine concentrations in physiology related research and the healthcare field.
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Affiliation(s)
- Moemi Tatsumi
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Wataru Hoshino
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Yuya Kodama
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Techawaree Ueatrongchit
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Kazutoshi Takahashi
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Hiroki Yamaguchi
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Uno Tagami
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Hiroshi Miyano
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Toshimi Mizukoshi
- Institute for Innovation, Ajinomoto Co., Inc., Kawasaki, Kanagawa, 210-8681, Japan.
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22
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Masuo S, Tsuda Y, Namai T, Minakawa H, Shigemoto R, Takaya N. Enzymatic Cascade in Pseudomonas that Produces Pyrazine from α-Amino Acids. Chembiochem 2019; 21:353-359. [PMID: 31322801 DOI: 10.1002/cbic.201900448] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Indexed: 12/31/2022]
Abstract
Pyrazines are widespread chemical compounds that include pheromones and odors. Herein, a novel mechanism used by Pseudomonas fluorescens SBW25 to biosynthesize monocyclic pyrazines is reported. Heterologous expression of the papABC genes that synthesize the natural α-amino acid 4-aminophenylalanine (4APhe), together with three adjacent papDEF genes of unknown function, in Escherichia coli resulted in the production of 2,5-dimethyl-3,6-bis(4-aminobenzyl)pyrazine (DMBAP), which comprised two symmetrical aminobenzyl moieties derived from 4APhe. It is found that PapD is a novel amino acid C-acetyltransferase, which decarboxylates and transfers acetyl residues to 4APhe, to generate an α-aminoketone, which spontaneously dehydrates and condenses to give dihydro DMBAP. PapF is a novel oxidase in the amine oxidase superfamily that oxidizes dihydro DMBAP to yield the pyrazine ring of DMBAP. These two enzymes constitute a unique mechanism for synthesizing monocyclic pyrazines and might serve as a novel strategy for the enzymatic synthesis of pyrazine derivatives from natural α-amino acids.
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Affiliation(s)
- Shunsuke Masuo
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yusuke Tsuda
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Tomohito Namai
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hajime Minakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Ryosuke Shigemoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Naoki Takaya
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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23
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Rosini E, Pollegioni L. A comprehensive practical laboratory course on protein engineering: Evolution of a glycine oxidase variant active on the herbicide glyphosate. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:689-699. [PMID: 31444933 DOI: 10.1002/bmb.21291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/01/2019] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Protein engineering represents a modern approach to generate novel proteins for the different fields of biotechnology. Here, we report about an 8-day laboratory activity in which students generate enzyme variants to degrade the herbicide glyphosate. The students conduct a true research experiment in an important field (bioremediation by novel, engineered enzymes) and are introduced to widely used techniques in molecular biology and protein biochemistry laboratories. Based on a docking analysis of glycine (the original substrate) and of glyphosate into the active site of glycine oxidase, residues putatively involved in substrate selectivity are identified that will become the target of site-saturation mutagenesis. Each group of students focuses on the library generated at one position and selects the most active variant based on colorimetric screening. Following protein overexpression in Escherichia coli, the selected glycine oxidase variants are purified and their kinetic properties on glycine and glyphosate assessed. The best variant identified by the whole class is then used for detecting the herbicide in water. With the help of the professor, students can improve technical skills, ability to evaluate results, team work activity, and critical thinking. © 2019 International Union of Biochemistry and Molecular Biology, 47(6):689-699, 2019.
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Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
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24
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Production of nonnatural straight-chain amino acid 6-aminocaproate via an artificial iterative carbon-chain-extension cycle. Metab Eng 2019; 55:23-32. [DOI: 10.1016/j.ymben.2019.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 06/13/2019] [Accepted: 06/15/2019] [Indexed: 12/23/2022]
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25
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Kim NY, Goddard TN, Sohn S, Spiegel DA, Crawford JM. Biocatalytic Reversal of Advanced Glycation End Product Modification. Chembiochem 2019; 20:2402-2410. [PMID: 31013547 DOI: 10.1002/cbic.201900158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 01/01/2023]
Abstract
Advanced glycation end products (AGEs) are a heterogeneous group of molecules that emerge from the condensation of sugars and proteins through the Maillard reaction. Despite a significant number of studies showing strong associations between AGEs and the pathologies of aging-related illnesses, it has been a challenge to establish AGEs as causal agents primarily due to the lack of tools in reversing AGE modifications at the molecular level. Herein, we show that MnmC, an enzyme involved in a bacterial tRNA-modification pathway, is capable of reversing the AGEs carboxyethyl-lysine (CEL) and carboxymethyl-lysine (CML) back to their native lysine structure. Combining structural homology analysis, site-directed mutagenesis, and protein domain dissection studies, we generated a variant of MnmC with improved catalytic properties against CEL in its free amino acid form. We show that this enzyme variant is also active on a CEL-modified peptidomimetic and an AGE-containing peptide that has been established as an authentic ligand of the receptor for AGEs (RAGE). Our data demonstrate that MnmC variants are promising lead catalysts toward the development of AGE-reversal tools and a better understanding of AGE biology.
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Affiliation(s)
- Nam Y Kim
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.,Chemical Biology Institute, Yale University, 600 West Campus Drive, West Haven, CT, 06516, USA
| | - Tyler N Goddard
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.,Chemical Biology Institute, Yale University, 600 West Campus Drive, West Haven, CT, 06516, USA
| | - Seungjung Sohn
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA
| | - David A Spiegel
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.,Department of Pharmacology, Yale School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Jason M Crawford
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT, 06511, USA.,Chemical Biology Institute, Yale University, 600 West Campus Drive, West Haven, CT, 06516, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, 295 Congress Avenue, New Haven, CT, 06536, USA
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26
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Kawasaki D, Chisuga T, Miyanaga A, Kudo F, Eguchi T. Structural Analysis of the Glycine Oxidase Homologue CmiS2 Reveals a Unique Substrate Recognition Mechanism for Formation of a β-Amino Acid Starter Unit in Cremimycin Biosynthesis. Biochemistry 2019; 58:2706-2709. [PMID: 31154757 DOI: 10.1021/acs.biochem.9b00444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The flavin adenine dinucleotide-dependent oxidase CmiS2 catalyzes the oxidation of N-carboxymethyl-3-aminononanoic acid to produce a 3-aminononanoic acid starter unit for the biosynthesis of cremimycin, a macrolactam polyketide. Although the sequence of CmiS2 is similar with that of the well-characterized glycine oxidase ThiO, the chemical structure of the substrate of CmiS2 is different from that of ThiO substrate glycine. Here, we present the biochemical and structural characterization of CmiS2. Kinetic analysis revealed that CmiS2 has a strong preference for N-carboxymethyl-3-aminononanoic acid over other substrates such as N-carboxymethyl-3-aminobutanoic acid and glycine, suggesting that CmiS2 recognizes the nonanoic acid moiety of the substrate as well as the glycine moiety. We determined the crystal structure of CmiS2 in complex with a substrate analogue, namely, S-carboxymethyl-3-thiononanoic acid, which enabled the identification of key amino acid residues involved in substrate recognition. We discovered that Asn49, Arg243, and Arg334 interact with the carboxyl group of the nonanoic acid moiety, while Pro46, Leu52, and Ile335 recognize the alkyl chain of the nonanoic acid moiety via hydrophobic interaction. These residues are highly conserved in CmiS2 homologues involved in the biosynthesis of related macrolactam polyketides but are not conserved in glycine oxidases such as ThiO. These results suggest that CmiS2-type enzymes employ a distinct mechanism of substrate recognition for the synthesis of β-amino acids.
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Affiliation(s)
- Daisuke Kawasaki
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Taichi Chisuga
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Akimasa Miyanaga
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Fumitaka Kudo
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
| | - Tadashi Eguchi
- Department of Chemistry , Tokyo Institute of Technology , 2-12-1 O-okayama , Meguro-ku, Tokyo 152-8551 , Japan
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27
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Kim SH, Shishido Y, Sogabe H, Rachadech W, Yorita K, Kato Y, Fukui K. Age- and gender-dependent D-amino acid oxidase activity in mouse brain and peripheral tissues: implication for aging and neurodegeneration. J Biochem 2019; 166:187-196. [DOI: 10.1093/jb/mvz025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/01/2019] [Indexed: 12/11/2022] Open
Abstract
Abstract
D-amino acid oxidase (DAO) is a flavoenzyme, catalysing oxidative deamination of D-amino acids to produce corresponding α-keto acids, ammonia and hydrogen peroxide. In our search for DAO activity among various tissues, we developed a sensitive assay based on hydrogen peroxide production involving enzyme-coupled colorimetric assay with peroxidase. We first optimized buffer components to extract DAO protein from mouse tissues. Here we show that DAO activity was detected in kidney, cerebellum, medulla oblongata, midbrain and spinal cord, but not in liver. In addition, we observed that DAO activity and expression were decreased in thoracic and lumbar regions of spinal cord in aged mice when compared with young mice, indicating that decreased DAO is involved in motoneuron degeneration during senescence. We also found gender difference in DAO activity in the kidney, suggesting that DAO activity is influenced by sexual dimorphism. We newly detected DAO activity in the epididymis, although undetected in testis. Furthermore, DAO activity was significantly higher in the caput region than corpus and cauda regions of epididymis, indicating that D-amino acids present in the testis are eliminated in epididymis. Taken together, age- and gender-dependent DAO activity in each organ may underlie the human pathophysiology regulated by D-amino acid metabolism.
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Affiliation(s)
- Soo Hyeon Kim
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Yuji Shishido
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Hirofumi Sogabe
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Wanitcha Rachadech
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Kazuko Yorita
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Yusuke Kato
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
| | - Kiyoshi Fukui
- Division of Enzyme Pathophysiology, Institute for Enzyme Research, Tokushima University, 3-18-15 Kuramoto, Tokushima, Japan
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28
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Maggi M, Scotti C. Enzymes in Metabolic Anticancer Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1148:173-199. [PMID: 31482500 DOI: 10.1007/978-981-13-7709-9_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cancer treatment has greatly improved over the last 50 years, but it remains challenging in several cases. Useful therapeutic targets are normally unique peculiarities of cancer cells that distinguish them from normal cells and that can be tackled with appropriate drugs. It is now known that cell metabolism is rewired during tumorigenesis and metastasis as a consequence of oncogene activation and oncosuppressors inactivation, leading to a new cellular homeostasis typically directed towards anabolism. Because of these modifications, cells can become strongly or absolutely dependent on specific substrates, like sugars, lipids or amino acids. Cancer addictions are a relevant target for therapy, as removal of an essential substrate can lead to their selective cell-cycle arrest or even to cell death, leaving normal cells untouched. Enzymes can act as powerful agents in this respect, as demonstrated by asparaginase, which has been included in the treatment of Acute Lymphoblastic Leukemia for half a century. In this review, a short outline of cancer addictions will be provided, focusing on the main cancer amino acid dependencies described so far. Therapeutic enzymes which have been already experimented at the clinical level will be discussed, along with novel potential candidates that we propose as new promising molecules. The intrinsic limitations of their present molecular forms, along with molecular engineering solutions to explore, will also be presented.
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Affiliation(s)
- Maristella Maggi
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy.
| | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
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29
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Progress in using threonine aldolases for preparative synthesis. Enzyme Microb Technol 2018; 119:1-9. [DOI: 10.1016/j.enzmictec.2018.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 06/19/2018] [Accepted: 07/17/2018] [Indexed: 12/28/2022]
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30
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Rosini E, Caldinelli L, Piubelli L. Assays of D-Amino Acid Oxidase Activity. Front Mol Biosci 2018; 4:102. [PMID: 29404340 PMCID: PMC5785730 DOI: 10.3389/fmolb.2017.00102] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/28/2017] [Indexed: 11/13/2022] Open
Abstract
D-amino acid oxidase (DAAO) is a well-known flavoenzyme that catalyzes the oxidative FAD-dependent deamination of D-amino acids. As a result of the absolute stereoselectivity and broad substrate specificity, microbial DAAOs have been employed as industrial biocatalysts in the production of semi-synthetic cephalosporins and enantiomerically pure amino acids. Moreover, in mammals, DAAO is present in specific brain areas and degrades D-serine, an endogenous coagonist of the N-methyl-D-aspartate receptors (NMDARs). Dysregulation of D-serine metabolism due to an altered DAAO functionality is related to pathological NMDARs dysfunctions such as in amyotrophic lateral sclerosis and schizophrenia. In this protocol paper, we describe a variety of direct assays based on the determination of molecular oxygen consumption, reduction of alternative electron acceptors, or α-keto acid production, of coupled assays to detect the hydrogen peroxide or the ammonium production, and an indirect assay of the α-keto acid production based on a chemical derivatization. These analytical assays allow the determination of DAAO activity both on recombinant enzyme preparations, in cells, and in tissue samples.
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Affiliation(s)
- Elena Rosini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- The Protein Factory Research Center, Politecnico of Milan and University of Insubria, Milan, Italy
| | - Laura Caldinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- The Protein Factory Research Center, Politecnico of Milan and University of Insubria, Milan, Italy
| | - Luciano Piubelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy
- The Protein Factory Research Center, Politecnico of Milan and University of Insubria, Milan, Italy
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31
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Ouedraogo D, Ball J, Iyer A, Reis RAG, Vodovoz M, Gadda G. Amine oxidation by d-arginine dehydrogenase in Pseudomonas aeruginosa. Arch Biochem Biophys 2017. [PMID: 28625766 DOI: 10.1016/j.abb.2017.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is a flavin-dependent oxidoreductase, which is part of a novel two-enzyme racemization system that functions to convert d-arginine to l-arginine. PaDADH contains a noncovalently linked FAD that shows the highest activity with d-arginine. The enzyme exhibits broad substrate specificity towards d-amino acids, particularly with cationic and hydrophobic d-amino acids. Biochemical studies have established the structure and the mechanistic properties of the enzyme. The enzyme is a true dehydrogenase because it displays no reactivity towards molecular oxygen. As established through solvent and multiple kinetic isotope studies, PaDADH catalyzes an asynchronous CH and NH bond cleavage via a hydride transfer mechanism. Steady-state kinetic studies with d-arginine and d-histidine are consistent with the enzyme following a ping-pong bi-bi mechanism. As shown by a combination of crystallography, kinetic and computational data, the shape and flexibility of loop L1 in the active site of PaDADH are important for substrate capture and broad substrate specificity.
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Affiliation(s)
- Daniel Ouedraogo
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Jacob Ball
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Archana Iyer
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Maria Vodovoz
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Giovanni Gadda
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States; Department of Biology, Georgia State University, Atlanta, GA 30302, United States; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302, United States; Center for Biotechnology and Drug Design, Georgia State University, Atlanta, GA 30302, United States.
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32
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Ouedraogo D, Souffrant M, Vasquez S, Hamelberg D, Gadda G. Importance of Loop L1 Dynamics for Substrate Capture and Catalysis in Pseudomonas aeruginosa d-Arginine Dehydrogenase. Biochemistry 2017; 56:2477-2487. [DOI: 10.1021/acs.biochem.7b00098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Daniel Ouedraogo
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Michael Souffrant
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Sheena Vasquez
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Donald Hamelberg
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
| | - Giovanni Gadda
- Department
of Chemistry, ‡Department of Biology, §Center for Diagnostics and Therapeutics, and ∥Center for Biotechnology
and Drug Design, Georgia State University, Atlanta, Georgia 30302, United States
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33
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Asn336 is involved in the substrate affinity of glycine oxidase from Bacillus cereus. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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34
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Meunier CNJ, Dallérac G, Le Roux N, Sacchi S, Levasseur G, Amar M, Pollegioni L, Mothet JP, Fossier P. D-Serine and Glycine Differentially Control Neurotransmission during Visual Cortex Critical Period. PLoS One 2016; 11:e0151233. [PMID: 27003418 PMCID: PMC4803205 DOI: 10.1371/journal.pone.0151233] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 02/25/2016] [Indexed: 12/18/2022] Open
Abstract
N-methyl-D-aspartate receptors (NMDARs) play a central role in synaptic plasticity. Their activation requires the binding of both glutamate and d-serine or glycine as co-agonist. The prevalence of either co-agonist on NMDA-receptor function differs between brain regions and remains undetermined in the visual cortex (VC) at the critical period of postnatal development. Here, we therefore investigated the regulatory role that d-serine and/or glycine may exert on NMDARs function and on synaptic plasticity in the rat VC layer 5 pyramidal neurons of young rats. Using selective enzymatic depletion of d-serine or glycine, we demonstrate that d-serine and not glycine is the endogenous co-agonist of synaptic NMDARs required for the induction and expression of Long Term Potentiation (LTP) at both excitatory and inhibitory synapses. Glycine on the other hand is not involved in synaptic efficacy per se but regulates excitatory and inhibitory neurotransmission by activating strychnine-sensitive glycine receptors, then producing a shunting inhibition that controls neuronal gain and results in a depression of synaptic inputs at the somatic level after dendritic integration. In conclusion, we describe for the first time that in the VC both D-serine and glycine differentially regulate somatic depolarization through the activation of distinct synaptic and extrasynaptic receptors.
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Affiliation(s)
- Claire N. J. Meunier
- Institut de Neuroscience Paris-Saclay (NeuroPSI), UMR 9197 CNRS-Université Paris-Sud, Bât 446, F-91405, Orsay cedex, France
| | - Glenn Dallérac
- Aix-Marseille University, CRN2M UMR7286 CNRS, 51 Bd Pierre Dramard, 13344, Marseille, France
| | - Nicolas Le Roux
- Institut de Neuroscience Paris-Saclay (NeuroPSI), UMR 9197 CNRS-Université Paris-Sud, Bât 446, F-91405, Orsay cedex, France
| | - Silvia Sacchi
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, via J.H. Dunant 3, Varese, Italy
- “The Protein Factory”, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano, ICRM-CNR, Milano, Italy
- Università degli Studi dell’Insubria, via Mancinelli 7, Milano, Italy
| | - Grégoire Levasseur
- Aix-Marseille University, CRN2M UMR7286 CNRS, 51 Bd Pierre Dramard, 13344, Marseille, France
| | - Muriel Amar
- Institut de Neuroscience Paris-Saclay (NeuroPSI), UMR 9197 CNRS-Université Paris-Sud, Bât 446, F-91405, Orsay cedex, France
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, via J.H. Dunant 3, Varese, Italy
- “The Protein Factory”, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano, ICRM-CNR, Milano, Italy
- Università degli Studi dell’Insubria, via Mancinelli 7, Milano, Italy
| | - Jean-Pierre Mothet
- Aix-Marseille University, CRN2M UMR7286 CNRS, 51 Bd Pierre Dramard, 13344, Marseille, France
- * E-mail: (PF); (JPM)
| | - Philippe Fossier
- Institut de Neuroscience Paris-Saclay (NeuroPSI), UMR 9197 CNRS-Université Paris-Sud, Bât 446, F-91405, Orsay cedex, France
- * E-mail: (PF); (JPM)
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35
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Zhang K, Guo Y, Yao P, Lin Y, Kumar A, Liu Z, Wu G, Zhang L. Characterization and directed evolution of BliGO, a novel glycine oxidase from Bacillus licheniformis. Enzyme Microb Technol 2016; 85:12-8. [PMID: 26920475 DOI: 10.1016/j.enzmictec.2015.12.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 12/18/2022]
Abstract
Glycine oxidase (GO) has great potential for use in biosensors, industrial catalysis and agricultural biotechnology. In this study, a novel GO (BliGO) from a marine bacteria Bacillus licheniformis was cloned and characterized. BliGO showed 62% similarity to the well-studied GO from Bacillus subtilis. The optimal activity of BliGO was observed at pH 8.5 and 40°C. Interestingly, BliGO retained 60% of the maximum activity at 0°C, suggesting it is a cold-adapted enzyme. The kinetic parameters on glyphosate (Km, kcat and k(cat)/K(m)) of BliGO were 11.22 mM, 0.08 s(-1), and 0.01 mM(-1) s(-1), respectively. To improve the catalytic activity to glyphosate, the BliGO was engineered by directed evolution. With error-prone PCR and two rounds of DNA shuffling, the most evolved mutant SCF-4 was obtained from 45,000 colonies, which showed 7.1- and 8-fold increase of affinity (1.58 mM) and catalytic efficiency (0.08 mM(-1) s(-1)) to glyphosate, respectively. In contrast, its activity to glycine (the natural substrate of GO) decreased by 113-fold. Structure modeling and site-directed mutation study indicated that Ser51 in SCF-4 involved in the binding of enzyme with glyphosate and played a crucial role in the improvement of catalytic efficiency.
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Affiliation(s)
- Kai Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiming Guo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Pei Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongjun Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ashok Kumar
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziduo Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lili Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Crops, College of Life Science, Tarim University, Alar 843300, China.
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36
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Campillo-Brocal JC, Lucas-Elío P, Sanchez-Amat A. Distribution in Different Organisms of Amino Acid Oxidases with FAD or a Quinone As Cofactor and Their Role as Antimicrobial Proteins in Marine Bacteria. Mar Drugs 2015; 13:7403-18. [PMID: 26694422 PMCID: PMC4699246 DOI: 10.3390/md13127073] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 11/27/2015] [Accepted: 12/08/2015] [Indexed: 12/27/2022] Open
Abstract
Amino acid oxidases (AAOs) catalyze the oxidative deamination of amino acids releasing ammonium and hydrogen peroxide. Several kinds of these enzymes have been reported. Depending on the amino acid isomer used as a substrate, it is possible to differentiate between l-amino acid oxidases and d-amino acid oxidases. Both use FAD as cofactor and oxidize the amino acid in the alpha position releasing the corresponding keto acid. Recently, a novel class of AAOs has been described that does not contain FAD as cofactor, but a quinone generated by post-translational modification of residues in the same protein. These proteins are named as LodA-like proteins, after the first member of this group described, LodA, a lysine epsilon oxidase synthesized by the marine bacterium Marinomonas mediterranea. In this review, a phylogenetic analysis of all the enzymes described with AAO activity has been performed. It is shown that it is possible to recognize different groups of these enzymes and those containing the quinone cofactor are clearly differentiated. In marine bacteria, particularly in the genus Pseudoalteromonas, most of the proteins described as antimicrobial because of their capacity to generate hydrogen peroxide belong to the group of LodA-like proteins.
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Affiliation(s)
- Jonatan C Campillo-Brocal
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Patricia Lucas-Elío
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
| | - Antonio Sanchez-Amat
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain.
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37
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Han H, Zhu B, Fu X, You S, Wang B, Li Z, Zhao W, Peng R, Yao Q. Overexpression of D-amino acid oxidase from Bradyrhizobium japonicum, enhances resistance to glyphosate in Arabidopsis thaliana. PLANT CELL REPORTS 2015; 34:2043-51. [PMID: 26350405 DOI: 10.1007/s00299-015-1850-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/21/2015] [Accepted: 07/27/2015] [Indexed: 05/17/2023]
Abstract
KEY MESSAGE The glyphosate resistance in Escherichia coli and Arabidopsis was due to D-amino acid oxidase expression. Transgenic glyphosate-resistant crops have a high percentage in the total area devoted to transgenic crops worldwide. D-amino acid oxidase (DAAO) can metabolize glyphosate by oxidative cleavage of the carbon-nitrogen bond on the carboxyl side and yield aminomethyl phosphonic acid and glyoxylate, which are less toxic to plants than glyphosate. To date, reports on the use of DAAO to enhance glyphosate resistance in plants are lacking. In this paper, we report synthesis, and codon usage optimization for plant expression, of the DAAO gene by successive polymerase chain reaction from Bradyrhizobium japonicum. To confirm the glyphosate resistance of the DAAO gene, the recombinant plasmid pYPX251 (GenBank Accession No: AY178046) harboring the wild-type DAAO gene was transformed into DH5α. The positive transformants grew well both on solid and in liquid M9 medium containing 200 mM glyphosate. The optimized DAAO gene was transformed into Arabidopsis and 9 days after application of 10 mM glyphosate, the 4-week-old wild-type plants all died; by contrast, transgenic plants could grow normally. The proline content and peroxidase activity showed that glyphosate could induce proline accumulation and produce reactive oxygen species.
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Affiliation(s)
- Hongjuan Han
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Bo Zhu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Xiaoyan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Shuanghong You
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
- College of Horticulture Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Zhenjun Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Wei Zhao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Agro-Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 2901 Beidi Rd, Shanghai, 201106, People's Republic of China.
- College of Horticulture Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Yao P, Lin Y, Wu G, Lu Y, Zhan T, Kumar A, Zhang L, Liu Z. Improvement of glycine oxidase by DNA shuffling, and site-saturation mutagenesis of F247 residue. Int J Biol Macromol 2015; 79:965-70. [PMID: 26025077 DOI: 10.1016/j.ijbiomac.2015.05.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 05/17/2015] [Accepted: 05/19/2015] [Indexed: 01/17/2023]
Abstract
Glyphosate is a broad spectrum herbicide widely used throughout the world, and it could be degraded by glycine oxidase (GO) through CN bond cleavage. For a better understanding of the structure-function relationship and improving the activity of B3S1 (GO from Bacillus cereus), DNA shuffling was performed. A mutant B4S7 (The Km, Vmax, kcat and kcat/Km values on glyphosate were 0.1 mM, 0.002401 mM min(-1), 3.62 min(-1) and 36.2 mM(-1) min(-1), respectively. The four parameters on glycine were 50.34 mM, 0.001983 mM min(-1), 2.18 min(-1) and 0.04 mM(-1) min(-1), respectively) was obtained from 10,000 clones, which presented a 3.9-fold increase of the specificity constant (the kcat/Km ratio between glyphosate and glycine) compared with B3S1. Especially, the Km value of B4S7 to glyphosate was much less than those of the reported GO. Structure modeling and molecular docking indicated that the novel mutation point F247S was close to the active site of the enzyme. To identify the role of the site, the remaining 19 amino acids were introduced into the site by site-saturation mutagenesis. The result showed that compared with B3S1, the specificity constant of mutant F247S and F247R increased 0.64-fold and 1.04-fold, respectively. While the specificity constant of mutant F247E decreased 2.01-fold. Therefore, the site 247 plays a crucial role in regulating the substrate specificity. This study provides new information on the structure-function relationship of glycine oxidase and the development of glyphosate-tolerant crops.
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Affiliation(s)
- Pei Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongjun Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yulin Lu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Zhan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ashok Kumar
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lili Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Crops, College of Life Science, Tarim University, Alar 843300, China.
| | - Ziduo Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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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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Tani Y, Miyake R, Yukami R, Dekishima Y, China H, Saito S, Kawabata H, Mihara H. Functional expression of L-lysine α-oxidase from Scomber japonicus in Escherichia coli for one-pot synthesis of L-pipecolic acid from DL-lysine. Appl Microbiol Biotechnol 2014; 99:5045-54. [PMID: 25547835 DOI: 10.1007/s00253-014-6308-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 12/05/2014] [Accepted: 12/09/2014] [Indexed: 11/24/2022]
Abstract
L-Pipecolic acid is a key component of biologically active molecules and a pharmaceutically important chiral building block. It can be stereoselectively produced from L-lysine by a two-step bioconversion involving L-lysine α-oxidase and ∆(1)-piperideine-2-carboxylae (Pip2C) reductase. In this study, we focused on an L-lysine α-oxidase from Scomber japonicus that was originally identified as an apoptosis-inducing protein (AIP) and applied the enzyme to one-pot fermentation of L-pipecolic acid in Escherichia coli. A synthetic gene coding for an AIP was expressed in E. coli, and the recombinant enzyme was purified and characterized. The purified enzyme was determined to be a homodimer with a molecular mass of 133.9 kDa. The enzyme essentially exhibited the same substrate specificity as the native enzyme. Optimal temperature and pH for the enzymatic reaction were 70 °C and 7.4, respectively. The enzyme was stable below 60 °C and at a pH range of 5.5-7.5 but was markedly inhibited by Co(2+). To establish a one-pot fermentation system for the synthesis of optically pure L-pipecolic acid from DL-lysine, an E. coli strain carrying a plasmid encoding AIP, Pip2C reductase from Pseudomonas putida, lysine racemase from P. putida, and glucose dehydrogenase from Bacillus subtilis was constructed. The one-pot process produced 45.1 g/L of L-pipecolic acid (87.4 % yield from DL-lysine) after a 46-h reaction with high optical purity (>99.9 % enantiomeric excess).
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Affiliation(s)
- Yasushi Tani
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
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Molla G, Nardini M, Motta P, D'Arrigo P, Panzeri W, Pollegioni L. Aminoacetone oxidase from Streptococcus oligofermentans belongs to a new three-domain family of bacterial flavoproteins. Biochem J 2014; 464:387-99. [PMID: 25269103 DOI: 10.1042/bj20140972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The aaoSo gene from Streptococcus oligofermentans encodes a 43 kDa flavoprotein, aminoacetone oxidase (SoAAO), which was reported to possess a low catalytic activity against several different L-amino acids; accordingly, it was classified as an L-amino acid oxidase. Subsequently, SoAAO was demonstrated to oxidize aminoacetone (a pro-oxidant metabolite), with an activity ~25-fold higher than the activity displayed on L-lysine, thus lending support to the assumption of aminoacetone as the preferred substrate. In the present study, we have characterized the SoAAO structure-function relationship. SoAAO is an FAD-containing enzyme that does not possess the classical properties of the oxidase/dehydrogenase class of flavoproteins (i.e. no flavin semiquinone formation is observed during anaerobic photoreduction as well as no reaction with sulfite) and does not show a true L-amino acid oxidase activity. From a structural point of view, SoAAO belongs to a novel protein family composed of three domains: an α/β domain corresponding to the FAD-binding domain, a β-domain partially modulating accessibility to the coenzyme, and an additional α-domain. Analysis of the reaction products of SoAAO on aminoacetone showed 2,5-dimethylpyrazine as the main product; we propose that condensation of two aminoacetone molecules yields 3,6-dimethyl-2,5-dihydropyrazine that is subsequently oxidized to 2,5-dimethylpyrazine. The ability of SoAAO to bind two molecules of the substrate analogue O-methylglycine ligand is thought to facilitate the condensation reaction. A specialized role for SoAAO in the microbial defence mechanism related to aminoacetone catabolism through a pathway yielding dimethylpyrazine derivatives instead of methylglyoxal can be proposed.
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Affiliation(s)
- Gianluca Molla
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
| | - Marco Nardini
- ‡Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Paolo Motta
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
| | - Paola D'Arrigo
- †The Protein Factory, Centro Interuniversitario di Biotecnologie Proteiche, Politecnico di Milano, ICRM CNR Milano, and Università degli Studi deII'Insubria, Varese, Italy
| | - Walter Panzeri
- ║CNR-Istituto di Chimica del Riconoscimento Molecolare, Politecnico di Milano, via Mancinelli 7, 20131 Milano, Italy
| | - Loredano Pollegioni
- *Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J.H. Dunant 3, 21100 Varese, ltaly
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Tani Y, Omatsu K, Saito S, Miyake R, Kawabata H, Ueda M, Mihara H. Heterologous expression of l-lysine α-oxidase from Scomber japonicus in Pichia pastoris and functional characterization of the recombinant enzyme. J Biochem 2014; 157:201-10. [PMID: 25359785 DOI: 10.1093/jb/mvu064] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fish have a complex self-defense mechanism against microbial invasion. Recently, l-lysine α-oxidases have been identified from a number of fish species as a novel type of antibacterial protein in the integument. These enzymes exhibit strict substrate specificity for l-lysine, but the underlying mechanisms and details of their catalytic properties remain unknown. In this study, a synthetic gene coding for Scomber japonicus l-lysine α-oxidase, originally termed AIP (for apoptosis-inducing protein), was expressed in Pichia pastoris, and the recombinant enzyme (rAIP) was purified and characterized. rAIP exhibited essentially the same substrate specificity as the native enzyme, catalyzing the oxidative deamination of l-lysine as an exclusive substrate. rAIP was N-glycosylated and remained active over a wide range of pH, with an optimal pH of 7.5. The enzyme was stable in the pH range from 4.5 to 10.0 and was thermally stable up to 60°C. A molecular modelling of rAIP and a comparative structure/sequence analysis with homologous enzymes indicate that Asp(220) and Asp(320) are the substrate-binding residues that are likely to confer exclusive substrate specificity for l-lysine on the fish enzymes.
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Affiliation(s)
- Yasushi Tani
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan
| | - Koichiro Omatsu
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan
| | - Shigeki Saito
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan
| | - Ryoma Miyake
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan
| | - Hiroshi Kawabata
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan
| | - Makoto Ueda
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan
| | - Hisaaki Mihara
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; R-GIRO, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; Mitsubishi Chemical Group Science and Technology Research Center, Inc., Yokohama, Kanagawa 227-8502, Japan; and API Corporation, Yokohama, Kanagawa 227-8502, Japan
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Gannavaram S, Sirin S, Sherman W, Gadda G. Mechanistic and Computational Studies of the Reductive Half-Reaction of Tyrosine to Phenylalanine Active Site Variants of d-Arginine Dehydrogenase. Biochemistry 2014; 53:6574-83. [PMID: 25243743 DOI: 10.1021/bi500917q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Sarah Sirin
- Schrödinger, LLC, 120 West 45st Street, New York, New York 10036, United States
| | - Woody Sherman
- Schrödinger, LLC, 120 West 45st Street, New York, New York 10036, United States
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Nicolia A, Ferradini N, Molla G, Biagetti E, Pollegioni L, Veronesi F, Rosellini D. Expression of an evolved engineered variant of a bacterial glycine oxidase leads to glyphosate resistance in alfalfa. J Biotechnol 2014; 184:201-8. [PMID: 24905148 DOI: 10.1016/j.jbiotec.2014.05.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 05/14/2014] [Accepted: 05/16/2014] [Indexed: 11/27/2022]
Abstract
The main strategy for resistance to the herbicide glyphosate in plants is the overexpression of an herbicide insensitive, bacterial 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). A glyphosate resistance strategy based on the ability to degrade the herbicide can be useful to reduce glyphosate phytotoxicity to the crops. Here we present the characterization of glyphosate resistance in transgenic alfalfa (Medicago sativa L.) expressing a plant-optimized variant of glycine oxidase (GO) from Bacillus subtilis, evolved in vitro by a protein engineering approach to efficiently degrade glyphosate. Two constructs were used, one with (GO(TP+)) and one without (GO(TP-)) the pea rbcS plastid transit peptide. Molecular and biochemical analyses confirmed the stable integration of the transgene and the correct localization of the plastid-imported GO protein. Transgenic alfalfa plants were tested for glyphosate resistance both in vitro and in vivo. Two GO(TP+) lines showed moderate resistance to the herbicide in both conditions. Optimization of expression of this GO variant may allow to attain sufficient field resistance to glyphosate herbicides, thus providing a resistance strategy based on herbicide degradation.
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Affiliation(s)
- A Nicolia
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy.
| | - N Ferradini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - G Molla
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J.H. Dunant 3, 21100 Varese, Italy; Centro Interuniversitario di Ricerca in Biotecnologie Proteiche The Protein Factory, Politecnico di Milano, ICRM CNR Milano and Università degli studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - E Biagetti
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - L Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli studi dell'Insubria, via J.H. Dunant 3, 21100 Varese, Italy; Centro Interuniversitario di Ricerca in Biotecnologie Proteiche The Protein Factory, Politecnico di Milano, ICRM CNR Milano and Università degli studi dell'Insubria, via Mancinelli 7, 20131 Milano, Italy
| | - F Veronesi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
| | - D Rosellini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy
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45
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Rosini E, Piubelli L, Molla G, Frattini L, Valentino M, Varriale A, D'Auria S, Pollegioni L. Novel biosensors based on optimized glycine oxidase. FEBS J 2014; 281:3460-72. [DOI: 10.1111/febs.12873] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/27/2014] [Accepted: 06/09/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
| | - Luciano Piubelli
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
| | - Luca Frattini
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
| | - Mattia Valentino
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
- CNR - Istituto di Chimica del Riconoscimento Molecolare; Sezione Adolfo Quilico; Milano Italy
| | | | - Sabato D'Auria
- CNR - Istituto di Biochimica delle Proteine; Napoli Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita; Università degli studi dell'Insubria; Varese Italy
- The Protein Factory; Centro Interuniversitario di Biotecnologie Proteiche; Politecnico di Milano; ICRM CNR Milano; Università degli studi dell'Insubria; Milano Italy
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Astroglial d-serine is the endogenous co-agonist at the presynaptic NMDA receptor in rat entorhinal cortex. Neuropharmacology 2014; 83:118-27. [PMID: 24747728 DOI: 10.1016/j.neuropharm.2014.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 03/17/2014] [Accepted: 04/07/2014] [Indexed: 12/17/2022]
Abstract
Presynaptic NMDA receptors facilitate the release of glutamate at excitatory cortical synapses and are involved in regulation of synaptic dynamics and plasticity. At synapses in the entorhinal cortex these receptors are tonically activated and provide a positive feedback modulation of the level of background excitation. NMDA receptor activation requires obligatory occupation of a co-agonist binding site, and in the present investigation we have examined whether this site on the presynaptic receptor is activated by endogenous glycine or d-serine. We used whole-cell patch clamp recordings of spontaneous AMPA receptor-mediated synaptic currents from rat entorhinal cortex neurones in vitro as a monitor of presynaptic glutamate release. Addition of exogenous glycine or d-serine had minimal effects on spontaneous release, suggesting that the co-agonist site was endogenously activated and likely to be saturated in our slices. This was supported by the observation that a co-agonist site antagonist reduced the frequency of spontaneous currents. Depletion of endogenous glycine by enzymatic breakdown with a bacterial glycine oxidase had little effect on glutamate release, whereas d-serine depletion with a yeast d-amino acid oxidase significantly reduced glutamate release, suggesting that d-serine is the endogenous agonist. Finally, the effects of d-serine depletion were mimicked by compromising astroglial cell function, and this was rescued by exogenous d-serine, indicating that astroglial cells are the provider of the d-serine that tonically activates the presynaptic NMDA receptor. We discuss the significance of these observations for the aetiology of epilepsy and possible targeting of the presynaptic NMDA receptor in anticonvulsant therapy.
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Identity of endogenous NMDAR glycine site agonist in amygdala is determined by synaptic activity level. Nat Commun 2013; 4:1760. [PMID: 23612301 PMCID: PMC3641574 DOI: 10.1038/ncomms2779] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 03/21/2013] [Indexed: 11/08/2022] Open
Abstract
Mechanisms of N-methyl-D-aspartate receptor-dependent synaptic plasticity contribute to the acquisition and retention of conditioned fear memory. However, synaptic rules which may determine the extent of N-methyl-D-aspartate receptor activation in the amygdala, a key structure implicated in fear learning, remain unknown. Here we show that the identity of the N-methyl-D-aspartate receptor glycine site agonist at synapses in the lateral nucleus of the amygdala may depend on the level of synaptic activation. Tonic activation of N-methyl-D-aspartate receptors at synapses in the amygdala under low activity conditions is supported by ambient D-serine, whereas glycine may be released from astrocytes in response to afferent impulses. The release of glycine may decode the increases in afferent activity levels into enhanced N-methyl-D-aspartate receptor-mediated synaptic events, serving an essential function in the induction of N-methyl-D-aspartate receptor-dependent long-term potentiation in fear conditioning pathways.
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Zhan T, Zhang K, Chen Y, Lin Y, Wu G, Zhang L, Yao P, Shao Z, Liu Z. Improving glyphosate oxidation activity of glycine oxidase from Bacillus cereus by directed evolution. PLoS One 2013; 8:e79175. [PMID: 24223901 PMCID: PMC3818420 DOI: 10.1371/journal.pone.0079175] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/20/2013] [Indexed: 11/18/2022] Open
Abstract
Glyphosate, a broad spectrum herbicide widely used in agriculture all over the world, inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, and glycine oxidase (GO) has been reported to be able to catalyze the oxidative deamination of various amines and cleave the C-N bond in glyphosate. Here, in an effort to improve the catalytic activity of the glycine oxidase that was cloned from a glyphosate-degrading marine strain of Bacillus cereus (BceGO), we used a bacteriophage T7 lysis-based method for high-throughput screening of oxidase activity and engineered the gene encoding BceGO by directed evolution. Six mutants exhibiting enhanced activity toward glyphosate were screened from two rounds of error-prone PCR combined with site directed mutagenesis, and the beneficial mutations of the six evolved variants were recombined by DNA shuffling. Four recombinants were generated and, when compared with the wild-type BceGO, the most active mutant B3S1 showed the highest activity, exhibiting a 160-fold increase in substrate affinity, a 326-fold enhancement in catalytic efficiency against glyphosate, with little difference between their pH and temperature stabilities. The role of these mutations was explored through structure modeling and molecular docking, revealing that the Arg(51) mutation is near the active site and could be an important residue contributing to the stabilization of glyphosate binding, while the role of the remaining mutations is unclear. These results provide insight into the application of directed evolution in optimizing glycine oxidase function and have laid a foundation for the development of glyphosate-tolerant crops.
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Affiliation(s)
- Tao Zhan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Kai Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yangyan Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yongjun Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Lili Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, College of Life Science, Tarim University, Alar, Xinjiang, P. R. China
| | - Pei Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, P. R. China
| | - Ziduo Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
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49
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Campillo-Brocal JC, Lucas-Elio P, Sanchez-Amat A. Identification in Marinomonas mediterranea of a novel quinoprotein with glycine oxidase activity. Microbiologyopen 2013; 2:684-94. [PMID: 23873697 PMCID: PMC3948610 DOI: 10.1002/mbo3.107] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/29/2013] [Accepted: 06/07/2013] [Indexed: 12/02/2022] Open
Abstract
A novel enzyme with lysine-epsilon oxidase activity was previously described in the marine bacterium Marinomonas mediterranea. This enzyme differs from other l-amino acid oxidases in not being a flavoprotein but containing a quinone cofactor. It is encoded by an operon with two genes lodA and lodB. The first one codes for the oxidase, while the second one encodes a protein required for the expression of the former. Genome sequencing of M. mediterranea has revealed that it contains two additional operons encoding proteins with sequence similarity to LodA. In this study, it is shown that the product of one of such genes, Marme_1655, encodes a protein with glycine oxidase activity. This activity shows important differences in terms of substrate range and sensitivity to inhibitors to other glycine oxidases previously described which are flavoproteins synthesized by Bacillus. The results presented in this study indicate that the products of the genes with different degrees of similarity to lodA detected in bacterial genomes could constitute a reservoir of different oxidases.
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50
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Branduardi P, Longo V, Berterame NM, Rossi G, Porro D. A novel pathway to produce butanol and isobutanol in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:68. [PMID: 23642236 PMCID: PMC3662618 DOI: 10.1186/1754-6834-6-68] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/25/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND The sustainable production of biofuels remains one of the major issues of the upcoming years. Among the number of most desirable molecules to be produced, butanol and isobutanol deserve a prominent place. They have superior liquid-fuel features in respect to ethanol. Particularly, butanol has similar properties to gasoline and thus it has the potential to be used as a substitute for gasoline in currently running engines. Clostridia are recognized as natural and good butanol producers and are employed in the industrial-scale production of solvents. Due to their complex metabolic characteristics and to the difficulty of performing genetic manipulations, in recent years the Clostridia butanol pathway was expressed in other microorganisms such as Escherichia coli and Saccharomyces cerevisiae, but in yeast the obtained results were not so promising. An alternative way for producing fusel alcohol is to exploit the degradation pathway of aminoacids released from protein hydrolysis, where proteins derive from exhausted microbial biomasses at the end of the fermentation processes. RESULTS It is known that wine yeasts can, at the end of the fermentation process, accumulate fusel alcohols, and butanol is among them. Despite it was quite obvious to correlate said production with aminoacid degradation, a putative native pathway was never proposed. Starting from literature data and combining information about different organisms, here we demonstrate how glycine can be the substrate for butanol and isobutanol production, individuating at least one gene encoding for the necessary activities leading to butanol accumulation. During a kinetic of growth using glycine as substrate, butanol and isobutanol accumulate in the medium up to 92 and 58 mg/L, respectively. CONCLUSIONS Here for the first time we demonstrate an alternative metabolic pathway for butanol and isobutanol production in the yeast S. cerevisiae, using glycine as a substrate. Doors are now opened for a number of optimizations, also considering that starting from an aminoacid mixture as a side stream process, a fusel alcohol blend can be generated.
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Affiliation(s)
- Paola Branduardi
- University of Milano Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | - Valeria Longo
- University of Milano Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
| | | | - Giorgia Rossi
- Current address: PTA (Schweiz) GmbH, Hohlstrasse 192, Zürich, CH-8004, Switzerland
| | - Danilo Porro
- University of Milano Bicocca, Piazza della Scienza 2, Milano, 20126, Italy
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