1
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Wang YL, Chang CY, Hsu NS, Lo IW, Lin KH, Chen CL, Chang CF, Wang ZC, Ogasawara Y, Dairi T, Maruyama C, Hamano Y, Li TL. N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry. Nat Commun 2023; 14:2528. [PMID: 37137912 PMCID: PMC10156733 DOI: 10.1038/s41467-023-38218-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a noncanonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 Å apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N-O or O-S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.
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Affiliation(s)
- Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chin-Yuan Chang
- Department of Biology Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan
| | - Ning-Shian Hsu
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - I-Wen Lo
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Hung Lin
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chun-Liang Chen
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Chi-Fon Chang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Zhe-Chong Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yasushi Ogasawara
- Graduate School of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Tohru Dairi
- Graduate School of Engineering, Hokkaido University, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan
| | - Chitose Maruyama
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan
- Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan
| | - Yoshimitsu Hamano
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan.
- Fukui Bioincubation Center (FBIC), Fukui Prefectural University, Eiheiji-cho, Fukui, 910-1195, Japan.
| | - Tsung-Lin Li
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan.
- Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.
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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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3
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Chen R, Wang S, Sun Y, Li H, Wan S, Lin F, Xu H. Comparison of Glyphosate-Degradation Ability of Aldo-Keto Reductase (AKR4) Proteins in Maize, Soybean and Rice. Int J Mol Sci 2023; 24:ijms24043421. [PMID: 36834831 PMCID: PMC9966811 DOI: 10.3390/ijms24043421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Genes that participate in the degradation or isolation of glyphosate in plants are promising, for they endow crops with herbicide tolerance with a low glyphosate residue. Recently, the aldo-keto reductase (AKR4) gene in Echinochloa colona (EcAKR4) was identified as a naturally evolved glyphosate-metabolism enzyme. Here, we compared the glyphosate-degradation ability of theAKR4 proteins from maize, soybean and rice, which belong to a clade containing EcAKR4 in the phylogenetic tree, by incubation of glyphosate with AKR proteins both in vivo and in vitro. The results indicated that, except for OsALR1, the other proteins were characterized as glyphosate-metabolism enzymes, with ZmAKR4 ranked the highest activity, and OsAKR4-1 and OsAKR4-2 exhibiting the highest activity among the AKR4 family in rice. Moreover, OsAKR4-1 was confirmed to endow glyphosate-tolerance at the plant level. Our study provides information on the mechanism underlying the glyphosate-degradation ability of AKR proteins in crops, which enables the development of glyphosate-resistant crops with a low glyphosate residue, mediated by AKRs.
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Affiliation(s)
| | | | | | | | | | - Fei Lin
- Correspondence: (F.L.); (H.X.); Tel.: +86-20-85285127 (H.X.)
| | - Hanhong Xu
- Correspondence: (F.L.); (H.X.); Tel.: +86-20-85285127 (H.X.)
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4
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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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Johnson ZT, Jared N, Peterson JK, Li J, Smith EA, Walper SA, Hooe SL, Breger JC, Medintz IL, Gomes C, Claussen JC. Enzymatic Laser-Induced Graphene Biosensor for Electrochemical Sensing of the Herbicide Glyphosate. GLOBAL CHALLENGES (HOBOKEN, NJ) 2022; 6:2200057. [PMID: 36176938 PMCID: PMC9463521 DOI: 10.1002/gch2.202200057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Glyphosate is a globally applied herbicide yet it has been relatively undetectable in-field samples outside of gold-standard techniques. Its presumed nontoxicity toward humans has been contested by the International Agency for Research on Cancer, while it has been detected in farmers' urine, surface waters and crop residues. Rapid, on-site detection of glyphosate is hindered by lack of field-deployable and easy-to-use sensors that circumvent sample transportation to limited laboratories that possess the equipment needed for detection. Herein, the flavoenzyme, glycine oxidase, immobilized on platinum-decorated laser-induced graphene (LIG) is used for selective detection of glyphosate as it is a substrate for GlyOx. The LIG platform provides a scaffold for enzyme attachment while maintaining the electronic and surface properties of graphene. The sensor exhibits a linear range of 10-260 µ m, detection limit of 3.03 µ m, and sensitivity of 0.991 nA µ m -1. The sensor shows minimal interference from the commonly used herbicides and insecticides: atrazine, 2,4-dichlorophenoxyacetic acid, dicamba, parathion-methyl, paraoxon-methyl, malathion, chlorpyrifos, thiamethoxam, clothianidin, and imidacloprid. Sensor function is further tested in complex river water and crop residue fluids, which validate this platform as a scalable, direct-write, and selective method of glyphosate detection for herbicide mapping and food analysis.
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Affiliation(s)
| | - Nathan Jared
- Department of Mechanical EngineeringIowa State UniversityAmesIA50011USA
| | - John K. Peterson
- Department of Mechanical EngineeringIowa State UniversityAmesIA50011USA
| | - Jingzhe Li
- Department of ChemistryIowa State UniversityAmesIA50011USA
- The Ames LaboratoryU.S. Department of EnergyAmesIA50011USA
| | - Emily A. Smith
- Department of ChemistryIowa State UniversityAmesIA50011USA
- The Ames LaboratoryU.S. Department of EnergyAmesIA50011USA
| | - Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashington, D.C20375USA
| | - Shelby L. Hooe
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashington, D.C20375USA
- National Research CouncilWashington, DC20001USA
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashington, D.C20375USA
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900U.S. Naval Research LaboratoryWashington, D.C20375USA
| | - Carmen Gomes
- Department of Mechanical EngineeringIowa State UniversityAmesIA50011USA
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6
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Anshuman Gogoi, Linkon Bharali. Conversion of Glycine to Oxalate in Presence of CuSO4⋅5H2O and Isonicotinamide. RUSS J INORG CHEM+ 2022. [DOI: 10.1134/s0036023622050072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Pirillo V, Orlando M, Tessaro D, Pollegioni L, Molla G. An Efficient Protein Evolution Workflow for the Improvement of Bacterial PET Hydrolyzing Enzymes. Int J Mol Sci 2021; 23:ijms23010264. [PMID: 35008691 PMCID: PMC8745736 DOI: 10.3390/ijms23010264] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/23/2021] [Accepted: 12/24/2021] [Indexed: 12/23/2022] Open
Abstract
Enzymatic degradation is a promising green approach to bioremediation and recycling of the polymer poly(ethylene terephthalate) (PET). In the past few years, several PET-hydrolysing enzymes (PHEs) have been discovered, and new variants have been evolved by protein engineering. Here, we report on a straightforward workflow employing semi-rational protein engineering combined to a high-throughput screening of variant libraries for their activity on PET nanoparticles. Using this approach, starting from the double variant W159H/S238F of Ideonella sakaiensis 201-F6 PETase, the W159H/F238A-ΔIsPET variant, possessing a higher hydrolytic activity on PET, was identified. This variant was stabilized by introducing two additional known substitutions (S121E and D186H) generating the TS-ΔIsPET variant. By using 0.1 mg mL−1 of TS-ΔIsPET, ~10.6 mM of degradation products were produced in 2 days from 9 mg mL−1 PET microparticles (~26% depolymerization yield). Indeed, TS-ΔIsPET allowed a massive degradation of PET nanoparticles (>80% depolymerization yield) in 1.5 h using only 20 μg of enzyme mL−1. The rationale underlying the effect on the catalytic parameters due to the F238A substitution was studied by enzymatic investigation and molecular dynamics/docking analysis. The present workflow is a well-suited protocol for the evolution of PHEs to help generate an efficient enzymatic toolbox for polyester degradation.
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Affiliation(s)
- Valentina Pirillo
- “The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (V.P.); (M.O.)
| | - Marco Orlando
- “The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (V.P.); (M.O.)
| | - Davide Tessaro
- Dipartimento di Chimica, Materiali e Ingegneria Chimica “Giulio Natta”, Politecnico di Milano, p.za L. da Vinci 32, 20133 Milano, Italy;
| | - Loredano Pollegioni
- “The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (V.P.); (M.O.)
- Correspondence: (L.P.); (G.M.)
| | - Gianluca Molla
- “The Protein Factory 2.0”, Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell’Insubria, Via J.H. Dunant 3, 21100 Varese, Italy; (V.P.); (M.O.)
- Correspondence: (L.P.); (G.M.)
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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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9
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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: 4] [Impact Index Per Article: 1.3] [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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10
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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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11
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d-Aspartate oxidase: distribution, functions, properties, and biotechnological applications. Appl Microbiol Biotechnol 2020; 104:2883-2895. [DOI: 10.1007/s00253-020-10439-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 01/28/2020] [Accepted: 02/05/2020] [Indexed: 12/16/2022]
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12
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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: 2] [Impact Index Per Article: 0.4] [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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13
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Molla G, Chaves‐Sanjuan A, Savinelli A, Nardini M, Pollegioni L. Structure and kinetic properties of humand‐aspartate oxidase, the enzyme‐controllingd‐aspartate levels in brain. FASEB J 2019; 34:1182-1197. [DOI: 10.1096/fj.201901703r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Gianluca Molla
- Dipartimento di Biotecnologie e Scienze della Vita Università degli studi dell’Insubria Varese Italy
| | | | - Antonio Savinelli
- Dipartimento di Biotecnologie e Scienze della Vita Università degli studi dell’Insubria Varese Italy
| | - Marco Nardini
- Dipartimento di Bioscienze Università degli studi di Milano Milano Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita Università degli studi dell’Insubria Varese Italy
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14
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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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15
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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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16
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Pollegioni L, Sacchi S, Murtas G. Human D-Amino Acid Oxidase: Structure, Function, and Regulation. Front Mol Biosci 2018; 5:107. [PMID: 30547037 PMCID: PMC6279847 DOI: 10.3389/fmolb.2018.00107] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/12/2018] [Indexed: 12/11/2022] Open
Abstract
D-Amino acid oxidase (DAAO) is an FAD-containing flavoenzyme that catalyzes with absolute stereoselectivity the oxidative deamination of all natural D-amino acids, the only exception being the acidic ones. This flavoenzyme plays different roles during evolution and in different tissues in humans. Its three-dimensional structure is well conserved during evolution: minute changes are responsible for the functional differences between enzymes from microorganism sources and those from humans. In recent years several investigations focused on human DAAO, mainly because of its role in degrading the neuromodulator D-serine in the central nervous system. D-Serine is the main coagonist of N-methyl D-aspartate receptors, i.e., excitatory amino acid receptors critically involved in main brain functions and pathologic conditions. Human DAAO possesses a weak interaction with the FAD cofactor; thus, in vivo it should be largely present in the inactive, apoprotein form. Binding of active-site ligands and the substrate stabilizes flavin binding, thus pushing the acquisition of catalytic competence. Interestingly, the kinetic efficiency of the enzyme on D-serine is very low. Human DAAO interacts with various proteins, in this way modulating its activity, targeting, and cell stability. The known properties of human DAAO suggest that its activity must be finely tuned to fulfill a main physiological function such as the control of D-serine levels in the brain. At present, studies are focusing on the epigenetic modulation of human DAAO expression and the role of post-translational modifications on its main biochemical properties at the cellular level.
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Affiliation(s)
- Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Silvia Sacchi
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
| | - Giulia Murtas
- Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi dell'Insubria, Varese, Italy
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17
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Berini F, Presti I, Beltrametti F, Pedroli M, Vårum KM, Pollegioni L, Sjöling S, Marinelli F. Production and characterization of a novel antifungal chitinase identified by functional screening of a suppressive-soil metagenome. Microb Cell Fact 2017; 16:16. [PMID: 28137256 PMCID: PMC5282697 DOI: 10.1186/s12934-017-0634-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 01/20/2017] [Indexed: 01/20/2023] Open
Abstract
Background Through functional screening of a fosmid library, generated from a phytopathogen-suppressive soil metagenome, the novel antifungal chitinase—named Chi18H8 and belonging to family 18 glycosyl hydrolases—was previously discovered. The initial extremely low yield of Chi18H8 recombinant production and purification from Escherichia coli cells (21 μg/g cell) limited its characterization, thus preventing further investigation on its biotechnological potential. Results We report on how we succeeded in producing hundreds of milligrams of pure and biologically active Chi18H8 by developing and scaling up to a high-yielding, 30 L bioreactor process, based on a novel method of mild solubilization of E. coli inclusion bodies in lactic acid aqueous solution, coupled with a single step purification by hydrophobic interaction chromatography. Chi18H8 was characterized as a Ca2+-dependent mesophilic chitobiosidase, active on chitin substrates at acidic pHs and possessing interesting features, such as solvent tolerance, long-term stability in acidic environment and antifungal activity against the phytopathogens Fusarium graminearum and Rhizoctonia solani. Additionally, Chi18H8 was found to operate according to a non-processive endomode of action on a water-soluble chitin-like substrate. Conclusions Expression screening of a metagenomic library may allow access to the functional diversity of uncultivable microbiota and to the discovery of novel enzymes useful for biotechnological applications. A persisting bottleneck, however, is the lack of methods for large scale production of metagenome-sourced enzymes from genes of unknown origin in the commonly used microbial hosts. To our knowledge, this is the first report on a novel metagenome-sourced enzyme produced in hundreds-of-milligram amount by recovering the protein in the biologically active form from recombinant E. coli inclusion bodies. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0634-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Francesca Berini
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy. .,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy.
| | - Ilaria Presti
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy.,Chemo Biosynthesis, Corana, Pavia, Italy
| | | | | | - Kjell M Vårum
- NOBIPOL, Department of Biotechnology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy
| | - Sara Sjöling
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Flavia Marinelli
- Department of Biotechnology and Life Sciences, University of Insubria, Varese, Italy.,"The Protein Factory Research Center", Politecnico di Milano and University of Insubria, Varese, Italy
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18
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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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19
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Motta P, Molla G, Pollegioni L, Nardini M. Structure-Function Relationships in l-Amino Acid Deaminase, a Flavoprotein Belonging to a Novel Class of Biotechnologically Relevant Enzymes. J Biol Chem 2016; 291:10457-75. [PMID: 27022028 DOI: 10.1074/jbc.m115.703819] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 01/11/2023] Open
Abstract
l-Amino acid deaminase from Proteus myxofaciens (PmaLAAD) is a membrane flavoenzyme that catalyzes the deamination of neutral and aromatic l-amino acids into α-keto acids and ammonia. PmaLAAD does not use dioxygen to re-oxidize reduced FADH2 and thus does not produce hydrogen peroxide; instead, it uses a cytochrome b-like protein as an electron acceptor. Although the overall fold of this enzyme resembles that of known amine or amino acid oxidases, it shows the following specific structural features: an additional novel α+β subdomain placed close to the putative transmembrane α-helix and to the active-site entrance; an FAD isoalloxazine ring exposed to solvent; and a large and accessible active site suitable to bind large hydrophobic substrates. In addition, PmaLAAD requires substrate-induced conformational changes of part of the active site, particularly in Arg-316 and Phe-318, to achieve the correct geometry for catalysis. These studies are expected to pave the way for rationally improving the versatility of this flavoenzyme, which is critical for biocatalysis of enantiomerically pure amino acids.
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Affiliation(s)
- Paolo Motta
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese
| | - Gianluca Molla
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, The Protein Factory, Politecnico di Milano and Università degli Studi deII'Insubria, 21100 Varese, and
| | - Loredano Pollegioni
- From the Dipartimento di Biotecnologie e Scienze della Vita, Università degli Studi deII'Insubria, via J. H. Dunant 3, 21100 Varese, The Protein Factory, Politecnico di Milano and Università degli Studi deII'Insubria, 21100 Varese, and
| | - Marco Nardini
- the Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, 20133 Milano, Italy
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20
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Jacewicz A, Schnell R, Lindqvist Y, Schneider G. Crystal structure of the flavoenzyme PA4991 from Pseudomonas aeruginosa. Acta Crystallogr F Struct Biol Commun 2016; 72:105-11. [PMID: 26841760 PMCID: PMC4741190 DOI: 10.1107/s2053230x15024437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 12/18/2015] [Indexed: 11/13/2022] Open
Abstract
The locus PA4991 in Pseudomonas aeruginosa encodes an open reading frame that has been identified as essential for the virulence and/or survival of this pathogenic organism in the infected host. Here, it is shown that this gene encodes a monomeric FAD-binding protein of molecular mass 42.2 kDa. The structure of PA4991 was determined by a combination of molecular replacement using a search model generated with Rosetta and phase improvement by a low-occupancy heavy-metal derivative. PA4991 belongs to the GR2 family of FAD-dependent oxidoreductases, comprising an FAD-binding domain typical of the glutathione reductase family and a second domain dominated by an eight-stranded mixed β-sheet. Most of the protein-FAD interactions are via the FAD-binding domain, but the isoalloxazine ring is located at the domain interface and interacts with residues from both domains. A comparison with the structurally related glycine oxidase and glycerol-3-phosphate dehydrogenase shows that in spite of very low amino-acid sequence identity (<18%) several active-site residues involved in substrate binding in these enzymes are conserved in PA4991. However, enzymatic assays show that PA4991 does not display amino-acid oxidase or glycerol-3-phosphate dehydrogenase activities, suggesting that it requires different substrates for activity.
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Affiliation(s)
- Agata Jacewicz
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Robert Schnell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Ylva Lindqvist
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
| | - Gunter Schneider
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden
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21
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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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22
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Hossain GS, Shin HD, Li J, Wang M, Du G, Liu L, Chen J. Integrating error-prone PCR and DNA shuffling as an effective molecular evolution strategy for the production of α-ketoglutaric acid byl-amino acid deaminase. RSC Adv 2016. [DOI: 10.1039/c6ra02940j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
l-Amino acid deaminases (LAADs; EC 1.4.3.2) belong to a family of amino acid dehydrogenases that catalyze the formation of α-keto acids froml-amino acids.
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Affiliation(s)
- Gazi Sakir Hossain
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
| | - Hyun-dong Shin
- School of Chemical and Biomolecular Engineering
- Georgia Institute of Technology
- Atlanta
- USA
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
- China
| | - Miao Wang
- School of Food Science and Technology
- Jiangnan University
- Wuxi 214122
- China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
- China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
- China
| | - Jian Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology
- Ministry of Education
- Jiangnan University
- Wuxi 214122
- China
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23
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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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24
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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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25
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Elkhal CK, Kean KM, Parsonage D, Maenpuen S, Chaiyen P, Claiborne A, Karplus PA. Structure and proposed mechanism of L-α-glycerophosphate oxidase from Mycoplasma pneumoniae. FEBS J 2015; 282:3030-42. [PMID: 25688572 DOI: 10.1111/febs.13233] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/29/2015] [Accepted: 02/12/2015] [Indexed: 12/17/2022]
Abstract
UNLABELLED The formation of H2 O2 by the FAD-dependent L-α-glycerophosphate oxidase (GlpO) is important for the pathogenesis of Streptococcus pneumoniae and Mycoplasma pneumoniae. The structurally known GlpO from Streptococcus sp. (SspGlpO) is similar to the pneumococcal protein (SpGlpO) and provides a guide for drug design against that target. However, M. pneumoniae GlpO (MpGlpO), having < 20% sequence identity with structurally known GlpOs, appears to represent a second type of GlpO that we designate as type II GlpOs. In the present study, the recombinant His-tagged MpGlpO structure is described at an approximate resolution of 2.5 Å, solved by molecular replacement using, as a search model, the Bordetella pertussis protein 3253 (Bp3253), comprising a protein of unknown function solved by structural genomics efforts. Recombinant MpGlpO is an active oxidase with a turnover number of approximately 580 min(-1), whereas Bp3253 showed no GlpO activity. No substantial differences exist between the oxidized and dithionite-reduced MpGlpO structures. Although, no liganded structures were determined, a comparison with the tartrate-bound Bp3253 structure and consideration of residue conservation patterns guided the construction of a model for L-α-glycerophosphate (Glp) recognition and turnover by MpGlpO. The predicted binding mode also appears relevant for the type I GlpOs (such as SspGlpO) despite differences in substrate recognition residues, and it implicates a histidine conserved in type I and II Glp oxidases and dehydrogenases as the catalytic acid/base. The present study provides a solid foundation for guiding further studies of the mitochondrial Glp dehydrogenases, as well as for continued studies of M. pneumoniae and S. pneumoniae glycerol metabolism and the development of novel therapeutics targeting MpGlpO and SpGlpO. DATABASE Structural data have been deposited in the Protein Data Bank under accession numbers 4X9M (oxidized) and 4X9N (reduced).
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Affiliation(s)
- Callia K Elkhal
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Kelsey M Kean
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Derek Parsonage
- Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center of Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Al Claiborne
- Center for Structural Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
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26
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Lemire BD. A structural model for FOXRED1, an FAD-dependent oxidoreductase necessary for NADH: Ubiquinone oxidoreductase (complex I) assembly. Mitochondrion 2015; 22:9-16. [PMID: 25765152 DOI: 10.1016/j.mito.2015.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/27/2015] [Accepted: 02/27/2015] [Indexed: 01/06/2023]
Abstract
The biogenesis of mitochondrial respiratory chain components is complex. Mammalian complex I (NADH:ubiquinone oxidoreductase) contains 44 different subunits, an FMN and seven iron-sulfur centers. Its assembly involves at least twelve additional proteins, called assembly factors. One of these is FOXRED1, a 486-amino acid FAD-dependent oxidoreductase. FOXRED1 is a member of the d-amino acid oxidase (DAO) family. A structural model of FOXRED1 reveals a large substrate-binding cavity and a putative oxygen-binding site. These features strongly suggest that FOXRED1 is catalytically active as an oxidoreductase. A metabolic role for FOXRED1 in the biogenesis of complex I should be considered.
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Affiliation(s)
- Bernard D Lemire
- Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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27
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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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28
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Weiß MS, Pavlidis IV, Vickers C, Höhne M, Bornscheuer UT. Glycine Oxidase Based High-Throughput Solid-Phase Assay for Substrate Profiling and Directed Evolution of (R)- and (S)-Selective Amine Transaminases. Anal Chem 2014; 86:11847-53. [DOI: 10.1021/ac503445y] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin S. Weiß
- Institute of Biochemistry,
Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Ioannis V. Pavlidis
- Institute of Biochemistry,
Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Clare Vickers
- Institute of Biochemistry,
Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Matthias Höhne
- Institute of Biochemistry,
Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Uwe T. Bornscheuer
- Institute of Biochemistry,
Department of Biotechnology and Enzyme Catalysis, Greifswald University, Felix Hausdorff-Str. 4, 17487 Greifswald, Germany
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29
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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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30
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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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31
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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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32
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Kalliokoski T, Olsson TSG, Vulpetti A. Subpocket analysis method for fragment-based drug discovery. J Chem Inf Model 2013; 53:131-41. [PMID: 23327721 DOI: 10.1021/ci300523r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Although two binding sites might be dissimilar overall, they might still bind the same fragments if they share suitable subpockets. Information about shared subpockets can be therefore used in fragment-based drug design to suggest new fragments or to replace existing fragments within an already known compound. A novel computational method called SubCav is described which allows the similarity searching and alignment of subpockets from a PDB-wide database against a user-defined query. The method is based on pharmacophoric fingerprints combined with a subpocket alignment algorithm. SubCav was shown to be effective in producing reasonable alignments for subpockets with low sequence similarity and be able to retrieve relevant subpockets from a large database of structures including those with different folds. It can also be used to analyze subpockets inside a protein family to facilitate drug design and to rationalize compound selectivity.
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Affiliation(s)
- Tuomo Kalliokoski
- Novartis Institutes for Biomedical Research, Postfach, CH-4002 Basel, Switzerland
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33
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Kinjo AR, Nakamura H. Composite structural motifs of binding sites for delineating biological functions of proteins. PLoS One 2012; 7:e31437. [PMID: 22347478 PMCID: PMC3275580 DOI: 10.1371/journal.pone.0031437] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 01/08/2012] [Indexed: 11/19/2022] Open
Abstract
Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures.
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Affiliation(s)
- Akira R Kinjo
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
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34
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Pollegioni L, Schonbrunn E, Siehl D. Molecular basis of glyphosate resistance-different approaches through protein engineering. FEBS J 2011; 278:2753-66. [PMID: 21668647 PMCID: PMC3145815 DOI: 10.1111/j.1742-4658.2011.08214.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glyphosate (N-phosphonomethyl-glycine) is the most widely used herbicide in the world: glyphosate-based formulations exhibit broad-spectrum herbicidal activity with minimal human and environmental toxicity. The extraordinary success of this simple, small molecule is mainly attributable to the high specificity of glyphosate for the plant enzyme enolpyruvyl shikimate-3-phosphate synthase in the shikimate pathway, leading to the biosynthesis of aromatic amino acids. Starting in 1996, transgenic glyphosate-resistant plants were introduced, thus allowing application of the herbicide to the crop (post-emergence) to remove emerged weeds without crop damage. This review focuses on mechanisms of resistance to glyphosate as obtained through natural diversity, the gene-shuffling approach to molecular evolution, and a rational, structure-based approach to protein engineering. In addition, we offer a rationale for the means by which the modifications made have had their intended effect.
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Affiliation(s)
- Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze Molecolari, Università degli Studi dell'Insubria, Varese, Italy.
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35
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New biotech applications from evolved D-amino acid oxidases. Trends Biotechnol 2011; 29:276-83. [PMID: 21397351 DOI: 10.1016/j.tibtech.2011.01.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 01/24/2011] [Accepted: 01/27/2011] [Indexed: 11/20/2022]
Abstract
D-Amino acid oxidase (DAAO) is a well-known flavoenzyme that catalyzes the oxygen-dependent oxidative deamination of amino acid D-isomers with absolute stereospecificity, which results in α-keto acids, ammonia and hydrogen peroxide. Recently, the extraordinary functional plasticity of DAAO has become evident; in turn, boosting research on this flavoprotein. Protein engineering has allowed for a redesign of DAAO substrate specificity, oxygen affinity, cofactor binding, stability, and oligomeric state. We review recent developments in utilizing DAAO, including as a biocatalyst for resolving racemic amino acid mixtures, as a tool for biosensing, and as a new mechanism of herbicide resistance. Perspectives for future biotechnological applications of this oxidative biocatalyst are also outlined.
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36
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Gene cloning and characterization of glycine oxidase from newly isolated Bacillus subtilis strain R5. Biologia (Bratisl) 2010. [DOI: 10.2478/s11756-010-0141-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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37
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Jamil F, Afza Gardner QTA, Bashir Q, Rashid N, Akhtar M. Mechanistic and Stereochemical Studies of Glycine Oxidase from Bacillus subtilis Strain R5. Biochemistry 2010; 49:7377-83. [DOI: 10.1021/bi100553n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Farrukh Jamil
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | | | - Qamar Bashir
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
| | - Muhammad Akhtar
- School of Biological Sciences, University of the Punjab, New Campus, Lahore 54590, Pakistan
- School of Biological Sciences, University of Southampton, Southampton SO16 7PX, U.K
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38
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Pedotti M, Rosini E, Molla G, Moschetti T, Savino C, Vallone B, Pollegioni L. Glyphosate resistance by engineering the flavoenzyme glycine oxidase. J Biol Chem 2009; 284:36415-36423. [PMID: 19864430 PMCID: PMC2794757 DOI: 10.1074/jbc.m109.051631] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 10/12/2009] [Indexed: 11/06/2022] Open
Abstract
Glycine oxidase from Bacillus subtilis is a homotetrameric flavoprotein of great potential biotechnological use because it catalyzes the oxidative deamination of various amines and d-isomer of amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Glyphosate (N-phosphonomethylglycine), a broad spectrum herbicide, is an interesting synthetic amino acid: this compound inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids in plants and certain bacteria. In recent years, transgenic crops resistant to glyphosate were mainly generated by overproducing the plant enzyme or by introducing a 5-enolpyruvylshikimate-3-phosphate synthase insensitive to this herbicide. In this work, we propose that the enzymatic oxidation of glyphosate could be an effective alternative to this important biotechnological process. To reach this goal, we used a rational design approach (together with site saturation mutagenesis) to generate a glycine oxidase variant more active on glyphosate than on the physiological substrate glycine. The glycine oxidase containing three point mutations (G51S/A54R/H244A) reaches an up to a 210-fold increase in catalytic efficiency and a 15,000-fold increase in the specificity constant (the k(cat)/K(m) ratio between glyphosate and glycine) as compared with wild-type glycine oxidase. The inspection of its three-dimensional structure shows that the alpha2-alpha3 loop (comprising residues 50-60 and containing two of the mutated residues) assumes a novel conformation and that the newly introduced residue Arg(54) could be the key residue in stabilizing glyphosate binding and destabilizing glycine positioning in the binding site, thus increasing efficiency on the herbicide.
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Affiliation(s)
- Mattia Pedotti
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Tommaso Moschetti
- Department of Biochemical Sciences, "Sapienza," University of Rome, 00185 Rome, Italy
| | - Carmelinda Savino
- Consiglio Nazionale delle Richerche Institute of Molecular Biology and Pathology, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences, "Sapienza," University of Rome, 00185 Rome, Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy.
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39
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FAD binding in glycine oxidase from Bacillus subtilis. Biochimie 2009; 91:1499-508. [DOI: 10.1016/j.biochi.2009.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 09/05/2009] [Indexed: 11/21/2022]
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40
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Forneris F, Battaglioli E, Mattevi A, Binda C. New roles of flavoproteins in molecular cell biology: histone demethylase LSD1 and chromatin. FEBS J 2009; 276:4304-12. [PMID: 19624733 DOI: 10.1111/j.1742-4658.2009.07142.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lysine-specific demethylase 1 (LSD1) is an enzyme that removes methyl groups from mono- and dimethylated Lys4 of histone H3, a post-translational modification associated with gene activation. Human LSD1 was the first histone demethylase to be discovered and this enzymatic activity is conserved among eukaryotes. LSD1 has been identified in a number of chromatin-remodeling complexes that control gene transcription and its demethylase activity has also been linked to pathological processes including tumorigenesis. The 852-residue sequence of LSD1 comprises an amine oxidase domain which identifies a family of enzymes that catalyze the FAD-dependent oxidation of amine substrates ranging from amino acids to aromatic neurotransmitters. Among these proteins, LSD1 is peculiar in that it acts on a protein substrate in the nuclear environment of chromatin-remodeling complexes. This functional divergence occurred during evolution from the eubacteria to eukaryotes by acquisition of additional domains such as the SWIRM domain. The N-terminal part of LSD1, predicted to be disordered, contains linear motifs that might represent functional sites responsible for the association of this enzyme with a variety of transcriptional protein complexes. LSD1 shares structural features with other flavin amine oxidases, including the overall fold of the amine oxidase domain region and details in the active site that are relevant for amine substrate oxidation.
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Affiliation(s)
- Federico Forneris
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Italy
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41
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Pedotti M, Ghisla S, Motteran L, Molla G, Pollegioni L. Catalytic and redox properties of glycine oxidase from Bacillus subtilis. Biochimie 2009; 91:604-12. [DOI: 10.1016/j.biochi.2009.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
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Martínez-Martínez I, Kaiser C, Rohde A, Ellert A, García-Carmona F, Sanchez-Ferrer A, Luttmann R. High-Level Production of Bacillus subtilis Glycine Oxidase by Fed-Batch Cultivation of Recombinant Escherichia coli Rosetta (DE3). Biotechnol Prog 2008; 23:645-51. [PMID: 17474758 DOI: 10.1021/bp0603917] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A fed-batch process for the high cell density cultivation of Escherichia coli Rosetta (DE3) and the production of the recombinant protein glycine oxidase (GOX) from Bacillus subtilis was developed. GOX is a deaminating enzyme that shares substrate specificity with d-amino acid oxidase and sarcosine oxidase and has great biotechnological potential. The B. subtilis gene coding for GOX was expressed in E. coli Rosetta under the strong inducible T7 promotor of the pET28a vector. Exponential feeding based on the specific growth rate and a starvation period for acetate utilization was used to control cell growth, acetate production, and reconsumption and glucose consumption during fed-batch cultivation. Expression of GOX was induced at three different cell densities (20, 40, and 60 g . L(-1)). When cells were induced at intermediate cell density, the amount of GOX produced was 20 U . g(-1) cell dry weight and 1154 U . L(-1) with a final intracellular protein concentration corresponding to approximately 37% of the total cell protein concentration. These values were higher than those previously published for GOX expression and also represent a drastic decrease of 26-fold in the cost of the culture medium.
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Affiliation(s)
- Irene Martínez-Martínez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, University of Murcia, Campus Espinardo, E-30071 Murcia, Spain
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Properties and applications of microbial D-amino acid oxidases: current state and perspectives. Appl Microbiol Biotechnol 2008; 78:1-16. [DOI: 10.1007/s00253-007-1282-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 11/09/2007] [Accepted: 11/09/2007] [Indexed: 10/22/2022]
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Martínez-Martínez I, Navarro-Fernández J, García-Carmona F, Sánchez-Ferrer A. Implication of a mutation in the flavin binding site on the specific activity and substrate specificity of glycine oxidase from Bacillus subtilis produced by directed evolution. J Biotechnol 2008; 133:1-8. [PMID: 17976850 DOI: 10.1016/j.jbiotec.2007.07.950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 07/10/2007] [Accepted: 07/20/2007] [Indexed: 11/18/2022]
Abstract
Directed evolution was used to expand the substrate specificity and functionality of glycine oxidase by using a high-throughput screening assay based on the 4-aminoantipyrine peroxidase system, with a coefficient of variance below 4%. After screening the library, one mutant with the desired changes was found. The mutant was purified and characterized, showing important changes compared to the wild-type, especially towards cyclic d-amino acids. Amino acid substitution of Ile15 for Val, where the consensus sequence for flavin binding site is placed, seems to be responsible for these changes in specific activity and substrate specificity. The effect of this mutation was explained by using a computer-based three-dimensional model.
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Affiliation(s)
- Irene Martínez-Martínez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, University of Murcia, Campus Espinardo, E-30071 Murcia, Spain
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Martínez-Martínez I, Navarro-Fernández J, García-Carmona F, Takami H, Sánchez-Ferrer A. Characterization and structural modeling of a novel thermostable glycine oxidase from Geobacillus kaustophilus HTA426. Proteins 2007; 70:1429-41. [PMID: 17894345 DOI: 10.1002/prot.21690] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Glycine oxidase from Geobacillus kaustophilus HTA426 (GOXK) is a 43 kDa monomer flavoenzyme containing noncovalently bound FAD. The induction of the enzyme resulted in the expression of a fully soluble protein with higher specific activity than those previously reported for GOX from B. subtilis (GOXB). A study of the kinetic properties of this novel GOXK revealed the lowest KM values for most of the substrates analyzed, with the exception of D-proline which kept a similar value and had the highest Vmax value reported. The Vmax/KM ratio maintained a substrate preference of GOXK for amines of small size, like glycine, sarcosine, N-ethyl-glycine, and glycine-ethyl-ester. GOXK presented good stability at 60-70 degrees C and in alkaline media (pH 6-9.5). The putative tridimensional structure was modeled by sequence alignment and by comparing the changes between GOXK and GOXB, and the residues that could be responsible for the substrate specificity as well as those essential for the catalytic activity were found. The comparison between the possible topology of GOXK with that of GOXB showed changes at the putative interactions between monomers for the building of the tetrameric oligomerization.
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Affiliation(s)
- Irene Martínez-Martínez
- Department of Biochemistry and Molecular Biology-A, Faculty of Biology, University of Murcia, Campus Espinardo, E-30071 Murcia, Spain
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Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 2007; 282:28791-28799. [PMID: 17573341 DOI: 10.1074/jbc.m703759200] [Citation(s) in RCA: 306] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
In this report, a genome-scale reconstruction of Bacillus subtilis metabolism and its iterative development based on the combination of genomic, biochemical, and physiological information and high-throughput phenotyping experiments is presented. The initial reconstruction was converted into an in silico model and expanded in a four-step iterative fashion. First, network gap analysis was used to identify 48 missing reactions that are needed for growth but were not found in the genome annotation. Second, the computed growth rates under aerobic conditions were compared with high-throughput phenotypic screen data, and the initial in silico model could predict the outcomes qualitatively in 140 of 271 cases considered. Detailed analysis of the incorrect predictions resulted in the addition of 75 reactions to the initial reconstruction, and 200 of 271 cases were correctly computed. Third, in silico computations of the growth phenotypes of knock-out strains were found to be consistent with experimental observations in 720 of 766 cases evaluated. Fourth, the integrated analysis of the large-scale substrate utilization and gene essentiality data with the genome-scale metabolic model revealed the requirement of 80 specific enzymes (transport, 53; intracellular reactions, 27) that were not in the genome annotation. Subsequent sequence analysis resulted in the identification of genes that could be putatively assigned to 13 intracellular enzymes. The final reconstruction accounted for 844 open reading frames and consisted of 1020 metabolic reactions and 988 metabolites. Hence, the in silico model can be used to obtain experimentally verifiable hypothesis on the metabolic functions of various genes.
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Affiliation(s)
- You-Kwan Oh
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093-0412 and
| | - Bernhard O Palsson
- Department of Bioengineering, University of California at San Diego, La Jolla, California 92093-0412 and
| | - Sung M Park
- Genomatica, Inc., San Diego, California 92121
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Boselli A, Rosini E, Marcone GL, Sacchi S, Motteran L, Pilone MS, Pollegioni L, Molla G. Glycine oxidase from Bacillus subtilis: role of histidine 244 and methionine 261. Biochimie 2007; 89:1372-80. [PMID: 17573175 DOI: 10.1016/j.biochi.2007.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2007] [Accepted: 04/27/2007] [Indexed: 11/24/2022]
Abstract
The reactions of several mutants at position 244 and 261 of bacterial glycine oxidase (GO) were studied by stopped-flow and steady-state kinetic methods. Substituting H244 with phenylalanine, glutamate, and glutamine and M261 with histidine and tyrosine did not affect the expression of GO and the physicochemical properties of bound FAD. All the H244 and M261 mutants of GO we prepared retained activity in both steady-state and stopped-flow kinetic studies, indicating they do not serve as key elements in glycine and sarcosine oxidation. We demonstrated that the substitution of H244 significantly affected the rate of flavin reduction with glycine even if this change did not modify the turnover number, which is frequently increased compared to wild-type GO. However, substitution of M261 affected the interaction with substrates/inhibitors and the rate of flavin reduction with sarcosine and resulted in a decrease in turnover number and efficiency with all the substrates tested. The considerable decrease in the rate of flavin reduction changed the conditions such that it was partially rate-limiting in the catalytic cycle compared to the wild-type GO. Our studies show some similarities, but also major differences, in the catalytic mechanism of GO and other flavooxidases also active on glycine and sarcosine and give insight into the mode of modulation of catalysis and substrate specificities.
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Affiliation(s)
- Angelo Boselli
- Department of Biotechnology and Molecular Sciences, University of Insubria, via JH Dunant 3, 21100, Varese, Italy
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Dasu VV, Nakada Y, Ohnishi-Kameyama M, Kimura K, Itoh Y. Characterization and a role of Pseudomonas aeruginosa spermidine dehydrogenase in polyamine catabolism. Microbiology (Reading) 2006; 152:2265-2272. [PMID: 16849793 DOI: 10.1099/mic.0.28920-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pseudomonas aeruginosaPAO1 has two possible catabolic pathways of spermidine and spermine; one includes thespuAandspuBproducts with unknown functions and the other involves spermidine dehydrogenase (SpdH; EC 1.5.99.6) encoded by an unknown gene. The properties of SpdH inP. aeruginosaPAO1 were characterized and the correspondingspdHgene in this strain identified. The deduced SpdH (620 residues, calculatedMrof 68 861) had a signal sequence of 28 amino acids at the amino terminal and a potential transmembrane segment between residues 76 and 92, in accordance with membrane location of the enzyme. Purified SpdH oxidatively cleaved spermidine into 1,3-diaminopropane and 4-aminobutyraldehyde with a specific activity of 37 units (mg protein)−1and aKmvalue of 36 μM. The enzyme also hydrolysed spermine into spermidine and 3-aminopropanaldehyde with a specific activity of 25 units (mg protein)−1and aKmof 18 μM. Knockout ofspdHhad no apparent effect on the utilization of both polyamines, suggesting that this gene is minimally involved in polyamine catabolism. However, whenspdHwas fused to the polyamine-inducible promoter ofspuA, it fully restored the ability of aspuAmutant to utilize spermidine. It is concluded that SpdH can perform a catabolic rolein vivo, butP. aeruginosaPAO1 does not produce sufficient amounts of the enzyme to execute this function.
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Affiliation(s)
- Veeranki Venkata Dasu
- National Food Research Institute, Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642, Japan
| | - Yuji Nakada
- National Food Research Institute, Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642, Japan
| | | | - Keitarou Kimura
- National Food Research Institute, Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642, Japan
| | - Yoshifumi Itoh
- Akita Research Institute for Food and Brewing, Sanuki 4-26, Araya-machi, Akita 010-1623, Japan
- National Food Research Institute, Kannondai 2-1-12, Tsukuba, Ibaraki 305-8642, Japan
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Rossi F, Gatto V, Marzotto M, Torriani S. A Genetic Insight Into Peptide and Amino-Acid Utilization by Propionibacterium freudenreichii LMG 16415. Curr Microbiol 2006; 52:464-8. [PMID: 16732457 DOI: 10.1007/s00284-005-0353-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Accepted: 02/10/2006] [Indexed: 11/26/2022]
Abstract
In this note the genetic characterization of the peptide degrading system of Propionibacterium freudenreichii was addressed. Genomic fragments of P. freudenreichii subsp. freudenreichii LMG 16415 were cloned in Escherichia coli XL1 Blue, and those leading to an increase in peptidase-like activity using chromogenic substrates aminoacyl-beta-naphtylamides (aminoacyl-betaNA) were isolated and sequenced. This strategy allowed the identification of partial gene regions of P. freudenreichii LMG 16415 with significant similarity to proteins directly or indirectly involved in peptide and amino acid metabolism, i.e., an oligopeptide transporter, a D-amino acid oxidase, a muropeptidase, and an ABC transporter involved in osmoregulation similar to glycine betaine transporters.
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Affiliation(s)
- Franca Rossi
- Dipartimento Scientifico e Tecnologico, Università degli Studi di Verona, Strada Le Grazie 15, 37134, Verona, Italy
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50
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Panatier A, Theodosis DT, Mothet JP, Touquet B, Pollegioni L, Poulain DA, Oliet SHR. Glia-Derived d-Serine Controls NMDA Receptor Activity and Synaptic Memory. Cell 2006; 125:775-84. [PMID: 16713567 DOI: 10.1016/j.cell.2006.02.051] [Citation(s) in RCA: 651] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2005] [Revised: 01/03/2006] [Accepted: 02/28/2006] [Indexed: 02/05/2023]
Abstract
The NMDA receptor is a key player in excitatory transmission and synaptic plasticity in the central nervous system. Its activation requires the binding of both glutamate and a co-agonist like D-serine to its glycine site. As D-serine is released exclusively by astrocytes, we studied the physiological impact of the glial environment on NMDA receptor-dependent activity and plasticity. To this end, we took advantage of the changing astrocytic ensheathing of neurons occurring in the supraoptic nucleus during lactation. We provide direct evidence that in this hypothalamic structure the endogenous co-agonist of NMDA receptors is D-serine and not glycine. Consequently, the degree of astrocytic coverage of neurons governs the level of glycine site occupancy on the NMDA receptor, thereby affecting their availability for activation and thus the activity dependence of long-term synaptic changes. Such a contribution of astrocytes to synaptic metaplasticity fuels the emerging concept that astrocytes are dynamic partners of brain signaling.
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