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Dong C, Cui S, Ren J, Gong G, Zha J, Wu X. Engineering of bacteria towards programmed autolysis: why, how, and when? Microb Cell Fact 2024; 23:293. [PMID: 39465360 PMCID: PMC11514776 DOI: 10.1186/s12934-024-02566-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 10/11/2024] [Indexed: 10/29/2024] Open
Abstract
Programmed autolytic bacteria, also termed controlled self-disruptive or self-destructive bacteria, are bacterial systems that express certain lytic genes and undergo cell lysis at a predetermined time point to release the intracellular contents or to commit suicide. Such systems have wide applications in high-throughput screening of protein libraries, synthesis and recovery of bio-products, population control of heterogeneous cultures or synthetic co-cultures, drug delivery, and food fermentation. Recently, great achievements have been reported regarding on-demand control of cell autolysis for different purposes, highlighting the potential of autolytic strains in biomanufacturing and biomedicine. In this review article, we first introduce the various applications of such bacteria, followed by a summarization of the approaches used in the establishment of autolytic bacterial systems, including cell autolysis mediated by cell wall hydrolases with or without facilitating proteins and by membrane-disturbing proteins. Next, we describe in detail the methodologies adopted to control and initiate cell lysis, including induction by chemical inducers, stimulation by physical signals, auto-induction by metabolic status or nutrient limitation, and constitutive expression of the lytic genes. This article is ended with discussions on the remaining problems and possible future directions. This review provides comprehensive information on autolytic bacteria and insightful guidance to the development of highly efficient, robust, and smart autolytic bacterial platforms.
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Affiliation(s)
- Changying Dong
- College of Biological and Pharmaceutical Engineering, Jilin Agricultural Science and Technology University, 77 Hanlin Road, City of Jilin, 132101, Jilin, China.
| | - Shenghao Cui
- College of Biological and Pharmaceutical Engineering, Jilin Agricultural Science and Technology University, 77 Hanlin Road, City of Jilin, 132101, Jilin, China
| | - Jialuan Ren
- School of Food Science and Engineering, School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Guoli Gong
- School of Food Science and Engineering, School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China
| | - Jian Zha
- School of Food Science and Engineering, School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China.
- Xi'an Key Laboratory of Antiviral and Antimicrobial-Resistant Bacteria Therapeutics Research, Xi'an, 710021, Shaanxi, China.
| | - Xia Wu
- School of Food Science and Engineering, School of Biological and Pharmaceutical Sciences, Shaanxi University of Science and Technology, Xi'an, 710021, Shaanxi, China.
- Xi'an Key Laboratory of Antiviral and Antimicrobial-Resistant Bacteria Therapeutics Research, Xi'an, 710021, Shaanxi, China.
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Liu W, Tang D, Shi R, Lian J, Huang L, Cai J, Xu Z. Efficient production ofS‐adenosyl‐l‐methionine fromdl‐methionine in metabolic engineeredSaccharomyces cerevisiae. Biotechnol Bioeng 2019; 116:3312-3323. [DOI: 10.1002/bit.27157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/25/2019] [Accepted: 08/26/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Wei Liu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological EngineeringZhejiang University Hangzhou China
| | - Dandan Tang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological EngineeringZhejiang University Hangzhou China
- State Key Laboratory of Clean Energy Utilization, College of Energy EngineeringZhejiang University Hangzhou China
| | - Rui Shi
- Department of Food Science and TechnologyCollege of Light Industry and Food Engineering, Nanjing Forestry University Nanjing China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological EngineeringZhejiang University Hangzhou China
- Center for Synthetic Biology, College of Chemical and Biological EngineeringZhejiang University Hangzhou China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological EngineeringZhejiang University Hangzhou China
| | - Jin Cai
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological EngineeringZhejiang University Hangzhou China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological EngineeringZhejiang University Hangzhou China
- Center for Synthetic Biology, College of Chemical and Biological EngineeringZhejiang University Hangzhou China
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3
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Zheng J, Yang T, Zhou J, Xu M, Zhang X, Rao Z, Yang S. Efficient production of d-amino acid oxidase in Escherichia coli by a trade-off between its expression and biomass using N-terminal modification. BIORESOURCE TECHNOLOGY 2017; 243:716-723. [PMID: 28711799 DOI: 10.1016/j.biortech.2017.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 07/01/2017] [Accepted: 07/03/2017] [Indexed: 06/07/2023]
Abstract
Native d-amino acid oxidase (DAAO) that is expressed mostly as inclusion body and its toxicity for E. coli hamper efficient heterologous expression. In this study, the soluble expression of DAAO from Rhodosporidium toruloides (RtDAAO) was improved in E. coli through N-terminal modification, but the cell biomass was decreased. Then a trade-off between DAAO expression and biomass was achieved to obtain the highest volumetric activity of DAAO through regulated the number of N-terminus histidine residues. When variant 2H3G was fused with three N-terminus histidine residues, the volumetric activity was increased by 3.1 times and the biomass was not significant change compared with the wild type. Finally, the N-terminus disordered region of RtDAAO (HSQK) was replaced with HHHG and the variant enzyme activity reached 80.7U/mL (with a 40 percent of inactive DAAO reduced) in a 7.5L fermenter in 24h.
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Affiliation(s)
- Junxian Zheng
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Junping Zhou
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.
| | - Shangtian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
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4
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Development of a multi-enzymatic desymmetrization and its application for the biosynthesis of l -norvaline from dl -norvaline. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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5
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Parmeggiani F, Lovelock SL, Weise NJ, Ahmed ST, Turner NJ. Synthesis of d- and l-Phenylalanine Derivatives by Phenylalanine Ammonia Lyases: A Multienzymatic Cascade Process. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 127:4691-4694. [PMID: 27478261 PMCID: PMC4955227 DOI: 10.1002/ange.201410670] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/08/2015] [Indexed: 11/08/2022]
Abstract
The synthesis of substituted d-phenylalanines in high yield and excellent optical purity, starting from inexpensive cinnamic acids, has been achieved with a novel one-pot approach by coupling phenylalanine ammonia lyase (PAL) amination with a chemoenzymatic deracemization (based on stereoselective oxidation and nonselective reduction). A simple high-throughput solid-phase screening method has also been developed to identify PALs with higher rates of formation of non-natural d-phenylalanines. The best variants were exploited in the chemoenzymatic cascade, thus increasing the yield and ee value of the d-configured product. Furthermore, the system was extended to the preparation of those l-phenylalanines which are obtained with a low ee value using PAL amination.
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Affiliation(s)
- Fabio Parmeggiani
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester (UK)
| | - Sarah L. Lovelock
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester (UK)
| | - Nicholas J. Weise
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester (UK)
| | - Syed T. Ahmed
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester (UK)
| | - Nicholas J. Turner
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester (UK)
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Parmeggiani F, Lovelock SL, Weise NJ, Ahmed ST, Turner NJ. Synthesis of D- and L-phenylalanine derivatives by phenylalanine ammonia lyases: a multienzymatic cascade process. Angew Chem Int Ed Engl 2015; 54:4608-11. [PMID: 25728350 PMCID: PMC4531825 DOI: 10.1002/anie.201410670] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 01/08/2015] [Indexed: 11/25/2022]
Abstract
The synthesis of substituted d-phenylalanines in high yield and excellent optical purity, starting from inexpensive cinnamic acids, has been achieved with a novel one-pot approach by coupling phenylalanine ammonia lyase (PAL) amination with a chemoenzymatic deracemization (based on stereoselective oxidation and nonselective reduction). A simple high-throughput solid-phase screening method has also been developed to identify PALs with higher rates of formation of non-natural d-phenylalanines. The best variants were exploited in the chemoenzymatic cascade, thus increasing the yield and ee value of the d-configured product. Furthermore, the system was extended to the preparation of those l-phenylalanines which are obtained with a low ee value using PAL amination.
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Affiliation(s)
- Fabio Parmeggiani
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, M1 7DN, Manchester (UK)
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7
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High-level soluble and functional expression of Trigonopsis variabilis D-amino acid oxidase in Escherichia coli. Bioprocess Biosyst Eng 2014; 37:1517-26. [PMID: 24425540 DOI: 10.1007/s00449-013-1123-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/30/2013] [Indexed: 10/25/2022]
Abstract
D-Amino acid oxidase is an important biocatalyst used in a variety of fields, and its economically justified level recombinant expression in Escherichia coli has not been established. To accomplish this, after a single Phe54Tyr substitution, fusion proteins of D-amino acid oxidase from Trigonopsis variabilis (TvDAO) with 6 × His-tags were constructed and expressed in E. coli. The effects of his-tags fusing position were revealed. Significant increase in holoenzyme percent and protein solubility made N-terminus tagged TvDAO (termed NHDAO) a suitable choice for TvDAO production. However, reduced cell growth and protein production rates were also observed for the NHDAO bearing strains. To optimize the performance of NHDAO production, changes of culture medium were tested. Finally, a production of 140 U/mL or 3.48 g active enzyme per liter which accounted for 41.4 % of the total protein, and a specific activity of 16.68 U/mg for the crude extract, were achieved in a 3.7 L fermenter in 28.5 h. This indicated a possibility for functional and economical TvDAO expression in E. coli to meet the industrial need.
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8
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One-step production of α-ketoglutaric acid from glutamic acid with an engineered l-amino acid deaminase from Proteus mirabilis. J Biotechnol 2013; 164:97-104. [DOI: 10.1016/j.jbiotec.2013.01.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/05/2013] [Accepted: 01/09/2013] [Indexed: 11/23/2022]
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9
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Kopf J, Hormigo D, García JL, Acebal C, de la Mata I, Arroyo M. Inhibition of Recombinant D-Amino Acid Oxidase from Trigonopsis variabilisby Salts. Enzyme Res 2011; 2011:158541. [PMID: 21423676 PMCID: PMC3057018 DOI: 10.4061/2011/158541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 01/01/2011] [Indexed: 11/20/2022] Open
Abstract
Inhibition of recombinant D-amino acid oxidase fromTrigonopsis variabilis(TvDAAO) activity in the presence of different sodium salts and potassium chloride is reported. A competitive inhibition pattern by sodium chloride was observed, and an inhibition constant value ofKi=85 mM was calculated. Direct connection of NaCl inhibition with FAD cofactor dissociation was confirmed by measuring the fluorescence of tryptophanyl residues of the holoenzyme.
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Affiliation(s)
- Jessica Kopf
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
| | - Daniel Hormigo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
| | - José Luis García
- Departamento de Biología Medioambiental, Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carmen Acebal
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
| | - Isabel de la Mata
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
| | - Miguel Arroyo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain
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10
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Redo VA, Novikova EK, Eldarov MA. Expression of modified oxidase of D-aminoacids of Trigonopsis variabilis in methylotrophic yeasts Pichia pastoris. APPL BIOCHEM MICRO+ 2011. [DOI: 10.1134/s0003683811010133] [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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11
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Chen Y, Goldberg SL, Hanson RL, Parker WL, Gill I, Tully TP, Montana MA, Goswami A, Patel RN. Enzymatic Preparation of an (S)-Amino Acid from a Racemic Amino Acid. Org Process Res Dev 2010. [DOI: 10.1021/op1001534] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yijun Chen
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Steven L. Goldberg
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Ronald L. Hanson
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - William L. Parker
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Iqbal Gill
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Thomas P. Tully
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Michael A. Montana
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Animesh Goswami
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
| | - Ramesh N. Patel
- Process Research and Development, Bristol-Myers Squibb, One Squibb Drive, New Brunswick, New Jersey 08903, U.S.A
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12
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Gholizadeh A, Kohnehrouz BB. Molecular cloning and expression in Escherichia coli of an active fused Zea mays L. D-amino acid oxidase. BIOCHEMISTRY (MOSCOW) 2009; 74:137-44. [PMID: 19267668 DOI: 10.1134/s0006297909020035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
D-Amino acid oxidase (DAAO) is an FAD-dependent enzyme that metabolizes D-amino acids in microbes and animals. However, such ability has not been identified in plants so far. We predicted a complete DAAO coding sequence consisting of 1158 bp and encoding a protein of 386 amino acids. We cloned this sequence from the leaf cDNA population of maize plants that could utilize D-alanine as a nitrogen source and grow normally on media containing D-Ala at the concentrations of 100 and 1000 ppm. For more understanding of DAAO ability in maize plant, we produced a recombinant plasmid by the insertion of isolated cDNA into the pMALc2X Escherichia coli expression vector, downstream of the maltose-binding protein coding sequence. The pMALc2X-DAAO vector was used to transform the TB1 strain of E. coli cells. Under normal growth conditions, fused DAAO (with molecular weight of about 78 kDa) was expressed up to 5 mg/liter of bacterial cells. The expressed product was purified by affinity chromatography and subjected to in vitro DAAO activity assay in the presence of five different D-amino acids. Fused DAAO could oxidize D-alanine and D-aspartate, but not D-leucine, D-isoleucine, and D-serine. The cDNA sequence reported in this paper has been submitted to EMBL databases under accession number AM407717.
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Affiliation(s)
- A Gholizadeh
- Research Institute for Fundamental Sciences, University of Tabriz, Iran.
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13
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Ma XF, Yu HM, Wen C, Luo H, Li Q, Shen ZY. Triple fusion of d-amino acid oxidase from Trigonopsis variabilis with polyhistidine and Vitreoscilla hemoglobin. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0022-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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14
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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: 0.8] [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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15
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Optimization of culture condition for the production of D-amino acid oxidase in a recombinant Escherichia coli. BIOTECHNOL BIOPROC E 2008. [DOI: 10.1007/s12257-008-0005-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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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: 4.7] [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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17
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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: 5] [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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18
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Stability and stabilization of D-amino acid oxidase from the yeast Trigonopsis variabilis. Biochem Soc Trans 2007; 35:1588-92. [DOI: 10.1042/bst0351588] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The use of DAO (D-amino acid oxidase) for the conversion of cephalosporin C has provided a significant case for the successful implementation of an O2-dependent biocatalyst on an industrial scale. Improvement of the operational stability of the immobilized oxidase is, however, an important goal of ongoing process optimization. We have examined DAO from the yeast Trigonopsis variabilis with the aim of developing a rational basis for the stabilization of the enzyme activity at elevated temperature and under conditions of substrate turnover. Loss of activity in the resting enzyme can occur via different paths of denaturation. Partial thermal unfolding and release of the FAD cofactor, kinetically coupled with aggregation, contribute to the overall inactivation rate of the oxidase at 50°C. Oxidation of Cys108 into a stable cysteine sulfinic acid causes both decreased activity and stability of the enzyme. Strategies to counteract each of the denaturation steps in DAO are discussed. Fusion to a pull-down domain is a novel approach to produce DAO as protein-based insoluble particles that display high enzymatic activity per unit mass of catalyst.
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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: 0.8] [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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Arroyo M, Menéndez M, García JL, Campillo N, Hormigo D, de la Mata I, Castillón MP, Acebal C. The role of cofactor binding in tryptophan accessibility and conformational stability of His-tagged d-amino acid oxidase from Trigonopsis variabilis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:556-65. [PMID: 17466607 DOI: 10.1016/j.bbapap.2007.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 03/07/2007] [Accepted: 03/07/2007] [Indexed: 11/30/2022]
Abstract
d-amino acid oxidase from Trigonopsis variabilis (TvDAAO) is a flavoenzyme with high biotechnological and industrial interest. The overexpression and purification of the apoprotein form of a recombinant His-tagged TvDAAO allowed us to go deep into the structural differences between apoenzyme and holoenzyme, and on the cofactor binding and its contribution to enzyme stability. A significant decrease in intrinsic fluorescence emission took place upon FAD binding, associated to cofactor induced conformational transitions or subunit dimerization that could affect the local environment of protein tryptophan residues. Furthermore, acrylamide-quenching experiments indicated that one of the five tryptophan residues of TvDAAO became less accessible upon FAD binding. A K(d)=1.5+/-0.1x10(-7) M for the dissociation of FAD from TvDAAO was calculated from binding experiments based on both quenching of FAD fluorescence and activity titration curves. Secondary structure prediction indicated that TvDAAO is a mixed alpha/beta protein with 8 alpha-helices and 14 beta-sheets connected by loops. Prediction results were in good agreement with the estimates obtained by circular dichroism which indicated that both the apoenzyme and the holoenzyme had the same structural component ratios: 34% alpha-helix content, 20% beta-structure content (14% antiparallel and 6% parallel beta-sheet), 15% beta-turns and 31% of random structure. Circular dichroism thermal-transition curves suggested single-step denaturation processes with apparent midpoint transition temperatures (T(m)) of 37.9 degrees C and 41.4 degrees C for the apoenzyme and the holoenzyme, respectively. A three-dimensional model of TvDAAO built by homology modelling and consistent with the spectroscopic studies is shown. Comparing our results with those reported for pig kidney (pkDAAO) and Rhodotorula gracilis (RgDAAO) d-amino acid oxidases, a "head-to-head" interaction between subunits in the TvDAAO dimer might be expected.
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Affiliation(s)
- Miguel Arroyo
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain.
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21
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Geueke B, Weckbecker A, Hummel W. Overproduction and characterization of a recombinant D-amino acid oxidase from Arthrobacter protophormiae. Appl Microbiol Biotechnol 2007; 74:1240-7. [PMID: 17279391 DOI: 10.1007/s00253-006-0776-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2006] [Revised: 11/17/2006] [Accepted: 11/17/2006] [Indexed: 11/26/2022]
Abstract
A screening of soil samples for D-amino acid oxidase (D-AAO) activity led to the isolation and identification of the gram-positive bacterium Arthrobacter protophormiae. After purification of the wild-type D-AAO, the gene sequence was determined and designated dao. An alignment of the deduced primary structure with eukaryotic D-AAOs and D-aspartate oxidases showed that the D-AAO from A. protophormiae contains five of six conserved regions; the C-terminal type 1 peroxisomal targeting signal that is typical for D-AAOs from eukaryotic origin is missing. The dao gene was cloned and expressed in Escherichia coli. The purified recombinant D-AAO had a specific activity of 180 U mg protein(-1) for D-methionine and was slightly inhibited in the presence of L-methionine. Mainly, basic and hydrophobic D-amino acids were oxidized by the strictly enantioselective enzyme. After a high cell density fermentation, 2.29 x 10(6) U of D-AAO were obtained from 15 l of fermentation broth.
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Affiliation(s)
- Birgit Geueke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Research Centre Jülich, 52426 Jülich, Germany.
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22
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Zheng H, Zhu T, Chen J, Zhao Y, Jiang W, Zhao G, Yang S, Yang Y. Construction of recombinant Escherichia coli D11/pMSTO and its use in enzymatic preparation of 7-aminocephalosporanic acid in one pot. J Biotechnol 2007; 129:400-5. [PMID: 17349708 DOI: 10.1016/j.jbiotec.2007.01.021] [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: 10/08/2006] [Revised: 01/14/2007] [Accepted: 01/26/2007] [Indexed: 10/23/2022]
Abstract
The main drawback in the industrial production of 7-aminocephalosporanic acid is the accumulation of intermediate (AKA-7-ACA) and destruction of substrate (cephalosporin C) catalyzed by catalase and beta-lactamase. To overcome the adverse effect of these enzymes on the conversion process, Escherichia coli D11 with mutation of katG, katE and ampC genes was constructed by P1 phage transduction, which enabled it not to produce catalase and beta-lactamase, respectively. At the same time, recA mutation in D11 increased the stability of foreign plasmid. With D11 used as host, both d-amino acid oxidase and GL-7-ACA acylase were cloned and expressed by the recombinant plasmids of pMSS or pMSTO, and the production of two enzymes could be increased by addition of 1.0% glucose. Cells of recombinant strain D11/pMSTO could directly convert cephalosporin C into 7-aminocephalosporanic acid at 25 degrees C, with the yield of more than 74%. The data suggested that the constructed D11/pMSTO could be an alternative catalyst for production of 7-aminocephalosporanic acid in one pot.
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Affiliation(s)
- Huabao Zheng
- College of Life Sciences, Zhejiang University, Hangzhou 310029, China
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Dib I, Stanzer D, Nidetzky B. Trigonopsis variabilis D-amino acid oxidase: control of protein quality and opportunities for biocatalysis through production in Escherichia coli. Appl Environ Microbiol 2006; 73:331-3. [PMID: 17056691 PMCID: PMC1797113 DOI: 10.1128/aem.01569-06] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Trigonopsis variabilis D-amino acid oxidase accounts for 35% of Escherichia coli protein when added D-methionine suppresses the toxic activity of the recombinant product. Permeabilized E. coli cells are reusable and stabilized enzyme preparations. The purified oxidase lacks the microheterogeneity of the natural enzyme. Oriented immobilization of a chimeric oxidase maintains 80% of the original activity in microparticle-bound enzymes.
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Affiliation(s)
- Iskandar Dib
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, Petersgasse 12/I, A-8010 Graz, Austria
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24
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Synergistic effect of co-expressing d-amino acid oxidase with T7 lysozyme on self-disruption of Escherichia coli cell. Biochem Eng J 2006. [DOI: 10.1016/j.bej.2005.08.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Zheng H, Wang X, Chen J, Zhu K, Zhao Y, Yang Y, Yang S, Jiang W. Expression, purification, and immobilization of His-tagged D-amino acid oxidase of Trigonopsis variabilis in Pichia pastoris. Appl Microbiol Biotechnol 2005; 70:683-9. [PMID: 16217653 DOI: 10.1007/s00253-005-0158-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Revised: 08/26/2005] [Accepted: 08/31/2005] [Indexed: 10/25/2022]
Abstract
High-level expression of D: -amino acid oxidase (DAO) has been reported in Pichia pastoris by integrating the DAO gene under the control of the alcohol oxidase promoter (PAOX1). However, the time taken to reach peak product concentration is usually long (approximately 43 h), and cultivation requires tight regulation of methanol feeding. In this paper, we describe the expression of His-tagged DAO (HDAO) in P. pastoris using the glyceraldehydes-3-phosphate dehydrogenase promoter (PGAP). The maximal level of HDAO expression using the PGAP integrant is attained in 13 h and is equal to that obtained using the PAOX1 integrant in 43 h. We also explored the possibility of secreting HDAO in P. pastoris. In-frame fusion of Saccharomyces cerevisiae alpha-factor secretion signal under a PGAP or PAOX1 resulted in low-level secretion of active HDAO, which was not of practical use. The intracellularly expressed HDAO under PGAP was purified by agar-based affinity support and then immobilized on Amberzyme oxirane resin. The immobilized HDAO, with specific activity of 75 U g-1 (wet weight), could be recycled more than 14 times without significant loss of activity. The data suggest that intracellular production of HDAO under PGAP, followed by affinity purification and immobilization on oxirane resin, may serve as an effective process for the manufacture of immobilized DAO for industrial application.
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Affiliation(s)
- Huabao Zheng
- College of Life Sciences, Zhejiang University, Hangzhou 310029, China
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26
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Liu X, He G, Wang X, Chen Q, Qian X, Lin W, Li D, Gu N, Feng G, He L. Association of DAAO with schizophrenia in the Chinese population. Neurosci Lett 2005; 369:228-33. [PMID: 15464270 DOI: 10.1016/j.neulet.2004.07.078] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2004] [Revised: 07/21/2004] [Accepted: 07/23/2004] [Indexed: 10/26/2022]
Abstract
Recently, the gene called DAAO was reported to be associated with schizophrenia in the French Canadian populations. Here, we report a result obtained in the study of our large collection of 547 schizophrenia cases and 536 controls in the Chinese population. Six single-nucleotide polymorphisms (SNPs) were genotyped at and around the DAAO locus, covering a 10-kb region entirely encompassing the complementary DNA sequences of DAAO. We found statistically significant differences in allele distributions on one marker: SNP rs3741775 (P = 0.0000001). In the haplotype analysis based on the information of linkage-disequilibrium block across this gene locus, we demonstrated a highly significant association between schizophrenia and a DAAO haplotype (P = 2.0173 x 10(-21)), which therefore provides an independent statistical support for association of the DAAO gene with schizophrenia and indicates that the DAAO gene may play a significant role in the etiology of schizophrenia in the Han Chinese.
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Affiliation(s)
- Xinmin Liu
- Bio-X Life Science Research Center, Shanghai Jiao Tong University, Hao Ran Building, 1954 Huashan Road, P.O. Box 501, Shanghai 200030, PR China
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27
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D-amino acid oxidase: structure, catalytic mechanism, and practical application. BIOCHEMISTRY (MOSCOW) 2005. [DOI: 10.1007/pl00021754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Tishkov VI, Khoronenkova SV. D-amino acid oxidase: structure, catalytic mechanism, and practical application. BIOCHEMISTRY (MOSCOW) 2005. [DOI: 10.1007/s10541-005-0004-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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29
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Tishkov VI, Khoronenkova SV. D-amino acid oxidase: structure, catalytic mechanism, and practical application. BIOCHEMISTRY (MOSCOW) 2005. [DOI: 10.1007/s10541-005-0050-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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30
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Takeuchi A, Hashiyama K, Arai R, Makino O. Isolation of a series of single missense mutants of a dna gene of phage .PHI.29, gene 1, utilizing their inhibitory effect on E. coli growth. Genes Genet Syst 2005; 80:377-83. [PMID: 16394589 DOI: 10.1266/ggs.80.377] [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] [Indexed: 11/23/2022] Open
Abstract
Gene 1 product (gp1) of Bacillus subtilis phage psi29 is known to promote DNA replication of the phage. Although its role in the DNA replication is not clear, gp1 is reported to exhibit multiple characteristics, including RNA binding, cell membrane localization, and self-association. To investigate these characteristics, we undertook the isolation of a series of missense mutants of gene 1 bearing substitutions at various regions. During cloning of gene 1, we found that its expression severely inhibited the growth of its host Escherichia coli cells. In this study, we utilized this growth-inhibition phenomenon to screen a random library muta-genized by error-prone PCR, expecting that mutants which could not inhibit cell growth would be affected in the authentic functions of gp1. Using this approach, we obtained 31 different mutants bearing single amino acid substitutions at 26 positions along the entire length of gp1. As a preliminary analysis of these mutants, we compared the deduced amino acid sequences of gp1s from psi29 and its related phages PZA, B103 and M2. Alignment of these sequences revealed three conserved regions, i.e. a hydrophobic region near the carboxyl terminus (assumed to be involved in the membrane localization and self-association of gp1), coiled-coil motif (essential for self-association), and a region of unknown function near the amino terminus. Interestingly, many of the substitutions in the isolated mutants occurred at strongly conserved residues in these regions and affected characteristic features of the regions (e.g. hydrophobicity of the hydrophobic region). These substitutions are expected to affect authentic functions of gp1, and the mutants will be useful for studies of the structure and functions of gp1.
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Affiliation(s)
- Ari Takeuchi
- Department of Genetics, Life Science Institute, Sophia University, Tokyo, Japan
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31
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Khang YH, Kim IW, Hah YR, Hwangbo JH, Kang KK. Fusion protein of Vitreoscilla hemoglobin with D-amino acid oxidase enhances activity and stability of biocatalyst in the bioconversion process of cephalosporin C. Biotechnol Bioeng 2003; 82:480-8. [PMID: 12632405 DOI: 10.1002/bit.10592] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this study we constructed an artificial flavohemoprotein by fusing Vitreoscilla hemoglobin (VHb) with D-amino acid oxidase (DAO) of Rhodotorula gracilis to determine whether bacterial hemoglobin can be used as an oxygen donor to immobilized flavoenzyme. This chimeric enzyme significantly enhanced DAO activity and stability in the bioconversion process of cephalosporin C. In a 200-mL bioreactor, the catalytic efficiency of immobilized VHb-DAO against cephalosporin C was 12.5-fold higher than that of immobilized DAO, and the operational stability of the immobilized VHb-DAO was approximately threefold better than that of the immobilized DAO. In the scaled-up bioprocess with a 5-L bioreactor, immobilized VHb-DAO (2500 U/L) resulted in 99% bioconversion of 120 mM cephalosporin C within 60 min at an oxygen flow rate of 0.2 (v/v) x min. Ninety percent of the initial activity of immobilized VHb-DAO could be maintained at up to 50 cycles of the enzymatic reaction without exogenous addition of H(2)O(2) and flavin adenine dinucleotide (FAD). The purity of the final product, glutaryl-7-aminocephalosporanic acid, was confirmed to be 99.77% by high-performance liquid chromatography (HPLC) analysis. Relative specificity of immobilized VHb-DAO on D-alpha-aminoadipic acid, a precursor in cephalosporin C biosynthesis, increased twofold, compared with that of immobilized DAO, suggesting that conformational modification of the VHb-DAO fusion protein may be altered in favor of cephalosporin C.
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Affiliation(s)
- Yong-Ho Khang
- Department of Applied Microbiology, Yeungnam University, Gyeongsan, 712-749, Republic of Korea.
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32
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Isoai A, Kimura H, Reichert A, Schörgendorfer K, Nikaido K, Tohda H, Giga-Hama Y, Mutoh N, Kumagai H. Production of D-amino acid oxidase (DAO) of Trigonopsis variabilis in Schizosaccharomyces pombe and the characterization of biocatalysts prepared with recombinant cells. Biotechnol Bioeng 2002; 80:22-32. [PMID: 12209783 DOI: 10.1002/bit.10345] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The cDNA of D-amino acid oxidase (DAO) gene isolated from Trigonopsis variabilis was expressed in Schizosaccharomyces pombe. A clone, ASP327-10, transformed with plasmid vector, pTL2M5DAO, expressed catalytically active DAO in the presence of G418, and converted Cephalosprin C to alpha-ketoadipyl-7-cephalosporanic acid (KA-7-ACA) and glutaryl-7-aminocephalosporanic acid (GL-7-ACA). Biocatalysts were prepared using ASP327-10 and T. variabilis, and evaluated to demonstrate the feasibility of recombinant S. pombe for industrial application. The cells were immobilized by crosslinking polyethylene imine after glutardialdehyde (GDA) fixation and permeabilization by alkaline treatment. Although the biocatalyst prepared from ASP327-10 exhibited DAO activity, catalase activity still remained fully even after permeabilization, under which condition, the catalase activity of T. variabilis decreased to 20-30%. Heat treatment was required before cell fixation by GDA to inactivate the catalase in S. pombe. This improved the efficiency of bioconversion to GL-7-ACA, but caused poor mechanical strength in the biocatalyst of S. pombe. To overcome this weakness, a catalase-deficient host strain was obtained by ethylmethansulfate mutagenesis. Moreover, taking economics into consideration, the integrative vector, pTL2M5DAO-8XL, with multi-copies of expression cassette was constructed to express DAO in S. pombe even in the absence of G418. The newly established integrant, ASP417-7, did not exhibit any catalase activity so that heat treatment was not required. The obtained integrant and its biocatalyst were significantly improved in GL-7ACA conversion ability and mechanical strength. This study demonstrates that the established integrant is a potential candidate as an alternative source of DAO enzyme.
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Affiliation(s)
- Atsushi Isoai
- ASPEX Division, Asahi Glass Co. Ltd., 1150 Hazawa, Kanagawa, Yokohama 221-8755, Japan.
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