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Gu P, Ma Q, Zhao S, Li Q, Gao J. Alanine dehydrogenases from four different microorganisms: characterization and their application in L-alanine production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:123. [PMID: 37537629 PMCID: PMC10401832 DOI: 10.1186/s13068-023-02373-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Alanine dehydrogenase (AlaDH) belongs to oxidoreductases, and it exists in several different bacteria species and plays a key role in microbial carbon and nitrogen metabolism, spore formation and photosynthesis. In addition, AlaDH can also be applied in biosynthesis of L-alanine from cheap carbon source, such as glucose. RESULTS To achieve a better performance of L-alanine accumulation, system evaluation and comparison of different AlaDH with potential application value are essential. In this study, enzymatic properties of AlaDH from Bacillus subtilis 168 (BsAlaDH), Bacillus cereus (BcAlaDH), Mycobacterium smegmatis MC2 155 (MsAlaDH) and Geobacillus stearothermophilus (GsAlaDH) were firstly carefully investigated. Four different AlaDHs have few similarities in optimum temperature and optimum pH, while they also exhibited significant differences in enzyme activity, substrate affinity and enzymatic reaction rate. The wild E. coli BL21 with these four AlaDHs could produce 7.19 g/L, 7.81 g/L, 6.39 g/L and 6.52 g/L of L-alanine from 20 g/L glucose, respectively. To further increase the L-alanine titer, competitive pathways for L-alanine synthesis were completely blocked in E. coli. The final strain M-6 could produce 80.46 g/L of L-alanine with a yield of 1.02 g/g glucose after 63 h fed-batch fermentation, representing the highest yield for microbial L-alanine production. CONCLUSIONS Enzyme assay, biochemical characterization and structure analysis of BsAlaDH, BcAlaDH, MsAlaDH and GsAlaDH were carried out. In addition, application potential of these four AlaDHs in L-alanine productions were explored. The strategies here can be applied for developing L-alanine producing strains with high titers.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Qianqian Ma
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Shuo Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
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2
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Yin X, Gong W, Zhan Z, Wei W, Li M, Jiao J, Chen B, Liu L, Li W, Gao Z. Mining and engineering of valine dehydrogenases from a hot spring sediment metagenome for the synthesis of chiral non-natural L-amino acids. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Chen R, Liao YT, Gao TT, Zhang YM, Lu LH, Wang CH. Novel Salt-Tolerant Leucine Dehydrogenase from Marine Pseudoalteromonas rubra DSM 6842. Mol Biotechnol 2022; 64:1270-1278. [PMID: 35578070 DOI: 10.1007/s12033-022-00505-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
This study reported the cloning, expression, and characterization of a new salt-tolerant leucine dehydrogenase (PrLeuDH) from Pseudoalteromonas rubra DSM 6842. A codon-optimized 1038 bp gene encoding PrLeuDH was successfully expressed on pET-22b( +) in E. coli BL21(DE3). The purified recombinant PrLeuDH showed a single band of about 38.7 kDa on SDS-PAGE. It exhibited the maximum activity at 40 °C and pH 10.5, while kept high activities in the range of 25-45 °C and pH 9.5-12. The Km value and turnover number kcat for leucine of PrLeuDH were 2.23 ± 0.12 mM and 35.39 ± 0.05 s-1, respectively, resulting in a catalytic efficiency kcat/Km of 15.87 s-1/mM. Importantly, PrLeuDH remained 92.1 ± 2.67% active in the presence of 4.0 M NaCl. The study provides the first in-depth understanding of LeuDH from marine Pseudoalteromonas rubra, meanwhile the unique properties of high activity at low temperature and high salt tolerance make it a promising biocatalyst for the synthesis of non-protein amino acids and α-ketoacids under special conditions in pharmaceutical industry.
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Affiliation(s)
- Rui Chen
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Yu-Ting Liao
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Tian-Tian Gao
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Yan-Mei Zhang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Liang-Hua Lu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China
| | - Cheng-Hua Wang
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue East Road, Nanning, 530004, People's Republic of China.
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Cen YK, Gong H, Xue YP, Zheng YG. Biosynthesis of l-phosphinothricin with enzymes from chromosomal integrated expression in E. coli. 3 Biotech 2021; 11:477. [PMID: 34777934 DOI: 10.1007/s13205-021-03037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/18/2021] [Indexed: 11/25/2022] Open
Abstract
Phosphinothricin (PPT) is one of the most prevalently using herbicides. The commercial phosphinothricin products are generally in the form of a racemic mixture, of which only the l-phosphinothricin (L-PPT) gives herbicidal function. Synthesis of optically pure L-PPT by deracemization of D/L-PPT is a promising way to cut down the environmental burden and manufacturing cost. To convert D/L-PPT to L-PPT, we expressed the catalytic enzymes by genomic integration in E. coli. The whole production was implemented in two steps in one pot using four catalytic enzymes, namely d-amino acid oxidase, catalase, glutamate dehydrogenase, and glucose dehydrogenase. Finally, after a series of process optimization, the results showed that with our system the overall L-PPT yield reached 86%. Our study demonstrated a new strategy for L-PPT synthesis, based on enzymes from chromosomal integrated expression, which does not depend on antibiotic selection, and shows a high potential for future industrial application.
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Affiliation(s)
- Yu-Ke Cen
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Huo Gong
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
- Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014 China
- National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014 People's Republic of China
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Xiong T, Bai Y, Fan TP, Zheng X, Cai Y. Biosynthesis of phenylpyruvic acid from l-phenylalanine using chromosomally engineered Escherichia coli. Biotechnol Appl Biochem 2021; 69:1909-1916. [PMID: 34554609 DOI: 10.1002/bab.2256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 09/14/2021] [Indexed: 11/09/2022]
Abstract
The efficiency of whole-cell biotransformation is often affected by the genetic instability of plasmid-based expression systems, which require selective pressure to maintain the stability of the plasmids. To circumvent this shortcoming, we constructed a chromosome engineering strain for the synthesis of phenylpyruvic acid (PPA) from l-phenylalanine. First, l-amino acid deaminase (pmLAAD) from Proteus myxofaciens was incorporated into Escherichia coli BL21 (DE3) chromosome and the copy numbers of pmLAAD were increased by chemically induced chromosomal evolution (CIChE). Fifty-nine copies of pmLAAD were obtained in E. coli BL8. The PPA titer of E. coli BL8 reached 2.22 g/L at 6 h. Furthermore, the deletion of lacI improved PPA production. In the absence of isopropyl-β-d-thiogalactopyranoside, the resulting strain, E. coli BL8△recA△lacI, produced 2.65 g/L PPA at 6 h and yielded a 19.37% increase in PPA production compared to E. coli BL8△recA. Finally, the engineered E. coli BL8△recA△lacI strain achieved 19.14 g/L PPA at 24 h in a 5-L bioreactor.
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Affiliation(s)
- Tianzhen Xiong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Yajun Bai
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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A three-component monooxygenase from Rhodococcus wratislaviensis may expand industrial applications of bacterial enzymes. Commun Biol 2021; 4:16. [PMID: 33398074 PMCID: PMC7782822 DOI: 10.1038/s42003-020-01555-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022] Open
Abstract
The high-valent iron-oxo species formed in the non-heme diiron enzymes have high oxidative reactivity and catalyze difficult chemical reactions. Although the hydroxylation of inert methyl groups is an industrially promising reaction, utilizing non-heme diiron enzymes as such a biocatalyst has been difficult. Here we show a three-component monooxygenase system for the selective terminal hydroxylation of α-aminoisobutyric acid (Aib) into α-methyl-D-serine. It consists of the hydroxylase component, AibH1H2, and the electron transfer component. Aib hydroxylation is the initial step of Aib catabolism in Rhodococcus wratislaviensis C31-06, which has been fully elucidated through a proteome analysis. The crystal structure analysis revealed that AibH1H2 forms a heterotetramer of two amidohydrolase superfamily proteins, of which AibHm2 is a non-heme diiron protein and functions as a catalytic subunit. The Aib monooxygenase was demonstrated to be a promising biocatalyst that is suitable for bioprocesses in which the inert C–H bond in methyl groups need to be activated. Makoto Hibi et al. report a novel three-component monooxygenase system in Rhodococcus wratislaviensis. This enzyme catalyzes the activation of an inert C–H bond and may be potentially important as a biocatalyst for industrial applications.
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Okada CY, dos Santos CY, Jurberg ID. Blue light-promoted N–H insertion of amides, isatins, sulfonamides and imides into aryldiazoacetates: Synthesis of unnatural α-aryl amino acid derivatives. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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8
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Grzechowiak M, Sliwiak J, Jaskolski M, Ruszkowski M. Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism. FRONTIERS IN PLANT SCIENCE 2020; 11:754. [PMID: 32655590 PMCID: PMC7326016 DOI: 10.3389/fpls.2020.00754] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/12/2020] [Indexed: 05/24/2023]
Abstract
Glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)+-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). In current perception, GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways. GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD+-specific, NAD+/NADP+ dual-specific, and NADP+-specific. We determined in this work that the mitochondrial AtGDH1 isozyme from A. thaliana is NAD+-specific. Altogether, A. thaliana expresses three GDH isozymes (AtGDH1-3) targeted to mitochondria, of which AtGDH2 has an extra EF-hand motif and is stimulated by calcium. Our enzymatic assays of AtGDH1 established that its sensitivity to calcium is negligible. In vivo the AtGDH1-3 enzymes form homo- and heterohexamers of varied composition. We solved the crystal structure of recombinant AtGDH1 in the apo-form and in complex with NAD+ at 2.59 and 2.03 Å resolution, respectively. We demonstrate also that both in the apo form and in 1:1 complex with NAD+, it forms D 3-symmetric homohexamers. A subunit of AtGDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and of domain II which binds coenzyme. Most of the subunits in our crystal structures, including those in NAD+ complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the AtGDH1-NAD+ hexamer contains a serendipitous 2OG molecule in the active site, causing a dramatic (∼25°) closure of the domains. We provide convincing evidence that the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30). We also identified several MPD [(+/-)-2-methyl-2,4-pentanediol] binding sites with conserved sequence. Although AtGDH1 is insensitive to MPD in our assays, the observation of druggable sites opens a potential for non-competitive herbicide design.
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Affiliation(s)
- Marta Grzechowiak
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Joanna Sliwiak
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Mariusz Jaskolski
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Milosz Ruszkowski
- Center for Biocrystallographic Research Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
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9
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Cheng F, Li H, Zhang K, Li QH, Xie D, Xue YP, Zheng YG. Tuning amino acid dehydrogenases with featured sequences for L-phosphinothricin synthesis by reductive amination. J Biotechnol 2020; 312:35-43. [PMID: 32135177 DOI: 10.1016/j.jbiotec.2020.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/16/2020] [Accepted: 03/01/2020] [Indexed: 01/23/2023]
Abstract
Biosynthesizing unnatural chiral amino acids is challenging due to the limited reductive amination activity of amino acid dehydrogenase (AADH). Here, for the asymmetric synthesis of l-phosphinothricin from 2-oxo-4-[(hydroxy)(methyl)phosphinoyl]butyric acid (PPO), a glutamate dehydrogenase gene (named GluDH3) from Pseudomonas monteilii was selected, cloned and expressed in Escherichia coli (E. coli). To boost its activity, a "two-step"-based computational approach was developed and applied to select the potential beneficial amino acid positions on GluDH3. l-phosphinothricin was synthesized by GluDH-catalyzed asymmetric amination using the d-glucose dehydrogenase from Exiguobacterium sibiricum (EsGDH) for NADPH regeneration. Using lyophilized E. coli cells that co-expressed GluDH3_V375S and EsGDH, up to 89.04 g L-1 PPO loading was completely converted to l-phosphinothricin within 30 min at 35 °C with a space-time yield of up to 4.752 kg·L-1·d-1. The beneficial substitution V375S with increased polar interactions between K90, T193, and substrate PPO exhibited 168.2-fold improved catalytic efficiency (kcat/KM) and 344.8-fold enhanced specific activity. After the introduction of serine residues into other GluDHs at specific positions, forty engineered GluDHs exhibited the catalytic functions of "glufosinate dehydrogenase" towards PPO.
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Affiliation(s)
- Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Heng Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Kai Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Qing-Hua Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Dong Xie
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, 310014, PR China
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10
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Yin X, Liu Y, Meng L, Zhou H, Wu J, Yang L. Semi-rational hinge engineering: modulating the conformational transformation of glutamate dehydrogenase for enhanced reductive amination activity towards non-natural substrates. Catal Sci Technol 2020. [DOI: 10.1039/c9cy02576f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The hinge region was identified to be a promising hotspot for activity engineering of GluDHs, providing a potent alternative for developing high-performance biocatalysts toward valuable optically pure l-amino acid production.
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Affiliation(s)
- Xinjian Yin
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Yayun Liu
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Lijun Meng
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Haisheng Zhou
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Jianping Wu
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
| | - Lirong Yang
- Institute of Bioengineering
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- China
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Liu S, Zhang X, Liu F, Xu M, Yang T, Long M, Zhou J, Osire T, Yang S, Rao Z. Designing of a Cofactor Self-Sufficient Whole-Cell Biocatalyst System for Production of 1,2-Amino Alcohols from Epoxides. ACS Synth Biol 2019; 8:734-743. [PMID: 30840437 DOI: 10.1021/acssynbio.8b00364] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Optically pure 1,2-amino alcohols are highly valuable products as intermediates for chiral pharmaceutical products. Here we designed an environmentally friendly non-natural biocatalytic cascade for efficient synthesis of 1,2-amino alcohols from cheaper epoxides. A redesignated ω-transaminase PAKω-TA was tested and showed good bioactivity at a lower pH than other reported transaminases. The cascade was efficiently constructed as a single one-pot E. coli recombinant, by coupling SpEH (epoxide hydrolase), MnADH (alcohol dehydrogenase), and PAKω-TA. Furthermore, RBS regulation strategy was used to overcome the rate limiting step by increasing expression of MnADH. For cofactor regeneration and amino donor source, an interesting point was involved as that a cofactor self-sufficient system was designed by expression of GluDH. It established a "bridge" between the cofactor and the cosubstrate, such that the cofactor self-sufficient system could release cofactor (NADP+) and cosubstrate (l-Glutamine) regenerated simultaneously. The recombinant E. coli BL21 (SGMP) with cofactor self-sufficient whole-cell cascade biocatalysis showed high ee value (>99%) and high yield, with 99.6% conversion of epoxide ( S)-1a to 1,2-amino alcohol ( S)-1d in 10 h. It further converted ( S)-2a-5a to ( S)-2d-5d with varying conversion rates ranging between 65-96.4%. This study first provides one-step synthesis of optically pure 1,2-amino alcohols from ( S)-epoxides employing a synthetic redox-self-sufficient cascade.
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Affiliation(s)
- Song Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fei Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Mengfei Long
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Junping Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tolbert Osire
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shangtian Yang
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, United States
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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Xia X, Qin W, Zhu H, Wang X, Jiang J, Hu J. How Streptococcus suis serotype 2 attempts to avoid attack by host immune defenses. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2019; 52:516-525. [PMID: 30954397 DOI: 10.1016/j.jmii.2019.03.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 02/20/2019] [Accepted: 03/07/2019] [Indexed: 01/08/2023]
Abstract
Streptococcus suis (S. suis) type 2 (SS2) is an important zoonotic pathogen that causes swine streptococcosis, a widespread infectious disease that occurs in pig production areas worldwide and causes serious economic losses in the pork industry. Hosts recognize pathogen-associated molecular patterns (PAMPs) through pattern recognition receptors (PRRs) to activate both innate and acquired immune responses. However, S. suis has evolved multiple mechanisms to escape host defenses. Pathogenic proteins, such as enolase, double-component regulatory systems, factor H-combining proteins and other pathogenic and virulence factors, contribute to immune escape by evading host phagocytosis, reactive oxygen species (ROS), complement-mediated immune destruction, etc. SS2 can prevent neutrophil extracellular trap (NET) formation to avoid being trapped by porcine neutrophils and disintegrate host immunoglobulins via IgA1 hydrolases and IgM proteases. Currently, the pathogenesis of arthritis and meningitis caused by SS2 infection remains unclear, and further studies are necessary to elucidate it. Understanding immune evasion mechanisms after SS2 infection is important for developing high-efficiency vaccines and targeted drugs.
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Affiliation(s)
- Xiaojing Xia
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China; Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, China; Postdoctoral Research Station, Henan Agriculture University, Zhengzhou, China
| | - Wanhai Qin
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Amsterdam Infection & Immunity, Meibergdreef 9, 1105AZ Amsterdam, Netherlands
| | - Huili Zhu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China
| | - Xin Wang
- College of Agriculture and Forestry Science, Linyi University, Linyi, China
| | - Jinqing Jiang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China.
| | - Jianhe Hu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, China; Postdoctoral Research Base, Henan Institute of Science and Technology, Xinxiang, China.
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Żymańczyk-Duda E, Dunal N, Brzezińska-Rodak M, Osiewała A, Olszewski TK, Klimek-Ochab M, Serafin-Lewańczuk M. First biological conversion of chiral heterophosphonate derivative - Scaling and paths of conversion discussion. Bioorg Chem 2019; 93:102751. [PMID: 30709702 DOI: 10.1016/j.bioorg.2019.01.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/21/2019] [Accepted: 01/24/2019] [Indexed: 01/09/2023]
Abstract
Presented work describes the first approach for the biocatalytic resolution of racemic mixtures of heterophosphonate derivative. Penicillium funiculosum and Rhodotorula mucilaginosa were successfully applied for the biological conversion of racemic mixture of 1-amino-1-(3'-pyridyl)methylphosphonic acid 3. Both microorganisms carried out the kinetically driven process leading to conversion of one from the substrate enantiomers, leaving the second one unreacted. Application of R. mucilaginosa allowed obtaining pure enantiomer of the substrate (yield 100%, e.e 100% - unreacted isomer) after 24 h of biotransformation of 3 in the laboratory scale process (Method E), applying biocatalyst pre-treatment step - 24 h of starvation. In case of other biocatalyst, application of whole cells of P. funiculosum in laboratory scale process, also resulted in conversion of the racemic mixture of substrate 3via oxidative deamination into ketone derivative, which was then bioreduced (second step of the process) into 1-hydroxy-1-(3'-pyridyl)methylphosphonic acid 4. This time two products were isolated: unreacted substrate and hydroxy compound 4. Conversion degree ranged from 30% (standard procedure, method A) to even 70% (with extra addition of sodium pyruvate - method B2). However, in this case, bioconversion was not enantioselective - products: amino- and hydroxyderivative were obtained as racemic mixtures. Both biocatalysts were also tested towards the scaling so other biocatalytic procedures were introduced - with immobilized fungal mycelium. In case of Rhodotorula mucilaginosa this approach failed (data not shown) but Penicillium funiculosum turned out to be active and also selective. Thus, application of this biocatalyst in the half-preparative scale, continuous-flow bioprocess (Method C2) resulted in the obtaining of pure S-3 (100% e.e.) isomer with the 100% of conversion degree, without any side products. Recorded NMR spectra allowed confirming the reaction progress and its selectivity and also postulating possible mechanism of conversion.
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Affiliation(s)
- Ewa Żymańczyk-Duda
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| | - Natalia Dunal
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Małgorzata Brzezińska-Rodak
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Angelika Osiewała
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Tomasz K Olszewski
- Department of Organic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Magdalena Klimek-Ochab
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Monika Serafin-Lewańczuk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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Yin X, Liu Y, Meng L, Zhou H, Wu J, Yang L. Rational Molecular Engineering of Glutamate Dehydrogenases for Enhancing Asymmetric Reductive Amination of Bulky α-Keto Acids. Adv Synth Catal 2018. [DOI: 10.1002/adsc.201801251] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Xinjian Yin
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Yayun Liu
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Lijun Meng
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Haisheng Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering; Zhejiang University; Hangzhou 310027 People's Republic of China
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15
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Yin X, Wu J, Yang L. Efficient reductive amination process for enantioselective synthesis of L-phosphinothricin applying engineered glutamate dehydrogenase. Appl Microbiol Biotechnol 2018; 102:4425-4433. [DOI: 10.1007/s00253-018-8910-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/25/2018] [Accepted: 02/28/2018] [Indexed: 11/24/2022]
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16
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Phogosee S, Hibino T, Kageyama H, Waditee-Sirisattha R. Bifunctional alanine dehydrogenase from the halotolerant cyanobacterium Aphanothece halophytica: characterization and molecular properties. Arch Microbiol 2018; 200:719-727. [DOI: 10.1007/s00203-018-1481-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/11/2018] [Accepted: 01/18/2018] [Indexed: 11/28/2022]
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17
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Jung J, Nidetzky B. Evidence of a sequestered imine intermediate during reduction of nitrile to amine by the nitrile reductase QueF from Escherichia coli. J Biol Chem 2018; 293:3720-3733. [PMID: 29339556 DOI: 10.1074/jbc.m117.804583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/30/2017] [Indexed: 11/06/2022] Open
Abstract
In the biosynthesis of the tRNA-inserted nucleoside queuosine, the nitrile reductase QueF catalyzes conversion of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1), a biologically unique four-electron reduction of a nitrile to an amine. The QueF mechanism involves a covalent thioimide adduct between the enzyme and preQ0 that undergoes reduction to preQ1 in two NADPH-dependent steps, presumably via an imine intermediate. Protecting a labile imine from interception by water is fundamental to QueF catalysis for proper enzyme function. In the QueF from Escherichia coli, the conserved Glu89 and Phe228 residues together with a mobile structural element composing the catalytic Cys190 form a substrate-binding pocket that secludes the bound preQ0 completely from solvent. We show here that residue substitutions (E89A, E89L, and F228A) targeted at opening up the binding pocket weakened preQ0 binding at the preadduct stage by up to +10 kJ/mol and profoundly affected catalysis. Unlike wildtype enzyme, the QueF variants, including L191A and I192A, were no longer selective for preQ1 formation. The E89A, E89L, and F228A variants performed primarily (≥90%) a two-electron reduction of preQ0, releasing hydrolyzed imine (7-formyl-7-deazaguanine) as the product. The preQ0 reduction by L191A and I192A gave preQ1 and 7-formyl-7-deazaguanine at a 4:1 and 1:1 ratio, respectively. The proportion of 7-formyl-7-deazaguanine in total product increased with increasing substrate concentration, suggesting a role for preQ0 in a competitor-induced release of the imine intermediate. Collectively, these results provide direct evidence for the intermediacy of an imine in the QueF-catalyzed reaction. They reveal determinants of QueF structure required for imine sequestration and hence for a complete nitrile-to-amine conversion by this class of enzymes.
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Affiliation(s)
- Jihye Jung
- From the Austrian Centre of Industrial Biotechnology and.,the Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, A-8010 Graz, Austria
| | - Bernd Nidetzky
- From the Austrian Centre of Industrial Biotechnology and .,the Institute of Biotechnology and Biochemical Engineering, NAWI Graz, Graz University of Technology, A-8010 Graz, Austria
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18
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Sellés Vidal L, Kelly CL, Mordaka PM, Heap JT. Review of NAD(P)H-dependent oxidoreductases: Properties, engineering and application. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:327-347. [PMID: 29129662 DOI: 10.1016/j.bbapap.2017.11.005] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/27/2017] [Accepted: 11/08/2017] [Indexed: 11/27/2022]
Abstract
NAD(P)H-dependent oxidoreductases catalyze the reduction or oxidation of a substrate coupled to the oxidation or reduction, respectively, of a nicotinamide adenine dinucleotide cofactor NAD(P)H or NAD(P)+. NAD(P)H-dependent oxidoreductases catalyze a large variety of reactions and play a pivotal role in many central metabolic pathways. Due to the high activity, regiospecificity and stereospecificity with which they catalyze redox reactions, they have been used as key components in a wide range of applications, including substrate utilization, the synthesis of chemicals, biodegradation and detoxification. There is great interest in tailoring NAD(P)H-dependent oxidoreductases to make them more suitable for particular applications. Here, we review the main properties and classes of NAD(P)H-dependent oxidoreductases, the types of reactions they catalyze, some of the main protein engineering techniques used to modify their properties and some interesting examples of their modification and application.
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Affiliation(s)
- Lara Sellés Vidal
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Ciarán L Kelly
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Paweł M Mordaka
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - John T Heap
- Centre for Synthetic Biology and Innovation, Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom.
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19
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Zhang C, Wang Z, Zhang D, Zhou J, Lu C, Su X, Ding D. Proteomics and 1H NMR-based metabolomics analysis of pathogenic Vibrio vulnificus aquacultures isolated from sewage drains. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:23704-23713. [PMID: 28864971 DOI: 10.1007/s11356-017-0007-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/22/2017] [Indexed: 06/07/2023]
Abstract
Vibrio bacteria live in both marine and freshwater habitats and are associated with aquatic animals. Vibrio vulnificus is a pathogenic bacterium that infects people and livestock. It is usually found in offshore waters or within fish and shellfish. This study presents a comparative proteomic analysis of the outer membrane protein (OMP) changes in V. vulnificus proteins after stimulation with sewage from sewage drains. Using two-dimensional electrophoresis followed by MALDI-TOF MS/MS, 32 protein spots with significant differences in abundance were identified and characterized. These identified proteins were found to be involved in various functional categories, including catalysis, transport, membrane proteins progresses, receptor activity, energy metabolism, cytokine activity, and protein metabolism. The mRNA expression levels of 12 differential proteins were further assessed by qRT-PCR. Seven genes including carboxypeptidase, hemoglobin receptor, succinate dehydrogenase iron-sulfur subunit, ATP synthase subunit alpha, thioredoxin, succinyl-CoA synthetase subunit, and alanine dehydrogenase were downregulated upon stimulation, whereas the protein expression levels HupA receptor, type I secretion outer membrane protein, glutamine synthetase, superoxide dismutase, OmpU, and VuuA were upregulated. 1H NMR spectra showed 18 dysregulated metabolites from V. vulnificus after the sewage stimulation and the pathogenicity was enhanced after that.
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Affiliation(s)
- Chundan Zhang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Zhonghua Wang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Dijun Zhang
- School of Marine Science, Ningbo University, Ningbo, China
| | - Jun Zhou
- School of Marine Science, Ningbo University, Ningbo, China
| | - Chenyang Lu
- School of Marine Science, Ningbo University, Ningbo, China
| | - Xiurong Su
- School of Marine Science, Ningbo University, Ningbo, China.
| | - Dewen Ding
- School of Marine Science, Ningbo University, Ningbo, China.
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20
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Sharma M, Mangas‐Sanchez J, Turner NJ, Grogan G. NAD(P)H-Dependent Dehydrogenases for the Asymmetric Reductive Amination of Ketones: Structure, Mechanism, Evolution and Application. Adv Synth Catal 2017; 359:2011-2025. [PMID: 30008635 PMCID: PMC6033044 DOI: 10.1002/adsc.201700356] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/11/2017] [Indexed: 11/16/2022]
Abstract
Asymmetric reductive aminations are some of the most important reactions in the preparation of active pharmaceuticals, as chiral amines feature in many of the world's most important drugs. Although many enzymes have been applied to the synthesis of chiral amines, the development of reductive amination reactions that use enzymes is attractive, as it would permit the one-step transformation of readily available prochiral ketones into chiral amines of high optical purity. However, as most natural "reductive aminase" activities operate on keto acids, and many are able to use only ammonia as the amine donor, there is considerable scope for the engineering of natural enzymes for the reductive amination of ketones, and also for the preparation of secondary amines using alkylamines as donors. This review summarises research into the development of NAD(P)H-dependent dehydrogenases for the reductive amination of ketones, including amino acid dehydrogenases (AADHs), natural amine dehydrogenases (AmDHs), opine dehydrogenases (OpDHs) and imine reductases (IREDs). In each case knowledge of the structure and mechanism of the enzyme class is addressed, with a further description of the engineering of those enzymes for the reductive amination of ketones towards primary and also secondary amine products.
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Affiliation(s)
- Mahima Sharma
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkYO10 5DDYorkU.K.
| | - Juan Mangas‐Sanchez
- School of ChemistryUniversity of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK.
| | - Nicholas J. Turner
- School of ChemistryUniversity of ManchesterManchester Institute of Biotechnology131 Princess StreetManchesterM1 7DNUK.
| | - Gideon Grogan
- York Structural Biology LaboratoryDepartment of ChemistryUniversity of YorkYO10 5DDYorkU.K.
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21
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Szymańska-Majchrzak J, Pałka K, Kańska M. Isotopic effects in mechanistic studies of biotransformations of fluorine derivatives of L-alanine catalysed by L-alanine dehydrogenase. Appl Radiat Isot 2017; 123:21-25. [DOI: 10.1016/j.apradiso.2017.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/12/2017] [Accepted: 02/02/2017] [Indexed: 11/30/2022]
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22
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Structural Insights into l-Tryptophan Dehydrogenase from a Photoautotrophic Cyanobacterium, Nostoc punctiforme. Appl Environ Microbiol 2017; 83:AEM.02710-16. [PMID: 27815281 DOI: 10.1128/aem.02710-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 10/31/2016] [Indexed: 01/08/2023] Open
Abstract
l-Tryptophan dehydrogenase from Nostoc punctiforme NIES-2108 (NpTrpDH), despite exhibiting high amino acid sequence identity (>30%)/homology (>50%) with NAD(P)+-dependent l-Glu/l-Leu/l-Phe/l-Val dehydrogenases, exclusively catalyzes reversible oxidative deamination of l-Trp to 3-indolepyruvate in the presence of NAD+ Here, we determined the crystal structure of the apo form of NpTrpDH. The structure of the NpTrpDH monomer, which exhibited high similarity to that of l-Glu/l-Leu/l-Phe dehydrogenases, consisted of a substrate-binding domain (domain I, residues 3 to 133 and 328 to 343) and an NAD+/NADH-binding domain (domain II, residues 142 to 327) separated by a deep cleft. The apo-NpTrpDH existed in an open conformation, where domains I and II were apart from each other. The subunits dimerized themselves mainly through interactions between amino acid residues around the β-1 strand of each subunit, as was observed in the case of l-Phe dehydrogenase. The binding site for the substrate l-Trp was predicted by a molecular docking simulation and validated by site-directed mutagenesis. Several hydrophobic residues, which were located in the active site of NpTrpDH and possibly interacted with the side chain of the substrate l-Trp, were arranged similarly to that found in l-Leu/l-Phe dehydrogenases but fairly different from that of an l-Glu dehydrogenase. Our crystal structure revealed that Met-40, Ala-69, Ile-74, Ile-110, Leu-288, Ile-289, and Tyr-292 formed a hydrophobic cluster around the active site. The results of the site-directed mutagenesis experiments suggested that the hydrophobic cluster plays critical roles in protein folding, l-Trp recognition, and catalysis. Our results provide critical information for further characterization and engineering of this enzyme. IMPORTANCE In this study, we determined the three-dimensional structure of l-Trp dehydrogenase, analyzed its various site-directed substitution mutants at residues located in the active site, and obtained the following informative results. Several residues in the active site form a hydrophobic cluster, which may be a part of the hydrophobic core essential for protein folding. To our knowledge, there is no previous report demonstrating that a hydrophobic cluster in the active site of any l-amino acid dehydrogenase may have a critical impact on protein folding. Furthermore, our results suggest that this hydrophobic cluster could strictly accommodate l-Trp. These studies show the structural characteristics of l-Trp dehydrogenase and hence would facilitate novel applications of l-Trp dehydrogenase.
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23
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Ren X, O’Hanlon JA, Morris M, Robertson J, Wong LL. Synthesis of Imidazolidin-4-ones via a Cytochrome P450-Catalyzed Intramolecular C–H Amination. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02189] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xinkun Ren
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | - Jack A. O’Hanlon
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield
Road, Oxford OX1 3TA, United Kingdom
| | - Melloney Morris
- Syngenta
UK, Jealott’s Hill International Research Centre, Bracknell RG42 6EY, United Kingdom
| | - Jeremy Robertson
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield
Road, Oxford OX1 3TA, United Kingdom
| | - Luet Lok Wong
- Department
of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
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24
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da Silva ES, Gómez-Vallejo V, Baz Z, Llop J, López-Gallego F. Efficient Enzymatic Preparation of (13) N-Labelled Amino Acids: Towards Multipurpose Synthetic Systems. Chemistry 2016; 22:13619-26. [PMID: 27515007 DOI: 10.1002/chem.201602471] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Indexed: 01/27/2023]
Abstract
Nitrogen-13 can be efficiently produced in biomedical cyclotrons in different chemical forms, and its stable isotopes are present in the majority of biologically active molecules. Hence, it may constitute a convenient alternative to Fluorine-18 and Carbon-11 for the preparation of positron-emitter-labelled radiotracers; however, its short half-life demands for the development of simple, fast, and efficient synthetic processes. Herein, we report the one-pot, enzymatic and non-carrier-added synthesis of the (13) N-labelled amino acids l-[(13) N]alanine, [(13) N]glycine, and l-[(13) N]serine by using l-alanine dehydrogenase from Bacillus subtilis, an enzyme that catalyses the reductive amination of α-keto acids by using nicotinamide adenine dinucleotide (NADH) as the redox cofactor and ammonia as the amine source. The integration of both l-alanine dehydrogenase and formate dehydrogenase from Candida boidinii in the same reaction vessel to facilitate the in situ regeneration of NADH during the radiochemical synthesis of the amino acids allowed a 50-fold decrease in the concentration of the cofactor without compromising reaction yields. After optimization of the experimental conditions, radiochemical yields were sufficient to carry out in vivo imaging studies in small rodents.
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Affiliation(s)
- Eunice S da Silva
- Radiochemistry and Nuclear Imaging Group, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain
| | - Vanessa Gómez-Vallejo
- Radiochemistry Platform, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain
| | - Zuriñe Baz
- Radiochemistry and Nuclear Imaging Group, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain
| | - Jordi Llop
- Radiochemistry and Nuclear Imaging Group, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain.
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Group, CIC biomaGUNE, Paseo Miramón 182, 20009, San Sebastián, Guipúzcoa, Spain. .,IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Bizkaia, Spain.
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26
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Fernandes P, Aldeborgh H, Carlucci L, Walsh L, Wasserman J, Zhou E, Lefurgy ST, Mundorff EC. Alteration of substrate specificity of alanine dehydrogenase. Protein Eng Des Sel 2014; 28:29-35. [PMID: 25538307 DOI: 10.1093/protein/gzu053] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The l-alanine dehydrogenase (AlaDH) has a natural history that suggests it would not be a promising candidate for expansion of substrate specificity by protein engineering: it is the only amino acid dehydrogenase in its fold family, it has no sequence or structural similarity to any known amino acid dehydrogenase, and it has a strong preference for l-alanine over all other substrates. By contrast, engineering of the amino acid dehydrogenase superfamily members has produced catalysts with expanded substrate specificity; yet, this enzyme family already contains members that accept a broad range of substrates. To test whether the natural history of an enzyme is a predictor of its innate evolvability, directed evolution was carried out on AlaDH. A single mutation identified through molecular modeling, F94S, introduced into the AlaDH from Mycobacterium tuberculosis (MtAlaDH) completely alters its substrate specificity pattern, enabling activity toward a range of larger amino acids. Saturation mutagenesis libraries in this mutant background additionally identified a double mutant (F94S/Y117L) showing improved activity toward hydrophobic amino acids. The catalytic efficiencies achieved in AlaDH are comparable with those that resulted from similar efforts in the amino acid dehydrogenase superfamily and demonstrate the evolvability of MtAlaDH specificity toward other amino acid substrates.
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Affiliation(s)
- Puja Fernandes
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Hannah Aldeborgh
- Chemistry Department, Vassar College, Poughkeepsie, NY 12604, USA
| | - Lauren Carlucci
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Lauren Walsh
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Jordan Wasserman
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Edward Zhou
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Scott T Lefurgy
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
| | - Emily C Mundorff
- Chemistry Department, Hofstra University, Hempstead, NY 11549, USA
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27
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Biochemical characterization of an L-tryptophan dehydrogenase from the photoautotrophic cyanobacterium Nostoc punctiforme. Enzyme Microb Technol 2014; 60:40-6. [PMID: 24835098 DOI: 10.1016/j.enzmictec.2014.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/27/2014] [Accepted: 04/02/2014] [Indexed: 01/01/2023]
Abstract
An NAD(+)-dependent l-tryptophan dehydrogenase from Nostoc punctiforme NIES-2108 (NpTrpDH) was cloned and overexpressed in Escherichia coli. The recombinant NpTrpDH with a C-terminal His6-tag was purified to homogeneity using a Ni-NTA agarose column, and was found to be a homodimer with a molecular mass of 76.1kDa. The enzyme required NAD(+) and NADH as cofactors for oxidative deamination and reductive amination, respectively, but not NADP(+) or NADPH. l-Trp was the preferred substrate for deamination, though l-Phe was deaminated at a much lower rate. The enzyme exclusively aminated 3-indolepyruvate; phenylpyruvate was inert. The pH optima for the deamination of l-Trp and amination of 3-indolpyruvate were 11.0 and 7.5, respectively. For deamination of l-Trp, maximum enzymatic activity was observed at 45°C. NpTrpDH retained more than 80% of its activity after incubation for 30min at pHs ranging from 5.0 to 11.5 or incubation for 10min at temperatures up to 40°C. Unlike l-Trp dehydrogenases from higher plants, NpTrpDH activity was not activated by metal ions. Typical Michaelis-Menten kinetics were observed for NAD(+) and l-Trp for oxidative deamination, but with reductive amination there was marked substrate inhibition by 3-indolepyruvate. NMR analysis of the hydrogen transfer from the C4 position of the nicotinamide moiety of NADH showed that NpTrpDH has a pro-S (B-type) stereospecificity similar to the Glu/Leu/Phe/Val dehydrogenase family.
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28
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Patel RN. Biocatalytic synthesis of chiral alcohols and amino acids for development of pharmaceuticals. Biomolecules 2013; 3:741-77. [PMID: 24970190 PMCID: PMC4030968 DOI: 10.3390/biom3040741] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 09/22/2013] [Accepted: 09/23/2013] [Indexed: 01/18/2023] Open
Abstract
Chirality is a key factor in the safety and efficacy of many drug products and thus the production of single enantiomers of drug intermediates and drugs has become increasingly important in the pharmaceutical industry. There has been an increasing awareness of the enormous potential of microorganisms and enzymes derived there from for the transformation of synthetic chemicals with high chemo-, regio- and enatioselectivities. In this article, biocatalytic processes are described for the synthesis of chiral alcohols and unntural aminoacids for pharmaceuticals.
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Affiliation(s)
- Ramesh N Patel
- SLRP Associates Consultation in Biotechnology, 572 Cabot Hill Road, Bridgewater, NJ 08807, USA.
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Rios-Solis L, Bayir N, Halim M, Du C, Ward J, Baganz F, Lye G. Non-linear kinetic modelling of reversible bioconversions: Application to the transaminase catalyzed synthesis of chiral amino-alcohols. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Design of a recombinant Escherichia coli for producing L-phenylalanine from glycerol. World J Microbiol Biotechnol 2012; 28:2937-43. [PMID: 22806734 DOI: 10.1007/s11274-012-1104-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
Abstract
A recombinant Escherichia coli was engineered to produce the commercially important amino acid L-phenylalanine (L-Phe) using glycerol as the carbon source. Compared to the conventionally used glucose and sucrose, glycerol is a less expensive carbon source. As phenylalanine dehydrogenase (PheDH) activity is involved in the last step of L-Phe synthesis in E. coli, a phenylalanine dehydrogenase gene (phedh) from the thermotolerant Bacillus lentus was cloned into pRSFDuet-1 (pPheDH) and expressed in E. coli BL21(DE3). The resulting clone had a limited ability to produce L-Phe from glycerol, possibly because of a poor glycerol uptake by the cell, or an inability to excrete L-Phe, or both. Therefore, yddG gene encoding an aromatic amino acid exporter and glpF gene encoding a glycerol transport facilitator were coexpressed with the phedh in a reengineered E. coli. In a glycerol medium, the maximum L-Phe production rates of the clones pPY (phedh and yddG genes) and pPYF (phedh, yddG and glpF genes) were 1.4- and 1.8-fold higher than the maximum production rate of the pPheDH clone. The better producing pPYF clone was further evaluated in a 5 l stirred-tank fermenter (37 °C, an aeration rate of 1 vvm, an agitation speed of 400 rpm). In the fermenter, the maximum concentration of L-Phe (366 mg/l) was achieved in a much shorter period compared to in the shake flasks. In the latter, the highest titer of L-Phe was only 76 % of the maximum value attained in the fermenter.
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Amenábar MJ, Blamey JM. Purification and characterization of a thermostable glutamate dehydrogenase from a thermophilic bacterium isolated from a sterilization drying oven. BMB Rep 2012; 45:91-5. [PMID: 22360886 DOI: 10.5483/bmbrep.2012.45.2.91] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Glutamate dehydrogenase from axenic bacterial cultures of a new microorganism, called GWE1, isolated from the interior of a sterilization drying oven, was purified by anion-exchange and molecular-exclusion liquid chromatography. The apparent molecular mass of the native enzyme was 250.5 kDa and was shown to be an hexamer with similar subunits of molecular mass 40.5 kDa. For glutamate oxidation, the enzyme showed an optimal pH and temperature of 8.0 and 70 degrees C, respectively. In contrast to other glutamate dehydrogenases isolated from bacteria, the enzyme isolated in this study can use both NAD(+) and NADP(+) as electron acceptors, displaying more affinity for NADP(+) than for NAD(+). No activity was detected with NADH or NADPH, 2-oxoglutarate and ammonia. The enzyme was exceptionally thermostable, maintaining more than 70% of activity after incubating at 100(o)C for more than five hours suggesting being one of the most thermoestable enzymes reported in the family of dehydrogenases.
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Affiliation(s)
- Maximiliano J Amenábar
- Fundación Científica y Cultural Biociencia, José Domingo Cañas 2280, Nuñoa, Santiago, Chile.
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de Vladar HP. Amino acid fermentation at the origin of the genetic code. Biol Direct 2012; 7:6. [PMID: 22325238 PMCID: PMC3376031 DOI: 10.1186/1745-6150-7-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 02/10/2012] [Indexed: 01/15/2023] Open
Abstract
There is evidence that the genetic code was established prior to the existence of proteins, when metabolism was powered by ribozymes. Also, early proto-organisms had to rely on simple anaerobic bioenergetic processes. In this work I propose that amino acid fermentation powered metabolism in the RNA world, and that this was facilitated by proto-adapters, the precursors of the tRNAs. Amino acids were used as carbon sources rather than as catalytic or structural elements. In modern bacteria, amino acid fermentation is known as the Stickland reaction. This pathway involves two amino acids: the first undergoes oxidative deamination, and the second acts as an electron acceptor through reductive deamination. This redox reaction results in two keto acids that are employed to synthesise ATP via substrate-level phosphorylation. The Stickland reaction is the basic bioenergetic pathway of some bacteria of the genus Clostridium. Two other facts support Stickland fermentation in the RNA world. First, several Stickland amino acid pairs are synthesised in abiotic amino acid synthesis. This suggests that amino acids that could be used as an energy substrate were freely available. Second, anticodons that have complementary sequences often correspond to amino acids that form Stickland pairs. The main hypothesis of this paper is that pairs of complementary proto-adapters were assigned to Stickland amino acids pairs. There are signatures of this hypothesis in the genetic code. Furthermore, it is argued that the proto-adapters formed double strands that brought amino acid pairs into proximity to facilitate their mutual redox reaction, structurally constraining the anticodon pairs that are assigned to these amino acid pairs. Significance tests which randomise the code are performed to study the extent of the variability of the energetic (ATP) yield. Random assignments can lead to a substantial yield of ATP and maintain enough variability, thus selection can act and refine the assignments into a proto-code that optimises the energetic yield. Monte Carlo simulations are performed to evaluate the establishment of these simple proto-codes, based on amino acid substitutions and codon swapping. In all cases, donor amino acids are assigned to anticodons composed of U+G, and have low redundancy (1-2 codons), whereas acceptor amino acids are assigned to the the remaining codons. These bioenergetic and structural constraints allow for a metabolic role for amino acids before their co-option as catalyst cofactors. Reviewers: this article was reviewed by Prof. William Martin, Prof. Eörs Szathmáry (nominated by Dr. Gáspár Jékely) and Dr. Ádám Kun (nominated by Dr. Sandor Pongor)
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L-aspartate dehydrogenase: features and applications. Appl Microbiol Biotechnol 2011; 93:503-16. [PMID: 22120624 DOI: 10.1007/s00253-011-3730-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Revised: 10/30/2011] [Accepted: 11/14/2011] [Indexed: 10/15/2022]
Abstract
L-amino acid dehydrogenases are a group of enzymes that catalyze the reversible oxidative deamination of L-amino acids to their corresponding 2-oxoacids, using either nicotinamide adenine dinucleotide (NAD(+)) or nicotinamide adenine dinucleotide phosphate (NADP(+)) as cofactors. These enzymes have been studied widely because of their potential applications in the synthesis of amino acids for use in production of pharmaceutical peptides, herbicides and insecticides, in biosensors or diagnostic kits, and development of coenzyme regeneration systems for industrial processes. This article presents a review of the currently available data about the recently discovered amino acid dehydrogenase superfamily member L-aspartate dehydrogenase (L-AspDH), their relevant catalytic properties and speculated physiological roles, and potential for biotechnological applications. The proposed classification of L-AspDH on the basis of bioinformatic information and potential role in vivo into NadB (NAD biosynthesis-related) and non-NadB type is unique. In particular, the mesophilic non-NadB type L-AspDH is a novel group of amino acid dehydrogenases with great promise as potential industrial biocatalysts owing to their relatively high catalytic properties at room temperature. Considering that only a few L-AspDH homologs have been characterized so far, identification and prodigious enzymological research of the new members will be necessary to shed light on the gray areas pertaining to these enzymes.
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Disruption of the gene encoding glutamate dehydrogenase affects growth, amino acids catabolism and survival of Lactobacillus plantarum UC1001. Int Dairy J 2011. [DOI: 10.1016/j.idairyj.2010.09.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Vashishtha AK, West AH, Cook PF. Chemical mechanism of saccharopine reductase from Saccharomyces cerevisiae. Biochemistry 2009; 48:5899-907. [PMID: 19449898 DOI: 10.1021/bi900599s] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Saccharopine reductase (SR) [saccharopine dehydrogenase (l-glutamate forming), EC 1.5.1.10] catalyzes the condensation of l-alpha-aminoadipate-delta-semialdehyde (AASA) with l-glutamate to give an imine, which is reduced by NADPH to give saccharopine. An acid-base chemical mechanism has been proposed for SR on the basis of pH-rate profiles and solvent deuterium kinetic isotope effects. A finite solvent isotope effect is observed indicating that proton(s) are in flight in the rate-limiting step(s) and likely the same step is limiting under both limiting and saturating substrate concentrations. A concave upward proton inventory suggests that more than one proton is transferred in a single transition state, likely a conformation change required to open the site and release products. Two groups are involved in the acid-base chemistry of the reaction. One of these groups catalyzes the steps involved in forming the imine between the alpha-amine of glutamate and the aldehyde of AASA. The group, which has a pK(a) of about 8, is observed in the pH-rate profiles for V(1) and V(1)/K(Glu) and must be protonated for optimal activity. It is also observed in the V(2) and V(2)/K(Sacc) pH-rate profiles and is required unprotonated. The second group, which has a pK(a) of 5.6, accepts a proton from the alpha-amine of glutamate so that it can act as a nucleophile in forming a carbinolamine upon attack of the carbonyl of AASA.
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Affiliation(s)
- Ashwani Kumar Vashishtha
- Department of Chemistry and Biochemistry, University of Oklahoma, 620 Parrington Oval, Norman, Oklahoma 73019, USA
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Chemoenzymatic Synthesis of Chiral Pharmaceutical Intermediates. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2009. [DOI: 10.1201/9781420077070.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Lazzi C, Bove CG, Marsano RM, Neviani E. Transcriptional analysis of the gdhA gene in Streptococcus thermophilus. J Appl Microbiol 2009; 107:1358-66. [PMID: 19486386 DOI: 10.1111/j.1365-2672.2009.04317.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To study the transcriptional analysis of glutamate dehydrogenase gene, involved in the amino acid conversion to aroma compound in Streptococcus thermophilus. METHODS AND RESULTS Analysis of the gdhA gene nucleotide sequence of S. thermophilus CNRZ1066 revealed that the coding region is 1353 nucleotides long. The deduced amino acids sequence exhibits the putative GDH active site and some conserved domains characteristic of family I of hexameric GDHs. Phylogenetic analysis revealed that the gdh gene of S. thermophilus clustered with the orthologues of other streptococci such as Streptococcus mutans, Streptococcus agalactiae and Streptococcus infantarius. Studying the structural organization of the gdhA locus the amino acid similarity of GDHs was higher than 87%, but the locus organization was not conserved. A dominant transcript of approximately 1.4 kbp was revealed by Northern blot hybridization, suggesting that gdhA mRNA is monocystronic. Primer extension showed that transcription start point of gdhA was localized 43 bp upstream of the potential start codon (ATG). CONCLUSIONS The gdhA represents a monocistronic operon highly conserved in phylogenetic-related bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY A deeper knowledge of gdh transcriptional mechanisms could lead to develop S. thermophilus industrial starter cultures with optimized aromatic properties.
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Affiliation(s)
- C Lazzi
- Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, Viale Usberti 11/A, Parma 43100, Italy.
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Li M, Allen A, Smith TJ. High throughput screening reveals several new classes of glutamate dehydrogenase inhibitors. Biochemistry 2007; 46:15089-102. [PMID: 18044977 DOI: 10.1021/bi7018783] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Glutamate dehydrogenase (GDH) has been shown to play a regulatory role in insulin secretion by pancreatic beta-cells. The most compelling evidence of this comes from features of the hyperinsulism/hyperammonemia (HI/HA) syndrome where a dominant mutation causes the loss of inhibition by GTP, and from studies that link leucine (and its analogue BCH) activation of GDH to stimulation of insulin secretion. This suggests that GDH may represent a new and novel drug target to control a variety of insulin disorders. Recently we demonstrated that a subset of green tea polyphenols are potent inhibitors of glutamate dehydrogenase in vitro and can efficaciously block BCH stimulation of insulin secretion. In these current studies, we extend our search for GDH inhibitors using high throughput methods to pan through more than 27,000 compounds. A number of known and new inhibitors were identified with IC50s in the low micromolar range. These new inhibitors were found to act via apparently different mechanisms with some inhibiting the reaction in a positively cooperative manner, the inhibition by only some of the compounds was reversed by ADP, and one compound was found to stabilize the enzyme against thermal denaturation. Therefore, these new compounds not only are new leads in the treatment of hyperactive GDH but also are useful in dissecting the complex allosteric nature of the enzyme.
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Affiliation(s)
- Ming Li
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132, USA
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40
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Kaulmann U, Smithies K, Smith ME, Hailes HC, Ward JM. Substrate spectrum of ω-transaminase from Chromobacterium violaceum DSM30191 and its potential for biocatalysis. Enzyme Microb Technol 2007. [DOI: 10.1016/j.enzmictec.2007.05.011] [Citation(s) in RCA: 177] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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41
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Mohamadi HS, Omidinia E, Dinarvand R. Evaluation of recombinant phenylalanine dehydrogenase behavior in aqueous two-phase partitioning. Process Biochem 2007. [DOI: 10.1016/j.procbio.2007.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Vedha-Peters K, Gunawardana M, Rozzell JD, Novick SJ. Creation of a broad-range and highly stereoselective D-amino acid dehydrogenase for the one-step synthesis of D-amino acids. J Am Chem Soc 2007; 128:10923-9. [PMID: 16910688 PMCID: PMC2533268 DOI: 10.1021/ja0603960] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using both rational and random mutagenesis, we have created the first known broad substrate range, nicotinamide cofactor dependent, and highly stereoselective d-amino acid dehydrogenase. This new enzyme is capable of producing d-amino acids via the reductive amination of the corresponding 2-keto acid with ammonia. This biocatalyst was the result of three rounds of mutagenesis and screening performed on the enzyme meso-diaminopimelate d-dehydrogenase. The first round targeted the active site of the wild-type enzyme and produced mutants that were no longer strictly dependent on the native substrate. The second and third rounds produced mutants that had an increased substrate range including straight- and branched-aliphatic amino acids and aromatic amino acids. The very high selectivity toward the d-enantiomer (95 to >99% ee) was shown to be preserved even after the addition of the five mutations found in the three rounds of mutagenesis and screening. This new enzyme could complement and improve upon current methods for d-amino acid synthesis.
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Affiliation(s)
- Kavitha Vedha-Peters
- BioCatalytics, Inc., 129 North Hill Avenue, Suite 103, Pasadena, California 91106, USA
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43
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Choudhury R, Punekar NS. Competitive inhibition of glutamate dehydrogenase reaction. FEBS Lett 2007; 581:2733-6. [PMID: 17531979 DOI: 10.1016/j.febslet.2007.05.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 05/14/2007] [Accepted: 05/14/2007] [Indexed: 11/18/2022]
Abstract
Irrespective of their pyridine nucleotide specificity, all glutamate dehydrogenases share a common chemical mechanism that involves an enzyme bound 'iminoglutarate' intermediate. Three compounds, structurally related to this intermediate, were tested for the inhibition of purified NADP-glutamate dehydrogenases from two Aspergilli, as also the bovine liver NAD(P)-glutamate dehydrogenase. 2-Methyleneglutarate, closely resembling iminoglutarate, was a potent competitive inhibitor of the glutamate dehydrogenase reaction. This is the first report of a non-aromatic structure with a better glutamate dehydrogenase inhibitory potency than aryl carboxylic acids such as isophthalate. A suitably located 2-methylene group to mimic the iminium ion could be exploited to design inhibitors of other amino acid dehydrogenases.
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Affiliation(s)
- Rajarshi Choudhury
- Biotechnology Group, SBB, Indian Institute of Technology, Powai, Mumbai, India
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44
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Matsumoto M, Nishimura Y. Hydrogen production by fermentation using acetic acid and lactic acid. J Biosci Bioeng 2007; 103:236-41. [PMID: 17434426 DOI: 10.1263/jbb.103.236] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Accepted: 12/07/2006] [Indexed: 11/17/2022]
Abstract
Microbial hydrogen production from sho-chu post-distillation slurry solution (slurry solution) containing large amounts of organic acids was investigated. The highest hydrogen producer, Clostridium diolis JPCC H-3, was isolated from natural environment and produced hydrogen at 6.03+/-0.15 ml from 5 ml slurry solution in 30 h. Interestingly, the concentration of acetic acid and lactic acid in the slurry solution decreased during hydrogen production. The substrates for hydrogen production by C. diolis JPCC H-3, in particular organic acids, were investigated in an artificial medium. No hydrogen was produced from acetic acid, propionic acid, succinic acid, or citric acid on their own. Hydrogen and butyric acid were produced from a mixture of acetic acid and lactic acid, showing that C. diolis. JPCC H-3 could produce hydrogen from acetic acid and lactic acid. Furthermore, calculation of the Gibbs free energy strongly suggests that this reaction would proceed. In this paper, we describe for the first time microbial hydrogen production from acetic acid and lactic acid by fermentation.
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Affiliation(s)
- Mitsufumi Matsumoto
- Technology Development Center, Wakamatsu Research Institute, Biotechnology Laboratory, Electric Power Development Co., Ltd, 1 Yanagasaki, Wakamatsu, Kitakyushu, Fukuoka 808-0111, Japan.
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45
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Forbes CD, Myung J, Szewczak AA, Landro JA. A high-throughput competitive scintillation proximity aminoacyl–tRNA synthetase charging assay to measure amino acid concentration. Anal Biochem 2007; 363:246-54. [PMID: 17316538 DOI: 10.1016/j.ab.2007.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 01/12/2007] [Accepted: 01/20/2007] [Indexed: 10/23/2022]
Abstract
An enhanced method to measure the concentration of individual naturally occurring free amino acids in solution is described. This relatively simple but robust method combines two previously reported procedures: the use of scintillation proximity assay (SPA) technology to measure aminoacyl-tRNA synthetase (aaRS) activity and the use of aaRS activity to measure amino acid concentration using the enzymatic isotope dilution technique. The format described is called an aaRS competitive scintillation proximity assay (cSPA). This cSPA takes advantage of competition between a fixed concentration of radiolabeled amino acid and an unknown concentration of the same nonradiolabeled amino acid for its cognate tRNA catalyzed by the aaRS specific for that amino acid. Under equilibrium conditions, in the case of limiting tRNA, the rate of the enzyme-catalyzed reaction relative to substrate concentration becomes irrelevant and the enzymatic isotopic dilution technique becomes the simple isotopic dilution technique. Due to the exquisite specificity of the reaction, a crude mixture of tRNAs and aaRSs can be used to detect the concentration of a particular amino acid without interference from noncognate amino acids. When used to monitor aminopeptidase M activity, this assay produced similar results in time course and inhibition experiments as compared with a traditional fluorescent assay. High-throughput compatibility was demonstrated by screening 12,000 compounds against aminopeptidase M in 384-well microtiter plates with Z factors ranging from 0.53 to 0.70. This competitive assay can be used as a general method to detect amino acids at concentrations less than 100 nM and to monitor enzyme activity in biological samples, and it is amenable to high-throughput screening.
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Li C, Allen A, Kwagh J, Doliba NM, Qin W, Najafi H, Collins HW, Matschinsky FM, Stanley CA, Smith TJ. Green tea polyphenols modulate insulin secretion by inhibiting glutamate dehydrogenase. J Biol Chem 2006; 281:10214-21. [PMID: 16476731 DOI: 10.1074/jbc.m512792200] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Insulin secretion by pancreatic beta-cells is stimulated by glucose, amino acids, and other metabolic fuels. Glutamate dehydrogenase (GDH) has been shown to play a regulatory role in this process. The importance of GDH was underscored by features of hyperinsulinemia/hyperammonemia syndrome, where a dominant mutation causes the loss of inhibition by GTP and ATP. Here we report the effects of green tea polyphenols on GDH and insulin secretion. Of the four compounds tested, epigallocatechin gallate (EGCG) and epicatechin gallate were found to inhibit GDH with nanomolar ED(50) values and were therefore found to be as potent as the physiologically important inhibitor GTP. Furthermore, we have demonstrated that EGCG inhibits BCH-stimulated insulin secretion, a process that is mediated by GDH, under conditions where GDH is no longer inhibited by high energy metabolites. EGCG does not affect glucose-stimulated insulin secretion under high energy conditions where GDH is probably fully inhibited. We have further shown that these compounds act in an allosteric manner independent of their antioxidant activity and that the beta-cell stimulatory effects are directly correlated with glutamine oxidation. These results demonstrate that EGCG, much like the activator of GDH (BCH), can facilitate dissecting the complex regulation of insulin secretion by pharmacologically modulating the effects of GDH.
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Affiliation(s)
- Changhong Li
- Donald Danforth Plant Science Center, 975 Warson Road, St. Louis, MO 63132, USA
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Noor S, Punekar NS. Allosteric NADP-glutamate dehydrogenase from aspergilli: purification, characterization and implications for metabolic regulation at the carbon-nitrogen interface. MICROBIOLOGY-SGM 2005; 151:1409-1419. [PMID: 15870451 DOI: 10.1099/mic.0.27751-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
NADP-dependent glutamate dehydrogenase (NADP-GDH) mediates fungal ammonium assimilation through reductive synthesis of glutamate from 2-oxoglutarate. By virtue of its position at the interface of carbon and nitrogen metabolism, biosynthetic NADP-GDH is a potential candidate for metabolic control. In order to facilitate characterization, a new and effective dye-affinity method was devised to purify NADP-GDH from two aspergilli, Aspergillus niger and Aspergillus nidulans. The A. niger NADP-GDH was characterized at length and its kinetic interaction constants with glutamate (Km 34.7 mM) and ammonium (Km 1.05 mM; Ki 0.4 mM) were consistent with an anabolic role. Isophthalate, 2-methyleneglutarate and 2,4-pyridinedicarboxylate were significant inhibitors, with respective Ki values of 6.9, 9.2 and 202.0 microM. The A. niger enzyme showed allosteric properties and a sigmoid response (nH=2.5) towards 2-oxoglutarate saturation. The co-operative behaviour was a feature common to NADP-GDH from Aspergillus awamori, A. nidulans and Aspergillus oryzae. NADP-GDH may therefore be a crucial determinant in adjusting 2-oxoglutarate flux between the tricarboxylic acid cycle and glutamate biosynthesis in aspergilli.
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Affiliation(s)
- Shahid Noor
- Biotechnology Group, School of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai - 400076, India
| | - Narayan S Punekar
- Biotechnology Group, School of Bioscience and Bioengineering, Indian Institute of Technology Bombay, Mumbai - 400076, India
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48
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Paradisi F, Woolfson R, Geoghegan KF, Engel PC. Identification of the residue responsible for catalysing regeneration of activity in the inactive glutamate dehydrogenase mutant D165N. FEBS Lett 2005; 579:2830-2. [PMID: 15878554 DOI: 10.1016/j.febslet.2005.03.098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2005] [Revised: 03/30/2005] [Accepted: 03/31/2005] [Indexed: 11/19/2022]
Abstract
Previously a mutant of clostridial glutamate dehydrogenase with the catalytic Asp-165 replaced by Asn was shown to regain activity through spontaneous, specific deamidation of this residue. A double mutant D165N/K125A has now been constructed, in which the catalytic Lys is also replaced. This was successfully over-expressed and according to several criteria appears to be correctly folded. The double mutant was incubated for 35 days under conditions where D165N reactivates. LC-MS analysis of tryptic digests of timed samples showed no significant deamidation. This confirms that the reactivation of D165N is a consequence of the catalytic chemistry of the enzyme's active site.
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Affiliation(s)
- Francesca Paradisi
- Department of Biochemistry, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Ireland
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49
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Mihara H, Muramatsu H, Kakutani R, Yasuda M, Ueda M, Kurihara T, Esaki N. N-methyl-L-amino acid dehydrogenase from Pseudomonas putida. A novel member of an unusual NAD(P)-dependent oxidoreductase superfamily. FEBS J 2005; 272:1117-23. [PMID: 15720386 DOI: 10.1111/j.1742-4658.2004.04541.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We found N-methyl-L-amino acid dehydrogenase activity in various bacterial strains, such as Pseudomonas putida and Bacillus alvei, and cloned the gene from P. putida ATCC12633 into Escherichia coli. The enzyme purified to homogeneity from recombinant E. coli catalyzed the NADPH-dependent formation of N-alkyl-L-amino acids from the corresponding alpha-oxo acids (e.g. pyruvate, phenylpyruvate, and hydroxypyruvate) and alkylamines (e.g. methylamine, ethylamine, and propylamine). Ammonia was inert as a substrate, and the enzyme was clearly distinct from conventional NAD(P)-dependent amino acid dehydrogenases, such as alanine dehydrogenase (EC 1.4.1.1). NADPH was more than 300 times more efficient than NADH as a hydrogen donor in the enzymatic reductive amination. Primary structure analysis revealed that the enzyme belongs to a new NAD(P)-dependent oxidoreductase superfamily, the members of which show no sequence homology to conventional NAD(P)-dependent amino acid dehydrogenases and opine dehydrogenases.
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Affiliation(s)
- Hisaaki Mihara
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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Gunawardana SC, Liu YJ, Macdonald MJ, Straub SG, Sharp GWG. Anaplerotic input is sufficient to induce time-dependent potentiation of insulin release in rat pancreatic islets. Am J Physiol Endocrinol Metab 2004; 287:E828-33. [PMID: 15475511 DOI: 10.1152/ajpendo.00381.2003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nutrients that induce biphasic insulin release, such as glucose and leucine, provide acetyl-CoA and anaplerotic input in the beta-cell. The first phase of release requires increased ATP production leading to increased intracellular Ca(2+) concentration ([Ca(2+)](i)). The second phase requires increased [Ca(2+)](i) and anaplerosis. There is strong evidence to indicate that the second phase is due to augmentation of Ca(2+)-stimulated release via the K(ATP) channel-independent pathway. To test whether the phenomenon of time-dependent potentiation (TDP) has similar properties to the ATP-sensitive K(+) channel-independent pathway, we monitored the ability of different agents that provide acetyl-CoA and anaplerotic input or both of these inputs to induce TDP. The results show that anaplerotic input is sufficient to induce TDP. Interestingly, among the agents tested, the nonsecretagogue glutamine, the nonhydrolyzable analog of leucine aminobicyclo[2.2.1]heptane-2-carboxylic acid, and succinic acid methyl ester all induced TDP, and all significantly increased alpha-ketoglutarate levels in the islets. In conclusion, anaplerosis that enhances the supply and utilization of alpha-ketoglutarate in the tricarboxylic acid cycle appears to play an essential role in the generation of TDP.
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Affiliation(s)
- Subhadra C Gunawardana
- Dept. of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
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