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Schwarze CM, Petersen M. Phenylalanine ammonia-lyases and 4-coumaric acid coenzyme A ligases in Chara braunii, Marchantia polymorpha, and Physcomitrium patens as extant model organisms for plant terrestrialization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39052447 DOI: 10.1111/tpj.16950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
The conquest of land posed severe problems to plants which they had to cope with by adapting biosynthetic capacities. Adaptations to respond to UV irradiation, water loss, pathogen and herbivore defense, and the earth's pull were essential. Chemical compounds alleviating these problems can be synthesized by the phenylpropanoid pathway, the core of which are three enzymes: phenylalanine ammonia-lyase (PAL), cinnamic acid 4-hydroxylase, and 4-coumaric acid coenzyme A-ligase (4CL). The genomes of model organisms, Chara braunii as aquatic alga and the two bryophytes Physcomitrium patens and Marchantia polymorpha, were searched for sequences encoding PAL and 4CL and selected sequences heterologously expressed in Escherichia coli for biochemical characterization. Several possible isoforms were identified for both enzymes in Marchantia polymorpha and Physcomitrium patens, while only one or two isoforms could be retrieved for Chara braunii. Active forms of both enzymes were found in all three organisms, although the catalytic efficiencies varied in a wide range. l-Phenylalanine was accepted as best substrate by all PAL-like enzymes, despite annotations in some cases suggesting different activities. The substrate spectrum of 4CLs was more diverse, but caffeic and/or 4-coumaric acids generally were the best-accepted substrates. Our investigations show that PAL and 4CL, important enzymes for the formation of phenolic compounds, are present and active in extant charophytes and bryophytes as model organisms for the conquest of land.
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Affiliation(s)
- Christoph Michael Schwarze
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, Marburg, 35037, Germany
| | - Maike Petersen
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, Marburg, 35037, Germany
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2
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Jangra N, Kawatra A, Datten B, Gupta S, Gulati P. Recent trends in targeted delivery of smart nanocarrier-based microbial enzymes for therapeutic applications. Drug Discov Today 2024; 29:103915. [PMID: 38340953 DOI: 10.1016/j.drudis.2024.103915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/19/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
Smart carrier-based immobilization has widened the use of enzymes for the treatment of several disorders. Large surface areas, tunable morphology, and surface modification ability aid the targeted and controlled release of therapeutic enzymes from such formulations. Smart nanocarriers, such as polymeric carriers, liposomes, and silica have also increased the stability, half-life, and permeability of these enzymes. In this review, summarize recent advances in the smart immobilization of microbial enzymes and their development as precision nanomedicine for the treatment of cancer, thrombosis, phenylketonuria (PKU), and wound healing. We also discuss the challenges and measures to be adopted for the successful clinical translation of these formulations.
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Affiliation(s)
- Nikita Jangra
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Anubhuti Kawatra
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Bharti Datten
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Shefali Gupta
- Department of Industrial Microbiology, Sam Higginbottom University of Agriculture Technology and Sciences (SHUATS), Allahabad, Uttar Pradesh
| | - Pooja Gulati
- Medical Microbiology and Bioprocess Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
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Brack Y, Sun C, Yi D, Bornscheuer UT. Systematic Analysis of the MIO-forming Residues of Aromatic Ammonia Lyases. Chembiochem 2024; 25:e202400016. [PMID: 38323706 DOI: 10.1002/cbic.202400016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
Aromatic ammonia lyases (AALs) and tyrosine/phenylalanine ammonia mutases (TAM/PAM) are 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO)-dependent enzymes. Usually, the MIO moiety is autocatalytically formed from the tripeptide Ala-Ser-Gly (ASG) and acts as an electrophile during the enzymatic reaction. However, the MIO-forming residues (ASG) have some diversity in this enzyme class. In this work, a systematic investigation on the variety of MIO-forming residues was carried out using in-depth sequence analyses. Several protein clusters of AAL-like enzymes with unusual MIO-forming residues such as ACG, TSG, SSG, and CSG were identified, including two novel histidine ammonia lyases and one PAM with CSG and TSG residues, respectively, as well as three novel ergothioneine trimethylammonia lyases without MIO motif. The mutagenesis of common MIO-groups confirmed the function of these MIO variants, which provides good starting points for future functional prediction and mutagenesis research of AALs.
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Affiliation(s)
- Yannik Brack
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| | - Chenghai Sun
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| | - Dong Yi
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
- National Key Laboratory of Lead Druggability Research, Research Center for Systems Biosynthesis, China State Institute of Pharmaceutical Industry, Gebaini Road 285, 201203, Shanghai, China
| | - Uwe T Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
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4
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Brack Y, Sun C, Yi D, Bornscheuer UT. Exploring the Substrate Switch Motif of Aromatic Ammonia Lyases. Chembiochem 2023; 24:e202300584. [PMID: 37747300 DOI: 10.1002/cbic.202300584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 09/26/2023]
Abstract
Aromatic ammonia lyases (AALs) are important enzymes for biocatalysis as they enable the asymmetric synthesis of chiral l-α-amino acids from the corresponding α,β-unsaturated precursors. AALs have very similar protein structures and active site pockets but exhibit strict substrate specificity towards tyrosine, phenylalanine, or histidine. Herein, through systematic bioinformatics and structural analysis, we discovered eight new motifs of amino acid residues in AALs. After introducing them - as well as four already known motifs - into different AALs, we learned that altering the substrate specificity by engineering the substrate switch motif in phenylalanine ammonia lyases (PALs), phenylalanine/tyrosine ammonia lyases (PTALs), and tyrosine ammonia lyases (TALs) was only partially successful. However, we discovered that three previously unknown residue combinations introduced a substrate switch from tyrosine to phenylalanine in TAL, which was converted up to 20-fold better compared to the wild-type TAL enzyme.
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Affiliation(s)
- Yannik Brack
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| | - Chenghai Sun
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
| | - Dong Yi
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
- Department of Biopharmaceuticals, China State Institute of Pharmaceutical Industry, Gebaini Road 285, 201203, Shanghai, P. R. China
| | - Uwe T Bornscheuer
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Straße 4, 17489, Greifswald, Germany
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5
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Tachibana R, Zhang K, Zou Z, Burgener S, Ward TR. A Customized Bayesian Algorithm to Optimize Enzyme-Catalyzed Reactions. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:12336-12344. [PMID: 37621696 PMCID: PMC10445256 DOI: 10.1021/acssuschemeng.3c02402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/21/2023] [Indexed: 08/26/2023]
Abstract
Design of experiments (DoE) plays an important role in optimizing the catalytic performance of chemical reactions. The most commonly used DoE relies on the response surface methodology (RSM) to model the variable space of experimental conditions with the fewest number of experiments. However, the RSM leads to an exponential increase in the number of required experiments as the number of variables increases. Herein we describe a Bayesian optimization algorithm (BOA) to optimize the continuous parameters (e.g., temperature, reaction time, reactant and enzyme concentrations, etc.) of enzyme-catalyzed reactions with the aim of maximizing performance. Compared to existing Bayesian optimization methods, we propose an improved algorithm that leads to better results under limited resources and time for experiments. To validate the versatility of the BOA, we benchmarked its performance with biocatalytic C-C bond formation and amination for the optimization of the turnover number. Gratifyingly, up to 80% improvement compared to RSM and up to 360% improvement vs previous Bayesian optimization algorithms were obtained. Importantly, this strategy enabled simultaneous optimization of both the enzyme's activity and selectivity for cross-benzoin condensation.
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Affiliation(s)
- Ryo Tachibana
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4058, Basel, Switzerland
- National
Center of Competence in Research (NCCR) “Catalysis”,
ETHZ, 8093 Zurich, Switzerland
| | - Kailin Zhang
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4058, Basel, Switzerland
| | - Zhi Zou
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4058, Basel, Switzerland
| | - Simon Burgener
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4058, Basel, Switzerland
| | - Thomas R. Ward
- Department
of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, CH-4058, Basel, Switzerland
- National
Center of Competence in Research (NCCR) “Molecular Systems
Engineering”, 4058 Basel, Switzerland
- National
Center of Competence in Research (NCCR) “Catalysis”,
ETHZ, 8093 Zurich, Switzerland
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Phenylalanine Ammonia-Lyase: A Key Gene for Color Discrimination of Edible Mushroom Flammulina velutipes. J Fungi (Basel) 2023; 9:jof9030339. [PMID: 36983507 PMCID: PMC10053379 DOI: 10.3390/jof9030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/07/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
In nature; Flammulina velutipes, also known as winter mushrooms, vary in the color of their fruiting bodies, from black, yellow, pale yellow, or beige to white. The purpose of this study was to compare the genome sequences of different colored strains of F. velutipes and to identify variations in the genes associated with fruiting body color. Comparative genomics of six F. velutipes strains revealed 70 white-strain-specific variations, including single nucleotide polymorphisms (SNPs) and insertions/deletions (indels), in the genome sequences. Among them, 36 variations were located in the open reading frames, and only one variation was identified as a mutation with a disruptive in-frame deletion (ΔGCGCAC) within the annotated gene phenylalanine ammonia-lyase 1 (Fvpal1). This mutation was found to cause a deletion, without a frameshift, of two amino acids at positions 112 and 113 (arginine and threonine, respectively) in the Fvpal1 gene of the white strain. Specific primers to detect this mutation were designed, and amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) was performed to evaluate whether the mutation is color specific for the F. velutipes fruiting body. PCR analysis of a total of 95 F. velutipes strains revealed that this mutation was present only in white strains. In addition, monospores of the heterozygous mutant were isolated, and whether this mutation was related to the color of the fruiting body was evaluated by a mating assay. In the mating analysis of monospores with mutations in Fvpal1, it was found that this mutation plays an important role in determining the color of the fruiting body. Furthermore, the deletion (Δ112RT113) in Fvpal1 is located between motifs that play a key role in the catalytic function of FvPAL1. These results suggest that this mutation can be used as an effective marker for the color-specific breeding of F. velutipes, a representative edible mushroom.
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7
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Biochemical Characterization of Novel Phenylalanine Ammonia-Lyase from Spirulina CPCC-695. Protein J 2022; 41:414-423. [PMID: 35713742 DOI: 10.1007/s10930-022-10063-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2022] [Indexed: 10/18/2022]
Abstract
Phenylalanine ammonia lyase (PAL) catalyzes the deamination of phenylalanine to cinnamic acid and ammonia. It plays a crucial role in the formation of secondary metabolites through the phenylpropanoid pathway. Recently there has been growing interest in exploring the biochemical properties of PAL for its clinical and commercial applications. PAL as a key component has been used in metabolic engineering and synthetic biology. Due to its high substrate specificity and catalytic efficacy, PAL has opened a new area of interest in the biomedical field. PAL has been frequently used in the enzyme replacement therapy of phenylketonuria, cancer treatment and microbial production of l-phe the precursor of noncalorific sweetener aspartame (Methyl L-α-aspartyl-l-phenylalaninate), antimicrobial and health supplements. PAL occurs in few plants, fungi, bacteria, and cyanobacteria. The present investigation is a preliminary study in which an attempt has been made for the isolation, partial purification, and biochemical characterization of PAL (crude and partially purified) from Spirulina CPCC-695. Partially purified PAL exhibited higher enzymatic activity and protein content than the crude enzyme. Molecular weight of the crude and partially purified PAL was ~ 66 kDa. The optimum temperature and pH for PAL activity was observed as 30 ℃ and 8.0 respectively. l-Phe was the most preferred substrate (100 mM) whereas gallic acid showed maximum inhibition of PAL activity. Enzyme kinetics suggested good catalytic efficacy of the PAL enzyme and affinity towards substrate. Both the enzyme (crude and partially purified) showed less than 5% haemolysis suggesting the biocompatible nature of PAL.
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8
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Jagtap SS, Deewan A, Liu JJ, Walukiewicz HE, Yun EJ, Jin YS, Rao CV. Integrating transcriptomic and metabolomic analysis of the oleaginous yeast Rhodosporidium toruloides IFO0880 during growth under different carbon sources. Appl Microbiol Biotechnol 2021; 105:7411-7425. [PMID: 34491401 DOI: 10.1007/s00253-021-11549-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/18/2021] [Accepted: 08/22/2021] [Indexed: 12/31/2022]
Abstract
Rhodosporidium toruloides is an oleaginous yeast capable of producing a variety of biofuels and bioproducts from diverse carbon sources. Despite numerous studies showing its promise as a platform microorganism, little is known about its metabolism and physiology. In this work, we investigated the central carbon metabolism in R. toruloides IFO0880 using transcriptomics and metabolomics during growth on glucose, xylose, acetate, or soybean oil. These substrates were chosen because they can be derived from plants. Significant changes in gene expression and metabolite concentrations were observed during growth on these four substrates. We mapped these changes onto the governing metabolic pathways to better understand how R. toruloides reprograms its metabolism to enable growth on these substrates. One notable finding concerns xylose metabolism, where poor expression of xylulokinase induces a bypass leading to arabitol production. Collectively, these results further our understanding of central carbon metabolism in R. toruloides during growth on different substrates. They may also help guide the metabolic engineering and development of better models of metabolism for R. toruloides.Key points• Gene expression and metabolite concentrations were significantly changed.• Reduced expression of xylulokinase induces a bypass leading to arabitol production.• R. toruloides reprograms its metabolism to allow growth on different substrates.
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Affiliation(s)
- Sujit Sadashiv Jagtap
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois At Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois At Urbana-Champaign, Urbana, IL, USA
| | - Anshu Deewan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois At Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois At Urbana-Champaign, Urbana, IL, USA
| | - Jing-Jing Liu
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois At Urbana-Champaign, Urbana, IL, USA
| | - Hanna E Walukiewicz
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois At Urbana-Champaign, Urbana, IL, USA
- Department of Chemical and Biomolecular Engineering, University of Illinois At Urbana-Champaign, Urbana, IL, USA
| | - Eun Ju Yun
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois At Urbana-Champaign, Urbana, IL, USA
- Department of Biotechnology, Graduate School, Korea University, Seoul, Republic of Korea
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois At Urbana-Champaign, Urbana, IL, USA
- Department of Food Science and Human Nutrition, University of Illinois At Urbana-Champaign, Urbana, IL, USA
| | - Christopher V Rao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois At Urbana-Champaign, Urbana, IL, USA.
- Department of Chemical and Biomolecular Engineering, University of Illinois At Urbana-Champaign, Urbana, IL, USA.
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Yi D, Bayer T, Badenhorst CPS, Wu S, Doerr M, Höhne M, Bornscheuer UT. Recent trends in biocatalysis. Chem Soc Rev 2021; 50:8003-8049. [PMID: 34142684 PMCID: PMC8288269 DOI: 10.1039/d0cs01575j] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Indexed: 12/13/2022]
Abstract
Biocatalysis has undergone revolutionary progress in the past century. Benefited by the integration of multidisciplinary technologies, natural enzymatic reactions are constantly being explored. Protein engineering gives birth to robust biocatalysts that are widely used in industrial production. These research achievements have gradually constructed a network containing natural enzymatic synthesis pathways and artificially designed enzymatic cascades. Nowadays, the development of artificial intelligence, automation, and ultra-high-throughput technology provides infinite possibilities for the discovery of novel enzymes, enzymatic mechanisms and enzymatic cascades, and gradually complements the lack of remaining key steps in the pathway design of enzymatic total synthesis. Therefore, the research of biocatalysis is gradually moving towards the era of novel technology integration, intelligent manufacturing and enzymatic total synthesis.
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Affiliation(s)
- Dong Yi
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Shuke Wu
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Mark Doerr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Matthias Höhne
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University GreifswaldFelix-Hausdorff-Str. 4D-17487 GreifswaldGermany
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10
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Xue F, Liu Z, Yu Y, Wu Y, Jin Y, Yang M, Ma L. Codon-Optimized Rhodotorula glutinis PAL Expressed in Escherichia coli With Enhanced Activities. Front Bioeng Biotechnol 2021; 8:610506. [PMID: 33614604 PMCID: PMC7886678 DOI: 10.3389/fbioe.2020.610506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
PAL (phenylalanine ammonia lyase) is important for secondary metabolite production in plants and microorganisms. There is broad interest in engineering PAL for its biocatalytic applications in industry, agriculture, and medicine. The production of quantities of high-activity enzymes has been explored by gene cloning and heterogeneous expression of the corresponding protein. Here, we cloned the cDNA of Rhodotorula glutinis PAL (RgPAL) and introduced codon optimization to improve protein expression in Escherichia coli and enzyme activities in vitro. The RgPAL gene was cloned by reverse transcription and named pal-wt. It had a full-length of 2,121 bp and encoded a 706-amino-acid protein. The pal-wt was inefficiently expressed in E. coli, even when the expression host and physical conditions were optimized. Therefore, codon optimization was used to obtain the corresponding gene sequence, named pal-opt, in order to encode the same amino acid for the RgPAL protein. The recombinant protein encoded by pal-opt, named PAL-opt, was successfully expressed in E. coli and then purified to detect its enzymatic activity in vitro. Consequently, 55.33 ± 0.88 mg/L of PAL-opt protein with a specific activity of 1,219 ± 147 U/mg and Km value of 609 μM for substrate L-phenylalanine was easily obtained. The enzyme protein also displayed tyrosine ammonia lyase (TAL)–specific activity of 80 ± 2 U/mg and Km value of 13.3 μM for substrate L-tyrosine. The bifunctional enzyme RgPAL/TAL (PAL-opt) and its easy expression advantage will provide an important basis for further applications.
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Affiliation(s)
- Feiyan Xue
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Zihui Liu
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Yue Yu
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Yangjie Wu
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Yuxin Jin
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Mingfeng Yang
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
| | - Lanqing Ma
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, College of Bioscience and Resources Environment, Beijing University of Agriculture, Beijing, China
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11
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Akram M, Rasool A, An T, Feng X, Li C. Metabolic engineering of Yarrowia lipolytica for liquiritigenin production. Chem Eng Sci 2021. [DOI: 10.1016/j.ces.2020.116177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Fouilloux H, Thomas CM. Production and Polymerization of Biobased Acrylates and Analogs. Macromol Rapid Commun 2021; 42:e2000530. [DOI: 10.1002/marc.202000530] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/23/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Hugo Fouilloux
- PSL University Chimie ParisTech CNRS Institut de Recherche de Chimie Paris Paris 75005 France
| | - Christophe M. Thomas
- PSL University Chimie ParisTech CNRS Institut de Recherche de Chimie Paris Paris 75005 France
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13
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Hou Y, Pi C, Feng X, Wang Y, Fu S, Zhang X, Zhao L, Wei Y. Antitumor Activity In Vivo and Vitro of New Chiral Derivatives of Baicalin and Induced Apoptosis via the PI3K/Akt Signaling Pathway. Mol Ther Oncolytics 2020; 19:67-78. [PMID: 33072864 PMCID: PMC7533372 DOI: 10.1016/j.omto.2020.08.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/27/2020] [Indexed: 01/07/2023] Open
Abstract
In this study, a pair of chiral baicalin (BA) derivatives were synthesized by combining BA with phenylalanine methyl ester based on molecular docking technology, namely BAD and BAL. Cell cytotoxicity trails showed that the cell growth inhibitory effects of both BAD and BAL were increased by 8- to 12-fold compared with BA on A549 cells. Flow cytometry showed that the apoptotic rates of 50 μg/mL BA, BAD, and BAL to A549 cells for 48 h were 17.94%, 24.32%, and 39.69%, respectively. Western blotting analysis showed that BAD and BAL could promote Bax, caspase-3, and caspase-9 expression and inhibit Bcl-2 expression by inhibiting the expression of p-Akt. The tumor inhibition rates of BA, BAD, and BAL in nude mice of tumor-bearing experiment lasting for 24 days were 35.01%, 53.30%, and 59.35%, respectively. These results in vitro and in vivo showed that BAL had higher antitumor activity than did BAD and BA, which were related to promotion of the apoptosis of tumor cells by inhibiting the expression of p-Akt on PI3K/Akt pathway. This study provides an experimental basis for the development of a new configuration of BA for the treatment of cancer.
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Affiliation(s)
- Yi Hou
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, No. 3-5, Zhongshan Road, Jiangyang District, Luzhou, Sichuan 646000, P.R. China
| | - Chao Pi
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, No. 3-5, Zhongshan Road, Jiangyang District, Luzhou, Sichuan 646000, P.R. China
| | - Xianhu Feng
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, No. 3-5, Zhongshan Road, Jiangyang District, Luzhou, Sichuan 646000, P.R. China
| | - Yuanyuan Wang
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, No. 3-5, Zhongshan Road, Jiangyang District, Luzhou, Sichuan 646000, P.R. China
| | - Shaozhi Fu
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, No. 25, Taiping Street, Luzhou, Sichuan 646000, P.R. China
| | - Xiaomei Zhang
- Institute of Chinese Medicine and Pharmaceutical Chemistry, Chongqing Academy of Chinese Materia Medica, No. 34, Nanshan Road, Nanshan Street, Nan’an District, Chongqing 400065, P.R. China
| | - Ling Zhao
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, No. 3-5, Zhongshan Road, Jiangyang District, Luzhou, Sichuan 646000, P.R. China
| | - Yumeng Wei
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, No. 3-5, Zhongshan Road, Jiangyang District, Luzhou, Sichuan 646000, P.R. China
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Biomedical applications of microbial phenylalanine ammonia lyase: Current status and future prospects. Biochimie 2020; 177:142-152. [PMID: 32828824 DOI: 10.1016/j.biochi.2020.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/01/2020] [Accepted: 08/18/2020] [Indexed: 12/18/2022]
Abstract
Phenylalanine ammonia lyase (PAL) has recently emerged as an important therapeutic enzyme with several biomedical applications. The enzyme catabolizes l-phenylalanine to trans-cinnamate and ammonia. PAL is widely distributed in higher plants, some algae, ferns, and microorganisms, but absent in animals. Although microbial PAL has been extensively exploited in the past for producing industrially important metabolites, its high substrate specificity and catalytic efficacy lately spurred interest in its biomedical applications. PEG-PAL drug named Palynziq™, isolated from Anabaena variabilis has been recently approved for the treatment of adult phenylketonuria (PKU) patients. Further, it has exhibited high potency in regressing tumors and treating tyrosine related metabolic abnormalities like tyrosinemia. Several therapeutically valuable metabolites have been biosynthesized via its catalytic action including dietary supplements, antimicrobial peptides, aspartame, amino-acids, and their derivatives. This review focuses on all the prospective biomedical applications of PAL. It also provides an overview of the structure, production parameters, and various strategies to improve the therapeutic potential of this enzyme. Engineered PAL with improved pharmacodynamic and pharmacokinetic properties will further establish this enzyme as a highly efficient biological drug.
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15
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Dong FS, Lv MY, Wang JP, Shi XP, Liang XX, Liu YW, Yang F, Zhao H, Chai JF, Zhou S. Transcriptome analysis of activated charcoal-induced growth promotion of wheat seedlings in tissue culture. BMC Genet 2020; 21:69. [PMID: 32631217 PMCID: PMC7336497 DOI: 10.1186/s12863-020-00877-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 06/25/2020] [Indexed: 11/18/2022] Open
Abstract
Background Activated charcoal (AC) is highly adsorbent and is often used to promote seedling growth in plant tissue culture; however, the underlying molecular mechanism remains unclear. In this study, root and leaf tissues of 10-day-old seedlings grown via immature embryo culture in the presence or absence of AC in the culture medium were subjected to global transcriptome analysis by RNA sequencing to provide insights into the effects of AC on seedling growth. Results In total, we identified 18,555 differentially expressed genes (DEGs). Of these, 11,182 were detected in the roots and 7373 in the leaves. In seedlings grown in the presence of AC, 9460 DEGs were upregulated and 7483 DEGs were downregulated in the presence of AC as compared to the control. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed 254 DEG-enriched pathways, 226 of which were common between roots and leaves. Further analysis of the major metabolic pathways revealed that AC stimulated the expression of nine genes in the phenylpropanoid biosynthesis pathway, including PLA, CYP73A, COMT, CYP84A, and 4CL, the protein products of which promote cell differentiation and seedling growth. Further, AC upregulated genes involved in plant hormone signaling related to stress resistance and disease resistance, including EIN3, BZR1, JAR1, JAZ, and PR1, and downregulated genes related to plant growth inhibition, including BKI1, ARR-B, DELLA, and ABF. Conclusions Growth medium containing AC promotes seedling growth by increasing the expression of certain genes in the phenylpropanoid biosynthesis pathway, which are related to cell differentiation and seedling growth, as well as genes involved in plant hormone signaling, which is related to resistance.
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Affiliation(s)
- Fu-Shuang Dong
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050000, China
| | - Meng-Yu Lv
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050000, China
| | - Jin-Ping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050000, China
| | - Xue-Ping Shi
- The Semi-arid Agriculture Engineering & Technology Research Center of P.R. China, Shijiazhuang, 050000, China
| | - Xin-Xia Liang
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050000, China
| | - Yong-Wei Liu
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050000, China
| | - Fan Yang
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050000, China
| | - He Zhao
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050000, China
| | - Jian-Fang Chai
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050000, China
| | - Shuo Zhou
- Institute of Genetics and Physiology, Hebei Academy of Agriculture and Forestry Sciences, Plant Genetic Transformation Center of Hebei Province, Shijiazhuang, 050000, China.
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Arafa AM, Abdel-Ghany AE, El-Dahmy SI, Abdelaziz S, El-Ayouty Y, El-Sayed ASA. Purification and Characterization of Anabaena flos-aquae Phenylalanine Ammonia-Lyase as a Novel Approach for Myristicin Biotransformation. J Microbiol Biotechnol 2020; 30:622-632. [PMID: 31581382 PMCID: PMC9728195 DOI: 10.4014/jmb.1908.08009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Phenylalanine ammonia-lyase (PAL) catalyzes the reversible deamination of phenylalanine to cinnamic acid and ammonia. Algae have been considered as biofactories for PAL production, however, biochemical characterization of PAL and its potency for myristicin biotransformation into MMDA (3-methoxy-4, 5-methylenedioxyamphetamine) has not been studied yet. Thus, PAL from Anabaena flos-aquae and Spirulina platensis has been purified, comparatively characterized and its affinity to transform myristicin was assessed. The specific activity of purified PAL from S. platensis (73.9 μmol/mg/min) and A. flos-aquae (30.5 μmol/mg/min) was increased by about 2.9 and 2.4 folds by gel-filtration comparing to their corresponding crude enzymes. Under denaturing-PAGE, a single proteineous band with a molecular mass of 64 kDa appeared for A. flos-aquae and S. platensis PAL. The biochemical properties of the purified PAL from both algal isolates were determined comparatively. The optimum temperature of S. platensis and A. flos-aquae PAL for forward or reverse activity was reported at 30°C, while the optimum pH for PAL enzyme isolated from A. flos-aquae was 8.9 for forward and reverse activities, and S. platensis PAL had maximum activities at pH 8.9 and 8 for forward and reverse reactions, respectively. Luckily, the purified PALs have the affinity to hydroaminate the myristicin to MMDA successfully in one step. Furthermore, a successful method for synthesis of MMDA from myristicin in two steps was also established. Gas chromatography-mass spectrometry (GC-MS) analysis was conducted to track the product formation.
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Affiliation(s)
- Asmaa M. Arafa
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Afaf E. Abdel-Ghany
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Samih I. El-Dahmy
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Sahar Abdelaziz
- Department of Pharmacognosy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Yassin El-Ayouty
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Ashraf S. A. El-Sayed
- Enzymology and Fungal Biotechnology Lab (EFBL), Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt,Corresponding author Phone: +2-01024686495 E-mail:
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A microparticulate based formulation to protect therapeutic enzymes from proteolytic digestion: phenylalanine ammonia lyase as case study. Sci Rep 2020; 10:3651. [PMID: 32107425 PMCID: PMC7046617 DOI: 10.1038/s41598-020-60463-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/10/2020] [Indexed: 11/08/2022] Open
Abstract
AbstractPhenylketonuria is a genetic disorder affecting the metabolism of phenylalanine (phe) due to a deficiency in the enzyme phenylalanine hydroxylase. This disorder is characterized by an elevated phe blood level, which can lead to severe intellectual disabilities in newborns. The current strategy to prevent these devastating consequences is limited to a life-long phe-free diet, which implies major lifestyle changes and restrictions. Recently, an injectable enzyme replacement therapy, Pegvaliase, has been approved for treating phenylketonuria, but is associated with significant side-effects. In this study a phe-metabolizing system suitable for oral delivery is designed to overcome the need for daily injections. Active phenylalanine ammonia-lyase (PAL), an enzyme that catalyses phe metabolism, is loaded into mesoporous silica microparticles (MSP) with pore sizes ranging from 10 to 35 nm. The surface of the MSP is lined with a semipermeable barrier to allow permeation of phe while blocking digestive enzymes that degrade PAL. The enzymatic activity can be partially preserved in vitro by coating the MSP with poly(allylamine) and poly(acrylic acid)-bowman birk (protease inhibitor) conjugate. The carrier system presented herein may provide a general approach to overcome gastro-intestinal proteolytic digestion and to deliver active enzymes to the intestinal lumen for prolonged local action.
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18
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The production of L- and D-phenylalanines using engineered phenylalanine ammonia lyases from Petroselinum crispum. Sci Rep 2019; 9:20123. [PMID: 31882791 PMCID: PMC6934771 DOI: 10.1038/s41598-019-56554-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/12/2019] [Indexed: 12/17/2022] Open
Abstract
The biocatalytic synthesis of l- and d-phenylalanine analogues of high synthetic value have been developed using as biocatalysts mutant variants of phenylalanine ammonia lyase from Petroselinum crispum (PcPAL), specifically tailored towards mono-substituted phenylalanine and cinnamic acid substrates. The catalytic performance of the engineered PcPAL variants was optimized within the ammonia elimination and ammonia addition reactions, focusing on the effect of substrate concentration, biocatalyst:substrate ratio, reaction buffer and reaction time, on the conversion and enantiomeric excess values. The optimal conditions provided an efficient preparative scale biocatalytic procedure of valuable phenylalanines, such as (S)-m-methoxyphenylalanine (Y = 40%, ee > 99%), (S)-p-bromophenylalanine (Y = 82%, ee > 99%), (S)-m-(trifluoromethyl)phenylalanine (Y = 26%, ee > 99%), (R)-p-methylphenylalanine, (Y = 49%, ee = 95%) and (R)-m-(trifluoromethyl)phenylalanine (Y = 34%, ee = 93%).
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19
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Funnell-Harris DL, Sattler SE, O'Neill PM, Gries T, Tetreault HM, Clemente TE. Response of Sorghum Enhanced in Monolignol Biosynthesis to Stalk Rot Pathogens. PLANT DISEASE 2019; 103:2277-2287. [PMID: 31215851 DOI: 10.1094/pdis-09-18-1622-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
To increase phenylpropanoid constituents and energy content in the versatile C4 grass sorghum (Sorghum bicolor [L.] Moench), sorghum genes for proteins related to monolignol biosynthesis were overexpressed: SbMyb60 (transcriptional activator), SbPAL (phenylalanine ammonia lyase), SbCCoAOMT (caffeoyl coenzyme A [CoA] 3-O-methyltransferase), Bmr2 (4-coumarate:CoA ligase), and SbC3H (coumaroyl shikimate 3-hydroxylase). Overexpression lines were evaluated for responses to stalk pathogens under greenhouse and field conditions. Greenhouse-grown plants were inoculated with Fusarium thapsinum (Fusarium stalk rot) and Macrophomina phaseolina (charcoal rot), which cause yield-reducing diseases. F. thapsinum-inoculated overexpression plants had mean lesion lengths not significantly different than wild-type, except for significantly smaller lesions on two of three SbMyb60 and one of two SbCCoAOMT lines. M. phaseolina-inoculated overexpression lines had lesions not significantly different from wild-type except one SbPAL line (of two lines studied) with mean lesion lengths significantly larger. Field-grown SbMyb60 and SbCCoAOMT overexpression plants were inoculated with F. thapsinum. Mean lesions of SbMyb60 lines were similar to wild-type, but one SbCCoAOMT had larger lesions, whereas the other line was not significantly different than wild-type. Because overexpression of SbMyb60, Bmr2, or SbC3H may not render sorghum more susceptible to stalk rots, these lines may provide sources for development of sorghum with increased phenylpropanoid concentrations.
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Affiliation(s)
- Deanna L Funnell-Harris
- Wheat, Sorghum and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
| | - Scott E Sattler
- Wheat, Sorghum and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Patrick M O'Neill
- Wheat, Sorghum and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68583
| | - Tammy Gries
- Wheat, Sorghum and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Hannah M Tetreault
- Wheat, Sorghum and Forage Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Lincoln, NE 68583
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
| | - Thomas E Clemente
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583
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20
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Bogart JW, Bowers AA. Dehydroamino acids: chemical multi-tools for late-stage diversification. Org Biomol Chem 2019; 17:3653-3669. [PMID: 30849157 PMCID: PMC6637761 DOI: 10.1039/c8ob03155j] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
α,β-Dehydroamino acids (dhAAs) are noncanonical amino acids that are found in a wide array of natural products and can be easily installed into peptides and proteins. dhAAs exhibit remarkable synthetic flexibility, readily undergoing a number of reactions, such as polar and single-electron additions, transition metal catalyzed cross-couplings, and cycloadditions. Because of the relatively mild conditions required for many of these reactions, dhAAs are increasingly being used as orthogonal chemical handles for late-stage modification of biomolecules. Still, only a fraction of the chemical reactivity of dhAAs has been exploited in such biorthogonal applications. Herein, we provide an overview of the broad spectrum of chemical reactivity of dhAAs, with special emphasis on recent efforts to adapt such transformations for biomolecules such as natural products, peptides, and proteins. We also discuss examples of enzymes from natural product biosynthetic pathways that have been found to catalyze many similar reactions; these enzymes provide mild, regio- and stereoselective, biocatalytic alternatives for future development. We anticipate that the continued investigation of the innate reactivity of dhAAs will furnish a diverse portfolio dhAA-based chemistries for use in chemical biology and drug discovery.
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Affiliation(s)
- Jonathan W Bogart
- Division of Chemical Biology and Medicinal Chemistry Eshelman School of Pharmacy, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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21
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Wu S, Zhou Y, Li Z. Biocatalytic selective functionalisation of alkenes via single-step and one-pot multi-step reactions. Chem Commun (Camb) 2019; 55:883-896. [PMID: 30566124 DOI: 10.1039/c8cc07828a] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Alkenes are excellent starting materials for organic synthesis due to the versatile reactivity of C[double bond, length as m-dash]C bonds and the easy availability of many unfunctionalised alkenes. Direct regio- and/or enantioselective conversion of alkenes into functionalised (chiral) compounds has enormous potential for industrial applications, and thus has attracted the attention of researchers for extensive development using chemo-catalysis over the past few years. On the other hand, many enzymes have also been employed for conversion of alkenes in a highly selective and much greener manner to offer valuable products. Herein, we review recent advances in seven well-known types of biocatalytic conversion of alkenes. Remarkably, recent mechanism-guided directed evolution and enzyme cascades have enabled the development of seven novel types of single-step and one-pot multi-step functionalisation of alkenes, some of which are even unattainable via chemo-catalysis. These new reactions are particularly highlighted in this feature article. Overall, we present an ever-expanding enzyme toolbox for various alkene functionalisations inspiring further research in this fast-developing theme.
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Affiliation(s)
- Shuke Wu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585.
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22
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Nepal KK, Wang G. Streptomycetes: Surrogate hosts for the genetic manipulation of biosynthetic gene clusters and production of natural products. Biotechnol Adv 2019; 37:1-20. [PMID: 30312648 PMCID: PMC6343487 DOI: 10.1016/j.biotechadv.2018.10.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/04/2018] [Accepted: 10/05/2018] [Indexed: 12/23/2022]
Abstract
Due to the worldwide prevalence of multidrug-resistant pathogens and high incidence of diseases such as cancer, there is an urgent need for the discovery and development of new drugs. Nearly half of the FDA-approved drugs are derived from natural products that are produced by living organisms, mainly bacteria, fungi, and plants. Commercial development is often limited by the low yield of the desired compounds expressed by the native producers. In addition, recent advances in whole genome sequencing and bioinformatics have revealed an abundance of cryptic biosynthetic gene clusters within microbial genomes. Genetic manipulation of clusters in the native host is commonly used to awaken poorly expressed or silent gene clusters, however, the lack of feasible genetic manipulation systems in many strains often hinders our ability to engineer the native producers. The transfer of gene clusters into heterologous hosts for expression of partial or entire biosynthetic pathways is an approach that can be used to overcome this limitation. Heterologous expression also facilitates the chimeric fusion of different biosynthetic pathways, leading to the generation of "unnatural" natural products. The genus Streptomyces is especially known to be a prolific source of drugs/antibiotics, its members are often used as heterologous expression hosts. In this review, we summarize recent applications of Streptomyces species, S. coelicolor, S. lividans, S. albus, S. venezuelae and S. avermitilis, as heterologous expression systems.
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Affiliation(s)
- Keshav K Nepal
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA
| | - Guojun Wang
- Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 U.S. 1 North, Fort Pierce, FL 34946, USA.
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Rahmatabadi SS, Sadeghian I, Ghasemi Y, Sakhteman A, Hemmati S. Identification and characterization of a sterically robust phenylalanine ammonia-lyase among 481 natural isoforms through association of in silico and in vitro studies. Enzyme Microb Technol 2018; 122:36-54. [PMID: 30638507 DOI: 10.1016/j.enzmictec.2018.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 11/14/2018] [Accepted: 12/09/2018] [Indexed: 10/27/2022]
Abstract
The enzyme phenylalanine ammonia lyase (PAL) is of special importance for the treatment of phenylketonuria patients. The aim of this study was to find a stable recombinant PAL with suitable kinetic properties among all natural PAL producing species using in silico and experimental approaches. To find such a stable PAL among 481 natural isoforms, 48,000 of 3-D models were predicted using the Modeller 9.10 program and evaluated by Ramachandran plot. Correlation analysis between Ramachandran plot and the energy of different thermodynamic components indicated that this plot could be an appropriate tool to predict protein stability. Hence, PAL6 from Lotus japonicus (LjPAL6) was selected as a stable isoform. Molecular dynamic (MD) simulation for 50 ns and docking has been conducted for LjPAL6-phenylalanine complex. The best PAL-phenylalanine frame was selected by re-docking with l-phenylalanine (L-Phe) and root-mean-square deviation (RMSD) value. MD simulation showed that the complex has a good stability, depicted by the low RMSD value, binding free energy and hydrogen bindings. Docking results showed that LjPAL6 has a high affinity toward l-Phe according to the low level of binding free energy. By overexpressing Ljpal6 in E. coli BL21, a total of 33.5 mg/l of protein was obtained, which has been increased to 83.7 mg/l via the optimization of LjPAL6 production using response surface methodology. The optimal pH and temperature were 8.5 and 50 °C, respectively. LjPAL6 showed a specific activity of 42 nkat/mg protein, with Km, Kcat and Kcat/Km values of 0.483 mM, 7 S-1 and 14.5 S-1 mM-1 for l-phe, respectively. In conclusion, finding models with the most reasonable stereo-chemical quality and lowest numbers of steric clashes would result in easier folding. Hence, in silico analyses of bulk data from natural origin will lead one to find an optimal model for in vitro studies and drug design.
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Affiliation(s)
- Seyyed Soheil Rahmatabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Issa Sadeghian
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Owji H, Hemmati S. A comprehensive in silico characterization of bacterial signal peptides for the excretory production of Anabaena variabilis phenylalanine ammonia lyase in Escherichia coli. 3 Biotech 2018; 8:488. [PMID: 30498661 DOI: 10.1007/s13205-018-1517-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/13/2018] [Indexed: 12/30/2022] Open
Abstract
Anabaena variabilis double mutant (C503S/C565S) phenylalanine ammonia-lyase (PAL) is an appealing enzyme in the enzyme-replacement therapy of phenylketonuria. Yet abundant production of this enzyme has been of concern for industrial production. In this study, we have characterized 1175 bacterial signal peptides (SPs) and identified the most efficient ones for the excretory production of mutant AvPAL. Analysis by SignalP 4.1 revealed that more than 61% of SPs had a D-score greater than 0.7, denoting to be highly efficient. The optimum length of a bacterial SP was 25-30. The preferable net positive charge and the second residue of N-region were + 2 and Lys/Arg, respectively. Highly efficient SPs possessed 3-5 Leus in their H-region and A/L/VXA-FF cleavage site. Highly efficient SPs were from Escherichia coli, corroborating the necessity of an agreement between SPs and the host. Physiochemical characterization of mutant AvPAL conjugates via ProtParam and PROSOII, revealed that ~ 99.5% of proteins would not be entraped in inclusion bodies. Secretory pathways were identified by EffectiveDB and more than 98% of SPs were cleavable. Chimeras were modeled using the I-TASSER program, being evaluated by the Ramachandran plots. The mRNA secondary structure of mutant AvPAL upon linkage to SPs was assessed using the mfold program. It was shown that the linkage of a SP does not affect mutant AvPAL's stability at the protein or mRNA level. AllergenFP tool demonstrated that chimeras were not allergen. SPs, including FMF4_ECOLX, E2BB_ECOLX, and LPTA_ECOLI exhibited the highest propensity for secretion and appropriate features in all analyses.
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Affiliation(s)
- Hajar Owji
- 1Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- 2Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- 1Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- 2Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Wanat W, Talma M, Hurek J, Pawełczak M, Kafarski P. Substituted phosphonic analogues of phenylglycine as inhibitors of phenylalanine ammonia lyase from potatoes. Biochimie 2018; 151:119-127. [PMID: 29890205 DOI: 10.1016/j.biochi.2018.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/06/2018] [Indexed: 11/26/2022]
Abstract
A series of phosphonic acid analogues of phenylglycine variously substituted in phenyl ring have been synthesized and evaluated for their inhibitory activity towards potato l-phenylalanine ammonia lyase. Most of the compounds appeared to act as moderate (micromolar) inhibitors of the enzyme. Analysis of their binding performed using molecular modeling have shown that they might be bound either in active site of the enzyme or in the non-physiologic site. The latter one is located in adjoining deep site nearby the to the entrance channel for substrate into active site.
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Affiliation(s)
- Weronika Wanat
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Michał Talma
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - Józef Hurek
- Department of Chemistry, University of Opole, ul. Oleska 48, 45-052, Opole, Poland
| | - Małgorzata Pawełczak
- Department of Chemistry, University of Opole, ul. Oleska 48, 45-052, Opole, Poland
| | - Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
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Park YK, Nicaud JM, Ledesma-Amaro R. The Engineering Potential of Rhodosporidium toruloides as a Workhorse for Biotechnological Applications. Trends Biotechnol 2017; 36:304-317. [PMID: 29132754 DOI: 10.1016/j.tibtech.2017.10.013] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 12/30/2022]
Abstract
Moving our society towards a bioeconomy requires efficient and sustainable microbial production of chemicals and fuels. Rhodotorula (Rhodosporidium) toruloides is a yeast that naturally synthesizes substantial amounts of specialty chemicals and has been recently engineered to (i) enhance its natural production of lipids and carotenoids, and (ii) produce novel industrially relevant compounds. The use of R. toruloides by companies and research groups has exponentially increased in recent years as a result of recent improvements in genetic engineering techniques and the availability of multiomics information on its genome and metabolism. This review focuses on recent engineering approaches in R. toruloides for bioproduction and explores its potential as a biotechnological chassis.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- Micalis Institute, Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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Dreßen A, Hilberath T, Mackfeld U, Rudat J, Pohl M. Phenylalanine ammonia lyase from Arabidopsis thaliana ( At PAL2): A potent MIO-enzyme for the synthesis of non-canonical aromatic alpha-amino acids. J Biotechnol 2017; 258:158-166. [DOI: 10.1016/j.jbiotec.2017.04.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/28/2017] [Accepted: 04/28/2017] [Indexed: 11/15/2022]
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Parmeggiani F, Weise NJ, Ahmed ST, Turner NJ. Synthetic and Therapeutic Applications of Ammonia-lyases and Aminomutases. Chem Rev 2017; 118:73-118. [DOI: 10.1021/acs.chemrev.6b00824] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fabio Parmeggiani
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Weise
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Syed T. Ahmed
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
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Dreßen A, Hilberath T, Mackfeld U, Billmeier A, Rudat J, Pohl M. Phenylalanine ammonia lyase from Arabidopsis thaliana (AtPAL2): A potent MIO-enzyme for the synthesis of non-canonical aromatic alpha-amino acids: Part I: Comparative characterization to the enzymes from Petroselinum crispum (PcPAL1) and Rhodosporidium toruloides (RtPAL). J Biotechnol 2017; 258:148-157. [PMID: 28392421 DOI: 10.1016/j.jbiotec.2017.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
Phenylalanine ammonia lyase (PAL) from Arabidopsis thaliana (AtPAL2) was comparatively characterized to the well-studied enzyme from parsley (PcPAL1) and Rhodosporidium toruloides (RtPAL) with respect to kinetic parameters for the deamination and the amination reaction, pH- and temperature optima and the substrate range of the amination reaction. Whereas both plant enzymes are specific for phenylalanine, the bifunctional enzyme from Rhodosporidium toruloides shows KM-values for L-Phe and L-Tyr in the same order of magnitude and, compared to both plant enzymes, a 10-15-fold higher activity. At 30°C all enzymes were sufficiently stable with half-lives of 3.4days (PcPAL1), 4.6days (AtPAL2) and 9.7days (RtPAL/TAL). Very good results for the amination of various trans-cinnamic acid derivatives were obtained using E. coli cells as whole cell biocatalysts in ammonium carbonate buffer. Investigation of the substrate ranges gave interesting results for the newly tested enzymes from A. thaliana and R. toruloides. Only the latter accepts besides 4-hydroxy-CA also 3-methoxy-4-hydroxy-CA as a substrate, which is an interesting intermediate for the formation of pharmaceutically relevant L-Dopa. AtPAL2 is a very good catalyst for the formation of (S)-3-F-Phe, (S)-4-F-Phe and (S)-2-Cl-Phe. Such non-canonical amino acids are valuable building blocks for the formation of various drug molecules.
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Affiliation(s)
- Alana Dreßen
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Thomas Hilberath
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Ursula Mackfeld
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Arne Billmeier
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| | - Jens Rudat
- Karlsruhe Institute of Technology (KIT), Institute of Process Engineering in Life Sciences, Section: Technical Biology, Engler-Bunte-Ring 3, D-76131 Karlsruhe, Germany.
| | - Martina Pohl
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
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Bell SM, Wendt DJ, Zhang Y, Taylor TW, Long S, Tsuruda L, Zhao B, Laipis P, Fitzpatrick PA. Formulation and PEGylation optimization of the therapeutic PEGylated phenylalanine ammonia lyase for the treatment of phenylketonuria. PLoS One 2017; 12:e0173269. [PMID: 28282402 PMCID: PMC5345807 DOI: 10.1371/journal.pone.0173269] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 02/11/2017] [Indexed: 01/03/2023] Open
Abstract
Phenylketonuria (PKU) is a genetic metabolic disease in which the decrease or loss of phenylalanine hydroxylase (PAH) activity results in elevated, neurotoxic levels of phenylalanine (Phe). Due to many obstacles, PAH enzyme replacement therapy is not currently an option. Treatment of PKU with an alternative enzyme, phenylalanine ammonia lyase (PAL), was first proposed in the 1970s. However, issues regarding immunogenicity, enzyme production and mode of delivery needed to be overcome. Through the evaluation of PAL enzymes from multiple species, three potential PAL enzymes from yeast and cyanobacteria were chosen for evaluation of their therapeutic potential. The addition of polyethylene glycol (PEG, MW = 20,000), at a particular ratio to modify the protein surface, attenuated immunogenicity in an animal model of PKU. All three PEGylated PAL candidates showed efficacy in a mouse model of PKU (BTBR Pahenu2) upon subcutaneous injection. However, only PEGylated Anabaena variabilis (Av) PAL-treated mice demonstrated sustained low Phe levels with weekly injection and was the only PAL evaluated that maintained full enzymatic activity upon PEGylation. A PEGylated recombinant double mutant version of AvPAL (Cys503Ser/Cys565Ser), rAvPAL-PEG, was selected for drug development based on its positive pharmacodynamic profile and favorable expression titers. PEGylation was shown to be critical for rAvPAL-PEG efficacy as under PEGylated rAvPAL had a lower pharmacodynamic effect. rAvPAL and rAvPAL-PEG had poor stability at 4°C. L-Phe and trans-cinnamate were identified as activity stabilizing excipients. rAvPAL-PEG is currently in Phase 3 clinical trials to assess efficacy in PKU patients.
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Affiliation(s)
- Sean M. Bell
- BioMarin Pharmaceutical, Novato, California, United States of America
- * E-mail:
| | - Dan J. Wendt
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Yanhong Zhang
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Timothy W. Taylor
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Shinong Long
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Laurie Tsuruda
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Bin Zhao
- BioMarin Pharmaceutical, Novato, California, United States of America
| | - Phillip Laipis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, United States of America
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Zoń J, Miziak P. 1-Aminobenzocyclobutene-1-phosphonic Acid and Related Compounds as Inhibitors of Phenylalanine Ammonia-Lyase. Chem Biodivers 2017; 14. [PMID: 28171693 DOI: 10.1002/cbdv.201600488] [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: 12/22/2016] [Accepted: 02/03/2017] [Indexed: 11/11/2022]
Abstract
Five new geminal aminocycloalkanephosphonic acids (4 - 8) containing both an aromatic ring and a cycloalkane ring were synthesized and evaluated as potential inhibitors of buckwheat phenylalanine ammonia-lyase (PAL). Within the set of compounds which are related to 2-aminoindane-2-phosphonic acid (AIP, 3), a known powerful inhibitor of PAL, racemic 1-aminobenzocyclobutene-1-phosphonic acid (4), was six times weaker than AIP as an in vitro inhibitor of buckwheat PAL, but six times stronger than AIP as an in vivo inhibitor of phenylalanine-derived anthocyanin synthesis in buckwheat.
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Affiliation(s)
- Jerzy Zoń
- Department of Thermodynamics, Theory of Machine and Thermal Systems, Faculty of Mechanical and Power Engineering, Wrocław University of Science and Technology, 27 Wybrzeże Wyspiańskiego St., 50-370, Wrocław, Poland
| | - Piotr Miziak
- Department of Thermodynamics, Theory of Machine and Thermal Systems, Faculty of Mechanical and Power Engineering, Wrocław University of Science and Technology, 27 Wybrzeże Wyspiańskiego St., 50-370, Wrocław, Poland
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Barron CC, Sponagle BJD, Arivalagan P, D'Cunha GB. Optimization of oligomeric enzyme activity in ionic liquids using Rhodotorula glutinis yeast phenylalanine ammonia lyase. Enzyme Microb Technol 2016; 96:151-156. [PMID: 27871376 DOI: 10.1016/j.enzmictec.2016.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/08/2016] [Accepted: 10/17/2016] [Indexed: 11/17/2022]
Abstract
Phenylalanine ammonia lyase (E.C.4.3.1.24, PAL) activity of Rhodotorula glutinis yeast has been demonstrated in four commonly used ionic liquids. PAL forward reaction was carried out in 1-butyl-3-methylimidazolium methyl sulfate ([BMIM][MeSO4]), 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) and 1-butyl-3-methylimidazolium lactate ([BMIM][lactate]). Our experiments have revealed that PAL is catalytically active in ionic liquids and the enzyme activity in ([BMIM][PF6]) is comparable to that obtained in aqueous buffer medium. Different conditions were optimized for maximal PAL forward activity including time of incubation (30.0min)L-phenylalanine substrate concentration (30.0mM), nature of buffer (50.0mM Tris-HCl), pH (9.0), temperature (37°C), and speed of agitation (100 rev min-1). Under these optimized conditions, about 83% conversion of substrate to product was obtained for the PAL forward reaction that was determined using UV spectroscopy at 290nm. PAL reverse reaction in ([BMIM][PF6]) was determined spectrophotometrically at 520nm; and about 59% substrate conversion was obtained. This data provides further knowledge in enzyme biocatalysis in non-aqueous media, and may be of importance when studying the function of other oligomeric/multimeric proteins and enzymes in ionic liquids.
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Affiliation(s)
| | - Brandon J D Sponagle
- Department of Chemistry, Cape Breton University, 1250 Grand Lake Road, Sydney, Nova Scotia, B1P 6L2, Canada
| | - Pugazhendhi Arivalagan
- Department of Environmental Engineering, Daegu University, Gyeongbuk, 712-714, South Korea
| | - Godwin B D'Cunha
- Department of Chemistry, Cape Breton University, 1250 Grand Lake Road, Sydney, Nova Scotia, B1P 6L2, Canada.
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Alternative fermentation pathway of cinnamic acid production via phenyllactic acid. Appl Microbiol Biotechnol 2016; 100:8701-9. [DOI: 10.1007/s00253-016-7623-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 05/02/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
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MacDonald MC, Arivalagan P, Barre DE, MacInnis JA, D’Cunha GB. Rhodotorula glutinis Phenylalanine/Tyrosine Ammonia Lyase Enzyme Catalyzed Synthesis of the Methyl Ester of para-Hydroxycinnamic Acid and its Potential Antibacterial Activity. Front Microbiol 2016; 7:281. [PMID: 27014206 PMCID: PMC4781862 DOI: 10.3389/fmicb.2016.00281] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/22/2016] [Indexed: 11/13/2022] Open
Abstract
Biotransformation of L-tyrosine methyl ester (L-TM) to the methyl ester of para- hydroxycinnamic acid (p-HCAM) using Rhodotorula glutinis yeast phenylalanine/tyrosine ammonia lyase (PTAL; EC 4.3.1.26) enzyme was successfully demonstrated for the first time; progress of the reaction was followed by spectrophotometric determination at 315 nm. The following conditions were optimized for maximal formation of p-HCAM: pH (8.5), temperature (37°C), speed of agitation (50 rpm), enzyme concentration (0.080 μM), and substrate concentration (0.50 mM). Under these conditions, the yield of the reaction was ∼15% in 1 h incubation period and ∼63% after an overnight (∼18 h) incubation period. The product (p-HCAM) of the reaction of PTAL with L-TM was confirmed using Nuclear Magnetic Resonance spectroscopy (NMR). Fourier Transform Infra-Red spectroscopy (FTIR) was carried out to rule out potential hydrolysis of p-HCAM during overnight incubation. Potential antibacterial activity of p-HCAM was tested against several strains of Gram-positive and Gram-negative bacteria. This study describes a synthetically useful transformation, and could have future clinical and industrial applications.
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Affiliation(s)
| | - Pugazhendhi Arivalagan
- Department of Environmental Biotechnology, School of Environmental Sciences, Bharathidasan UniversityTiruchirappalli, India
| | - Douglas E. Barre
- Department of Health Sciences and Emergency Management, Cape Breton UniversitySydney, NS, Canada
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Metabolic engineering of Escherichia coli for the production of cinnamaldehyde. Microb Cell Fact 2016; 15:16. [PMID: 26785776 PMCID: PMC4719340 DOI: 10.1186/s12934-016-0415-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/07/2016] [Indexed: 11/16/2022] Open
Abstract
Background Plant parasitic nematodes are harmful to agricultural crops and plants, and may cause severe yield losses. Cinnamaldehyde, a volatile, yellow liquid commonly used as a flavoring or food additive, is increasingly becoming a popular natural nematicide because of its high nematicidal activity and, there is a high demand for the development of a biological platform to produce cinnamaldehyde. Results We engineered Escherichia coli as an eco-friendly biological platform for the production of cinnamaldehyde. In E. coli, cinnamaldehyde can be synthesized from intracellular l-phenylalanine, which requires the activities of three enzymes: phenylalanine-ammonia lyase (PAL), 4-coumarate:CoA ligase (4CL), and cinnamoyl-CoA reductase (CCR). For the efficient production of cinnamaldehyde in E. coli, we first examined the activities of enzymes from different sources and a gene expression system for the selected enzymes was constructed. Next, the metabolic pathway for l-phenylalanine biosynthesis was engineered to increase the intracellular pool of l-phenylalanine, which is a main precursor of cinnamaldehyde. Finally, we tried to produce cinnamaldehyde with the engineered E. coli. According to this result, cinnamaldehyde production as high as 75 mg/L could be achieved, which was about 35-fold higher compared with that in the parental E. coli W3110 harboring a plasmid for cinnamaldehyde biosynthesis. We also confirmed that cinnamaldehyde produced by our engineered E. coli had a nematicidal activity similar to the activity of commercial cinnamaldehyde by nematicidal assays against Bursaphelenchus xylophilus. Conclusion As a potential natural pesticide, cinnamaldehyde was successfully produced in E. coli by construction of the biosynthesis pathway and, its production titer was also significantly increased by engineering the metabolic pathway of l-phenylalanine. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0415-9) contains supplementary material, which is available to authorized users.
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36
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Vargas-Tah A, Gosset G. Production of Cinnamic and p-Hydroxycinnamic Acids in Engineered Microbes. Front Bioeng Biotechnol 2015; 3:116. [PMID: 26347861 PMCID: PMC4542537 DOI: 10.3389/fbioe.2015.00116] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/30/2015] [Indexed: 11/13/2022] Open
Abstract
The aromatic compounds cinnamic and p-hydroxycinnamic acids (pHCAs) are phenylpropanoids having applications as precursors for the synthesis of thermoplastics, flavoring, cosmetic, and health products. These two aromatic acids can be obtained by chemical synthesis or extraction from plant tissues. However, both manufacturing processes have shortcomings, such as the generation of toxic subproducts or a low concentration in plant material. Alternative production methods are being developed to enable the biotechnological production of cinnamic and (pHCAs) by genetically engineering various microbial hosts, including Escherichia coli, Saccharomyces cerevisiae, Pseudomonas putida, and Streptomyces lividans. The natural capacity to synthesize these aromatic acids is not existent in these microbial species. Therefore, genetic modification have been performed that include the heterologous expression of genes encoding phenylalanine ammonia-lyase and tyrosine ammonia-lyase activities, which catalyze the conversion of l-phenylalanine (l-Phe) and l-tyrosine (l-Tyr) to cinnamic acid and (pHCA), respectively. Additional host modifications include the metabolic engineering to increase carbon flow from central metabolism to the l-Phe or l-Tyr biosynthetic pathways. These strategies include the expression of feedback insensitive mutant versions of enzymes from the aromatic pathways, as well as genetic modifications to central carbon metabolism to increase biosynthetic availability of precursors phosphoenolpyruvate and erythrose-4-phosphate. These efforts have been complemented with strain optimization for the utilization of raw material, including various simple carbon sources, as well as sugar polymers and sugar mixtures derived from plant biomass. A systems biology approach to production strains characterization has been limited so far and should yield important data for future strain improvement.
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Affiliation(s)
- Alejandra Vargas-Tah
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca , Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México , Cuernavaca , Mexico
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Kim J, Park H, Han JG, Oh J, Choi HK, Kim SH, Sung GH. Regulation of a phenylalanine ammonia lyase (BbPAL) by calmodulin in response to environmental changes in the entomopathogenic fungus Beauveria bassiana. Environ Microbiol 2015; 17:4484-94. [PMID: 25970691 DOI: 10.1111/1462-2920.12898] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/01/2015] [Accepted: 05/05/2015] [Indexed: 11/30/2022]
Abstract
Phenylalanine ammonia lyase (PAL, E.C. 4.3.1.5) catalyses the deamination of L -phenylalanine to trans-cinnamic acid and ammonia, facilitating a critical step in the phenylpropanoid pathway that produces a variety of secondary metabolites. In this study, we isolated BbPAL gene in the entomopathogenic fungus Beauveria bassiana. According to multiple sequence alignment, homology modelling and in vitro PAL activity, we demonstrated that BbPAL acts as a typical PAL enzyme in B. bassiana. BbPAL interacted with calmodulin (CaM) in vitro and in vivo, indicating that BbPAL is a novel CaM-binding protein. The functional role of CaM in BbPAL action was to negatively regulate the BbPAL activity in B. bassiana. High-performance liquid chromatography analysis revealed that L -phenylalanine was reduced and trans-cinnamic acid was increased in response to the CaM inhibitor W-7. Dark conditions suppressed BbPAL activity in B. bassiana, compared with light. In addition, heat and cold stresses inhibited BbPAL activity in B. bassiana. Interestingly, these negative effects of BbPAL activity by dark, heat and cold conditions were recovered by W-7 treatment, suggesting that the inhibitory mechanism is mediated through stimulation of CaM activity. Therefore, this work suggests that BbPAL plays a role in the phenylpropanoid pathway mediated by environmental stimuli via the CaM signalling pathway.
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Affiliation(s)
- Jiyoung Kim
- Institute of Life Science and Biotechnology, Sungkyunkwan University, Suwon, 440-746, Korea
| | - Hyesung Park
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 369-873, Korea
| | - Jae-Gu Han
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, 369-873, Korea
| | - Junsang Oh
- College of Pharmacy, Chung-Ang University, Seoul, 156-756, Korea
| | - Hyung-Kyoon Choi
- College of Pharmacy, Chung-Ang University, Seoul, 156-756, Korea
| | - Seong Hwan Kim
- Department of Microbiology, Dankook University, Cheonan, 330-714, Korea
| | - Gi-Ho Sung
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 210-701, Korea.,Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Korea
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38
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Zang Y, Jiang T, Cong Y, Zheng Z, Ouyang J. Molecular Characterization of a Recombinant Zea mays Phenylalanine Ammonia-Lyase (ZmPAL2) and Its Application in trans-Cinnamic Acid Production from L-Phenylalanine. Appl Biochem Biotechnol 2015; 176:924-37. [PMID: 25947617 DOI: 10.1007/s12010-015-1620-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/06/2015] [Indexed: 10/23/2022]
Abstract
Phenylalanine ammonia-lyase (PAL) is one of the most extensively studied enzymes with its crucial role in secondary phenylpropanoid metabolism of plants. Recently, its demand has been increased for aromatic chemical production, but its applications in trans-cinnamic acid production were not much explored. In the present study, a putative PAL gene from Zea mays designated as ZmPAL2 was expressed and characterized in Escherichia coli BL21 (DE3). The recombinant ZmPAL2 exhibited a high PAL activity (7.14 U/mg) and a weak tyrosine ammonia-lyase activity. The optimal temperature of ZmPAL2 was 55 °C, and the thermal stability results showed that about 50 % of enzyme activity remained after a treatment at 60 °C for 6 h. The recombinant ZmPAL2 is a good candidate for the production of trans-cinnamic acid. The vitro conversion indicated that the recombinant ZmPAL2 could effectively catalyze the L-phenylalanine to trans-cinnamic acid, and the trans-cinnamic acid concentration can reach up to 5 g/l.
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Affiliation(s)
- Ying Zang
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, People's Republic of China
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Wang D, Ho L, Faith J, Ono K, Janle EM, Lachcik PJ, Cooper BR, Jannasch AH, D'Arcy BR, Williams BA, Ferruzzi MG, Levine S, Zhao W, Dubner L, Pasinetti GM. Role of intestinal microbiota in the generation of polyphenol-derived phenolic acid mediated attenuation of Alzheimer's disease β-amyloid oligomerization. Mol Nutr Food Res 2015; 59:1025-40. [PMID: 25689033 DOI: 10.1002/mnfr.201400544] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 01/29/2015] [Accepted: 01/30/2015] [Indexed: 12/24/2022]
Abstract
SCOPE Grape seed polyphenol extract (GSPE) is receiving increasing attention for its potential preventative and therapeutic roles in Alzheimer's disease (AD) and other age-related neurodegenerative disorders. The intestinal microbiota is known to actively convert many dietary polyphenols, including GSPE, to phenolic acids. There is limited information on the bioavailability and bioactivity of GSPE-derived phenolic acid in the brain. METHODS AND RESULTS We orally administered GSPE to rats and investigated the bioavailability of 12 phenolic acids known to be generated by microbiota metabolism of anthocyanidins. GSPE treatment significantly increased the content of two of the phenolic acids in the brain: 3-hydroxybenzoic acid and 3-(3´-hydroxyphenyl)propionic acid, resulting in the brain accumulations of the two phenolic acids at micromolar concentrations. We also provided evidence that 3-hydroxybenzoic acid and 3-(3´-hydroxyphenyl)propionic acid potently interfere with the assembly of β-amyloid peptides into neurotoxic β-amyloid aggregates that play key roles in AD pathogenesis. CONCLUSION Our observation suggests important contribution of the intestinal microbiota to the protective activities of GSPE (as well as other polyphenol preparations) in AD. Outcomes from our studies support future preclinical and clinical investigations exploring the potential contributions of the intestinal microbiota in protecting against the onset/progression of AD and other neurodegenerative conditions.
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Affiliation(s)
- Dongjie Wang
- Center of Nutrition and Food Sciences, ARC center of Excellence in Plant Cell Walls, The University of Queensland, Brisbane, Queensland, Australia
| | - Lap Ho
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NJ, USA
| | - Jeremiah Faith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NJ, USA
| | - Kenjiro Ono
- Department of Neurology and Neurobiology and Aging, Kanazawa University Graduate School of Medical Science, Kanazawa, Japan
| | - Elsa M Janle
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Pamela J Lachcik
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Bruce R Cooper
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Amber H Jannasch
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Bruce R D'Arcy
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Barbara A Williams
- Center of Nutrition and Food Sciences, ARC center of Excellence in Plant Cell Walls, The University of Queensland, Brisbane, Queensland, Australia
| | - Mario G Ferruzzi
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA.,Department of Food Science, Purdue University, West Lafayette, IN, USA
| | - Samara Levine
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NJ, USA
| | - Wei Zhao
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NJ, USA
| | - Lauren Dubner
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NJ, USA
| | - Giulio M Pasinetti
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NJ, USA.,Geriatric Research and Clinical Center, James J. Peter Veterans Affairs Medical Center, Bronx, NY, USA
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40
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Cui J, Liang L, Han C, Lin Liu R. Stabilization of Phenylalanine Ammonia Lyase from Rhodotorula glutinis by Encapsulation in Polyethyleneimine-Mediated Biomimetic Silica. Appl Biochem Biotechnol 2015; 176:999-1011. [PMID: 25906687 DOI: 10.1007/s12010-015-1624-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Accepted: 04/06/2015] [Indexed: 02/03/2023]
Abstract
Phenylalanine ammonia lyase (PAL) from Rhodotorula glutinis was encapsulated within polyethyleneimine-mediated biomimetic silica. The main factors in the preparation of biomimetic silica were optimized by response surface methodology (RSM). Compared to free PAL (about 2 U), the encapsulated PAL retained more than 43 % of their initial activity after 1 h of incubation time at 60 °C, whereas free PAL lost most of activity in the same conditions. It was clearly indicated that the thermal stability of PAL was improved by encapsulation. Moreover, the encapsulated PAL exhibited the excellent stability of the enzyme against denaturants and storage stability, and pH stability was improved by encapsulation. Operational stability of 7 reaction cycles showed that the encapsulated PAL was stable. Nevertheless, the K m value of encapsulated PAL in biomimetic silica was higher than that of the free PAL due to lower total surface area and increased mass transfer resistance.
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Affiliation(s)
- Jiandong Cui
- Research Center for Fermentation Engineering of Hebei, College of Bioscience and Bioengineering, Hebei University of Science and Technology, 70 Yuhua East Road, Shijiazhang, 050018, People's Republic of China,
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41
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Kong JQ. Phenylalanine ammonia-lyase, a key component used for phenylpropanoids production by metabolic engineering. RSC Adv 2015. [DOI: 10.1039/c5ra08196c] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Phenylalanine ammonia-lyase, a versatile enzyme with industrial and medical applications.
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Affiliation(s)
- Jian-Qiang Kong
- Institute of Materia Medica
- Chinese Academy of Medical Sciences & Peking Union Medical College
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines & Ministry of Health Key Laboratory of Biosynthesis of Natural Products
- Beijing
- China
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42
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Cui JD, Li LL, Zhao YM. Simple Technique for Preparing Stable and Recyclable Cross-Linked Enzyme Aggregates with Crude-Pored Microspherical Silica Core. Ind Eng Chem Res 2014. [DOI: 10.1021/ie5021206] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jian Dong Cui
- Research
Center for Fermentation Engineering of Hebei, College of Bioscience
and Bioengineering, Hebei University of Science and Technology, 26 YuXiang Street, Shijiazhang 050000, P. R. China
- National
Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, HaiDian District, Beijing, 100080, P. R. China
- Key
Laboratory of Industry Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, 29 Thirteenth Street, Tianjin 300457, P. R. China
| | - Lian Lian Li
- Research
Center for Fermentation Engineering of Hebei, College of Bioscience
and Bioengineering, Hebei University of Science and Technology, 26 YuXiang Street, Shijiazhang 050000, P. R. China
| | - Ya Min Zhao
- Research
Center for Fermentation Engineering of Hebei, College of Bioscience
and Bioengineering, Hebei University of Science and Technology, 26 YuXiang Street, Shijiazhang 050000, P. R. China
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