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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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2
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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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Geng X, Gao Z, Zhao L, Zhang S, Wu J, Yang Q, Liu S, Chen X. Comparative transcriptome analysis of resistant and susceptible wheat in response to Rhizoctonia cerealis. BMC PLANT BIOLOGY 2022; 22:235. [PMID: 35534832 PMCID: PMC9087934 DOI: 10.1186/s12870-022-03584-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Sheath blight is an important disease caused by Rhizoctonia cerealis that affects wheat yields worldwide. No wheat varieties have been identified with high resistance or immunity to sheath blight. Understanding the sheath blight resistance mechanism is essential for controlling this disease. In this study, we investigated the response of wheat to Rhizoctonia cerealis infection by analyzing the cytological changes and transcriptomes of common wheat 7182 with moderate sensitivity to sheath blight and H83 with moderate resistance. RESULTS The cytological observation showed that the growth of Rhizoctonia cerealis on the surface and its expansion inside the leaf sheath tissue were more rapid in the susceptible material. According to the transcriptome sequencing results, a total of 88685 genes were identified in both materials, including 20156 differentially expressed genes (DEGs) of which 12087 was upregulated genes and 8069 was downregulated genes. At 36 h post-inoculation, compared with the uninfected control, 11498 DEGs were identified in resistant materials, with 5064 downregulated genes and 6434 upregulated genes, and 13058 genes were detected in susceptible materials, with 6759 downregulated genes and 6299 upregulated genes. At 72 h post-inoculation, compared with the uninfected control, 6578 DEGs were detected in resistant materials, with 2991 downregulated genes and 3587 upregulated genes, and 7324 genes were detected in susceptible materials, with 4119 downregulated genes and 3205 upregulated genes. Functional annotation and enrichment analysis showed that the main pathways enriched for the DEGs included biosynthesis of secondary metabolites, carbon metabolism, plant hormone signal transduction, and plant-pathogen interaction. In particular, phenylpropane biosynthesis pathway is specifically activated in resistant variety H83 after infection. Many DEGs also belonged to the MYB, AP2, NAC, and WRKY transcription factor families. CONCLUSIONS Thus, we suggest that the normal functioning of plant signaling pathways and differences in the expression of key genes and transcription factors in some important metabolic pathways may be important for defending wheat against sheath blight. These findings may facilitate further exploration of the sheath blight resistance mechanism in wheat and the cloning of related genes.
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Affiliation(s)
- Xingxia Geng
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhen Gao
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Li Zhao
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shufa Zhang
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jun Wu
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qunhui Yang
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shuhui Liu
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinhong Chen
- Shaanxi Key Laboratory of Genetic Engineering for Plant Breeding, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Bata Z, Molnár Z, Madaras E, Molnár B, Sánta-Bell E, Varga A, Leveles I, Qian R, Hammerschmidt F, Paizs C, Vértessy BG, Poppe L. Substrate Tunnel Engineering Aided by X-ray Crystallography and Functional Dynamics Swaps the Function of MIO-Enzymes. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00266] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Zsófia Bata
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Zsófia Molnár
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Erzsébet Madaras
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Bence Molnár
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Evelin Sánta-Bell
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Andrea Varga
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
| | - Ibolya Leveles
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Renzhe Qian
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, A-1090 Vienna, Austria
| | - Friedrich Hammerschmidt
- Institute of Organic Chemistry, University of Vienna, Währinger Str. 38, A-1090 Vienna, Austria
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
| | - Beáta G. Vértessy
- Institute of Enzymology, ELKH Research Center of Natural Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Biocatalysis and Biotransformation Research Centre, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Arany János Str. 11, RO-400028 Cluj-Napoca, Romania
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5
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Sagharyan M, Ganjeali A, Cheniany M, Mousavi Kouhi SM. Optimization of Callus Induction with Enhancing Production of Phenolic Compounds Production and Antioxidants Activity in Callus Cultures of Nepeta binaloudensis Jamzad (Lamiaceae). IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2621. [PMID: 34056026 PMCID: PMC8148645 DOI: 10.30498/ijb.2020.2621] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND World Health Organization (WHO) reported that more than 80% of people in the world use herbal traditional medicines nowadays. Many endemic medicinal plants, especially Nepeta species, are facing to extinction as a result of high harvesting, limited distribution, and habitat destruction.Tissue culture is a successful method for plant secondary metabolites production. Nepeta binaloudensis is a medicinal plant belonging to family Lamiaceae. OBJECTIVE Our study was focused on devising an optimum procedure for callus induction and phenolic compounds production in N. binaloudensis. First, we are focused on finding suitable explants and media for callus induction. Then, subsequent experiments were conducted to find an optimal concentration of plant growth regulators (PGRs) and reduced- glutathione for maximum biomass production, and phenolic compounds production in calli. MATERIAL AND METHOD In this study, the usage of whole plant grown in Hoagland nutrient solution, were used as a source of explants. Also, different media including, ½ MS, MS, and B5 and different combination of PGRs (NAA and BAP) were used for optimization of calli induction. RESULTS Based on the results of the first experiment, leaf-originated explants, and macro half strength MS (½ MS) medium were used for the next experiments. The highest FW (Fresh Weight) and DW (Dry Weight) of calli were observed in ½ MS medium, supplemented with 2 μM/L reduced-glutathione, 2 mg.L-1 BAP, and 2 mg.L-1 NAA. The maximum amount of total phenolic, flavonoid, tannin contents and free-radical scavenger were observed in calli which were grown in ½ MS medium supplemented with 2 μM/L reduced-glutathione, 2 mg.L-1 BAP, and 2 mg.L-1 NAA. CONCLUSION Our study finds the optimum condition for calli induction and phenolic compounds production in N. binaloudensis.
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Affiliation(s)
- Mostafa Sagharyan
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ali Ganjeali
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Monireh Cheniany
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
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6
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Kendall IP, Woodward P, Clark JP, Styring AK, Hanna JV, Evershed RP. Compound-specific δ 15N values express differences in amino acid metabolism in plants of varying lignin content. PHYTOCHEMISTRY 2019; 161:130-138. [PMID: 30826700 DOI: 10.1016/j.phytochem.2019.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/27/2018] [Accepted: 01/15/2019] [Indexed: 06/09/2023]
Abstract
Amino acid δ15N values of foliage of various plant taxa, grown at the experimental farm stations of North Wyke, UK and Bad Lauchstädt, Germany were determined by GC-C-IRMS. The difference between δ15N values of glutamate (Glx) and phenylalanine (Phe) were found to differ significantly between woody and herbaceous plants, with mean Δ15NGlx-Phe (i.e. δ15NPhe - δ15NGlx) values of -9.3 ± 1.6‰ and -5.8 ± 2.1‰, respectively. These differences in values are hypothesised to be due to the involvement of Phe in the phenylpropanoid pathway, by which lignin and other phenolic secondary metabolites are produced, leading to isotopic fractionation and enrichment of the remaining Phe pool available for protein biosynthesis. This results in the more negative Δ15NGlx-Phe values observed in woody plants relative to herbaceous plants, as the former are assumed to produce more lignin. To test this assumption, plant leaf tissue lignin concentrations were estimated by solid state 13C cross-polarisation, magic-angle-spinning (CPMAS) NMR spectroscopy for a subset of plants, which showed that tree foliage has a higher concentration of lignin (12.6 wt%) than herbaceous foliage (6.3 wt%). The correlation of lignin concentration with Δ15NGlx-Phe values demonstrates that the difference in these values with plant type is indeed due to differential production of lignin. The ability to estimate the lignin content of plants from amino acid δ15N values will, to give one example, allow refinement of estimates of herbivore diet in present and past ecosystems, enabling more accurate environmental niche modelling.
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Affiliation(s)
- Iain P Kendall
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Peter Woodward
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Joshua P Clark
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Amy K Styring
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; Present Address: Institut für Archäologische Wissenschaften, Goethe-Universität Frankfurt Am Main, Frankfurt, Germany
| | - John V Hanna
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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7
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Yoshikawa M, Luo W, Tanaka G, Konishi Y, Matsuura H, Takahashi K. Wounding stress induces phenylalanine ammonia lyases, leading to the accumulation of phenylpropanoids in the model liverwort Marchantia polymorpha. PHYTOCHEMISTRY 2018; 155:30-36. [PMID: 30064058 DOI: 10.1016/j.phytochem.2018.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 07/19/2018] [Accepted: 07/21/2018] [Indexed: 06/08/2023]
Abstract
Wounding stress induces the biosynthesis of various specialized metabolites in plants. In this study, wounding induced the biosynthesis of luteolin, apigenin, and isoriccardin C, which are biosynthesized through the phenylpropanoid pathway, in the model liverwort Marchantia polymorpha L (Marchantiaceae). Recombinant M. polymorpha phenylalanine ammonia lyases (MpPALs) exhibited PAL activity in vitro and converted phenylalanine into trans-cinnamic acid. Based on semi-quantitative RT-PCR analysis, the expression levels of the MpPAL genes were up-regulated after wounding. α-Aminooxy-β-phenylpropionic acid, a PAL inhibitor, suppressed the production of wounding-induced phenolic compounds, luteolin, apigenin, and isoriccardin C, in M. polymorpha. Thus, PAL is a committed step in the biosynthesis of phenylpropanoids in response to wounding in M. polymorpha. This study suggests that wound-induced specialized metabolites such as phenylpropanoids comprise a conserved defense system in land plants.
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Affiliation(s)
- Mayu Yoshikawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Weifeng Luo
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Genta Tanaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yuka Konishi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Hideyuki Matsuura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Kosaku Takahashi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
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8
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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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9
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Pająk M, Pałka K, Winnicka E, Kańska M. The chemo- enzymatic synthesis of labeled l-amino acids and some of their derivatives. J Radioanal Nucl Chem 2018; 317:643-666. [PMID: 30100649 PMCID: PMC6061101 DOI: 10.1007/s10967-018-5932-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Indexed: 01/14/2023]
Abstract
This review compiles the combined chemical and enzymatic synthesis of aromatic l-amino acids (l-phenylalanine, l-tyrosine, l-DOPA, l-tryptophan, and their derivatives and precursors) specifically labeled with carbon and hydrogen isotopes, which were elaborated in our research group by the past 20 years. These compounds could be then employed to characterize the mechanisms of enzymatic reactions via kinetic and solvent isotope effects methods.
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Affiliation(s)
- Małgorzata Pająk
- Department of Chemistry, Warsaw University, Pasteur 1 Str., 02-093 Warsaw, Poland
| | - Katarzyna Pałka
- Department of Chemistry, Warsaw University, Pasteur 1 Str., 02-093 Warsaw, Poland
| | - Elżbieta Winnicka
- Department of Chemistry, Warsaw University, Pasteur 1 Str., 02-093 Warsaw, Poland
| | - Marianna Kańska
- Department of Biochemistry, 2nd Faculty of Medicine, Medical University of Warsaw, 61 Zwirki i Wigury Av., 02-091 Warsaw, Poland
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10
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Jun SY, Sattler SA, Cortez GS, Vermerris W, Sattler SE, Kang C. Biochemical and Structural Analysis of Substrate Specificity of a Phenylalanine Ammonia-Lyase. PLANT PHYSIOLOGY 2018; 176:1452-1468. [PMID: 29196539 PMCID: PMC5813539 DOI: 10.1104/pp.17.01608] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 11/28/2017] [Indexed: 05/18/2023]
Abstract
Phenylalanine ammonia-lyase (PAL) is the first enzyme of the general phenylpropanoid pathway catalyzing the nonoxidative elimination of ammonia from l-phenylalanine to give trans-cinnamate. In monocots, PAL also displays tyrosine ammonia lyase (TAL) activity, leading to the formation of p-coumaric acid. The catalytic mechanism and substrate specificity of a major PAL from sorghum (Sorghum bicolor; SbPAL1), a strategic plant for bioenergy production, were deduced from crystal structures, molecular docking, site-directed mutagenesis, and kinetic and thermodynamic analyses. This first crystal structure of a monocotyledonous PAL displayed a unique conformation in its flexible inner loop of the 4-methylidene-imidazole-5-one (MIO) domain compared with that of dicotyledonous plants. The side chain of histidine-123 in the MIO domain dictated the distance between the catalytic MIO prosthetic group created from 189Ala-Ser-Gly191 residues and the bound l-phenylalanine and l-tyrosine, conferring the deamination reaction through either the Friedel-Crafts or E2 reaction mechanism. Several recombinant mutant SbPAL1 enzymes were generated via structure-guided mutagenesis, one of which, H123F-SbPAL1, has 6.2 times greater PAL activity without significant TAL activity. Additional PAL isozymes of sorghum were characterized and categorized into three groups. Taken together, this approach identified critical residues and explained substrate preferences among PAL isozymes in sorghum and other monocots, which can serve as the basis for the engineering of plants with enhanced biomass conversion properties, disease resistance, or nutritional quality.
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Affiliation(s)
- Se-Young Jun
- Department of Chemistry, Washington State University, Pullman, Washington 99164
| | - Steven A Sattler
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99163
| | - Gabriel S Cortez
- Department of Chemistry, Washington State University, Pullman, Washington 99164
| | - Wilfred Vermerris
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, and Genetics Institute, University of Florida, Gainesville, Florida 32610
| | - Scott E Sattler
- United States Department of Agriculture-Agricultural Research Service, Wheat, Sorghum, and Forage Research Unit, and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, Washington 99164
- School of Molecular Biosciences, Washington State University, Pullman, Washington 99163
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11
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Bata Z, Qian R, Roller A, Horak J, Bencze LC, Paizs C, Hammerschmidt F, Vértessy BG, Poppe L. A Methylidene Group in the Phosphonic Acid Analogue of Phenylalanine Reverses the Enantiopreference of Binding to Phenylalanine Ammonia-Lyases. Adv Synth Catal 2017; 359:2109-2120. [PMID: 28919846 PMCID: PMC5573973 DOI: 10.1002/adsc.201700428] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 05/02/2017] [Indexed: 12/19/2022]
Abstract
Aromatic amino acid ammonia‐lyases and aromatic amino acid 2,3‐aminomutases contain the post‐translationally formed prosthetic 3,5‐dihydro‐4‐methylidene‐5H‐imidazol‐5‐one (MIO) group. MIO enzymes catalyze the stereoselective synthesis of α‐ or β‐amino acid enantiomers, making these chemical processes environmentally friendly and affordable. Characterization of novel inhibitors enables structural understanding of enzyme mechanism and recognizes promising herbicide candidates as well. The present study found that both enantiomers of the aminophosphonic acid analogue of the natural substrate phenylalanine and a novel derivative bearing a methylidene at the β‐position inhibited phenylalanine ammonia‐lyases (PAL), representing MIO enzymes. X‐ray methods unambiguously determined the absolute configuration of all tested enantiomers during their synthesis. Enzyme kinetic measurements revealed the enantiomer of the methylidene‐substituted substrate analogue as being a mirror image relation to the natural l‐phenylalanine as the strongest inhibitor. Isothermal titration calorimetry (ITC) confirmed the binding constants and provided a detailed analysis of the thermodynamic driving forces of ligand binding. Molecular docking suggested that binding of the (R)‐ and (S)‐enantiomers is possible by a mirror image packing. ![]()
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Affiliation(s)
- Zsófia Bata
- Department of Organic Chemistry and Technology Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary.,Institute of Enzymology HAS-Research Center of Natural Sciences, Budapest, H-1117 Magyar tudósok krt. 2. Budapest Hungary
| | - Renzhe Qian
- Institute of Organic Chemistry University of Vienna Währinger Str. 38 1090 Vienna Austria
| | - Alexander Roller
- Institute of Inorganic Chemistry University of Vienna Währinger Str. 42. A-1090 Vienna Austria
| | - Jeannie Horak
- Institute of Pharmaceutical Sciences Pharmaceutical (Bio-)Analysis Eberhard-Karls-University Tübingen Auf der Morgensstelle 872076 Tübingen Germany
| | - László Csaba Bencze
- Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
| | | | - Beáta G Vértessy
- Institute of Enzymology HAS-Research Center of Natural Sciences, Budapest, H-1117 Magyar tudósok krt. 2. Budapest Hungary.,Department of Applied Biotechnology and Food Science Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary
| | - László Poppe
- Department of Organic Chemistry and Technology Budapest University of Technology and Economics Műegyetem rkp. 3. H-1111 Budapest Hungary.,Biocatalysis and Biotransformation Research Centre Faculty of Chemistry and Chemical Engineering Babeş-Bolyai University of Cluj-Napoca Arany János Str. 11400028 Cluj-Napoca Romania
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12
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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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13
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Lin CI, McCarty RM, Liu HW. The Enzymology of Organic Transformations: A Survey of Name Reactions in Biological Systems. Angew Chem Int Ed Engl 2017; 56:3446-3489. [PMID: 27505692 PMCID: PMC5477795 DOI: 10.1002/anie.201603291] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 01/05/2023]
Abstract
Chemical reactions that are named in honor of their true, or at least perceived, discoverers are known as "name reactions". This Review is a collection of biological representatives of named chemical reactions. Emphasis is placed on reaction types and catalytic mechanisms that showcase both the chemical diversity in natural product biosynthesis as well as the parallels with synthetic organic chemistry. An attempt has been made, whenever possible, to describe the enzymatic mechanisms of catalysis within the context of their synthetic counterparts and to discuss the mechanistic hypotheses for those reactions that are currently active areas of investigation. This Review has been categorized by reaction type, for example condensation, nucleophilic addition, reduction and oxidation, substitution, carboxylation, radical-mediated, and rearrangements, which are subdivided by name reactions.
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Affiliation(s)
- Chia-I Lin
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Reid M McCarty
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
| | - Hung-Wen Liu
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, and Department of Chemistry, University of Texas at Austin, Austin, TX, 78731, USA
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14
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Sergeant K, Printz B, Gutsch A, Behr M, Renaut J, Hausman JF. Didehydrophenylalanine, an abundant modification in the beta subunit of plant polygalacturonases. PLoS One 2017; 12:e0171990. [PMID: 28207764 PMCID: PMC5313189 DOI: 10.1371/journal.pone.0171990] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/30/2017] [Indexed: 01/07/2023] Open
Abstract
The structure and the activity of proteins are often regulated by transient or stable post- translational modifications (PTM). Different from well-known, abundant modifications such as phosphorylation and glycosylation some modifications are limited to one or a few proteins across a broad range of related species. Although few examples of the latter type are known, the evolutionary conservation of these modifications and the enzymes responsible for their synthesis suggest an important physiological role. Here, the first observation of a new, fold-directing PTM is described. During the analysis of alfalfa cell wall proteins a -2Da mass shift was observed on phenylalanine residues in the repeated tetrapeptide FxxY of the beta-subunit of polygalacturonase. This modular protein is known to be involved in developmental and stress-responsive processes. The presence of this modification was confirmed using in-house and external datasets acquired by different commonly used techniques in proteome studies. Based on these analyses it was found that all identified phenylalanine residues in the sequence FxxY of this protein were modified to α,β-didehydro-Phe (ΔPhe). Besides showing the reproducible identification of ΔPhe in different species arguments that substantiate the fold-determining role of ΔPhe are given.
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Affiliation(s)
- Kjell Sergeant
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
- * E-mail:
| | - Bruno Printz
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
- Université catholique de Louvain, Earth and Life Institute Agronomy, Groupe de Recherche en Physiologie Végétale Louvain-la-Neuve, Belgium
| | - Annelie Gutsch
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
- University of Hasselt, Centre for Environmental Sciences, Environmental Biology, Diepenbeek, Belgium
| | - Marc Behr
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
- Université catholique de Louvain, Earth and Life Institute Agronomy, Groupe de Recherche en Physiologie Végétale Louvain-la-Neuve, Belgium
| | - Jenny Renaut
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
| | - Jean-Francois Hausman
- Luxembourg Institute of Science and Technology (LIST), Environmental Research and Innovation (ERIN) department, Esch-sur-Alzette, Luxembourg
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15
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Lin C, McCarty RM, Liu H. Die Enzymologie organischer Umwandlungen: Namensreaktionen in biologischen Systemen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201603291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Chia‐I. Lin
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Reid M. McCarty
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
| | - Hung‐wen Liu
- Division of Chemical Biology and Medicinal Chemistry College of Pharmacy, and Department of Chemistry University of Texas at Austin Austin TX 78731 USA
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16
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Bencze LC, Filip A, Bánóczi G, Toşa MI, Irimie FD, Gellért Á, Poppe L, Paizs C. Expanding the substrate scope of phenylalanine ammonia-lyase from Petroselinum crispum towards styrylalanines. Org Biomol Chem 2017; 15:3717-3727. [DOI: 10.1039/c7ob00562h] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The substrate scope of phenylalanine ammonia-lyase from Petroselinum crispum (PcPAL) towards the l-enantiomers of racemic styrylalanines rac-1a–d were extended by reshaping the aromatic binding pocket of the active site of PcPAL by point mutations of F137.
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Affiliation(s)
- László Csaba Bencze
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Alina Filip
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Gergely Bánóczi
- Department of Organic Chemistry and Technology
- Budapest University of Technology and Economics
- H-1111 Budapest
- Hungary
| | - Monica Ioana Toşa
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Florin Dan Irimie
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Ákos Gellért
- Agricultural Institute
- Centre of Agricultural Research
- Hungarian Academy of Sciences
- H-2462 Martonvásár
- Hungary
| | - László Poppe
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Centre
- Faculty of Chemistry and Chemical Engineering
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
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17
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Kańska M, Jemielity J, Pająk M, Pałka K, Podsadni K, Winnicka E. Kinetic and solvent isotope effects on biotransformation of aromatic amino acids and their derivatives. J Labelled Comp Radiopharm 2016; 59:627-634. [DOI: 10.1002/jlcr.3419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 05/09/2016] [Accepted: 05/23/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Marianna Kańska
- Department of Biochemistry; Medical University of Warsaw, 2nd Faculty of Medicine; 101 Zwirki i Wigury Av., 02-089 Warsaw Poland
- Department of Chemistry; Warsaw University; 1 Pasteur Str., 02-093 Warsaw Poland
| | - Jacek Jemielity
- University of Warsaw; Centre of New Technologies; 2c Banacha Str., 02-097 Warsaw Poland
| | - Małgorzata Pająk
- Department of Chemistry; Warsaw University; 1 Pasteur Str., 02-093 Warsaw Poland
| | - Katarzyna Pałka
- Department of Chemistry; Warsaw University; 1 Pasteur Str., 02-093 Warsaw Poland
| | - Katarzyna Podsadni
- Department of Biochemistry; Medical University of Warsaw, 2nd Faculty of Medicine; 101 Zwirki i Wigury Av., 02-089 Warsaw Poland
| | - Elżbieta Winnicka
- Department of Chemistry; Warsaw University; 1 Pasteur Str., 02-093 Warsaw Poland
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18
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Khan T, Abbasi BH, Khan MA, Shinwari ZK. Differential Effects of Thidiazuron on Production of Anticancer Phenolic Compounds in Callus Cultures of Fagonia indica. Appl Biochem Biotechnol 2016; 179:46-58. [PMID: 26758711 DOI: 10.1007/s12010-016-1978-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/03/2016] [Indexed: 11/30/2022]
Abstract
Fagonia indica, a very important anticancer plant, has been less explored for its in vitro potential. This is the first report on thidiazuron (TDZ)-mediated callogenesis and elicitation of commercially important phenolic compounds. Among the five different plant growth regulators tested, TDZ induced comparatively higher fresh biomass, 51.0 g/100 mL and 40.50 g/100 mL for stem and leaf explants, respectively, after 6 weeks of culture time. Maximum total phenolic content (202.8 μg gallic acid equivalent [GAE]/mL for stem-derived callus and 161.3 μg GAE/mL for leaf-derived callus) and total flavonoid content (191.03 μg quercetin equivalent [QE]/mL for stem-derived callus and 164.83 μg QE/mL for leaf-derived callus) were observed in the optimized callus cultures. The high-performance liquid chromatography (HPLC) data indicated higher amounts of commercially important anticancer secondary metabolites such as gallic acid (125.10 ± 5.01 μg/mL), myricetin (32.5 ± 2.05 μg/mL), caffeic acid (12.5 ± 0.52 μg/mL), catechin (9.4 ± 1.2 μg/mL), and apigenin (3.8 ± 0.45 μg/mL). Owing to the greater phenolic content, a better 2-2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging activity (69.45 % for stem explant and 63.68 % for leaf explant) was observed in optimized calluses. The unusually higher biomass and the enhanced amount of phenolic compounds as a result of lower amounts of TDZ highlight the importance of this multipotent hormone as elicitor in callus cultures of F. indica.
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Affiliation(s)
- Tariq Khan
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Bilal Haider Abbasi
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
- Pakistan Academy of Sciences, Islamabad, Pakistan.
| | - Mubarak Ali Khan
- Biotechnology Program, Department of Environmental Sciences, COMSATS Institute of Information Technology (CIIT), Abbottabad, Pakistan
| | - Zabta Khan Shinwari
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Pakistan Academy of Sciences, Islamabad, Pakistan
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19
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Weiser D, Bencze LC, Bánóczi G, Ender F, Kiss R, Kókai E, Szilágyi A, Vértessy BG, Farkas Ö, Paizs C, Poppe L. Phenylalanine Ammonia-Lyase-Catalyzed Deamination of an Acyclic Amino Acid: Enzyme Mechanistic Studies Aided by a Novel Microreactor Filled with Magnetic Nanoparticles. Chembiochem 2015; 16:2283-8. [DOI: 10.1002/cbic.201500444] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Diána Weiser
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - László Csaba Bencze
- Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Gergely Bánóczi
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Ferenc Ender
- Department of Electron Devices; Budapest University of Technology and Economics; Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Róbert Kiss
- Gedeon Richter Plc. Gyömrői út 19-21; 1103 Budapest Hungary
| | - Eszter Kókai
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - András Szilágyi
- Department of Physical Chemistry and Materials Science; Budapest University of Technology and Economics; Budafoki út 8 1111 Budapest Hungary
| | - Beáta G. Vértessy
- Institute of Enzymology; Research Centre for Natural Sciences of Hungarian Academy of Sciences; Magyar tudósok körútja 2 1117 Budapest Hungary
- Department of Biotechnology and Food Sciences; Budapest University of Technology and Economics; Szt. Gellért tér 4 1111 Budapest Hungary
| | - Ödön Farkas
- Department of Organic Chemistry; Eötvös Lóránd University; Pázmány Péter sétány 1A 1117 Budapest Hungary
| | - Csaba Paizs
- Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - László Poppe
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
- SynBiocat Ltd.; Lázár deák u 4/1 1173 Budapest Hungary
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20
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Highly Active and Specific Tyrosine Ammonia-Lyases from Diverse Origins Enable Enhanced Production of Aromatic Compounds in Bacteria and Saccharomyces cerevisiae. Appl Environ Microbiol 2015; 81:4458-76. [PMID: 25911487 DOI: 10.1128/aem.00405-15] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/20/2015] [Indexed: 11/20/2022] Open
Abstract
Phenylalanine and tyrosine ammonia-lyases form cinnamic acid and p-coumaric acid, which are precursors of a wide range of aromatic compounds of biotechnological interest. Lack of highly active and specific tyrosine ammonia-lyases has previously been a limitation in metabolic engineering approaches. We therefore identified 22 sequences in silico using synteny information and aiming for sequence divergence. We performed a comparative in vivo study, expressing the genes intracellularly in bacteria and yeast. When produced heterologously, some enzymes resulted in significantly higher production of p-coumaric acid in several different industrially important production organisms. Three novel enzymes were found to have activity exclusively for phenylalanine, including an enzyme from the low-GC Gram-positive bacterium Brevibacillus laterosporus, a bacterial-type enzyme from the amoeba Dictyostelium discoideum, and a phenylalanine ammonia-lyase from the moss Physcomitrella patens (producing 230 μM cinnamic acid per unit of optical density at 600 nm [OD600]) in the medium using Escherichia coli as the heterologous host). Novel tyrosine ammonia-lyases having higher reported substrate specificity than previously characterized enzymes were also identified. Enzymes from Herpetosiphon aurantiacus and Flavobacterium johnsoniae resulted in high production of p-coumaric acid in Escherichia coli (producing 440 μM p-coumaric acid OD600 unit(-1) in the medium) and in Lactococcus lactis. The enzymes were also efficient in Saccharomyces cerevisiae, where p-coumaric acid accumulation was improved 5-fold over that in strains expressing previously characterized tyrosine ammonia-lyases.
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21
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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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22
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Gamir J, Sánchez-Bel P, Flors V. Molecular and physiological stages of priming: how plants prepare for environmental challenges. PLANT CELL REPORTS 2014; 33:1935-49. [PMID: 25113544 DOI: 10.1007/s00299-014-1665-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 05/18/2023]
Abstract
Being sessile organisms, plants must respond to various challenges in the environment. The priming process consists of three clear stages. The first stage includes all the cellular changes in the absence of the challenge so-called pre-challenge priming stage. These changes are expected to be rather subtle, affecting the preparation of the plant to properly manage subsequent responses to pathogens with no major fitness costs. Most of the research that has been conducted at this stage has been dedicated to the study of changes in gene expression and protein phosphorylation. However, the metabolic changes that occur during the pre-challenge priming stage are poorly understood. The second stage affects the early to late stages of the defence response, which occurs after the interaction with a pathogen has been established. Most studies involving priming are dedicated to the molecular events that take place during this stage. Most studies have shown that defence priming is strongly hormonally regulated; however, there is also evidence of the involvement of phenolic derivative compounds and many other secondary metabolites, leading to stronger and faster plant responses. The third priming phase ranges from long lasting defence priming to trans-generational acquired resistance. Long-term metabolic transitions, that occur in the offspring of primed plants, remain to be elucidated. Here we review existing information in the literature that relates to the metabolic changes that occur during all three defence priming stages and highlight the metabolic transitions that are associated with the stimulation of priming and the characteristics of the pathogens whenever possible.
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Affiliation(s)
- J Gamir
- Metabolic Integration and Cell Signaling Group, Plant Physiology Section, Department of CAMN, Universitat Jaume I, Avd Vicente Sos Baynat, 12071, Castellón, Spain
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23
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Nascimento KJT, Debona D, França SKS, Gonçalves MGM, DaMatta FM, Rodrigues FÁ. Soybean Resistance to Cercospora sojina Infection Is Reduced by Silicon. PHYTOPATHOLOGY 2014; 104:1183-91. [PMID: 24805073 DOI: 10.1094/phyto-02-14-0047-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Frogeye leaf spot, caused by Cercospora sojina, is one of the most important leaf diseases of soybean worldwide. Silicon (Si) is known to increase the resistance of several plant species to pathogens. The cultivars Bossier and Conquista, which are susceptible and resistant, respectively, to frogeye leaf spot, supplied and nonsupplied with Si were examined for the activities of defense enzymes and the concentrations of total soluble phenolics (TSP) and lignin-thioglycolic acid (LTGA) derivatives at 8, 14, and 16 days after inoculation (dai) with C. sojina. The importance of cell wall degrading enzymes (CWDE) to the infection process of C. sojina and the effect of Si on their activities were also determined. Soybean plants were grown in hydroponic culture containing either 0 or 2 mM Si (-Si and +Si, respectively) and noninoculated or C. sojina inoculated. Severity of frogeye leaf spot was higher in cultivar Bossier plants than cultivar Conquista and also in the +Si plants compared with their -Si counterparts. Except for the concentrations of TSP and LTGA derivatives, activities of defense enzymes and the CWDE did not change for +Si noninoculated plants regardless of the cultivar. The activities of lipoxygenases, phenylalanine ammonia-lyases, chitinases, and polyphenoloxidases as well as the activities of CWDE decreased for the +Si inoculated plants. The results from this study demonstrated that defense enzyme activities decreased in soybean plants supplied with Si, which compromised resistance to C. sojina infection.
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24
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Ratnayake ND, Liu N, Kuhn LA, Walker KD. Ring-Substituted α-Arylalanines for Probing Substituent Effects on the Isomerization Reaction Catalyzed by an Aminomutase. ACS Catal 2014. [DOI: 10.1021/cs500474s] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Nishanka Dilini Ratnayake
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Nan Liu
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Leslie A. Kuhn
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin D. Walker
- Department of Chemistry, ‡Department of Biochemistry and Molecular Biology, and §Computer Science & Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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25
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Lovelock SL, Lloyd RC, Turner NJ. Phenylalanine Ammonia Lyase Catalyzed Synthesis of Amino Acids by an MIO-Cofactor Independent Pathway. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201311061] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Lovelock SL, Lloyd RC, Turner NJ. Phenylalanine Ammonia Lyase Catalyzed Synthesis of Amino Acids by an MIO-Cofactor Independent Pathway. Angew Chem Int Ed Engl 2014; 53:4652-6. [DOI: 10.1002/anie.201311061] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Indexed: 11/08/2022]
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27
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Jewgiński M, Krzciuk-Gula J, Makowski M, Latajka R, Kafarski P. Conformation of dehydropentapeptides containing four achiral amino acid residues - controlling the role of L-valine. Beilstein J Org Chem 2014; 10:660-6. [PMID: 24778717 PMCID: PMC3999861 DOI: 10.3762/bjoc.10.58] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/05/2014] [Indexed: 12/01/2022] Open
Abstract
Structural studies of pentapeptides containing an achiral block, built from two dehydroamino acid residues (ΔZPhe and ΔAla) and two glycines, as well as one chiral L-Val residue were performed using NMR spectroscopy. The key role of the L-Val residue in the generation of the secondary structure of peptides is discussed. The obtained results suggest that the strongest influence on the conformation of peptides arises from a valine residue inserted at the C-terminal position. The most ordered conformation was found for peptide Boc-Gly-ΔAla-Gly-ΔZPhe-Val-OMe (3), which adopts a right-handed helical conformation.
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Affiliation(s)
- Michał Jewgiński
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Joanna Krzciuk-Gula
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Maciej Makowski
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Rafał Latajka
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paweł Kafarski
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wrocław University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
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28
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Nestl BM, Hammer SC, Nebel BA, Hauer B. New generation of biocatalysts for organic synthesis. Angew Chem Int Ed Engl 2014; 53:3070-95. [PMID: 24520044 DOI: 10.1002/anie.201302195] [Citation(s) in RCA: 230] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 02/04/2023]
Abstract
The use of enzymes as catalysts for the preparation of novel compounds has received steadily increasing attention over the past few years. High demands are placed on the identification of new biocatalysts for organic synthesis. The catalysis of more ambitious reactions reflects the high expectations of this field of research. Enzymes play an increasingly important role as biocatalysts in the synthesis of key intermediates for the pharmaceutical and chemical industry, and new enzymatic technologies and processes have been established. Enzymes are an important part of the spectrum of catalysts available for synthetic chemistry. The advantages and applications of the most recent and attractive biocatalysts--reductases, transaminases, ammonia lyases, epoxide hydrolases, and dehalogenases--will be discussed herein and exemplified by the syntheses of interesting compounds.
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Affiliation(s)
- Bettina M Nestl
- Technische Biochemie, Universität Stuttgart, Stuttgart (Germany)
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Nestl BM, Hammer SC, Nebel BA, Hauer B. Biokatalysatoren für die organische Synthese - die neue Generation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201302195] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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Wang ZB, Chen X, Wang W, Cheng KD, Kong JQ. Transcriptome-wide identification and characterization of Ornithogalum saundersiae phenylalanine ammonia lyase gene family. RSC Adv 2014. [DOI: 10.1039/c4ra03385j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Transcriptome-wide identification and characterization ofOrnithogalum saundersiaephenylalanine ammonia lyase gene family.
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Affiliation(s)
- Zhi-Biao Wang
- 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
| | - Xi Chen
- 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
| | - Wei Wang
- 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
| | - Ke-Di Cheng
- 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
| | - 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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WU JW, SHI Y, ZHU YX, WANG YC, GONG HJ. Mechanisms of Enhanced Heavy Metal Tolerance in Plants by Silicon: A Review. PEDOSPHERE 2013; 23:815-825. [PMID: 0 DOI: 10.1016/s1002-0160(13)60073-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
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32
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Aritua V, Achor D, Gmitter FG, Albrigo G, Wang N. Transcriptional and microscopic analyses of citrus stem and root responses to Candidatus Liberibacter asiaticus infection. PLoS One 2013; 8:e73742. [PMID: 24058486 PMCID: PMC3772824 DOI: 10.1371/journal.pone.0073742] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 07/30/2013] [Indexed: 11/18/2022] Open
Abstract
Huanglongbing (HLB) is the most destructive disease that affects citrus worldwide. The disease has been associated with Candidatus Liberibacter. HLB diseased citrus plants develop a multitude of symptoms including zinc and copper deficiencies, blotchy mottle, corky veins, stunting, and twig dieback. Ca. L. asiaticus infection also seriously affects the roots. Previous study focused on gene expression of leaves and fruit to Ca. L. asiaticus infection. In this study, we compared the gene expression levels of stems and roots of healthy plants with those in Ca. L. asiaticus infected plants using microarrays. Affymetrix microarray analysis showed a total of 988 genes were significantly altered in expression, of which 885 were in the stems, and 111 in the roots. Of these, 551 and 56 were up-regulated, while 334 and 55 were down-regulated in the stem and root samples of HLB diseased trees compared to healthy plants, respectively. Dramatic differences in the transcriptional responses were observed between citrus stems and roots to Ca. L. asiaticus infection, with only 8 genes affected in both the roots and stems. The affected genes are involved in diverse cellular functions, including carbohydrate metabolism, cell wall biogenesis, biotic and abiotic stress responses, signaling and transcriptional factors, transportation, cell organization, protein modification and degradation, development, hormone signaling, metal handling, and redox. Microscopy analysis showed the depletion of starch in the roots of the infected plants but not in healthy plants. Collapse and thickening of cell walls were observed in HLB affected roots, but not as severe as in the stems. This study provides insight into the host response of the stems and roots to Ca. L. asiaticus infection.
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Affiliation(s)
- Valente Aritua
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, Florida, United States of America
| | - Diann Achor
- Citrus Research and Education Center, University of Florida, Lake Alfred, Florida, United States of America
| | - Frederick G. Gmitter
- Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Gene Albrigo
- Citrus Research and Education Center, Department of Horticultural Sciences, University of Florida, Lake Alfred, Florida, United States of America
| | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Lake Alfred, Florida, United States of America
- * E-mail:
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Cloning, expression and characterization of phenylalanine ammonia-lyase from Rhodotorula glutinis. Biotechnol Lett 2013; 35:751-6. [PMID: 23338700 DOI: 10.1007/s10529-013-1140-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Accepted: 01/08/2013] [Indexed: 10/27/2022]
Abstract
The industrial-scale production of phenylalanine ammonia-lyase (PAL) mainly uses strains of Rhodotorula. However, the PAL gene from Rhodotorula has not been cloned. Here, the full-length gene of PAL from Rhodotorula glutinis was isolated. It was 2,121 bp, encoding a polypeptide with 706 amino acids and a calculated MW of 75.5 kDa. Though R. glutinis is an anamorph of Rhodosporium toruloides, the amino acid sequences of PALs them are not the same (about 74 % identity). PAL was expressed in E. coli and characterized. Its specific activity was 4.2 U mg(-1) and the k cat/K m was 1.9 × 10(4) mM(-1) s(-1), exhibiting the highest catalytic ability among the reported PALs. The genetic and biochemical information reported here should facilitate future application in industry.
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Toşa MI, Brem J, Mantu A, Irimie FD, Paizs C, Rétey J. The Interaction of Nitrophenylalanines with Wild Type and Mutant 4-Methylideneimidazole-5-one-less Phenylalanine Ammonia Lyase. ChemCatChem 2013. [DOI: 10.1002/cctc.201200536] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Strom S, Wanninayake U, Ratnayake ND, Walker KD, Geiger JH. Insights into the Mechanistic Pathway of thePantoea agglomeransPhenylalanine Aminomutase. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108525] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Strom S, Wanninayake U, Ratnayake ND, Walker KD, Geiger JH. Insights into the Mechanistic Pathway of thePantoea agglomeransPhenylalanine Aminomutase. Angew Chem Int Ed Engl 2012; 51:2898-902. [DOI: 10.1002/anie.201108525] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/26/2012] [Indexed: 11/11/2022]
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Hyun MW, Yun YH, Kim JY, Kim SH. Fungal and Plant Phenylalanine Ammonia-lyase. MYCOBIOLOGY 2011; 39:257-65. [PMID: 22783113 PMCID: PMC3385129 DOI: 10.5941/myco.2011.39.4.257] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 11/04/2011] [Accepted: 11/04/2011] [Indexed: 05/02/2023]
Abstract
L-Phenylalanine is one of the essential amino acids that cannot be synthesized in mammals in adequate amounts to meet the requirements for protein synthesis. Fungi and plants are able to synthesize phenylalanine via the shikimic acid pathway. L-Phenylalanine, derived from the shikimic acid pathway, is used directly for protein synthesis in plants or metabolized through the phenylpropanoid pathway. This phenylpropanoid metabolism leads to the biosynthesis of a wide array of phenylpropanoid secondary products. The first step in this metabolic sequence involves the action of phenylalanine ammonia-lyase (PAL). The discovery of PAL enzyme in fungi and the detection of (14)CO(2) production from (14)C-ring-labeled phenylalanine and cinnamic acid demonstrated that certain fungi can degrade phenylalanine by a pathway involving an initial deamination to cinnamic acid, as happens in plants. In this review, we provide background information on PAL and a recent update on the presence of PAL genes in fungi.
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Affiliation(s)
- Min Woo Hyun
- Department of Microbiology and Institute of Basic Sciences, Dankook University, Cheonan 330-714, Korea
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Wu B, Szymański W, Heberling MM, Feringa BL, Janssen DB. Aminomutases: mechanistic diversity, biotechnological applications and future perspectives. Trends Biotechnol 2011; 29:352-62. [PMID: 21477876 DOI: 10.1016/j.tibtech.2011.02.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 02/22/2011] [Accepted: 02/23/2011] [Indexed: 11/26/2022]
Abstract
Aminomutases carry out the chemically challenging exchange of a hydrogen atom and an amine substituent present on neighboring carbon atoms. In recent years, aminomutases have been intensively investigated for their biophysical, structural and mechanistic characteristics. The reactions catalyzed by these enzymes have considerable potential for biotechnological applications. Here, we present an overview of this diverse group of enzymes, with a focus on enzymatic mechanisms and recent developments in their use in applied biocatalysis.
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Affiliation(s)
- Bian Wu
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
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Bartsch S, Bornscheuer UT. Mutational analysis of phenylalanine ammonia lyase to improve reactions rates for various substrates. Protein Eng Des Sel 2010; 23:929-33. [PMID: 21036782 DOI: 10.1093/protein/gzq089] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phenylalanine ammonia lyases (PAL) catalyze the reversible, non-reductive amination of trans-cinnamic acid to l-phenylalanine in the presence of high ammonia concentrations. Since neither cofactor recycling nor other additives are needed and by this asymmetric synthesis theoretical yields of 100% can be reached, it is an interesting reaction for industrial processes. In this study we demonstrate the superior properties of p-nitro-cinnamic acid (p-n-CA) in the amination reaction using the PAL from Petroselinum crispum (pcPAL). By focused-directed evolution, three mutants were identified showing increased reaction rates and decreased substrate inhibition. Together, the F137V mutant with p-n-CA showed a 15-fold increased reaction rate compared with the pcPAL WT with the natural cinnamic acid. The high reaction rates were also proven in preparative scale experiments. Activities towards other p-substituted cinnamic acids showing different electronic effects of the substituent were analyzed. Focused-directed evolution around the carboxylic acid- and amine-binding site always decreased PAL activity, due to a sensitive H-bond network.
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Affiliation(s)
- Sebastian Bartsch
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
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40
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Rhee SG, Cho CS. Blot-based detection of dehydroalanine-containing glutathione peroxidase with the use of biotin-conjugated cysteamine. Methods Enzymol 2010; 474:23-34. [PMID: 20609902 DOI: 10.1016/s0076-6879(10)74002-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dehydroalanine (DHA), alpha,beta-unsaturated amino acid, is found in the position corresponding to the serine, cysteine, and selenocysteine (Sec) residues of various proteins. Proteinaceous Sec is readily oxidized and subsequently undergoes beta-elimination to produce DHA. Glutathione peroxidase (GPx), which contains a Sec at the active site, is irreversibly inactivated by its own substrate as the result of the oxidation of selenium atom followed by the conversion of oxidized Sec to DHA. We developed a convenient method for estimation of the amount of DHA-GPx1 in cell homogenates. This blot-based method depends on specific addition of biotin-conjugated cysteamine to the DHA residue followed by detection of biotinylated protein based on its interaction with streptavidin. The method required an immunoprecipitation of GPx1 before labeling with the cysteamine derivative because many other proteins contain DHA. With the use of this method, we found that conversion of the Sec residue at the active site of GPx1 to DHA occurred during aging of red blood cells (RBCs) in vivo as well as in RBCs exposed to H(2)O(2) generated either externally by glucose oxidase or internally as a result of aniline-induced Hb autoxidation. Accordingly, the content of DHA-GPx1 in each RBC likely reflects total oxidative stress experienced by the cell during its lifetime of 120 days. Previous studies suggested that the activity of GPx1 in RBCs is most influenced by lifestyle and environmental factors such as the use of dietary supplements and smoking habit. Therefore, DHA-GPx1 in RBCs might be a suitable surrogate marker for evaluation of oxidative stress in the body. Our blot-based method for the detection of DHA-GPx1 will be very useful for evaluation of such stress. In addition, similar blot detection method can be devised for other proteins for which immunoprecipitating antibodies are available.
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Affiliation(s)
- Sue Goo Rhee
- Division of Life and Pharmaceutical Sciences, Ewha Womans University, Seodaemun-gu, Seoul, Korea
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41
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Rétey J, Paizs C, Ioana Toşa M, Csaba Bencze L, Brem J, Dan Irimie F. 2-Amino-3-(5-phenylfuran-2-yl)propionic Acids and 5-Phenylfuran-2-ylacrylic Acids are Novel Substrates of Phenylalanine Ammonia-Lyase. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)60] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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42
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Structure and chemistry of 4-methylideneimidazole-5-one containing enzymes. Curr Opin Chem Biol 2009; 13:460-8. [PMID: 19620019 DOI: 10.1016/j.cbpa.2009.06.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Accepted: 06/12/2009] [Indexed: 11/21/2022]
Abstract
The prosthetic group 4-methylideneimidazole-5-one (MIO) is the catalytic component of the ammonia lyase class of enzymes. This family is responsible for the processing of amino acids in a variety of metabolic pathways through the elimination of ammonia to form unsaturated products. Recently, new chemistry has been attributed to this family with the discovery of MIO-based aminomutases. The mechanism of electrophilic chemistry catalyzed by MIO-based enzymes has been investigated for several decades. Recent X-ray crystal structures of members of the family have provided novel insight into the molecular basis for catalysis and substrate recognition. In addition, the inclusion of aminomutases in natural product biosynthetic pathways has spurned recent advances toward rational engineering and chemoenzymatic applications.
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Su V, Hsu BD. Isolation and Sequencing a Genomic DNA Encoding for Phenylalanine Ammonia-Lyase fromPhalaenopsis. ACTA ACUST UNITED AC 2009; 14:442-9. [PMID: 15018355 DOI: 10.1080/10425170310001628883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The enzyme L-phenylalanine ammonia-lyase is universally present in higher plants and it catalyzes the first committed reaction for a central pathway that generates hundreds of different phenylpropanoid metabolites including anthocyanin, the main pigments in flowers. In this study, we have successfully isolated and analyzed a phenylalanine ammonia-lyase gene from Phalaenopsis. The gene spans 3265bp and consists of two exons and one intron and encodes a polypeptide of 703 amino acid residues.
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Affiliation(s)
- Vincent Su
- Department of Life Science, National Tsing Hua University, Hsin-Chu 30055, Taiwan
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44
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Asano Y, Kato Y, Levy C, Baker P, Rice D. Structure and Function of Amino Acid Ammonia-lyases. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420410001703496] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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45
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Zhu S, Sun L, Zhou J. Effects of nitric oxide fumigation on phenolic metabolism of postharvest Chinese winter jujube (Zizyphus jujuba Mill. cv. Dongzao) in relation to fruit quality. Lebensm Wiss Technol 2009. [DOI: 10.1016/j.lwt.2008.12.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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46
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Bartsch S, Bornscheuer UT. A single residue influences the reaction mechanism of ammonia lyases and mutases. Angew Chem Int Ed Engl 2009; 48:3362-5. [PMID: 19343746 DOI: 10.1002/anie.200900337] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
All ways lead to Rome? Computer modeling and kinetic measurements identified a distinct residue in Phe/Tyr ammonia lyases (PAL/TAL) which controls whether the Friedel-Crafts or an E(1)cB reaction mechanism takes place. Hence, Glu484 in pcPAL favors the Friedel-Crafts reaction (see picture, MIO = 4-methylidene imidazol-5-one) whereas an Asn in TAL gives an elimination reaction. These mechanistic investigations also reveal activity of a PAL mutant and a TAL towards an amino alcohol.
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Affiliation(s)
- Sebastian Bartsch
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, Greifswald University, Felix-Hausdorff-Strasse 4, 17487 Greifswald, Germany
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47
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Bartsch S, Bornscheuer U. Einfluss einer einzelnen Aminosäure auf den Reaktionsmechanismus von Ammonium-Lyasen und -Mutasen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900337] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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48
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McIntosh JA, Donia MS, Schmidt EW. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds. Nat Prod Rep 2009; 26:537-59. [PMID: 19642421 PMCID: PMC2975598 DOI: 10.1039/b714132g] [Citation(s) in RCA: 192] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Ribosomally synthesized bacterial natural products rival the nonribosomal peptides in their structural and functional diversity. The last decade has seen substantial progress in the identification and characterization of biosynthetic pathways leading to ribosomal peptide natural products with new and unusual structural motifs. In some of these cases, the motifs are similar to those found in nonribosomal peptides, and many are constructed by convergent or even paralogous enzymes. Here, we summarize the major structural and biosynthetic categories of ribosomally synthesized bacterial natural products and, where applicable, compare them to their homologs from nonribosomal biosynthesis.
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Affiliation(s)
- John A. McIntosh
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
| | - Mohamed S. Donia
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, 30 South 2000 East Rm 201, Salt Lake City, UT 84112 USA
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Bazukyan IL, Vardanyan AE, Hambardzumyan AA, Tozalakyan PV, Popov YG. Catalytic properties of Rhodotorula aurantiaca KM-1 phenylalanine ammonia-lyase. APPL BIOCHEM MICRO+ 2009. [DOI: 10.1134/s0003683809010037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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50
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Dybala-Defratyka A, Szatkowski L, Kaminski R, Wujec M, Siwek A, Paneth P. Kinetic isotope effects on dehalogenations at an aromatic carbon. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:7744-7750. [PMID: 19031855 DOI: 10.1021/es800276y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In order to interpret the observed isotopic fractionation it is necessaryto understand its relationship with the isotope effect(s) on steps that occur during the conversion of the initial reactant to the final product. We examine this relationship from the biochemical point of view and elaborate on the consequences of the assumptions that it is based on. We illustrate the discrepancies between theoretical and experimental interpretation of kinetic isotope effects on examples of dehalogenation reactions that occur at an aromatic carbon atom. The examples include 4-chlorobenzoyl-CoA dehalogenase-catalyzed conversion of 4-chlorobenzoyl-CoA to 4-hydroxybenzoyl-CoA, dehaloperoxidase-catalyzed conversion of 2,4,6-trichlorophenol to 2,6-dichloroquinone, and spontaneous hydrolysis of atrazine at pH 12. For this latter reaction we have measured the chlorine kinetic isotope effect and estimated its value theoretically at the DFT level of theory. Results of chlorine kinetic isotope effects suggest that the studied dechlorination reactions proceed in a single step with significant weakening of the carbon-chlorine bond in the transition state.
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Affiliation(s)
- Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Technical University of Lodz, Zeromskiego 116, 90-924 Lodz, Poland
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