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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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Mejía-Manzano LA, Ortiz-Alcaráz CI, Parra Daza LE, Suarez Medina L, Vargas-Cortez T, Fernández-Niño M, González Barrios AF, González-Valdez J. Saccharomyces cerevisiae biofactory to produce naringenin using a systems biology approach and a bicistronic vector expression strategy in flavonoid production. Microbiol Spectr 2024; 12:e0337423. [PMID: 38088543 PMCID: PMC10871697 DOI: 10.1128/spectrum.03374-23] [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: 10/17/2023] [Accepted: 11/21/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Flavonoids are a group of compounds generally produced by plants with proven biological activity, which have recently beeen recommended for the treatment and prevention of diseases and ailments with diverse causes. In this study, naringenin was produced in adequate amounts in yeast after in silico design. The four genes of the involved enzymes from several organisms (bacteria and plants) were multi-expressed in two vectors carrying each two genes linked by a short viral peptide sequence. The batch kinetic behavior of the product, substrate, and biomass was described at lab scale. The engineered strain might be used in a more affordable and viable bioprocess for industrial naringenin procurement.
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Affiliation(s)
| | | | - Laura E. Parra Daza
- School of Engineering and Science, Tecnologico de Monterrey, Monterrey, Nuevo León, Mexico
- Department of Chemical and Food Engineering, Grupo de Diseño de Productos y Procesos (GDPP), Universidad de los Andes, Bogotá, Colombia
| | - Lina Suarez Medina
- Department of Chemical and Food Engineering, Grupo de Diseño de Productos y Procesos (GDPP), Universidad de los Andes, Bogotá, Colombia
| | - Teresa Vargas-Cortez
- School of Engineering and Science, Tecnologico de Monterrey, Monterrey, Nuevo León, Mexico
| | - Miguel Fernández-Niño
- Department of Chemical and Food Engineering, Grupo de Diseño de Productos y Procesos (GDPP), Universidad de los Andes, Bogotá, Colombia
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Halle, Germany
| | - Andrés Fernando González Barrios
- Department of Chemical and Food Engineering, Grupo de Diseño de Productos y Procesos (GDPP), Universidad de los Andes, Bogotá, Colombia
| | - José González-Valdez
- School of Engineering and Science, Tecnologico de Monterrey, Monterrey, Nuevo León, Mexico
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Pérez-Valero Á, Ye S, Magadán-Corpas P, Villar CJ, Lombó F. Metabolic engineering in Streptomyces albidoflavus for the biosynthesis of the methylated flavonoids sakuranetin, acacetin, and genkwanin. Microb Cell Fact 2023; 22:234. [PMID: 37964284 PMCID: PMC10648386 DOI: 10.1186/s12934-023-02247-3] [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: 07/24/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Flavonoids are important plant secondary metabolites showing antioxidant, antitumor, anti-inflammatory, and antiviral activities, among others. Methylated flavonoids are particularly interesting compared to non-methylated ones due to their greater stability and intestinal absorption, which improves their oral bioavailability. In this work we have stablished a metabolic engineered strain of Streptomyces albidoflavus with enhanced capabilities for flavonoid production, achieving a 1.6-fold increase in the biosynthesis of naringenin with respect to the parental strain. This improved strain, S. albidoflavus UO-FLAV-004, has been used for the heterologous biosynthesis of the methylated flavonoids sakuranetin, acacetin and genkwanin. The achieved titers of sakuranetin and acacetin were 8.2 mg/L and 5.8 mg/L, respectively. The genkwanin titers were 0.8 mg/L, with a bottleneck identified in this producing strain. After applying a co-culture strategy, genkwanin production titers reached 3.5 mg/L, which represents a 4.4-fold increase. To our knowledge, this study presents the first biosynthesis of methylated flavonoids in not only any Streptomyces species, but also in any Gram-positive bacteria.
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Affiliation(s)
- Álvaro Pérez-Valero
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Suhui Ye
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Patricia Magadán-Corpas
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Claudio J Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain.
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Parra Daza LE, Suarez Medina L, Tafur Rangel AE, Fernández-Niño M, Mejía-Manzano LA, González-Valdez J, Reyes LH, González Barrios AF. Design and Assembly of a Biofactory for (2 S)-Naringenin Production in Escherichia coli: Effects of Oxygen Transfer on Yield and Gene Expression. Biomolecules 2023; 13:biom13030565. [PMID: 36979500 PMCID: PMC10046166 DOI: 10.3390/biom13030565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/17/2023] [Accepted: 03/02/2023] [Indexed: 03/30/2023] Open
Abstract
The molecule (2S)-naringenin is a scaffold molecule with several nutraceutical properties. Currently, (2S)-naringenin is obtained through chemical synthesis and plant isolation. However, these methods have several drawbacks. Thus, heterologous biosynthesis has emerged as a viable alternative to its production. Recently, (2S)-naringenin production studies in Escherichia coli have used different tools to increase its yield up to 588 mg/L. In this study, we designed and assembled a bio-factory for (2S)-naringenin production. Firstly, we used several parametrized algorithms to identify the shortest pathway for producing (2S)-naringenin in E. coli, selecting the genes phenylalanine ammonia lipase (pal), 4-coumarate: CoA ligase (4cl), chalcone synthase (chs), and chalcone isomerase (chi) for the biosynthetic pathway. Then, we evaluated the effect of oxygen transfer on the production of (2S)-naringenin at flask (50 mL) and bench (4 L culture) scales. At the flask scale, the agitation rate varied between 50 rpm and 250 rpm. At the bench scale, the dissolved oxygen was kept constant at 5% DO (dissolved oxygen) and 40% DO, obtaining the highest (2S)-naringenin titer (3.11 ± 0.14 g/L). Using genome-scale modeling, gene expression analysis (RT-qPCR) of oxygen-sensitive genes was obtained.
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Affiliation(s)
- Laura E Parra Daza
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
| | - Lina Suarez Medina
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
| | - Albert E Tafur Rangel
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
| | - Miguel Fernández-Niño
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, 06120 Halle, Germany
| | - Luis Alberto Mejía-Manzano
- Tecnológico de Monterrey, School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur, Monterrey 64849, NL, Mexico
| | - José González-Valdez
- Tecnológico de Monterrey, School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur, Monterrey 64849, NL, Mexico
| | - Luis H Reyes
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
| | - Andrés Fernando González Barrios
- Grupo de Diseño de Productos y Procesos (GDPP), Department of Chemical and Food Engineering, Universidad de Los Andes, Bogotá 110311, Colombia
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Pant S, Huang Y. Genome-wide studies of PAL genes in sorghum and their responses to aphid infestation. Sci Rep 2022; 12:22537. [PMID: 36581623 PMCID: PMC9800386 DOI: 10.1038/s41598-022-25214-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/28/2022] [Indexed: 12/30/2022] Open
Abstract
Phenylalanine ammonia-lyase (PAL, EC 4.3.1.25) plays a crucial role in plant adaptation to biotic and abiotic stresses. However, the current knowledge about PAL proteins in sorghum is essentially lacking. Thus, in this study we aimed to analyze the PAL family genes in sorghum using a genome-wide approach and to explore the role of PAL genes in host plant resistance to aphids via SA-mediated defense signaling. Here, we report gene structural features of 8 PAL (SbPAL) genes in sorghum (Sorghum bicolor), their phylogeny, protein motifs and promoter analysis. Furthermore, we demonstrated that the SbPAL genes were induced by sugarcane aphid (SCA) infestation and SbPAL exhibited differential gene expression in susceptible and resistant genotypes. PAL activity assays further validated upregulated expression of the SbPAL genes in a resistant genotype. In addition, exogenous application of SA reduced plant damage and suppressed aphid population growth and fecundity in susceptible genotype, suggesting that those SbPAL genes act as positive regulator of the SA-mediated defense signaling pathway to combat aphid pests in sorghum. This study provides insights for further examination of the defense role of PAL in sorghum against other pests and pathogens.
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Affiliation(s)
- Shankar Pant
- grid.508981.dUnited States Department of Agriculture - Agricultural Research Service (USDA-ARS), Plant Science Research Laboratory, Stillwater, OK 74075 USA
| | - Yinghua Huang
- grid.508981.dUnited States Department of Agriculture - Agricultural Research Service (USDA-ARS), Plant Science Research Laboratory, Stillwater, OK 74075 USA
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Wang J, Zhang N, Huang Y, Li S, Zhang G. Simple and efficient enzymatic procedure for p-coumaric acid synthesis: Complete bioconversion and biocatalyst recycling under alkaline condition. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Photoactive yellow protein (PYP) is a model photoreceptor. It binds a p-coumaric acid as a chromophore, thus enabling blue light sensing. The first discovered single-domain PYP from Halorhodospira halophila has been studied thoroughly in terms of its structural dynamics and photochemical properties. However, the evolutionary origins and biological role of PYP homologs are not well understood. Here, we show that PYP is an evolutionarily novel domain family of the ubiquitous PAS (Per-Arnt-Sim) superfamily. It likely originated from the phylum Myxococcota and was then horizontally transferred to representatives of a few other bacterial phyla. We show that PYP is associated with signal transduction either by domain fusion or by genome context. Key cellular functions modulated by PYP-initiated signal transduction pathways likely involve gene expression, motility, and biofilm formation. We identified three clades of the PYP family, one of which is poorly understood and potentially has novel functional properties. The Tyr42, Glu46, and Cys69 residues that are involved in p-coumaric acid binding in the model PYP from H. halophila are well conserved in the PYP family. However, we also identified cases where substitutions in these residues might have led to neofunctionalization, such as the proposed transition from light to redox sensing. Overall, this study provides definition, a newly built hidden Markov model, and the current genomic landscape of the PYP family and sets the stage for the future exploration of its signaling mechanisms and functional diversity. IMPORTANCE Photoactive yellow protein is a model bacterial photoreceptor. For many years, it was considered a prototypical model of the ubiquitous PAS domain superfamily. Here, we show that, in fact, the PYP family is evolutionarily novel, restricted to a few bacterial phyla and distinct from other PAS domains. We also reveal the diversity of PYP-containing signal transduction proteins and their potential mechanisms.
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Transcriptome of the coralline alga Calliarthron tuberculosum (Corallinales, Rhodophyta) reveals convergent evolution of a partial lignin biosynthesis pathway. PLoS One 2022; 17:e0266892. [PMID: 35834440 PMCID: PMC9282553 DOI: 10.1371/journal.pone.0266892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/13/2022] [Indexed: 11/19/2022] Open
Abstract
The discovery of lignins in the coralline red alga Calliarthron tuberculosum raised new questions about the deep evolution of lignin biosynthesis. Here we present the transcriptome of C. tuberculosum supported with newly generated genomic data to identify gene candidates from the monolignol biosynthetic pathway using a combination of sequence similarity-based methods. We identified candidates in the monolignol biosynthesis pathway for the genes 4CL, CCR, CAD, CCoAOMT, and CSE but did not identify candidates for PAL, CYP450 (F5H, C3H, C4H), HCT, and COMT. In gene tree analysis, we present evidence that these gene candidates evolved independently from their land plant counterparts, suggesting convergent evolution of a complex multistep lignin biosynthetic pathway in this red algal lineage. Additionally, we provide tools to extract metabolic pathways and genes from the newly generated transcriptomic and genomic datasets. Using these methods, we extracted genes related to sucrose metabolism and calcification. Ultimately, this transcriptome will provide a foundation for further genetic and experimental studies of calcifying red algae.
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Brack Y, Sun C, Yi D, Bornscheuer U. Discovery of novel tyrosine ammonia lyases for the enzymatic synthesis of p-coumaric acid. Chembiochem 2022; 23:e202200062. [PMID: 35352477 PMCID: PMC9321829 DOI: 10.1002/cbic.202200062] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/29/2022] [Indexed: 11/09/2022]
Abstract
p‐Coumaric acid (p‐CA) is a key precursor for the biosynthesis of flavonoids. Tyrosine ammonia lyases (TALs) specifically catalyze the synthesis of p‐CA from l‐tyrosine, which is a convenient enzymatic pathway. To explore novel and highly active TALs, a phylogenetic tree‐building approach was conducted including 875 putative TALs and 46 putative phenylalanine/tyrosine ammonia lyases (PTALs). Among them, 5 TALs and 3 PTALs were successfully characterized and found to exhibit the proposed enzymatic activity. The TAL from Chryseobacterium luteum sp. nov (TALclu) has the highest affinity (Km=0.019 mm) and conversion efficiency (kcat/Km=1631 s−1 ⋅ mm−1) towards l‐tyrosine. The reaction conditions for two purified enzymes and their E. coli recombinant cells were optimized and p‐CA yields of 2.03 g/L after 8 hours by TALclu and 2.35 g/L after 24 h by TAL from Rivularia sp. PCC 7116 (TALrpc) in whole cells were achieved. These TALs are thus candidates for the construction of whole‐cell systems to produce the flavonoid precursor p‐CA.
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Affiliation(s)
- Yannik Brack
- University of Greifswald: Universitat Greifswald, Institute of Biochemistry, GERMANY
| | - Chenghai Sun
- University of Greifswald: Universitat Greifswald, Institute of Biochemistry, GERMANY
| | - Dong Yi
- University of Greifswald: Universitat Greifswald, Institute of Biochemistry, GERMANY
| | - Uwe Bornscheuer
- Greifswald University, Dept. of Biotechnology & Enzyme Catalysis, Felix-Hausdorff-Str. 4, 17487, Greifswald, GERMANY
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Shen J, Zerkle AL, Claire MW. Nitrogen Cycling and Biosignatures in a Hyperarid Mars Analog Environment. ASTROBIOLOGY 2022; 22:127-142. [PMID: 34652219 PMCID: PMC8861911 DOI: 10.1089/ast.2021.0012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/11/2021] [Indexed: 05/20/2023]
Abstract
The hyperarid Atacama Desert is a unique Mars-analog environment with a large near-surface soil nitrate reservoir due to the lack of rainfall leaching for millennia. We investigated nitrogen (N) cycling and organic matter dynamics in this nitrate-rich terrestrial environment by analyzing the concentrations and isotopic compositions of nitrate, organic C, and organic N, coupled with microbial pathway-enzyme inferences, across a naturally occurring rainfall gradient. Nitrate deposits in sites with an annual precipitation of <10 mm carry atmospheric δ15N, δ18O, and Δ17O signatures, while these values are overprinted by biological cycling in sites with >15 mm annual precipitation. Metagenomic analyses suggest that the Atacama Desert harbors a unique biological nitrogen cycle driven by nitrifier denitrification, nitric oxide dioxygenase-driven alternative nitrification, and organic N loss pathways. Nitrate assimilation is the only nitrate consumption pathway available in the driest sites, although some hyperarid sites also support organisms with ammonia lyase- and nitric oxide synthase-driven organic N loss. Nitrifier denitrification is enhanced in the "transition zone" desert environments, which are generally hyperarid but see occasional large rainfall events, and shifts to nitric oxide dioxygenase-driven alternative nitrifications in wetter arid sites. Since extremophilic microorganisms tend to exploit all reachable nutrients, both N and O isotope fractionations during N transformations are reduced. These results suggest that N cycling on the more recent dry Mars might be dominated by nitrate assimilation that cycles atmospheric nitrate and exchanges water O during intermittent wetting, resulting stable isotope biosignatures could shift away from martian atmospheric nitrate endmember. Early wetter Mars could nurture putative life that metabolized nitrate with traceable paleoenvironmental isotopic markers similar to microbial denitrification and nitrification stored in deep subsurface.
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Affiliation(s)
- Jianxun Shen
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, United Kingdom
- Address correspondence to: Jianxun Shen, Centre for Exoplanet Science, School of Earth and Environmental Sciences, University of St Andrews, Irvine Building, North Street, St Andrews KY16 9AL, United Kingdom, USA
| | - Aubrey L. Zerkle
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, United Kingdom
| | - Mark W. Claire
- School of Earth and Environmental Sciences and Centre for Exoplanet Science, University of St Andrews, St Andrews, United Kingdom
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Martín JF, Liras P. Comparative Molecular Mechanisms of Biosynthesis of Naringenin and Related Chalcones in Actinobacteria and Plants: Relevance for the Obtention of Potent Bioactive Metabolites. Antibiotics (Basel) 2022; 11:antibiotics11010082. [PMID: 35052959 PMCID: PMC8773403 DOI: 10.3390/antibiotics11010082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/01/2022] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
Naringenin and its glycosylated derivative naringin are flavonoids that are synthesized by the phenylpropanoid pathway in plants. We found that naringenin is also formed by the actinobacterium Streptomyces clavuligerus, a well-known microorganism used to industrially produce clavulanic acid. The production of naringenin in S. clavuligerus involves a chalcone synthase that uses p-coumaric as a starter unit and a P450 monoxygenase, encoded by two adjacent genes (ncs-ncyP). The p-coumaric acid starter unit is formed by a tyrosine ammonia lyase encoded by an unlinked, tal, gene. Deletion and complementation studies demonstrate that these three genes are required for biosynthesis of naringenin in S. clavuligerus. Other actinobacteria chalcone synthases use caffeic acid, ferulic acid, sinapic acid or benzoic acid as starter units in the formation of different antibiotics and antitumor agents. The biosynthesis of naringenin is restricted to a few Streptomycess species and the encoding gene cluster is present also in some Saccharotrix and Kitasatospora species. Phylogenetic comparison of S. clavuligerus naringenin chalcone synthase with homologous proteins of other actinobacteria reveal that this protein is closely related to chalcone synthases that use malonyl-CoA as a starter unit for the formation of red-brown pigment. The function of the core enzymes in the pathway, such as the chalcone synthase and the tyrosine ammonia lyase, is conserved in plants and actinobacteria. However, S. clavuligerus use a P450 monooxygenase proposed to complete the cyclization step of the naringenin chalcone, whereas this reaction in plants is performed by a chalcone isomerase. Comparison of the plant and S. clavuligerus chalcone synthases indicates that they have not been transmitted between these organisms by a recent horizontal gene transfer phenomenon. We provide a comprehensive view of the molecular genetics and biochemistry of chalcone synthases and their impact on the development of antibacterial and antitumor compounds. These advances allow new bioactive compounds to be obtained using combinatorial strategies. In addition, processes of heterologous expression and bioconversion for the production of naringenin and naringenin-derived compounds in yeasts are described.
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Kukil K, Lindberg P. Expression of phenylalanine ammonia lyases in Synechocystis sp. PCC 6803 and subsequent improvements of sustainable production of phenylpropanoids. Microb Cell Fact 2022; 21:8. [PMID: 35012528 PMCID: PMC8750797 DOI: 10.1186/s12934-021-01735-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/29/2021] [Indexed: 11/18/2022] Open
Abstract
Background Phenylpropanoids represent a diverse class of industrially important secondary metabolites, synthesized in plants from phenylalanine and tyrosine. Cyanobacteria have a great potential for sustainable production of phenylpropanoids directly from CO2, due to their photosynthetic lifestyle with a fast growth compared to plants and the ease of generating genetically engineered strains. This study focuses on photosynthetic production of the starting compounds of the phenylpropanoid pathway, trans-cinnamic acid and p-coumaric acid, in the unicellular cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis). Results A selected set of phenylalanine ammonia lyase (PAL) enzymes from different organisms was overexpressed in Synechocystis, and the productivities of the resulting strains compared. To further improve the titer of target compounds, we evaluated the use of stronger expression cassettes for increasing PAL protein levels, as well as knock-out of the laccase gene slr1573, as this was previously reported to prevent degradation of the target compounds in the cell. Finally, to investigate the effect of growth conditions on the production of trans-cinnamic and p-coumaric acids from Synechocystis, cultivation conditions promoting rapid, high density growth were tested. Comparing the different PALs, the highest specific titer was achieved for the strain AtC, expressing PAL from Arabidopsis thaliana. A subsequent increase of protein level did not improve the productivity. Production of target compounds in strains where the slr1573 laccase had been knocked out was found to be lower compared to strains with wild type background, and the Δslr1573 strains exhibited a strong phenotype of slower growth rate and lower pigment content. Application of a high-density cultivation system for the growth of production strains allowed reaching the highest total titers of trans-cinnamic and p-coumaric acids reported so far, at around 0.8 and 0.4 g L−1, respectively, after 4 days. Conclusions Production of trans-cinnamic acid, unlike that of p-coumaric acid, is not limited by the protein level of heterologously expressed PAL in Synechocystis. High density cultivation led to higher titres of both products, while knocking out slr1573 did not have a positive effect on production. This work contributes to capability of exploiting the primary metabolism of cyanobacteria for sustainable production of plant phenylpropanoids. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01735-8.
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Affiliation(s)
- Kateryna Kukil
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Box 523, SE 751 20, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University, Box 523, SE 751 20, Uppsala, Sweden.
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Effendi SSW, Xue C, Tan SI, Ng IS. Whole-cell biocatalyst of recombinant tyrosine ammonia lyase with fusion protein and integrative chaperone in Escherichia coli for high-level p-Coumaric acid production. J Taiwan Inst Chem Eng 2021. [DOI: 10.1016/j.jtice.2021.08.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Abstract
Phenylalanine ammonia-lyase (PAL) links the plant primary and secondary metabolisms, and its product, trans-cinnamic acid, is derived into thousands of diverse phenylpropanoids. Bambusa oldhamii BoPAL4 has broad substrate specificity using L-phenylalanine, L-tyrosine, and L-3,4-dihydroxy phenylalanine (L-DOPA) as substrates to yield trans-cinnamic acid, p-coumaric acid, and caffeic acid, respectively. The optimum reaction pH of BoPAL4 for three substrates was measured at 9.0, 8.5, and 9.0, respectively. The optimum reaction temperatures of BoPAL4 for three substrates were obtained at 50, 60, and 40 °C, respectively. The Km values of BoPAL4 for three substrates were 2084, 98, and 956 μM, respectively. The kcat values of BoPAL4 for three substrates were 1.44, 0.18, and 0.06 σ−1, respectively. The major substrate specificity site mutant, BoPAL4-H123F, showed better affinity toward L-phenylalanine by decreasing its Km value to 640 μM and increasing its kcat value to 1.87 s−1. In comparison to wild-type BoPAL4, the specific activities of BoPAL4-H123F using L-tyrosine and L-DOPA as substrates retained 5.4% and 17.8% residual activities. Therefore, L-phenylalanine, L-tyrosine, and L-DOPA are bona fide substrates for BoPAL4.
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15
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Marín L, Gutiérrez-Del-Río I, Villar CJ, Lombó F. De novo biosynthesis of garbanzol and fustin in Streptomyces albus based on a potential flavanone 3-hydroxylase with 2-hydroxylase side activity. Microb Biotechnol 2021; 14:2009-2024. [PMID: 34216097 PMCID: PMC8449655 DOI: 10.1111/1751-7915.13874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/26/2022] Open
Abstract
Flavonoids are important plant secondary metabolites, which were shown to have antioxidant, anti-inflammatory or antiviral activities. Heterologous production of flavonoids in engineered microbial cell factories is an interesting alternative to their purification from plant material representing the natural source. The use of engineered bacteria allows to produce specific compounds, independent of soil, climatic or other plant-associated production parameters. The initial objective of this study was to achieve an engineered production of two interesting flavanonols, garbanzol and fustin, using Streptomyces albus as the production host. Unexpectedly, the engineered strain produced several flavones and flavonols in the absence of the additional expression of a flavone synthase (FNS) or flavonol synthase (FLS) gene. It turned out that the heterologous flavanone 3-hydroxylase (F3H) has a 2-hydroxylase side activity, which explains the observed production of 7,4'-dihydroxyflavone, resokaempferol, kaempferol and apigenin, as well as the biosynthesis of the extremely rare 2-hydroxylated intermediates 2-hydroxyliquiritigenin, 2-hydroxynaringenin and probably licodione. Other related metabolites, such as quercetin, dihydroquercetin and eriodictyol, have also been detected in culture extracts of this recombinant strain. Hence, the enzymatic versatility of S. albus can be conveniently exploited for the heterologous production of a large diversity of plant metabolites of the flavonoid family.
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Affiliation(s)
- Laura Marín
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Ignacio Gutiérrez-Del-Río
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Claudio Jesús Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
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16
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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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17
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Cai M, Wu Y, Qi H, He J, Wu Z, Xu H, Qiao M. Improving the Level of the Tyrosine Biosynthesis Pathway in Saccharomyces cerevisiae through HTZ1 Knockout and Atmospheric and Room Temperature Plasma (ARTP) Mutagenesis. ACS Synth Biol 2021; 10:49-62. [PMID: 33395268 DOI: 10.1021/acssynbio.0c00448] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years, many studies have been conducted on the expression of multiple aromatic compounds by Saccharomyces cerevisiae. The concentration of l-tyrosine, as a precursor of such valuable compounds, is crucial for the biosynthesis of aromatic metabolites. In this study, a novel function of HTZ1 was found to be related to tyrosine biosynthesis, which has not yet been reported. Knockout of this gene could significantly improve the ability of yeast cells to synthesize tyrosine, and its p-coumaric acid (p-CA) titer was approximately 3.9-fold higher than that of the wild-type strain BY4742. Subsequently, this strain was selected for random mutagenesis through an emerging mutagenesis technique, namely, atmospheric and room temperature plasma (ARTP). After two rounds of mutagenesis, five tyrosine high-producing mutants were obtained. The highest production of p-CA was 7.6-fold higher than that of the wild-type strain. Finally, transcriptome data of the htz1Δ strain and the five mutants were analyzed. The genome of mutagenic strains was also resequenced to reveal the mechanism underlying the high titer of tyrosine. This system of target engineering combined with random mutagenesis to screen excellent mutants provides a new basis for synthetic biology.
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Affiliation(s)
- Miao Cai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Yuzhen Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Hang Qi
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Jiaze He
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Zhenzhou Wu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Haijin Xu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, PR China
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18
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Jeandet P, Vannozzi A, Sobarzo-Sánchez E, Uddin MS, Bru R, Martínez-Márquez A, Clément C, Cordelier S, Manayi A, Nabavi SF, Rasekhian M, El-Saber Batiha G, Khan H, Morkunas I, Belwal T, Jiang J, Koffas M, Nabavi SM. Phytostilbenes as agrochemicals: biosynthesis, bioactivity, metabolic engineering and biotechnology. Nat Prod Rep 2021; 38:1282-1329. [PMID: 33351014 DOI: 10.1039/d0np00030b] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 1976 to 2020. Although constituting a limited chemical family, phytostilbenes represent an emblematic group of molecules among natural compounds. Ever since their discovery as antifungal compounds in plants and their ascribed role in human health and disease, phytostilbenes have never ceased to arouse interest for researchers, leading to a huge development of the literature in this field. Owing to this, the number of references to this class of compounds has reached the tens of thousands. The objective of this article is thus to offer an overview of the different aspects of these compounds through a large bibliography analysis of more than 500 articles. All the aspects regarding phytostilbenes will be covered including their chemistry and biochemistry, regulation of their biosynthesis, biological activities in plants, molecular engineering of stilbene pathways in plants and microbes as well as their biotechnological production by plant cell systems.
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Affiliation(s)
- Philippe Jeandet
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment (DAFNAE), University of Padova, 35020 Legnaro, PD, Italy
| | - Eduardo Sobarzo-Sánchez
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Campus Vida, 15782 Santiago de Compostela, Spain and Instituto de Investigación e Innovación en Salud, Facultad de Ciencias de la Salud, Universidad Central de Chile, Chile
| | - Md Sahab Uddin
- Department of Pharmacy, Southeast University, Dhaka, Bangladesh and Neuroscience Research Network, Dhaka, Bangladesh
| | - Roque Bru
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Ascension Martínez-Márquez
- Plant Proteomics and Functional Genomics Group, Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Christophe Clément
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Sylvain Cordelier
- Research Unit "Induced Resistance and Plant Bioprotection", EA 4707, SFR Condorcet FR CNRS 3417, Faculty of Sciences, University of Reims Champagne-Ardenne, PO Box 1039, 51687 Reims Cedex 2, France.
| | - Azadeh Manayi
- Medicinal Plants Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, 1417614411 Tehran, Iran
| | - Seyed Fazel Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran 14359-16471, Iran
| | - Mahsa Rasekhian
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Haroon Khan
- Department of Pharmacy, Faculty of Chemical and Life Sciences, Abdul Wali Khan University Mardan, 23200, Pakistan
| | - Iwona Morkunas
- Department of Plant Physiology, Poznań University of Life Sciences, Wołyńska 35, 60-637 Poznań, Poland
| | - Tarun Belwal
- Zhejiang University, College of Biosystems Engineering and Food Science, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Zhejiang Key Laboratory for Agri-Food Processing, Hangzhou 310058, The People's Republic of China
| | - Jingjie Jiang
- Dorothy and Fred Chau '71 Constellation Professor, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Room 4005D, 110 8th Street, Troy, NY 12180, USA
| | - Mattheos Koffas
- Dorothy and Fred Chau '71 Constellation Professor, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Room 4005D, 110 8th Street, Troy, NY 12180, USA
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran 14359-16471, Iran
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19
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Behzadipour Y, Sadeghian I, Ghaffarian Bahraman A, Hemmati S. Introducing a delivery system for melanogenesis inhibition in melanoma B16F10 cells mediated by the conjugation of tyrosine ammonia-lyase and a TAT-penetrating peptide. Biotechnol Prog 2020; 37:e3071. [PMID: 32840065 DOI: 10.1002/btpr.3071] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/12/2020] [Accepted: 08/21/2020] [Indexed: 12/16/2022]
Abstract
Hyperpigmentation disorders negatively influence an individual's quality of life and may cause emotional distress. Over the years, various melanogenesis inhibitors (mainly tyrosinase inhibitors) have been developed, most of which with low efficacy or high toxicity. Although metabolic engineering by deviation in the flux of substrate is of considerable interest, trials to develop a melanogenesis inhibitor based on L-tyrosine (L-Tyr) restriction are missing. We propose a novel proteinaceous melanogenesis inhibitor called tyrosine ammonia-lyase (TAL), an enzyme that catalyzes the conversion of L-Tyr to p-coumaric acid and ammonia. Since the cell membrane can act as a barrier for intracellular protein delivery, we have covalently conjugated a recombinant TAL enzyme from Rhodobacter sphaeroides (RsTAL) to a trans-activator of transcription (TAT) cell-penetrating peptide (CPP) to afford the intracellular delivery. The heterologously expressed TAT-RsTAL fusion protein was delivered successfully into B16F10 melanocytes as confirmed by the direct fluorescence microscopy with increased intensity from 30 to 180 min. TAT-RsTAL showed sufficient intracellular activity of about 0.83 ± 0.04 and 0.34 ± 0.03 nmol•mg-1 •s-1 for the native and inclusion body-extracted conjugates, respectively. The conjugate inhibited melanin biosynthesis in B16F10 cells in a time-dependent manner. Melanin accumulation was inhibited by 12.7 ± 6.2%, 28.2 ± 5.7%, and 33.9 ± 2.9% compared to the nontreated control groups after 24, 48, and 72 hr of incubation, respectively. L-Tyr restriction had no significant effect on the cell viability up to a concentration of 100 μgml-1 even after 72 hr. According to the observed hypopigmentary effect of the conjugate in this study, TAT-RsTAL can be suggested as a melanogenesis inhibitor for further investigations.
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Affiliation(s)
- Yasaman Behzadipour
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Issa Sadeghian
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Ghaffarian Bahraman
- Department of Pharmacology and Toxicology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Occupational Environment Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.,Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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20
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Optimization of the l-tyrosine metabolic pathway in Saccharomyces cerevisiae by analyzing p-coumaric acid production. 3 Biotech 2020; 10:258. [PMID: 32550099 DOI: 10.1007/s13205-020-02223-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022] Open
Abstract
In this study, we applied a series of genetic modifications to wild-type S. cerevisiae strain BY4741 to address the bottlenecks in the l-tyrosine pathway. A tyrosine ammonia-lyase (TAL) gene from Rhodobacter capsulatus, which can catalyze conversion of l-tyrosine into p-coumaric acid, was overexpressed to facilitate the analysis of l-tyrosine and test the strain's capability to synthesize heterologous derivatives. First, we enhanced the supply of precursors by overexpressing transaldolase gene TAL1, enolase II gene ENO2, and pentafunctional enzyme gene ARO1 resulting in a 1.55-fold increase in p-coumaric acid production. Second, feedback inhibition of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase and chorismate mutase was relieved by overexpressing the mutated feedback-resistant ARO4 K229L and ARO7 G141S , and a 3.61-fold improvement of p-coumaric acid production was obtained. Finally, formation of byproducts was decreased by deleting pyruvate decarboxylase gene PDC5 and phenylpyruvate decarboxylase gene ARO10, and p-coumaric acid production was increased 2.52-fold. The best producer-when TAL1, ENO2, ARO1, ARO4 K229L , ARO7 G141S , and TAL were overexpressed, and PDC5 and ARO10 were deleted-increased p-coumaric acid production by 14.08-fold (from 1.4 to 19.71 mg L-1). Our study provided a valuable insight into the optimization of l-tyrosine metabolic pathway.
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21
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Miranda RR, Silva M, Barisón MJ, Silber AM, Iulek J. Crystal structure of histidine ammonia-lyase from Trypanosoma cruzi. Biochimie 2020; 175:181-188. [PMID: 32464165 DOI: 10.1016/j.biochi.2020.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 04/10/2020] [Accepted: 05/17/2020] [Indexed: 10/24/2022]
Abstract
Chagas disease is one of seventeen neglected tropical diseases according to the World Health Organization (WHO). The histidine-glutamate metabolic pathway is an oxidative route that has shown to be relevant for the bioenergetics in Trypanosoma cruzi, the etiological agent for Chagas disease. Histidine ammonia-lyase participates in the first stage of the histidine catabolism, catalyzing the conversion of l-histidine into urocanate. This work presents the three-dimensional (3D) structure of Trypanosoma cruzi histidine ammonia-lyase enzyme (TcHAL) and some comparisons of it to homologous structures. The enzyme was expressed, purified and assayed for crystallization, what allowed the obtainment of crystals of sufficient quality to collect X-ray diffraction data up to 2.55 Å resolution. After refinement, some structural analyses indicated that the structure does not contain the active site protection domain, in opposition to previously known 3D structures from plants and fungi phenylalanine ammonia-lyase, therefore, it is the first structure of eukaryotic ammonia-lyases that lacks this domain.
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Affiliation(s)
- Robson R Miranda
- Department of Chemistry, State University of Ponta Grossa, Brazil
| | - Marcio Silva
- Department of Education, Federal Technological University of Paraná, Brazil
| | - Maria J Barisón
- Department of Parasitology, Institute of Biomedical Sciences, University of São, Paulo, Brazil
| | - Ariel M Silber
- Department of Parasitology, Institute of Biomedical Sciences, University of São, Paulo, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, Brazil.
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22
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Xu JJ, Fang X, Li CY, Yang L, Chen XY. General and specialized tyrosine metabolism pathways in plants. ABIOTECH 2020; 1:97-105. [PMID: 36304719 PMCID: PMC9590561 DOI: 10.1007/s42994-019-00006-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/06/2019] [Indexed: 11/25/2022]
Abstract
The tyrosine metabolism pathway serves as a starting point for the production of a variety of structurally diverse natural compounds in plants, such as tocopherols, plastoquinone, ubiquinone, betalains, salidroside, benzylisoquinoline alkaloids, and so on. Among these, tyrosine-derived metabolites, tocopherols, plastoquinone, and ubiquinone are essential to plant survival. In addition, this pathway provides us essential micronutrients (e.g., vitamin E and ubiquinone) and medicine (e.g., morphine, salidroside, and salvianolic acid B). However, our knowledge of the plant tyrosine metabolism pathway remains rudimentary, and genes encoding the pathway enzymes have not been fully defined. In this review, we summarize and discuss recent advances in the tyrosine metabolism pathway, key enzymes, and important tyrosine-derived metabolites in plants.
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Affiliation(s)
- Jing-Jing Xu
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602 People’s Republic of China
| | - Xin Fang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences Kunming, Kunming, 650201 Yunnan People’s Republic of China
| | - Chen-Yi Li
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
- University of Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
| | - Lei Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602 People’s Republic of China
| | - Xiao-Ya Chen
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Plant Science Research Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602 People’s Republic of China
- State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences/Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032 People’s Republic of China
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23
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Cui P, Zhong W, Qin Y, Tao F, Wang W, Zhan J. Characterization of two new aromatic amino acid lyases from actinomycetes for highly efficient production of p-coumaric acid. Bioprocess Biosyst Eng 2020; 43:1287-1298. [PMID: 32198549 DOI: 10.1007/s00449-020-02325-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/04/2020] [Indexed: 12/31/2022]
Abstract
p-Coumaric acid (p-CA) is a bioactive natural product and an important industrial material for pharmaceuticals and nutraceuticals. It can be synthesized from deamination of L-tyrosine by tyrosine ammonia lyase (TAL). In this work, we discovered two aromatic amino acid lyase genes, Sas-tal and Sts-tal, from Saccharothrix sp. NRRL B-16348 and Streptomyces sp. NRRL F-4489, respectively, and expressed them in Escherichia coli BL21(DE3). The two enzymes were functionally characterized as TAL. The optimum reaction temperature for Sas-TAL and Sts-TAL is 55 °C and 50 °C, respectively; while, the optimum pH for both TALs is 11. Sas-TAL had a kcat/Km value of 6.2 μM-1 min-1, while Sts-TAL had a much higher efficiency with a kcat/Km value of 78.3 μM-1 min-1. Both Sts-TAL and Sas-TAL can also take L-phenylalanine as the substrate to yield trans-cinnamic acid, and Sas-TAL showed much higher phenylalanine ammonia lyase activity than Sts-TAL. Using E. coli/Sts-TAL as a whole-cell biocatalyst, the productivity of p-CA reached 2.88 ± 0.12 g (L h)-1, which represents the highest efficiency for microbial production of p-CA. Therefore, this work not only reports the identification of two new TALs from actinomycetes, but also provides an efficient way to produce the industrially valuable material p-CA.
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Affiliation(s)
- Peiwu Cui
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310030, Zhejiang, China.,TCM and Ethnomedicine Innovation and Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China.,Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
| | - Weihong Zhong
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310030, Zhejiang, China
| | - Yong Qin
- Hangzhou Viablife Biotech Co., Ltd., 1 Jingyi Road, Yuhang District, Hangzhou, 311113, Zhejiang, China
| | - Fuping Tao
- Hangzhou Viablife Biotech Co., Ltd., 1 Jingyi Road, Yuhang District, Hangzhou, 311113, Zhejiang, China
| | - Wei Wang
- TCM and Ethnomedicine Innovation and Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China.
| | - Jixun Zhan
- TCM and Ethnomedicine Innovation and Development Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, 410208, Hunan, China. .,Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA.
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Exploring the therapeutic potential of modern and ancestral phenylalanine/tyrosine ammonia-lyases as supplementary treatment of hereditary tyrosinemia. Sci Rep 2020; 10:1315. [PMID: 31992763 PMCID: PMC6987202 DOI: 10.1038/s41598-020-57913-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/07/2020] [Indexed: 12/01/2022] Open
Abstract
Phenylalanine/tyrosine ammonia-lyases (PAL/TALs) have been approved by the FDA for treatment of phenylketonuria and may harbour potential for complementary treatment of hereditary tyrosinemia Type I. Herein, we explore ancestral sequence reconstruction as an enzyme engineering tool to enhance the therapeutic potential of PAL/TALs. We reconstructed putative ancestors from fungi and compared their catalytic activity and stability to two modern fungal PAL/TALs. Surprisingly, most putative ancestors could be expressed as functional tetramers in Escherichia coli and thus retained their ability to oligomerize. All ancestral enzymes displayed increased thermostability compared to both modern enzymes, however, the increase in thermostability was accompanied by a loss in catalytic turnover. One reconstructed ancestral enzyme in particular could be interesting for further drug development, as its ratio of specific activities is more favourable towards tyrosine and it is more thermostable than both modern enzymes. Moreover, long-term stability assessment showed that this variant retained substantially more activity after prolonged incubation at 25 °C and 37 °C, as well as an increased resistance to incubation at 60 °C. Both of these factors are indicative of an extended shelf-life of biopharmaceuticals. We believe that ancestral sequence reconstruction has potential for enhancing the properties of enzyme therapeutics, especially with respect to stability. This work further illustrates that resurrection of putative ancestral oligomeric proteins is feasible and provides insight into the extent of conservation of a functional oligomerization surface area from ancestor to modern enzyme.
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25
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Barros J, Dixon RA. Plant Phenylalanine/Tyrosine Ammonia-lyases. TRENDS IN PLANT SCIENCE 2020; 25:66-79. [PMID: 31679994 DOI: 10.1016/j.tplants.2019.09.011] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 05/13/2023]
Abstract
Aromatic amino acid deaminases are key enzymes mediating carbon flux from primary to secondary metabolism in plants. Recent studies have uncovered a tyrosine ammonia-lyase that contributes to the typical characteristics of grass cell walls and contributes to about 50% of the total lignin synthesized by the plant. Grasses are currently preferred bioenergy feedstocks and lignin is the most important limiting factor in the conversion of plant biomass to liquid biofuels, as well as being an abundant renewable carbon source that can be industrially exploited. Further research on the structure, evolution, regulation, and biological function of functionally distinct ammonia-lyases has multiple implications for improving the economics of the agri-food and biofuel industries.
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Affiliation(s)
- Jaime Barros
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Richard A Dixon
- BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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26
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Development of an effective protein-labeling system based on smart fluorogenic probes. J Biol Inorg Chem 2019; 24:443-455. [PMID: 31152238 DOI: 10.1007/s00775-019-01669-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 12/23/2022]
Abstract
Proteins are an important component of living systems and play a crucial role in various physiological functions. Fluorescence imaging of proteins is a powerful tool for monitoring protein dynamics. Fluorescent protein (FP)-based labeling methods are frequently used to monitor the movement and interaction of cellular proteins. However, alternative methods have also been developed that allow the use of synthetic fluorescent probes to target a protein of interest (POI). Synthetic fluorescent probes have various advantages over FP-based labeling methods. They are smaller in size than the fluorescent proteins, offer a wide variety of colors and have improved photochemical properties. There are various chemical recognition-based labeling techniques that can be used for labeling a POI with a synthetic probe. In this review, we focus on the development of protein-labeling systems, particularly the SNAP-tag, BL-tag, and PYP-tag systems, and understanding the fluorescence behavior of the fluorescently labeled target protein in these systems. We also discuss the smart fluorogenic probes for these protein-labeling systems and their applications. The fluorogenic protein labeling will be a useful tool to investigate complex biological phenomena in future work on cell biology.
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Affiliation(s)
- Shahi Imam Reja
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masafumi Minoshima
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan.
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27
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Brechun KE, Zhen D, Jaikaran A, Borisenko V, Kumauchi M, Hoff WD, Arndt KM, Woolley GA. Detection of Incorporation of p-Coumaric Acid into Photoactive Yellow Protein Variants in Vivo. Biochemistry 2019; 58:2682-2694. [DOI: 10.1021/acs.biochem.9b00279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Katherine E. Brechun
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, Brandenburg 14476, Germany
| | - Danlin Zhen
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Anna Jaikaran
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Vitali Borisenko
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
| | - Masato Kumauchi
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, Oklahoma 74078, United States
| | - Wouter D. Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, 307 Life Sciences East, Stillwater, Oklahoma 74078, United States
| | - Katja M. Arndt
- Molecular Biotechnology, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Potsdam, Brandenburg 14476, Germany
| | - G. Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S 3H6, Canada
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28
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Huccetogullari D, Luo ZW, Lee SY. Metabolic engineering of microorganisms for production of aromatic compounds. Microb Cell Fact 2019; 18:41. [PMID: 30808357 PMCID: PMC6390333 DOI: 10.1186/s12934-019-1090-4] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 02/19/2019] [Indexed: 01/09/2023] Open
Abstract
Metabolic engineering has been enabling development of high performance microbial strains for the efficient production of natural and non-natural compounds from renewable non-food biomass. Even though microbial production of various chemicals has successfully been conducted and commercialized, there are still numerous chemicals and materials that await their efficient bio-based production. Aromatic chemicals, which are typically derived from benzene, toluene and xylene in petroleum industry, have been used in large amounts in various industries. Over the last three decades, many metabolically engineered microorganisms have been developed for the bio-based production of aromatic chemicals, many of which are derived from aromatic amino acid pathways. This review highlights the latest metabolic engineering strategies and tools applied to the biosynthesis of aromatic chemicals, many derived from shikimate and aromatic amino acids, including L-phenylalanine, L-tyrosine and L-tryptophan. It is expected that more and more engineered microorganisms capable of efficiently producing aromatic chemicals will be developed toward their industrial-scale production from renewable biomass.
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Affiliation(s)
- Damla Huccetogullari
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Zi Wei Luo
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program) and Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon, 34141, Republic of Korea.
- BioProcess Engineering Research Center and Bioinformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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29
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Preczenhak AP, Orsi B, Lima GPP, Tezotto-Uliana JV, Minatel IO, Kluge RA. Cysteine enhances the content of betalains and polyphenols in fresh-cut red beet. Food Chem 2019; 286:600-607. [PMID: 30827652 DOI: 10.1016/j.foodchem.2019.02.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/09/2019] [Accepted: 02/10/2019] [Indexed: 01/21/2023]
Abstract
This study investigated the effectiveness of cysteine in conservation of bioactive compounds and the antioxidant capacity of minimally processed red beet. After red beet minimal processing increasing cysteine concentrations were applied, corresponding to control, 2 mM, 4 mM, 8 mM and 16 mM. Assay was performed over 15 d to evaluate the polyphenols, betalains, antioxidant capacity and enzymatic activity of polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL). Cysteine enhanced the gallic acid, caffeic acid, chlorogenic acid, kaempferol and betalain contents until 6 d of storage. Subsequently, dosages of cysteine above 4 mM maintained gallic acid, kaempferol and betalains contents. Cysteine appears to influence the phenylpropanoid pathway, favoring the accumulation of polyphenols and betalains. In red beet, cysteine did not inhibit PPO activity but enhanced PAL activity. Betalains contribute more than phenolics to the antioxidant capacity, and their relationship with cysteine has not been thoroughly elucidated to date.
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Affiliation(s)
- Ana Paula Preczenhak
- Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz' - University of Sao Paulo, Pádua Dias 11, 13.418-900 Piracicaba, Sao Paulo, Brazil.
| | - Bruna Orsi
- Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz' - University of Sao Paulo, Pádua Dias 11, 13.418-900 Piracicaba, Sao Paulo, Brazil
| | - Giuseppina P Pereira Lima
- Sao Paulo State University, Department of Chemistry and Biochemistry, Institute of Bioscience, 18.618-000 Botucatu, Sao Paulo, Brazil
| | - Jaqueline V Tezotto-Uliana
- Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz' - University of Sao Paulo, Pádua Dias 11, 13.418-900 Piracicaba, Sao Paulo, Brazil
| | - Igor Otávio Minatel
- Sao Paulo State University, Department of Chemistry and Biochemistry, Institute of Bioscience, 18.618-000 Botucatu, Sao Paulo, Brazil
| | - Ricardo Alfredo Kluge
- Department of Biological Sciences, Escola Superior de Agricultura 'Luiz de Queiroz' - University of Sao Paulo, Pádua Dias 11, 13.418-900 Piracicaba, Sao Paulo, Brazil
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30
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Production of methylparaben in Escherichia coli. ACTA ACUST UNITED AC 2019; 46:91-99. [DOI: 10.1007/s10295-018-2102-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/27/2018] [Indexed: 10/27/2022]
Abstract
Abstract
Since the 1930s, parabens have been employed widely as preservatives in food, pharmaceutical, and personal care products. These alkyl esters of benzoic acid occur naturally in a broad range of plant species, where they are thought to enhance overall fitness through disease resistance and allelopathy. Current manufacture of parabens relies on chemical synthesis and the processing of 4-hydroxybenzoate as a precursor. A variety of bio-based production platforms have targeted 4-hydroxybenzoate for a greener alternative to chemical manufacturing, but parabens have yet to be made in microbes. Here, we deploy the plant enzyme benzoic acid carboxyl methyltransferase together with four additional recombinant enzymes to produce methylparaben in Escherichia coli. The feasibility of a tyrosine-dependent route to methylparaben is explored, establishing a framework for linking paraben production to emerging high-tyrosine E. coli strains. However, our use of a unique plant enzyme for bio-based methylparaben biosynthesis is potentially applicable to any microbial system engineered for the manufacture of 4-hydroxybenzoate.
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31
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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: 20] [Impact Index Per Article: 3.3] [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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32
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Marín L, Gutiérrez-del-Río I, Entrialgo-Cadierno R, Villar CJ, Lombó F. De novo biosynthesis of myricetin, kaempferol and quercetin in Streptomyces albus and Streptomyces coelicolor. PLoS One 2018; 13:e0207278. [PMID: 30440014 PMCID: PMC6237366 DOI: 10.1371/journal.pone.0207278] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/29/2018] [Indexed: 01/16/2023] Open
Abstract
Flavonols are a flavonoid subfamily widely distributed in plants, including several ones of great importance in human and animal diet (apple, tomato, broccoli, onion, beans, tea). These polyphenolic nutraceuticals exert potent antimicrobial (membrane potential disruptors), antioxidant (free-radical scavengers), pharmacokinetic (CYP450 modulators), anti-inflammatory (lipoxygenase inhibitors), antiangiogenic (VEGF inhibitors) and antitumor (cyclin inhibitors) activities. Biotechnological production of these nutraceuticals, for example via heterologous biosynthesis in industrial actinomycetes, is favored since in plants these polyphenols appear as inactive glycosylated derivatives, in low concentrations or as part of complex mixtures with other polyphenolic compounds. In this work, we describe the de novo biosynthesis of three important flavonols, myricetin, kaempferol and quercetin, in the industrially relevant actinomycetes Streptomyces coelicolor and S. albus. De novo biosynthesis of kaempferol, myricetin and quercetin in actinomycetes has not been described before.
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Affiliation(s)
- Laura Marín
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias) Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
| | - Ignacio Gutiérrez-del-Río
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias) Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
| | - Rodrigo Entrialgo-Cadierno
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias) Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
| | - Claudio J. Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias) Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias) Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Principality of Asturias, Spain
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Decoene T, Peters G, De Maeseneire SL, De Mey M. Toward Predictable 5'UTRs in Saccharomyces cerevisiae: Development of a yUTR Calculator. ACS Synth Biol 2018; 7:622-634. [PMID: 29366325 DOI: 10.1021/acssynbio.7b00366] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fine-tuning biosynthetic pathways is crucial for the development of economic feasible microbial cell factories. Therefore, the use of computational models able to predictably design regulatory sequences for pathway engineering proves to be a valuable tool, especially for modifying genes at the translational level. In this study we developed a computational approach for the de novo design of 5'-untranslated regions (5'UTRs) in Saccharomyces cerevisiae with a predictive outcome on translation initiation rate. On the basis of existing data, a partial least-squares (PLS) regression model was trained and showed good performance on predicting protein abundances of an independent test set. This model was further used for the construction of a "yUTR calculator" that can design 5'UTR sequences with a diverse range of desired translation efficiencies. The predictive power of our yUTR calculator was confirmed in vivo by different representative case studies. As such, these results show the great potential of data driven approaches for reliable pathway engineering in S. cerevisiae.
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Affiliation(s)
- Thomas Decoene
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Gert Peters
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Sofie L. De Maeseneire
- Centre
for Industrial Biotechnology and Biocatalysis, Ghent University, Coupure
links 653, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
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34
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Csuka P, Juhász V, Kohári S, Filip A, Varga A, Sátorhelyi P, Bencze LC, Barton H, Paizs C, Poppe L. Pseudomonas fluorescensStrain R124 Encodes Three Different MIO Enzymes. Chembiochem 2018; 19:411-418. [DOI: 10.1002/cbic.201700530] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Pál Csuka
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Vivien Juhász
- Department of Organic Chemistry and Technology; Budapest University of Technology and Economics; Műegyetem rkp. 3 1111 Budapest Hungary
| | - Szabolcs Kohári
- Fermentia Microbiological Ltd; Berlini út 47-49 1049 Budapest Hungary
| | - Alina Filip
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Andrea Varga
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Péter Sátorhelyi
- Fermentia Microbiological Ltd; Berlini út 47-49 1049 Budapest Hungary
| | - László Csaba Bencze
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
| | - Hazel Barton
- Department of Biology; The University of Akron; ASEC West Tower 178 Akron OH 44325 USA
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; 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
- Biocatalysis and Biotransformation Research Center; Faculty of Chemistry and Chemical Engineering; Babeş-Bolyai University of Cluj-Napoca; Arany János str. 11 400028 Cluj-Napoca Romania
- SynBiocat Ltd; Szilasliget u. 3 1172 Budapest Hungary
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35
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Mao J, Liu Q, Li Y, Yang J, Song X, Liu X, Xu H, Qiao M. A high-throughput method for screening of L-tyrosine high-yield strains by Saccharomyces cerevisiae. J GEN APPL MICROBIOL 2018; 64:198-201. [DOI: 10.2323/jgam.2017.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jiwei Mao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University
| | - Quanli Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University
| | - Yuanzi Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University
| | - Jiuxia Yang
- Department of Microbiology, College of Life Sciences, Nankai University
| | - Xinhao Song
- Department of Microbiology, College of Life Sciences, Nankai University
| | - Xiao Liu
- Department of Microbiology, College of Life Sciences, Nankai University
| | - Haijin Xu
- Department of Microbiology, College of Life Sciences, Nankai University
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University
- Department of Microbiology, College of Life Sciences, Nankai University
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36
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Wu G, Nielson JR, Peterson RT, Winter JM. Bonnevillamides, Linear Heptapeptides Isolated from a Great Salt Lake-Derived Streptomyces sp. Mar Drugs 2017; 15:md15070195. [PMID: 28672784 PMCID: PMC5532637 DOI: 10.3390/md15070195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/13/2017] [Accepted: 06/19/2017] [Indexed: 11/22/2022] Open
Abstract
Streptomyces sp. GSL-6B was isolated from sediment collected from the Great Salt Lake and investigation of its organic extract led to the isolation of three new linear heptapeptides, bonnevillamides A (1), B (2), and C (3). The bonnevillamides represent a new class of linear peptides featuring unprecedented non-proteinogenic amino acids. All three peptides contain the newly characterized bonnevillic acid moiety (3-(3,5-dichloro-4-methoxyphenyl)-2-hydroxyacrylic acid), as well as a heavily modified proline residue. Moreover, in bonnevillamide A, the terminal proline residue found in bonnevillamides B and C is replaced with 4-methyl-azetidine-2-carboxylic acid methyl ester. The structures of the three heptapeptides were elucidated by NMR, high-resolution electrospray ionization mass spectroscopy (HRESIMS), and LC-MS/MS, and the absolute configuration of all proteinogenic amino acid residues were determined by advanced Marfey’s method. Bonnevillamides A, B and C were evaluated for their effects on zebrafish embryo development. All three heptapeptides were shown to modulate heart growth and cardiac function, with bonnevillamide B having the most pronounced effect.
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Affiliation(s)
- Guangwei Wu
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
| | - Jason R Nielson
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Randall T Peterson
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, UT 84112, USA.
| | - Jaclyn M Winter
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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37
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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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38
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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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39
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Mao J, Liu Q, Song X, Wang H, Feng H, Xu H, Qiao M. Combinatorial analysis of enzymatic bottlenecks of l-tyrosine pathway by p-coumaric acid production in Saccharomyces cerevisiae. Biotechnol Lett 2017; 39:977-982. [DOI: 10.1007/s10529-017-2322-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/09/2017] [Indexed: 10/20/2022]
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40
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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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41
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Sánchez-Murcia PA, Bueren-Calabuig JA, Camacho-Artacho M, Cortés-Cabrera Á, Gago F. Stepwise Simulation of 3,5-Dihydro-5-methylidene-4H-imidazol-4-one (MIO) Biogenesis in Histidine Ammonia-lyase. Biochemistry 2016; 55:5854-5864. [DOI: 10.1021/acs.biochem.6b00744] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pedro A. Sánchez-Murcia
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Juan A. Bueren-Calabuig
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Marta Camacho-Artacho
- Structural
Biology Department, Centro Nacional de Investigaciones Oncológicas (CNIO), E-28029 Madrid, Spain
| | - Álvaro Cortés-Cabrera
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
| | - Federico Gago
- Área
de Farmacología, Departamento de Ciencias Biomédicas,
Unidad Asociada al IQM-CSIC, Universidad de Alcalá, E-28805 Alcalá de Henares, Spain
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42
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Optogenetic Inhibitor of the Transcription Factor CREB. ACTA ACUST UNITED AC 2016; 22:1531-1539. [PMID: 26590638 DOI: 10.1016/j.chembiol.2015.09.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 09/11/2015] [Accepted: 09/24/2015] [Indexed: 01/28/2023]
Abstract
Current approaches for optogenetic control of transcription do not mimic the activity of endogenous transcription factors, which act at numerous sites in the genome in a complex interplay with other factors. Optogenetic control of dominant negative versions of endogenous transcription factors provides a mechanism for mimicking the natural regulation of gene expression. Here we describe opto-DN-CREB, a blue-light-controlled inhibitor of the transcription factor CREB created by fusing the dominant negative inhibitor A-CREB to photoactive yellow protein (PYP). A light-driven conformational change in PYP prevents coiled-coil formation between A-CREB and CREB, thereby activating CREB. Optogenetic control of CREB function was characterized in vitro, in HEK293T cells, and in neurons where blue light enabled control of expression of the CREB targets NR4A2 and c-Fos. Dominant negative inhibitors exist for numerous transcription factors; linking these to optogenetic domains offers a general approach for spatiotemporal control of native transcriptional events.
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43
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Gao F, Gao T, Zhou K, Zeng W. Small Molecule-Photoactive Yellow Protein Labeling Technology in Live Cell Imaging. Molecules 2016; 21:molecules21091163. [PMID: 27589715 PMCID: PMC6273459 DOI: 10.3390/molecules21091163] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/09/2016] [Accepted: 08/16/2016] [Indexed: 12/18/2022] Open
Abstract
Characterization of the chemical environment, movement, trafficking and interactions of proteins in live cells is essential to understanding their functions. Labeling protein with functional molecules is a widely used approach in protein research to elucidate the protein location and functions both in vitro and in live cells or in vivo. A peptide or a protein tag fused to the protein of interest and provides the opportunities for an attachment of small molecule probes or other fluorophore to image the dynamics of protein localization. Here we reviewed the recent development of no-wash small molecular probes for photoactive yellow protein (PYP-tag), by the means of utilizing a quenching mechanism based on the intramolecular interactions, or an environmental-sensitive fluorophore. Several fluorogenic probes have been developed, with fast labeling kinetics and cell permeability. This technology allows quick live-cell imaging of cell-surface and intracellular proteins without a wash-out procedure.
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Affiliation(s)
- Feng Gao
- Powder Metallurgy Research Institute of Central South University, Changsha 410013, China.
- The Third Xiangya Hospital, Central South University, Changsha 410013, China.
| | - Tang Gao
- School of Pharmaceutical Sciences, Central South University, Changsha 410013, China.
| | - Kechao Zhou
- Powder Metallurgy Research Institute of Central South University, Changsha 410013, China.
| | - Wenbin Zeng
- School of Pharmaceutical Sciences, Central South University, Changsha 410013, China.
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44
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Characterization of mutants of a tyrosine ammonia-lyase from Rhodotorula glutinis. Appl Microbiol Biotechnol 2016; 100:10443-10452. [DOI: 10.1007/s00253-016-7672-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 05/09/2016] [Accepted: 06/08/2016] [Indexed: 10/21/2022]
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45
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Walter T, Wijewardena D, Walker KD. Mutation of Aryl Binding Pocket Residues Results in an Unexpected Activity Switch in an Oryza sativa Tyrosine Aminomutase. Biochemistry 2016; 55:3497-503. [DOI: 10.1021/acs.biochem.6b00331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tyler Walter
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Devinda Wijewardena
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
| | - Kevin D. Walker
- Department
of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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46
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Barros J, Serrani-Yarce JC, Chen F, Baxter D, Venables BJ, Dixon RA. Role of bifunctional ammonia-lyase in grass cell wall biosynthesis. NATURE PLANTS 2016; 2:16050. [PMID: 27255834 DOI: 10.1038/nplants.2016.50] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/10/2016] [Indexed: 05/18/2023]
Abstract
L-Phenylalanine ammonia-lyase (PAL) is the first enzyme in the biosynthesis of phenylpropanoid-derived plant compounds such as flavonoids, coumarins and the cell wall polymer lignin. The cell walls of grasses possess higher proportions of syringyl (S)-rich lignins and high levels of esterified coumaric acid compared with those of dicotyledonous plants, and PAL from grasses can also possess tyrosine ammonia-lyase (TAL) activity, the reason for which has remained unclear. Using phylogenetic, transcriptomic and in vitro biochemical analyses, we identified a single homotetrameric bifunctional ammonia-lyase (PTAL) among eight BdPAL enzymes in the model grass species Brachypodium distachyon. (13)C isotope labelling experiments along with BdPTAL1-downregulation in transgenic plants showed that the TAL activity of BdPTAL1 can provide nearly half of the total lignin deposited in Brachypodium, with a preference for S-lignin and wall-bound coumarate biosynthesis, indicating that PTAL function is linked to the characteristic features of grass cell walls. Furthermore, isotope dilution experiments suggest that the pathways to lignin from L-phenylalanine and L-tyrosine are distinct beyond the formation of 4-coumarate, supporting the organization of lignin synthesis enzymes in one or more metabolons.
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Affiliation(s)
- Jaime Barros
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Juan C Serrani-Yarce
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Fang Chen
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - David Baxter
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
| | - Barney J Venables
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
| | - Richard A Dixon
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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47
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Busto E, Simon RC, Richter N, Kroutil W. One-Pot, Two-Module Three-Step Cascade To Transform Phenol Derivatives to Enantiomerically Pure (R)- or (S)-p-Hydroxyphenyl Lactic Acids. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00030] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Eduardo Busto
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010-Graz, Austria
| | - Robert C. Simon
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010-Graz, Austria
| | - Nina Richter
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010-Graz, Austria
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria
| | - Wolfgang Kroutil
- Institute
of Chemistry, University of Graz, NAWI Graz, Heinrichstrasse 28, A-8010-Graz, Austria
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48
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Busto E, Gerstmann M, Tobola F, Dittmann E, Wiltschi B, Kroutil W. Systems biocatalysis: para-alkenylation of unprotected phenols. Catal Sci Technol 2016. [DOI: 10.1039/c6cy01947a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Commercially available phenol derivatives were transformed with pyruvate to form a new C–C bond leading to the correspondingpara-coumaric acids and only one molecule of water as an innocent side product in buffer.
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Affiliation(s)
- Eduardo Busto
- Department of Chemistry
- NAWI Graz
- BioTechMed Graz
- University of Graz
- 8010 Graz
| | | | - Felix Tobola
- Austrian Centre of Industrial Biotechnology (ACIB)
- 8010 Graz
- Austria
| | - Edmund Dittmann
- Austrian Centre of Industrial Biotechnology (ACIB)
- 8010 Graz
- Austria
| | - Birgit Wiltschi
- Austrian Centre of Industrial Biotechnology (ACIB)
- 8010 Graz
- Austria
| | - Wolfgang Kroutil
- Department of Chemistry
- NAWI Graz
- BioTechMed Graz
- University of Graz
- 8010 Graz
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49
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Varga A, Bánóczi G, Nagy B, Bencze LC, Toşa MI, Gellért Á, Irimie FD, Rétey J, Poppe L, Paizs C. Influence of the aromatic moiety in α- and β-arylalanines on their biotransformation with phenylalanine 2,3-aminomutase from Pantoea agglomerans. RSC Adv 2016. [DOI: 10.1039/c6ra02964g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In this study enantiomer selective isomerization of various racemic α- and β-arylalanines catalysed by phenylalanine 2,3-aminomutase from Pantoea agglomerans (PaPAM) was investigated.
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Affiliation(s)
- Andrea Varga
- Biocatalysis and Biotransformation Research Group
- 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
| | - Botond Nagy
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - László Csaba Bencze
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - Monica Ioana Toşa
- Biocatalysis and Biotransformation Research Group
- 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
| | - Florin Dan Irimie
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
| | - János Rétey
- Institute of Organic Chemistry
- Karlsruhe Institute of Technology
- D-76128 Karlsruhe
- Germany
| | - László Poppe
- Department of Organic Chemistry and Technology
- Budapest University of Technology and Economics
- H-1111 Budapest
- Hungary
- SynBiocat Ltd
| | - Csaba Paizs
- Biocatalysis and Biotransformation Research Group
- Babeş-Bolyai University of Cluj-Napoca
- RO-400028 Cluj-Napoca
- Romania
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50
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Álvarez-Álvarez R, Botas A, Albillos SM, Rumbero A, Martín JF, Liras P. Molecular genetics of naringenin biosynthesis, a typical plant secondary metabolite produced by Streptomyces clavuligerus. Microb Cell Fact 2015; 14:178. [PMID: 26553209 PMCID: PMC4640377 DOI: 10.1186/s12934-015-0373-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/29/2015] [Indexed: 01/07/2023] Open
Abstract
Background Some types of flavonoid intermediates seemed to be restricted to plants. Naringenin is a typical plant metabolite, that has never been reported to be produced in prokariotes. Naringenin is formed by the action of a chalcone synthase using as starter 4-coumaroyl-CoA, which in dicotyledonous plants derives from phenylalanine by the action of a phenylalanine ammonia lyase. Results A compound produced by Streptomyces clavuligerus has been identified by LC–MS and NMR as naringenin and coelutes in HPLC with a naringenin standard. Genome mining of S. clavuligerus revealed the presence of a gene for a chalcone synthase (ncs), side by side to a gene encoding a P450 cytochrome (ncyP) and separated from a gene encoding a Pal/Tal ammonia lyase (tal). Deletion of any of these genes results in naringenin non producer mutants. Complementation with the deleted gene restores naringenin production in the transformants. Furthermore, naringenin production increases in cultures supplemented with phenylalanine or tyrosine. Conclusion This is the first time that naringenin is reported to be produced naturally in a prokariote. Interestingly three non-clustered genes are involved in naringenin production, which is unusual for secondary metabolites. A tentative pathway for naringenin biosynthesis has been proposed. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0373-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rubén Álvarez-Álvarez
- Microbiology Section, Department of Molecular Biology, Faculty of Biology and Environmental Sciences, Vegazana Campus, University of León, León, 24071, Spain. .,Institute of Biotechnology, INBIOTEC, Av. Real 1, León, 24006, Spain.
| | - Alma Botas
- Institute of Biotechnology, INBIOTEC, Av. Real 1, León, 24006, Spain.
| | - Silvia M Albillos
- Institute of Biotechnology, INBIOTEC, Av. Real 1, León, 24006, Spain.
| | - Angel Rumbero
- Organic Chemistry Department, University Autónoma of Madrid, Cantoblanco, 28049, Madrid, Spain.
| | - Juan F Martín
- Microbiology Section, Department of Molecular Biology, Faculty of Biology and Environmental Sciences, Vegazana Campus, University of León, León, 24071, Spain.
| | - Paloma Liras
- Microbiology Section, Department of Molecular Biology, Faculty of Biology and Environmental Sciences, Vegazana Campus, University of León, León, 24071, Spain.
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