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Roda-Garcia JJ, Haro-Moreno JM, López-Pérez M. Evolutionary pathways for deep-sea adaptation in marine planktonic Actinobacteriota. Front Microbiol 2023; 14:1159270. [PMID: 37234526 PMCID: PMC10205998 DOI: 10.3389/fmicb.2023.1159270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
The deep ocean, one of the largest ecosystems on earth, is dominated by microorganisms that are keystones in the regulation of biogeochemical cycles. However, the evolutionary pathways underlying the specific adaptations required (e.g., high pressure and low temperature) by this unique niche remain understudied. Here, we analyzed the first representatives belonging to the order Acidimicrobiales, a group of marine planktonic Actinobacteriota, that specifically inhabits the aphotic zone of the oceanic water column (>200 m). Compared with their epipelagic counterparts, deep-sea representatives showed the same evolution in genome architecture with higher GC content, longer intergenic spaces as well as higher nitrogen (N-ARSC) and lower carbon (C-ARSC) content in encoded amino acid residue side chains consistent with the higher nitrogen concentration and lower carbon concentration in deep waters compared to the photic zone. Metagenomic recruitment showed distribution patterns that allowed the description of different ecogenomic units within the three deep water-associated genera defined by our phylogenomic analyses (UBA3125, S20-B6 and UBA9410). The entire genus UBA3125 was found exclusively associated with oxygen minimum zones linked to the acquisition of genes involved in denitrification. Genomospecies of genus S20-B6 recruited in samples from both mesopelagic (200-1,000 m) and bathypelagic (1000-4,000 m) zones, including polar regions. Diversity in the genus UBA9410 was higher, with genomospecies widely distributed in temperate zones, others in polar regions, and the only genomospecies associated with abyssal zones (>4,000 m). At the functional level, groups beyond the epipelagic zone have a more complex transcriptional regulation including in their genomes a unique WhiB paralog. In addition, they showed higher metabolic potential for organic carbon and carbohydrate degradation as well as the ability to accumulate glycogen as a source of carbon and energy. This could compensate for energy metabolism in the absence of rhodopsins, which is only present in genomes associated with the photic zone. The abundance in deep samples of cytochrome P450 monooxygenases associated with the genomes of this order suggests an important role in remineralization of recalcitrant compounds throughout the water column.
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2
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Zhang L, Zhou X, Hu C, Yao S, Shi L, Niu T, Li X, Tong L, Zhang J, Ma T, Xia W. CO 2 improves the anaerobic biodegradation intensity and selectivity of heterocyclic hydrocarbons in heavy oil. ENVIRONMENTAL RESEARCH 2023; 224:115541. [PMID: 36828250 DOI: 10.1016/j.envres.2023.115541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/14/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Heterocyclic hydrocarbons pollution generated by oil spills and oilfield wastewater discharges threatens the ecological environment and human health. Here we described a strategy that combines the greenhouse gas CO2 reduction with microbial remediation. In the presence of nitrate, CO2 can improve the biodegradation efficiency of the resins and asphaltenes in heavy oil, particularly the biodegradation selectivity of the polar heterocyclic compounds by the newly isolated Klebsiella michiganensis. This strain encoded 80 genes for the xenobiotic biodegradation and metabolism, and can efficiently utilize CO2 when degrading heavy oil. The total abundance of resins and asphaltenes decreased significantly with CO2, from 40.816% to 26.909%, to 28.873% with O2, and to 36.985% with N2. The transcripts per million (TPM) value of accA gene was 57.81 under CO2 condition, while respectively 8.86 and 21.23 under O2 and N2 conditions. Under CO2 condition, the total relative percentage of N1-type heterocyclic compounds was selectively decreased from 32.25% to 22.78%, resulting in the heavy oil viscosity decreased by 46.29%. These results demonstrated a novel anaerobic degradation mechanism that CO2 can promote the anaerobic biodegradation of heterocyclic hydrocarbons in heavy oil, which provides a promising biotreatment technology for the oil-contaminated water.
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Affiliation(s)
- Lu Zhang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Xiangyu Zhou
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Chuxiao Hu
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Shun Yao
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, PR China
| | - Lei Shi
- Xinjiang Xinyitong Petroleum Technology Co.,Ltd, Karamay, 834000, PR China
| | - Tong Niu
- School of Public Health, Jilin University, Changchun, 130012, PR China
| | - Xin Li
- Xinli Oil Production Plant, Jilin Oilfield, PetroChina, Songyuan, 138001, PR China
| | - Lihua Tong
- Oil & Gas Survey, China Geological Survey, Beijing, 100083, PR China
| | - Jiaqiang Zhang
- The Key Laboratory of Unconventional Petroleum Geology, China Geological Survey, Beijing, 100083, PR China
| | - Ting Ma
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
| | - Wenjie Xia
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, PR China.
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3
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Engineering of Microbial Substrate Promiscuous CYP105A5 for Improving the Flavonoid Hydroxylation. Catalysts 2022. [DOI: 10.3390/catal12101157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Bacterial cytochrome P450 (CYP) enzymes are versatile biocatalysts that are responsible for the biotransformation of diverse endogenous substances. CYP105A5 from Streptomyces sp. showed substrate flexibility with different flavonoids and was able to catalyze O-demethylation of biochanin A, regioselective C3′-hydroxylation of daidzein, genistein, and naringenin, and additional C8-hydroxylation for daidzein using heterologous redox partners putidaredoxin and putidaredoxin reductase. By rational design of substrate-binding pocket based on experimental data, homology modeling, and molecular docking analysis, we enhanced the product formation rate of flavonoids. The double mutant L100A/I302A and L100A/I408N exhibited greatly enhanced in vivo conversion rates for flavonoid hydroxylation. Particularly, the L100A/I302A mutant’s kcat/Km values and in vivo conversion rate increased by 1.68-fold and 2.57-fold, respectively, for naringenin. Overall, our result might facilitate the potential use of CYP105A5 for future modification and application in whole-cell biocatalysts for the production of valuable polyphenols.
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Srdič M, Fessner ND, Yildiz D, Glieder A, Spiertz M, Schwaneberg U. Preparative Production of Functionalized (N- and O-Heterocyclic) Polycyclic Aromatic Hydrocarbons by Human Cytochrome P450 3A4 in a Bioreactor. Biomolecules 2022; 12:biom12020153. [PMID: 35204652 PMCID: PMC8961652 DOI: 10.3390/biom12020153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 11/16/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and their N- and O-containing derivatives (N-/O-PAHs) are environmental pollutants and synthetically attractive building blocks in pharmaceuticals. Functionalization of PAHs can be achieved via C-H activation by cytochrome P450 enzymes (e.g., P450 CYP3A4) in an environmentally friendly manner. Despite its broad substrate scope, the contribution of CYP3A4 to metabolize common PAHs in humans was found to be small. We recently showcased the potential of CYP3A4 in whole-cell biocatalysis with recombinant yeast Komagataella phaffii (Pichia pastoris) catalysts for the preparative-scale synthesis of naturally occurring metabolites in humans. In this study, we aimed at exploring the substrate scope of CYP3A4 towards (N-/O)-PAHs and conducted a bioconversion experiment at 10 L scale to validate the synthetic potential of CYP3A4 for the preparative-scale production of functionalized PAH metabolites. Hydroxylated products were purified and characterized using HPLC and NMR analysis. In total, 237 mg of fluorenol and 48 mg of fluorenone were produced from 498 mg of fluorene, with peak productivities of 27.7 μmol/L/h for fluorenol and 5.9 μmol/L/h for fluorenone; the latter confirmed that CYP3A4 is an excellent whole-cell biocatalyst for producing authentic human metabolites.
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Affiliation(s)
- Matic Srdič
- SeSaM-Biotech GmbH, 52074 Aachen, Germany;
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Nico D. Fessner
- Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, 8010 Graz, Austria;
| | - Deniz Yildiz
- DWI—Leibniz Institute for Interactive Materials, 52074 Aachen, Germany;
- Institute for Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | | | - Markus Spiertz
- SeSaM-Biotech GmbH, 52074 Aachen, Germany;
- Correspondence: (M.S.); (U.S.)
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI—Leibniz Institute for Interactive Materials, 52074 Aachen, Germany;
- Correspondence: (M.S.); (U.S.)
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Subedi P, Kim KH, Hong YS, Lee JH, Oh TJ. Enzymatic Characterization and Comparison of Two Steroid Hydroxylases CYP154C3-1 and CYP154C3-2 from Streptomyces Species. J Microbiol Biotechnol 2021; 31:464-474. [PMID: 33397832 PMCID: PMC9705902 DOI: 10.4014/jmb.2010.10020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/15/2020] [Accepted: 12/31/2020] [Indexed: 12/15/2022]
Abstract
Bacterial cytochrome P450 (CYP) enzymes are responsible for the hydroxylation of diverse endogenous substances with a heme molecule used as a cofactor. This study characterized two CYP154C3 proteins from Streptomyces sp. W2061 (CYP154C3-1) and Streptomyces sp. KCCM40643 (CYP154C3-2). The enzymatic activity assays of both CYPs conducted using heterologous redox partners' putidaredoxin and putidaredoxin reductase showed substrate flexibility with different steroids and exhibited interesting product formation patterns. The enzymatic characterization revealed good activity over a pH range of 7.0 to 7.8 and the optimal temperature range for activity was 30 to 37°C. The major product was the C16-hydroxylated product and the kinetic profiles and patterns of the generated hydroxylated products differed between the two enzymes. Both enzymes showed a higher affinity toward progesterone, with CYP154C3-1 demonstrating slightly higher activity than CYP154C3-2 for most of the substrates. Oxidizing agents (diacetoxyiodo) benzene (PIDA) and hydrogen peroxide (H2O2) were also utilized to actively support the redox reactions, with optimum conversion achieved at concentrations of 3 mM and 65 mM, respectively. The oxidizing agents affected the product distribution, influencing the type and selectivity of the CYP-catalyzed reaction. Additionally, CYP154C3s also catalyzed the C-C bond cleavage of steroids. Therefore, CYP154C3s may be a good candidate for the production of modified steroids for various biological uses.
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Affiliation(s)
- Pradeep Subedi
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea
| | - Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang-eup, Chungbuk 28116, Republic of Korea
| | - Joo-Ho Lee
- Genome-Based BioIT Convergence Institute, Asan 31460, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea,Genome-Based BioIT Convergence Institute, Asan 31460, Republic of Korea,Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asan 31460, Republic of Korea,Corresponding author Phone: +82-41-530-2677 Fax: +82-41-530-2279 E-mail:
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De Luca V, Mandrich L. Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects. Protein Pept Lett 2020; 27:400-410. [PMID: 31868141 DOI: 10.2174/0929866527666191223141205] [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: 11/27/2018] [Revised: 10/30/2019] [Accepted: 11/07/2019] [Indexed: 11/22/2022]
Abstract
Enzymes are among the most studied biological molecules because better understanding enzymes structure and activity will shed more light on their biological processes and regulation; from a biotechnological point of view there are many examples of enzymes used with the aim to obtain new products and/or to make industrial processes less invasive towards the environment. Enzymes are known for their high specificity in the recognition of a substrate but considering the particular features of an increasing number of enzymes this is not completely true, in fact, many enzymes are active on different substrates: this ability is called enzyme promiscuity. Usually, promiscuous activities have significantly lower kinetic parameters than to that of primary activity, but they have a crucial role in gene evolution. It is accepted that gene duplication followed by sequence divergence is considered a key evolutionary mechanism to generate new enzyme functions. In this way, promiscuous activities are the starting point to increase a secondary activity in the main activity and then get a new enzyme. The primary activity can be lost or reduced to a promiscuous activity. In this review we describe the differences between substrate and enzyme promiscuity, and its rule in gene evolution. From a practical point of view the knowledge of promiscuity can facilitate the in vitro progress of proteins engineering, both for biomedical and industrial applications. In particular, we report cases regarding esterases, phosphotriesterases and cytochrome P450.
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Affiliation(s)
- Valentina De Luca
- Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 111, 80131, Naples, Italy
| | - Luigi Mandrich
- Research Institute on Terrestrial Ecosystems, National Research Council, Via Pietro Castellino, 111, 80131, Naples, Italy
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7
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A Novel Thermostable Cytochrome P450 from Sequence-Based Metagenomics of Binh Chau Hot Spring as a Promising Catalyst for Testosterone Conversion. Catalysts 2020. [DOI: 10.3390/catal10091083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Biotechnological applications of cytochromes P450 show difficulties, such as low activity, thermal and/or solvent instability, narrow substrate specificity and redox partner dependence. In an attempt to overcome these limitations, an exploitation of novel thermophilic P450 enzymes from nature via uncultured approaches is desirable due to their great advantages that can resolve nearly all mentioned impediments. From the metagenomics library of the Binh Chau hot spring, an open reading frame (ORF) encoding a thermostable cytochrome P450—designated as P450-T3—which shared 66.6% amino acid sequence identity with CYP109C2 of Sorangium cellulosum So ce56 was selected for further identification and characterization. The ORF was synthesized artificially and heterologously expressed in Escherichia coli C43(DE3) using the pET17b system. The purified enzyme had a molecular weight of approximately 43 kDa. The melting temperature of the purified enzyme was 76.2 °C and its apparent half-life at 60 °C was 38.7 min. Redox partner screening revealed that P450-T3 was reduced well by the mammalian AdR-Adx4-108 and the yeast Arh1-Etp1 redox partners. Lauric acid, palmitic acid, embelin, retinoic acid (all-trans) and retinoic acid (13-cis) demonstrated binding to P450-T3. Interestingly, P450-T3 also bound and converted testosterone. Overall, P450-T3 might become a good candidate for biocatalytic applications on a larger scale.
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8
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Alejo-González K, Hanson-Viana E, Vazquez-Duhalt R. Enzymatic detoxification of organophosphorus pesticides and related toxicants. JOURNAL OF PESTICIDE SCIENCE 2018; 43:1-9. [PMID: 30363124 PMCID: PMC6140661 DOI: 10.1584/jpestics.d17-078] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/08/2018] [Indexed: 05/20/2023]
Abstract
Millions of cases of pesticide intoxication occur yearly and represent a public health problem. In addition, pesticide poisoning is the preferred suicidal method in rural areas. The use of enzymes for the treatment of intoxication due to organophosphorus pesticides was proposed decades ago. Several enzymes are able to transform organophosphorus compounds such as pesticides and nerve agents. Some specific enzymatic treatments have been proposed, including direct enzyme injection, liposome and erythrocytes carriers, PEGylated preparations and extracorporeal enzymatic treatments. Nevertheless, no enzymatic treatments are currently available. In this work, the use of enzymes for treating of organophosphorus pesticide intoxication is critically reviewed and the remaining challenges are discussed.
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Affiliation(s)
- Karla Alejo-González
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera Tijuana-Ensenada, Ensenada, Baja California 22760 México
| | - Erik Hanson-Viana
- Facultad de Medicina, Universidad Autónoma de Baja California, Mexicali, Mexico
| | - Rafael Vazquez-Duhalt
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 carretera Tijuana-Ensenada, Ensenada, Baja California 22760 México
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9
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Lo HC, Ryan JD, Kerr JB, Clark DS, Fish RH. Bioorganometallic chemistry: Co-factor regeneration, enzyme recognition of biomimetic 1,4-NADH analogs, and organic synthesis; tandem catalyzed regioselective formation of N-substituted-1,4-dihydronicotinamide derivatives with [Cp*Rh(bpy)H]+, coupled to chiral S-alcohol formation with HLADH, and engineered cytochrome P450s, for selective C-H oxidation reactions. J Organomet Chem 2017. [DOI: 10.1016/j.jorganchem.2017.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Holtmann D, Fraaije MW, Arends IWCE, Opperman DJ, Hollmann F. The taming of oxygen: biocatalytic oxyfunctionalisations. Chem Commun (Camb) 2015; 50:13180-200. [PMID: 24902635 DOI: 10.1039/c3cc49747j] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scope and limitations of oxygenases as catalysts for preparative organic synthesis is discussed.
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Affiliation(s)
- Dirk Holtmann
- DECHEMA Research Institute, Theodor-Heuss-Allee 25, 60486 Frankfurt am Main, Germany
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11
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Paul CE, Churakova E, Maurits E, Girhard M, Urlacher VB, Hollmann F. In situ formation of H2O2 for P450 peroxygenases. Bioorg Med Chem 2014; 22:5692-6. [DOI: 10.1016/j.bmc.2014.05.074] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/23/2014] [Accepted: 05/28/2014] [Indexed: 11/25/2022]
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12
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Roh C. Characterization of a biocatalyst catalyzing biotransformation of highly branched fatty acids. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2014. [DOI: 10.1016/j.bcab.2014.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Evaluation of coumarin-based fluorogenic P450 BM3 substrates and prospects for competitive inhibition screenings. Anal Biochem 2014; 456:70-81. [PMID: 24708937 DOI: 10.1016/j.ab.2014.03.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 12/17/2022]
Abstract
Fluorescence-based assays for the cytochrome P450 BM3 monooxygenase from Bacillus megaterium address an attractive biotechnological challenge by facilitating enzyme engineering and the identification of potential substrates of this highly promising biocatalyst. In the current study, we used the scarcity of corresponding screening systems as an opportunity to evaluate a novel and continuous high-throughput assay for this unique enzyme. A set of nine catalytically diverse P450 BM3 variants was constructed and tested toward the native substrate-inspired fluorogenic substrate 12-(4-trifluoromethylcoumarin-7-yloxy)dodecanoic acid. Particularly high enzyme-mediated O-dealkylation yielding the fluorescent product 7-hydroxy-4-trifluoromethylcoumarin was observed with mutants containing the F87V substitution, with A74G/F87V showing the highest catalytic efficiency (0.458 min(-1)μM(-1)). To simplify the assay procedure and show its versatility, different modes of application were successfully demonstrated, including (i) the direct use of NADPH or its oxidized form NADP(+) along with diverse NADPH recycling systems for electron supply, (ii) the use of cell-free lysates and whole-cell preparations as the biocatalyst source, and (iii) its use for competitive inhibition screens to identify or characterize substrates and inhibitors. A detailed comparison with known, fluorescence-based P450 BM3 assays finally emphasizes the relevance of our contribution to the ongoing research.
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14
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Biocatalytic production of 5-hydroxy-2-adamantanone by P450cam coupled with NADH regeneration. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Rabe KS, Niemeyer CM. Screening for cytochrome P450 reactivity with a reporter enzyme. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2013; 987:149-56. [PMID: 23475675 DOI: 10.1007/978-1-62703-321-3_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The identification of novel substrates of cytochrome P450 enzymes by high-throughput screening assays is of utmost importance to further increase the scope of these enzymes for future applications. Most screens are either confined to individual substrate analogues or hampered by low throughput due to elaborate analysis techniques. Here we describe a general high-throughput screening assay that interrogates the activity of P450 enzymes with the aid of catalase as a reporter enzyme.
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Affiliation(s)
- Kersten S Rabe
- Fakultät Chemie, Biologisch-Chemische Mikrostrukturtechnik, Technische Universität Dortmund, Dortmund, Germany
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17
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Sun R, Song HC, Yang YH, Yang P, Yang DY, Shen KZ, Xu YB, Gao YX, Chen YG, Dong JY. Microbiological transformation of the triterpene nigranoic acid by the freshwater fungus Dictyosporium heptasporum. JOURNAL OF ASIAN NATURAL PRODUCTS RESEARCH 2013; 15:433-440. [PMID: 23600754 DOI: 10.1080/10286020.2013.778833] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The microbiological transformation of the triterpene nigranoic acid (3,4-secocycloarta-4(28),24(Z)-diene-3,26-dioic acid) (1) to 3,4-secocycloarta-4(28),17(20),24(Z)-triene-7β-hydroxy-16β,26-lactone-3-oic acid (2) and 3,4-secocycloarta-4(28),17(20)(Z),24(Z)-triene-7β-hydroxy-16β-methoxy-3,26-dioic acid (3) by the freshwater fungus Dictyosporium heptasporum YMF1.01213 has been demonstrated. The structures of the biotransformation products were determined by spectroscopic and MS analyses. Compound 2, characterized by the presence of a formed C-16/C-26 ester bridge, provided a novel nine-membered lactone ring structural skeleton for 3,4-secocycloartane triterpenoid derivatives. In addition, Compounds 1-3 exhibited weak anti-HIV activity in vitro. Compounds 2 and 3 were reported for the first time as natural product derivatives.
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Affiliation(s)
- Rong Sun
- School of Life Science, Southwest University, Chongqing 400715, China
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18
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Biotransformation of isoflavone using enzymatic reactions. Molecules 2013; 18:3028-40. [PMID: 23467013 PMCID: PMC6270586 DOI: 10.3390/molecules18033028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 02/25/2013] [Accepted: 03/04/2013] [Indexed: 11/16/2022] Open
Abstract
The roles of cytochrome P450 monooxygenases (CYPs) from Streptomyces spp. which are called the "treasure islands" for natural products for medicine and antibiotics are not well understood. Substrate specificity studies on CYPs may give a solution for elucidation of their roles. Based on homology sequence information, the CYP105D7 of a soluble cytochrome P450 known as heme protein from Streptomyces avermitilis MA4680 was expressed using the T7 promoter of the bacterial expression vector pET24ma, over-expressed in Escherichia coli system and characterized. An engineered whole cell system for daidzein hydroxylation was constructed using an exogenous electron transport system from ferredoxin reductase (PdR) and ferredoxin (Pdx). Also, an in vitro reaction study showed the purified CYP105D7 enzyme, using NADH-dependent-reducing equivalents of a redox partner from Pseudomonas putida, hydroxylated daidzein at the 3' position of the B ring to produce 7,3,'4' trihydroxyisoflavone. The hydroxylated position was confirmed by GC-MS analysis. The turnover number of the enzyme was 0.69 μmol 7,3,'4'-trihydroxyisoflavone produced per μmol P450 per min. This enzyme CYP105D7 represents a novel type of 3'-hydroxylase for daidzein hydroxylation. A P450 inhibitor such as coumarin significantly (ca.98%) inhibited the daidzein hydroxylation activity.
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19
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Lu Y, Jiang JG. Application of Enzymatic Method in the Extraction and Transformation of Natural Botanical Active Ingredients. Appl Biochem Biotechnol 2013; 169:923-40. [DOI: 10.1007/s12010-012-0026-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 12/05/2012] [Indexed: 10/27/2022]
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20
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Braun A, Halwachs B, Geier M, Weinhandl K, Guggemos M, Marienhagen J, Ruff AJ, Schwaneberg U, Rabin V, Torres Pazmiño DE, Thallinger GG, Glieder A. MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2012; 2012:bas028. [PMID: 22730453 PMCID: PMC3381223 DOI: 10.1093/database/bas028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mutational events as well as the selection of the optimal variant are essential steps in the evolution of living organisms. The same principle is used in laboratory to extend the natural biodiversity to obtain better catalysts for applications in biomanufacturing or for improved biopharmaceuticals. Furthermore, single mutation in genes of drug-metabolizing enzymes can also result in dramatic changes in pharmacokinetics. These changes are a major cause of patient-specific drug responses and are, therefore, the molecular basis for personalized medicine. MuteinDB systematically links laboratory-generated enzyme variants (muteins) and natural isoforms with their biochemical properties including kinetic data of catalyzed reactions. Detailed information about kinetic characteristics of muteins is available in a systematic way and searchable for known mutations and catalyzed reactions as well as their substrates and known products. MuteinDB is broadly applicable to any known protein and their variants and makes mutagenesis and biochemical data searchable and comparable in a simple and easy-to-use manner. For the import of new mutein data, a simple, standardized, spreadsheet-based data format has been defined. To demonstrate the broad applicability of the MuteinDB, first data sets have been incorporated for selected cytochrome P450 enzymes as well as for nitrilases and peroxidases. Database URL:http://www.MuteinDB.org
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Affiliation(s)
- Andreas Braun
- Institute of Molecular Biotechnology, Graz University of Technology, 8010 Graz, Austria
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21
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Ueno T, Ohki T, Watanabe Y. Molecular engineering of cytochrome P450 and myoglobin for selective oxygenations. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s108842460400026x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Aspects of protein engineering of cytochrome P450 (P450) and myoglobin ( Mb ) to construct selective oxygenation catalysts have been described. Heme enzymes are known as biocatalysts for various oxidations but the design of substrate specificity has still remained one of the significant challenges because of dynamic nature of enzyme-substrate interactions. In particular, P450s are the most interesting targets among the heme enzymes because they are able to catalyze many types of monooxygenations such as hydroxylation, epoxidation, and sulfoxidation with high selectivity. Thus, many researchers have made efforts to convert the selectivity for natural substrates into that for unnatural substrates by several protein engineering approaches. On the other hand, we have reported a rational design of Mb to convert its oxygen carrier function into that of peroxidase or peroxygenase. The Mb mutants prepared in our work afford oxo-ferryl porphyrin radical cation (compound I) as observable species in Mb for the first time. Furthermore, some of the mutants we have constructed are useful for enantioselective oxygenations by oxygen transfer from the Mb -compound I to substrates.
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Affiliation(s)
- Takafumi Ueno
- Research Center for Materials Science, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Takahiro Ohki
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
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Choi KY, Jung E, Jung DH, Pandey BP, Yun H, Park HY, Kazlauskas RJ, Kim BG. Cloning, expression and characterization of CYP102D1, a self-sufficient P450 monooxygenase from Streptomyces avermitilis. FEBS J 2012; 279:1650-62. [PMID: 22188665 DOI: 10.1111/j.1742-4658.2011.08462.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Among 33 cytochrome P450s (CYPs) of Streptomyces avermitilis, CYP102D1 encoded by the sav575 gene is naturally a unique and self-sufficient CYP. Since the native cyp102D1 gene could not be expressed well in Escherichia coli, its expression was attempted using codon-optimized synthetic DNA. The gene was successfully overexpressed and the recombinant CYP102D1 was functionally active, showing a Soret peak at 450 nm in the reduced CO difference spectrum. FMN/FAD isolated from the reductase domain showed the same fluorescence in thin layer chromatography separation as the authentic standards. Characterization of the substrate specificity of CYP102D1 based on NADPH oxidation rate revealed that it catalysed the oxidation of saturated and unsaturated fatty acids with very good regioselectivity, similar to other CYP102A families depending on NADPH supply. In particular, CYP102D1 catalysed the rapid oxidation of myristoleic acid with a k(cat)/K(m) value of 453.4 ± 181.5 μM(-1)·min(-1). Homology models of CYP102D1 based on other members of the CYP102A family allowed us to alter substrate specificity to aromatic compounds such as daidzein. Interestingly, replacement of F96V/M246I in the active site increased catalytic activity for daidzein with a k(cat)/K(m) value of 100.9 ± 10.4 μM(-1)·min(-1) (15-fold).
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Affiliation(s)
- Kwon-Young Choi
- School of Chemical and Biological Engineering, Institute of Bioengineering, Seoul National University, Seoul, South Korea
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23
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Rea V, Kolkman AJ, Vottero E, Stronks EJ, Ampt KAM, Honing M, Vermeulen NPE, Wijmenga SS, Commandeur JNM. Active site substitution A82W improves the regioselectivity of steroid hydroxylation by cytochrome P450 BM3 mutants as rationalized by spin relaxation nuclear magnetic resonance studies. Biochemistry 2012; 51:750-60. [PMID: 22208729 DOI: 10.1021/bi201433h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cytochrome P450 BM3 from Bacillus megaterium is a monooxygenase with great potential for biotechnological applications. In this paper, we present engineered drug-metabolizing P450 BM3 mutants as a novel tool for regioselective hydroxylation of steroids at position 16β. In particular, we show that by replacing alanine at position 82 with a tryptophan in P450 BM3 mutants M01 and M11, the selectivity toward 16β-hydroxylation for both testosterone and norethisterone was strongly increased. The A82W mutation led to a ≤42-fold increase in V(max) for 16β-hydroxylation of these steroids. Moreover, this mutation improves the coupling efficiency of the enzyme, which might be explained by a more efficient exclusion of water from the active site. The substrate affinity for testosterone increased at least 9-fold in M11 with tryptophan at position 82. A change in the orientation of testosterone in the M11 A82W mutant as compared to the orientation in M11 was observed by T(1) paramagnetic relaxation nuclear magnetic resonance. Testosterone is oriented in M11 with both the A- and D-ring protons closest to the heme iron. Substituting alanine at position 82 with tryptophan results in increased A-ring proton-iron distances, consistent with the relative decrease in the level of A-ring hydroxylation at position 2β.
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Affiliation(s)
- V Rea
- LACDR/Division of Molecular Toxicology, Department of Pharmacochemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Abstract
P450(BM3) (CYP102A1), a fatty acid hydroxylase from Bacillus megaterium, has been extensively studied over a period of almost forty years. The enzyme has been redesigned to catalyse the oxidation of non-natural substrates as diverse as pharmaceuticals, terpenes and gaseous alkanes using a variety of engineering strategies. Crystal structures have provided a basis for several of the catalytic effects brought about by mutagenesis, while changes to reduction potentials, inter-domain electron transfer rates and catalytic parameters have yielded functional insights. Areas of active research interest include drug metabolite production, the development of process-scale techniques, unravelling general mechanistic aspects of P450 chemistry, methane oxidation, and improving selectivity control to allow the synthesis of fine chemicals. This review draws together the disparate research themes and places them in a historical context with the aim of creating a resource that can be used as a gateway to the field.
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Affiliation(s)
- Christopher J C Whitehouse
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, UK
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Hartog AF, van Herk T, Wever R. Efficient Regeneration of NADPH in a 3-Enzyme Cascade Reaction by in situ Generation of Glucose 6-Phosphate from Glucose and Pyrophosphate. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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27
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Lombard M, Salard I, Sari MA, Mansuy D, Buisson D. A new cytochrome P450 belonging to the 107L subfamily is responsible for the efficient hydroxylation of the drug terfenadine by Streptomyces platensis. Arch Biochem Biophys 2011; 508:54-63. [DOI: 10.1016/j.abb.2011.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 01/10/2011] [Accepted: 01/12/2011] [Indexed: 11/26/2022]
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Martin AS, Rovinosa J, Carrasco A, Orejarena S, Soto-Delgado J, Contreras R, Chamy MC. Microbial Transformation of Marine Halogenated Sesquiterpenes. Nat Prod Commun 2010. [DOI: 10.1177/1934578x1000501203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The sesquiterpene pacifenol is one of the main constituents of the red alga Laurencia claviformis. Earlier work on the semisynthetic derivatives of pacifenol afforded a series of halogenated sesquiterpenes. The aim of the present work was to obtain new hydroxylated derivatives of halogenated sesquiterpenes by means of microbial transformation using Aspergillus níger, Gibberella fujikuroi and Mucor plumbeus. The best results were obtained with M. plumbeus. The microbiological transformation by M. plumbeus of pacifenol, and two semisynthetic derivatives, is described. The structures of the new compounds obtained were determined by spectroscopic means.
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Affiliation(s)
- Aurelio San Martin
- Universidad de Chile, Facultad de Ciencias, Casilla 653, Santiago, Chile
| | - Juana Rovinosa
- Universidad de Chile, Facultad de Ciencias, Casilla 653, Santiago, Chile
| | - Alvaro Carrasco
- Universidad de Chile, Facultad de Ciencias, Casilla 653, Santiago, Chile
| | - Silvia Orejarena
- Universidad de Chile, Facultad de Ciencias, Casilla 653, Santiago, Chile
| | - Jorge Soto-Delgado
- Universidad de Chile, Facultad de Ciencias, Casilla 653, Santiago, Chile
| | - Renato Contreras
- Universidad de Chile, Facultad de Ciencias, Casilla 653, Santiago, Chile
| | - M. Cristina Chamy
- Depto de Química, Universidad Andrés Bello, Avda Los Fresnos 52, Viña del Mar, Chile
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29
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Sirim D, Widmann M, Wagner F, Pleiss J. Prediction and analysis of the modular structure of cytochrome P450 monooxygenases. BMC STRUCTURAL BIOLOGY 2010; 10:34. [PMID: 20950472 PMCID: PMC3224734 DOI: 10.1186/1472-6807-10-34] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 10/15/2010] [Indexed: 02/05/2023]
Abstract
Background Cytochrome P450 monooxygenases (CYPs) form a vast and diverse family of highly variable sequences. They catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. Despite their differences in sequence and substrate specificity, the structures of CYPs are highly similar. Although being in research focus for years, factors mediating selectivity and activity remain vague. Description This systematic comparison of CYPs based on the Cytochrome P450 Engineering Database (CYPED) involved sequence and structure analysis of more than 8000 sequences. 31 structures have been applied to generate a reliable structure-based HMM profile in order to predict structurally conserved regions. Therefore, it was possible to automatically transfer these modules on CYP sequences without any secondary structure information, to analyze substrate interacting residues and to compare interaction sites with redox partners. Conclusions Functionally relevant structural sites of CYPs were predicted. Regions involved in substrate binding were analyzed in all sequences among the CYPED. For all CYPs that require a reductase, two reductase interaction sites were identified and classified according to their length. The newly gained insights promise an improvement of engineered enzyme properties for potential biotechnological application. The annotated sequences are accessible on the current version of the CYPED. The prediction tool can be applied to any CYP sequence via the web interface at http://www.cyped.uni-stuttgart.de/cgi-bin/strpred/dosecpred.pl.
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Affiliation(s)
- Demet Sirim
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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30
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Rabe KS, Erkelenz M, Kiko K, Niemeyer CM. Peroxidase activity of bacterial cytochrome P450 enzymes: Modulation by fatty acids and organic solvents. Biotechnol J 2010; 5:891-9. [DOI: 10.1002/biot.201000028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Khatri Y, Girhard M, Romankiewicz A, Ringle M, Hannemann F, Urlacher VB, Hutter MC, Bernhardt R. Regioselective hydroxylation of norisoprenoids by CYP109D1 from Sorangium cellulosum So ce56. Appl Microbiol Biotechnol 2010; 88:485-95. [PMID: 20645086 DOI: 10.1007/s00253-010-2756-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/29/2010] [Accepted: 06/29/2010] [Indexed: 11/26/2022]
Abstract
Sesquiterpenes are particularly interesting as flavorings and fragrances or as pharmaceuticals. Regio- or stereoselective functionalizations of terpenes are one of the main goals of synthetic organic chemistry, which are possible through radical reactions but are not selective enough to introduce the desired chiral alcohol function into those compounds. Cytochrome P450 monooxygenases are versatile biocatalysts and are capable of performing selective oxidations of organic molecules. We were able to demonstrate that CYP109D1 from Sorangium cellulosum So ce56 functions as a biocatalyst for the highly regioselective hydroxylation of norisoprenoids, alpha- and beta-ionone, which are important aroma compounds of floral scents. The substrates alpha- and beta-ionone were regioselectively hydroxylated to 3-hydroxy-alpha-ionone and 4-hydroxy-beta-ionone, respectively, which was confirmed by (1)H NMR and (13)C NMR. The results of docking alpha- and beta-ionone into a homology model of CYP109D1 gave a rational explanation for the regio-selectivity of the hydroxylation. Kinetic studies revealed that alpha- and beta-ionone can be hydroxylated with nearly identical V (max) and K (m) values. This is the first comprehensive investigation of the regioselective hydroxylation of norisoprenoids by CYP109D1.
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Affiliation(s)
- Yogan Khatri
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
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32
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Mitsukura K, Sakamoto H, Kubo H, Yoshida T, Nagasawa T. Bioconversion of 1-adamantanol to 1,3-adamantanediol using Streptomyces sp. SA8 oxidation system. J Biosci Bioeng 2010; 109:550-3. [DOI: 10.1016/j.jbiosc.2009.11.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Revised: 11/30/2009] [Accepted: 11/30/2009] [Indexed: 11/29/2022]
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Smith EM, Wilson JY. Assessment of cytochrome P450 fluorometric substrates with rainbow trout and killifish exposed to dexamethasone, pregnenolone-16alpha-carbonitrile, rifampicin, and beta-naphthoflavone. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2010; 97:324-333. [PMID: 20167382 DOI: 10.1016/j.aquatox.2010.01.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 12/23/2009] [Accepted: 01/05/2010] [Indexed: 05/28/2023]
Abstract
Cytochrome P450s (CYPs) are important xenobiotic metabolizing proteins. While their functions are well understood in mammals, CYP function in non-mammalian vertebrate systems is much less defined, with function often inferred from mammalian data, assuming similar function across vertebrate species. In this study, we investigate whether in vivo treatment with known mammalian CYP inducers can alter the in vitro catalytic activity of fish microsomes using eleven fluorescent CYP-mediated substrates. We investigate the basal metabolism and induction potential for hepatic CYPs in two fish species, rainbow trout (Oncorhynchus mykiss) and killifish (Fundulus heteroclitus). Species differences were found in the baseline metabolism of these substrates. Killifish have significantly higher metabolic rates for all tested substrates except 7-benzyloxyquinoline and 7-benzyloxy-4-trifluoromethylcoumarin (both mammalian CYP3A substrates); significant differences were also seen between male and female killifish. Treatment with dexamethasone, pregnenolone-16alpha-carbonitrile, and rifampicin did not cause broad, measurable CYP induction in either fish species. In trout, dexamethasone (100 mg kg(-1)) significantly induced 3-cyano-7-ethoxycoumarin metabolism and rifampicin (100 mg kg(-1)) induced the dealkylation of 7-methoxyresorufin, although both were highly variable. Female killifish exposed to pregnenolone-16alpha-carbonitrile (100 mg kg(-1)) showed significantly higher metabolism of 7-pentoxyresorufin. Overall, dexamethasone, pregnenolone-16alpha-carbonitrile and rifampicin did not appear to consistently increase CYP activity in fish. Trout treated with 10 or 50 mg kg(-1) beta-naphthoflavone (BNF), a CYP1A inducer, showed significantly induced activity across almost all substrates tested, exceptions being 7-benzyloxyquinoline, 7-benzyloxy-4-trifluoromethylcoumarin and dibenzylfluorescein. 7-Methoxy-4-(aminomethyl)coumarin, a typical CYP2D substrate in mammals, was not metabolized by untreated fish liver microsomes; however, treatment with BNF significantly induced the metabolism of this substrate in trout. Induced substrate metabolism in BNF-treated microsomes was only correlated across selective substrates, suggesting that BNF induces multiple CYPs in fish liver. These include the known BNF inducible CYP1s plus a number of as yet unidentified fish CYPs. Overall, many of these catalytic assays could be valuable tools for identification of the function of specific CYP subfamilies and individual isoforms in fish.
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Affiliation(s)
- Emily M Smith
- Department of Biology, McMaster University, Hamilton, Ontario L8S4K1, Canada
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34
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Lamb DC, Lei L, Zhao B, Yuan H, Jackson CJ, Warrilow AGS, Skaug T, Dyson PJ, Dawson ES, Kelly SL, Hachey DL, Waterman MR. Streptomyces coelicolor A3(2) CYP102 protein, a novel fatty acid hydroxylase encoded as a heme domain without an N-terminal redox partner. Appl Environ Microbiol 2010; 76:1975-80. [PMID: 20097805 PMCID: PMC2838009 DOI: 10.1128/aem.03000-09] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Accepted: 01/15/2010] [Indexed: 11/20/2022] Open
Abstract
The gene from Streptomyces coelicolor A3(2) encoding CYP102B1, a recently discovered CYP102 subfamily which exists solely as a single P450 heme domain, has been cloned, expressed in Escherichia coli, purified, characterized, and compared to its fusion protein family members. Purified reconstitution metabolism experiments with spinach ferredoxin, ferredoxin reductase, and NADPH revealed differences in the regio- and stereoselective metabolism of arachidonic acid compared to that of CYP102A1, exclusively producing 11,12-epoxyeicosa-5,8,14-trienoic acid in addition to the shared metabolites 18-hydroxy arachidonic acid and 14,15-epoxyeicosa-5,8,11-trienoic acid. Consequently, in order to elucidate the physiological function of CYP102B1, transposon mutagenesis was used to generate an S. coelicolor A3(2) strain lacking CYP102B1 activity and the phenotype was assessed.
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Affiliation(s)
- David C Lamb
- Institute of Life Science and Swansea Medical School, Grove Building, Swansea University, Swansea SA2 8PP, United Kingdom.
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Furuya T, Kino K. Genome mining approach for the discovery of novel cytochrome P450 biocatalysts. Appl Microbiol Biotechnol 2010; 86:991-1002. [DOI: 10.1007/s00253-010-2450-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/13/2010] [Accepted: 01/13/2010] [Indexed: 10/19/2022]
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Protein engineering of microbial enzymes. Curr Opin Microbiol 2010; 13:274-82. [PMID: 20171138 DOI: 10.1016/j.mib.2010.01.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Revised: 01/14/2010] [Accepted: 01/15/2010] [Indexed: 11/20/2022]
Abstract
Protein engineering has emerged as an important tool to overcome the limitations of natural enzymes as biocatalysts. Recent advances have mainly focused on applying directed evolution to enzymes, especially important for organic synthesis, such as monooxygenases, ketoreductases, lipases or aldolases in order to improve their activity, enantioselectivity, and stability. The combination of directed evolution and rational protein design using computational tools is becoming increasingly important in order to explore enzyme sequence-space and to create improved or novel enzymes. These developments should allow to further expand the application of microbial enzymes in industry.
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Ning J, Wu TH, Tian Y, Wang CY, Tian G, Zhang BJ, Liu KX, Ma XC. Identification of cinobufagin metabolites in the bile of rats. Xenobiotica 2009; 40:48-54. [DOI: 10.3109/00498250903331049] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Perez DI, Grau MM, Arends IWCE, Hollmann F. Visible light-driven and chloroperoxidase-catalyzed oxygenation reactions. Chem Commun (Camb) 2009:6848-50. [PMID: 19885500 DOI: 10.1039/b915078a] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Robust peroxidase-catalyzed enantiospecific oxyfunctionalizations can be achieved by simple light-driven in situ generation of hydrogen peroxide.
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Affiliation(s)
- Daniel I Perez
- Department of Biotechnology, Biocatalysis and Organic Chemistry, Delft University of Technology, Julianalaan 136, Delft, 2628 BL, The Netherlands
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39
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Roh C, Choi KY, Pandey BP, Kim BG. Hydroxylation of daidzein by CYP107H1 from Bacillus subtilis 168. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcatb.2008.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Eckstein M, Daußmann T, Kragl U. Recent Developments in NAD(P)H Regeneration for Enzymatic Reductions in One- and Two-Phase Systems. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420410001692769] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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Ryan JD, Fish RH, Clark DS. Engineering cytochrome P450 enzymes for improved activity towards biomimetic 1,4-NADH cofactors. Chembiochem 2009; 9:2579-82. [PMID: 18816544 DOI: 10.1002/cbic.200800246] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jessica D Ryan
- Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA
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Craig JW, Chang FY, Brady SF. Natural products from environmental DNA hosted in Ralstonia metallidurans. ACS Chem Biol 2009; 4:23-8. [PMID: 19146479 DOI: 10.1021/cb8002754] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metagenomic studies designed to access new small molecules from the heterologous expression of environmental DNA have focused on the use of two model systems, Escherichia coli and Streptomyces spp., as heterologous hosts. Accessing the biosynthetic potential of DNA extracted from the bacteria present in environmental samples will require the development of a more diverse collection of model bacterial hosts that can be used for screening environmental DNA libraries. In this study the bacterium Ralstonia metallidurans was explored as a heterologous host. Here we report the isolation and characterization of both novel and known metabolites from pigmented and antibacterially active clones found in R. metallidurans based environmental DNA libraries. The clones found in this study do not confer the production of clone-specific metabolites to E. coli, validating R. metallidurans as an orthogonal expression host that can be used to expand the number of metabolites found in future metagenomic discovery efforts.
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Affiliation(s)
- Jeffrey W. Craig
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065
| | - Fang-Yuan Chang
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065
| | - Sean F. Brady
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, New York 10065
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Versatile capacity of shuffled cytochrome P450s for dye production. Appl Microbiol Biotechnol 2008; 82:203-10. [PMID: 19107474 DOI: 10.1007/s00253-008-1812-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 11/21/2008] [Accepted: 12/05/2008] [Indexed: 10/21/2022]
Abstract
DNA family shuffling is a relatively new method of directed evolution used to create novel enzymes in order to improve their existing properties or to develop new features. This method of evolution in vitro has one basic requirement: a high similarity of initial parental sequences. Cytochrome P450 enzymes are relatively well conserved in their amino acid sequences. Members of the same family can have more than 40% of sequence identity at the protein level and are therefore good candidates for DNA family shuffling. These xenobiotic-metabolising enzymes have an ability to metabolise a wide range of chemicals and produce a variety of products including blue pigments such as indigo. By applying the specifically designed DNA family shuffling approach, catalytic properties of cytochrome P450 enzymes were further extended in the chimeric progeny to include a new range of blue colour formations. This mini-review evokes the possibility of exploiting directed evolution of cytochrome P450s and the novel enzymes created by DNA family shuffling for the production of new dyes.
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Choi KY, Roh C, Pandey BP, Lee N, Kim T, Kim S, Kim BG. Functional expression of cytochrome P450s in Escherichia coli for the biotransformation of daidzein to produce ortho-specific monohydroxylation. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Rabe KS, Gandubert VJ, Spengler M, Erkelenz M, Niemeyer CM. Engineering and assaying of cytochrome P450 biocatalysts. Anal Bioanal Chem 2008; 392:1059-73. [PMID: 18622752 DOI: 10.1007/s00216-008-2248-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 06/11/2008] [Accepted: 06/12/2008] [Indexed: 11/29/2022]
Abstract
Cytochrome P450s constitute a highly fascinating superfamily of enzymes which catalyze a broad range of reactions. They are essential for drug metabolism and promise industrial applications in biotechnology and biosensing. The constant search for cytochrome P450 enzymes with enhanced catalytic performances has generated a large body of research. This review will concentrate on two key aspects related to the identification and improvement of cytochrome P450 biocatalysts, namely the engineering and assaying of these enzymes. To this end, recent advances in cytochrome P450 development are reported and commonly used screening methods are surveyed.
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Affiliation(s)
- Kersten S Rabe
- Fakultät für Chemie, Biologisch-Chemische Mikrostrukturtechnik, Technische Universität Dortmund, Otto-Hahn-Strabetae 6, 44227, Dortmund, Germany
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Ryan JD, Clark DS. P450cam biocatalysis in surfactant-stabilized two-phase emulsions. Biotechnol Bioeng 2008; 99:1311-9. [PMID: 18098319 DOI: 10.1002/bit.21772] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cytochrome P450 monooxygenases (P450s) are powerful biocatalysts that have the ability to oxidize a broad range of substrates, often at non-reactive carbon centers. However, incorporation of P450s into synthetic schemes has so far been limited to a few whole-cell transformations. P450 substrates are often hydrophobic and have low water solubility, limiting the amount of product that can be produced. To help overcome this limitation, we have examined P450cam activity in two-phase hexane/water emulsions with and without the anionic surfactant, bis(2-ethylhexyl) sulfosuccinate sodium salt (AOT). Hydroxylation of camphor to hydroxycamphor by the three- component P450cam system was chosen as the model reaction, and regeneration of NADH was accomplished with yeast alcohol dehydrogenase (YADH). P450cam was activated in the surfactant-free emulsions, and addition of AOT improved the activity even further, at least over the range of camphor concentrations for which initial rates were readily measurable in all media. The largest observed rate enhancement was 4.5-fold. Nearly 50-times more product was formed in the surfactant-stabilized emulsions than was achieved in aqueous buffer, with total turnover numbers reaching 28,900 for P450cam and 11,800 for YADH. In the absence of surfactant, the two-phase reaction appeared to be mass-transfer limited, while inclusion of AOT alleviated transport limitations and/or afforded a larger interfacial area for P450 activation. The oxidation of hydroxycamphor to 2,5-diketocamphane was also observed, owing to the large concentration of hydroxycamphor relative to camphor in the aqueous phase of the two-phase emulsion. This competing reaction was accompanied by the uncoupled oxidation of NADH (i.e., NADH oxidation without formation of 2,5-diketocamphane), which reduced the availability of NADH for camphor oxidation and further limited the yield of hydroxycamphor in the two-phase emulsions. These results indicate that a surfactant-stabilized two-phase emulsion is a promising reaction medium for practical P450 biocatalysis, although its effectiveness for a given P450/substrate combination can depend on several factors, including competitive or sequential reactions, product inhibition, and NAD(P)H uncoupling.
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Affiliation(s)
- Jessica D Ryan
- Department of Chemical Engineering, University of California, Berkeley, California 94720, USA
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Ye M, Guo D. A new bufadienolide obtained from the biotransformation of cinobufagin byAlternaria alternata. Nat Prod Res 2008; 22:26-30. [DOI: 10.1080/14786410601130141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Gandubert VJ, Torres E, Niemeyer CM. Investigation of cytochrome P450-modified cadmium sulfide quantum dots as photocatalysts. ACTA ACUST UNITED AC 2008. [DOI: 10.1039/b805526b] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Affiliation(s)
- Elizabeth M. J. Gillam
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Brisbane, Australia 4072
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Yun CH, Kim KH, Kim DH, Jung HC, Pan JG. The bacterial P450 BM3: a prototype for a biocatalyst with human P450 activities. Trends Biotechnol 2007; 25:289-98. [PMID: 17532492 DOI: 10.1016/j.tibtech.2007.05.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 03/20/2007] [Accepted: 05/09/2007] [Indexed: 11/18/2022]
Abstract
The use of cytochrome P450 (P450 or CYP) enzymes as biocatalysts for the production of fine chemicals, including pharmaceuticals, has been of increasing interest, primarily owing to their catalytic diversity and broad substrate range. CYP102A1 (P450 BM3) from Bacillus megaterium integrates an entire monooxygenase system into one polypeptide and represents an appropriate prokaryotic model for industrial applications of mammalian P450 activities. CYP102A1 not only exhibits the highest catalytic activity ever detected in a P450 monooxygenase but also provides a potentially versatile biocatalyst for the production of human P450 metabolites. CYP102A1 can be further engineered to be a drug-metabolizing enzyme, making it a promising candidate to use as a biocatalyst in drug discovery and synthesis.
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Affiliation(s)
- Chul-Ho Yun
- School of Biological Sciences and Technology and Hormone Research Center, Chonnam National University, Gwangju 500-757, Republic of Korea.
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