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Guo M, Lv H, Chen H, Dong S, Zhang J, Liu W, He L, Ma Y, Yu H, Chen S, Luo H. Strategies on biosynthesis and production of bioactive compounds in medicinal plants. CHINESE HERBAL MEDICINES 2024; 16:13-26. [PMID: 38375043 PMCID: PMC10874775 DOI: 10.1016/j.chmed.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/05/2023] [Accepted: 01/26/2023] [Indexed: 02/21/2024] Open
Abstract
Medicinal plants are a valuable source of essential medicines and herbal products for healthcare and disease therapy. Compared with chemical synthesis and extraction, the biosynthesis of natural products is a very promising alternative for the successful conservation of medicinal plants, and its rapid development will greatly facilitate the conservation and sustainable utilization of medicinal plants. Here, we summarize the advances in strategies and methods concerning the biosynthesis and production of natural products of medicinal plants. The strategies and methods mainly include genetic engineering, plant cell culture engineering, metabolic engineering, and synthetic biology based on multiple "OMICS" technologies, with paradigms for the biosynthesis of terpenoids and alkaloids. We also highlight the biosynthetic approaches and discuss progress in the production of some valuable natural products, exemplifying compounds such as vindoline (alkaloid), artemisinin and paclitaxel (terpenoids), to illustrate the power of biotechnology in medicinal plants.
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Affiliation(s)
- Miaoxian Guo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Haizhou Lv
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Hongyu Chen
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shuting Dong
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jianhong Zhang
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Wanjing Liu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Liu He
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yimian Ma
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Hua Yu
- Key Laboratory of Hangzhou City for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Shilin Chen
- Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hongmei Luo
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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Chen M, Petriti V, Mondal A, Jiang Y, Ding Y. Direct aromatic nitration by bacterial P450 enzymes. Methods Enzymol 2023; 693:307-337. [PMID: 37977734 PMCID: PMC10928822 DOI: 10.1016/bs.mie.2023.09.008] [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] [Indexed: 11/19/2023]
Abstract
Nitro aromatics have broad applications in industry, agriculture, and pharmaceutics. However, their industrial production is faced with many challenges including poor selectivity, heavy pollution and safety concerns. Nature provides multiple strategies for aromatic nitration, which opens the door for the development of green and efficient biocatalysts. Our group's efforts focused on a unique bacterial cytochrome P450 TxtE that originates from the biosynthetic pathway of phytotoxin thaxtomins, which can install a nitro group at C4 of l-Trp indole ring. TxtE is a Class I P450 and its reaction relies on a pair of redox partners ferredoxin and ferredoxin reductase for essential electron transfer. To develop TxtE as an efficient nitration biocatalyst, we created artificial self-sufficient P450 chimeras by fusing TxtE with the reductase domain of the bacterial P450BM3 (BM3R). We evaluated the catalytic performance of the chimeras with different lengths of the linker connecting TxtE and BM3R domains and identified one with a 14-amino-acid linker (TB14) to give the best activity. In addition, we demonstrated the broad substrate scope of the engineered biocatalyst by screening diverse l-Trp analogs. In this chapter, we provide a detailed procedure for the development of aromatic nitration biocatalysts, including the construction of P450 fusion chimeras, biochemical characterization, determination of catalytic parameters, and testing of enzyme-substrate scope. These protocols can be followed to engineer other P450 enzymes and illustrate the processes of biocatalytic development for the synthesis of nitro chemicals.
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Affiliation(s)
- Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Vanisa Petriti
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Amit Mondal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Yujia Jiang
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, College of Pharmacy, University of Florida, Gainesville, FL, United States.
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Salisbury LJ, Fletcher SJ, Stok JE, Churchman LR, Blanchfield JT, De Voss JJ. Characterization of the cholesterol biosynthetic pathway in Dioscorea transversa. J Biol Chem 2023:104768. [PMID: 37142228 DOI: 10.1016/j.jbc.2023.104768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Cholesterol is the precursor of bioactive plant metabolites such as steroidal saponins. An Australian plant, Dioscorea transversa, produces only two steroidal saponins: 1β-hydroxyprotoneogracillin and protoneogracillin. Here, we used D. transversa as a model in which to elucidate the biosynthetic pathway to cholesterol, a precursor to these compounds. Preliminary transcriptomes of D. transversa rhizome and leaves were constructed, annotated, and analyzed. We identified a novel sterol side chain reductase (SSR) as a key initiator of cholesterol biosynthesis in this plant. By complementation in yeast, we determine that this SSR reduces Δ24,28 double bonds required for phytosterol biogenesis, as well as Δ24,25 double bonds. The latter function is believed to initiate cholesterogenesis by reducing cycloartenol to cycloartanol. Through heterologous expression, purification and enzymatic reconstitution we also demonstrate that the D. transversa sterol demethylase (CYP51) effectively demethylates obtusifoliol, an intermediate of phytosterol biosynthesis and 4-desmethyl-24,25-dihydrolanosterol, a postulated downstream intermediate of cholesterol biosynthesis. In summary, we investigated specific steps of the cholesterol biosynthetic pathway, providing further insight into the downstream production of bioactive steroidal saponin metabolites.
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Wang H, Jiang G, Liang N, Dong T, Shan M, Yao M, Wang Y, Xiao W, Yuan Y. Systematic Engineering to Enhance 8-Hydroxygeraniol Production in Yeast. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4319-4327. [PMID: 36857414 DOI: 10.1021/acs.jafc.2c09028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
8-Hydroxygeraniol, an important component of insect sex pheromones and defensive secretions, can be used as a potential biological insect repellent in agriculture. Microbial production provides sustainable and green means to efficiently gain 8-hydroxygeraniol. The conversion of geraniol to 8-hydroxygeraniol by P450 geraniol-8-hydroxylase (G8H) was regarded as the bottleneck for 8-hydroxygeraniol production. Herein, an integrated strategy consisting of the fitness between G8H and cytochrome P450 reductase (CPR), endoplasmic reticulum (ER) engineering, and reduced nicotinamide adenine dinucleotide phosphate (NADPH) supply is implemented to enhance the production of 8-hydroxygeraniol in Saccharomyces cerevisiae. The titer of 8-hydroxygeraniol was gradually increased by 2.1-fold (up to 158.1 mg/L). Moreover, dehydrogenase ADH6 and reductase ARI1 responsible for the reduction of 8-hydroxygeraniol toward shunt products were also deleted, elevating 8-hydroxygeraniol production to 238.9 mg/L at the shake flask level. Consequently, more than 1.0 g/L 8-hydroxygeraniol in S. cerevisiae was achieved in 5.0 L fed-batch fermentation by a carbon restriction strategy, which was the highest-reported titer in microbes so far. Our work not only provides a sustainable way for de novo biosynthesis of 8-hydroxygeraniol but also sets a good reference in P450 engineering in microbes.
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Affiliation(s)
- Herong Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Guozhen Jiang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Nan Liang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Tianyu Dong
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Mengying Shan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen 518071, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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Meng S, Ji Y, Zhu L, Dhoke GV, Davari MD, Schwaneberg U. The molecular basis and enzyme engineering strategies for improvement of coupling efficiency in cytochrome P450s. Biotechnol Adv 2022; 61:108051. [DOI: 10.1016/j.biotechadv.2022.108051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 11/28/2022]
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Qiao JW, Fan YL, Wu BJ, Bai TT, Wang YH, Zhang ZF, Wang D, Liu TX. Downregulation of NADPH-cytochrome P450 reductase via RNA interference increases the susceptibility of Acyrthosiphon pisum to desiccation and insecticides. INSECT SCIENCE 2022; 29:1105-1119. [PMID: 34723412 DOI: 10.1111/1744-7917.12982] [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: 07/04/2021] [Revised: 10/14/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Nicotinamide adenine dinucleotide phosphate (NADPH)-cytochrome P450 reductase (CPR) is involved in the metabolism of endogenous and exogenous substances, and detoxification of insecticides. RNA interference (RNAi) of CPR in certain insects causes developmental defects and enhanced susceptibility to insecticides. However, the CPR of Acyrthosiphon pisum has not been characterized, and its function is still not understood. In this study, we investigated the biochemical functions of A. pisum CPR (ApCPR). ApCPR was found to be transcribed in all developmental stages and was abundant in the embryo stage, and in the gut, head, and abdominal cuticle. After optimizing the dose and silencing duration of RNAi for downregulating ApCPR, we found that ApCPR suppression resulted in a significant decrease in the production of cuticular and internal hydrocarbon contents, and of cuticular waxy coatings. Deficiency in cuticular hydrocarbons (CHCs) decreased the survival rate of A. pisum under desiccation stress and increased its susceptibility to contact insecticides. Moreover, desiccation stress induced a significant increase in ApCPR mRNA levels. We further confirmed that ApCPR participates in CHC production. These results indicate that ApCPR modulates CHC production, desiccation tolerance, and insecticide susceptibility in A. pisum, and presents a novel target for pest control.
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Affiliation(s)
- Jian-Wen Qiao
- State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yong-Liang Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Bing-Jin Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Tian-Tian Bai
- State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Ying-Hao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Zhan-Feng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Dun Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Tong-Xian Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong Province, China
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Ducharme J, Sevrioukova IF, Thibodeaux CJ, Auclair K. Structural Dynamics of Cytochrome P450 3A4 in the Presence of Substrates and Cytochrome P450 Reductase. Biochemistry 2021; 60:2259-2271. [PMID: 34196520 DOI: 10.1021/acs.biochem.1c00178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the most important drug-metabolizing enzyme in humans and has been associated with harmful drug interactions. The activity of CYP3A4 is known to be modulated by several compounds and by the electron transfer partner, cytochrome P450 reductase (CPR). The underlying mechanism of these effects, however, is poorly understood. We have used hydrogen-deuterium exchange mass spectrometry to investigate the impact of binding of CPR and of three different substrates (7-benzyloxy-4-trifluoromethyl-coumarin, testosterone, and progesterone) on the conformational dynamics of CYP3A4. Here, we report that interaction of CYP3A4 with substrates or with the oxidized or reduced forms of CPR leads to a global rigidification of the CYP3A4 structure. This was evident from the suppression of deuterium exchange in several regions of CYP3A4, including regions known to be involved in protein-protein interactions (helix C) and substrate binding and specificity (helices B' and E, and loop K/β1). Furthermore, the bimodal isotopic distributions observed for some CYP3A4-derived peptides were drastically impacted upon binding to CPR and/or substrates, suggesting the existence of stable CYP3A4 conformational populations that are perturbed by ligand/CPR binding. The results have implications for understanding the mechanisms of ligand binding, allostery, and catalysis in CYP enzymes.
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Affiliation(s)
- Julie Ducharme
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Irina F Sevrioukova
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
| | - Christopher J Thibodeaux
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8
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Abstract
Transmembrane proteins involved in metabolic redox reactions and photosynthesis catalyse a plethora of key energy-conversion processes and are thus of great interest for bioelectrocatalysis-based applications. The development of membrane protein modified electrodes has made it possible to efficiently exchange electrons between proteins and electrodes, allowing mechanistic studies and potentially applications in biofuels generation and energy conversion. Here, we summarise the most common electrode modification and their characterisation techniques for membrane proteins involved in biofuels conversion and semi-artificial photosynthesis. We discuss the challenges of applications of membrane protein modified electrodes for bioelectrocatalysis and comment on emerging methods and future directions, including recent advances in membrane protein reconstitution strategies and the development of microbial electrosynthesis and whole-cell semi-artificial photosynthesis.
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Bokel A, Rühlmann A, Hutter MC, Urlacher VB. Enzyme-Mediated Two-Step Regio- and Stereoselective Synthesis of Potential Rapid-Acting Antidepressant (2S,6S)-Hydroxynorketamine. ACS Catal 2020. [DOI: 10.1021/acscatal.9b05384] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ansgar Bokel
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Ansgar Rühlmann
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Michael C. Hutter
- Center for Bioinformatics, Saarland University, Campus E2.1, 66123 Saarbruecken, Germany
| | - Vlada B. Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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Stok JE, Giang PD, Wong SH, De Voss JJ. Exploring the substrate specificity of Cytochrome P450 cin. Arch Biochem Biophys 2019; 672:108060. [PMID: 31356780 DOI: 10.1016/j.abb.2019.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 11/25/2022]
Abstract
Cytochromes P450 are enzymes that catalyse the oxidation of a wide variety of compounds that range from small volatile compounds, such as monoterpenes to larger compounds like steroids. These enzymes can be modified to selectively oxidise substrates of interest, thereby making them attractive for applications in the biotechnology industry. In this study, we screened a small library of terpenes and terpenoid compounds against P450cin and two P450cin mutants, N242A and N242T, that have previously been shown to affect selectivity. Initial screening indicated that P450cin could catalyse the oxidation of most of the monoterpenes tested; however, sesquiterpenes were not substrates for this enzyme or the N242A mutant. Additionally, both P450cin mutants were found to be able to oxidise other bicyclic monoterpenes. For example, the oxidation of (R)- and (S)-camphor by N242T favoured the production of 5-endo-hydroxycamphor (65-77% of the total products, dependent on the enantiomer), which was similar to that previously observed for (R)-camphor with N242A (73%). Selectivity was also observed for both (R)- and (S)-limonene where N242A predominantly produced the cis-limonene 1,2-epoxide (80% of the products following (R)-limonene oxidation) as compared to P450cin (23% of the total products with (R)-limonene). Of the three enzymes screened, only P450cin was observed to catalyse the oxidation of the aromatic terpene p-cymene. All six possible hydroxylation products were generated from an in vivo expression system catalysing the oxidation of p-cymene and were assigned based on 1H NMR and GC-MS fragmentation patterns. Overall, these results have provided the foundation for pursuing new P450cin mutants that can selectively oxidise various monoterpenes for biocatalytic applications.
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Affiliation(s)
- Jeanette E Stok
- School of Chemistry and Molecular Biosciences, The University of Queensland, Australia
| | - Peter D Giang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Australia
| | - Siew Hoon Wong
- School of Chemistry and Molecular Biosciences, The University of Queensland, Australia
| | - James J De Voss
- School of Chemistry and Molecular Biosciences, The University of Queensland, Australia.
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Pathak RK, Baunthiyal M, Pandey D, Kumar A. Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities. 3 Biotech 2018; 8:454. [PMID: 30370195 PMCID: PMC6195494 DOI: 10.1007/s13205-018-1473-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
With the continuous increase in the population of developing countries and decline of natural resources, there is an urgent need to qualitatively and quantitatively augment crop productivity by using new tools and technologies for improvement of agriculturally important traits. The new scientific and technological omics-based approaches have enabled us to deal with several issues and challenges faced by modern agricultural system and provided us novel opportunities for ensuring food and nutritional security. Recent developments in sequencing techniques have made available huge amount of genomic and transcriptomic data on model and cultivated crop plants including Arabidopsis thaliana, Oryza sativa, Triticum aestivum etc. The sequencing data along with other data generated through several omics platforms have significantly influenced the disciplines of crop sciences. Gene discovery and expression profiling-based technologies are offering enormous opportunities to the scientific community which can now apply marker-assisted selection technology to assess and enhance diversity in their collected germplasm, introgress essential traits from new sources and investigate genes that control key traits of crop plants. Utilization of omics science and technologies for crop productivity, protection and management has recently been receiving a lot of attention; the majority of the efforts have been put into signifying the possible applications of various omics technologies in crop plant sciences. This article highlights the background of challenges and opportunities for augmentation of crop productivity through interventions of omics technologies in India.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Mamta Baunthiyal
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Present Address: Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
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Brummund J, Müller M, Schmitges T, Kaluzna I, Mink D, Hilterhaus L, Liese A. Process development for oxidations of hydrophobic compounds applying cytochrome P450 monooxygenases in-vitro. J Biotechnol 2016; 233:143-50. [PMID: 27396939 DOI: 10.1016/j.jbiotec.2016.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/06/2016] [Accepted: 07/06/2016] [Indexed: 11/18/2022]
Abstract
Cytochrome P450 monooxygenases are a unique family of enzymes that are able to catalyze regio- and stereospecific oxidations for a broad substrate range. However, due to limited enzyme activities and stabilities, hydrophobicity of substrates, as well as the necessity of a continuous electron and oxygen supply the implementation of P450s for industrial processes remains challenging. Aim of this study was to point out key aspects for the development of an efficient synthesis concept for cytochrome P450 catalyzed oxidations. In order to regenerate the natural cofactor NADPH, a glucose dehydrogenase was applied. The low water soluble terpene α-ionone was used as substrate for the model reaction system. The studies reveal that an addition of surfactants in combination with low volumetric amounts of co-solvent can significantly increase substrate availability and reaction rates. Furthermore, these additives facilitated a reliable sampling procedure during the process. Another key factor for the process design was the oxygen supply. Based on various investigations, a bubble-aerated stirred tank reactor in batch mode represents a promising reactor concept for P450 oxidations. Main restriction of the investigated reaction system was the low process stability of the P450 monooxygenase, characterized by maximum total turnover numbers of ∼4100molα-ionone/molP450.
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Affiliation(s)
- Jan Brummund
- Hamburg University of Technology, Institute of Technical Biocatalysis, Denickestr. 15, 21073 Hamburg, Germany
| | - Monika Müller
- DSM Chemical Technology R&D B.V., Urmonderbaan 22, P.O. Box 18, 6160 MD Geleen, The Netherlands
| | - Thomas Schmitges
- DSM Chemical Technology R&D B.V., Urmonderbaan 22, P.O. Box 18, 6160 MD Geleen, The Netherlands
| | - Iwona Kaluzna
- DSM Chemical Technology R&D B.V., Urmonderbaan 22, P.O. Box 18, 6160 MD Geleen, The Netherlands
| | - Daniel Mink
- DSM Chemical Technology R&D B.V., Urmonderbaan 22, P.O. Box 18, 6160 MD Geleen, The Netherlands
| | - Lutz Hilterhaus
- Hamburg University of Technology, Institute of Technical Biocatalysis, Denickestr. 15, 21073 Hamburg, Germany
| | - Andreas Liese
- Hamburg University of Technology, Institute of Technical Biocatalysis, Denickestr. 15, 21073 Hamburg, Germany.
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13
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Ordered chimerogenesis applied to CYP2B P450 enzymes. Biochim Biophys Acta Gen Subj 2016; 1860:1395-403. [DOI: 10.1016/j.bbagen.2016.03.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/12/2016] [Accepted: 03/20/2016] [Indexed: 12/11/2022]
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14
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Stok JE, Hall EA, Stone IS, Noble MC, Wong SH, Bell SG, De Voss JJ. In vivo and in vitro hydroxylation of cineole and camphor by cytochromes P450CYP101A1, CYP101B1 and N242A CYP176A1. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.03.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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15
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Davydov DR. Molecular organization of the microsomal oxidative system: a new connotation for an old term. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2016. [DOI: 10.1134/s1990750816010042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kern F, Khatri Y, Litzenburger M, Bernhardt R. CYP267A1 and CYP267B1 from Sorangium cellulosum So ce56 are Highly Versatile Drug Metabolizers. Drug Metab Dispos 2016; 44:495-504. [DOI: 10.1124/dmd.115.068486] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/02/2016] [Indexed: 11/22/2022] Open
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17
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Davydov DR. [Molecular organization of the microsomal oxidative system: a new connotation for an old term]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:176-87. [PMID: 25978385 DOI: 10.18097/pbmc20156102176] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The central role that cytochromes P450 play in the metabolism of drugs and other xenobiotics makes these enzymes a major subject for studies of drug disposition, adverse drug effects and drug-drug interactions. Although there has been tremendous success in delineating P450 mechanisms, the concept of the drug-metabolizing ensemble as a functionally integrated system remains undeveloped. However, eukaryotic cells typically possess a multitude of different P450 enzymes that are co-localized in the membrane of endoplasmic reticulum (ER) and interact with each other with the formation of dynamic heteromeric complexes (mixed oligomers). Appreciation of the importance of developing an integral, systems approach to the ensemble of cytochromes P450 as an integral system inspired growing interest of researchers to the molecular organization of microsomal monooxygenase, which remained in the focus of research of academician Archakov for over 40 years. Fundamental studies carried out under his guidance have an important impact on our current concepts in this area. Further exploration of the molecular organization of the system of microsomal monooxygenase as an integral multienzyme and multifunctional system will have an essential impact on our understanding of the key factors that determine the changes in human drug metabolism and other P450-related functions in development, aging, and disease, as well as under influence of drugs, food ingredients, and environmental contaminants.
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Affiliation(s)
- D R Davydov
- Institute of Biomedical Chemistry, Moscow, Russia; Department of Chemistry, Washington State University, Washington, USA
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18
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Pearsall SM, Rowley CN, Berry A. Advances in Pathway Engineering for Natural Product Biosynthesis. ChemCatChem 2015. [DOI: 10.1002/cctc.201500602] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Sarah M. Pearsall
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Christopher N. Rowley
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
| | - Alan Berry
- Astbury Centre for Structural Molecular Biology; University of Leeds; Leeds LS2 9JT UK
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Schiffer L, Anderko S, Hobler A, Hannemann F, Kagawa N, Bernhardt R. A recombinant CYP11B1 dependent Escherichia coli biocatalyst for selective cortisol production and optimization towards a preparative scale. Microb Cell Fact 2015; 14:25. [PMID: 25880059 PMCID: PMC4347555 DOI: 10.1186/s12934-015-0209-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/18/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human mitochondrial CYP11B1 catalyzes a one-step regio- and stereoselective 11β-hydroxylation of 11-deoxycortisol yielding cortisol which constitutes not only the major human stress hormone but also represents a commercially relevant therapeutic drug due to its anti-inflammatory and immunosuppressive properties. Moreover, it is an important intermediate in the industrial production of synthetic pharmaceutical glucocorticoids. CYP11B1 thus offers a great potential for biotechnological application in large-scale synthesis of cortisol. Because of its nature as external monooxygenase, CYP11B1-dependent steroid hydroxylation requires reducing equivalents which are provided from NADPH via a redox chain, consisting of adrenodoxin reductase (AdR) and adrenodoxin (Adx). RESULTS We established an Escherichia coli based whole-cell system for selective cortisol production from 11-deoxycortisol by recombinant co-expression of the demanded 3 proteins. For the subsequent optimization of the whole-cell activity 3 different approaches were pursued: Firstly, CYP11B1 expression was enhanced 3.3-fold to 257 nmol∗L(-1) by site-directed mutagenesis of position 23 from glycine to arginine, which was accompanied by a 2.6-fold increase in cortisol yield. Secondly, the electron transfer chain was engineered in a quantitative manner by introducing additional copies of the Adx cDNA in order to enhance Adx expression on transcriptional level. In the presence of 2 and 3 copies the initial linear conversion rate was greatly accelerated and the final product concentration was improved 1.4-fold. Thirdly, we developed a screening system for directed evolution of CYP11B1 towards higher hydroxylation activity. A culture down-scale to microtiter plates was performed and a robot-assisted, fluorescence-based conversion assay was applied for the selection of more efficient mutants from a random library. CONCLUSIONS Under optimized conditions a maximum productivity of 0.84 g cortisol∗L(-1)∗d(-1) was achieved, which clearly shows the potential of the developed system for application in the pharmaceutical industry.
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Affiliation(s)
- Lina Schiffer
- Department of Biochemistry, Saarland University, 66123, Saarbrücken, Germany.
| | - Simone Anderko
- Department of Biochemistry, Saarland University, 66123, Saarbrücken, Germany.
| | - Anna Hobler
- Department of Biochemistry, Saarland University, 66123, Saarbrücken, Germany.
| | - Frank Hannemann
- Department of Biochemistry, Saarland University, 66123, Saarbrücken, Germany.
| | - Norio Kagawa
- Department of Biochemistry, Saarland University, 66123, Saarbrücken, Germany.
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, 66123, Saarbrücken, Germany.
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20
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Litzenburger M, Kern F, Khatri Y, Bernhardt R. Conversions of tricyclic antidepressants and antipsychotics with selected P450s from Sorangium cellulosum So ce56. Drug Metab Dispos 2014; 43:392-9. [PMID: 25550480 DOI: 10.1124/dmd.114.061937] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Human cytochromes P450 (P450s) play a major role in the biotransformation of drugs. The generated metabolites are important for pharmaceutical, medical, and biotechnological applications and can be used for derivatization or toxicological studies. The availability of human drug metabolites is restricted and alternative ways of production are requested. For this, microbial P450s turned out to be a useful tool for the conversion of drugs and related derivatives. Here, we used 10 P450s from the myxobacterium Sorangium cellulosum So ce56, which have been cloned, expressed, and purified. The P450s were investigated concerning the conversion of the antidepressant drugs amitriptyline, clomipramine, imipramine, and promethazine; the antipsychotic drugs carbamazepine, chlorpromazine, and thioridazine, as well as their precursors, iminodibenzyl and phenothiazine. Amitriptyline, chlorpromazine, clomipramine, imipramine, and thioridazine are efficiently converted during the in vitro reaction and were chosen to upscale the production by an Escherichia coli-based whole-cell bioconversion system. Two different approaches, a whole-cell system using M9CA medium and a system using resting cells in buffer, were used for the production of sufficient amounts of metabolites for NMR analysis. Amitriptyline, clomipramine, and imipramine are converted to the corresponding 10-hydroxylated products, whereas the conversion of chlorpromazine and thioridazine leads to a sulfoxidation in position 5. It is shown for the first time that myxobacterial P450s are efficient to produce known human drug metabolites in a milligram scale, revealing their ability to synthesize pharmaceutically important compounds.
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Affiliation(s)
- Martin Litzenburger
- Institut für Biochemie, Universität des Saarlandes, Saarbruecken, Germany (M.L., F.K., Y.K., R.B.)
| | - Fredy Kern
- Institut für Biochemie, Universität des Saarlandes, Saarbruecken, Germany (M.L., F.K., Y.K., R.B.)
| | - Yogan Khatri
- Institut für Biochemie, Universität des Saarlandes, Saarbruecken, Germany (M.L., F.K., Y.K., R.B.)
| | - Rita Bernhardt
- Institut für Biochemie, Universität des Saarlandes, Saarbruecken, Germany (M.L., F.K., Y.K., R.B.)
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21
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Lee JH, Nam DH, Lee SH, Park JH, Park SJ, Lee SH, Park CB, Jeong KJ. New platform for cytochrome p450 reaction combining in situ immobilization on biopolymer. Bioconjug Chem 2014; 25:2101-4. [PMID: 25322062 DOI: 10.1021/bc500404j] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We describe an efficienct chemical conversion platform with in situ immobilization of P450-BM3 on poly(3-hydroxybutyrate) granules. Through fusion with phasin, P450-BM3 is easily immobilized on poly(3-hydroxybutyrate) granules in Escherichia coli. In our work, the immobilized P450 exhibited higher stability and catalytic activity compared to free P450 against changes of pH, temperature, and concentrations of urea and ions. Through quick recovery of immobilized enzyme, the P450-P(3HB) complex successfully catalyzed an O-dealkylation reaction several times with maintained activity. Using the robust P450-P(3HB) complex, we performed a P450-catalyzed reaction on a preparative reactor scale (100 mL) and high-level production (12.3 μM) of 7-hydroxycoumarine from 7-ethoxycoumarin could be achieved.
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Affiliation(s)
- Jae Hyung Lee
- Department of Chemical and Biomolecular Engineering, and ‡Department of Materials Science and Engineering, Korea Advanced Institute of Science and Technology , 335 Science Road, Daejeon 305-701, Republic of Korea
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22
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Sharma A, Rao VK, Kamboj DV, Upadhyay S, Shaik M, Shrivastava AR, Jain R. Sensitive detection of staphylococcal enterotoxin B (SEB) using quantum dots by various methods with special emphasis on an electrochemical immunoassay approach. RSC Adv 2014. [DOI: 10.1039/c4ra02563f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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Bernhardt R, Urlacher VB. Cytochromes P450 as promising catalysts for biotechnological application: chances and limitations. Appl Microbiol Biotechnol 2014; 98:6185-203. [PMID: 24848420 DOI: 10.1007/s00253-014-5767-7] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 01/08/2023]
Abstract
Cytochromes P450 (CYPs) belong to the superfamily of heme b containing monooxygenases with currently more than 21,000 members. These enzymes accept a vast range of organic molecules and catalyze diverse reactions. These extraordinary capabilities of CYP systems that are unmet by other enzymes make them attractive for biotechnology. However, the complexity of these systems due to the need of electron transfer from nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) via redox partner proteins for the initial hydroxylation step limits a broader technical implementation of CYP enzymes. There have been several reviews during the past years tackling the potential CYPs for synthetic application. The aim of this review is to give a critical overview about possibilities and chances for application of these interesting catalysts as well as to discuss drawbacks and problems related to their use. Solutions to overcome these limitations will be demonstrated, and several selected examples of successful CYP applications under industrial conditions will be reviewed.
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Affiliation(s)
- Rita Bernhardt
- Institute of Biochemistry, Saarland University, 66123, Saarbrücken, Germany,
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24
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Montemiglio LC, Macone A, Ardiccioni C, Avella G, Vallone B, Savino C. Redirecting P450 EryK Specificity by Rational Site-Directed Mutagenesis. Biochemistry 2013; 52:3678-87. [DOI: 10.1021/bi400223j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Linda Celeste Montemiglio
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
| | - Alberto Macone
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
| | - Chiara Ardiccioni
- Departments of Physiology & Cellular Biophysics, Columbia University College of Physicians & Surgeons, Russ Berrie Pavilion, 1150 St. Nicholas Avenue, New York, New York 10032, United States
| | - Giovanna Avella
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
| | - Beatrice Vallone
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
| | - Carmelinda Savino
- Istituto Pasteur-Fondazione
Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del
CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, Piazzale A. Moro
5, 00185 Rome, Italy
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25
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Engineering and application of P450 monooxygenases in pharmaceutical and metabolite synthesis. Curr Opin Chem Biol 2013; 17:271-5. [DOI: 10.1016/j.cbpa.2013.01.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/29/2013] [Accepted: 01/31/2013] [Indexed: 11/21/2022]
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26
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Dong MS, Lee SB, Kim HJ. Co-expression of human cytochrome b5 increases expression of cytochrome P450 3A4 in Escherichia coli by stabilizing mRNA. Protein Expr Purif 2013; 89:44-50. [PMID: 23459292 DOI: 10.1016/j.pep.2013.02.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 01/22/2013] [Accepted: 02/06/2013] [Indexed: 01/26/2023]
Abstract
CYP3A4 is the most abundant cytochrome P450 in the human liver. The expression level of CYP3A4 when coexpressed with cytochrome b(5) (cyt b(5)) in Escherichia coli was 20-60% higher than that when it was expressed alone over an extended period (48-72 h). This time-dependent elevation in coexpression with cyt b(5) was a result of an increase in CYP3A4 mRNA half-life; no significant change in CYP3A4 degradation was seen in the bacterial protease fraction. These results suggest that the higher CYP3A4 levels observed upon coexpression with cyt b(5) primarily resulted from CYP3A4 mRNA stabilization by cyt b(5).
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Affiliation(s)
- Mi-Sook Dong
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Republic of Korea.
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27
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Ichinose H. Cytochrome P450 of wood-rotting basidiomycetes and biotechnological applications. Biotechnol Appl Biochem 2013; 60:71-81. [PMID: 23586994 DOI: 10.1002/bab.1061] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 11/09/2012] [Indexed: 12/23/2022]
Abstract
Wood-rotting basidiomycetes possess superior metabolic functions to degrade woody biomass, and these activities are indispensable for the carbon cycle of the biosphere. As well as basic studies of the biochemistry of basidiomycetes, many researchers have been focusing on utilizing basidiomycetes and/or their enzymes in the biotechnology sector; therefore, the unique activities of their extracellular and intracellular enzymes have been widely demonstrated. A rich history of applied study has established that basidiomycetes are capable of metabolizing a series of endogeneous and exogeneous compounds using cytochrome P450s (P450s). Recently, whole genome sequence analyses have revealed large-scale divergences in basidiomycetous P450s. The tremendous variation in P450s implies that basidiomycetes have vigorously diversified monooxygenase functions to acquire metabolic adaptations such as lignin degradation, secondary metabolite production, and xenobiotics detoxification. However, fungal P450s discovered from genome projects are often categorized into novel families and subfamilies, making it difficult to predict catalytic functions by sequence comparison. Experimental screening therefore remains essential to elucidate the catalytic potential of individual P450s, even in this postgenomic era. This paper archives the known metabolic capabilities of basidiomycetes, focusing on their P450s, outlines the molecular diversity of basidiomycetous P450s, and introduces new functions revealed by functionomic studies using a recently developed, rapid, functional screening system.
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28
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29
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Prabhulkar S, Tian H, Wang X, Zhu JJ, Li CZ. Engineered proteins: redox properties and their applications. Antioxid Redox Signal 2012; 17:1796-822. [PMID: 22435347 PMCID: PMC3474195 DOI: 10.1089/ars.2011.4001] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 03/20/2012] [Accepted: 03/21/2012] [Indexed: 10/28/2022]
Abstract
Oxidoreductases and metalloproteins, representing more than one third of all known proteins, serve as significant catalysts for numerous biological processes that involve electron transfers such as photosynthesis, respiration, metabolism, and molecular signaling. The functional properties of the oxidoreductases/metalloproteins are determined by the nature of their redox centers. Protein engineering is a powerful approach that is used to incorporate biological and abiological redox cofactors as well as novel enzymes and redox proteins with predictable structures and desirable functions for important biological and chemical applications. The methods of protein engineering, mainly rational design, directed evolution, protein surface modifications, and domain shuffling, have allowed the creation and study of a number of redox proteins. This review presents a selection of engineered redox proteins achieved through these methods, resulting in a manipulation in redox potentials, an increase in electron-transfer efficiency, and an expansion of native proteins by de novo design. Such engineered/modified redox proteins with desired properties have led to a broad spectrum of practical applications, ranging from biosensors, biofuel cells, to pharmaceuticals and hybrid catalysis. Glucose biosensors are one of the most successful products in enzyme electrochemistry, with reconstituted glucose oxidase achieving effective electrical communication with the sensor electrode; direct electron-transfer-type biofuel cells are developed to avoid thermodynamic loss and mediator leakage; and fusion proteins of P450s and redox partners make the biocatalytic generation of drug metabolites possible. In summary, this review includes the properties and applications of the engineered redox proteins as well as their significance and great potential in the exploration of bioelectrochemical sensing devices.
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Affiliation(s)
- Shradha Prabhulkar
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
| | - Hui Tian
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Xiaotang Wang
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida
| | - Jun-Jie Zhu
- Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Chen-Zhong Li
- Nanobioengineering/Bioelectronics Laboratory, Department of Biomedical Engineering, Florida International University, Miami, Florida
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30
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Schumacher SD, Jose J. Expression of active human P450 3A4 on the cell surface of Escherichia coli by Autodisplay. J Biotechnol 2012; 161:113-20. [DOI: 10.1016/j.jbiotec.2012.01.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 01/17/2012] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
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Engineering of Human CYP3A Enzymes by Combination of Activating Polymorphic Variants. Appl Biochem Biotechnol 2012; 168:785-96. [DOI: 10.1007/s12010-012-9819-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 08/01/2012] [Indexed: 01/20/2023]
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Abstract
Natural products and their derivatives play an important role in modern healthcare as frontline treatments for many diseases and as inspiration for chemically synthesized therapeutics. With advances in sequencing and recombinant DNA technology, many of the biosynthetic pathways responsible for the production of these chemically complex yet valuable compounds have been elucidated. With an ever-expanding toolkit of biosynthetic components, metabolic engineering is an increasingly powerful method to improve natural product titers and generate novel compounds. Heterologous production platforms have enabled access to pathways from difficult to culture strains, systems biology and metabolic modeling tools have resulted in increasing predictive and analytic capabilities, advances in expression systems and regulation have enabled the fine-tuning of pathways for increased efficiency, and characterization of individual pathway components has facilitated the construction of hybrid pathways for the production of new compounds. These advances in the many aspects of metabolic engineering not only have yielded fascinating scientific discoveries but also make it an increasingly viable approach for the optimization of natural product biosynthesis.
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Affiliation(s)
- Lauren B Pickens
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
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Whole-cell hydroxylation of n-octane by Escherichia coli strains expressing the CYP153A6 operon. Appl Microbiol Biotechnol 2012; 96:1507-16. [PMID: 22410745 DOI: 10.1007/s00253-012-3984-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/11/2012] [Accepted: 02/17/2012] [Indexed: 10/28/2022]
Abstract
CYP153A6 is a well-studied terminal alkane hydroxylase which has previously been expressed in Pseudomonas putida and Escherichia coli by using the pCom8 plasmid. In this study, CYP153A6 was successfully expressed in E. coli BL21(DE3) by cloning the complete operon from Mycobacterium sp. HXN-1500, also encoding the ferredoxin reductase and ferredoxin, into pET28b(+). LB medium with IPTG as well as auto-induction medium was used to express the proteins under the T7 promoter. A maximum concentration of 1.85 μM of active CYP153A6 was obtained when using auto-induction medium, while with IPTG induction of LB cultures, the P450 concentration peaked at 0.6-0.8 μM. Since more biomass was produced in auto-induction medium, the specific P450 content was often almost the same, 0.5-1.0 μmol P450 g (DCW)⁻¹, for both methods. Analytical scale whole-cell biotransformations of n-octane were conducted with resting cells, and it was found that high P450 content in biomass did not necessarily result in high octanol production. Whole cells from LB cultures induced with IPTG gave higher specific and volumetric octanol formation rates than biomass from auto-induction medium. A maximum of 8.7 g octanol L (BRM)⁻¹ was obtained within 24 h (0.34 g L (BRM)⁻¹ h⁻¹) with IPTG-induced cells containing only 0.20 μmol P450 g (DCW)⁻¹, when glucose (22 g L (BRM)⁻¹) was added for cofactor regeneration.
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34
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Ichinose H. Molecular and Functional Diversity of Fungal Cytochrome P450s. Biol Pharm Bull 2012; 35:833-7. [DOI: 10.1248/bpb.35.833] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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35
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Urlacher VB, Girhard M. Cytochrome P450 monooxygenases: an update on perspectives for synthetic application. Trends Biotechnol 2012; 30:26-36. [DOI: 10.1016/j.tibtech.2011.06.012] [Citation(s) in RCA: 342] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 06/10/2011] [Accepted: 06/16/2011] [Indexed: 01/14/2023]
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Kumar S, Jin M, Weemhoff JL. Cytochrome P450-Mediated Phytoremediation using Transgenic Plants: A Need for Engineered Cytochrome P450 Enzymes. ACTA ACUST UNITED AC 2012; 3. [PMID: 25298920 PMCID: PMC4186655 DOI: 10.4172/2157-7463.1000127] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
There is an increasing demand for versatile and ubiquitous Cytochrome P450 (CYP) biocatalysts for biotechnology, medicine, and bioremediation. In the last decade there has been an increase in realization of the power of CYP biocatalysts for detoxification of soil and water contaminants using transgenic plants. However, the major limitations of mammalian CYP enzymes are that they require CYP reductase (CPR) for their activity, and they show relatively low activity, stability, and expression. On the other hand, bacterial CYP enzymes show limited substrate diversity and usually do not metabolize herbicides and industrial contaminants. Therefore, there has been a considerable interest for biotechnological industries and the scientific community to design CYP enzymes to improve their catalytic efficiency, stability, expression, substrate diversity, and the suitability of P450-CPR fusion enzymes. Engineered CYP enzymes have potential for transgenic plants-mediated phytoremediation of herbicides and environmental contaminants. In this review we discuss: 1) the role of CYP enzymes in phytoremediation using transgenic plants, 2) problems associated with wild-type CYP enzymes in phytoremediation, and 3) examples of engineered CYP enzymes and their potential role in transgenic plant-mediated phytoremediation.
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Affiliation(s)
| | - Mengyao Jin
- School of Pharmacy, University of Missouri, USA
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37
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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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38
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Tran NH, Huynh N, Bui T, Nguyen Y, Huynh P, Cooper ME, Cheruzel LE. Light-initiated hydroxylation of lauric acid using hybrid P450 BM3 enzymes. Chem Commun (Camb) 2011; 47:11936-8. [PMID: 21975564 DOI: 10.1039/c1cc15124j] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed hybrid P450 BM3 enzymes consisting of a Ru(II)-diimine photosensitizer covalently attached to non-native single cysteine residues of P450 BM3 heme domain mutants. These enzymes are capable, upon light activation, of selectively hydroxylating lauric acid with 40 times higher total turnover numbers compared to the peroxide shunt.
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Affiliation(s)
- Ngoc-Han Tran
- San José State University, Department of Chemistry, One Washington Square, San José, CA 95192-0101, USA
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Molecular identification and functional characterization of cytochrome P450 monooxygenases from the brown-rot basidiomycete Postia placenta. Arch Microbiol 2011; 194:243-53. [DOI: 10.1007/s00203-011-0753-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/19/2011] [Accepted: 09/02/2011] [Indexed: 12/21/2022]
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Traylor MJ, Ryan JD, Arnon ES, Dordick JS, Clark DS. Rapid and quantitative measurement of metabolic stability without chromatography or mass spectrometry. J Am Chem Soc 2011; 133:14476-9. [PMID: 21766815 DOI: 10.1021/ja203172c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic stability measurements are a critical component of preclinical drug development. Available measurement strategies rely on chromatography and mass spectrometry, which are expensive and labor intensive. We have developed a general method to determine the metabolic stability of virtually any compound by quantifying cofactors in the mechanism of cytochrome P450 enzymes using fluorescence intensity measurements. While many previous studies have shown that simple measurements of cofactor depletion do not correlate with substrate conversion (i.e., metabolic stability) in P450 systems, the present work employs a reaction engineering approach to simplify the overall rate equation, thus allowing the accurate and quantitative determination of substrate depletion from simultaneous measurements of NADPH and oxygen depletion. This method combines the accuracy and generality of chromatography with the ease, throughput, and real-time capabilities of fluorescence.
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Affiliation(s)
- Matthew J Traylor
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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42
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Krishnan S, Schenkman JB, Rusling JF. Bioelectronic delivery of electrons to cytochrome P450 enzymes. J Phys Chem B 2011; 115:8371-80. [PMID: 21591685 DOI: 10.1021/jp201235m] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450s (cyt P450s) are the major oxidative enzymes in human oxidative metabolism of drugs and xenobiotic chemicals. In nature, the iron heme cyt P450s utilize oxygen and electrons delivered from NADPH by a reductase enzyme to oxidize substrates stereo- and regioselectively. Significant research has been directed toward achieving these events electrochemically. This Feature Article discusses the direct electrochemistry of cyt P450s in thin films and the utilization of such films for electrochemically driven biocatalysis. Maintaining and confirming structural integrity and catalytic activity of cyt P450s in films is an essential feature of these efforts. We highlight here our efforts to elucidate the influence of iron heme spin state and secondary structure of human cyt P450s on voltammetric and biocatalytic properties, using methodologies to quantitatively describe the dynamics of these processes in thin films. We also describe the first cyt P450/reductase films that accurately mimic the natural biocatalytic pathway and show how they can be used with voltammetry to elucidate key mechanistic features. Such bioelectronic cyt P450 systems have high value for future drug development, toxicity screening, fundamental investigations, and chemical synthesis systems.
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Affiliation(s)
- Sadagopan Krishnan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
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Strohmeier GA, Pichler H, May O, Gruber-Khadjawi M. Application of Designed Enzymes in Organic Synthesis. Chem Rev 2011; 111:4141-64. [DOI: 10.1021/cr100386u] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Gernot A. Strohmeier
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Oliver May
- DSM—Innovative Synthesis BV, Geleen, P.O. Box 18, 6160 MD Geleen, The Netherlands
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Larsen AT, May EM, Auclair K. Predictable Stereoselective and Chemoselective Hydroxylations and Epoxidations with P450 3A4. J Am Chem Soc 2011; 133:7853-8. [PMID: 21528858 DOI: 10.1021/ja200551y] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Aaron T. Larsen
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
| | - Erin M. May
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
| | - Karine Auclair
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec, Canada H3A 2K6
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Insight into functional diversity of cytochrome P450 in the white-rot basidiomycete Phanerochaete chrysosporium: Involvement of versatile monooxygenase. Biochem Biophys Res Commun 2011; 407:118-23. [DOI: 10.1016/j.bbrc.2011.02.121] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 02/24/2011] [Indexed: 01/25/2023]
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Biotechnological synthesis of drug metabolites using human cytochrome P450 isozymes heterologously expressed in fission yeast. Bioanalysis 2011; 1:821-30. [PMID: 21083140 DOI: 10.4155/bio.09.53] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cytochrome P450 mono-oxygenases (CYPs) are the major enzymes involved in the metabolism of drugs and poisons in humans. The variation of their activity - due to genetic polymorphisms or enzyme inhibition/induction - potentially increases the risk of side effects or toxicity. Studies on CYP-dependent metabolism are important in drug-development or toxicity studies. Reference standards of drug metabolites required for such studies, especially in the context of metabolites in safety testing (MIST), are often not commercially available and their classical chemical synthesis can be cumbersome. Recently, a biotechnological approach using human CYP isozymes heterologously expressed in fission yeast was developed for the synthesis of drug metabolites. Among other aspects, this approach has the distinct advantages that the reactions run under mild conditions and that only the final product must be isolated and characterized. This review overviews the first practical applications of this new approach and discusses the selection of substrates, metabolites and fission yeast strains as well as important aspects of incubation, product isolation and clean-up.
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Jung ST, Lauchli R, Arnold FH. Cytochrome P450: taming a wild type enzyme. Curr Opin Biotechnol 2011; 22:809-17. [PMID: 21411308 DOI: 10.1016/j.copbio.2011.02.008] [Citation(s) in RCA: 226] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2011] [Accepted: 02/11/2011] [Indexed: 11/18/2022]
Abstract
Protein engineering of cytochrome P450 monooxygenases (P450s) has been very successful in generating valuable non-natural activities and properties, allowing these powerful catalysts to be used for the synthesis of drug metabolites and in biosynthetic pathways for the production of precursors of artemisinin and paclitaxel. Collected experience indicates that the P450s are highly 'evolvable' - they are particularly robust to mutation in their active sites and readily accept new substrates and exhibit new selectivities. Their ability to adapt to new challenges upon mutation may reflect the nonpolar nature of their active sites as well as their high degree of conformational variability.
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Affiliation(s)
- Sang Taek Jung
- Divison of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
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Davydov DR. Microsomal monooxygenase as a multienzyme system: the role of P450-P450 interactions. Expert Opin Drug Metab Toxicol 2011; 7:543-58. [PMID: 21395496 DOI: 10.1517/17425255.2011.562194] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION There is increasing evidence of physical interactions (association) among cytochromes P450 in the membranes of the endoplasmic reticulum. Functional consequences of these interactions are often underestimated. AREAS COVERED This article provides a comprehensive overview of available experimental material regarding P450-P450 interactions. Special emphasis is given to the interactions between different P450 species and to the functional consequences of homo- and heterooligomerization. EXPERT OPINION Recent advances provide conclusive evidence for a substantial degree of P450 oligomerization in membranes. Interactions between different P450 species resulting in the formation of mixed oligomers with altered activity and substrate specificity have been demonstrated clearly. There are important indications that oligomerization impedes electron flow to a fraction of the P450 population, which renders some P450 species nonfunctional. Functional consequences of P450-P450 interactions make the integrated properties of the microsomal monooxygenase remarkably different from a simple summation of the properties of the individual P450 species. This complexity compromises the predictive power of the current in vitro models of drug metabolism and warrants an urgent need for development of new model systems that consider the interactions of multiple P450 species.
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Affiliation(s)
- Dmitri R Davydov
- University of California - San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
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Construction and application of a functional library of cytochrome P450 monooxygenases from the filamentous fungus Aspergillus oryzae. Appl Environ Microbiol 2011; 77:3147-50. [PMID: 21378053 DOI: 10.1128/aem.02491-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A functional library of cytochrome P450 monooxygenases from Aspergillus oryzae (AoCYPs) was constructed in which 121 isoforms were coexpressed with yeast NADPH-cytochrome P450 oxidoreductase in Saccharomyces cerevisiae. Using this functional library, novel catalytic functions of AoCYPs, such as catalytic potentials of CYP57B3 against genistein, were elucidated for the first time. Comprehensive functional screening promises rapid characterization of catalytic potentials and utility of AoCYPs.
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