1
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Zhang Z, Huang L, Zhang ZJ, Xu JH, Yu HL. Rational Design of Taxadiene Hydroxylase by Ancestral Enzyme Construction and the Elucidation of Key Amino Acids. Biochemistry 2023; 62:3214-3221. [PMID: 37902563 DOI: 10.1021/acs.biochem.3c00411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2023]
Abstract
Cytochrome P450 monooxygenases (CYP450s) play an important role in the biosynthesis of natural products by activating inert C-H bonds and inserting hydroxyl groups. However, the activities of most plant-derived CYP450s are extremely low, limiting the heterologous biosynthesis of natural products. Traditional enzyme engineering methods, either rational or screening-based, are not suitable for CYP450s because of the lack of crystal structures and high-throughput screening methods for this class of enzymes. CYP725A4 is the first hydroxylase involved in the biosynthesis pathway of Taxol. Its low activity, promiscuity, and multispecificity make it a bottleneck in Taxol biosynthesis. Here, we identified key amino acids that affect the in vivo activity of CYP725A4 by constructing the ancestral enzymes of CYP725A4. We obtained positive mutants that showed an improved yield of hydroxylated products based on the key amino acids identified, providing guidance for the modification of other CYP450s involved in the biosynthesis of natural products.
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Affiliation(s)
- Zihan Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Longhao Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Zhi-Jun Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, East China University of Science and Technology, Shanghai 200237, China
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2
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Lu J. Genome-Wide Comparative Profiles of Triterpenoid Biosynthesis Genes in Ginseng and Pseudo Ginseng Medicinal Plants. Life (Basel) 2023; 13:2227. [PMID: 38004367 PMCID: PMC10672587 DOI: 10.3390/life13112227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/05/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Saponin-rich medicinal plants, particularly ginseng and Pseudo ginseng, are valuable in traditional medical practice due to the presence of different saponins. These plants benefit from natural saponins/triterpenoids drugs, such as Ginsenosides, Gypenosides, Platycodins, and Lancemasides. Ginsenosides are highly required for research and functional materials preparation in industrial practices, and some compounds, like Compound-K, have been taken to human trials for various therapeutic applications. To elucidate the genes/transcripts profiles responsible for secondary metabolites and ginsenoside biosynthesis in Ginseng and Pseudo ginseng plant genomes, a comparative analysis was conducted in this study. Nine plant genomes with a 99% BUSCO completeness score were used, resulting in 49 KEGG secondary metabolite pathways, 571 cytochromes genes with 42 families, and 3529 carbohydrate genes with 103 superfamilies. The comparative analysis revealed 24 genes/transcripts belonging to the CYP716 family, which is involved in the ginsenoside biosynthesis pathway. Additionally, it found that various ginsenosides demonstrated strong binding affinity with twelve targets, with ginsenoside Rg3, Rg2, Rh1, Rh5, F3, Rh9, Panaxadione, Protopanaxatriol, Floral ginsenoside C, and Floral ginsenoside E exhibiting the highest binding affinities with the tested enzymes. Since these groups of enzymes are not yet fully characterized for Pseudo ginseng plants in the interconversion of triterpenoids, this comparative bioinformatics analysis could aid experimentalists in selecting and conducting characterization with practical knowledge.
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Affiliation(s)
- Jing Lu
- Division of General Education, Seokyeong University, Seoul 02173, Republic of Korea
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3
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Lappe A, Luelf UJ, Keilhammer M, Bokel A, Urlacher VB. Bacterial cytochrome P450 enzymes: Semi-rational design and screening of mutant libraries in recombinant Escherichia coli cells. Methods Enzymol 2023; 693:133-170. [PMID: 37977729 DOI: 10.1016/bs.mie.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Bacterial cytochromes P450 (P450s) have been recognized as attractive targets for biocatalysis and protein engineering. They are soluble cytosolic enzymes that demonstrate higher stability and activity than their membrane-associated eukaryotic counterparts. Many bacterial P450s possess broad substrate spectra and can be produced in well-known expression hosts like Escherichia coli at high levels, which enables quick and convenient mutant libraries construction. However, the majority of bacterial P450s interacts with two auxiliary redox partner proteins, which significantly increase screening efforts. We have established recombinant E. coli cells for screening of P450 variants that rely on two separate redox partners. In this chapter, a case study on construction of a selective P450 to synthesize a precursor of several chemotherapeutics, (-)-podophyllotoxin, is described. The procedure includes co-expression of P450 and redox partner genes in E. coli with subsequent whole-cell conversion of the substrate (-)-deoxypodophyllotoxin in 96-deep-well plates. By omitting the chromatographic separation while measuring mass-to-charge ratios specific for the substrate and product via MS in so-called multiple injections in a single experimental run (MISER) LC/MS, the analysis time could be drastically reduced to roughly 1 min per sample. Screening results were verified by using isolated P450 variants and purified redox partners.
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Affiliation(s)
- Alessa Lappe
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - U Joost Luelf
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mirco Keilhammer
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ansgar Bokel
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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4
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Jóźwik IK, Bombino E, Abdulmughni A, Hartz P, Rozeboom HJ, Wijma HJ, Kappl R, Janssen DB, Bernhardt R, Thunnissen AMWH. Regio- and stereoselective steroid hydroxylation by CYP109A2 from Bacillus megaterium explored by X-ray crystallography and computational modeling. FEBS J 2023; 290:5016-5035. [PMID: 37453052 DOI: 10.1111/febs.16906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/31/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
The P450 monooxygenase CYP109A2 from Bacillus megaterium DSM319 was previously found to convert vitamin D3 (VD3) to 25-hydroxyvitamin D3. Here, we show that this enzyme is also able to convert testosterone in a highly regio- and stereoselective manner to 16β-hydroxytestosterone. To reveal the structural determinants governing the regio- and stereoselective steroid hydroxylation reactions catalyzed by CYP109A2, two crystal structures of CYP109A2 were solved in similar closed conformations, one revealing a bound testosterone in the active site pocket, albeit at a nonproductive site away from the heme-iron. To examine whether the closed crystal structures nevertheless correspond to a reactive conformation of CYP109A2, docking and molecular dynamics (MD) simulations were performed with testosterone and vitamin D3 (VD3) present in the active site. These MD simulations were analyzed for catalytically productive conformations, the relative occurrences of which were in agreement with the experimentally determined stereoselectivities if the predicted stability of each carbon-hydrogen bond was taken into account. Overall, the first-time determination and analysis of the catalytically relevant 3D conformation of CYP109A2 will allow for future small molecule ligand screening in silico, as well as enabling site-directed mutagenesis toward improved enzymatic properties of this enzyme.
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Affiliation(s)
- Ilona K Jóźwik
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Elvira Bombino
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Ammar Abdulmughni
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Philip Hartz
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Henriette J Rozeboom
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Hein J Wijma
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Reinhard Kappl
- Department of Biophysics, CIPMM, School of Medicine, Saarland University, Saarbrücken, Germany
| | - Dick B Janssen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Andy-Mark W H Thunnissen
- Biotransformation and Biocatalysis, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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5
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Hu B, Zhao X, Wang E, Zhou J, Li J, Chen J, Du G. Efficient heterologous expression of cytochrome P450 enzymes in microorganisms for the biosynthesis of natural products. Crit Rev Biotechnol 2023; 43:227-241. [PMID: 35129020 DOI: 10.1080/07388551.2022.2029344] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Natural products, a chemically and structurally diverse class of molecules, possess a wide spectrum of biological activities, have been used therapeutically for millennia, and have provided many lead compounds for the development of synthetic drugs. Cytochrome P450 enzymes (P450s, CYP) are widespread in nature and are involved in the biosynthesis of many natural products. P450s are heme-containing enzymes that use molecular oxygen and the hydride donor NAD(P)H (coupled via enzymic redox partners) to catalyze the insertion of oxygen into C-H bonds in a regio- and stereo-selective manner, effecting hydroxylation and several other reactions. With the rapid development of systems biology, numerous novel P450s have been identified for the biosynthesis of natural products, but there are still several challenges to the efficient heterologous expression of active P450s. This review covers recent developments in P450 research and development, including the properties and functions of P450s, discovery and mining of novel P450s, modification and screening of P450 mutants, improved heterologous expression of P450s in microbial hosts, efficient whole-cell transformation with P450s, and current applications of P450s for the biosynthesis of natural products. This resource provides a solid foundation for the application of highly active and stable P450s in microbial cell factories to biosynthesize natural products.
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Affiliation(s)
- Baodong Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China
| | - Xinrui Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China
| | - Endao Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianghua Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Science Center for Future Foods, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
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6
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Whole genome sequence characterization of Aspergillus terreus ATCC 20541 and genome comparison of the fungi A. terreus. Sci Rep 2023; 13:194. [PMID: 36604572 PMCID: PMC9814666 DOI: 10.1038/s41598-022-27311-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/29/2022] [Indexed: 01/06/2023] Open
Abstract
Aspergillus terreus is well-known for lovastatin and itaconic acid production with biomedical and commercial importance. The mechanisms of metabolite formation have been extensively studied to improve their yield through genetic engineering. However, the combined repertoire of carbohydrate-active enzymes (CAZymes), cytochrome P450s (CYP) enzymes, and secondary metabolites (SMs) in the different A. terreus strains has not been well studied yet, especially with respect to the presence of biosynthetic gene clusters (BGCs). Here we present a 30 Mb whole genome sequence of A. terreus ATCC 20541 in which we predicted 10,410 protein-coding genes. We compared the CAZymes, CYPs enzyme, and SMs across eleven A. terreus strains, and the results indicate that all strains have rich pectin degradation enzyme and CYP52 families. The lovastatin BGC of lovI was linked with lovF in A. terreus ATCC 20541, and the phenomenon was not found in the other strains. A. terreus ATCC 20541 lacked a non-ribosomal peptide synthetase (AnaPS) participating in acetylaszonalenin production, which was a conserved protein in the ten other strains. Our results present a comprehensive analysis of CAZymes, CYPs enzyme, and SM diversities in A. terreus strains and will facilitate further research in the function of BGCs associated with valuable SMs.
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7
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Wang Y, Malaco Morotti AL, Xiao Y, Wang Z, Wu S, Chen J, Tatsis EC. Decoding the Cytochrome P450 Catalytic Activity in Divergence of Benzophenone and Xanthone Biosynthetic Pathways. ACS Catal 2022. [DOI: 10.1021/acscatal.2c03405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ya Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ana Luisa Malaco Morotti
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
| | - Yiren Xiao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Wu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun 666303, China
| | - Evangelos C. Tatsis
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy
of Sciences, Shanghai 200032, China
- CEPAMS - CAS-JIC Centre of Excellence for Plant and Microbial Sciences, Shanghai 20032, China
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8
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P450 gene duplication and divergence led to the evolution of dual novel functions and insecticide cross-resistance in the brown planthopper Nilaparvata lugens. PLoS Genet 2022; 18:e1010279. [PMID: 35727851 PMCID: PMC9249207 DOI: 10.1371/journal.pgen.1010279] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/01/2022] [Accepted: 06/01/2022] [Indexed: 11/19/2022] Open
Abstract
The sustainable control of many highly damaging insect crop pests and disease vectors is threatened by the evolution of insecticide resistance. As a consequence, strategies have been developed that aim to prevent or delay resistance development by rotating or mixing insecticides with different modes of action (MoA). However, these approaches can be compromised by the emergence of mechanisms that confer cross-resistance to insecticides with different MoA. Despite the applied importance of cross-resistance, its evolutionary underpinnings remain poorly understood. Here we reveal how a single gene evolved the capacity to detoxify two structurally unrelated insecticides with different MoA. Using transgenic approaches we demonstrate that a specific variant of the cytochrome P450 CYP6ER1, previously shown to confer resistance to the neonicotinoid imidacloprid in the brown planthopper, N. lugens, also confers cross-resistance to the phenylpyrazole ethiprole. CYP6ER1 is duplicated in resistant strains, and we show that while the acquisition of mutations in two encoded substrate recognition sites (SRS) of one of the parologs led to resistance to imidacloprid, a different set of mutations, outside of known SRS, are primarily responsible for resistance to ethiprole. Epistatic interactions between these mutations and their genetic background suggest that the evolution of dual resistance from the same gene copy involved functional trade-offs in respect to CYP6ER1 catalytic activity for ethiprole versus imidacloprid. Surprisingly, the mutations leading to ethiprole and imidacloprid resistance do not confer the ability to detoxify the insecticide fipronil, another phenylpyrazole with close structural similarity to ethiprole. Taken together, these findings reveal how gene duplication and divergence can lead to the evolution of multiple novel functions from a single gene. From an applied perspective they also demonstrate how cross-resistance to structurally unrelated insecticides can evolve, and illustrate the difficulty in predicting cross-resistance profiles mediated by metabolic mechanisms. The evolution of mechanisms that confer resistance to insecticides of different mode of action (MoA) threatens to undermine the primary strategy used to manage insecticide resistance based on the rotation of insecticides of different MoA. Despite its importance, our understanding of how cross-resistance evolves remains surprisingly poor. Here, we uncover the mechanisms by which a single gene, CYP6ER1, encoding a cytochrome P450 enzyme, evolved resistance to two insecticides of different MoA, namely the neonicotinoid imidacloprid and the phenylpyrazole ethiprole. We have previously shown that CYP6ER1 is duplicated in imidacloprid resistant strains of the brown planthopper, N. lugens. In the current study we demonstrate that two different sets of mutations, occurring in the same copy of CYP6ER1, were key to conferring the de novo ability to detoxify imidacloprid and ethiprole. We uncover complex interactions between these mutations and their genetic background that provide strong evidence of functional trade-offs associated with evolving dual resistance. Our findings provide fundamental and applied insights into the versatility of gene duplication in providing opportunities for functional innovation during the evolution of adaptive traits and reveal the mechanisms by which dual novel functions can arise from single genes.
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9
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Peng W, Fu Y, Jia B, Sun X, Wang Y, Deng Z, Lin S, Liang R. Metabolism analysis of 17α-ethynylestradiol by Pseudomonas citronellolis SJTE-3 and identification of the functional genes. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127045. [PMID: 34488099 DOI: 10.1016/j.jhazmat.2021.127045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Synthetic estrogens are the most hazardous and persistent environmental estrogenic contaminants, with few reports on their biodegradation. Pseudomonas citronellolis SJTE-3 degraded natural steroids efficiently and metabolized 17α-ethynylestradiol (EE2) with the addition of different easily used energy sources (glucose, peptone, ethanol, yeast extract, fulvic acid and ammonia). Over 92% of EE2 (1 mg/L) and 55% of EE2 (10 mg/L) in culture were removed in seven days with the addition of 0.1% ethanol, and the EE2-biotransforming efficiency increased with the increasing ethanol concentrations. Two novel intermediate metabolites of EE2 (C22H22O and C18H34O2) were identified with high-performance liquid chromatography (HPLC) and GC-Orbitrap/MS. Comparative analysis and genome mining revealed strain SJTE-3 contained a unique genetic basis for EE2 metabolism, and the putative EE2-degrading genes exhibited dispersed distribution. The EE2 metabolism of strain SJTE-3 was inducible and the transcription of eight genes were significantly induced by EE2. Three genes (sdr3, yjcH and cyp2) encoding a short-chain dehydrogenase, a membrane transporter and a cytochrome P450 hydroxylase, respectively, were vital for EE2 metabolism in strain SJTE-3; their over-expression accelerated EE2 metabolic processes and advanced the generation of intermediate metabolites. This work could promote the study of bacterial EE2 metabolism mechanisms and facilitate efficient bioremediation for EE2 pollution.
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Affiliation(s)
- Wanli Peng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yali Fu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ben Jia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xin Sun
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yanqiu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuangjun Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Rubing Liang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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Qiu Y, Diao H, Zheng Y, Wu R. Multiscale Simulations on the Catalytic Plasticity of CYP76AH1. Front Chem 2021; 9:689731. [PMID: 34150721 PMCID: PMC8207200 DOI: 10.3389/fchem.2021.689731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The catalytic promiscuity and fidelity of cytochrome P450 enzymes are widespread in the skeletal modification of terpenoid natural products and have attracted much attention. CYP76AH1 is involved in key modification reactions in the biosynthetic pathway of tanshinone, a well-known medicinal norditerpenoid. In this work, classical molecular dynamic simulations, metadynamics, and DFT calculations were performed to investigate the protein conformational dynamics, ligand binding poses, and catalytic reaction mechanism in wide-type and mutant CYP76AH1. Our results not only reveal a plausible enzymatic mechanism for mutant CYP76AH1 leading to various products but also provide valuable guidance for rational protein engineering of the CYP76 family.
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Affiliation(s)
- Yufan Qiu
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hongjuan Diao
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ying Zheng
- Research Center of Integrative Medicine, School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruibo Wu
- Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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11
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Sharifian S, Homaei A, Kamrani E, Etzerodt T, Patel S. New insights on the marine cytochrome P450 enzymes and their biotechnological importance. Int J Biol Macromol 2020; 142:811-821. [DOI: 10.1016/j.ijbiomac.2019.10.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/02/2019] [Accepted: 10/02/2019] [Indexed: 01/09/2023]
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12
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Schmitz LM, Rosenthal K, Lütz S. Recent advances in heme biocatalysis engineering. Biotechnol Bioeng 2019; 116:3469-3475. [PMID: 31483477 DOI: 10.1002/bit.27156] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/17/2019] [Accepted: 08/29/2019] [Indexed: 01/13/2023]
Abstract
Heme enzymes have the potential to be widely used as biocatalysts due to their capability to perform a vast variety of oxidation reactions. In spite of their versatility, the application of heme enzymes was long time-limited for the industry due to their low activity and stability in large scale processes. The identification of novel natural biocatalysts and recent advances in protein engineering have led to new reactions with a high application potential. The latest creation of a serine-ligated mutant of BM3 showed an efficient transfer of reactive carbenes into C═C bonds of olefins reaching total turnover numbers of more than 60,000 and product titers of up to 27 g/L-1 . This prominent example shows that heme enzymes are becoming competitive to chemical syntheses while being already advantageous in terms of high yield, regioselectivity, stereoselectivity and environmentally friendly reaction conditions. Advances in reactor concepts and the influencing parameters on reaction performance are also under investigation resulting in improved productivities and increased stability of the heme biocatalytic systems. In this mini review, we briefly present the latest advancements in the field of heme enzymes towards increased reaction scope and applicability.
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Affiliation(s)
- Lisa Marie Schmitz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Katrin Rosenthal
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
| | - Stephan Lütz
- Department of Biochemical and Chemical Engineering, TU Dortmund University, Dortmund, Germany
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13
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Schmitz LM, Schäper J, Rosenthal K, Lütz S. Accessing the Biocatalytic Potential for C−H‐Activation by Targeted Genome Mining and Screening. ChemCatChem 2019. [DOI: 10.1002/cctc.201901273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Lisa Marie Schmitz
- Chair for Bioprocess Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University Emil-Figge-Straße 66 Dortmund 44227 Germany
| | - Jonas Schäper
- Chair for Bioprocess Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University Emil-Figge-Straße 66 Dortmund 44227 Germany
| | - Katrin Rosenthal
- Chair for Bioprocess Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University Emil-Figge-Straße 66 Dortmund 44227 Germany
| | - Stephan Lütz
- Chair for Bioprocess Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University Emil-Figge-Straße 66 Dortmund 44227 Germany
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Using targeted next-generation sequencing to characterize genetic differences associated with insecticide resistance in Culex quinquefasciatus populations from the southern U.S. PLoS One 2019; 14:e0218397. [PMID: 31269040 PMCID: PMC6608931 DOI: 10.1371/journal.pone.0218397] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/31/2019] [Indexed: 11/19/2022] Open
Abstract
Resistance to insecticides can hamper the control of mosquitoes such as Culex quinquefasciatus, known to vector arboviruses such as West Nile virus and others. The strong selective pressure exerted on a mosquito population by the use of insecticides can result in heritable genetic changes associated with resistance. We sought to characterize genetic differences between insecticide resistant and susceptible Culex quinquefasciatus mosquitoes using targeted DNA sequencing. To that end, we developed a panel of 122 genes known or hypothesized to be involved in insecticide resistance, and used an Ion Torrent PGM sequencer to sequence 125 unrelated individuals from seven populations in the southern U.S. whose resistance phenotypes to permethrin and malathion were known from previous CDC bottle bioassay testing. Data analysis consisted of discovering SNPs (Single Nucleotide Polymorphism) and genes with evidence of copy number variants (CNVs) statistically associated with resistance. Ten of the seventeen genes found to be present in higher copy numbers were experimentally validated with real-time PCR. Of those, six, including the gene with the knock-down resistance (kdr) mutation, showed evidence of a ≥ 1.5 fold increase compared to control DNA. The SNP analysis revealed 228 unique SNPs that had significant p-values for both a Fisher’s Exact Test and the Cochran-Armitage Test for Trend. We calculated the population frequency for each of the 64 nonsynonymous SNPs in this group. Several genes not previously well characterized represent potential candidates for diagnostic assays when further validation is conducted.
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15
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Transcriptional Profiles of Secondary Metabolite Biosynthesis Genes and Cytochromes in the Leaves of Four Papaver Species. DATA 2018. [DOI: 10.3390/data3040055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Poppies are well-known plants in the family Papaveraceae that are rich in alkaloids. This family contains 61 species, and in this study we sequenced the transcriptomes of four species’ (Papaver rhoeas, Papaver nudicaule, Papaver fauriei, and Papaver somniferum) leaves. These transcripts were systematically assessed for the expression of secondary metabolite biosynthesis (SMB) genes and cytochromes, and their expression profiles were assessed for use in bioinformatics analyses. This study contributed 265 Gb (13 libraries with three biological replicates) of leaf transcriptome data from three Papaver plant developmental stages. Sequenced transcripts were assembled into 815 Mb of contigs, including 226 Mb of full-length transcripts. The transcripts for 53 KEGG pathways, 55 cytochrome superfamilies, and benzylisoquinoline alkaloid biosynthesis (BIA) were identified and compared to four other alkaloid-rich genomes. Additionally, 22 different alkaloids and their relative expression profiles in three developmental stages of Papaver species were assessed by targeted metabolomics using LC-QTOF-MS/MS. Collectively, the results are given in co-occurrence heat-maps to help researchers obtain an overview of the transcripts and their differential expression in the Papaver development life cycle, particularly in leaves. Moreover, this dataset will be a valuable resource to derive hypotheses to mitigate an array of Papaver developmental and secondary metabolite biosynthesis issues in the future.
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16
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Forman V, Bjerg-Jensen N, Dyekjær JD, Møller BL, Pateraki I. Engineering of CYP76AH15 can improve activity and specificity towards forskolin biosynthesis in yeast. Microb Cell Fact 2018; 17:181. [PMID: 30453976 PMCID: PMC6240942 DOI: 10.1186/s12934-018-1027-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/12/2018] [Indexed: 12/20/2022] Open
Abstract
Background Forskolin is a high-value diterpenoid produced exclusively by the Lamiaceae plant Coleus forskohlii. Today forskolin is used pharmaceutically for its adenyl-cyclase activating properties. The limited availability of pure forskolin is currently hindering its full utilization, thus a new environmentally friendly, scalable and sustainable strategy is needed for forskolin production. Recently, the entire biosynthetic pathway leading to forskolin was elucidated. The key steps of the pathway are catalyzed by cytochrome P450 enzymes (CYPs), which have been shown to be the limiting steps of the pathway. Here we study whether protein engineering of the substrate recognition sites (SRSs) of CYPs can improve their efficiency towards forskolin biosynthesis in yeast. Results As a proof of concept, we engineered the enzyme responsible for the first putative oxygenation step of the forskolin pathway: the conversion of 13R-manoyl oxide to 11-oxo-13R-manoyl oxide, catalyzed by the CYP76AH15. Four CYP76AH15 variants—engineered in the SRS regions—yielded at least a twofold increase of 11-oxo-13R-manoyl oxide when expressed in yeast cells grown in microtiter plates. The highest titers (5.6-fold increase) were observed with the variant A99I, mutated in the SRS1 region. Double or triple CYP76AH15 mutant variants resulted in additional enzymes with optimized performances. Moreover, in planta CYP76AH15 can synthesize ferruginol from miltiradiene. In this work, we showed that the mutants affecting 11-oxo-13R-manoyl oxide synthesis, do not affect ferruginol production, and vice versa. The best performing variant, A99I, was utilized to reconstruct the forskolin biosynthetic pathway in yeast cells. Although these strains showed increased 11-oxo-manoyl oxide production and higher accumulation of other pathway intermediates compared to the native CYP76AH15, lower production of forskolin was observed. Conclusions As demonstrated for CYP76AH15, site-directed mutagenesis of SRS regions of plant CYPs may be an efficient and targeted approach to increase the performance of these enzymes. Although in this work we have managed to achieve higher efficiency and specificity of the first CYP of the pathway, further work is necessary in order to increase the overall production of forskolin in yeast cells. Electronic supplementary material The online version of this article (10.1186/s12934-018-1027-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Victor Forman
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.,Evolva A/S, Copenhagen, Denmark
| | | | | | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark.,bioSYNergy, Center for Synthetic Biology, 1871, Frederiksberg C, Denmark.,VILLUM, Research Center for Plant Plasticity, 1871, Frederiksberg C, Denmark
| | - Irini Pateraki
- Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark. .,bioSYNergy, Center for Synthetic Biology, 1871, Frederiksberg C, Denmark.
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17
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Oh J, Shin Y, Ha IJ, Lee MY, Lee SG, Kang BC, Kyeong D, Kim D. Transcriptome Profiling of Two Ornamental and Medicinal Papaver Herbs. Int J Mol Sci 2018; 19:ijms19103192. [PMID: 30332811 PMCID: PMC6213990 DOI: 10.3390/ijms19103192] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/05/2018] [Accepted: 10/11/2018] [Indexed: 01/04/2023] Open
Abstract
The Papaver spp. (Papaver rhoeas (Corn poppy) and Papaver nudicaule (Iceland poppy)) genera are ornamental and medicinal plants that are used for the isolation of alkaloid drugs. In this study, we generated 700 Mb of transcriptome sequences with the PacBio platform. They were assembled into 120,926 contigs, and 1185 (82.2%) of the benchmarking universal single-copy orthologs (BUSCO) core genes were completely present in our assembled transcriptome. Furthermore, using 128 Gb of Illumina sequences, the transcript expression was assessed at three stages of Papaver plant development (30, 60, and 90 days), from which we identified 137 differentially expressed transcripts. Furthermore, three co-occurrence heat maps are generated from 51 different plant genomes along with the Papaver transcriptome, i.e., secondary metabolite biosynthesis, isoquinoline alkaloid biosynthesis (BIA) pathway, and cytochrome. Sixty-nine transcripts in the BIA pathway along with 22 different alkaloids (quantified with LC-QTOF-MS/MS) were mapped into the BIA KEGG map (map00950). Finally, we identified 39 full-length cytochrome transcripts and compared them with other genomes. Collectively, this transcriptome data, along with the expression and quantitative metabolite profiles, provides an initial recording of secondary metabolites and their expression related to Papaver plant development. Moreover, these profiles could help to further detail the functional characterization of the various secondary metabolite biosynthesis and Papaver plant development associated problems.
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Affiliation(s)
- Jaehyeon Oh
- Genomics Division, National Institute of Agricultural Science, RDA, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si 54874, Jeollabuk-do, Korea.
| | - Younhee Shin
- Data Science Center, Insilicogen Inc., Yongin-si 16954, Gyeonggi-do, Korea.
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea.
| | - In Jin Ha
- Korean Medicine Clinical Trial Center (K-CTC), Kyung Hee University Korean Medicine Hospital, Seoul 02447, Korea.
| | - Min Young Lee
- Korean Medicine Clinical Trial Center (K-CTC), Kyung Hee University Korean Medicine Hospital, Seoul 02447, Korea.
| | - Seok-Geun Lee
- Korean Medicine Clinical Trial Center (K-CTC), Kyung Hee University Korean Medicine Hospital, Seoul 02447, Korea.
- KHU-KIST Department of Converging Science & Technology, Kyung Hee University, Seoul 02447, Korea.
| | - Byeong-Chul Kang
- Data Science Center, Insilicogen Inc., Yongin-si 16954, Gyeonggi-do, Korea.
| | - Dongsoo Kyeong
- Data Science Center, Insilicogen Inc., Yongin-si 16954, Gyeonggi-do, Korea.
| | - Dowan Kim
- Genomics Division, National Institute of Agricultural Science, RDA, 370, Nongsaengmyeong-ro, Wansan-gu, Jeonju-si 54874, Jeollabuk-do, Korea.
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18
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Xu LH, Du YL. Rational and semi-rational engineering of cytochrome P450s for biotechnological applications. Synth Syst Biotechnol 2018; 3:283-290. [PMID: 30533540 PMCID: PMC6263019 DOI: 10.1016/j.synbio.2018.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 01/08/2023] Open
Abstract
The cytochrome P450 enzymes are ubiquitous heme-thiolate proteins performing regioselective and stereoselective oxygenation reactions in cellular metabolism. Due to their broad substrate scope and catalytic versatility, P450 enzymes are also attractive candidates for many industrial and biopharmaceutical applications. For particular uses, enzyme properties of P450s can be further optimized through directed evolution, rational, and semi-rational engineering approaches, all of which introduce mutations within the P450 structures. In this review, we describe the recent applications of these P450 engineering approaches and highlight the key regions and residues that have been identified using such approaches. These “hotspots” lie within critical functional areas of the P450 structure, including the active site, the substrate access channel, and the redox partner interaction interface.
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Affiliation(s)
- Lian-Hua Xu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Corresponding author.
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Corresponding author.
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19
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Tavanti M, Porter JL, Levy CW, Gómez Castellanos JR, Flitsch SL, Turner NJ. The crystal structure of P450-TT heme-domain provides the first structural insights into the versatile class VII P450s. Biochem Biophys Res Commun 2018; 501:846-850. [PMID: 29738765 DOI: 10.1016/j.bbrc.2018.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 05/02/2018] [Indexed: 02/06/2023]
Abstract
The first crystal structure of a class VII P450, CYP116B46 from Tepidiphilus thermophilus, has been solved at 1.9 Å resolution. The structure reveals overall conservation of the P450-fold and a water conduit around the I-helix. Active site residues have been identified and sequence comparisons have been made with other class VII enzymes. A structure similarity search demonstrated that the P450-TT structure is similar to enzymes capable of oxy-functionalization of fatty acids, terpenes, macrolides, steroids and statins. The insight gained from solving this structure will provide a guideline for future engineering and modelling studies on this catalytically promiscuous class of enzymes.
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Affiliation(s)
- Michele Tavanti
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - Joanne L Porter
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - Colin W Levy
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom
| | - J Rubén Gómez Castellanos
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Sabine L Flitsch
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom.
| | - Nicholas J Turner
- Manchester Institute of Biotechnology (MIB), School of Chemistry, The University of Manchester, 131Princess Street, M1 7DN, Manchester, United Kingdom.
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20
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Khatri Y, Jóźwik IK, Ringle M, Ionescu IA, Litzenburger M, Hutter MC, Thunnissen AMWH, Bernhardt R. Structure-Based Engineering of Steroidogenic CYP260A1 for Stereo- and Regioselective Hydroxylation of Progesterone. ACS Chem Biol 2018; 13:1021-1028. [PMID: 29509407 DOI: 10.1021/acschembio.8b00026] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The production of regio- and stereoselectively hydroxylated steroids is of high pharmaceutical interest and can be achieved by cytochrome P450-based biocatalysts. CYP260A1 from Sorangium cellulosum strain So ce56 catalyzes hydroxylation of C19 or C21 steroids at the very unique 1α-position. However, the conversion of progesterone (PROG) by CYP260A1 is very unselective. In order to improve its selectivity we applied a semirational protein engineering approach, resulting in two different, highly regio- and stereoselective mutants by replacing a single serine residue (S276) of the substrate recognition site 5 with an asparagine or isoleucine. The S276N mutant converted PROG predominantly into 1α-hydroxy-PROG, while the S276I mutant led to 17α-hydroxy-PROG. We solved the high-resolution crystal structures of the PROG-bound S276N and S276I mutants, which revealed two different binding modes of PROG in the active site. The orientations were consistent with the exclusive 1α- (pro-1α binding mode) and 17α-hydroxylation (pro-17α-binding mode) of S276N and S276I, respectively. We observed that water-mediated hydrogen bonds contribute to the stabilization of the polar C3 and C17 substituents of PROG. Both binding modes of PROG may be stabilized in the wild-type enzyme. The change in regioselectivity is mainly driven by destabilizing the alternative binding mode due to steric hindrance and hydrogen bond disruption, caused by the mutations of Ser276. Thus, for the first time, the change in the selectivity of cytochrome P450-mediated steroid hydroxylation created by rational mutagenesis can be explained by the obtained 3D structures of the substrate-bound mutants, providing the basis for further experiments to engineer the biocatalyst toward novel steroid hydroxylation positions.
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Affiliation(s)
- Yogan Khatri
- Department of Biochemistry, Campus B2.2, 66123, Saarland University, Saarbrücken, Germany
| | - Ilona K. Jóźwik
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Michael Ringle
- Department of Biochemistry, Campus B2.2, 66123, Saarland University, Saarbrücken, Germany
| | | | - Martin Litzenburger
- Department of Biochemistry, Campus B2.2, 66123, Saarland University, Saarbrücken, Germany
| | | | - Andy-Mark W. H. Thunnissen
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Rita Bernhardt
- Department of Biochemistry, Campus B2.2, 66123, Saarland University, Saarbrücken, Germany
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21
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Buchholz PCF, Fademrecht S, Pleiss J. Percolation in protein sequence space. PLoS One 2017; 12:e0189646. [PMID: 29261740 PMCID: PMC5738032 DOI: 10.1371/journal.pone.0189646] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/28/2017] [Indexed: 01/08/2023] Open
Abstract
The currently known protein sequences are not distributed equally in sequence space, but cluster into families. Analyzing the cluster size distribution gives a glimpse of the large and unknown extant protein sequence space, which has been explored during evolution. For six protein superfamilies with different fold and function, the cluster size distributions followed a power law with slopes between 2.4 and 3.3, which represent upper limits to the cluster distribution of extant sequences. The power law distribution of cluster sizes is in accordance with percolation theory and strongly supports connectedness of extant sequence space. Percolation of extant sequence space has three major consequences: (1) It transforms our view of sequence space as a highly connected network where each sequence has multiple neighbors, and each pair of sequences is connected by many different paths. A high degree of connectedness is a necessary condition of efficient evolution, because it overcomes the possible blockage by sign epistasis and reciprocal sign epistasis. (2) The Fisher exponent is an indicator of connectedness and saturation of sequence space of each protein superfamily. (3) All clusters are expected to be connected by extant sequences that become apparent as a higher portion of extant sequence space becomes known. Being linked to biochemically distinct homologous families, bridging sequences are promising enzyme candidates for applications in biotechnology because they are expected to have substrate ambiguity or catalytic promiscuity.
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Affiliation(s)
- Patrick C. F. Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Silvia Fademrecht
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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22
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Jung E, Park BG, Yoo HW, Kim J, Choi KY, Kim BG. Semi-rational engineering of CYP153A35 to enhance ω-hydroxylation activity toward palmitic acid. Appl Microbiol Biotechnol 2017; 102:269-277. [DOI: 10.1007/s00253-017-8584-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 09/01/2017] [Accepted: 10/09/2017] [Indexed: 01/14/2023]
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23
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Magistrato A, Sgrignani J, Krause R, Cavalli A. Single or Multiple Access Channels to the CYP450s Active Site? An Answer from Free Energy Simulations of the Human Aromatase Enzyme. J Phys Chem Lett 2017; 8:2036-2042. [PMID: 28423275 DOI: 10.1021/acs.jpclett.7b00697] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cytochromes P450 (CYP450s), in particular, CYP19A1 and CYP17A1, are key clinical targets of breast and prostate anticancer therapies, critical players in drug metabolism, and their overexpression in tumors is associated with drug resistance. In these enzymes, ligand (substrates, drugs) metabolism occurs in deeply buried active sites accessible only via several grueling channels, whose exact biological role remains unclear. Gaining direct insights on the mechanism by which ligands travel in and out is becoming increasingly important given that channels are involved in the modulation of binding/dissociation kinetics and the specificity of ligands toward a CYP450. This has profound implications for enzymatic efficiency and drug efficacy/toxicity. Here, by applying free energy methods, for a cumulative simulation time of 20 μs, we provide detailed atomistic characterization and free energy profiles of the entry/exit routes preferentially followed by a substrate (androstenedione) and a last-generation inhibitor (letrozole) to/from the catalytic site of CYP19A1 (the human aromatase (HA) enzyme), a key clinical target against breast cancer, studied here as prototypical CYP450. Despite the remarkably different size/shape/hydrophobicity of the ligands, two channels appear accessible to their entrance, while only one exit route appears to be preferential. Our study shows that the preferential paths may be conserved among different CYP450s. Moreover, our results highlight that, at least in the case of HA, ligand channeling is associated with large enzyme structural rearrangements. A wise choice of the computational method and very long simulations are, thus, required to obtain fully converged quantitative free energy profiles, which might be used to design novel biocatalysts or next-generation cytochrome inhibitors with an in silico tuned Km.
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Affiliation(s)
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI) , Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - Rolf Krause
- Institute of Computational Science, Faculty of Informatics, Università della Svizzera Italiana (USI) , Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI) , Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
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24
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Characterization of cytochrome P450 CYP109E1 from Bacillus megaterium as a novel vitamin D 3 hydroxylase. J Biotechnol 2016; 243:38-47. [PMID: 28043840 DOI: 10.1016/j.jbiotec.2016.12.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/26/2016] [Accepted: 12/28/2016] [Indexed: 12/31/2022]
Abstract
In this study the ability of CYP109E1 from Bacillus megaterium to metabolize vitamin D3 (VD3) was investigated. In an in vitro system using bovine adrenodoxin reductase (AdR) and adrenodoxin (Adx4-108), VD3 was converted by CYP109E1 into several products. Furthermore, a whole-cell system in B. megaterium MS941 was established. The new system showed a conversion of 95% after 24h. By NMR analysis it was found that CYP109E1 catalyzes hydroxylation of VD3 at carbons C-24 and C-25, resulting in the formation of 24(S)-hydroxyvitamin D3 (24S(OH)VD3), 25-hydroxyvitamin D3 (25(OH)VD3) and 24S,25-dihydroxyvitamin D3 (24S,25(OH)2VD3). Through time dependent whole-cell conversion of VD3, we identified that the formation of 24S,25(OH)2VD3 by CYP109E1 is derived from VD3 via the intermediate 24S(OH)VD3. Moreover, using docking analysis and site-directed mutagenesis, we identified important active site residues capable of determining substrate specificity and regio-selectivity. HPLC analysis of the whole-cell conversion with the I85A-mutant revealed an increased selectivity towards 25-hydroxylation of VD3 compared with the wild type activity, resulting in an approximately 2-fold increase of 25(OH)VD3 production (45mgl-1day-1) compared to wild type (24.5mgl-1day-1).
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25
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Jóźwik IK, Kiss FM, Gricman Ł, Abdulmughni A, Brill E, Zapp J, Pleiss J, Bernhardt R, Thunnissen AMWH. Structural basis of steroid binding and oxidation by the cytochrome P450 CYP109E1 from Bacillus megaterium. FEBS J 2016; 283:4128-4148. [PMID: 27686671 PMCID: PMC5132081 DOI: 10.1111/febs.13911] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/15/2016] [Accepted: 09/27/2016] [Indexed: 01/08/2023]
Abstract
Cytochrome P450 monooxygenases (P450s) are attractive enzymes for the pharmaceutical industry, in particular, for applications in steroidal drug synthesis. Here, we report a comprehensive functional and structural characterization of CYP109E1, a novel steroid‐converting cytochrome P450 enzyme identified from the genome of Bacillus megaterium DSM319. In vitro and whole‐cell in vivo turnover experiments, combined with binding assays, revealed that CYP109E1 is able to hydroxylate testosterone at position 16β. Related steroids with bulky substituents at carbon C17, like corticosterone, bind to the enzyme without being converted. High‐resolution X‐ray structures were solved of a steroid‐free form of CYP109E1 and of complexes with testosterone and corticosterone. The structural analysis revealed a highly dynamic active site at the distal side of the heme, which is wide open in the absence of steroids, can bind four ordered corticosterone molecules simultaneously, and undergoes substantial narrowing upon binding of single steroid molecules. In the crystal structures, the single bound steroids adopt unproductive binding modes coordinating the heme‐iron with their C3‐keto oxygen. Molecular dynamics (MD) simulations suggest that the steroids may also bind in ~180° reversed orientations with the C16 carbon and C17‐substituents pointing toward the heme, leading to productive binding of testosterone explaining the observed regio‐ and stereoselectivity. The X‐ray structures and MD simulations further identify several residues with important roles in steroid binding and conversion, which could be confirmed by site‐directed mutagenesis. Taken together, our results provide unique insights into the CYP109E1 activity, substrate specificity, and regio/stereoselectivity. Database The atomic coordinates and structure factors have been deposited in the Protein Data Bank with accession codes 5L90 (steroid‐free CYP109E1), 5L91 (CYP109E1‐COR4), 5L94 (CYP109E1‐TES), and 5L92 (CYP109E1‐COR). Enzymes Cytochrome P450 monooxygenase CYP109E1, EC 1.14.14.1, UniProt ID: D5DKI8, Adrenodoxin reductase EC 1.18.1.6.
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Affiliation(s)
- Ilona K Jóźwik
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
| | - Flora M Kiss
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Łukasz Gricman
- Institute of Technical Biochemistry, University of Stuttgart, Germany
| | - Ammar Abdulmughni
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Elisa Brill
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Josef Zapp
- Pharmaceutical Biology, Saarland University, Saarbrücken, Germany
| | - Juergen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Germany
| | - Rita Bernhardt
- Institute of Biochemistry, Saarland University, Saarbrücken, Germany
| | - Andy-Mark W H Thunnissen
- Laboratory of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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26
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Buchholz PCF, Vogel C, Reusch W, Pohl M, Rother D, Spieß AC, Pleiss J. BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments. Chembiochem 2016; 17:2093-2098. [DOI: 10.1002/cbic.201600462] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Patrick C. F. Buchholz
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Waldemar Reusch
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Martina Pohl
- IBG-1: Biotechnology; Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Dörte Rother
- IBG-1: Biotechnology; Forschungszentrum Jülich GmbH; 52425 Jülich Germany
| | - Antje C. Spieß
- Institute of Biochemical Engineering; Technical University of Braunschweig; Rebenring 56 38106 Braunschweig Germany
- RWTH Aachen University; AVT.EPT; Worringerweg 1 52074 Aachen Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
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Notonier S, Gricman Ł, Pleiss J, Hauer B. Semirational Protein Engineering of CYP153AM.aq. -CPRBM3 for Efficient Terminal Hydroxylation of Short- to Long-Chain Fatty Acids. Chembiochem 2016; 17:1550-7. [PMID: 27251775 DOI: 10.1002/cbic.201600207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/07/2022]
Abstract
The regioselective terminal hydroxylation of alkanes and fatty acids is of great interest in a variety of industrial applications, such as in cosmetics, in fine chemicals, and in the fragrance industry. The chemically challenging activation and oxidation of non-activated C-H bonds can be achieved with cytochrome P450 enzymes. CYP153AM.aq. -CPRBM3 is an artificial fusion construct consisting of the heme domain from Marinobacter aquaeolei and the reductase domain of CYP102A1 from Bacillus megaterium. It has the ability to hydroxylate medium- and long-chain fatty acids selectively at their terminal positions. However, the activity of this interesting P450 construct needs to be improved for applications in industrial processes. For this purpose, the design of mutant libraries including two consecutive steps of mutagenesis is demonstrated. Targeted positions and residues chosen for substitution were based on semi-rational protein design after creation of a homology model of the heme domain of CYP153AM.aq. , sequence alignments, and docking studies. Site-directed mutagenesis was the preferred method employed to address positions within the binding pocket, whereas diversity was created with the aid of a degenerate codon for amino acids located at the substrate entrance channel. Combining the successful variants led to the identification of a double variant-G307A/S233G-that showed alterations of one position within the binding pocket and one position located in the substrate access channel. This double variant showed twofold increased activity relative to the wild type for the terminal hydroxylation of medium-chain-length fatty acids. This variant furthermore showed improved activity towards short- and long-chain fatty acids and enhanced stability in the presence of higher concentrations of fatty acids.
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Affiliation(s)
- Sandra Notonier
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Łukasz Gricman
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry, Universität Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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Gricman Ł, Weissenborn MJ, Hoffmann SM, Borlinghaus N, Hauer B, Pleiss J. Redox Partner Interaction Sites in Cytochrome P450 Monooxygenases:In SilicoAnalysis and Experimental Validation. ChemistrySelect 2016. [DOI: 10.1002/slct.201600369] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Martin J. Weissenborn
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Sara M. Hoffmann
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Niels Borlinghaus
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
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29
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Bifunctional CYP81AA proteins catalyse identical hydroxylations but alternative regioselective phenol couplings in plant xanthone biosynthesis. Nat Commun 2016; 7:11472. [PMID: 27145837 PMCID: PMC4858744 DOI: 10.1038/ncomms11472] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 03/30/2016] [Indexed: 01/01/2023] Open
Abstract
Xanthones are natural products present in plants and microorganisms. In plants, their biosynthesis starts with regioselective cyclization of 2,3′,4,6-tetrahydroxybenzophenone to either 1,3,5- or 1,3,7-trihydroxyxanthones, catalysed by cytochrome P450 (CYP) enzymes. Here we isolate and express CYP81AA-coding sequences from Hypericum calycinum and H. perforatum in yeast. Microsomes catalyse two consecutive reactions, that is, 3′-hydroxylation of 2,4,6-trihydroxybenzophenone and C–O phenol coupling of the resulting 2,3′,4,6-tetrahydroxybenzophenone. Relative to the inserted 3′-hydroxyl, the orthologues Hc/HpCYP81AA1 cyclize via the para position to form 1,3,7-trihydroxyxanthone, whereas the paralogue HpCYP81AA2 directs cyclization to the ortho position, yielding the isomeric 1,3,5-trihydroxyxanthone. Homology modelling and reciprocal mutagenesis reveal the impact of S375, L378 and A483 on controlling the regioselectivity of HpCYP81AA2, which is converted into HpCYP81AA1 by sextuple mutation. However, the reciprocal mutations in HpCYP81AA1 barely affect its regiospecificity. Product docking rationalizes the alternative C–O phenol coupling reactions. Our results help understand the machinery of bifunctional CYPs. Xanthones are pharmacologically and biosynthetically intriguing compounds. Here, the authors identify two cytochrome P450 enzymes, which hydroxylate and cyclize the benzophenone precursor to either 1,3,7- or 1,3,5-trihydroxyxanthones, and pinpoint residues that determine the alternative regioselectivities.
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30
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Weissenborn MJ, Notonier S, Lang SL, Otte KB, Herter S, Turner NJ, Flitsch SL, Hauer B. Whole-cell microtiter plate screening assay for terminal hydroxylation of fatty acids by P450s. Chem Commun (Camb) 2016; 52:6158-61. [PMID: 27074906 DOI: 10.1039/c6cc01749e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A readily available galactose oxidase (GOase) variant was used to develop a whole cell screening assay. This endpoint detection system was applied in a proof-of-concept approach by screening a focussed mutant library. This led to the discovery of the thus far most active P450 Marinobacter aquaeolei mutant catalysing the terminal hydroxylation of fatty acids.
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Affiliation(s)
- Martin J Weissenborn
- Institute of Technical Biochemistry, Universitaet Stuttgart, Allmandring 31, 70569 Stuttgart, Germany.
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31
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Eichler A, Gricman Ł, Herter S, Kelly PP, Turner NJ, Pleiss J, Flitsch SL. Enantioselective Benzylic Hydroxylation Catalysed by P450 Monooxygenases: Characterisation of a P450cam Mutant Library and Molecular Modelling. Chembiochem 2016; 17:426-32. [DOI: 10.1002/cbic.201500536] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Indexed: 12/30/2022]
Affiliation(s)
- Anja Eichler
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Łukasz Gricman
- Institute for Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Susanne Herter
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Paul P. Kelly
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Nicholas J. Turner
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
| | - Jürgen Pleiss
- Institute for Technical Biochemistry; University of Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Sabine L. Flitsch
- School of Chemistry; Manchester Institute of Biotechnology; University of Manchester; 131 Princess Street Manchester M1 7DN UK
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Kelly PP, Eichler A, Herter S, Kranz DC, Turner NJ, Flitsch SL. Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions. Beilstein J Org Chem 2015; 11:1713-1720. [PMID: 26664590 PMCID: PMC4660908 DOI: 10.3762/bjoc.11.186] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/03/2015] [Indexed: 12/27/2022] Open
Abstract
Cytochrome P450 monooxygenases are useful biocatalysts for C-H activation, and there is a need to expand the range of these enzymes beyond what is naturally available. A panel of 93 variants of active self-sufficient P450cam[Tyr96Phe]-RhFRed fusion enzymes with a broad diversity in active site amino acids was developed by screening a large mutant library of 16,500 clones using a simple, highly sensitive colony-based colorimetric screen against indole. These mutants showed distinct fingerprints of activity not only when screened in oxidations of substituted indoles but also for unrelated oxidations such as benzylic hydroxylations.
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Affiliation(s)
- Paul P Kelly
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Anja Eichler
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Susanne Herter
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - David C Kranz
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J Turner
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
| | - Sabine L Flitsch
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, M1 7DN, Manchester, United Kingdom
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