1
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Yi G, Zou H, Long T, Osire T, Wang L, Wei X, Long M, Rao Z, Liao G. Novel cytochrome P450s for various hydroxylation of steroids from filamentous fungi. BIORESOURCE TECHNOLOGY 2024; 394:130244. [PMID: 38145763 DOI: 10.1016/j.biortech.2023.130244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 12/27/2023]
Abstract
Hydroxylated steroids are value-added products with diverse biological activities mediated by cytochrome P450 enzymes, however, few has been thoroughly characterized in fungi. This study introduces a rapid identification strategy for filamentous fungi P450 enzymes through transcriptome and bioinformatics analysis. Five novel enzymes (CYP68J5, CYP68L10, CYP68J3, CYP68N1 and CYP68N3) were identified and characterized in Saccharomyces cerevisiae or Aspergillus oryzae. Molecular docking and dynamics simulations were employed to elucidate hydroxylation preferences of CYP68J5 (11α, 7α bihydroxylase) and CYP68N1 (11α hydroxylase). Additionally, redox partners (cytochrome P450 reductase and cytochrome b5) and ABC transporter were co-expressed with CYP68N1 to enhance 11α-OH-androstenedione (11α-OH-4AD) production. The engineered cell factory, co-expressing CPR1 and CYP68N1, achieved a significant increase of 11α-OH-4AD production, reaching 0.845 g·L-1, which increased by 14 times compared to the original strain. This study provides a comprehensive approach for identifying and implementing novel cytochrome P450 enzymes, paving the way for sustainable production of steroidal products.
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Affiliation(s)
- Guojuan Yi
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Hanlu Zou
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Tao Long
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Tolbert Osire
- Faculty of Biology, Shenzhen MSU-BIT University, 1 University Park Road, Shenzhen, Guangdong 518172, China
| | - Lin Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Xiaoyun Wei
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China
| | - Mengfei Long
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China.
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Guojian Liao
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China.
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2
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Wang Y, Pan H, Wang F, Shen C. Microbial P450 repertoire (P450ome) and its application feasibility in pharmaceutical industry, chemical industry, and environmental protection. Biotechnol Bioeng 2024; 121:7-25. [PMID: 37767638 DOI: 10.1002/bit.28565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/13/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023]
Abstract
Cytochrome P450s (CYPs) are heme-thiolated enzymes that catalyze the oxidation of C-H bonds in a regio- and stereo-selective manner. CYPs are widely present in the biological world. With the completion of more biological genome sequencing, the number and types of P450 enzymes have increased rapidly. P450 in microorganisms is easy to clone and express, rich in catalytic types, and strong in substrate adaptability, which has good application potential. Although the number of P450 enzymes found in microorganisms is huge, the function of most of the microorganism P450s has not been studied, and it contains a large number of excellent biocatalysts to be developed. This review is based on the P450 groups in microorganisms. First, it reviews the distribution of P450 groups in different microbial species, and then studies the application of microbial P450 enzymes in the pharmaceutical industry, chemical industry and environmental pollutant treatment in recent years. And focused on the application fields of P450 enzymes of different families to guide the selection of suitable P450s from the huge P450 library. In view of the current shortcomings of microbial P450 in the application process, the final solution is the most likely to assist the application of P450 enzymes in large-scale, that is, whole cell transformation combined with engineering, fusion P450 combined with immobilization technology.
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Affiliation(s)
- Yongfa Wang
- College of Chemical & Pharmaceutical Engineering, Hebei University of Science & Technology, Shijiazhuang, China
| | - Hao Pan
- College of Chemical & Pharmaceutical Engineering, Hebei University of Science & Technology, Shijiazhuang, China
| | - Fuhao Wang
- College of Chemical & Pharmaceutical Engineering, Hebei University of Science & Technology, Shijiazhuang, China
| | - Chen Shen
- College of Chemical & Pharmaceutical Engineering, Hebei University of Science & Technology, Shijiazhuang, China
- State Key Laboratory Breeding Base-Hebei Province Key Laboratory of Molecular Chemistry for Drug, Hebei University of Science & Technology, Shijiazhuang, China
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3
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Gao Q, Ma B, Wang Q, Zhang H, Fushinobu S, Yang J, Lin S, Sun K, Han BN, Xu LH. Improved 2α-Hydroxylation Efficiency of Steroids by CYP154C2 Using Structure-Guided Rational Design. Appl Environ Microbiol 2023; 89:e0218622. [PMID: 36847541 PMCID: PMC10056965 DOI: 10.1128/aem.02186-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/01/2023] [Indexed: 03/01/2023] Open
Abstract
Cytochrome P450 enzymes are promising biocatalysts for industrial use because they catalyze site-selective C-H oxidation and have diverse catalytic reactions and a broad substrate range. In this study, the 2α-hydroxylation activity of CYP154C2 from Streptomyces avermitilis MA-4680T toward androstenedione (ASD) was identified by an in vitro conversion assay. The testosterone (TES)-bound structure of CYP154C2 was solved at 1.42 Å, and this structure was used to design eight mutants, including single, double, and triple mutants, to improve the conversion efficiency. Mutants L88F/M191F and M191F/V285L were found to enhance the conversion rates significantly (i.e., 8.9-fold and 7.4-fold for TES, 46.5-fold and 19.5-fold for ASD, respectively) compared with the wild-type (WT) enzyme while retaining high 2α-position selectivity. The substrate binding affinity of the L88F/M191F mutant toward TES and ASD was enhanced compared with that of WT CYP154C2, supporting the measured increase in the conversion efficiencies. Moreover, the total turnover number and kcat/Km of the L88F/M191F and M191F/V285L mutants increased significantly. Interestingly, all mutants containing L88F generated 16α-hydroxylation products, suggesting that L88 in CYP154C2 plays a vital role in substrate selectivity and that the amino acid corresponding to L88 in the 154C subfamily affects the orientation of steroid binding and substrate selectivity. IMPORTANCE Hydroxylated derivatives of steroids play essential roles in medicine. Cytochrome P450 enzymes selectively hydroxylate methyne groups on steroids, which can dramatically change their polarity, biological activity and toxicity. There is a paucity of reports on the 2α-hydroxylation of steroids, and documented 2α-hydroxylate P450s show extremely low conversion efficiency and/or low regio- and stereoselectivity. This study conducted crystal structure analysis and structure-guided rational engineering of CYP154C2 and efficiently enhanced the conversion efficiency of TES and ASD with high regio- and stereoselectivity. Our results provide an effective strategy and theoretical basis for the 2α-hydroxylation of steroids, and the structure-guided rational design of P450s should facilitate P450 applications in the biosynthesis of steroid drugs.
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Affiliation(s)
- Qilin Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Bingbing Ma
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qianwen Wang
- Ocean College, Zhejiang University, Zhoushan, China
| | - Hao Zhang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Jian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Susu Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Keke Sun
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Bing-Nan Han
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Lian-Hua Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Pardhe BD, Kwon KP, Park JK, Lee JH, Oh TJ. H 2O 2-Driven Hydroxylation of Steroids Catalyzed by Cytochrome P450 CYP105D18: Exploration of the Substrate Access Channel. Appl Environ Microbiol 2023; 89:e0158522. [PMID: 36511686 PMCID: PMC9888293 DOI: 10.1128/aem.01585-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/04/2022] [Indexed: 12/15/2022] Open
Abstract
CYP105D18 supports H2O2 as an oxygen surrogate for catalysis well and shows high H2O2 resistance capacity. We report the hydroxylation of different steroids using H2O2 as a cosubstrate. Testosterone was regiospecifically hydroxylated to 2β-hydroxytestosterone. Based on the experimental data and molecular docking, we predicted that hydroxylation of methyl testosterone and nandrolone would occur at position 2 in the A-ring, while hydroxylation of androstenedione and adrenosterone was predicted to occur in the B-ring. Further, structure-guided rational design of the substrate access channel was performed with the mutagenesis of residues S63, R82, and F184. Among the mutants, S63A showed a marked decrease in product formation, while F184A showed a significant increase in product formation in testosterone, nandrolone, methyl testosterone, androstenedione, and adrenosterone. The catalytic efficiency (kcat/Km) toward testosterone was increased 1.36-fold in the F184A mutant over that in the wild-type enzyme. These findings might facilitate the potential use of CYP105D18 and further engineering to establish the basis of biotechnological applications. IMPORTANCE The structural modification of steroids is a challenging chemical reaction. Modifying the core ring and the side chain improves the biological activity of steroids. In particular, bacterial cytochrome P450s are used as promiscuous enzymes for the activation of nonreactive carbons of steroids. In the present work, we reported the H2O2-mediated hydroxylation of steroids by CYP105D18, which also overcomes the use of expensive cofactors. Further, exploring the substrate access channel and modifying the bulky amino acid F184A increase substrate conversion while modifying the substrate recognizing amino acid S63 markedly decreases product formation. Exploring the substrate access channel and the rational design of CYP105D18 can improve the substrate conversion, which facilitates the engineering of P450s for industrial application.
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Affiliation(s)
- Bashu Dev Pardhe
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan-si, Chungnam, Republic of Korea
| | - Kyoung Pyo Kwon
- Department of Pharmaceutical Engineering and Biotechnology, Sunmoon University, Asan-si, Chungnam, Republic of Korea
| | - Jong Kook Park
- Department of Biomedical Science and Research Institute for Bioscience & Biotechnology, Hallym University, Chuncheon, Gangwon-do, Republic of Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Polar Sciences, University of Science and Technology, Incheon, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan-si, Chungnam, Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sunmoon University, Asan-si, Chungnam, Republic of Korea
- Genome-based BioIT Convergence Institute, Asan-si, Chungnam, Republic of Korea
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5
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Karpov MV, Nikolaeva VM, Fokina VV, Shutov AA, Kazantsev AV, Strizhov NI, Donova MV. Creation and Functional Analysis of Mycolicibacterium smegmatis Recombinant Strains Carrying the Bacillary Cytochromes CYP106A1 and CYP106A2 Genes. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822090058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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6
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Zhu R, Liu Y, Yang Y, Min Q, Li H, Chen L. Cytochrome P450 Monooxygenases Catalyse Steroid Nucleus Hydroxylation with Regio‐ and Stereo‐selectivity. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202200210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Lin S, Ma B, Gao Q, Yang J, Lai G, Lin R, Yang B, Han BN, Xu LH. The 16α-Hydroxylation of Progesterone by Cytochrome P450 107X1 from Streptomyces avermitilis. Chem Biodivers 2022; 19:e202200177. [PMID: 35426465 DOI: 10.1002/cbdv.202200177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/04/2022] [Indexed: 11/10/2022]
Abstract
Cytochrome P450 enzymes (CYPs or P450s) are ubiquitous heme-dependent enzymes that catalyze the monooxygenation of non-activated C-H bonds to modify the structure of the substrate. In this study, we heterologously expressed CYP107X1 from Streptomyces avermitilis and conducted in vitro substrate screening using the alternative redox partners putidaredoxin and putidaredoxin reductase. CYP107X1 catalyzed the 16α-hydroxylation of progesterone with regio- and stereoselectivity. The spectroscopic analyses showed that CYP107X1 bound progesterone with a relatively high Kd value of 65.3±38.9 μM. The Km and kcat values for progesterone were estimated to be 47.7±12.0 μM and 0.30 min-1 , respectively. Furthermore, a crystal structure was obtained of CYP107X1 bound with glycerol from the buffer solution. Interestingly, a conserved threonine was replaced with asparagine in CYP107X1, indicating that it may adopt an unnatural proton transfer process and play a crucial role in its catalytic activity.
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Affiliation(s)
- Susu Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Bingbing Ma
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qilin Gao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Jian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Gang Lai
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Runhao Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Bingxian Yang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Bing-Nan Han
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
| | - Lian-Hua Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China
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8
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Permana D, Niesel K, Ford MJ, Ichinose H. Latent Functions and Applications of Cytochrome P450 Monooxygenases from Thamnidium elegans: A Novel Biocatalyst for 14α-Hydroxylation of Testosterone. ACS OMEGA 2022; 7:13932-13941. [PMID: 35559141 PMCID: PMC9088945 DOI: 10.1021/acsomega.2c00430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/05/2022] [Indexed: 05/21/2023]
Abstract
Cytochrome P450 monooxygenases (P450s) are ubiquitous enzymes with high availability and diversity in nature. Fungi provide a diverse and complex array of P450s, and these enzymes play essential roles in various secondary metabolic processes. Besides the physiological impacts of P450s on fungal life, their versatile functions are attractive for use in advanced applications of the biotechnology sector. Herein, we report gene identification and functional characterization of P450s from the zygomycetous fungus Thamnidium elegans (TeCYPs). We identified 48 TeCYP genes, including two putative pseudogenes, from the whole-genome sequence of T. elegans. Furthermore, we constructed a functional library of TeCYPs and heterologously expressed 46 TeCYPs in Saccharomyces cerevisiae. Recombinants of S. cerevisiae were then used as whole-cell biocatalysts for bioconversion of various compounds. Catalytic potentials of various TeCYPs were demonstrated through a functionomic survey to convert a series of compounds, including steroidal substrates. Notably, CYP5312A4 was found to be highly active against testosterone. Based on nuclear magnetic resonance analysis, enzymatic conversion of testosterone to 14α-hydroxytestosterone by CYP5312A4 was demonstrated. This is the first report to identify a novel fungal P450 that catalyzes the 14α-hydroxylation of testosterone. In addition, we explored the latent potentials of TeCYPs using various substrates. This study provides a platform to further study the potential use of TeCYPs as catalysts in pharmaceutical and agricultural industries and biotechnology.
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Affiliation(s)
- Dani Permana
- Faculty
of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Research
Center for Environmental and Clean Technology, The National Research and Innovation Agency of the Republic of Indonesia
(BRIN), Bandung Advanced Science and Creative Engineering Space (BASICS), Jl. Cisitu, Bandung 40135, Indonesia
| | - Ksenia Niesel
- Bayer
AG, Industriepark Höchst, Frankfurt am Main 65926, Germany
| | | | - Hirofumi Ichinose
- Faculty
of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- . Phone/Fax: +81 (0)92-802-4666
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9
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Salama S, Habib MH, Hatti-Kaul R, Gaber Y. Reviewing a plethora of oxidative-type reactions catalyzed by whole cells of Streptomyces species. RSC Adv 2022; 12:6974-7001. [PMID: 35424663 PMCID: PMC8982256 DOI: 10.1039/d1ra08816e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/17/2022] [Indexed: 11/21/2022] Open
Abstract
Selective oxidation reactions represent a challenging task for conventional organic chemistry. Whole-cell biocatalysis provides a very convenient, easy to apply method to carry out different selective oxidation reactions including chemo-, regio-, and enantio-selective reactions. Streptomyces species are important biocatalysts as they can catalyze these selective reactions very efficiently owing to the wide diversity of enzymes and enzymatic cascades in their cell niche. In this review, we present and analyze most of the examples reported to date of oxidative reactions catalyzed by Streptomyces species as whole-cell biocatalysts. We discuss 33 different Streptomyces species and strains and the role they play in different oxidative reactions over the past five decades. The oxidative reactions have been classified into seven categories that include: hydroxylation of steroids/non-steroids, asymmetric sulfoxidations, oxidation of aldehydes, multi-step oxidations, oxidative cleavage, and N-oxidations. The role played by Streptomyces species as recombinant hosts catalyzing bio-oxidations has also been highlighted.
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Affiliation(s)
- Sara Salama
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University Beni-Suef 62517 Egypt
| | - Mohamed H Habib
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University Sweden
| | - Yasser Gaber
- Department of Pharmaceutical Microbiology and Immunology, Faculty of Pharmacy, Beni-Suef University Beni-Suef 62511 Egypt
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Mutah University Al-Karak 61710 Jordan
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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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11
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Subedi P, Kim KH, Hong YS, Lee JH, Oh TJ. Enzymatic Characterization and Comparison of Two Steroid Hydroxylases CYP154C3-1 and CYP154C3-2 from Streptomyces Species. J Microbiol Biotechnol 2021; 31:464-474. [PMID: 33397832 PMCID: PMC9705902 DOI: 10.4014/jmb.2010.10020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/15/2020] [Accepted: 12/31/2020] [Indexed: 12/15/2022]
Abstract
Bacterial cytochrome P450 (CYP) enzymes are responsible for the hydroxylation of diverse endogenous substances with a heme molecule used as a cofactor. This study characterized two CYP154C3 proteins from Streptomyces sp. W2061 (CYP154C3-1) and Streptomyces sp. KCCM40643 (CYP154C3-2). The enzymatic activity assays of both CYPs conducted using heterologous redox partners' putidaredoxin and putidaredoxin reductase showed substrate flexibility with different steroids and exhibited interesting product formation patterns. The enzymatic characterization revealed good activity over a pH range of 7.0 to 7.8 and the optimal temperature range for activity was 30 to 37°C. The major product was the C16-hydroxylated product and the kinetic profiles and patterns of the generated hydroxylated products differed between the two enzymes. Both enzymes showed a higher affinity toward progesterone, with CYP154C3-1 demonstrating slightly higher activity than CYP154C3-2 for most of the substrates. Oxidizing agents (diacetoxyiodo) benzene (PIDA) and hydrogen peroxide (H2O2) were also utilized to actively support the redox reactions, with optimum conversion achieved at concentrations of 3 mM and 65 mM, respectively. The oxidizing agents affected the product distribution, influencing the type and selectivity of the CYP-catalyzed reaction. Additionally, CYP154C3s also catalyzed the C-C bond cleavage of steroids. Therefore, CYP154C3s may be a good candidate for the production of modified steroids for various biological uses.
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Affiliation(s)
- Pradeep Subedi
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea
| | - Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea
| | - Young-Soo Hong
- Chemical Biology Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang-eup, Chungbuk 28116, Republic of Korea
| | - Joo-Ho Lee
- Genome-Based BioIT Convergence Institute, Asan 31460, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Sunmoon University, Asan 31460, Republic of Korea,Genome-Based BioIT Convergence Institute, Asan 31460, Republic of Korea,Department of BT-Convergent Pharmaceutical Engineering, Sunmoon University, Asan 31460, Republic of Korea,Corresponding author Phone: +82-41-530-2677 Fax: +82-41-530-2279 E-mail:
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12
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Bracco P, Wijma HJ, Nicolai B, Buitrago JAR, Klünemann T, Vila A, Schrepfer P, Blankenfeldt W, Janssen DB, Schallmey A. CYP154C5 Regioselectivity in Steroid Hydroxylation Explored by Substrate Modifications and Protein Engineering*. Chembiochem 2020; 22:1099-1110. [PMID: 33145893 PMCID: PMC8048783 DOI: 10.1002/cbic.202000735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/03/2020] [Indexed: 12/27/2022]
Abstract
CYP154C5 from Nocardia farcinica is a P450 monooxygenase able to hydroxylate a range of steroids with high regio- and stereoselectivity at the 16α-position. Using protein engineering and substrate modifications based on the crystal structure of CYP154C5, an altered regioselectivity of the enzyme in steroid hydroxylation had been achieved. Thus, conversion of progesterone by mutant CYP154C5 F92A resulted in formation of the corresponding 21-hydroxylated product 11-deoxycorticosterone in addition to 16α-hydroxylation. Using MD simulation, this altered regioselectivity appeared to result from an alternative binding mode of the steroid in the active site of mutant F92A. MD simulation further suggested that the entrance of water to the active site caused higher uncoupling in this mutant. Moreover, exclusive 15α-hydroxylation was observed for wild-type CYP154C5 in the conversion of 5α-androstan-3-one, lacking an oxy-functional group at C17. Overall, our data give valuable insight into the structure-function relationship of this cytochrome P450 monooxygenase for steroid hydroxylation.
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Affiliation(s)
- Paula Bracco
- Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Hein J Wijma
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Bastian Nicolai
- Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Jhon Alexander Rodriguez Buitrago
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Thomas Klünemann
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Agustina Vila
- Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Patrick Schrepfer
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Wulf Blankenfeldt
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124, Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
| | - Dick B Janssen
- Department of Biochemistry Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands
| | - Anett Schallmey
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstr. 7, 38106, Braunschweig, Germany
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13
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Zhu J, Shen C, Zhao W, Liu X, Liu J, Yu B. Regio- and stereoselective hydroxylation of testosterone by cytochrome P450 from Streptomyces griseus ATCC 13273. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1799990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Jinqian Zhu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Chen Shen
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Wanli Zhao
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Xiufeng Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Jihua Liu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Boyang Yu
- Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
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14
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Chen W, Fisher MJ, Leung A, Cao Y, Wong LL. Oxidative Diversification of Steroids by Nature-Inspired Scanning Glycine Mutagenesis of P450BM3 (CYP102A1). ACS Catal 2020. [DOI: 10.1021/acscatal.0c02077] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Wenyu Chen
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
| | - Matthew J. Fisher
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
| | - Aaron Leung
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
| | - Yang Cao
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
- Oxford Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Jiangsu 215123, P.R. China
| | - Luet L. Wong
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, U.K
- Oxford Suzhou Centre for Advanced Research, Ruo Shui Road, Suzhou Industrial Park, Jiangsu 215123, P.R. China
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15
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Wang Q, Ma B, Fushinobu S, Zhang C, Xu LH. Regio- and stereoselective hydroxylation of testosterone by a novel cytochrome P450 154C2 from Streptomyces avermitilis. Biochem Biophys Res Commun 2020; 522:355-361. [PMID: 31767148 DOI: 10.1016/j.bbrc.2019.11.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022]
Abstract
Cytochrome P450 enzymes (P450 or CYP) are some of the most versatile biocatalysts, and offer advantages for oxidizing unreactive C-H bonds in mild conditions. In this study, we identified a novel cytochrome P450 154C2 from Streptomyces avermitilis and characterized its function in 2α-hydroxylation of testosterone with regio- and stereoselectivity. To investigate the efficiency of electron transfer, we conducted biotransformation using two different P450 redox partners-RhFRED (RhF reductase domain) from Rhodococcus sp. and Pdx (putidaredoxin)/Pdr (putidaredoxin reductase) from Pseudomonas putida and revealed that RhFRED was more effective than Pdx/Pdr, especially in vivo. The Km and kcat values for testosterone were estimated to be 0.16 ± 0.05 mM and 0.13 ± 0.02 min-1, and kcat/Km was 0.81 min-1 mM-1. We also determined the crystal structure of the substrate-free form of CYP154C2 at 1.5 Å resolution. The structure has a closed conformation, and the substrate binding pocket is narrow, which can explain the strict substrate specificity of the enzyme.
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Affiliation(s)
- Qianwen Wang
- Ocean College, Zhejiang University, Dinghai, Zhoushan, Zhejiang, 316021, China
| | - Bingbing Ma
- Ocean College, Zhejiang University, Dinghai, Zhoushan, Zhejiang, 316021, China
| | - Shinya Fushinobu
- Department of Biotechnology, Graduate School of Agriculture and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Chunfang Zhang
- Ocean College, Zhejiang University, Dinghai, Zhoushan, Zhejiang, 316021, China.
| | - Lian-Hua Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang, 310018, China.
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16
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Pratush A, Ye X, Yang Q, Kan J, Peng T, Wang H, Huang T, Xiong G, Hu Z. Biotransformation strategies for steroid estrogen and androgen pollution. Appl Microbiol Biotechnol 2020; 104:2385-2409. [PMID: 31993703 DOI: 10.1007/s00253-020-10374-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 01/06/2020] [Accepted: 01/12/2020] [Indexed: 12/21/2022]
Abstract
The common steroid hormones are estrone (E1), 17β-estradiol (E2), estriol (E3), 17α-ethinylestradiol (EE2), and testosterone (T). These steroids are reported to contaminate the environment through wastewater treatment plants. Steroid estrogens are widespread in the aquatic environment and therefore pose a potential risk, as exposure to these compounds has adverse impacts on vertebrates. Excessive exposure to steroid estrogens causes endocrine disruption in aquatic vertebrates, which affects the normal sexual life of these animals. Steroid pollutants also cause several health problems in humans and other animals. Microbial degradation is an efficient method for removing hormone pollutants from the environment by remediation. Over the last two decades, microbial metabolism of steroids has gained considerable attention due to its higher efficiency to reduce pollutants from the environment. The present review is focused on the major causes of steroid pollution, concentrations of these pollutants in surface water, groundwater, drinking water, and wastewater, their effect on humans and aquatic animals, as well as recent efforts by various research groups that seek better ways to degrade steroids by aerobic and anaerobic microbial systems. Detailed overview of aerobic and anaerobic microbial biotransformation of steroid estrogens and testosterone present in the environment along with the active enzyme systems involved in these biotransformation reactions is described in the review article, which helps readers to understand the biotransformation mechanism of steroids in depth. Other measures such as co-metabolic degradation, consortia degradation, algal, and fungal steroid biotransformation are also discussed in detail.
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Affiliation(s)
- Amit Pratush
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Xueying Ye
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Qi Yang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Jie Kan
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Tao Peng
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Hui Wang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Tongwang Huang
- Biology Department, College of Science, Shantou University, Shantou, 515063, China
| | - Guangming Xiong
- Institute of Toxicology and Pharmacology for Natural Scientists, University Medical School, Schleswig-Holstein, Campus Kiel, Brunswiker Str. 10, 24105, Kiel, Germany
| | - Zhong Hu
- Biology Department, College of Science, Shantou University, Shantou, 515063, China.
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17
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Zhang X, Peng Y, Zhao J, Li Q, Yu X, Acevedo-Rocha CG, Li A. Bacterial cytochrome P450-catalyzed regio- and stereoselective steroid hydroxylation enabled by directed evolution and rational design. BIORESOUR BIOPROCESS 2020. [DOI: 10.1186/s40643-019-0290-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AbstractSteroids are the most widely marketed products by the pharmaceutical industry after antibiotics. Steroid hydroxylation is one of the most important functionalizations because their derivatives enable a higher biological activity compared to their less polar non-hydroxylated analogs. Bacterial cytochrome P450s constitute promising biocatalysts for steroid hydroxylation due to their high expression level in common workhorses like Escherichia coli. However, they often suffer from wrong or insufficient regio- and/or stereoselectivity, low activity, narrow substrate range as well as insufficient thermostability, which hampers their industrial application. Fortunately, these problems can be generally solved by protein engineering based on directed evolution and rational design. In this work, an overview of recent developments on the engineering of bacterial cytochrome P450s for steroid hydroxylation is presented.
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18
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Hydroxylation of Steroids by a Microbial Substrate-Promiscuous P450 Cytochrome (CYP105D7): Key Arginine Residues for Rational Design. Appl Environ Microbiol 2019; 85:AEM.01530-19. [PMID: 31540985 DOI: 10.1128/aem.01530-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/11/2019] [Indexed: 11/20/2022] Open
Abstract
Our previous study showed that CYP105D7, a substrate-promiscuous P450, catalyzes the hydroxylation of 1-deoxypentalenic acid, diclofenac, naringenin, and compactin. In this study, 14 steroid compounds were screened using recombinant Escherichia coli cells harboring genes encoding CYP105D7 and redox partners (Pdx/Pdr, RhFRED, and FdxH/FprD), and the screening identified steroid A-ring 2β- and D-ring 16β-hydroxylation activity. Wild-type CYP105D7 was able to catalyze the hydroxylation of five steroids (testosterone, progesterone, 4-androstene-3,17-dione, adrenosterone, and cortisone) with low (<10%) conversion rates. Structure-guided site-directed mutagenesis of arginine residues around the substrate entrance and active site showed that the R70A and R190A single mutants and an R70A/R190A double mutant exhibited greatly enhanced conversion rates for steroid hydroxylation. For the conversion of testosterone in particular, the R70A/R190A mutant's k cat/Km values increased 1.35-fold and the in vivo conversion rates increased significantly by almost 9-fold with high regio- and stereoselectivity. Molecular docking analysis revealed that when Arg70 and Arg190 were replaced with alanine, the volume of the substrate access and binding pocket increased 1.08-fold, which might facilitate improvement of the hydroxylation efficiency of steroids.IMPORTANCE Cytochrome P450 monooxygenases (P450s) are able to introduce oxygen atoms into nonreactive hydrocarbon compounds under mild conditions, thereby offering significant advantages compared to chemical catalysts. Promiscuous P450s with broad substrate specificity and reaction diversity have significant potential for applications in various fields, including synthetic biology. The study of the function, molecular mechanisms, and rational engineering of substrate-promiscuous P450s from microbial sources is important to fulfill this potential. Here, we present a microbial substrate-promiscuous P450, CYP105D7, which can catalyze hydroxylation of steroids. The loss of the bulky side chains of Arg70 and Arg190 in the active site and substrate entrance resulted in an up to 9-fold increase in the substrate conversion rate. These findings will support future rational and semirational engineering of P450s for applications as biocatalysts.
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19
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Distinct Regioselectivity of Fungal P450 Enzymes for Steroidal Hydroxylation. Appl Environ Microbiol 2019; 85:AEM.01182-19. [PMID: 31324634 DOI: 10.1128/aem.01182-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 06/25/2019] [Indexed: 01/25/2023] Open
Abstract
In this study, we identified two P450 enzymes (CYP5150AP3 and CYP5150AN1) from Thanatephorus cucumeris NBRC 6298 by combination of transcriptome sequencing and heterologous expression in Pichia pastoris The biotransformation of 11-deoxycortisol and testosterone by Pichia pastoris whole cells coexpressing the cyp5150ap3 and por genes demonstrated that the CYP5150AP3 enzyme possessed steroidal 7β-hydroxylase activities toward these substrates, and the regioselectivity was dependent on the structures of steroidal compounds. CYP5150AN1 catalyzed the 2β-hydroxylation of 11-deoxycortisol. It is interesting that they display different regioselectivity of hydroxylation from that of their isoenzyme, CYP5150AP2, which possesses 19- and 11β-hydroxylase activities.IMPORTANCE The steroidal hydroxylases CYP5150AP3 and CYP5150AN1 together with the previously characterized CYP5150AP2 belong to the CYP5150A family of P450 enzymes with high amino acid sequence identity, but they showed completely different regioselectivities toward 11-deoxycortisol, suggesting the regioselectivity diversity of steroidal hydroxylases of CYP5150 family. They are also distinct from the known bacterial and fungal steroidal hydroxylases in substrate specificity and regioselectivity. Biocatalytic hydroxylation is one of the important transformations for the functionalization of steroid nucleus rings but remains a very challenging task in organic synthesis. These hydroxylases are useful additions to the toolbox of hydroxylase enzymes for the functionalization of steroids at various positions.
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20
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Dangi B, Lee CW, Kim K, Park S, Yu E, Jeong C, Park H, Lee JH, Oh T. Characterization of two steroid hydroxylases from different
Streptomyces
spp. and their ligand‐bound and ‐unbound crystal structures. FEBS J 2018; 286:1683-1699. [DOI: 10.1111/febs.14729] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/20/2018] [Accepted: 12/09/2018] [Indexed: 01/04/2023]
Affiliation(s)
- Bikash Dangi
- Department of Life Science and Biochemical Engineering Sunmoon University Asansi Korea
| | - Chang Woo Lee
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
- Department of Polar Sciences University of Science and Technology Incheon Korea
| | - Ki‐Hwa Kim
- Department of Life Science and Biochemical Engineering Sunmoon University Asansi Korea
| | - Sun‐Ha Park
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
| | - Eun‐Ji Yu
- Department of Life Science and Biochemical Engineering Sunmoon University Asansi Korea
| | - Chang‐Sook Jeong
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
- Department of Polar Sciences University of Science and Technology Incheon Korea
| | - Hyun Park
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
- Department of Polar Sciences University of Science and Technology Incheon Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics Korea Polar Research Institute Incheon Korea
- Department of Polar Sciences University of Science and Technology Incheon Korea
| | - Tae‐Jin Oh
- Department of Life Science and Biochemical Engineering Sunmoon University Asansi Korea
- Genome‐based BioIT Convergence Institute Asansi Korea
- Department of Pharmaceutical Engineering and Biotechnology Sunmoon University Asansi Korea
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21
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Dangi B, Park H, Oh TJ. Effects of Alternative Redox Partners and Oxidizing Agents on CYP154C8 Catalytic Activity and Product Distribution. Chembiochem 2018; 19:2273-2282. [PMID: 30136363 DOI: 10.1002/cbic.201800284] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/23/2018] [Indexed: 12/11/2022]
Abstract
CYP154C8 catalyzes the hydroxylation of diverse steroids, as has previously been demonstrated, by using an NADH-dependent system including putidaredoxin and putidaredoxin reductase as redox partner proteins carrying electrons from NADH. In other reactions, CYP154C8 reconstituted with spinach ferredoxin and NADPH-dependent ferredoxin reductase displayed catalytic activity different from that of the NADH-dependent system. The NADPH-dependent system showed multistep oxidation of progesterone and other substrates including androstenedione, testosterone, and nandrolone. (Diacetoxyiodo)benzene was employed to generate compound I (FeO3+ ), actively supporting the redox reactions catalyzed by CYP154C8. In addition to 16α-hydroxylation, progesterone and 11-oxoprogesterone also underwent hydroxylation at the 6β-position in reactions supported by (diacetoxyiodo)benzene. CYP154C8 was active in the presence of high concentrations (>10 mm) of H2 O2 , with optimum conversion surprisingly being achieved at ≈75 mm H2 O2 . More importantly, H2 O2 tolerance by CYP154C8 was evident in the very low heme oxidation rate constant (K) even at high concentrations of H2 O2 . Our results demonstrate that alternative redox partners and oxidizing agents influence the catalytic efficiency and product distribution of a cytochrome P450 enzyme. More importantly, these choices affected the type and selectivity of reaction catalyzed by the P450 enzyme.
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Affiliation(s)
- Bikash Dangi
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Hyun Park
- Unit of Polar Genomics, Korea Polar Research Institute, Incheon, 21990, Republic of Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, 21990, Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Department of Pharmaceutical Engineering and Biotechnology, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Genome-based BioIT Convergence Institute, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
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22
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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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23
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Szaleniec M, Wojtkiewicz AM, Bernhardt R, Borowski T, Donova M. Bacterial steroid hydroxylases: enzyme classes, their functions and comparison of their catalytic mechanisms. Appl Microbiol Biotechnol 2018; 102:8153-8171. [PMID: 30032434 PMCID: PMC6153880 DOI: 10.1007/s00253-018-9239-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022]
Abstract
The steroid superfamily includes a wide range of compounds that are essential for living organisms of the animal and plant kingdoms. Structural modifications of steroids highly affect their biological activity. In this review, we focus on hydroxylation of steroids by bacterial hydroxylases, which take part in steroid catabolic pathways and play an important role in steroid degradation. We compare three distinct classes of metalloenzymes responsible for aerobic or anaerobic hydroxylation of steroids, namely: cytochrome P450, Rieske-type monooxygenase 3-ketosteroid 9α-hydroxylase, and molybdenum-containing steroid C25 dehydrogenases. We analyze the available literature data on reactivity, regioselectivity, and potential application of these enzymes in organic synthesis of hydroxysteroids. Moreover, we describe mechanistic hypotheses proposed for all three classes of enzymes along with experimental and theoretical evidences, which have provided grounds for their formulation. In case of the 3-ketosteroid 9α-hydroxylase, such a mechanistic hypothesis is formulated for the first time in the literature based on studies conducted for other Rieske monooxygenases. Finally, we provide comparative analysis of similarities and differences in the reaction mechanisms utilized by bacterial steroid hydroxylases.
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Affiliation(s)
- Maciej Szaleniec
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland.
| | - Agnieszka M Wojtkiewicz
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland
| | - Rita Bernhardt
- Lehrstuhl für Biochemie, Universität des Saarlandes, Campus B2 2, 66123, Saarbrücken, Germany
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Kraków, Poland
| | - Marina Donova
- G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Oblast, 142290, Russia
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24
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Dangi B, Kim KH, Kang SH, Oh TJ. Tracking Down a New Steroid-Hydroxylating Promiscuous Cytochrome P450: CYP154C8 fromStreptomycessp. W2233-SM. Chembiochem 2018. [DOI: 10.1002/cbic.201800018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bikash Dangi
- Department of Life Science and Biochemical Engineering; SunMoon University; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Ki-Hwa Kim
- Department of Life Science and Biochemical Engineering; SunMoon University; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
| | - Sang-Ho Kang
- Genomics Division; National Institute of Agricultural Sciences, RDA; Jeonju 54874 Republic of Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering; SunMoon University; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
- Department of Pharmaceutical Engineering and Biotechnology; SunMoon University; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
- Genome-based BioIT Convergence Institute; 70 Sunmoon-ro 221 Tangjeong-myeon Asan-si Chungnam 31460 Republic of Korea
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25
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Acevedo-Rocha CG, Gamble CG, Lonsdale R, Li A, Nett N, Hoebenreich S, Lingnau JB, Wirtz C, Fares C, Hinrichs H, Deege A, Mulholland AJ, Nov Y, Leys D, McLean KJ, Munro AW, Reetz MT. P450-Catalyzed Regio- and Diastereoselective Steroid Hydroxylation: Efficient Directed Evolution Enabled by Mutability Landscaping. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00389] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carlos G. Acevedo-Rocha
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Charles G. Gamble
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Richard Lonsdale
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Aitao Li
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University 368 Youyi Road, Wuchang Wuhan 430062, China
| | - Nathalie Nett
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Sabrina Hoebenreich
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
| | - Julia B. Lingnau
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Cornelia Wirtz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Christophe Fares
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Heike Hinrichs
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Alfred Deege
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, U.K
| | - Yuval Nov
- Department of Statistics, University of Haifa, Haifa 31905, Israel
| | - David Leys
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Kirsty J. McLean
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Andrew W. Munro
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Manfred T. Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany
- Department of Chemistry, Philipps-University, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany
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26
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Rühlmann A, Groth G, Urlacher VB. Characterization of CYP154F1 from Thermobifida fusca YX and Extension of Its Substrate Spectrum by Site-Directed Mutagenesis. Chembiochem 2018; 19:478-485. [PMID: 29266604 DOI: 10.1002/cbic.201700565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Indexed: 11/05/2022]
Abstract
Previous studies on cytochrome P450 monooxygenases (CYP) from family 154 reported their substrate promiscuity and high activity. Hence, herein, the uncharacterized family member CYP154F1 is described. Screening of more than 100 organic compounds revealed that CYP154F1 preferably accepts small linear molecules with a carbon chain length of 8-10 atoms. In contrast to thoroughly characterized CYP154E1, CYP154F1 has a much narrower substrate spectrum and lower activity. A structural alignment of homology models of CYP154F1 and CYP154E1 revealed few differences in the active sites of both family members. By gradual mutagenesis of the CYP154F1 active site towards those of CYP154E1, a key residue accounting for the different activities of both enzymes was identified at position 234. Substitution of T234 for large hydrophobic amino acids led to up to tenfold higher conversion rates of small substrates, such as geraniol. Replacement of T234 by small hydrophobic amino acids, valine or alanine, resulted in mutants with extended substrate spectra. These mutants are able to convert some of the larger substrates of CYP154E1, such as (E)-stilbene and (+)-nootkatone.
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Affiliation(s)
- Ansgar Rühlmann
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Georg Groth
- Institute of Biochemical Plant Physiology, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
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Hara Y, Arai MA, Sakai K, Ishikawa N, Gonoi T, Yaguchi T, Ishibashi M. Dehydropropylpantothenamide isolated by a co-culture of Nocardia tenerifensis IFM 10554T in the presence of animal cells. J Nat Med 2017; 72:280-289. [DOI: 10.1007/s11418-017-1161-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 11/30/2017] [Indexed: 10/18/2022]
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28
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Świzdor A, Panek A, Milecka-Tronina N. Hydroxylative activity of Aspergillus niger towards androst-4-ene and androst-5-ene steroids. Steroids 2017; 126:101-106. [PMID: 28827070 DOI: 10.1016/j.steroids.2017.08.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/05/2017] [Accepted: 08/14/2017] [Indexed: 11/27/2022]
Abstract
Aspergillus niger, one of fungal species most frequently used for experimental and industrial-scale biotransformations of various organic compounds, is generally known to transform steroids at 16β position. In this work, application of the strain A. niger KCH910 to bioconversion of dehydroepiandrosterone (DHEA), androstenediol and testosterone is described, with emphasis on the metabolic steps leading to the products. Evidence from this study indicated that incubated 5-ene steroids underwent bioconversion within two metabolic pathways: oxidation by the action of 3β-HSD (3β-hydroxysteroid dehydrogenase) to 4-ene steroids, and minor allylic hydroxylation to epimeric 7-alcohols. Further transformation of the 3-oxo-4-ene metabolites resulted in non-selective 16-hydroxylation. It is the first report on an A. niger strain able to introduce not only 16β- but also 16α-hydroxyl function into steroids.
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Affiliation(s)
- Alina Świzdor
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Anna Panek
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland.
| | - Natalia Milecka-Tronina
- Department of Chemistry, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
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29
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Rudolf JD, Chang CY, Ma M, Shen B. Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function. Nat Prod Rep 2017; 34:1141-1172. [PMID: 28758170 PMCID: PMC5585785 DOI: 10.1039/c7np00034k] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: up to January 2017Cytochrome P450 enzymes (P450s) are some of the most exquisite and versatile biocatalysts found in nature. In addition to their well-known roles in steroid biosynthesis and drug metabolism in humans, P450s are key players in natural product biosynthetic pathways. Natural products, the most chemically and structurally diverse small molecules known, require an extensive collection of P450s to accept and functionalize their unique scaffolds. In this review, we survey the current catalytic landscape of P450s within the Streptomyces genus, one of the most prolific producers of natural products, and comprehensively summarize the functionally characterized P450s from Streptomyces. A sequence similarity network of >8500 P450s revealed insights into the sequence-function relationships of these oxygen-dependent metalloenzymes. Although only ∼2.4% and <0.4% of streptomycete P450s have been functionally and structurally characterized, respectively, the study of streptomycete P450s involved in the biosynthesis of natural products has revealed their diverse roles in nature, expanded their catalytic repertoire, created structural and mechanistic paradigms, and exposed their potential for biomedical and biotechnological applications. Continued study of these remarkable enzymes will undoubtedly expose their true complement of chemical and biological capabilities.
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Affiliation(s)
- Jeffrey D Rudolf
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
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30
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Xiong S, Wang Y, Yao M, Liu H, Zhou X, Xiao W, Yuan Y. Cell foundry with high product specificity and catalytic activity for 21-deoxycortisol biotransformation. Microb Cell Fact 2017; 16:105. [PMID: 28610588 PMCID: PMC5470312 DOI: 10.1186/s12934-017-0720-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/06/2017] [Indexed: 12/22/2022] Open
Abstract
Background 21-deoxycortisol (21-DF) is the key intermediate to manufacture pharmaceutical glucocorticoids. Recently, a Japan patent has realized 21-DF production via biotransformation of 17-hydroxyprogesterone (17-OHP) by purified steroid 11β-hydroxylase CYP11B1. Due to the less costs on enzyme isolation, purification and stabilization as well as cofactors supply, whole-cell should be preferentially employed as the biocatalyst over purified enzymes. No reports as so far have demonstrated a whole-cell system to produce 21-DF. Therefore, this study aimed to establish a whole-cell biocatalyst to achieve 21-DF transformation with high catalytic activity and product specificity. Results In this study, Escherichia coli MG1655(DE3), which exhibited the highest substrate transportation rate among other tested chassises, was employed as the host cell to construct our biocatalyst by co-expressing heterologous CYP11B1 together with bovine adrenodoxin and adrenodoxin reductase. Through screening CYP11B1s (with mutagenesis at N-terminus) from nine sources, Homo sapiens CYP11B1 mutant (G25R/G46R/L52 M) achieved the highest 21-DF transformation rate at 10.6 mg/L/h. Furthermore, an optimal substrate concentration of 2.4 g/L and a corresponding transformation rate of 16.2 mg/L/h were obtained by screening substrate concentrations. To be noted, based on structural analysis of the enzyme-substrate complex, two types of site-directed mutations were designed to adjust the relative position between the catalytic active site heme and the substrate. Accordingly, 1.96-fold enhancement on 21-DF transformation rate (to 47.9 mg/L/h) and 2.78-fold improvement on product/by-product ratio (from 0.36 to 1.36) were achieved by the combined mutagenesis of F381A/L382S/I488L. Eventually, after 38-h biotransformation in shake-flask, the production of 21-DF reached to 1.42 g/L with a yield of 52.7%, which is the highest 21-DF production as known. Conclusions Heterologous CYP11B1 was manipulated to construct E. coli biocatalyst converting 17-OHP to 21-DF. Through the strategies in terms of (1) screening enzymes (with N-terminal mutagenesis) sources, (2) optimizing substrate concentration, and most importantly (3) rational design novel mutants aided by structural analysis, the 21-DF transformation rate was stepwise improved by 19.5-fold along with 4.67-fold increase on the product/byproduct ratio. Eventually, the highest 21-DF reported production was achieved in shake-flask after 38-h biotransformation. This study highlighted above described methods to obtain a high efficient and specific biocatalyst for the desired biotransformation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0720-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shuting Xiong
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Ying Wang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Mingdong Yao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Hong Liu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Xiao Zhou
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Wenhai Xiao
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
| | - Yingjin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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31
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Kiebist J, Schmidtke K, Zimmermann J, Kellner H, Jehmlich N, Ullrich R, Zänder D, Hofrichter M, Scheibner K. A Peroxygenase from Chaetomium globosum Catalyzes the Selective Oxygenation of Testosterone. Chembiochem 2017; 18:563-569. [PMID: 28103392 PMCID: PMC5363369 DOI: 10.1002/cbic.201600677] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Indexed: 01/18/2023]
Abstract
Unspecific peroxygenases (UPO, EC 1.11.2.1) secreted by fungi open an efficient way to selectively oxyfunctionalize diverse organic substrates, including less-activated hydrocarbons, by transferring peroxide-borne oxygen. We investigated a cell-free approach to incorporate epoxy and hydroxyl functionalities directly into the bulky molecule testosterone by a novel unspecific peroxygenase (UPO) that is produced by the ascomycetous fungus Chaetomium globosum in a complex medium rich in carbon and nitrogen. Purification by fast protein liquid chromatography revealed two enzyme fractions with the same molecular mass (36 kDa) and with specific activity of 4.4 to 12 U mg-1 . Although the well-known UPOs of Agrocybe aegerita (AaeUPO) and Marasmius rotula (MroUPO) failed to convert testosterone in a comparative study, the UPO of C. globosum (CglUPO) accepted testosterone as substrate and converted it with total turnover number (TTN) of up to 7000 into two oxygenated products: the 4,5-epoxide of testosterone in β-configuration and 16α-hydroxytestosterone. The reaction performed on a 100 mg scale resulted in the formation of about 90 % of the epoxide and 10 % of the hydroxylation product, both of which could be isolated with purities above 96 %. Thus, CglUPO is a promising biocatalyst for the oxyfunctionalization of bulky steroids and it will be a useful tool for the synthesis of pharmaceutically relevant steroidal molecules.
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Affiliation(s)
- Jan Kiebist
- Faculty of Environment and Natural SciencesBrandenburg University of Technology Cottbus-SenftenbergUniversitätsplatz 101968SenftenbergGermany
| | - Kai‐Uwe Schmidtke
- Faculty of Environment and Natural SciencesBrandenburg University of Technology Cottbus-SenftenbergUniversitätsplatz 101968SenftenbergGermany
| | - Jörg Zimmermann
- Faculty of Environment and Natural SciencesBrandenburg University of Technology Cottbus-SenftenbergUniversitätsplatz 101968SenftenbergGermany
| | - Harald Kellner
- Department of Bio- and Environmental SciencesTU DresdenInternational Institute ZittauMarkt 2302763ZittauGermany
| | - Nico Jehmlich
- Department of Molecular Systems BiologyHelmholtz-Centre for Environmental ResearchUFZPermoserstrasse 1504318LeipzigGermany
| | - René Ullrich
- Department of Bio- and Environmental SciencesTU DresdenInternational Institute ZittauMarkt 2302763ZittauGermany
| | | | - Martin Hofrichter
- Department of Bio- and Environmental SciencesTU DresdenInternational Institute ZittauMarkt 2302763ZittauGermany
| | - Katrin Scheibner
- Faculty of Environment and Natural SciencesBrandenburg University of Technology Cottbus-SenftenbergUniversitätsplatz 101968SenftenbergGermany
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32
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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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33
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Liu L, Yao Q, Ma Z, Ikeda H, Fushinobu S, Xu LH. Hydroxylation of flavanones by cytochrome P450 105D7 from Streptomyces avermitilis. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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34
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Identification, characterization and molecular adaptation of class I redox systems for the production of hydroxylated diterpenoids. Microb Cell Fact 2016; 15:86. [PMID: 27216162 PMCID: PMC4877809 DOI: 10.1186/s12934-016-0487-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 05/11/2016] [Indexed: 12/31/2022] Open
Abstract
Background De novo production of multi-hydroxylated diterpenoids is challenging due to the lack of efficient redox systems. Results In this study a new reductase/ferredoxin system from Streptomyces afghaniensis (AfR·Afx) was identified, which allowed the Escherichia coli-based production of the trihydroxylated diterpene cyclooctatin, a potent inhibitor of human lysophospholipase. This production system provides a 43-fold increase in cyclooctatin yield (15 mg/L) compared to the native producer. AfR·Afx is superior in activating the cylcooctatin-specific class I P450s CotB3/CotB4 compared to the conventional Pseudomonas putida derived PdR·Pdx model. To enhance the activity of the PdR·Pdx system, the molecular basis for these activity differences, was examined by molecular engineering. Conclusion We demonstrate that redox system engineering can boost and harmonize the catalytic efficiency of class I hydroxylase enzyme cascades. Enhancing CotB3/CotB4 activities also provided for identification of CotB3 substrate promiscuity and sinularcasbane D production, a functionalized diterpenoid originally isolated from the soft coral Sinularia sp. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0487-6) contains supplementary material, which is available to authorized users.
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35
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Hatakeyama M, Kitaoka T, Ichinose H. Heterologous expression of fungal cytochromes P450 (CYP5136A1 and CYP5136A3) from the white-rot basidiomycete Phanerochaete chrysosporium: Functionalization with cytochrome b5 in Escherichia coli. Enzyme Microb Technol 2016; 89:7-14. [PMID: 27233123 DOI: 10.1016/j.enzmictec.2016.03.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/14/2016] [Accepted: 03/08/2016] [Indexed: 12/21/2022]
Abstract
Cytochromes P450 from the white-rot basidiomycete Phanerochaete chrysosporium, CYP5136A1 and CYP5136A3, are capable of catalyzing oxygenation reactions of a wide variety of exogenous compounds, implying their significant roles in the metabolism of xenobiotics by the fungus. It is therefore interesting to explore their biochemistry to better understand fungal biology and to enable the use of fungal enzymes in the biotechnology sector. In the present study, we developed heterologous expression systems for CYP5136A1 and CYP5136A3 using the T7 RNA polymerase/promoter system in Escherichia coli. Expression levels of recombinant P450s were dramatically improved by modifications and optimization of their N-terminal amino acid sequences. A CYP5136A1 reaction system was reconstructed in E. coli whole cells by coexpression of CYP5136A1 and a redox partner, NADPH-dependent P450 reductase (CPR). The catalytic activity of CYP5136A1 was significantly increased when cytochrome b5 (Cyt-b5) was further coexpressed with CPR, indicating that Cyt-b5 supports electron transfer reactions from NAD(P)H to CYP5136A1. Notably, P450 reaction occurred in E. coli cells that harbored CYP5136A1 and Cyt-b5 but not CPR, implying that the reducing equivalents required for the P450 catalytic cycle were transferred via a CPR-independent pathway. Such an "alternative" electron transfer system in CYP5136A1 reaction was also demonstrated using purified enzymes in vitro. The fungal P450 reaction system may be associated with sophisticated electron transfer pathways.
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Affiliation(s)
- Mayumi Hatakeyama
- Faculty of Agriculture, Kyushu University, 6-10-(1) Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, 6-10-(1) Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
| | - Hirofumi Ichinose
- Faculty of Agriculture, Kyushu University, 6-10-(1) Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan.
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36
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Khatri Y, Ringle. M, Lisurek M, von Kries JP, Zapp J, Bernhardt R. Substrate Hunting for the Myxobacterial CYP260A1 Revealed New 1α-Hydroxylated Products from C-19 Steroids. Chembiochem 2015; 17:90-101. [DOI: 10.1002/cbic.201500420] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Yogan Khatri
- Universität des Saarlandes; Biochemie; Campus B2.2 66123 Saarbrücken Germany
| | - Michael Ringle.
- Universität des Saarlandes; Biochemie; Campus B2.2 66123 Saarbrücken Germany
| | - Michael Lisurek
- Forschungsinstitut für Molekulare Pharmakologie; Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Jens Peter von Kries
- Forschungsinstitut für Molekulare Pharmakologie; Robert-Rössle-Strasse 10 13125 Berlin Germany
| | - Josef Zapp
- Universität des Saarlandes; Pharmazeutische Biologie; Campus C2.2 66123 Saarbrücken Germany
| | - Rita Bernhardt
- Universität des Saarlandes; Biochemie; Campus B2.2 66123 Saarbrücken Germany
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Comparison of CYP106A1 and CYP106A2 from Bacillus megaterium – identification of a novel 11-oxidase activity. Appl Microbiol Biotechnol 2015; 99:8495-514. [DOI: 10.1007/s00253-015-6563-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Revised: 03/09/2015] [Accepted: 03/19/2015] [Indexed: 12/13/2022]
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38
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Herzog K, Bracco P, Onoda A, Hayashi T, Hoffmann K, Schallmey A. Enzyme-substrate complex structures of CYP154C5 shed light on its mode of highly selective steroid hydroxylation. ACTA ACUST UNITED AC 2014; 70:2875-89. [PMID: 25372679 DOI: 10.1107/s1399004714019129] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/25/2014] [Indexed: 01/06/2023]
Abstract
CYP154C5 from Nocardia farcinica is a bacterial cytochrome P450 monooxygenase active on steroid molecules. The enzyme has recently been shown to exhibit exclusive regioselectivity and stereoselectivity in the conversion of various pregnans and androstans, yielding 16α-hydroxylated steroid products. This makes the enzyme an attractive candidate for industrial application in steroid hormone synthesis. Here, crystal structures of CYP154C5 in complex with four different steroid molecules were solved at resolutions of up to 1.9 Å. These are the first reported P450 structures from the CYP154 family in complex with a substrate. The active site of CYP154C5 forms a flattened hydrophobic channel with two opposing polar regions, perfectly resembling the size and polarity distribution of the steroids and thus resulting in highly specific steroid binding with Kd values in the range 10-100 nM. Key enzyme-substrate interactions were identified that accounted for the exclusive regioselectivity and stereoselectivity of the enzyme. Additionally, comparison of the four CYP154C5-steroid structures revealed distinct structural differences, explaining the observed variations in kinetic data obtained for this P450 with the steroids pregnenolone, dehydroepiandrosterone, progesterone, androstenedione, testosterone and nandrolone. This will facilitate the generation of variants with improved activity or altered selectivity in the future by means of protein engineering.
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Affiliation(s)
- Konrad Herzog
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Paula Bracco
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
| | - Akira Onoda
- Department of Applied Chemistry, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kurt Hoffmann
- Institute of Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Anett Schallmey
- Junior Professorship for Biocatalysis, Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany
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