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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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2
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Molinaro C, Kawasaki Y, Wanyoike G, Nishioka T, Yamamoto T, Snedecor B, Robinson SJ, Gosselin F. Engineered Cytochrome P450-Catalyzed Oxidative Biaryl Coupling Reaction Provides a Scalable Entry into Arylomycin Antibiotics. J Am Chem Soc 2022; 144:14838-14845. [PMID: 35905381 DOI: 10.1021/jacs.2c06019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report herein the first example of a cytochrome P450-catalyzed oxidative carbon-carbon coupling process for a scalable entry into arylomycin antibiotic cores. Starting from wild-type hydroxylating cytochrome P450 enzymes and engineered Escherichia coli, a combination of enzyme engineering, random mutagenesis, and optimization of reaction conditions generated a P450 variant that affords the desired arylomycin core 2d in 84% assay yield. Furthermore, this process was demonstrated as a viable route for the production of the arylomycin antibiotic core on the gram scale. Finally, this new entry affords a viable, scalable, and practical route for the synthesis of novel Gram-negative antibiotics.
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Affiliation(s)
- Carmela Molinaro
- Department of Small Molecule Process Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yukie Kawasaki
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - George Wanyoike
- Production Technology Department, MicroBiopharm Japan Co. Ltd., 1808 Nakaizumi, Iwata, Shizuoka 438-0078, Japan
| | - Taiki Nishioka
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - Tsuyoshi Yamamoto
- Applied Microbiotechnology Department, MicroBiopharm Japan Co. Ltd., 156 Nakagawara, Kiyosu, Aichi 452-0915, Japan
| | - Brad Snedecor
- Department of Cell Culture and Bioprocess Operations, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Sarah J Robinson
- Department of Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Francis Gosselin
- Department of Small Molecule Process Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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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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4
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Affiliation(s)
- Judith Münch
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Pascal Püllmann
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West seventh Avenue, Tianjin 300308, China
- National Technology Innovation Center of Synthetic Biology, 32 West seventh Avenue, Tianjin 300308, China
| | - Martin J. Weissenborn
- Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Saale, Germany
- Institute of Chemistry, MartinLuther-University Halle-Wittenberg, Kurt-Mothes-Strasse 2, 06120, Halle, Saale, Germany
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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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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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7
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Binding modes of CYP106A2 redox partners determine differences in progesterone hydroxylation product patterns. Commun Biol 2018; 1:99. [PMID: 30271979 PMCID: PMC6123783 DOI: 10.1038/s42003-018-0104-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 06/27/2018] [Indexed: 11/17/2022] Open
Abstract
Natural redox partners of bacterial cytochrome P450s (P450s) are mostly unknown. Therefore, substrate conversions are performed with heterologous redox partners; in the case of CYP106A2 from Bacillus megaterium ATCC 13368, bovine adrenodoxin (Adx) and adrenodoxin reductase (AdR). Our aim was to optimize the redox system for CYP106A2 for improved product formation by testing 11 different combinations of redox partners. We found that electron transfer protein 1(516–618) showed the highest yield of the main product, 15β-hydroxyprogesterone, and, furthermore, produced a reduced amount of unwanted polyhydroxylated side products. Molecular protein–protein docking indicated that this is caused by subtle structural changes leading to alternative binding modes of both redox enzymes. Stopped-flow measurements analyzing the CYP106A2 reduction and showing substantial differences in the apparent rate constants supported this conclusion. The study provides for the first time to our knowledge rational explanations for differences in product patterns of a cytochrome P450 caused by difference in the binding mode of the redox partners. Tanja Sagadin et al. show that different redox systems can be used to tune the rate selectivity and yield of progesterone conversion by the cytochrome P450 CYP106A2. They screen 11 redox partner combinations and identify specific combinations that may be used to improve biotechnological production of mono- and polyhydroxylated products.
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Bakkes PJ, Riehm JL, Sagadin T, Rühlmann A, Schubert P, Biemann S, Girhard M, Hutter MC, Bernhardt R, Urlacher VB. Engineering of versatile redox partner fusions that support monooxygenase activity of functionally diverse cytochrome P450s. Sci Rep 2017; 7:9570. [PMID: 28852040 PMCID: PMC5575160 DOI: 10.1038/s41598-017-10075-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 08/04/2017] [Indexed: 12/12/2022] Open
Abstract
Most bacterial cytochrome P450 monooxygenases (P450s or CYPs) require two redox partner proteins for activity. To reduce complexity of the redox chain, the Bacillus subtilis flavodoxin YkuN (Y) was fused to the Escherichia coli flavodoxin reductase Fpr (R), and activity was tuned by placing flexible (GGGGS)n or rigid ([E/L]PPPP)n linkers (n = 1–5) in between. P-linker constructs typically outperformed their G-linker counterparts, with superior performance of YR-P5, which carries linker ([E/L]PPPP)5. Molecular dynamics simulations demonstrated that ([E/L]PPPP)n linkers are intrinsically rigid, whereas (GGGGS)n linkers are highly flexible and biochemical experiments suggest a higher degree of separation between the fusion partners in case of long rigid P-linkers. The catalytic properties of the individual redox partners were best preserved in the YR-P5 construct. In comparison to the separate redox partners, YR-P5 exhibited attenuated rates of NADPH oxidation and heme iron (III) reduction, while coupling efficiency was improved (28% vs. 49% coupling with B. subtilis CYP109B1, and 44% vs. 50% with Thermobifida fusca CYP154E1). In addition, YR-P5 supported monooxygenase activity of the CYP106A2 from Bacillus megaterium and bovine CYP21A2. The versatile YR-P5 may serve as a non-physiological electron transfer system for exploitation of the catalytic potential of other P450s.
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Affiliation(s)
- Patrick J Bakkes
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Jan L Riehm
- Center for Bioinformatics, Saarland University, Campus Building E2.1, 66123, Saarbrücken, Germany
| | - Tanja Sagadin
- Institute of Biochemistry, Saarland University, Campus Building B2.2, 66123, Saarbrücken, Germany
| | - Ansgar Rühlmann
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Peter Schubert
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Stefan Biemann
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Marco Girhard
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Michael C Hutter
- Center for Bioinformatics, Saarland University, Campus Building E2.1, 66123, Saarbrücken, Germany
| | - Rita Bernhardt
- Institute of Biochemistry, Saarland University, Campus Building B2.2, 66123, Saarbrücken, Germany
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
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Schmitz D, Janocha S, Kiss FM, Bernhardt R. CYP106A2-A versatile biocatalyst with high potential for biotechnological production of selectively hydroxylated steroid and terpenoid compounds. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:11-22. [PMID: 28780179 DOI: 10.1016/j.bbapap.2017.07.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 12/12/2022]
Abstract
CYP106A2 from Bacillus megaterium ATCC13368, was identified in the 1970s as one of the first bacterial steroid hydroxylases responsible for the conversion of progesterone to 15β-hydroxyprogesterone. Later on it has been proven to be a potent hydroxylase of numerous 3-oxo-Δ4 as well as 3-hydroxy-Δ5-steroids and has recently also been characterized as a regioselective allylic bacterial diterpene hydroxylase. The main hydroxylation position of CYP106A2 is thought to be influenced by the functional groups at C3 position in the steroid core leading to a favored 15β-hydroxylation of 3-oxo-Δ4-steroids and 7β-hydroxylation of 3-hydroxy-Δ5-steroids. However, in some cases the hydroxylation is not strictly selective, resulting in the formation of undesired side-products. To overcome the unspecific hydroxylations or, on the contrary, to gain more of these products in case they are of industrial interest, rational protein design and directed evolution have been successfully performed to shift the stereoselectivity of hydroxylation by CYP106A2. The subsequently obtained hydroxylated steroid and terpene derivatives are especially useful as drug metabolites and drug precursors for the pharmaceutical industry, due to their diverse biological properties and hardship of their chemical synthesis. As a soluble prokaryotic P450 with broad substrate spectrum and hydroxylating capacity, CYP106A2 is an outstanding candidate to establish bioconversion processes. It has been expressed with respectable yields in Escherichia coli and Bacillus megaterium and was applied for the preparative hydroxylation of several steroids and terpenes. Recently, the application of the enzyme was assessed under process conditions as well, depicting a successfully optimized process development and getting us closer to industrial scale process requirements and a future large scale application. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.
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Affiliation(s)
- Daniela Schmitz
- Department of Biochemistry, Saarland University, Campus B2.2, 66123 Saarbruecken, Germany
| | - Simon Janocha
- Department of Biochemistry, Saarland University, Campus B2.2, 66123 Saarbruecken, Germany
| | - Flora Marta Kiss
- Department of Biochemistry, Saarland University, Campus B2.2, 66123 Saarbruecken, Germany
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Campus B2.2, 66123 Saarbruecken, Germany.
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Nikolaus J, Nguyen KT, Virus C, Riehm JL, Hutter M, Bernhardt R. Engineering of CYP106A2 for steroid 9α- and 6β-hydroxylation. Steroids 2017; 120:41-48. [PMID: 28163026 DOI: 10.1016/j.steroids.2017.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/07/2017] [Accepted: 01/17/2017] [Indexed: 11/25/2022]
Abstract
CYP 106A2 from Bacillus megaterium ATCC 13368 has been described as a 15β-hydroxylase showing also minor 11α-, 9α- and 6β-hydroxylase activity for progesterone conversion. Previously, mutant proteins with a changed selectivity towards 11α-OH-progesterone have already been produced. The challenge of this work was to create mutant proteins with a higher regioselectivity towards hydroxylation at positions 9 and 6 of the steroid molecule. 9α-hydroxyprogesterone exhibits pharmaceutical importance, because it is a useful intermediate in the production of physiologically active substances which possess progestational activity. Sixteen mutant proteins were selected from a library containing mutated proteins created by a combination of site-directed and saturation mutagenesis of active site residues. Four mutant proteins out of these catalyzed the conversion of progesterone to 9α-OH-progesterone as a main product. For further optimization site-directed mutagenesis was performed. The introduction of seven mutations (D217V, A243V, A106T, F165L, T89N, T247V or T247W) into these four mutant proteins led to 28 new variants, which were also used for an in vivo conversion of progesterone. The best mutant protein, F165L/A395E/G397V, showed a ten-fold increase in the selectivity towards progesterone 9α-hydroxylation compared with the wild type CYP106A2. Also 6β-OH-progesterone is a pharmaceutically important compound, especially as intermediate for the production of drugs against breast cancer. For the rational design of mutant proteins with 6β-selectivity, docking of the 3D-structure of CYP106A2 with progesterone was performed. The introduction of three mutations (T247A, A243S, F173A) led to seven new mutant proteins. Clone A243S showed the greatest improvement in 6β-selectivity being more than ten-fold. Finally, an in vivo conversion of 11-deoxycorticosterone (DOC), testosterone and cortisol with the best five mutant proteins displaying 9α- or 6β-hydroxylation, respectively, of progesterone was performed to investigate whether the introduced mutations also effected the conversion of other substrates.
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Affiliation(s)
- Julia Nikolaus
- Department of Biochemistry, Saarland University, Campus B2.2, 66123 Saarbrücken, Germany
| | - Kim Thoa Nguyen
- Department of Biochemistry, Saarland University, Campus B2.2, 66123 Saarbrücken, Germany
| | - Cornelia Virus
- Department of Biochemistry, Saarland University, Campus B2.2, 66123 Saarbrücken, Germany
| | - Jan L Riehm
- Center for Bioinformatics, Saarland University, Campus E2.1, 66123 Saarbrücken, Germany
| | - Michael Hutter
- Center for Bioinformatics, Saarland University, Campus E2.1, 66123 Saarbrücken, Germany
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Campus B2.2, 66123 Saarbrücken, Germany.
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Janocha S, Carius Y, Hutter M, Lancaster CRD, Bernhardt R. Crystal Structure of CYP106A2 in Substrate-Free and Substrate-Bound Form. Chembiochem 2016; 17:852-60. [DOI: 10.1002/cbic.201500524] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Simon Janocha
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
| | - Yvonne Carius
- Department of Structural Biology, ZHMB; Saarland University; Building 60 66421 Homburg Germany
| | - Michael Hutter
- Center for Bioinformatics; Saarland University; Campus E2.1 66123 Saarbrücken Germany
| | - C. Roy D. Lancaster
- Department of Structural Biology, ZHMB; Saarland University; Building 60 66421 Homburg Germany
| | - Rita Bernhardt
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
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12
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Balabanova L, Golotin V, Podvolotskaya A, Rasskazov V. Genetically modified proteins: functional improvement and chimeragenesis. Bioengineered 2015. [PMID: 26211369 DOI: 10.1080/21655979.2015.1075674] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
This review focuses on the emerging role of site-specific mutagenesis and chimeragenesis for the functional improvement of proteins in areas where traditional protein engineering methods have been extensively used and practically exhausted. The novel path for the creation of the novel proteins has been created on the farther development of the new structure and sequence optimization algorithms for generating and designing the accurate structure models in result of x-ray crystallography studies of a lot of proteins and their mutant forms. Artificial genetic modifications aim to expand nature's repertoire of biomolecules. One of the most exciting potential results of mutagenesis or chimeragenesis finding could be design of effective diagnostics, bio-therapeutics and biocatalysts. A sampling of recent examples is listed below for the in vivo and in vitro genetically improvement of various binding protein and enzyme functions, with references for more in-depth study provided for the reader's benefit.
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Affiliation(s)
- Larissa Balabanova
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | - Vasily Golotin
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia.,b Far Eastern Federal University ; Vladivostok , Russia
| | | | - Valery Rasskazov
- a G.B. Elyakov Pacific Institute of Bioorganic Chemistry; Far Eastern Branch; Russian Academy of Science ; Vladivostok , Russia
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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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Janocha S, Schmitz D, Bernhardt R. Terpene hydroxylation with microbial cytochrome P450 monooxygenases. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 148:215-50. [PMID: 25682070 DOI: 10.1007/10_2014_296] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Terpenoids comprise a highly diverse group of natural products. In addition to their basic carbon skeleton, they differ from one another in their functional groups. Functional groups attached to the carbon skeleton are the basis of the terpenoids' diverse properties. Further modifications of terpene olefins include the introduction of acyl-, aryl-, or sugar moieties and usually start with oxidations catalyzed by cytochrome P450 monooxygenases (P450s, CYPs). P450s are ubiquitously distributed throughout nature, involved in essential biological pathways such as terpenoid biosynthesis as well as the tailoring of terpenoids and other natural products. Their ability to introduce oxygen into nonactivated C-H bonds is unique and makes P450s very attractive for applications in biotechnology. Especially in the field of terpene oxidation, biotransformation methods emerge as an attractive alternative to classical chemical synthesis. For this reason, microbial P450s depict a highly interesting target for protein engineering approaches in order to increase selectivity and activity, respectively. Microbial P450s have been described to convert industrial and pharmaceutically interesting terpenoids such as ionones, limone, valencene, resin acids, and triterpenes (including steroids) as well as vitamin D3. Highly selective and active mutants have been evolved by applying classical site-directed mutagenesis as well as directed evolution of proteins. As P450s usually depend on electron transfer proteins, mutagenesis has also been applied to improve the interactions between P450s and their respective redox partners. This chapter provides an overview of terpenoid hydroxylation reactions catalyzed by bacterial P450s and highlights the achievements made by protein engineering to establish productive hydroxylation processes.
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Affiliation(s)
- Simon Janocha
- Department of Biochemistry, Saarland University, Campus B2 2, 66123, Saarbruecken, Germany
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15
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Roiban GD, Reetz MT. Expanding the toolbox of organic chemists: directed evolution of P450 monooxygenases as catalysts in regio- and stereoselective oxidative hydroxylation. Chem Commun (Camb) 2015; 51:2208-24. [DOI: 10.1039/c4cc09218j] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cytochrome P450 enzymes (CYPs) have been used for more than six decades as catalysts for the CH-activating oxidative hydroxylation of organic compounds with formation of added-value products.
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Affiliation(s)
| | - Manfred T. Reetz
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
- Max-Planck-Institut für Kohlenforschung
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16
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Schmitz D, Zapp J, Bernhardt R. Steroid conversion with CYP106A2 - production of pharmaceutically interesting DHEA metabolites. Microb Cell Fact 2014; 13:81. [PMID: 24903845 PMCID: PMC4080778 DOI: 10.1186/1475-2859-13-81] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 04/13/2014] [Indexed: 12/13/2022] Open
Abstract
Background Steroids are lipophilic compounds with a gonane skeleton and play an important role in higher organisms. Due to different functionalizations - mainly hydroxylations - at the steroid molecule, they vary highly in their mode of action. The pharmaceutical industry is, therefore, interested in hydroxysteroids as therapeutic agents. The insertion of hydroxyl groups into a steroid core, however, is hardly accomplishable by classical chemical means; that is because microbial steroid hydroxylations are investigated and applied since decades. CYP106A2 is a cytochrome P450 monooxygenase from Bacillus megaterium ATCC 13368, which was first described in the late 1970s and which is capable to hydroxylate a variety of 3-oxo-delta4 steroids at position 15beta. CYP106A2 is a soluble protein, easy to express and to purify in high amounts, which makes this enzyme an interesting target for biotechnological purposes. Results In this work a focused steroid library was screened in vitro for new CYP106A2 substrates using a reconstituted enzyme assay. Five new substrates were identified, including dehydroepiandrosterone and pregnenolone. NMR-spectroscopy revealed that both steroids are mainly hydroxylated at position 7beta. In order to establish a biotechnological system for the preparative scale production of 7beta-hydroxylated dehydroepiandrosterone, whole-cell conversions with growing and resting cells of B. megaterium ATCC1336 the native host of CYP1062 and also with resting cells of a recombinant B. megaterium MS941 strain overexpressing CYP106A2 have been conducted and conversion rates of 400 muM/h (115 mg/l/h) were obtained. Using the B. megaterium MS941 overexpression strain, the selectivity of the reaction was improved from 0.7 to 0.9 for 7beta-OH-DHEA. Conclusions In this work we describe CYP106A2 for the first time as a regio-selective hydroxylase for 3-hydroxy-delta5 steroids. DHEA was shown to be converted to 7beta-OH-DHEA which is a highly interesting human metabolite, supposed to act as neuroprotective, anti-inflammatory and immune-modulatory agent. Optimization of the whole-cell system using different B. megaterium strains lead to a conversion of DHEA with B. megaterium showing high selectivity and conversion rates and displaying a volumetric yield of 103 mg/l/h 7beta-OH-DHEA.
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Affiliation(s)
| | | | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Campus B2 2, Saarbruecken 66123, Germany.
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Bernhardt R, Urlacher VB. Cytochromes P450 as promising catalysts for biotechnological application: chances and limitations. Appl Microbiol Biotechnol 2014; 98:6185-203. [PMID: 24848420 DOI: 10.1007/s00253-014-5767-7] [Citation(s) in RCA: 248] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 01/08/2023]
Abstract
Cytochromes P450 (CYPs) belong to the superfamily of heme b containing monooxygenases with currently more than 21,000 members. These enzymes accept a vast range of organic molecules and catalyze diverse reactions. These extraordinary capabilities of CYP systems that are unmet by other enzymes make them attractive for biotechnology. However, the complexity of these systems due to the need of electron transfer from nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) via redox partner proteins for the initial hydroxylation step limits a broader technical implementation of CYP enzymes. There have been several reviews during the past years tackling the potential CYPs for synthetic application. The aim of this review is to give a critical overview about possibilities and chances for application of these interesting catalysts as well as to discuss drawbacks and problems related to their use. Solutions to overcome these limitations will be demonstrated, and several selected examples of successful CYP applications under industrial conditions will be reviewed.
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Affiliation(s)
- Rita Bernhardt
- Institute of Biochemistry, Saarland University, 66123, Saarbrücken, Germany,
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Gricman Ł, Vogel C, Pleiss J. Conservation analysis of class-specific positions in cytochrome P450 monooxygenases: Functional and structural relevance. Proteins 2013; 82:491-504. [DOI: 10.1002/prot.24415] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 08/23/2013] [Accepted: 09/02/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Łukasz Gricman
- Institute of Technical Biochemistry, University of Stuttgart; 70569 Stuttgart Germany
| | - Constantin Vogel
- Institute of Technical Biochemistry, University of Stuttgart; 70569 Stuttgart Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart; 70569 Stuttgart Germany
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Stereo- and regioselectivity in the P450-catalyzed oxidative tandem difunctionalization of 1-methylcyclohexene. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.04.132] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Reetz MT. Laboratory evolution of stereoselective enzymes as a means to expand the toolbox of organic chemists. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.05.093] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Agudo R, Roiban GD, Reetz MT. Achieving regio- and enantioselectivity of P450-catalyzed oxidative CH activation of small functionalized molecules by structure-guided directed evolution. Chembiochem 2012; 13:1465-73. [PMID: 22711296 DOI: 10.1002/cbic.201200244] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Indexed: 11/08/2022]
Abstract
Directed evolution of the monooxygenase P450-BM3 utilizing iterative saturation mutagenesis at and near the binding site enables a high degree of both regio- and enantioselectivity in the oxidative hydroxylation of cyclohexene-1-carboxylic acid methyl ester. Wild-type P450-BM3 is 84% regioselective for the allylic 3-position with 34% enantioselectivity in favor of the R alcohol. Mutants enabling R selectivity (>95% ee) or S selectivity (>95% ee) were evolved, while reducing other oxidation products and thus maximizing regioselectivity to >93%. Control of the substrate-to-enzyme ratio is necessary for obtaining optimal and reproducible enantioselectivities, an observation which is important in future protein engineering of these mono-oxygenases. An E. coli strain capable of NADPH regeneration was also engineered, simplifying directed evolution of P450 enzymes in general. These synthetic results set the stage for subsequent stereoselective and stereospecific chemical transformations to form more complex compounds, thereby illustrating the viability of combining genetically altered enzymes as catalysts in organic chemistry with traditional chemical methods.
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Affiliation(s)
- Rubén Agudo
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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Nguyen KT, Virus C, Günnewich N, Hannemann F, Bernhardt R. Changing the Regioselectivity of a P450 from C15 to C11 Hydroxylation of Progesterone. Chembiochem 2012; 13:1161-6. [DOI: 10.1002/cbic.201100811] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Indexed: 11/11/2022]
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Schmitz D, Zapp J, Bernhardt R. Hydroxylation of the triterpenoid dipterocarpol with CYP106A2 from Bacillus megaterium. FEBS J 2012; 279:1663-74. [DOI: 10.1111/j.1742-4658.2012.08503.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kille S, Zilly FE, Acevedo JP, Reetz MT. Regio- and stereoselectivity of P450-catalysed hydroxylation of steroids controlled by laboratory evolution. Nat Chem 2011; 3:738-43. [PMID: 21860465 DOI: 10.1038/nchem.1113] [Citation(s) in RCA: 286] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/07/2011] [Indexed: 11/09/2022]
Abstract
A current challenge in synthetic organic chemistry is the development of methods that allow the regio- and stereoselective oxidative C-H activation of natural or synthetic compounds with formation of the corresponding alcohols. Cytochrome P450 enzymes enable C-H activation at non-activated positions, but the simultaneous control of both regio- and stereoselectivity is problematic. Here, we demonstrate that directed evolution using iterative saturation mutagenesis provides a means to solve synthetic problems of this kind. Using P450 BM3(F87A) as the starting enzyme and testosterone as the substrate, which results in a 1:1 mixture of the 2β- and 15β-alcohols, mutants were obtained that are 96-97% selective for either of the two regioisomers, each with complete diastereoselectivity. The mutants can be used for selective oxidative hydroxylation of other steroids without performing additional mutagenesis experiments. Molecular dynamics simulations and docking experiments shed light on the origin of regio- and stereoselectivity.
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Affiliation(s)
- Sabrina Kille
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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A new Bacillus megaterium whole-cell catalyst for the hydroxylation of the pentacyclic triterpene 11-keto-β-boswellic acid (KBA) based on a recombinant cytochrome P450 system. Appl Microbiol Biotechnol 2011; 93:1135-46. [DOI: 10.1007/s00253-011-3467-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 06/17/2011] [Accepted: 06/23/2011] [Indexed: 10/18/2022]
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Bleif S, Hannemann F, Lisurek M, von Kries JP, Zapp J, Dietzen M, Antes I, Bernhardt R. Identification of CYP106A2 as a Regioselective Allylic Bacterial Diterpene Hydroxylase. Chembiochem 2011; 12:576-82. [DOI: 10.1002/cbic.201000404] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Indexed: 11/06/2022]
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Khatri Y, Girhard M, Romankiewicz A, Ringle M, Hannemann F, Urlacher VB, Hutter MC, Bernhardt R. Regioselective hydroxylation of norisoprenoids by CYP109D1 from Sorangium cellulosum So ce56. Appl Microbiol Biotechnol 2010; 88:485-95. [PMID: 20645086 DOI: 10.1007/s00253-010-2756-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2010] [Revised: 06/29/2010] [Accepted: 06/29/2010] [Indexed: 11/26/2022]
Abstract
Sesquiterpenes are particularly interesting as flavorings and fragrances or as pharmaceuticals. Regio- or stereoselective functionalizations of terpenes are one of the main goals of synthetic organic chemistry, which are possible through radical reactions but are not selective enough to introduce the desired chiral alcohol function into those compounds. Cytochrome P450 monooxygenases are versatile biocatalysts and are capable of performing selective oxidations of organic molecules. We were able to demonstrate that CYP109D1 from Sorangium cellulosum So ce56 functions as a biocatalyst for the highly regioselective hydroxylation of norisoprenoids, alpha- and beta-ionone, which are important aroma compounds of floral scents. The substrates alpha- and beta-ionone were regioselectively hydroxylated to 3-hydroxy-alpha-ionone and 4-hydroxy-beta-ionone, respectively, which was confirmed by (1)H NMR and (13)C NMR. The results of docking alpha- and beta-ionone into a homology model of CYP109D1 gave a rational explanation for the regio-selectivity of the hydroxylation. Kinetic studies revealed that alpha- and beta-ionone can be hydroxylated with nearly identical V (max) and K (m) values. This is the first comprehensive investigation of the regioselective hydroxylation of norisoprenoids by CYP109D1.
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Affiliation(s)
- Yogan Khatri
- Department of Biochemistry, Saarland University, Saarbrücken, Germany
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Zehentgruber D, Hannemann F, Bleif S, Bernhardt R, Lütz S. Towards Preparative Scale Steroid Hydroxylation with Cytochrome P450 Monooxygenase CYP106A2. Chembiochem 2010; 11:713-21. [DOI: 10.1002/cbic.200900706] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Goñi G, Zöllner A, Lisurek M, Velázquez-Campoy A, Pinto S, Gómez-Moreno C, Hannemann F, Bernhardt R, Medina M. Cyanobacterial electron carrier proteins as electron donors to CYP106A2 from Bacillus megaterium ATCC 13368. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:1635-42. [DOI: 10.1016/j.bbapap.2009.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 07/02/2009] [Accepted: 07/17/2009] [Indexed: 11/15/2022]
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Virus C, Bernhardt R. Molecular evolution of a steroid hydroxylating cytochrome P450 using a versatile steroid detection system for screening. Lipids 2008; 43:1133-41. [PMID: 18830657 DOI: 10.1007/s11745-008-3236-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Accepted: 08/30/2008] [Indexed: 11/26/2022]
Abstract
Molecular evolution is a powerful tool for improving or changing activities of enzymes for their use in biotechnological processes. Cytochromes P450 are highly interesting enzymes for biotechnological purposes because they are able to hydroxylate a broad variety of substrates with high regio- and stereoselectivity. One promising steroid hydroxylating cytochrome P450 for biotechnological applications is CYP106A2 from Bacillus megaterium ATCC 13368. It is one of a few known bacterial cytochromes P450 able to transform steroids such as progesterone and 11-deoxycortisol. CYP106A2 can be easily expressed in Escherichia coli with a high yield and can be reconstituted using the adrenal redox proteins, adrenodoxin and adrenodoxin reductase. We developed a simple screening assay for this system and performed random mutagenesis of CYP106A2, yielding variants with improved 11-deoxycortisol and progesterone hydroxylation activity. After two generations of directed evolution, we were able to improve the k (cat)/K (m) of the 11-deoxycortisol hydroxylation by a factor of more than four. At the same time progesterone conversion was improved about 1.4-fold. Mapping the mutations identified in catalytically improved CYP106A2 variants into the structure of a CYP106A2 model suggests that these mutations influence the mobility of the F/G loop, and the interaction with the redox partner adrenodoxin. The results show the evolution of a soluble steroid hydroxylase as a potential new catalyst for the production of steroidogenic compounds.
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Affiliation(s)
- Cornelia Virus
- Naturwissenschaftlich-Technische Fakultät III, Institut für Biochemie, Universität des Saarlandes, Postfach 151150, 66041, Saarbrücken, Germany.
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