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Schulz V, Basu S, Freibert SA, Webert H, Boss L, Mühlenhoff U, Pierrel F, Essen LO, Warui DM, Booker SJ, Stehling O, Lill R. Functional spectrum and specificity of mitochondrial ferredoxins FDX1 and FDX2. Nat Chem Biol 2023; 19:206-217. [PMID: 36280795 PMCID: PMC10873809 DOI: 10.1038/s41589-022-01159-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/01/2022] [Indexed: 02/04/2023]
Abstract
Ferredoxins comprise a large family of iron-sulfur (Fe-S) proteins that shuttle electrons in diverse biological processes. Human mitochondria contain two isoforms of [2Fe-2S] ferredoxins, FDX1 (aka adrenodoxin) and FDX2, with known functions in cytochrome P450-dependent steroid transformations and Fe-S protein biogenesis. Here, we show that only FDX2, but not FDX1, is involved in Fe-S protein maturation. Vice versa, FDX1 is specific not only for steroidogenesis, but also for heme a and lipoyl cofactor biosyntheses. In the latter pathway, FDX1 provides electrons to kickstart the radical chain reaction catalyzed by lipoyl synthase. We also identified lipoylation as a target of the toxic antitumor copper ionophore elesclomol. Finally, the striking target specificity of each ferredoxin was assigned to small conserved sequence motifs. Swapping these motifs changed the target specificity of these electron donors. Together, our findings identify new biochemical tasks of mitochondrial ferredoxins and provide structural insights into their functional specificity.
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Affiliation(s)
- Vinzent Schulz
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Somsuvro Basu
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
- Freelance Medical Communications Consultant, Brno, Czech Republic
| | - Sven-A Freibert
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Holger Webert
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Linda Boss
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Ulrich Mühlenhoff
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany
| | - Fabien Pierrel
- Univ. of Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble, France
| | - Lars-O Essen
- Department of Biochemistry, Faculty of Chemistry, Philipps University of Marburg, Marburg, Germany
| | - Douglas M Warui
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- The Howard Hughes Medical Institute, The Pennsylvania State University, University Park, PA, USA
| | - Oliver Stehling
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany.
- Centre for Synthetic Microbiology, Synmikro, Marburg, Germany.
| | - Roland Lill
- Institute for Cytobiology, Philipps University of Marburg, Marburg, Germany.
- Centre for Synthetic Microbiology, Synmikro, Marburg, Germany.
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2
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Nguyen KT, Nguyen NL, Milhim M, Nguyen VT, Lai THN, Nguyen HH, Le TTX, Phan TTM, Bernhardt R. Characterization of a thermophilic cytochrome P450 of the CYP203A subfamily from Binh Chau hot spring in Vietnam. FEBS Open Bio 2020; 11:124-132. [PMID: 33176055 PMCID: PMC7780096 DOI: 10.1002/2211-5463.13033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 12/18/2022] Open
Abstract
Cytochromes P450 (CYPs or P450s) comprise a superfamily of heme-containing monooxygenases that are involved in a variety of biological processes. CYPs have broad utilities in industry, but most exhibit low thermostability, limiting their use on an industrial scale. Highly thermostable enzymes can be obtained from thermophiles in geothermal areas, including hot springs, offshore oil-producing wells and volcanoes. Here, we report the identification of a gene encoding for a thermophilic CYP from the Binh Chau hot spring metagenomic database, which was designated as P450-T2. The deduced amino acid sequence showed the highest identity of 73.15% with CYP203A1 of Rhodopseudomonas palustris, supporting that P450-T2 is a member of the CYP203A subfamily. Recombinant protein expression yielded 541 nm. The optimal temperature and pH of P450-T2 were 50 °C and 8.0, respectively. The half-life of P450-T2 was 50.2 min at 50 °C, and its melting temperature was 56.80 ± 0.08 °C. It was found to accept electrons from all tested redox partners systems, with BmCPR-Fdx2 being the most effective partner. Screening for putative substrates revealed binding of phenolic compounds, such as l-mimosine and emodin, suggesting a potential application of this new thermophilic P450 in the production of the corresponding hydroxylated products.
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Affiliation(s)
- Kim-Thoa Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Ngoc-Lan Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Mohammed Milhim
- Department of Biochemistry, Saarland University, Saarbrucken, Germany
| | - Van-Tung Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Hong-Nhung Lai
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Huy-Hoang Nguyen
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam.,Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Thanh-Xuan Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thi-Tuyet-Minh Phan
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Rita Bernhardt
- Department of Biochemistry, Saarland University, Saarbrucken, Germany
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3
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A Novel Thermostable Cytochrome P450 from Sequence-Based Metagenomics of Binh Chau Hot Spring as a Promising Catalyst for Testosterone Conversion. Catalysts 2020. [DOI: 10.3390/catal10091083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Biotechnological applications of cytochromes P450 show difficulties, such as low activity, thermal and/or solvent instability, narrow substrate specificity and redox partner dependence. In an attempt to overcome these limitations, an exploitation of novel thermophilic P450 enzymes from nature via uncultured approaches is desirable due to their great advantages that can resolve nearly all mentioned impediments. From the metagenomics library of the Binh Chau hot spring, an open reading frame (ORF) encoding a thermostable cytochrome P450—designated as P450-T3—which shared 66.6% amino acid sequence identity with CYP109C2 of Sorangium cellulosum So ce56 was selected for further identification and characterization. The ORF was synthesized artificially and heterologously expressed in Escherichia coli C43(DE3) using the pET17b system. The purified enzyme had a molecular weight of approximately 43 kDa. The melting temperature of the purified enzyme was 76.2 °C and its apparent half-life at 60 °C was 38.7 min. Redox partner screening revealed that P450-T3 was reduced well by the mammalian AdR-Adx4-108 and the yeast Arh1-Etp1 redox partners. Lauric acid, palmitic acid, embelin, retinoic acid (all-trans) and retinoic acid (13-cis) demonstrated binding to P450-T3. Interestingly, P450-T3 also bound and converted testosterone. Overall, P450-T3 might become a good candidate for biocatalytic applications on a larger scale.
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4
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Sagadin T, Riehm J, Putkaradze N, Hutter MC, Bernhardt R. Novel approach to improve progesterone hydroxylation selectivity by
CYP
106A2 via rational design of adrenodoxin binding. FEBS J 2019; 286:1240-1249. [DOI: 10.1111/febs.14722] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/09/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Tanja Sagadin
- Department of Biochemistry Saarland University Saarbrücken Germany
| | - Jan Riehm
- Center for Bioinformatics Saarland University Saarbrücken Germany
| | | | | | - Rita Bernhardt
- Department of Biochemistry Saarland University Saarbrücken Germany
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5
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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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Brengel C, Thomann A, Schifrin A, Allegretta G, Kamal AAM, Haupenthal J, Schnorr I, Cho SH, Franzblau SG, Empting M, Eberhard J, Hartmann RW. Biophysical Screening of a Focused Library for the Discovery of CYP121 Inhibitors as Novel Antimycobacterials. ChemMedChem 2017; 12:1616-1626. [DOI: 10.1002/cmdc.201700363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/04/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Alexander Schifrin
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
| | - Giuseppe Allegretta
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Ahmed A. M. Kamal
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Isabell Schnorr
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Sang Hyun Cho
- Institute for Tuberculosis Research; College of Pharmacy; University of Illinois at Chicago; 833 S. Wood Street Chicago IL 60612-7231 USA
| | - Scott G. Franzblau
- Institute for Tuberculosis Research; College of Pharmacy; University of Illinois at Chicago; 833 S. Wood Street Chicago IL 60612-7231 USA
| | - Martin Empting
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Jens Eberhard
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland, HIPS; Department for Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
- Department of Pharmacy; Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2.3 66123 Saarbrücken Germany
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7
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Harris KL, Thomson RES, Strohmaier SJ, Gumulya Y, Gillam EMJ. Determinants of thermostability in the cytochrome P450 fold. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1866:97-115. [PMID: 28822812 DOI: 10.1016/j.bbapap.2017.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/19/2017] [Accepted: 08/07/2017] [Indexed: 10/19/2022]
Abstract
Cytochromes P450 are found throughout the biosphere in a wide range of environments, serving a multitude of physiological functions. The ubiquity of the P450 fold suggests that it has been co-opted by evolution many times, and likely presents a useful compromise between structural stability and conformational flexibility. The diversity of substrates metabolized and reactions catalyzed by P450s makes them attractive starting materials for use as biocatalysts of commercially useful reactions. However, process conditions impose different requirements on enzymes to those in which they have evolved naturally. Most natural environments are relatively mild, and therefore most P450s have not been selected in Nature for the ability to withstand temperatures above ~40°C, yet industrial processes frequently require extended incubations at much higher temperatures. Thus, there has been considerable interest and effort invested in finding or engineering thermostable P450 systems. Numerous P450s have now been identified in thermophilic organisms and analysis of their structures provides information as to mechanisms by which the P450 fold can be stabilized. In addition, protein engineering, particularly by directed or artificial evolution, has revealed mutations that serve to stabilize particular mesophilic enzymes of interest. Here we review the current understanding of thermostability as it applies to the P450 fold, gleaned from the analysis of P450s characterized from thermophilic organisms and the parallel engineering of mesophilic forms for greater thermostability. We then present a perspective on how this information might be used to design stable P450 enzymes for industrial 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)
- Kurt L Harris
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Raine E S Thomson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Silja J Strohmaier
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Yosephine Gumulya
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia 4072, Australia.
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8
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Brengel C, Thomann A, Schifrin A, Eberhard J, Hartmann RW. Discovery and Biophysical Evaluation of First Low Nanomolar Hits Targeting CYP125 ofM. tuberculosis. ChemMedChem 2016; 11:2385-2391. [DOI: 10.1002/cmdc.201600361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/01/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Christian Brengel
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Andreas Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Alexander Schifrin
- Department of Biochemistry; Saarland University; Campus B2.2 66123 Saarbrücken Germany
| | - Jens Eberhard
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
| | - Rolf W. Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland; Department of Drug Design and Optimization; Campus E8.1 66123 Saarbrücken Germany
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry; Saarland University; Campus C2.3 66123 Saarbrücken Germany
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9
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Zanello P. The competition between chemistry and biology in assembling iron–sulfur derivatives. Molecular structures and electrochemistry. Part II. {[Fe2S2](SγCys)4} proteins. Coord Chem Rev 2014. [DOI: 10.1016/j.ccr.2014.08.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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10
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Bell SG, McMillan JHC, Yorke JA, Kavanagh E, Johnson EOD, Wong LL. Tailoring an alien ferredoxin to support native-like P450 monooxygenase activity. Chem Commun (Camb) 2012; 48:11692-4. [DOI: 10.1039/c2cc35968e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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11
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Kleser M, Hannemann F, Hutter M, Zapp J, Bernhardt R. CYP105A1 mediated 3-hydroxylation of glimepiride and glibenclamide using a recombinant Bacillus megaterium whole-cell catalyst. J Biotechnol 2011; 157:405-12. [PMID: 22202177 DOI: 10.1016/j.jbiotec.2011.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 11/17/2011] [Accepted: 12/12/2011] [Indexed: 11/15/2022]
Abstract
CYP105A1 from Streptomyces griseolus belongs to a widespread family of soluble prokaryotic cytochromes P450. For in vitro studies we established an electron transfer system, consisting of the ferredoxin Etp1(fd) and the ferredoxin reductase Arh1 from the fission yeast Schizosaccharomyces pombe. We investigated the metabolism of glibenclamide and glimepiride, hypoglycemic drugs of sulfonylurea type, and determined corresponding in vitro kinetic parameters. The resulting 3-cyclohexyl-hydroxylation activity towards glibenclamide and glimepiride was demonstrated by NMR analysis. Furthermore, the main product of glibenclamide, cis-3-hydroxy-glibenclamide is identical with the phase-1-metabolite of this drug in human. The orientation of glimepiride and glibenclamide in the active site of the enzyme is shown by a computational docking model. For high scale production of sulfonylurea derivatives, we designed whole-cell biocatalysts based on Bacillus megaterium MS941. Surprisingly, the system expressing only CYP105A1 showed a similar activity towards hydroxylation of glimepiride and glibenclamide compared to the system expressing additionally the redox partners, Arh1 and Etp1(fd)(516-618), indicating that the host strain provides a functional endogenous electron transfer system.
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Affiliation(s)
- Michael Kleser
- Universität des Saarlandes, Institut für Biochemie, Campus B2.2, 66123 Saarbrücken, Germany
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