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Zhan T, Jacoby C, Jede M, Knapp B, Ferlaino S, Günter A, Drepper F, Müller M, Weber S, Boll M. Bacterial stigmasterol degradation involving radical flavin delta-24 desaturase and molybdenum-dependent C26 hydroxylase. J Biol Chem 2024; 300:107243. [PMID: 38556086 PMCID: PMC11061730 DOI: 10.1016/j.jbc.2024.107243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/20/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024] Open
Abstract
Sterols are ubiquitous membrane constituents that persist to a large extent in the environment due to their water insolubility and chemical inertness. Recently, an oxygenase-independent sterol degradation pathway was discovered in a cholesterol-grown denitrifying bacterium Sterolibacterium (S.) denitrificans. It achieves hydroxylation of the unactivated primary C26 of the isoprenoid side chain to an allylic alcohol via a phosphorylated intermediate in a four-step ATP-dependent enzyme cascade. However, this pathway is incompatible with the degradation of widely distributed steroids containing a double bond at C22 in the isoprenoid side chain such as the plant sterol stigmasterol. Here, we have enriched a prototypical delta-24 desaturase from S. denitrificans, which catalyzes the electron acceptor-dependent oxidation of the intermediate stigmast-1,4-diene-3-one to a conjugated (22,24)-diene. We suggest an α4β4 architecture of the 440 kDa enzyme, with each subunit covalently binding an flavin mononucleotide cofactor to a histidyl residue. As isolated, both flavins are present as red semiquinone radicals, which can be reduced by stigmast-1,4-diene-3-one but cannot be oxidized even with strong oxidizing agents. We propose a mechanism involving an allylic radical intermediate in which two flavin semiquinones each abstract one hydrogen atom from the substrate. The conjugated delta-22,24 moiety formed allows for the subsequent hydroxylation of the terminal C26 with water by a heterologously produced molybdenum-dependent steroid C26 dehydrogenase 2. In conclusion, the pathway elucidated for delta-22 steroids achieves oxygen-independent hydroxylation of the isoprenoid side chain by bypassing the ATP-dependent formation of a phosphorylated intermediate.
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Affiliation(s)
- Tingyi Zhan
- Faculty of Biology, Department of Microbiology, University of Freiburg, Freiburg, Germany
| | - Christian Jacoby
- Faculty of Biology, Department of Microbiology, University of Freiburg, Freiburg, Germany
| | - Martin Jede
- Faculty of Biology, Department of Microbiology, University of Freiburg, Freiburg, Germany
| | - Bettina Knapp
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, Freiburg, Germany
| | - Sascha Ferlaino
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Andreas Günter
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Friedel Drepper
- Faculty of Biology, Department of Biochemistry and Functional Proteomics, University of Freiburg, Freiburg, Germany
| | - Michael Müller
- Institute of Pharmaceutical Sciences, University of Freiburg, Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, University of Freiburg, Freiburg, Germany
| | - Matthias Boll
- Faculty of Biology, Department of Microbiology, University of Freiburg, Freiburg, Germany.
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The Power of Biocatalysts for Highly Selective and Efficient Phosphorylation Reactions. Catalysts 2022. [DOI: 10.3390/catal12111436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Reactions involving the transfer of phosphorus-containing groups are of key importance for maintaining life, from biological cells, tissues and organs to plants, animals, humans, ecosystems and the whole planet earth. The sustainable utilization of the nonrenewable element phosphorus is of key importance for a balanced phosphorus cycle. Significant advances have been achieved in highly selective and efficient biocatalytic phosphorylation reactions, fundamental and applied aspects of phosphorylation biocatalysts, novel phosphorylation biocatalysts, discovery methodologies and tools, analytical and synthetic applications, useful phosphoryl donors and systems for their regeneration, reaction engineering, product recovery and purification. Biocatalytic phosphorylation reactions with complete conversion therefore provide an excellent reaction platform for valuable analytical and synthetic applications.
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Jacoby C, Ebenau-Jehle C, Saum K, Jehmlich N, von Bergen M, Brüls T, Boll M. Genes and enzymes involved in the biodegradation of the quaternary carbon compound pivalate in the denitrifying Thauera humireducens strain PIV-1. Environ Microbiol 2022; 24:3181-3194. [PMID: 35437936 DOI: 10.1111/1462-2920.16021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/17/2022] [Indexed: 11/28/2022]
Abstract
Quaternary carbon containing compounds exist in natural and fossil oil derived products and are used in chemical and pharmaceutical applications up to industrial scale. Due to the inaccessibility of the quaternary carbon atom for a direct oxidative or reductive attack, they are considered as persistent in the environment. Here, we investigated the unknown degradation of the quaternary carbon-containing model compound pivalate (2,2-dimethyl-propionate) in the denitrifying bacterium Thauera humireducens strain PIV-1 (formerly T. pivalivorans). We provide multiple evidence for a pathway comprising the activation to pivalyl-CoA and the carbon skeleton rearrangement to isovaleryl-CoA. Subsequent reactions proceed similar to the catabolic leucine degradation pathway such as the carboxylation to 3-methylglutaconyl-CoA and the cleavage of 3-methyl-3-hydroxyglutaryl-CoA to acetyl-CoA and acetoacetate. The completed genome of Thauera humireducens strain PIV-1 together with proteomic data was used to identify pivalate-upregulated gene clusters including genes putatively encoding pivalate CoA ligase and adenosylcobalamin-dependent pivalyl-CoA mutase. A pivalate-induced gene encoding a putative carboxylic acid CoA ligase was heterologously expressed, and its highly enriched product exhibited pivalate CoA ligase activity. The results provide first experimental insights into the biodegradation pathway of a quaternary carbon-containing model compound that serves as a blueprint for the degradation of related quaternary carbon-containing compounds. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Christian Jacoby
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Christa Ebenau-Jehle
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Katharina Saum
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Nico Jehmlich
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany.,Department of Molecular Systems Biology, Helmholtz,Centre for Environmental Research -.UFZ, 04318, Leipzig, Germany
| | - Martin von Bergen
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany.,Department of Molecular Systems Biology, Helmholtz,Centre for Environmental Research -.UFZ, 04318, Leipzig, Germany.,Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstr. 34, 04103, Leipzig, Germany
| | - Thomas Brüls
- Génomique métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Matthias Boll
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
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Haas TM, Mundinger S, Qiu D, Jork N, Ritter K, Dürr‐Mayer T, Ripp A, Saiardi A, Schaaf G, Jessen HJ. Stable Isotope Phosphate Labelling of Diverse Metabolites is Enabled by a Family of 18O-Phosphoramidites. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202112457. [PMID: 38505299 PMCID: PMC10947094 DOI: 10.1002/ange.202112457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 11/09/2022]
Abstract
Stable isotope labelling is state-of-the-art in quantitative mass spectrometry, yet often accessing the required standards is cumbersome and very expensive. Here, a unifying synthetic concept for 18O-labelled phosphates is presented, based on a family of modified 18O2-phosphoramidite reagents. This toolbox offers access to major classes of biologically highly relevant phosphorylated metabolites as their isotopologues including nucleotides, inositol phosphates, -pyrophosphates, and inorganic polyphosphates. 18O-enrichment ratios >95 % and good yields are obtained consistently in gram-scale reactions, while enabling late-stage labelling. We demonstrate the utility of the 18O-labelled inositol phosphates and pyrophosphates by assignment of these metabolites from different biological matrices. We demonstrate that phosphate neutral loss is negligible in an analytical setup employing capillary electrophoresis electrospray ionisation triple quadrupole mass spectrometry.
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Affiliation(s)
- Thomas M. Haas
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Stephan Mundinger
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Danye Qiu
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Nikolaus Jork
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
- CIBSS—The Center for Biological Signaling Studies &, Spemann Graduate School of Biology and Medicine (SGBM)Albert-Ludwigs-Universität FreiburgGermany
| | - Kevin Ritter
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Tobias Dürr‐Mayer
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Alexander Ripp
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Adolfo Saiardi
- Medical Research Council, Laboratory for molecular Cell BiologyUniversity College LondonUK
| | - Gabriel Schaaf
- INRES—Institut für Nutzpflanzenwissenschaften und RessourcenschutzUniversität BonnKarlrobert-Kreiten-Strasse 1353115BonnGermany
| | - Henning J. Jessen
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
- CIBSS—The Center for Biological Signaling Studies &, Spemann Graduate School of Biology and Medicine (SGBM)Albert-Ludwigs-Universität FreiburgGermany
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Haas TM, Mundinger S, Qiu D, Jork N, Ritter K, Dürr‐Mayer T, Ripp A, Saiardi A, Schaaf G, Jessen HJ. Stable Isotope Phosphate Labelling of Diverse Metabolites is Enabled by a Family of 18 O-Phosphoramidites. Angew Chem Int Ed Engl 2022; 61:e202112457. [PMID: 34734451 PMCID: PMC9298905 DOI: 10.1002/anie.202112457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Indexed: 11/12/2022]
Abstract
Stable isotope labelling is state-of-the-art in quantitative mass spectrometry, yet often accessing the required standards is cumbersome and very expensive. Here, a unifying synthetic concept for 18 O-labelled phosphates is presented, based on a family of modified 18 O2 -phosphoramidite reagents. This toolbox offers access to major classes of biologically highly relevant phosphorylated metabolites as their isotopologues including nucleotides, inositol phosphates, -pyrophosphates, and inorganic polyphosphates. 18 O-enrichment ratios >95 % and good yields are obtained consistently in gram-scale reactions, while enabling late-stage labelling. We demonstrate the utility of the 18 O-labelled inositol phosphates and pyrophosphates by assignment of these metabolites from different biological matrices. We demonstrate that phosphate neutral loss is negligible in an analytical setup employing capillary electrophoresis electrospray ionisation triple quadrupole mass spectrometry.
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Affiliation(s)
- Thomas M. Haas
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Stephan Mundinger
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Danye Qiu
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Nikolaus Jork
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
- CIBSS—The Center for Biological Signaling Studies &, Spemann Graduate School of Biology and Medicine (SGBM)Albert-Ludwigs-Universität FreiburgGermany
| | - Kevin Ritter
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Tobias Dürr‐Mayer
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Alexander Ripp
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
| | - Adolfo Saiardi
- Medical Research Council, Laboratory for molecular Cell BiologyUniversity College LondonUK
| | - Gabriel Schaaf
- INRES—Institut für Nutzpflanzenwissenschaften und RessourcenschutzUniversität BonnKarlrobert-Kreiten-Strasse 1353115BonnGermany
| | - Henning J. Jessen
- Institute of Organic ChemistryAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2179102Freiburg im BreisgauGermany
- CIBSS—The Center for Biological Signaling Studies &, Spemann Graduate School of Biology and Medicine (SGBM)Albert-Ludwigs-Universität FreiburgGermany
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