1
|
Fernández-Arévalo U, Fuchs J, Boll M, Díaz E. Transcriptional regulation of the anaerobic 3-hydroxybenzoate degradation pathway in Aromatoleum sp. CIB. Microbiol Res 2024; 288:127882. [PMID: 39216330 DOI: 10.1016/j.micres.2024.127882] [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: 05/07/2024] [Revised: 07/31/2024] [Accepted: 08/17/2024] [Indexed: 09/04/2024]
Abstract
Phenolic compounds are commonly found in anoxic environments, where they serve as both carbon and energy sources for certain anaerobic bacteria. The anaerobic breakdown of m-cresol, catechol, and certain lignin-derived compounds yields the central intermediate 3-hydroxybenzoate/3-hydroxybenzoyl-CoA. In this study, we have characterized the transcription and regulation of the hbd genes responsible for the anaerobic degradation of 3-hydroxybenzoate in the β-proteobacterium Aromatoleum sp. CIB. The hbd cluster is organized in three catabolic operons and a regulatory hbdR gene that encodes a dimeric transcriptional regulator belonging to the TetR family. HbdR suppresses the activity of the three catabolic promoters (PhbdN, PhbdE and PhbdH) by binding to a conserved palindromic operator box (ATGAATGAN4TCATTCAT). 3-Hydroxybenzoyl-CoA, the initial intermediate of the 3-hydroxybenzoate degradation pathway, along with benzoyl-CoA, serve as effector molecules that bind to HbdR inducing the expression of the hbd genes. Moreover, the hbd genes are subject to additional regulation influenced by the presence of non-aromatic carbon sources (carbon catabolite repression), and their expression is induced in oxygen-deprived conditions by the AcpR transcriptional activator. The prevalence of the hbd cluster among members of the Aromatoleum/Thauera bacterial group, coupled with its association with mobile genetic elements, suggests acquisition through horizontal gene transfer. These findings significantly enhance our understanding of the regulatory mechanisms governing the hbd gene cluster in bacteria, paving the way for further exploration into the anaerobic utilization/valorization of phenolic compounds derived from lignin.
Collapse
Affiliation(s)
- Unai Fernández-Arévalo
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain
| | - Jonathan Fuchs
- Faculty of Biology-Microbiology, University of Freiburg, Freiburg, Germany
| | - Matthias Boll
- Faculty of Biology-Microbiology, University of Freiburg, Freiburg, Germany
| | - Eduardo Díaz
- Department of Microbial and Plant Biotechnology, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Madrid, Spain.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Hollmann F, Opperman DJ, Paul CE. Biocatalytic Reduction Reactions from a Chemist's Perspective. Angew Chem Int Ed Engl 2021; 60:5644-5665. [PMID: 32330347 PMCID: PMC7983917 DOI: 10.1002/anie.202001876] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Indexed: 11/09/2022]
Abstract
Reductions play a key role in organic synthesis, producing chiral products with new functionalities. Enzymes can catalyse such reactions with exquisite stereo-, regio- and chemoselectivity, leading the way to alternative shorter classical synthetic routes towards not only high-added-value compounds but also bulk chemicals. In this review we describe the synthetic state-of-the-art and potential of enzymes that catalyse reductions, ranging from carbonyl, enone and aromatic reductions to reductive aminations.
Collapse
Affiliation(s)
- Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
- Department of BiotechnologyUniversity of the Free State205 Nelson Mandela DriveBloemfontein9300South Africa
| | - Diederik J. Opperman
- Department of BiotechnologyUniversity of the Free State205 Nelson Mandela DriveBloemfontein9300South Africa
| | - Caroline E. Paul
- Department of BiotechnologyDelft University of TechnologyVan der Maasweg 92629 HZDelftThe Netherlands
| |
Collapse
|
4
|
Hollmann F, Opperman DJ, Paul CE. Biokatalytische Reduktionen aus der Sicht eines Chemikers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001876] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Frank Hollmann
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629 HZ Delft Niederlande
- Department of Biotechnology University of the Free State 205 Nelson Mandela Drive Bloemfontein 9300 Südafrika
| | - Diederik J. Opperman
- Department of Biotechnology University of the Free State 205 Nelson Mandela Drive Bloemfontein 9300 Südafrika
| | - Caroline E. Paul
- Department of Biotechnology Delft University of Technology Van der Maasweg 9 2629 HZ Delft Niederlande
| |
Collapse
|
5
|
Merten C. Recent Advances in the Application of Vibrational Circular Dichroism Spectroscopy for the Characterization of Asymmetric Catalysts. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000876] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Christian Merten
- Fakultät für Chemie und Biochemie Organische Chemie II Ruhr Universität Bochum Universitätsstraße 150 44801 Bochum Germany
| |
Collapse
|
6
|
Abstract
Nowadays, biocatalysts have received much more attention in chemistry regarding their potential to enable high efficiency, high yield, and eco-friendly processes for a myriad of applications. Nature’s vast repository of catalysts has inspired synthetic chemists. Furthermore, the revolutionary technologies in bioengineering have provided the fast discovery and evolution of enzymes that empower chemical synthesis. This article attempts to deliver a comprehensive overview of the last two decades of investigation into enzymatic reactions and highlights the effective performance progress of bio-enzymes exploited in organic synthesis. Based on the types of enzymatic reactions and enzyme commission (E.C.) numbers, the enzymes discussed in the article are classified into oxidoreductases, transferases, hydrolases, and lyases. These applications should provide us with some insight into enzyme design strategies and molecular mechanisms.
Collapse
|
7
|
Schmid G, Scheffen M, Willistein M, Boll M. Oxygen detoxification by dienoyl-CoA oxidase involving flavin/disulfide cofactors. Mol Microbiol 2020; 114:17-30. [PMID: 32080908 DOI: 10.1111/mmi.14493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 11/30/2022]
Abstract
Class I benzoyl-CoA reductases (BCRs) are oxygen-sensitive key enzymes in the degradation of monocyclic aromatic compounds in anaerobic prokaryotes. They catalyze the ATP-dependent reductive dearomatization of their substrate to cyclohexa-1,5-diene-1-carboxyl-CoA (1,5-dienoyl-CoA). An aromatizing 1,5-dienoyl-CoA oxidase (DCO) activity has been proposed to protect BCRs from oxidative damage, however, the gene and its product involved have not been identified, yet. Here, we heterologously produced a DCO from the hyperthermophilic euryarchaeon Ferroglobus placidus that coupled the oxidation of two 1,5-dienoyl-CoA to benzoyl-CoA to the reduction of O2 to water at 80°C. DCO showed similarities to members of the old yellow enzyme family and contained FMN, FAD and an FeS cluster as cofactors. The O2 -dependent activation of inactive, reduced DCO is assigned to a redox thiol switch at Eo ' = -3 mV. We propose a catalytic cycle in which the active site FMN/disulfide redox centers are reduced by two 1,5-dienoyl-CoA (reductive half-cycle), followed by two consecutive two-electron transfer steps to molecular oxygen via peroxy- and hydroxyflavin intermediates yielding water (oxidative half-cycle). This work identified the enzyme involved in a unique oxygen detoxification process for an oxygen-sensitive catabolic enzyme.
Collapse
Affiliation(s)
- Georg Schmid
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Marieke Scheffen
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Max Willistein
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Matthias Boll
- Faculty of Biology - Microbiology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| |
Collapse
|
8
|
Spieker M, Saleem-Batcha R, Teufel R. Structural and Mechanistic Basis of an Oxepin-CoA Forming Isomerase in Bacterial Primary and Secondary Metabolism. ACS Chem Biol 2019; 14:2876-2886. [PMID: 31689071 DOI: 10.1021/acschembio.9b00742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Numerous aromatic compounds are aerobically degraded in bacteria via the central intermediate phenylacetic acid (paa). In one of the key steps of this widespread catabolic pathway, 1,2-epoxyphenylacetyl-CoA is converted by PaaG into the heterocyclic oxepin-CoA. PaaG thereby elegantly generates an α,β-unsaturated CoA ester that is predisposed to undergo β-oxidation subsequent to hydrolytic ring-cleavage. Moreover, oxepin-CoA serves as a precursor for secondary metabolites (e.g., tropodithietic acid) that act as antibiotics and quorum-sensing signals. Here we verify that PaaG adopts a second role in aromatic catabolism by converting cis-3,4-didehydroadipoyl-CoA into trans-2,3-didehydroadipoyl-CoA and corroborate a Δ3,Δ2-enoyl-CoA isomerase-like proton shuttling mechanism for both distinct substrates. Biochemical and structural investigations of PaaG reveal active site adaptations to the structurally different substrates and provide detailed insight into catalysis and control of stereospecificity. This work elucidates the mechanism of action of unusual isomerase PaaG and sheds new light on the ubiquitous enoyl-CoA isomerases of the crotonase superfamily.
Collapse
Affiliation(s)
- Melanie Spieker
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Raspudin Saleem-Batcha
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Robin Teufel
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| |
Collapse
|
9
|
Anselmann SEL, Löffler C, Stärk HJ, Jehmlich N, von Bergen M, Brüls T, Boll M. The class II benzoyl-coenzyme A reductase complex from the sulfate-reducing Desulfosarcina cetonica. Environ Microbiol 2019; 21:4241-4252. [PMID: 31430028 DOI: 10.1111/1462-2920.14784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/06/2019] [Accepted: 08/18/2019] [Indexed: 12/17/2022]
Abstract
Benzoyl-CoA reductases (BCRs) catalyse a key reaction in the anaerobic degradation pathways of monocyclic aromatic substrates, the dearomatization of benzoyl-CoA (BzCoA) to cyclohexa-1,5-diene-1-carboxyl-CoA (1,5-dienoyl-CoA) at the negative redox potential limit of diffusible enzymatic substrate/product couples (E°' = -622 mV). A 1-MDa class II BCR complex composed of the BamBCDEGHI subunits has so far only been isolated from the Fe(III)-respiring Geobacter metallireducens. It is supposed to drive endergonic benzene ring reduction at an active site W-pterin cofactor by flavin-based electron bifurcation. Here, we identified multiple copies of putative genes encoding the structural components of a class II BCR in sulfate reducing, Fe(III)-respiring and syntrophic bacteria. A soluble 950 kDa Bam[(BC)2 DEFGHI]2 complex was isolated from extracts of Desulfosarcina cetonica cells grown with benzoate/sulfate. Metal and cofactor analyses together with the identification of conserved binding motifs gave rise to 4 W-pterins, two selenocysteines, six flavin adenine dinucleotides, four Zn, and 48 FeS clusters. The complex exhibited 1,5-dienoyl-CoA-, NADPH- and ferredoxin-dependent oxidoreductase activities. Our results indicate that high-molecular class II BCR metalloenzyme machineries are remarkably conserved in strictly anaerobic bacteria with regard to subunit architecture and cofactor content, but their subcellular localization and electron acceptor preference may differ as a result of adaptations to variable energy metabolisms.
Collapse
Affiliation(s)
| | - Claudia Löffler
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| | - Hans-Joachim Stärk
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Martin von Bergen
- 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
- CEA, DRF, IBFJ, Genoscope, Evry, France.,CNRS-UMR8030, Université d'Evry Val d'Essonne and Université Paris-Saclay, Evry, France
| | - Matthias Boll
- Faculty of Biology - Microbiology, University of Freiburg, 79104, Freiburg, Germany
| |
Collapse
|
10
|
Merten C, Golub TP, Kreienborg NM. Absolute Configurations of Synthetic Molecular Scaffolds from Vibrational CD Spectroscopy. J Org Chem 2019; 84:8797-8814. [PMID: 31046276 DOI: 10.1021/acs.joc.9b00466] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Vibrational circular dichroism (VCD) spectroscopy is one of the most powerful techniques for the determination of absolute configurations (AC), as it does not require any specific UV/vis chromophores, no chemical derivatization, and no growth of suitable crystals. In the past decade, it has become increasingly recognized by chemists from various fields of synthetic chemistry such as total synthesis and drug discovery as well as from developers of asymmetric catalysts. This perspective article gives an overview about the most important experimental aspects of a VCD-based AC determination and explains the theoretical analysis. The comparison of experimental and computational spectra that leads to the final conclusion about the AC of the target molecules is described. In addition, the review summarizes unique VCD studies carried out in the period 2008-2018 that focus on the determination of unknown ACs of new compounds, which were obtained in its enantiopure form either through direct asymmetric synthesis or chiral chromatography.
Collapse
Affiliation(s)
- Christian Merten
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Tino P Golub
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| | - Nora M Kreienborg
- Ruhr Universität Bochum , Organische Chemie II , Universitätsstraße 150 , 44780 Bochum , Germany
| |
Collapse
|
11
|
Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors. Nat Commun 2019; 10:2074. [PMID: 31061390 PMCID: PMC6502838 DOI: 10.1038/s41467-019-10078-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/12/2019] [Indexed: 02/01/2023] Open
Abstract
Hydride transfers play a crucial role in a multitude of biological redox reactions and are mediated by flavin, deazaflavin or nicotinamide adenine dinucleotide cofactors at standard redox potentials ranging from 0 to –340 mV. 2-Naphthoyl-CoA reductase, a key enzyme of oxygen-independent bacterial naphthalene degradation, uses a low-potential one-electron donor for the two-electron dearomatization of its substrate below the redox limit of known biological hydride transfer processes at E°’ = −493 mV. Here we demonstrate by X-ray structural analyses, QM/MM computational studies, and multiple spectroscopy/activity based titrations that highly cooperative electron transfer (n = 3) from a low-potential one-electron (FAD) to a two-electron (FMN) transferring flavin cofactor is the key to overcome the resonance stabilized aromatic system by hydride transfer in a highly hydrophobic pocket. The results evidence how the protein environment inversely functionalizes two flavins to switch from low-potential one-electron to hydride transfer at the thermodynamic limit of flavin redox chemistry. The reduction of 2-naphtoyl-CoA to 5,6 dihydro-2-naphtoyl-CoA by 2-naphtoyl-CoA reductase is below the negative redox limit usually encountered in biological hydride transfer. Here, via X-ray crystallography and spectroscopic analysis, the authors elucidated the mechanism behind this.
Collapse
|